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Conserved domains on  [gi|1958787949|ref|XP_038934439|]
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potassium voltage-gated channel subfamily H member 3 isoform X1 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03192 super family cl33658
Voltage-dependent potassium channel; Provisional
 167-594 3.02e-25

Voltage-dependent potassium channel; Provisional


The actual alignment was detected with superfamily member PLN03192:

Pssm-ID: 215625 [Multi-domain]  Cd Length: 823  Bit Score: 113.04  E-value: 3.02e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  167 WDGFILLATLYVAVTVPYSVcvstAREPSAARGPPSVCDLAVEVLFILDIVLNFRTTFVSKSGQV-VFAPKSICLHYVTT 245
Cdd:PLN03192    64 WETLMVVLVAYSAWVYPFEV----AFLNASPKRGLEIADNVVDLFFAVDIVLTFFVAYIDPRTQLlVRDRKKIAVRYLST 139

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  246 WFLLDVIAALPFDLLHAF-----KVNV---YVGAHLLKTVRLLRLLRLLPRLDRYSQYSAVVLTLLMAVFALLAHWVACV 317
Cdd:PLN03192   140 WFLMDVASTIPFQALAYLitgtvKLNLsysLLGLLRFWRLRRVKQLFTRLEKDIRFSYFWIRCARLLSVTLFLVHCAGCL 219

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  318 wfyigqqeienseselpeigwlqelarrletpYYLVS-RSPDGGNSsgqsencsssgggseANGTGLELLGGPSLRSAYI 396
Cdd:PLN03192   220 --------------------------------YYLIAdRYPHQGKT---------------WIGAVIPNFRETSLWIRYI 252

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  397 TSLYFALSSLTSVGFGNVSANTDTEKIFSICTMLIGALMHAVVFGNVTAIIQRMYARRFLYHSRTRDLRDYIRIHRIPKP 476
Cdd:PLN03192   253 SAIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVEGTRRTMEFRNSIEAASNFVGRNRLPPR 332

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  477 LKQRMLEYFQATWAVNNgIDTTELLQSLPDELRADIAMHLHKEVLQ-LPLFEAASRGCLRALSLALRPAFCTPGEYLIHQ 555
Cdd:PLN03192   333 LKDQILAYMCLRFKAES-LNQQQLIDQLPKSICKSICQHLFLPVVEkVYLFKGVSREILLLLVTKMKAEYIPPREDVIMQ 411

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*...
gi 1958787949  556 GDALQALYFVCSGSMEVL----KGGTVLAILGKGDLIG-----CELPQ 594
Cdd:PLN03192   412 NEAPDDVYIVVSGEVEIIdsegEKERVVGTLGCGDIFGevgalCCRPQ 459
PRK13557 super family cl36263
histidine kinase; Provisional
 4-74 6.79e-13

histidine kinase; Provisional


The actual alignment was detected with superfamily member PRK13557:

Pssm-ID: 237425 [Multi-domain]  Cd Length: 540  Bit Score: 72.40  E-value: 6.79e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958787949    4 GCACSFLYGPDTSELVRQQIRKALDEHKEFKAELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHKDIS 74
Cdd:PRK13557    75 GNNCRFLQGPETDRATVAEVRDAIAERREIATEILNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVS 145
cyc_nuc_ocin super family cl28242
bacteriocin-type transport-associated protein; Members of this protein family are ...
 549-644 1.90e-06

bacteriocin-type transport-associated protein; Members of this protein family are uncharacterized and contain two copies of the cyclic nucleotide-binding domain pfam00027. Members are restricted to select cyanobacteria but are found regularly in association with a transport operon that, in turn, is associated with the production of putative bacteriocins. The models describing the transport operon are TIGR03794, TIGR03796, and TIGR03797.


The actual alignment was detected with superfamily member TIGR03896:

Pssm-ID: 274839 [Multi-domain]  Cd Length: 317  Bit Score: 51.05  E-value: 1.90e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  549 GEYLIHQGDALQALYFVCSGSMEVL----KGGTVLAILGKGDLIGcELPQREQVVKANADVKGLTYCVLQCLQLAGLHES 624
Cdd:TIGR03896  169 GTILIHEGGTVDALYILLYGEASLSispdGPGREVGSSRRGEILG-ETPFLNGSLPGTATVKAIENSVLLAIDKQQLAAK 247

                           90       100
                   ....*....|....*....|
gi 1958787949  625 LALYPEFAPRFSRGLRGELS 644
Cdd:TIGR03896  248 LQQDVGFASRFYRVIASLLS 267
 
Name Accession Description Interval E-value
PLN03192 PLN03192
Voltage-dependent potassium channel; Provisional
 167-594 3.02e-25

Voltage-dependent potassium channel; Provisional


Pssm-ID: 215625 [Multi-domain]  Cd Length: 823  Bit Score: 113.04  E-value: 3.02e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  167 WDGFILLATLYVAVTVPYSVcvstAREPSAARGPPSVCDLAVEVLFILDIVLNFRTTFVSKSGQV-VFAPKSICLHYVTT 245
Cdd:PLN03192    64 WETLMVVLVAYSAWVYPFEV----AFLNASPKRGLEIADNVVDLFFAVDIVLTFFVAYIDPRTQLlVRDRKKIAVRYLST 139

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  246 WFLLDVIAALPFDLLHAF-----KVNV---YVGAHLLKTVRLLRLLRLLPRLDRYSQYSAVVLTLLMAVFALLAHWVACV 317
Cdd:PLN03192   140 WFLMDVASTIPFQALAYLitgtvKLNLsysLLGLLRFWRLRRVKQLFTRLEKDIRFSYFWIRCARLLSVTLFLVHCAGCL 219

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  318 wfyigqqeienseselpeigwlqelarrletpYYLVS-RSPDGGNSsgqsencsssgggseANGTGLELLGGPSLRSAYI 396
Cdd:PLN03192   220 --------------------------------YYLIAdRYPHQGKT---------------WIGAVIPNFRETSLWIRYI 252

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  397 TSLYFALSSLTSVGFGNVSANTDTEKIFSICTMLIGALMHAVVFGNVTAIIQRMYARRFLYHSRTRDLRDYIRIHRIPKP 476
Cdd:PLN03192   253 SAIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVEGTRRTMEFRNSIEAASNFVGRNRLPPR 332

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  477 LKQRMLEYFQATWAVNNgIDTTELLQSLPDELRADIAMHLHKEVLQ-LPLFEAASRGCLRALSLALRPAFCTPGEYLIHQ 555
Cdd:PLN03192   333 LKDQILAYMCLRFKAES-LNQQQLIDQLPKSICKSICQHLFLPVVEkVYLFKGVSREILLLLVTKMKAEYIPPREDVIMQ 411

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*...
gi 1958787949  556 GDALQALYFVCSGSMEVL----KGGTVLAILGKGDLIG-----CELPQ 594
Cdd:PLN03192   412 NEAPDDVYIVVSGEVEIIdsegEKERVVGTLGCGDIFGevgalCCRPQ 459
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 525-635 1.19e-19

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 85.46  E-value: 1.19e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  525 LFEAASRGCLRALSLALRPAFCTPGEYLIHQGDALQALYFVCSGSMEVLKGG-----TVLAILGKGDLIGCELPQREQVv 599
Cdd:cd00038      1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDedgreQIVGFLGPGDLFGELALLGNGP- 79

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1958787949  600 kANADVKGLTYCVLQCLQLAGLHESLALYPEFAPRF 635
Cdd:cd00038     80 -RSATVRALTDSELLVLPRSDFRRLLQEYPELARRL 114
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 525-639 1.62e-16

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 76.67  E-value: 1.62e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949   525 LFEAASRGCLRALSLALRPAFCTPGEYLIHQGDALQALYFVCSGSMEVLK-----GGTVLAILGKGDLIGcELP-QREQV 598
Cdd:smart00100    1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKvledgEEQIVGTLGPGDFFG-ELAlLTNSR 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 1958787949   599 VKANADVKGLTYCVLQCLQLAGLHESLALYPEFAPRFSRGL 639
Cdd:smart00100   80 RAASAAAVALELATLLRIDFRDFLQLLPELPQLLLELLLEL 120
Ion_trans pfam00520
Ion transport protein; This family contains sodium, potassium and calcium ion channels. This ...
 167-454 3.11e-14

Ion transport protein; This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.


Pssm-ID: 459842 [Multi-domain]  Cd Length: 238  Bit Score: 73.46  E-value: 3.11e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  167 WDGFILLATLYVAVTVPYSVCVstaREPSAARGPPSVCDLAVEVLFILDIVLNFRTTFvsksgqvvfapksICLHYVTT- 245
Cdd:pfam00520    4 FELFILLLILLNTIFLALETYF---QPEEPLTTVLEILDYVFTGIFTLEMLLKIIAAG-------------FKKRYFRSp 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  246 WFLLDVIAALPFDLlhAFKVNVYVGAHLLKTVRLLRLLRLLPRLDRYSQYSAVVLTLLMAV-----FALLAHWVACVWFY 320
Cdd:pfam00520   68 WNILDFVVVLPSLI--SLVLSSVGSLSGLRVLRLLRLLRLLRLIRRLEGLRTLVNSLIRSLkslgnLLLLLLLFLFIFAI 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  321 IGQQeienseselpeigwlqelarrLETPYYLVSRSPDGGNSsgqseNCSSsgggseangtglellggpslrsaYITSLY 400
Cdd:pfam00520  146 IGYQ---------------------LFGGKLKTWENPDNGRT-----NFDN-----------------------FPNAFL 176

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958787949  401 FALSSLTSVGFGNVSANTDTEK-------IFSICTMLIGALMHAVVFGNVTAIIQRMYARR 454
Cdd:pfam00520  177 WLFQTMTTEGWGDIMYDTIDGKgefwayiYFVSFIILGGFLLLNLFIAVIIDNFQELTERT 237
PRK13557 PRK13557
histidine kinase; Provisional
 4-74 6.79e-13

histidine kinase; Provisional


Pssm-ID: 237425 [Multi-domain]  Cd Length: 540  Bit Score: 72.40  E-value: 6.79e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958787949    4 GCACSFLYGPDTSELVRQQIRKALDEHKEFKAELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHKDIS 74
Cdd:PRK13557    75 GNNCRFLQGPETDRATVAEVRDAIAERREIATEILNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVS 145
PAS COG2202
PAS domain [Signal transduction mechanisms];
4-77 4.71e-10

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 61.58  E-value: 4.71e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958787949    4 GCACSFLYGPDTSELVRQQIRKALDEHKEFKAELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHKDISETK 77
Cdd:COG2202     53 GKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRRKDGSLFWVELSISPVRDEDGEITGFVGIARDITERK 126
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 7-75 8.31e-09

PAS domain; This domain is found in many signalling proteins in which it functions as a sensor domain. It recognizes FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 463873 [Multi-domain]  Cd Length: 93  Bit Score: 53.62  E-value: 8.31e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949    7 CSFLYGPDTSElvrQQIRKALDEHKEFKA-ELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHKDISE 75
Cdd:pfam13426   27 ITDLFAEPEDS---ERLREALREGKAVREfEVVLYRKDGEPFPVLVSLAPIRDDGGELVGIIAILRDITE 93
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 534-643 2.65e-08

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 55.38  E-value: 2.65e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  534 LRALSLALRPAFCTPGEYLIHQGDALQALYFVCSGSMEVLK---GGT--VLAILGKGDLIGCELPQREQVVKANADVkgL 608
Cdd:COG0664      9 LEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRiseDGReqILGFLGPGDFFGELSLLGGEPSPATAEA--L 86

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1958787949  609 TYCVLQCLQLAGLHESLALYPEFAPRFSRGLRGEL 643
Cdd:COG0664     87 EDSELLRIPREDLEELLERNPELARALLRLLARRL 121
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 36-75 1.82e-06

Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.


Pssm-ID: 197509  Cd Length: 43  Bit Score: 45.64  E-value: 1.82e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|
gi 1958787949    36 ELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHKDISE 75
Cdd:smart00086    3 EYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITE 42
cyc_nuc_ocin TIGR03896
bacteriocin-type transport-associated protein; Members of this protein family are ...
 549-644 1.90e-06

bacteriocin-type transport-associated protein; Members of this protein family are uncharacterized and contain two copies of the cyclic nucleotide-binding domain pfam00027. Members are restricted to select cyanobacteria but are found regularly in association with a transport operon that, in turn, is associated with the production of putative bacteriocins. The models describing the transport operon are TIGR03794, TIGR03796, and TIGR03797.


Pssm-ID: 274839 [Multi-domain]  Cd Length: 317  Bit Score: 51.05  E-value: 1.90e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  549 GEYLIHQGDALQALYFVCSGSMEVL----KGGTVLAILGKGDLIGcELPQREQVVKANADVKGLTYCVLQCLQLAGLHES 624
Cdd:TIGR03896  169 GTILIHEGGTVDALYILLYGEASLSispdGPGREVGSSRRGEILG-ETPFLNGSLPGTATVKAIENSVLLAIDKQQLAAK 247

                           90       100
                   ....*....|....*....|
gi 1958787949  625 LALYPEFAPRFSRGLRGELS 644
Cdd:TIGR03896  248 LQQDVGFASRFYRVIASLLS 267
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 13-73 3.82e-05

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 43.78  E-value: 3.82e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958787949   13 PDTSELVRQQIRKALDEHKEFKAELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHKDI 73
Cdd:cd00130     43 PEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLVSLTPIRDEGGEVIGLLGVVRDI 103
 
Name Accession Description Interval E-value
PLN03192 PLN03192
Voltage-dependent potassium channel; Provisional
 167-594 3.02e-25

Voltage-dependent potassium channel; Provisional


Pssm-ID: 215625 [Multi-domain]  Cd Length: 823  Bit Score: 113.04  E-value: 3.02e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  167 WDGFILLATLYVAVTVPYSVcvstAREPSAARGPPSVCDLAVEVLFILDIVLNFRTTFVSKSGQV-VFAPKSICLHYVTT 245
Cdd:PLN03192    64 WETLMVVLVAYSAWVYPFEV----AFLNASPKRGLEIADNVVDLFFAVDIVLTFFVAYIDPRTQLlVRDRKKIAVRYLST 139

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  246 WFLLDVIAALPFDLLHAF-----KVNV---YVGAHLLKTVRLLRLLRLLPRLDRYSQYSAVVLTLLMAVFALLAHWVACV 317
Cdd:PLN03192   140 WFLMDVASTIPFQALAYLitgtvKLNLsysLLGLLRFWRLRRVKQLFTRLEKDIRFSYFWIRCARLLSVTLFLVHCAGCL 219

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  318 wfyigqqeienseselpeigwlqelarrletpYYLVS-RSPDGGNSsgqsencsssgggseANGTGLELLGGPSLRSAYI 396
Cdd:PLN03192   220 --------------------------------YYLIAdRYPHQGKT---------------WIGAVIPNFRETSLWIRYI 252

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  397 TSLYFALSSLTSVGFGNVSANTDTEKIFSICTMLIGALMHAVVFGNVTAIIQRMYARRFLYHSRTRDLRDYIRIHRIPKP 476
Cdd:PLN03192   253 SAIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVEGTRRTMEFRNSIEAASNFVGRNRLPPR 332

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  477 LKQRMLEYFQATWAVNNgIDTTELLQSLPDELRADIAMHLHKEVLQ-LPLFEAASRGCLRALSLALRPAFCTPGEYLIHQ 555
Cdd:PLN03192   333 LKDQILAYMCLRFKAES-LNQQQLIDQLPKSICKSICQHLFLPVVEkVYLFKGVSREILLLLVTKMKAEYIPPREDVIMQ 411

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*...
gi 1958787949  556 GDALQALYFVCSGSMEVL----KGGTVLAILGKGDLIG-----CELPQ 594
Cdd:PLN03192   412 NEAPDDVYIVVSGEVEIIdsegEKERVVGTLGCGDIFGevgalCCRPQ 459
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 525-635 1.19e-19

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 85.46  E-value: 1.19e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  525 LFEAASRGCLRALSLALRPAFCTPGEYLIHQGDALQALYFVCSGSMEVLKGG-----TVLAILGKGDLIGCELPQREQVv 599
Cdd:cd00038      1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDedgreQIVGFLGPGDLFGELALLGNGP- 79

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1958787949  600 kANADVKGLTYCVLQCLQLAGLHESLALYPEFAPRF 635
Cdd:cd00038     80 -RSATVRALTDSELLVLPRSDFRRLLQEYPELARRL 114
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 525-639 1.62e-16

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 76.67  E-value: 1.62e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949   525 LFEAASRGCLRALSLALRPAFCTPGEYLIHQGDALQALYFVCSGSMEVLK-----GGTVLAILGKGDLIGcELP-QREQV 598
Cdd:smart00100    1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKvledgEEQIVGTLGPGDFFG-ELAlLTNSR 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 1958787949   599 VKANADVKGLTYCVLQCLQLAGLHESLALYPEFAPRFSRGL 639
Cdd:smart00100   80 RAASAAAVALELATLLRIDFRDFLQLLPELPQLLLELLLEL 120
Ion_trans pfam00520
Ion transport protein; This family contains sodium, potassium and calcium ion channels. This ...
 167-454 3.11e-14

Ion transport protein; This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.


Pssm-ID: 459842 [Multi-domain]  Cd Length: 238  Bit Score: 73.46  E-value: 3.11e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  167 WDGFILLATLYVAVTVPYSVCVstaREPSAARGPPSVCDLAVEVLFILDIVLNFRTTFvsksgqvvfapksICLHYVTT- 245
Cdd:pfam00520    4 FELFILLLILLNTIFLALETYF---QPEEPLTTVLEILDYVFTGIFTLEMLLKIIAAG-------------FKKRYFRSp 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  246 WFLLDVIAALPFDLlhAFKVNVYVGAHLLKTVRLLRLLRLLPRLDRYSQYSAVVLTLLMAV-----FALLAHWVACVWFY 320
Cdd:pfam00520   68 WNILDFVVVLPSLI--SLVLSSVGSLSGLRVLRLLRLLRLLRLIRRLEGLRTLVNSLIRSLkslgnLLLLLLLFLFIFAI 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  321 IGQQeienseselpeigwlqelarrLETPYYLVSRSPDGGNSsgqseNCSSsgggseangtglellggpslrsaYITSLY 400
Cdd:pfam00520  146 IGYQ---------------------LFGGKLKTWENPDNGRT-----NFDN-----------------------FPNAFL 176

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958787949  401 FALSSLTSVGFGNVSANTDTEK-------IFSICTMLIGALMHAVVFGNVTAIIQRMYARR 454
Cdd:pfam00520  177 WLFQTMTTEGWGDIMYDTIDGKgefwayiYFVSFIILGGFLLLNLFIAVIIDNFQELTERT 237
PRK13557 PRK13557
histidine kinase; Provisional
 4-74 6.79e-13

histidine kinase; Provisional


Pssm-ID: 237425 [Multi-domain]  Cd Length: 540  Bit Score: 72.40  E-value: 6.79e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958787949    4 GCACSFLYGPDTSELVRQQIRKALDEHKEFKAELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHKDIS 74
Cdd:PRK13557    75 GNNCRFLQGPETDRATVAEVRDAIAERREIATEILNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVS 145
Ion_trans_2 pfam07885
Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
 395-449 1.67e-10

Ion channel; This family includes the two membrane helix type ion channels found in bacteria.


Pssm-ID: 462301 [Multi-domain]  Cd Length: 78  Bit Score: 58.05  E-value: 1.67e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1958787949  395 YITSLYFALSSLTSVGFGNVSANTDTEKIFSICTMLIGALMHAVVFGNVTAIIQR 449
Cdd:pfam07885   24 FLDALYFSFVTLTTVGYGDIVPLTDAGRLFTIFYILIGIPLFAIFLAVLGRFLTE 78
PRK13559 PRK13559
hypothetical protein; Provisional
 7-75 2.69e-10

hypothetical protein; Provisional


Pssm-ID: 237427 [Multi-domain]  Cd Length: 361  Bit Score: 63.30  E-value: 2.69e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958787949    7 CSFLYGPDTSELVRQQIRKALDEHKEFKAELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHKDISE 75
Cdd:PRK13559    91 CRFLQGAATDPIAVAKIRAAIAAEREIVVELLNYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTD 159
PRK13558 PRK13558
bacterio-opsin activator; Provisional
 4-77 4.19e-10

bacterio-opsin activator; Provisional


Pssm-ID: 237426 [Multi-domain]  Cd Length: 665  Bit Score: 63.70  E-value: 4.19e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958787949    4 GCACSFLYGPDTSELVRQQIRKALDEHKEFKAELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHKDISETK 77
Cdd:PRK13558   193 GRNCRFLQGEDTNEERVAELREAIDEERPTSVELRNYRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERK 266
PAS COG2202
PAS domain [Signal transduction mechanisms];
4-77 4.71e-10

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 61.58  E-value: 4.71e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958787949    4 GCACSFLYGPDTSELVRQQIRKALDEHKEFKAELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHKDISETK 77
Cdd:COG2202     53 GKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRRKDGSLFWVELSISPVRDEDGEITGFVGIARDITERK 126
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 7-75 8.31e-09

PAS domain; This domain is found in many signalling proteins in which it functions as a sensor domain. It recognizes FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 463873 [Multi-domain]  Cd Length: 93  Bit Score: 53.62  E-value: 8.31e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949    7 CSFLYGPDTSElvrQQIRKALDEHKEFKA-ELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHKDISE 75
Cdd:pfam13426   27 ITDLFAEPEDS---ERLREALREGKAVREfEVVLYRKDGEPFPVLVSLAPIRDDGGELVGIIAILRDITE 93
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 534-643 2.65e-08

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 55.38  E-value: 2.65e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  534 LRALSLALRPAFCTPGEYLIHQGDALQALYFVCSGSMEVLK---GGT--VLAILGKGDLIGCELPQREQVVKANADVkgL 608
Cdd:COG0664      9 LEALLAHLELRTLKKGEVLFREGDPADHLYFVLSGLVKLYRiseDGReqILGFLGPGDFFGELSLLGGEPSPATAEA--L 86

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1958787949  609 TYCVLQCLQLAGLHESLALYPEFAPRFSRGLRGEL 643
Cdd:COG0664     87 EDSELLRIPREDLEELLERNPELARALLRLLARRL 121
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 548-613 4.88e-07

Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 459637 [Multi-domain]  Cd Length: 89  Bit Score: 48.37  E-value: 4.88e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958787949  548 PGEYLIHQGDALQALYFVCSGSMEVLKGG-----TVLAILGKGDLIGcELP--QREqvvKANADVKGLTYCVL 613
Cdd:pfam00027    6 AGEVIFREGDPADSLYIVLSGKVKVYRTLedgreQILAVLGPGDFFG-ELAllGGE---PRSATVVALTDSEL 74
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 36-75 1.82e-06

Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.


Pssm-ID: 197509  Cd Length: 43  Bit Score: 45.64  E-value: 1.82e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|
gi 1958787949    36 ELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHKDISE 75
Cdd:smart00086    3 EYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITE 42
cyc_nuc_ocin TIGR03896
bacteriocin-type transport-associated protein; Members of this protein family are ...
 549-644 1.90e-06

bacteriocin-type transport-associated protein; Members of this protein family are uncharacterized and contain two copies of the cyclic nucleotide-binding domain pfam00027. Members are restricted to select cyanobacteria but are found regularly in association with a transport operon that, in turn, is associated with the production of putative bacteriocins. The models describing the transport operon are TIGR03794, TIGR03796, and TIGR03797.


Pssm-ID: 274839 [Multi-domain]  Cd Length: 317  Bit Score: 51.05  E-value: 1.90e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  549 GEYLIHQGDALQALYFVCSGSMEVL----KGGTVLAILGKGDLIGcELPQREQVVKANADVKGLTYCVLQCLQLAGLHES 624
Cdd:TIGR03896  169 GTILIHEGGTVDALYILLYGEASLSispdGPGREVGSSRRGEILG-ETPFLNGSLPGTATVKAIENSVLLAIDKQQLAAK 247

                           90       100
                   ....*....|....*....|
gi 1958787949  625 LALYPEFAPRFSRGLRGELS 644
Cdd:TIGR03896  248 LQQDVGFASRFYRVIASLLS 267
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 13-73 3.82e-05

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 43.78  E-value: 3.82e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958787949   13 PDTSELVRQQIRKALDEHKEFKAELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHKDI 73
Cdd:cd00130     43 PEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLVSLTPIRDEGGEVIGLLGVVRDI 103
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
16-77 7.11e-04

Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 42.91  E-value: 7.11e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958787949   16 SELVRQQIRKALDEHKEFKA-ELILYRKSGLPFWCLLDVIPIKNEKGEVALFLVSHkDISETK 77
Cdd:COG3852     59 DSPLRELLERALAEGQPVTErEVTLRRKDGEERPVDVSVSPLRDAEGEGGVLLVLR-DITERK 120
PLN02868 PLN02868
acyl-CoA thioesterase family protein
 522-627 3.86e-03

acyl-CoA thioesterase family protein


Pssm-ID: 178459 [Multi-domain]  Cd Length: 413  Bit Score: 40.86  E-value: 3.86e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958787949  522 QLPLFEAASRGCLRALSLALRPAFCTPGEYLIHQGDALQALYFVCSGSMEVLK----GGTVLAILGKGDLIGCELPQREQ 597
Cdd:PLN02868    12 SVPLLQRLPSSSLKKIAEVVVPKRYGKGEYVVREGEPGDGLYFIWKGEAEVSGpaeeESRPEFLLKRYDYFGYGLSGSVH 91

                           90       100       110
                   ....*....|....*....|....*....|
gi 1958787949  598 vvkaNADVKGLTYcvLQCLQLAglHESLAL 627
Cdd:PLN02868    92 ----SADVVAVSE--LTCLVLP--HEHCHL 113
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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