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Conserved domains on  [gi|1942121482|ref|WP_197276652|]
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hypothetical protein [Flavobacterium sp. KJJ]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
412-500 1.68e-11

DNA-binding transcriptional regulator, CsgD family [Transcription];


:

Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 63.24  E-value: 1.68e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 412 AIDIVLKRLEKNLNTDIWKEFEISFEQVHKSFFDKLTEDYPSLTPKDRRLCALLYLDLTTKEISQITGQSFKTIENARTR 491
Cdd:COG2771    86 LLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKR 165


                  ....*....
gi 1942121482 492 LRKKFDLTN 500
Cdd:COG2771   166 IYRKLGVSS 174
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 25-318 5.99e-09

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 57.05  E-value: 5.99e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  25 LQKTDWDRAIKYIELAETEAKKKKESELTLAGVYITSGKmysarevLDVALQYYLKAYDIYkkkgnlEEASKLENNLAII 104
Cdd:COG2956    19 LLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGE-------YDRAIRIHQKLLERD------PDRAEALLELAQD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 105 YAQGKNKEKALQCFLNVYRFQKSKNDAiklvkiLNNIGTLYL-SRNLDSSLNYFHKAEALNKSlknddlKVYVYTNLARA 183
Cdd:COG2956    86 YLKAGLLDRAEELLEKLLELDPDDAEA------LRLLAEIYEqEGDWEKAIEVLERLLKLGPE------NAHAYCELAEL 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 184 YVLKKNKTQADEYFNKAFSLLSNRVD-NLLQAFVYqsfseynLKEKNYDTVIVNAKRGLELCSENvysssgLDLNKMLYE 262
Cdd:COG2956   154 YLEQGDYDEAIEALEKALKLDPDCARaLLLLAELY-------LEQGDYEEAIAALERALEQDPDY------LPALPRLAE 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1942121482 263 VYVIKKDYKNAVYYFQKYNAIKDSINIEEKTVNIErIKLEQDYKARTQIKTLIEQK 318
Cdd:COG2956   221 LYEKLGDPEEALELLRKALELDPSDDLLLALADLL-ERKEGLEAALALLERQLRRH 275
 
Name Accession Description Interval E-value
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
412-500 1.68e-11

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 63.24  E-value: 1.68e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 412 AIDIVLKRLEKNLNTDIWKEFEISFEQVHKSFFDKLTEDYPSLTPKDRRLCALLYLDLTTKEISQITGQSFKTIENARTR 491
Cdd:COG2771    86 LLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKR 165


                  ....*....
gi 1942121482 492 LRKKFDLTN 500
Cdd:COG2771   166 IYRKLGVSS 174
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 25-318 5.99e-09

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 57.05  E-value: 5.99e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  25 LQKTDWDRAIKYIELAETEAKKKKESELTLAGVYITSGKmysarevLDVALQYYLKAYDIYkkkgnlEEASKLENNLAII 104
Cdd:COG2956    19 LLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGE-------YDRAIRIHQKLLERD------PDRAEALLELAQD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 105 YAQGKNKEKALQCFLNVYRFQKSKNDAiklvkiLNNIGTLYL-SRNLDSSLNYFHKAEALNKSlknddlKVYVYTNLARA 183
Cdd:COG2956    86 YLKAGLLDRAEELLEKLLELDPDDAEA------LRLLAEIYEqEGDWEKAIEVLERLLKLGPE------NAHAYCELAEL 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 184 YVLKKNKTQADEYFNKAFSLLSNRVD-NLLQAFVYqsfseynLKEKNYDTVIVNAKRGLELCSENvysssgLDLNKMLYE 262
Cdd:COG2956   154 YLEQGDYDEAIEALEKALKLDPDCARaLLLLAELY-------LEQGDYEEAIAALERALEQDPDY------LPALPRLAE 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1942121482 263 VYVIKKDYKNAVYYFQKYNAIKDSINIEEKTVNIErIKLEQDYKARTQIKTLIEQK 318
Cdd:COG2956   221 LYEKLGDPEEALELLRKALELDPSDDLLLALADLL-ERKEGLEAALALLERQLRRH 275
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 452-500 3.95e-05

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 41.36  E-value: 3.95e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1942121482  452 PSLTPKDRRLCALLYLDLTTKEISQITGQSFKTIENARTRLRKKFDLTN 500
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRS 50
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 23-254 6.49e-05

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 45.84  E-value: 6.49e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  23 LRLQKTDWDRAIKYIELAETEAKKKKESELTLAGVYITSGKMYSAREVL--------DVALQYYLKAY------DIYKKK 88
Cdd:TIGR02917 406 SKLSQGDPSEAIADLETAAQLDPELGRADLLLILSYLRSGQFDKALAAAkklekkqpDNASLHNLLGAiylgkgDLAKAR 485

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  89 GNLEEASKLE-------NNLAIIYAQGKNKEKALQCFLNVYRFQKSKNDAI-KLVKILNNIGT----------------- 143
Cdd:TIGR02917 486 EAFEKALSIEpdffpaaANLARIDIQEGNPDDAIQRFEKVLTIDPKNLRAIlALAGLYLRTGNeeeavawlekaaelnpq 565

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 144 -----LYLSRNLDSSLNYFHKAEALNKSLKNDDLKVYVYTNLARAYVLKKNKTQADEYFNKAFSLLSNRVDNLLQ-AFVY 217
Cdd:TIGR02917 566 eiepaLALAQYYLGKGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLlADAY 645

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1942121482 218 QSFseynlkeKNYDTVIVNAKRGLELCSENVYSSSGL 254
Cdd:TIGR02917 646 AVM-------KNYAKAITSLKRALELKPDNTEAQIGL 675
SNAP pfam14938
Soluble NSF attachment protein, SNAP; The soluble NSF attachment protein (SNAP) proteins are ...
 15-160 3.61e-04

Soluble NSF attachment protein, SNAP; The soluble NSF attachment protein (SNAP) proteins are involved in vesicular transport between the endoplasmic reticulum and Golgi apparatus. They act as adaptors between SNARE (integral membrane SNAP receptor) proteins and NSF (N-ethylmaleimide-sensitive factor). They are structurally similar to TPR repeats.


Pssm-ID: 405606 [Multi-domain]  Cd Length: 273  Bit Score: 42.55  E-value: 3.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  15 VELCSKIA--LRLQKtDWDRAIK-YIELAETEAKKKKESELtlAGVYITSGKMYSaREVLDVALQYYLKAYDIYKKKGNL 91
Cdd:pfam14938  27 ADLYIQAAnaYKLAK-NWEEAGEaFEKAAECQLKLGSKDEA--ANAYVEAAKCYK-KVDPEEAVRALEKAIEIYTEMGRF 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  92 EEASKLENNLAIIYAQ-GKNKEKAL--------------------QCFLNVYRFQKSKNDAIKLVKILNNIGTLYLSRNL 150
Cdd:pfam14938 103 RRAAKHKKEIAELYEQeLGDLEKAIeayeqaadwyegegasalanKCYLKVADLSAELEDYPKAIEIYEKVAKNSLENNL 182

                         170
                  ....*....|..
gi 1942121482 151 D--SSLNYFHKA 160
Cdd:pfam14938 183 LkySVKEYFLKA 194
GerE pfam00196
Bacterial regulatory proteins, luxR family;
453-500 1.48e-03

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 36.79  E-value: 1.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1942121482 453 SLTPKDRRLCALLYLDLTTKEISQITGQSFKTIENARTRLRKKFDLTN 500
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHS 49
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 410-495 6.28e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 37.33  E-value: 6.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 410 QQAIDIVLKRLEKNLNTDIWKEFEISFEQVHKSFFDKLTEdypsLTPKDRRLCALLYL-DLTTKEISQITGQSFKTIENA 488
Cdd:TIGR02937  71 KRRLRRELDLLEELLDSDPSPEEELEQEEEREALREALEK----LPEREREVLVLRYLeGLSYKEIAEILGISVGTVKRR 146


                  ....*..
gi 1942121482 489 RTRLRKK 495
Cdd:TIGR02937 147 LKRARKK 153
 
Name Accession Description Interval E-value
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
412-500 1.68e-11

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 63.24  E-value: 1.68e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 412 AIDIVLKRLEKNLNTDIWKEFEISFEQVHKSFFDKLTEDYPSLTPKDRRLCALLYLDLTTKEISQITGQSFKTIENARTR 491
Cdd:COG2771    86 LLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKR 165


                  ....*....
gi 1942121482 492 LRKKFDLTN 500
Cdd:COG2771   166 IYRKLGVSS 174
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 25-318 5.99e-09

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 57.05  E-value: 5.99e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  25 LQKTDWDRAIKYIELAETEAKKKKESELTLAGVYITSGKmysarevLDVALQYYLKAYDIYkkkgnlEEASKLENNLAII 104
Cdd:COG2956    19 LLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGE-------YDRAIRIHQKLLERD------PDRAEALLELAQD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 105 YAQGKNKEKALQCFLNVYRFQKSKNDAiklvkiLNNIGTLYL-SRNLDSSLNYFHKAEALNKSlknddlKVYVYTNLARA 183
Cdd:COG2956    86 YLKAGLLDRAEELLEKLLELDPDDAEA------LRLLAEIYEqEGDWEKAIEVLERLLKLGPE------NAHAYCELAEL 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 184 YVLKKNKTQADEYFNKAFSLLSNRVD-NLLQAFVYqsfseynLKEKNYDTVIVNAKRGLELCSENvysssgLDLNKMLYE 262
Cdd:COG2956   154 YLEQGDYDEAIEALEKALKLDPDCARaLLLLAELY-------LEQGDYEEAIAALERALEQDPDY------LPALPRLAE 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1942121482 263 VYVIKKDYKNAVYYFQKYNAIKDSINIEEKTVNIErIKLEQDYKARTQIKTLIEQK 318
Cdd:COG2956   221 LYEKLGDPEEALELLRKALELDPSDDLLLALADLL-ERKEGLEAALALLERQLRRH 275
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
54-243 5.22e-06

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 47.69  E-value: 5.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  54 LAGVYITSGKMYSAREVLDVALQYYLKAYDIYkkkgnlEEASKLENNLAIIYAQGKNKEKALQCFLNVYRFQkskndaIK 133
Cdd:COG0457     7 DAEAYNNLGLAYRRLGRYEEAIEDYEKALELD------PDDAEALYNLGLAYLRLGRYEEALADYEQALELD------PD 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 134 LVKILNNIGTLYLSR-NLDSSLNYFHKAEALNKSLknddlkVYVYTNLARAYVLKKNKTQADEYFNKAFSLLSNRVDNLL 212
Cdd:COG0457    75 DAEALNNLGLALQALgRYEEALEDYDKALELDPDD------AEALYNLGLALLELGRYDEAIEAYERALELDPDDADALY 148

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1942121482 213 -QAFVYQSFSEYNLKEKNYDTVIVNAKRGLEL 243
Cdd:COG0457   149 nLGIALEKLGRYEEALELLEKLEAAALAALLA 180
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 452-500 3.95e-05

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 41.36  E-value: 3.95e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1942121482  452 PSLTPKDRRLCALLYLDLTTKEISQITGQSFKTIENARTRLRKKFDLTN 500
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRS 50
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 23-254 6.49e-05

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 45.84  E-value: 6.49e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  23 LRLQKTDWDRAIKYIELAETEAKKKKESELTLAGVYITSGKMYSAREVL--------DVALQYYLKAY------DIYKKK 88
Cdd:TIGR02917 406 SKLSQGDPSEAIADLETAAQLDPELGRADLLLILSYLRSGQFDKALAAAkklekkqpDNASLHNLLGAiylgkgDLAKAR 485

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  89 GNLEEASKLE-------NNLAIIYAQGKNKEKALQCFLNVYRFQKSKNDAI-KLVKILNNIGT----------------- 143
Cdd:TIGR02917 486 EAFEKALSIEpdffpaaANLARIDIQEGNPDDAIQRFEKVLTIDPKNLRAIlALAGLYLRTGNeeeavawlekaaelnpq 565

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 144 -----LYLSRNLDSSLNYFHKAEALNKSLKNDDLKVYVYTNLARAYVLKKNKTQADEYFNKAFSLLSNRVDNLLQ-AFVY 217
Cdd:TIGR02917 566 eiepaLALAQYYLGKGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLlADAY 645

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1942121482 218 QSFseynlkeKNYDTVIVNAKRGLELCSENVYSSSGL 254
Cdd:TIGR02917 646 AVM-------KNYAKAITSLKRALELKPDNTEAQIGL 675
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
29-214 1.30e-04

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 43.46  E-value: 1.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  29 DWDRAIKYIELAETEAKKKKESELTLAGVYITSGKmysarevLDVALQYYLKAYDIykkkgNLEEASKLeNNLAIIYAQG 108
Cdd:COG0457    23 RYEEAIEDYEKALELDPDDAEALYNLGLAYLRLGR-------YEEALADYEQALEL-----DPDDAEAL-NNLGLALQAL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 109 KNKEKALQCFlnvyrfqkskNDAIKL----VKILNNIGTLYLSR-NLDSSLNYFHKAEALNKSLknddlkVYVYTNLARA 183
Cdd:COG0457    90 GRYEEALEDY----------DKALELdpddAEALYNLGLALLELgRYDEAIEAYERALELDPDD------ADALYNLGIA 153

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1942121482 184 YVLKKNKTQADEYFNKAFSLLSNRVDNLLQA 214
Cdd:COG0457   154 LEKLGRYEEALELLEKLEAAALAALLAAALG 184
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
104-203 1.81e-04

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 40.54  E-value: 1.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 104 IYAQGKNKEKALQCFLNVYRFQKSKNDAiklvkiLNNIGTLYLSrnldssLNYFHKAEALNKSLKNDDLKVYVYTNLARA 183
Cdd:COG3063     1 LYLKLGDLEEAEEYYEKALELDPDNADA------LNNLGLLLLE------QGRYDEAIALEKALKLDPNNAEALLNLAEL 68

                          90       100
                  ....*....|....*....|
gi 1942121482 184 YVLKKNKTQADEYFNKAFSL 203
Cdd:COG3063    69 LLELGDYDEALAYLERALEL 88
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 21-200 3.06e-04

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 42.79  E-value: 3.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  21 IALRLQKTDWDRAIKYIELAETEAKKKKESELTLAGVYITSGKmysarevLDVALQYYLKAYDIYKkkgNLEEASKLenn 100
Cdd:COG2956   117 AEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGD-------YDEAIEALEKALKLDP---DCARALLL--- 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 101 LAIIYAQGKNKEKALQCFLNVYRfqksknDAIKLVKILNNIGTLYLSRN-LDSSLNYFHKAEALNKSLknddlkvYVYTN 179
Cdd:COG2956   184 LAELYLEQGDYEEAIAALERALE------QDPDYLPALPRLAELYEKLGdPEEALELLRKALELDPSD-------DLLLA 250

                         170       180
                  ....*....|....*....|.
gi 1942121482 180 LARAYVLKKNKTQADEYFNKA 200
Cdd:COG2956   251 LADLLERKEGLEAALALLERQ 271
SNAP pfam14938
Soluble NSF attachment protein, SNAP; The soluble NSF attachment protein (SNAP) proteins are ...
 15-160 3.61e-04

Soluble NSF attachment protein, SNAP; The soluble NSF attachment protein (SNAP) proteins are involved in vesicular transport between the endoplasmic reticulum and Golgi apparatus. They act as adaptors between SNARE (integral membrane SNAP receptor) proteins and NSF (N-ethylmaleimide-sensitive factor). They are structurally similar to TPR repeats.


Pssm-ID: 405606 [Multi-domain]  Cd Length: 273  Bit Score: 42.55  E-value: 3.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  15 VELCSKIA--LRLQKtDWDRAIK-YIELAETEAKKKKESELtlAGVYITSGKMYSaREVLDVALQYYLKAYDIYKKKGNL 91
Cdd:pfam14938  27 ADLYIQAAnaYKLAK-NWEEAGEaFEKAAECQLKLGSKDEA--ANAYVEAAKCYK-KVDPEEAVRALEKAIEIYTEMGRF 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  92 EEASKLENNLAIIYAQ-GKNKEKAL--------------------QCFLNVYRFQKSKNDAIKLVKILNNIGTLYLSRNL 150
Cdd:pfam14938 103 RRAAKHKKEIAELYEQeLGDLEKAIeayeqaadwyegegasalanKCYLKVADLSAELEDYPKAIEIYEKVAKNSLENNL 182

                         170
                  ....*....|..
gi 1942121482 151 D--SSLNYFHKA 160
Cdd:pfam14938 183 LkySVKEYFLKA 194
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 454-500 8.40e-04

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 39.49  E-value: 8.40e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1942121482 454 LTPKDRRLCALLYLDLTTKEISQITGQSFKTIENARTRLRKKFDLTN 500
Cdd:COG2197    70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRN 116
GerE pfam00196
Bacterial regulatory proteins, luxR family;
453-500 1.48e-03

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 36.79  E-value: 1.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1942121482 453 SLTPKDRRLCALLYLDLTTKEISQITGQSFKTIENARTRLRKKFDLTN 500
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHS 49
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 25-284 5.13e-03

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 39.68  E-value: 5.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  25 LQKTDWDRAIKYIELAETEAKKKKESELTLAGVYITSGKMYSAREVLDVALQYYLKAYDIYKKKGNLEEAS-KLENNLAI 103
Cdd:TIGR02917 136 LGLGQLELAQKSYEQALAIDPRSLYAKLGLAQLALAENRFDEARALIDEVLTADPGNVDALLLKGDLLLSLgNIELALAA 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 104 I--YAQGKNKEKALQCFLNVYRFQKSKND-----AIKLVKILNN-IGTLYLSRNLDSSLNYFHKA-EALNKSLK-NDDLK 173
Cdd:TIGR02917 216 YrkAIALRPNNIAVLLALATILIEAGEFEeaekhADALLKKAPNsPLAHYLKALVDFQKKNYEDArETLQDALKsAPEYL 295

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 174 VYVYTNLARAYVLkKNKTQADEYFNKAFSLLSNRVDNLLQAFVYQsfseynLKEKNYDTVIVNAKRGLELCSENvysSSG 253
Cdd:TIGR02917 296 PALLLAGASEYQL-GNLEQAYQYLNQILKYAPNSHQARRLLASIQ------LRLGRVDEAIATLSPALGLDPDD---PAA 365

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1942121482 254 LDlnkMLYEVYVIKKDYKNAVYYFQKYNAIK 284
Cdd:TIGR02917 366 LS---LLGEAYLALGDFEKAAEYLAKATELD 393
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 74-214 6.05e-03

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 39.21  E-value: 6.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  74 ALQYYLKAYDIYKKKGNLEEAS-KLENNLAIIYAQGKNKEKALQCFlnvyrfqkskNDAIKL----VKILNNIGTLYlsr 148
Cdd:COG3914    90 ALGRYEEALALYRRALALNPDNaEALFNLGNLLLALGRLEEALAAL----------RRALALnpdfAEAYLNLGEAL--- 156

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 149 nldSSLNYFHKAEA-LNKSLKNDDLKVYVYTNLARAYVLKKNKTQADEYFNKAFSLLSNRVD---NLLQA 214
Cdd:COG3914   157 ---RRLGRLEEAIAaLRRALELDPDNAEALNNLGNALQDLGRLEEAIAAYRRALELDPDNADahsNLLFA 223
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 410-495 6.28e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 37.33  E-value: 6.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 410 QQAIDIVLKRLEKNLNTDIWKEFEISFEQVHKSFFDKLTEdypsLTPKDRRLCALLYL-DLTTKEISQITGQSFKTIENA 488
Cdd:TIGR02937  71 KRRLRRELDLLEELLDSDPSPEEELEQEEEREALREALEK----LPEREREVLVLRYLeGLSYKEIAEILGISVGTVKRR 146


                  ....*..
gi 1942121482 489 RTRLRKK 495
Cdd:TIGR02937 147 LKRARKK 153
NlpI COG4785
Lipoprotein NlpI, contains TPR repeats [Cell wall/membrane/envelope biogenesis];
32-224 9.52e-03

Lipoprotein NlpI, contains TPR repeats [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 443815 [Multi-domain]  Cd Length: 223  Bit Score: 37.59  E-value: 9.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482  32 RAIKYIELAETEAKKKKESELTLAGVYITSGKMYSAREVLDVALQYYLKAYDIYKKKGNLEEASKLENNLAIIYAQGKNK 111
Cdd:COG4785    10 LALALAAAAASKAAILLAALLFAAVLALAIALADLALALAAAALAAAALAAERIDRALALPDLAQLYYERGVAYDSLGDY 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942121482 112 EKALQCFLNvyrfqkskndAIKL----VKILNNIG-TLYLSRNLDSSLnyfhkaEALNKSLKNDDLKVYVYTNLARAYVL 186
Cdd:COG4785    90 DLAIADFDQ----------ALELdpdlAEAYNNRGlAYLLLGDYDAAL------EDFDRALELDPDYAYAYLNRGIALYY 153

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1942121482 187 KKNKTQADEYFNKAFSLLSNRVDNLLQAFVYQSFSEYN 224
Cdd:COG4785   154 LGRYELAIADLEKALELDPNDPERALWLYLAERKLDPE 191
 
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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