254780417

254780417

transcriptional regulator CarD family protein

GeneID in NCBI database:8209403Locus tag:CLIBASIA_01510
Protein GI in NCBI database:254780417Protein Accession:YP_003064830.1
Gene range:+(321338, 321904)Protein Length:188aa
Gene description:transcriptional regulator CarD family protein
COG prediction:[K] Transcriptional regulators, similar to M. xanthus CarD
KEGG prediction:transcriptional regulator CarD family protein; K07736 CarD family transcriptional regulator
SEED prediction:CarD-like transcriptional regulator
Pathway involved in KEGG:not defined
Subsystem involved in SEED:- none -
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------19
MTFQQKRDAMRQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLSSKSSKTEKSTSENQDKAA
ccHHHHHHHHHcccccccEEEccccccEEEEEEEEEEccccEEEEEEEEEccccEEEEEEHHHcccccccccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcccccccccccHHHHcc
ccccccccccccEEEcccEEEEcccccEEEEEEEEEEEcccEEEEEEEEEEcccEEEEEcHHHHHHccccccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHcccHHHcc
MTFQQKRDAMrqgfrtgehivypahgvgtiTEIKEQEVAGMKLEFFVIAfdkdkmclkvpvgkaIDIGMRKLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRdlhrtdsqpeksysERQLYESALNRMVREIAAvnsisepeaINLIEVnlsskssktekstsenqdkaa
mtfqqkrdamrqgfrtgehivypahGVGTITEIKEQEVAGMKLEFFVIafdkdkmclKVPVGKAIDIGMrklseahfveralklvrgkarvkrtmwsrraqeydakinsgdlIAIAEVVRDLhrtdsqpeksyserQLYESALNRMVREIAAvnsisepeaiNLIEvnlsskssktekstsenqdkaa
MTFQQKRDAMRQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLsskssktekstseNQDKAA
*****************EHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRG*************QEYDAKINSGDLIAIAEVVRDLH****************ESALNRMVREIAAVNSISEPEAINLI***********************
**********RQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLH************RQLYESALNRMVREIAAVNSISEPEAINLIEVNLS******************
*********MRQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLSS*****************
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MTFQQKRDAMRQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLSSKSSKTEKSTSENQDKAA
MTFQQKRDAMRQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLSSKSSKTEKSTSENQDKAA
MTFQQKRDAMRQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLSSKSSKTEKSTSENQDKAA

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target188 transcriptional regulator CarD family protein [Candidat
315122139188 transcriptional regulator CarD family protein [Candidat 1 4e-96
222150214223 transcriptional regulator CarD family [Agrobacterium vi 1 4e-74
15890014189 CarD family transcriptional regulator [Agrobacterium tu 1 5e-74
227823778189 putative transcriptional regulator, CarD family [Sinorh 1 6e-74
325294135189 transcriptional regulator, CarD family [Agrobacterium s 1 2e-73
15967010189 hypothetical protein SMc03874 [Sinorhizobium meliloti 1 1 4e-73
222087730190 transcriptional regulator protein [Agrobacterium radiob 1 8e-73
116254341190 CarD family transcriptional regulator [Rhizobium legumi 1 1e-72
150398306189 CarD family transcriptional regulator [Sinorhizobium me 1 2e-72
86359604190 CarD family transcriptional regulator [Rhizobium etli C 1 3e-72
>gi|315122139|ref|YP_004062628.1| transcriptional regulator CarD family protein [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 188 Back     alignment and organism information
 Score =  354 bits (908), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 171/188 (90%), Positives = 179/188 (95%)

Query: 1   MTFQQKRDAMRQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVP 60
           MT QQK+  MRQGF+TGEHIVYP HGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVP
Sbjct: 1   MTVQQKKSMMRQGFKTGEHIVYPTHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVP 60

Query: 61  VGKAIDIGMRKLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVR 120
           VGKAIDIGMRKLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVR
Sbjct: 61  VGKAIDIGMRKLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVR 120

Query: 121 DLHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLSSKSSKTEKST 180
           DL+RT++QPEKSYSERQLYESALNRMVRE+AAVNSISEPEAI+LIEVNLSSK  K EK T
Sbjct: 121 DLYRTENQPEKSYSERQLYESALNRMVREVAAVNSISEPEAIDLIEVNLSSKRPKDEKPT 180

Query: 181 SENQDKAA 188
           +ENQ KAA
Sbjct: 181 NENQCKAA 188


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222150214|ref|YP_002551171.1| transcriptional regulator CarD family [Agrobacterium vitis S4] Length = 223 Back     alignment and organism information
>gi|15890014|ref|NP_355695.1| CarD family transcriptional regulator [Agrobacterium tumefaciens str. C58] Length = 189 Back     alignment and organism information
>gi|227823778|ref|YP_002827751.1| putative transcriptional regulator, CarD family [Sinorhizobium fredii NGR234] Length = 189 Back     alignment and organism information
>gi|325294135|ref|YP_004279999.1| transcriptional regulator, CarD family [Agrobacterium sp. H13-3] Length = 189 Back     alignment and organism information
>gi|15967010|ref|NP_387363.1| hypothetical protein SMc03874 [Sinorhizobium meliloti 1021] Length = 189 Back     alignment and organism information
>gi|222087730|ref|YP_002546267.1| transcriptional regulator protein [Agrobacterium radiobacter K84] Length = 190 Back     alignment and organism information
>gi|116254341|ref|YP_770179.1| CarD family transcriptional regulator [Rhizobium leguminosarum bv. viciae 3841] Length = 190 Back     alignment and organism information
>gi|150398306|ref|YP_001328773.1| CarD family transcriptional regulator [Sinorhizobium medicae WSM419] Length = 189 Back     alignment and organism information
>gi|86359604|ref|YP_471496.1| CarD family transcriptional regulator [Rhizobium etli CFN 42] Length = 190 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target188 transcriptional regulator CarD family protein [Candidat
pfam0255998 pfam02559, CarD_TRCF, CarD-like/TRCF domain 1e-15
COG1329166 COG1329, COG1329, Transcriptional regulators, similar t 6e-50
>gnl|CDD|145606 pfam02559, CarD_TRCF, CarD-like/TRCF domain Back     alignment and domain information
>gnl|CDD|31520 COG1329, COG1329, Transcriptional regulators, similar to M Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 188 transcriptional regulator CarD family protein [Candidat
COG1329166 Transcriptional regulators, similar to M. xanthus CarD 100.0
PRK10689 1148 transcription-repair coupling factor; Provisional 99.88
TIGR00580 997 mfd transcription-repair coupling factor; InterPro: IPR 99.84
COG1197 1139 Mfd Transcription-repair coupling factor (superfamily I 99.84
pfam0255998 CarD_TRCF CarD-like/TRCF domain. CarD is a Myxococcus x 99.76
PRK06330 906 transcript cleavage factor/unknown domain fusion protei 93.09
>COG1329 Transcriptional regulators, similar to M Back     alignment and domain information
>PRK10689 transcription-repair coupling factor; Provisional Back     alignment and domain information
>TIGR00580 mfd transcription-repair coupling factor; InterPro: IPR004576 All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene Back     alignment and domain information
>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription] Back     alignment and domain information
>pfam02559 CarD_TRCF CarD-like/TRCF domain Back     alignment and domain information
>PRK06330 transcript cleavage factor/unknown domain fusion protein; Validated Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target188 transcriptional regulator CarD family protein [Candidat
2eyq_A 1151 Crystal Structure Of Escherichia Coli Transcription 3e-17
3mlq_E71 Crystal Structure Of The Thermus Thermophilus Trans 1e-09
>gi|90109237|pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair Coupling Factor Length = 1151 Back     alignment and structure
 Score = 92.2 bits (227), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 23/162 (14%), Positives = 47/162 (29%), Gaps = 16/162 (9%)

Query: 13  GFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKL 72
               G+ +V+  HGVG    +   E  G+  E+  +    +   L VPV     I     
Sbjct: 479 ELHIGQPVVHLEHGVGRYAGMTTLEAGGITGEYL-MLTYANDAKLYVPVSSLHLISRYAG 537

Query: 73  SEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKS 132
                    L  + G A                K         AE++    +  ++   +
Sbjct: 538 GAEE--NAPLHKLGGDA----------WSRARQKAAEKVRDVAAELLDIYAQRAAKEGFA 585

Query: 133 YSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLSSKSS 174
           +   +                 +  + +AIN +  ++    +
Sbjct: 586 FKHDR---EQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLA 624


>gi|308387853|pdb|3MLQ|E Chain E, Crystal Structure Of The Thermus Thermophilus Transcription-Repair Coupling Factor Rna Polymerase Interacting Domain With The Thermus Aquaticus Rna Polymerase Beta1 Domain Length = 71 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target188 transcriptional regulator CarD family protein [Candidat
3mlq_E71 Transcription-repair coupling factor; tudor, transferas 2e-05
>3mlq_E Transcription-repair coupling factor; tudor, transferase-transcription complex; 2.91A {Thermus thermophilus} Length = 71 Back     alignment and structure
 Score = 43.9 bits (104), Expect = 2e-05
 Identities = 15/49 (30%), Positives = 30/49 (61%), Gaps = 3/49 (6%)

Query: 14 FRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAF-DKDKMCLKVPV 61
             G+++++P HGVG    ++ +EV G+K ++ V+ +  + K  L +PV
Sbjct: 3  HMPGDYLIHPEHGVGQYLGLETREVLGVKRDYLVLRYKGEGK--LYLPV 49


Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target188 transcriptional regulator CarD family protein [Candidat
2eyq_A 1151 TRCF, transcription-repair coupling factor; MFD, SF2 AT 99.82
3mlq_E71 Transcription-repair coupling factor; tudor, transferas 99.28
2d7d_A661 Uvrabc system protein B; helicase, protein-DNA-ADP tern 97.53
>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1 Back     alignment and structure
Probab=99.82  E-value=5.3e-20  Score=147.53  Aligned_cols=148  Identities=16%  Similarity=0.237  Sum_probs=108.9

Q ss_pred             HHCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEECCCCCCEEEEECCCHHHCCCCCCCCCHHHHHHHHHCCCCCCC
Q ss_conf             31389986974878509997678986487302530220248885699805201210454334410246789850786644
Q gi|254780417|r   12 QGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARV   91 (188)
Q Consensus        12 ~~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~~~~~~l~vPv~~~~~~~~R~~~~~~e~~~l~~~l~~~~~~   91 (188)
                      ..+++||||||.+||||+|.|++++++.|..+||+.|+|. +++++|||+++.+.+..|...+....  -      ....
T Consensus       478 ~~L~~GDyVVH~dHGIGrY~GL~~i~v~g~~~DyL~IeYa-~~dkLyVPv~ql~lIskY~g~~~~~p--~------LdkL  548 (1151)
T 2eyq_A          478 AELHIGQPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYA-NDAKLYVPVSSLHLISRYAGGAEENA--P------LHKL  548 (1151)
T ss_dssp             TTCCTTCEEEETTTEEEEEEEEEEEESSSCEEEEEEEECG-GGCEEEEEGGGGGGEEECCCSCSSSC--C------CCCT
T ss_pred             HHCCCCCHHHHCCCCEEEEECCEEECCCCCCCCEEEEEEC-CCCEEEECHHHHHHHHHCCCCCCCCC--C------CCCC
T ss_conf             2067887113206764897132574036875552699975-89769746899877764037788887--1------6757


Q ss_pred             CCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHC
Q ss_conf             66550389999999851689999999999998410100000126899999999999774677489989999999998504
Q gi|254780417|r   92 KRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLSS  171 (188)
Q Consensus        92 ~~~~~~~R~~~~~~~lksgd~~~~a~vik~L~~~~~~k~l~~~e~~~l~~A~~~L~~Efa~~l~i~~eea~~~I~~~L~~  171 (188)
                      ....|.++...-++.+    ..-+.++++-...|...++.++....-   .++.|.+.|+|.+|.+|..|++.|..+|.+
T Consensus       549 G~~~W~k~K~kakk~i----~~iA~eLl~lyA~R~~~~~~~~~~~~~---~~~~~~~~~~~~~t~~q~~a~~~i~~~~~~  621 (1151)
T 2eyq_A          549 GGDAWSRARQKAAEKV----RDVAAELLDIYAQRAAKEGFAFKHDRE---QYQLFCDSFPFETTPDQAQAINAVLSDMCQ  621 (1151)
T ss_dssp             TCSHHHHHHHHHHHHH----HHHHHHHHHHHHHHHTSCCCCCCCCHH---HHHHHHHTCCSCCCHHHHHHHHHHHHHHHS
T ss_pred             CCHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHCCCCCCCCHH---HHHHHHHHCCCCCCHHHHHHHHHHHHHHHC
T ss_conf             8168999999999999----999999999999975203753045334---689999747766787799999999887606


Q ss_pred             CCCC
Q ss_conf             6753
Q gi|254780417|r  172 KSSK  175 (188)
Q Consensus       172 ~~~~  175 (188)
                      +.|.
T Consensus       622 ~~~~  625 (1151)
T 2eyq_A          622 PLAM  625 (1151)
T ss_dssp             SSCC
T ss_pred             CCHH
T ss_conf             8556



>3mlq_E Transcription-repair coupling factor; tudor, transferase-transcription complex; 2.91A {Thermus thermophilus} Back     alignment and structure
>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B* Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

No hit with e-value below 0.005

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target188 transcriptional regulator CarD family protein [Candidat
d2eyqa180 Transcription-repair coupling factor, RRCF, middle doma 99.25
d2eyqa3 233 Transcription-repair coupling factor, TRCF {Escherichia 92.74
>d2eyqa1 b.34.18.1 (A:466-545) Transcription-repair coupling factor, RRCF, middle domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: All beta proteins
fold: SH3-like barrel
superfamily: CarD-like
family: CarD-like
domain: Transcription-repair coupling factor, RRCF, middle domain
species: Escherichia coli [TaxId: 562]
Probab=99.25  E-value=4.4e-12  Score=95.07  Aligned_cols=62  Identities=23%  Similarity=0.363  Sum_probs=55.7

Q ss_pred             HHCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEECCCCCCEEEEECCCHHHCCCCCCCC
Q ss_conf             313899869748785099976789864873025302202488856998052012104543344
Q gi|254780417|r   12 QGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSE   74 (188)
Q Consensus        12 ~~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~~~~~~l~vPv~~~~~~~~R~~~~   74 (188)
                      ..+++||+|||.+||||+|.|++++++.|..+||+.|+|. +++++|||+++.+.+..+...+
T Consensus        10 ~~L~~GD~VVH~dhGIG~y~GL~~~~~~g~~~e~l~leY~-~~d~LyVPv~~~~~i~kY~g~~   71 (80)
T d2eyqa1          10 AELHIGQPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYA-NDAKLYVPVSSLHLISRYAGGA   71 (80)
T ss_dssp             TTCCTTCEEEETTTEEEEEEEEEEEESSSCEEEEEEEECG-GGCEEEEEGGGGGGEEECCCSC
T ss_pred             HHCCCCCEEEECCCCEEEEEEEEEEECCCCCCCEEEEEEC-CCCEEEEEHHHHCCEEECCCCC
T ss_conf             7587999998802591752322785127877855999986-8995997489933033315899



>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 188 transcriptional regulator CarD family protein [Can
2eyq_A_460-54485 (A:460-544) TRCF, transcription-repair coupling fa 8e-10
>2eyq_A (A:460-544) TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli}Length = 85 Back     alignment and structure
 Score = 57.9 bits (140), Expect = 8e-10
 Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 14 FRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLS 73
             G+ +V+  HGVG    +   E  G+  E+ ++ +  +   L VPV     I      
Sbjct: 21 LHIGQPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTY-ANDAKLYVPVSSLHLISRYAGG 79

Query: 74 EA 75
            
Sbjct: 80 AE 81


Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target188 transcriptional regulator CarD family protein [Candidat
2eyq_A_460-54485 TRCF, transcription-repair coupling factor; MFD, S 99.5
>2eyq_A (A:460-544) TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} Back     alignment and structure
Probab=99.50  E-value=3e-14  Score=111.49  Aligned_cols=66  Identities=21%  Similarity=0.321  Sum_probs=58.9

Q ss_pred             HHHHCCCCCEEECCCCCCEEEEEEEEEEECCCCHHHEEEECCCCCCEEEEECCCHHHCCCCCCCCCH
Q ss_conf             4531389986974878509997678986487302530220248885699805201210454334410
Q gi|254780417|r   10 MRQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAH   76 (188)
Q Consensus        10 ~~~~FkvGD~VVy~~~GVg~i~~I~~~~i~g~~~eyy~L~~~~~~~~l~vPv~~~~~~~~R~~~~~~   76 (188)
                      ...+|++||+|||++||||+|.||++++++|..++||+|+|. +++++|||+++.+.+..+...+..
T Consensus        17 d~~~l~~GD~VVh~~hGig~~~gi~~~~~~g~~~ey~~l~y~-~~~~l~VPv~~~~~i~ry~~~~~~   82 (85)
T 2eyq_A           17 NLAELHIGQPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYA-NDAKLYVPVSSLHLISRYAGGAEE   82 (85)
T ss_dssp             TCTTCCTTCEEEETTTEEEEEEEEEEEESSSCEEEEEEEECG-GGCEEEEEGGGGGGEEECCCSCSS
T ss_pred             CHHHCCCCCEEEEECCCHHHHCCEEEEECCCCCCCCEEEEEC-CCCEEEECHHHHHHHHHHHCCCCC
T ss_conf             043246774686601230101030553026776763035642-796498348999888875024667