254780440

254780440

transcription elongation factor GreA

GeneID in NCBI database:8209426Locus tag:CLIBASIA_01625
Protein GI in NCBI database:254780440Protein Accession:YP_003064853.1
Gene range:+(349818, 350294)Protein Length:158aa
Gene description:transcription elongation factor GreA
COG prediction:[K] Transcription elongation factor
KEGG prediction:greA; transcription elongation factor GreA; K03624 transcription elongation factor GreA
SEED prediction:Transcription elongation factor GreA
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Transcription factors bacterial
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-------16
MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI
ccccEEccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHcEEEccccccccEEEEccEEEEEEcccccEEEEEEEcHHHcccccccEEEccHHHHHHcccccccEEEEEccccEEEEEEEEEEEc
ccccccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHccccHHHHHHHHHHHHHccHHHHHHHHHHHHHccEEEEcccccccEEEEEEEEEEEEcccccEEEEEEEccccccHHcccEEcccHHHHHHHccccccEEEEEccccEEEEEEEEEEEc
mvdkipvtskgFDKIQQELRWRQQEERPRIIKAISEAraygdlsenAEYQAAKELQNLNEGRMAELENIITRAEVIdistmsgdriaFGATVSLVEknsgdkknyqivgdqeadvqsglvsiSSPIARALIGKELgdiisvnapggektYEILQVLWI
mvdkipvtskgfdkiqqelrwrqqeerprIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDiisvnapggektyEILQVLWI
MVDKIPVTSKGFDKIqqelrwrqqeerprIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI
**DKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI
MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI
****IPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI
MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI
MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI

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
Target158 transcription elongation factor GreA [Candidatus Liberi
315122111158 transcription elongation factor GreA [Candidatus Liberi 1 7e-77
190892720158 transcription elongation factor (transcript cleavage fa 1 8e-61
209550295158 transcription elongation factor GreA [Rhizobium legumin 1 2e-60
86358571158 transcription elongation factor GreA [Rhizobium etli CF 1 3e-60
241205678158 transcription elongation factor GreA [Rhizobium legumin 1 3e-60
116253164158 transcription elongation factor GreA [Rhizobium legumin 1 4e-60
227822120255 transcription elongation factor GreA [Sinorhizobium fre 1 7e-60
218671794158 transcription elongation factor GreA [Rhizobium etli GR 1 7e-60
47716785163 GreA [Sinorhizobium meliloti] Length = 163 1 2e-59
15965326158 transcription elongation factor GreA [Sinorhizobium mel 1 3e-59
>gi|315122111|ref|YP_004062600.1| transcription elongation factor GreA [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 158 Back     alignment and organism information
 Score =  289 bits (740), Expect = 7e-77,   Method: Compositional matrix adjust.
 Identities = 141/158 (89%), Positives = 151/158 (95%)

Query: 1   MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNE 60
           MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEAR+YGDLSENAEYQAAKELQ++NE
Sbjct: 1   MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARSYGDLSENAEYQAAKELQSMNE 60

Query: 61  GRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLV 120
           GR+AELENI T AEVIDIS MSG ++AFGATVSLV++ SGDKKNYQIVGDQEADVQSGLV
Sbjct: 61  GRIAELENITTCAEVIDISKMSGSKVAFGATVSLVDETSGDKKNYQIVGDQEADVQSGLV 120

Query: 121 SISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI 158
           SISSPIARALIGKELGD +SVNAPGG+K YEILQVLWI
Sbjct: 121 SISSPIARALIGKELGDTVSVNAPGGQKNYEILQVLWI 158


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|190892720|ref|YP_001979262.1| transcription elongation factor (transcript cleavage factor) protein [Rhizobium etli CIAT 652] Length = 158 Back     alignment and organism information
>gi|209550295|ref|YP_002282212.1| transcription elongation factor GreA [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 158 Back     alignment and organism information
>gi|86358571|ref|YP_470463.1| transcription elongation factor GreA [Rhizobium etli CFN 42] Length = 158 Back     alignment and organism information
>gi|241205678|ref|YP_002976774.1| transcription elongation factor GreA [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 158 Back     alignment and organism information
>gi|116253164|ref|YP_769002.1| transcription elongation factor GreA [Rhizobium leguminosarum bv. viciae 3841] Length = 158 Back     alignment and organism information
>gi|227822120|ref|YP_002826091.1| transcription elongation factor GreA [Sinorhizobium fredii NGR234] Length = 255 Back     alignment and organism information
>gi|218671794|ref|ZP_03521463.1| transcription elongation factor GreA [Rhizobium etli GR56] Length = 158 Back     alignment and organism information
>gi|47716785|gb|AAT37570.1| GreA [Sinorhizobium meliloti] Length = 163 Back     alignment and organism information
>gi|15965326|ref|NP_385679.1| transcription elongation factor GreA [Sinorhizobium meliloti 1021] Length = 158 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
Target158 transcription elongation factor GreA [Candidatus Liberi
PRK00226157 PRK00226, greA, transcription elongation factor GreA; R 4e-56
TIGR01462151 TIGR01462, greA, transcription elongation factor GreA 2e-46
PRK01885157 PRK01885, greB, transcription elongation factor GreB; R 1e-29
TIGR01461156 TIGR01461, greB, transcription elongation factor GreB 4e-25
PRK14720906 PRK14720, PRK14720, transcript cleavage factor/unknown 6e-23
PRK06330718 PRK06330, PRK06330, transcript cleavage factor/unknown 5e-15
PRK05753137 PRK05753, PRK05753, nucleoside diphosphate kinase regul 3e-07
PRK05892158 PRK05892, PRK05892, nucleoside diphosphate kinase regul 2e-05
COG0782151 COG0782, GreA, Transcription elongation factor [Transcr 3e-36
pfam0344971 pfam03449, GreA_GreB_N, domain 3e-21
pfam0127277 pfam01272, GreA_GreB, Transcription elongation factor, 7e-21
PRK06342160 PRK06342, PRK06342, transcription elongation factor reg 8e-12
>gnl|CDD|178936 PRK00226, greA, transcription elongation factor GreA; Reviewed Back     alignment and domain information
>gnl|CDD|130529 TIGR01462, greA, transcription elongation factor GreA Back     alignment and domain information
>gnl|CDD|179345 PRK01885, greB, transcription elongation factor GreB; Reviewed Back     alignment and domain information
>gnl|CDD|130528 TIGR01461, greB, transcription elongation factor GreB Back     alignment and domain information
>gnl|CDD|184804 PRK14720, PRK14720, transcript cleavage factor/unknown domain fusion protein; Provisional Back     alignment and domain information
>gnl|CDD|180531 PRK06330, PRK06330, transcript cleavage factor/unknown domain fusion protein; Validated Back     alignment and domain information
>gnl|CDD|180236 PRK05753, PRK05753, nucleoside diphosphate kinase regulator; Provisional Back     alignment and domain information
>gnl|CDD|180307 PRK05892, PRK05892, nucleoside diphosphate kinase regulator; Provisional Back     alignment and domain information
>gnl|CDD|31125 COG0782, GreA, Transcription elongation factor [Transcription] Back     alignment and domain information
>gnl|CDD|146205 pfam03449, GreA_GreB_N, domain Back     alignment and domain information
>gnl|CDD|144753 pfam01272, GreA_GreB, Transcription elongation factor, GreA/GreB, C-term Back     alignment and domain information
>gnl|CDD|180535 PRK06342, PRK06342, transcription elongation factor regulatory protein; Validated Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 158 transcription elongation factor GreA [Candidatus Liberi
TIGR01462155 greA transcription elongation factor GreA; InterPro: IP 100.0
PRK00226157 greA transcription elongation factor GreA; Reviewed 100.0
PRK01885159 greB transcription elongation factor GreB; Reviewed 100.0
TIGR01461157 greB transcription elongation factor GreB; InterPro: IP 100.0
PRK05892161 nucleoside diphosphate kinase regulator; Provisional 100.0
PRK06330906 transcript cleavage factor/unknown domain fusion protei 100.0
COG0782151 Uncharacterized conserved protein, YhbC family [Functio 100.0
PRK06342160 transcription elongation factor regulatory protein; Val 100.0
PRK05753135 nucleoside diphosphate kinase regulator; Provisional 99.96
pfam0127277 GreA_GreB Transcription elongation factor, GreA/GreB, C 99.88
pfam0344971 GreA_GreB_N domain. This domain adopts a long alpha-hai 99.84
PRK01490 435 tig trigger factor; Provisional 91.53
>TIGR01462 greA transcription elongation factor GreA; InterPro: IPR006359 Bacterial GreA and GreB IPR006358 from INTERPRO promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase (RNAP) , allowing RNA transcription to continue past template-encoded arresting sites Back     alignment and domain information
>PRK00226 greA transcription elongation factor GreA; Reviewed Back     alignment and domain information
>PRK01885 greB transcription elongation factor GreB; Reviewed Back     alignment and domain information
>TIGR01461 greB transcription elongation factor GreB; InterPro: IPR006358 Bacterial GreA IPR006359 from INTERPRO and GreB promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase, allowing RNA transcription to continue past template-encoded arresting sites Back     alignment and domain information
>PRK05892 nucleoside diphosphate kinase regulator; Provisional Back     alignment and domain information
>PRK06330 transcript cleavage factor/unknown domain fusion protein; Validated Back     alignment and domain information
>COG0782 Uncharacterized conserved protein, YhbC family [Function unknown] Back     alignment and domain information
>PRK06342 transcription elongation factor regulatory protein; Validated Back     alignment and domain information
>PRK05753 nucleoside diphosphate kinase regulator; Provisional Back     alignment and domain information
>pfam01272 GreA_GreB Transcription elongation factor, GreA/GreB, C-term Back     alignment and domain information
>pfam03449 GreA_GreB_N domain Back     alignment and domain information
>PRK01490 tig trigger factor; Provisional 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
Target158 transcription elongation factor GreA [Candidatus Liberi
1grj_A158 Grea Transcript Cleavage Factor From Escherichia Co 5e-36
2p4v_A158 Crystal Structure Of The Transcript Cleavage Factor 9e-30
2f23_A156 Crystal Structure Of Grea Factor Homolog 1 (Gfh1) P 1e-19
2eul_A156 Structure Of The Transcription Factor Gfh1. Length 2e-19
2etn_A157 Crystal Structure Of Thermus Aquaticus Gfh1 Length 4e-19
2pn0_A141 Prokaryotic Transcription Elongation Factor GreaGRE 7e-10
3bmb_A136 Crystal Structure Of A New Rna Polymerase Interacti 2e-08
gi|157831240|pdb|1GRJ|A Chain A, Grea Transcript Cleavage Factor From Escherichia Coli Length = 158 Back     alignment and structure
 Score =  154 bits (388), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 71/158 (44%), Positives = 114/158 (72%), Gaps = 1/158 (0%)

Query: 2   VDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEG 61
           +  IP+T +G +K+++EL + +   RP II AI+EAR +GDL ENAEY AA+E Q   EG
Sbjct: 1   MQAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEG 60

Query: 62  RMAELENIITRAEVIDISTMSGD-RIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLV 120
           R+ ++E  ++ A+VID++ M  + R+ FGATV+++  +S +++ Y+IVGD EAD +  L+
Sbjct: 61  RIKDIEAKLSNAQVIDVTKMPNNGRVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLI 120

Query: 121 SISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI 158
           S++SPIAR LIGKE  D++ +  PGGE  +E+++V ++
Sbjct: 121 SVNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVEYL 158


gi|166007061|pdb|2P4V|A Chain A, Crystal Structure Of The Transcript Cleavage Factor, Greb At 2.6a Resolution Length = 158 Back     alignment and structure
gi|109157536|pdb|2F23|A Chain A, Crystal Structure Of Grea Factor Homolog 1 (Gfh1) Protein Of Thermus Thermophilus Length = 156 Back     alignment and structure
gi|83754983|pdb|2EUL|A Chain A, Structure Of The Transcription Factor Gfh1. Length = 156 Back     alignment and structure
>gi|90109221|pdb|2ETN|A Chain A, Crystal Structure Of Thermus Aquaticus Gfh1 Length = 157 Back     alignment and structure
>gi|149243253|pdb|2PN0|A Chain A, Prokaryotic Transcription Elongation Factor GreaGREB FROM Nitrosomonas Europaea Length = 141 Back     alignment and structure
gi|210060903|pdb|3BMB|A Chain A, Crystal Structure Of A New Rna Polymerase Interacting Protein Length = 136 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target158 transcription elongation factor GreA [Candidatus Liberi
1grj_A158 GREA protein; transcript elongation factor, transcript 6e-36
2f23_A156 Anti-cleavage anti-GREA transcription factor GFH1; anti 9e-31
2p4v_A158 Transcription elongation factor GREB; transcript cleava 8e-30
2pn0_A141 Prokaryotic transcription elongation factor GREA/GREB; 2e-26
3bmb_A136 Regulator of nucleoside diphosphate kinase; RNA polymer 5e-26
>1grj_A GREA protein; transcript elongation factor, transcript cleavage factor, transcription regulation; 2.20A {Escherichia coli} SCOP: a.2.1.1 d.26.1.2 Length = 158 Back     alignment and structure
 Score =  145 bits (366), Expect = 6e-36
 Identities = 71/157 (45%), Positives = 113/157 (71%), Gaps = 1/157 (0%)

Query: 3   DKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGR 62
             IP+T +G +K+++EL + +   RP II AI+EAR +GDL ENAEY AA+E Q   EGR
Sbjct: 2   QAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGR 61

Query: 63  MAELENIITRAEVIDISTMSGD-RIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVS 121
           + ++E  ++ A+VID++ M  + R+ FGATV+++  +S +++ Y+IVGD EAD +  L+S
Sbjct: 62  IKDIEAKLSNAQVIDVTKMPNNGRVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLIS 121

Query: 122 ISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI 158
           ++SPIAR LIGKE  D++ +  PGGE  +E+++V ++
Sbjct: 122 VNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVEYL 158


>2f23_A Anti-cleavage anti-GREA transcription factor GFH1; anti-GREA GFH1 thermus thermophilus; 1.60A {Thermus thermophilus HB27} SCOP: a.2.1.1 d.26.1.2 PDB: 2eul_A 2etn_A Length = 156 Back     alignment and structure
>2p4v_A Transcription elongation factor GREB; transcript cleavage, GRE-factors, RNA polymerase; 2.60A {Escherichia coli} Length = 158 Back     alignment and structure
>2pn0_A Prokaryotic transcription elongation factor GREA/GREB; structural genomics, APC6349, PSI-2, protein structure initiative; HET: MSE; 1.70A {Nitrosomonas europaea} Length = 141 Back     alignment and structure
>3bmb_A Regulator of nucleoside diphosphate kinase; RNA polymerase, elongation factor, anti-GRE factor, RNA binding protein; 1.91A {Escherichia coli} Length = 136 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target158 transcription elongation factor GreA [Candidatus Liberi
1grj_A158 GREA protein; transcript elongation factor, transcript 100.0
2f23_A156 Anti-cleavage anti-GREA transcription factor GFH1; anti 100.0
2p4v_A158 Transcription elongation factor GREB; transcript cleava 100.0
3bmb_A136 Regulator of nucleoside diphosphate kinase; RNA polymer 99.96
2pn0_A141 Prokaryotic transcription elongation factor GREA/GREB; 99.96
3gty_X 433 Trigger factor, TF; chaperone-client complex, cell cycl 94.13
>1grj_A GREA protein; transcript elongation factor, transcript cleavage factor, transcription regulation; 2.20A {Escherichia coli} SCOP: a.2.1.1 d.26.1.2 Back     alignment and structure
Probab=100.00  E-value=0  Score=331.89  Aligned_cols=157  Identities=45%  Similarity=0.815  Sum_probs=153.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             98431488999999999999987248999999999975176222430489998876879999999974444210472101
Q gi|254780440|r    2 VDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTM   81 (158)
Q Consensus         2 ~~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~   81 (158)
                      |+++|||++||++|++||++|++++||++++.+++|+++|||||||+|++||++|+++++||++|+.+|++|+|++++..
T Consensus         1 m~~i~lT~~g~~~L~~EL~~L~~~~r~e~~~~i~~A~~~GDl~Enaey~aAk~~~~~~e~ri~~l~~~l~~a~ivd~~~~   80 (158)
T 1grj_A            1 MQAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQVIDVTKM   80 (158)
T ss_dssp             -CCEEEEHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHTTCCGGGCHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECGGGS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHCCEEEECCCCC
T ss_conf             98527799999999999999986301778988999886578222646899999999999999999976413499757668


Q ss_pred             CC-CCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEEC
Q ss_conf             33-211136579995347652359999631013345881501317899872888887899982897199999998979
Q gi|254780440|r   82 SG-DRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI  158 (158)
Q Consensus        82 ~~-~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~yi  158 (158)
                      +. ++|.|||+|++.|.+++++.+|+||||+|+||+.++||+.||||+||||+++||+|+|.+|+|...|+|++|+||
T Consensus        81 ~~~~~V~~Gs~V~l~d~~~~~~~~~~ivg~~ead~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~I~~I~y~  158 (158)
T 1grj_A           81 PNNGRVIFGATVTVLNLDSDEEQTYRIVGDDEADFKQNLISVNSPIARGLIGKEEDDVVVIKTPGGEVEFEVIKVEYL  158 (158)
T ss_dssp             CCCSBCCTTCEEEEEETTTTEEEEEEEECTTTCBGGGTEEESSSHHHHHHTTCBTTCEECC------CCEEEEEEECC
T ss_pred             CCCCEEEEEEEEEEEECCCCEEEEEEEECCHHHHCCCCEECCCCHHHHHHHCCCCCCEEEEECCCCCEEEEEEEEEEC
T ss_conf             999979951399999868854899998680553176883347787899983898999899983997489999999989



>2f23_A Anti-cleavage anti-GREA transcription factor GFH1; anti-GREA GFH1 thermus thermophilus; 1.60A {Thermus thermophilus HB27} SCOP: a.2.1.1 d.26.1.2 PDB: 2eul_A 2etn_A Back     alignment and structure
>2p4v_A Transcription elongation factor GREB; transcript cleavage, GRE-factors, RNA polymerase; 2.60A {Escherichia coli} Back     alignment and structure
>3bmb_A Regulator of nucleoside diphosphate kinase; RNA polymerase, elongation factor, anti-GRE factor, RNA binding protein; 1.91A {Escherichia coli} Back     alignment and structure
>2pn0_A Prokaryotic transcription elongation factor GREA/GREB; structural genomics, APC6349, PSI-2, protein structure initiative; HET: MSE; 1.70A {Nitrosomonas europaea} Back     alignment and structure
>3gty_X Trigger factor, TF; chaperone-client complex, cell cycle, cell division, chaperone, isomerase, rotamase, ribonucleoprotein; 3.40A {Thermotoga maritima} PDB: 3gu0_A 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

IdentityAlignment graphLength Definition E-value
Target 158 transcription elongation factor GreA [Candidatus Liberi
d1grja178 a.2.1.1 (A:2-79) GreA transcript cleavage protein, N-te 2e-19
d2f23a175 a.2.1.1 (A:3-77) GreA transcript cleavage protein, N-te 4e-16
d1grja279 d.26.1.2 (A:80-158) GreA transcript cleavage factor, C- 9e-19
d2f23a279 d.26.1.2 (A:78-156) GreA transcript cleavage factor, C- 5e-18
>d1grja1 a.2.1.1 (A:2-79) GreA transcript cleavage protein, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 78 Back     information, alignment and structure

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: GreA transcript cleavage protein, N-terminal domain
family: GreA transcript cleavage protein, N-terminal domain
domain: GreA transcript cleavage protein, N-terminal domain
species: Escherichia coli [TaxId: 562]
 Score = 89.0 bits (221), Expect = 2e-19
 Identities = 36/76 (47%), Positives = 55/76 (72%)

Query: 4  KIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRM 63
           IP+T +G +K+++EL + +   RP II AI+EAR +GDL ENAEY AA+E Q   EGR+
Sbjct: 2  AIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRI 61

Query: 64 AELENIITRAEVIDIS 79
           ++E  ++ A+VID++
Sbjct: 62 KDIEAKLSNAQVIDVT 77


>d2f23a1 a.2.1.1 (A:3-77) GreA transcript cleavage protein, N-terminal domain {Thermus thermophilus [TaxId: 274]} Length = 75 Back     information, alignment and structure
>d1grja2 d.26.1.2 (A:80-158) GreA transcript cleavage factor, C-terminal domain {Escherichia coli [TaxId: 562]} Length = 79 Back     information, alignment and structure
>d2f23a2 d.26.1.2 (A:78-156) GreA transcript cleavage factor, C-terminal domain {Thermus thermophilus [TaxId: 274]} Length = 79 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target158 transcription elongation factor GreA [Candidatus Liberi
d1grja178 GreA transcript cleavage protein, N-terminal domain {Es 99.9
d2f23a175 GreA transcript cleavage protein, N-terminal domain {Th 99.86
d1grja279 GreA transcript cleavage factor, C-terminal domain {Esc 99.88
d2f23a279 GreA transcript cleavage factor, C-terminal domain {The 99.83
d1t11a3113 Trigger factor PPIase domain {Vibrio cholerae [TaxId: 6 91.14
>d1grja1 a.2.1.1 (A:2-79) GreA transcript cleavage protein, N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: All alpha proteins
fold: Long alpha-hairpin
superfamily: GreA transcript cleavage protein, N-terminal domain
family: GreA transcript cleavage protein, N-terminal domain
domain: GreA transcript cleavage protein, N-terminal domain
species: Escherichia coli [TaxId: 562]
Probab=99.90  E-value=4.9e-24  Score=171.06  Aligned_cols=78  Identities=46%  Similarity=0.761  Sum_probs=75.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             843148899999999999998724899999999997517622243048999887687999999997444421047210
Q gi|254780440|r    3 DKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDIST   80 (158)
Q Consensus         3 ~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~   80 (158)
                      ++||||++||++|++||++|++++||+++++|++||++|||||||||++||++|+++++||.+|+..|++|+|||++.
T Consensus         1 e~iplT~eg~~~L~~EL~~L~~~~rpei~~~I~~Ar~~GDlsENaeY~aAKe~q~~~e~RI~eLe~~L~~a~IId~sk   78 (78)
T d1grja1           1 QAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQVIDVTK   78 (78)
T ss_dssp             CCEEEEHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHTTCCGGGCHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECGGG
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEECCCCC
T ss_conf             998988999999999999998833799999999999848863337789999999999999999999982763328999



>d2f23a1 a.2.1.1 (A:3-77) GreA transcript cleavage protein, N-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1grja2 d.26.1.2 (A:80-158) GreA transcript cleavage factor, C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2f23a2 d.26.1.2 (A:78-156) GreA transcript cleavage factor, C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1t11a3 d.26.1.1 (A:135-247) Trigger factor PPIase domain {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 158 transcription elongation factor GreA [Candidatus L
1grj_A_1-8383 (A:1-83) GREA protein; transcript elongation facto 2e-20
2f23_A_1-8080 (A:1-80) Anti-cleavage anti-GREA transcription fac 4e-19
2p4v_A_1-8282 (A:1-82) Transcription elongation factor GREB; tra 4e-19
1grj_A_84-15875 (A:84-158) GREA protein; transcript elongation fac 3e-19
2f23_A_81-15676 (A:81-156) Anti-cleavage anti-GREA transcription f 6e-18
2p4v_A_83-15876 (A:83-158) Transcription elongation factor GREB; t 2e-17
3bmb_A_52-13685 (A:52-136) Regulator of nucleoside diphosphate kin 5e-17
2pn0_A_55-14187 (A:55-141) Prokaryotic transcription elongation fa 2e-15
>1grj_A (A:1-83) GREA protein; transcript elongation factor, transcript cleavage factor, transcription regulation; 2.20A {Escherichia coli}Length = 83 Back     alignment and structure
 Score = 92.5 bits (230), Expect = 2e-20
 Identities = 37/83 (44%), Positives = 58/83 (69%)

Query: 2  VDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEG 61
          +  IP+T +G +K+++EL + +   RP II AI+EAR +GDL ENAEY AA+E Q   EG
Sbjct: 1  MQAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEG 60

Query: 62 RMAELENIITRAEVIDISTMSGD 84
          R+ ++E  ++ A+VID++ M  +
Sbjct: 61 RIKDIEAKLSNAQVIDVTKMPNN 83


>2f23_A (A:1-80) Anti-cleavage anti-GREA transcription factor GFH1; anti-GREA GFH1 thermus thermophilus; 1.60A {Thermus thermophilus HB27}Length = 80 Back     alignment and structure
>2p4v_A (A:1-82) Transcription elongation factor GREB; transcript cleavage, GRE-factors, RNA polymerase; 2.60A {Escherichia coli}Length = 82 Back     alignment and structure
>1grj_A (A:84-158) GREA protein; transcript elongation factor, transcript cleavage factor, transcription regulation; 2.20A {Escherichia coli}Length = 75 Back     alignment and structure
>2f23_A (A:81-156) Anti-cleavage anti-GREA transcription factor GFH1; anti-GREA GFH1 thermus thermophilus; 1.60A {Thermus thermophilus HB27}Length = 76 Back     alignment and structure
>2p4v_A (A:83-158) Transcription elongation factor GREB; transcript cleavage, GRE-factors, RNA polymerase; 2.60A {Escherichia coli}Length = 76 Back     alignment and structure
>3bmb_A (A:52-136) Regulator of nucleoside diphosphate kinase; RNA polymerase, elongation factor, anti-GRE factor, RNA binding protein; 1.91A {Escherichia coli}Length = 85 Back     alignment and structure
>2pn0_A (A:55-141) Prokaryotic transcription elongation factor GREA/GREB; structural genomics, APC6349, PSI-2, protein structure initiative; HET: MSE; 1.70A {Nitrosomonas europaea}Length = 87 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target158 transcription elongation factor GreA [Candidatus Liberi
1grj_A_1-8383 GREA protein; transcript elongation factor, transc 99.91
2p4v_A_1-8282 Transcription elongation factor GREB; transcript c 99.91
2f23_A_1-8080 Anti-cleavage anti-GREA transcription factor GFH1; 99.9
1grj_A_84-15875 GREA protein; transcript elongation factor, transc 99.86
3bmb_A_52-13685 Regulator of nucleoside diphosphate kinase; RNA po 99.85
2pn0_A_55-14187 Prokaryotic transcription elongation factor GREA/G 99.85
2f23_A_81-15676 Anti-cleavage anti-GREA transcription factor GFH1; 99.84
2p4v_A_83-15876 Transcription elongation factor GREB; transcript c 99.83
>1grj_A (A:1-83) GREA protein; transcript elongation factor, transcript cleavage factor, transcription regulation; 2.20A {Escherichia coli} Back     alignment and structure
Probab=99.91  E-value=2.4e-24  Score=175.56  Aligned_cols=83  Identities=45%  Similarity=0.751  Sum_probs=80.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             98431488999999999999987248999999999975176222430489998876879999999974444210472101
Q gi|254780440|r    2 VDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTM   81 (158)
Q Consensus         2 ~~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~   81 (158)
                      |+++|||++||++|++||++|++++||+++++|++||++|||||||||++||++|+++++||.+|+.+|++|+||+++..
T Consensus         1 m~~~~lT~eG~~kL~~EL~~L~~~~rpe~~~~i~~Ar~~GDlsENaeY~aAke~q~~le~RI~~Le~~L~~a~Iid~~~~   80 (83)
T 1grj_A            1 MQAIPMTLRGAEKLREELDFLKSVRRPEIIAAIAEAREHGDLKENAEYHAAREQQGFCEGRIKDIEAKLSNAQVIDVTKM   80 (83)
T ss_dssp             -CCEEEEHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHTTCCGGGCHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECGGGS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCEEECCCCC
T ss_conf             97555289999999999999986122778999999986578220747899999999999899999998621276134446


Q ss_pred             CCC
Q ss_conf             332
Q gi|254780440|r   82 SGD   84 (158)
Q Consensus        82 ~~~   84 (158)
                      ++|
T Consensus        81 ~~~   83 (83)
T 1grj_A           81 PNN   83 (83)
T ss_dssp             CCC
T ss_pred             CCC
T ss_conf             898



>2p4v_A (A:1-82) Transcription elongation factor GREB; transcript cleavage, GRE-factors, RNA polymerase; 2.60A {Escherichia coli} Back     alignment and structure
>2f23_A (A:1-80) Anti-cleavage anti-GREA transcription factor GFH1; anti-GREA GFH1 thermus thermophilus; 1.60A {Thermus thermophilus HB27} Back     alignment and structure
>1grj_A (A:84-158) GREA protein; transcript elongation factor, transcript cleavage factor, transcription regulation; 2.20A {Escherichia coli} Back     alignment and structure
>3bmb_A (A:52-136) Regulator of nucleoside diphosphate kinase; RNA polymerase, elongation factor, anti-GRE factor, RNA binding protein; 1.91A {Escherichia coli} Back     alignment and structure
>2pn0_A (A:55-141) Prokaryotic transcription elongation factor GREA/GREB; structural genomics, APC6349, PSI-2, protein structure initiative; HET: MSE; 1.70A {Nitrosomonas europaea} Back     alignment and structure
>2f23_A (A:81-156) Anti-cleavage anti-GREA transcription factor GFH1; anti-GREA GFH1 thermus thermophilus; 1.60A {Thermus thermophilus HB27} Back     alignment and structure
>2p4v_A (A:83-158) Transcription elongation factor GREB; transcript cleavage, GRE-factors, RNA polymerase; 2.60A {Escherichia coli} Back     alignment and structure