Citrus Sinensis ID: 021438

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310--
Protein Sequence
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNLKL
Secondary Structure (PSIPRED)
ccccccccccccccEEEEccccccccccccEEEccccccccccccccccccccccccccccccccccccccccEEEEEccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccEEEccccccEEcHHccEEEcccEccccccHEEccccccccccccccccccccccccccEEEEcccccccccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHccccHHHcccccHHHccc
Coil and Loop (DISEMBL)
MADSYCADCKRLTEVvfdhsagdticseCGLVLEaysvdetsewrifanessdhdpvrvggplnpllsggglstviakptaggstellsgslgklqarsshpdrNLIQAFKSISAMSDRLGLVTTIKDRANEIYKkvedqkplrgrnQEAIVAACLYIACrqenkprtvKEFCSVANGTTKKEIGRAKEFIVKHLEAemgqsvemgtiHASDYLRRFCSNLGMTNQAVKAAQEAVQKsedldirrspISVAAAVIYIITQLsndtkplkeISIVTRVAEGTIKNVYKDLFPHLariipdwfaneediknlkl
Flexible Loop (DISEMBL)
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFAnessdhdpvrVGGPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKsisamsdrlGLVTTIKDRANEIykkvedqkplrgrnQEAIVAACLYIACrqenkprtvKEFCSvangttkkeigRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQksedldirrsPISVAAAVIYIItqlsndtkplkeISIVTRVAEGTIKNVYKDLFPHLARiipdwfaneediknlkl
Low Complexity Region (SEG)
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVggplnpllsggglsTVIAKPTAggstellsgslgklQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNqavkaaqeavqkSEDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNLKL
Disordered region (IsUnstruct)
****YCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFAN**********************L*TV*******************************IQAFKSISAMSDRLGLVTTIKDRANEIYKKV*******GRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVK***********LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFAN*********
Disordered Region (DISOPRED)
**DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWR********************LLSGGGL********************************NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNLKL
Disordered Region (DISEMBL)
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGGSTELLSGSL*********PDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ**************LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNLKL
Disordered Region (DISPRO)
****YCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFAN***********GPLNPLLSGGGLSTVIAKPTA***TELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDI****L
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNLKL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	312	2.2.26 [Sep-21-2011]
P48513	313	Transcription initiation	yes	no	0.993	0.990	0.767	1e-144
Q8W0W3	312	Transcription initiation	yes	no	0.990	0.990	0.767	1e-142
Q9SS44	312	Transcription initiation	yes	no	0.993	0.993	0.752	1e-142
P48512	312	Transcription initiation	no	no	0.990	0.990	0.712	1e-133
P29052	315	Transcription initiation	yes	no	0.932	0.923	0.463	4e-67
P29054	316	Transcription initiation	N/A	no	0.926	0.914	0.442	3e-63
P62916	316	Transcription initiation	yes	no	0.926	0.914	0.436	1e-60
P62915	316	Transcription initiation	yes	no	0.926	0.914	0.436	1e-60
Q5R886	316	Transcription initiation	yes	no	0.926	0.914	0.436	1e-60
Q4R3J5	316	Transcription initiation	N/A	no	0.926	0.914	0.436	1e-60

>sp|P48513|TF2B_SOYBN Transcription initiation factor IIB OS=Glycine max GN=TFIIB1 PE=2 SV=1

 Score =  511 bits (1317), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 238/310 (76%), Positives = 274/310 (88%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           M+D++C+DCKR TEVVFDHSAGDT+CSECGLVLE++S+DETSEWR FANES D+DP RVG
Sbjct: 1   MSDAFCSDCKRQTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPNRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRL 120
           GP NPLL+ GGLSTVIAKP  GG  E LS SLG+ Q R S+PDR LIQAFK+I+ MSDRL
Sbjct: 61  GPSNPLLTDGGLSTVIAKPNGGGGGEFLSSSLGRWQNRGSNPDRALIQAFKTIATMSDRL 120

Query: 121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
           GLV TIKDRANEIYK+VEDQK  RGRNQ+A++AACLYIACRQE+KPRTVKE CSVANG T
Sbjct: 121 GLVATIKDRANEIYKRVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGAT 180

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           KKEIGRAKE+IVK L  E G +VEMGTIHA D++RRFCSNL M NQAVKAAQEAVQKSE+
Sbjct: 181 KKEIGRAKEYIVKQLGLENGNAVEMGTIHAGDFMRRFCSNLCMNNQAVKAAQEAVQKSEE 240

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
            DIRRSPIS+AAAVIYIITQLS+D KPLK+IS+ T VAEGTI+N YKDL+PH+++IIP+W
Sbjct: 241 FDIRRSPISIAAAVIYIITQLSDDKKPLKDISLATGVAEGTIRNSYKDLYPHVSKIIPNW 300

Query: 301 FANEEDIKNL 310
           +A EED+KNL
Sbjct: 301 YAKEEDLKNL 310

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.
Glycine max (taxid: 3847)

>sp|Q8W0W3|TF2B_ORYSJ Transcription initiation factor IIB OS=Oryza sativa subsp. japonica GN=TFIIB PE=1 SV=1

 Score =  504 bits (1299), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 238/310 (76%), Positives = 275/310 (88%), Gaps = 1/310 (0%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           M+DS+C DCK+ TEV FDHSAGDT+C+ECGLVLEA+SVDETSEWR FANESSD+DPVRVG
Sbjct: 1   MSDSFCPDCKKHTEVAFDHSAGDTVCTECGLVLEAHSVDETSEWRTFANESSDNDPVRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRL 120
           GP NPLL+ GGLSTVIAKP  G   E LS SLG+ Q R S+PDR+LI AF++I+ M+DRL
Sbjct: 61  GPTNPLLTDGGLSTVIAKPN-GAQGEFLSSSLGRWQNRGSNPDRSLILAFRTIANMADRL 119

Query: 121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
           GLV TIKDRANEIYKKVED K +RGRNQ+AI+AACLYIACRQE++PRTVKE CSVANG T
Sbjct: 120 GLVATIKDRANEIYKKVEDLKSIRGRNQDAILAACLYIACRQEDRPRTVKEICSVANGAT 179

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           KKEIGRAKEFIVK LE EMGQS+EMGTIHA D+LRRFCS LGM NQAVKAAQEAVQ+SE+
Sbjct: 180 KKEIGRAKEFIVKQLEVEMGQSMEMGTIHAGDFLRRFCSTLGMNNQAVKAAQEAVQRSEE 239

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
           LDIRRSPIS+AAAVIY+ITQLS+D KPLK+IS+ T VAEGTI+N YKDL+P+ +R+IP+ 
Sbjct: 240 LDIRRSPISIAAAVIYMITQLSDDKKPLKDISLATGVAEGTIRNSYKDLYPYASRLIPNT 299

Query: 301 FANEEDIKNL 310
           +A EED+KNL
Sbjct: 300 YAKEEDLKNL 309

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SS44|TF2B2_ARATH Transcription initiation factor IIB-2 OS=Arabidopsis thaliana GN=TFIIB2 PE=2 SV=1

 Score =  504 bits (1297), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 234/311 (75%), Positives = 275/311 (88%), Gaps = 1/311 (0%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           M+D++C+DCKR TEVVFDHSAGDT+CSECGLVLE++S+DETSEWR FANES D+DPVRVG
Sbjct: 1   MSDAFCSDCKRHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRL 120
           GP NPLL+ GGL+TVI+KP  G S + LS SLG+ Q R S+PDR LI AFK+I+ M+DRL
Sbjct: 61  GPTNPLLADGGLTTVISKPN-GSSGDFLSSSLGRWQNRGSNPDRGLIVAFKTIATMADRL 119

Query: 121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
           GLV TIKDRANEIYK+VEDQK  RGRNQ+A++AACLYIACRQE+KPRTVKE CSVANG T
Sbjct: 120 GLVATIKDRANEIYKRVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGAT 179

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           KKEIGRAKE+IVK L  E GQ VEMGTIHA D++RRFCSNLGMTNQ VKAAQE+VQKSE+
Sbjct: 180 KKEIGRAKEYIVKQLGLETGQLVEMGTIHAGDFMRRFCSNLGMTNQTVKAAQESVQKSEE 239

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
            DIRRSPIS+AAAVIYIITQLS++ KPL++IS+ T VAEGTI+N YKDL+PHL++IIP W
Sbjct: 240 FDIRRSPISIAAAVIYIITQLSDEKKPLRDISVATGVAEGTIRNSYKDLYPHLSKIIPAW 299

Query: 301 FANEEDIKNLK 311
           +A EED+KNL+
Sbjct: 300 YAKEEDLKNLQ 310

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Arabidopsis thaliana (taxid: 3702)

>sp|P48512|TF2B1_ARATH Transcription initiation factor IIB-1 OS=Arabidopsis thaliana GN=TFIIB1 PE=1 SV=1

 Score =  473 bits (1218), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 221/310 (71%), Positives = 264/310 (85%), Gaps = 1/310 (0%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           M+D+YC DCK+ TE+V DHSAGDT+CSECGLVLE++S+DETSEWR FANESS+ DP RVG
Sbjct: 1   MSDAYCTDCKKETELVVDHSAGDTLCSECGLVLESHSIDETSEWRTFANESSNSDPNRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRL 120
           GP NPLL+   L+TVIAKP  G S + LS SLG+ Q R+S+ DR LIQAFK+I+ MS+RL
Sbjct: 61  GPTNPLLADSALTTVIAKPN-GSSGDFLSSSLGRWQNRNSNSDRGLIQAFKTIATMSERL 119

Query: 121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
           GLV TIKDRANE+YK++EDQK  RGRNQ+A+ AACLYIACRQE+KPRT+KE C +ANG T
Sbjct: 120 GLVATIKDRANELYKRLEDQKSSRGRNQDALYAACLYIACRQEDKPRTIKEICVIANGAT 179

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           KKEIGRAK++IVK L  E GQSV++GTIHA D++RRFCSNL M+N AVKAAQEAVQKSE+
Sbjct: 180 KKEIGRAKDYIVKTLGLEPGQSVDLGTIHAGDFMRRFCSNLAMSNHAVKAAQEAVQKSEE 239

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
            DIRRSPIS+AA VIYIITQLS+D K LK+IS  T VAEGTI+N YKDL+PHL++I P W
Sbjct: 240 FDIRRSPISIAAVVIYIITQLSDDKKTLKDISHATGVAEGTIRNSYKDLYPHLSKIAPSW 299

Query: 301 FANEEDIKNL 310
           +A EED+KNL
Sbjct: 300 YAKEEDLKNL 309

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Arabidopsis thaliana (taxid: 3702)

>sp|P29052|TF2B_DROME Transcription initiation factor IIB OS=Drosophila melanogaster GN=TfIIB PE=2 SV=1

 Score =  254 bits (650), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 139/300 (46%), Positives = 189/300 (63%), Gaps = 9/300 (3%)

Query: 13  TEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGL 72
           + ++ D+ AGD ICSECGLV+    +D  SEWR F+NE S  DP RVGGP NPLLSGG L
Sbjct: 20  SPLIEDYRAGDMICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPLLSGGDL 79

Query: 73  STVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANE 132
           ST+I   T   S +       + +   S  DR+LI AFK IS+M+DR+ L  TI DRAN 
Sbjct: 80  STIIGPGTGSASFDAFGAPKYQNRRTMSSSDRSLISAFKEISSMADRINLPKTIVDRANN 139

Query: 133 IYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIV 192
           ++K+V D K L+GR+ +A  +ACLYIACRQE  PRT KE C+V+   +KKEIGR  +  +
Sbjct: 140 LFKQVHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSK-ISKKEIGRCFKLTL 198

Query: 193 KHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI--RRSPISV 250
           K LE     SV++  I  +D++ RFC+NL + N   +AA    +K+ ++DI   RSPISV
Sbjct: 199 KALET----SVDL--ITTADFMCRFCANLDLPNMVQRAATHIAKKAVEMDIVPGRSPISV 252

Query: 251 AAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
           AAA IY+ +Q S   +  KEI  +  VA+ TI+  YK ++PH A++ P+ F     I  L
Sbjct: 253 AAAAIYMASQASEHKRSQKEIGDIAGVADVTIRQSYKLMYPHAAKLFPEDFKFTTPIDQL 312

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Drosophila melanogaster (taxid: 7227)

>sp|P29054|TF2B_XENLA Transcription initiation factor IIB OS=Xenopus laevis GN=gtf2b PE=2 SV=1

 Score =  242 bits (617), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 132/298 (44%), Positives = 182/298 (61%), Gaps = 9/298 (3%)

Query: 15  VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLST 74
           +V D+ AGD ICSECGLV+    +D  SEWR F+N+ +  DP RVG   NPLLSGG L+T
Sbjct: 23  LVEDYRAGDMICSECGLVVGDRVIDVGSEWRTFSNDKAAADPSRVGDAQNPLLSGGDLTT 82

Query: 75  VIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIY 134
           +I K T   S +    S  + +   S  DR ++ AFK I+ MSDR+ L   I DR N ++
Sbjct: 83  MIGKGTGSASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITNMSDRINLPRNIIDRTNNLF 142

Query: 135 KKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194
           K+V +QK L+GR+ +AI +ACLYIACRQE  PRT KE C+V+   +KKEIGR  + I+K 
Sbjct: 143 KQVYEQKSLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSR-ISKKEIGRCFKLILKA 201

Query: 195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI--RRSPISVAA 252
           LE        +  I   D++ RFCSNLG+T Q   AA    +K+ +LD+   RSPISVAA
Sbjct: 202 LE------TNVDLITTGDFMSRFCSNLGLTKQVQMAATHIARKAVELDLVPGRSPISVAA 255

Query: 253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
           A IY+ +Q S + +  KEI  +  VA+ TI+  Y+ ++P    + P  F  +  +  L
Sbjct: 256 AAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPADFKFDTPVDKL 313

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Xenopus laevis (taxid: 8355)

>sp|P62916|TF2B_RAT Transcription initiation factor IIB OS=Rattus norvegicus GN=Gtf2b PE=2 SV=1

 Score =  233 bits (595), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 180/298 (60%), Gaps = 9/298 (3%)

Query: 15  VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLST 74
           +V D+ AGD IC ECGLV+    +D  SEWR F+N+ +  DP RVG   NPLLS G LST
Sbjct: 23  LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPLLSDGDLST 82

Query: 75  VIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIY 134
           +I K T   S +    S  + +   S  DR ++ AFK I+ M+DR+ L   I DR N ++
Sbjct: 83  MIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLF 142

Query: 135 KKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194
           K+V +QK L+GR  +AI +ACLYIACRQE  PRT KE C+V+   +KKEIGR  + I+K 
Sbjct: 143 KQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSR-ISKKEIGRCFKLILKA 201

Query: 195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI--RRSPISVAA 252
           LE     SV++  I   D++ RFCSNL +  Q   AA    +K+ +LD+   RSPISVAA
Sbjct: 202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAA 255

Query: 253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
           A IY+ +Q S + +  KEI  +  VA+ TI+  Y+ ++P    + P  F  +  +  L
Sbjct: 256 AAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPSDFKFDTPVDKL 313

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Rattus norvegicus (taxid: 10116)

>sp|P62915|TF2B_MOUSE Transcription initiation factor IIB OS=Mus musculus GN=Gtf2b PE=1 SV=1

 Score =  233 bits (595), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 180/298 (60%), Gaps = 9/298 (3%)

Query: 15  VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLST 74
           +V D+ AGD IC ECGLV+    +D  SEWR F+N+ +  DP RVG   NPLLS G LST
Sbjct: 23  LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPLLSDGDLST 82

Query: 75  VIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIY 134
           +I K T   S +    S  + +   S  DR ++ AFK I+ M+DR+ L   I DR N ++
Sbjct: 83  MIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLF 142

Query: 135 KKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194
           K+V +QK L+GR  +AI +ACLYIACRQE  PRT KE C+V+   +KKEIGR  + I+K 
Sbjct: 143 KQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSR-ISKKEIGRCFKLILKA 201

Query: 195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI--RRSPISVAA 252
           LE     SV++  I   D++ RFCSNL +  Q   AA    +K+ +LD+   RSPISVAA
Sbjct: 202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAA 255

Query: 253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
           A IY+ +Q S + +  KEI  +  VA+ TI+  Y+ ++P    + P  F  +  +  L
Sbjct: 256 AAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPSDFKFDTPVDKL 313

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Mus musculus (taxid: 10090)

>sp|Q5R886|TF2B_PONAB Transcription initiation factor IIB OS=Pongo abelii GN=GTF2B PE=2 SV=1

 Score =  233 bits (595), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 180/298 (60%), Gaps = 9/298 (3%)

Query: 15  VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLST 74
           +V D+ AGD IC ECGLV+    +D  SEWR F+N+ +  DP RVG   NPLLS G LST
Sbjct: 23  LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPLLSDGDLST 82

Query: 75  VIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIY 134
           +I K T   S +    S  + +   S  DR ++ AFK I+ M+DR+ L   I DR N ++
Sbjct: 83  MIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLF 142

Query: 135 KKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194
           K+V +QK L+GR  +AI +ACLYIACRQE  PRT KE C+V+   +KKEIGR  + I+K 
Sbjct: 143 KQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSR-ISKKEIGRCFKLILKA 201

Query: 195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI--RRSPISVAA 252
           LE     SV++  I   D++ RFCSNL +  Q   AA    +K+ +LD+   RSPISVAA
Sbjct: 202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAA 255

Query: 253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
           A IY+ +Q S + +  KEI  +  VA+ TI+  Y+ ++P    + P  F  +  +  L
Sbjct: 256 AAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTDFKFDTPVDKL 313

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Pongo abelii (taxid: 9601)

>sp|Q4R3J5|TF2B_MACFA Transcription initiation factor IIB OS=Macaca fascicularis GN=GTF2B PE=2 SV=1

 Score =  233 bits (595), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 180/298 (60%), Gaps = 9/298 (3%)

Query: 15  VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLST 74
           +V D+ AGD IC ECGLV+    +D  SEWR F+N+ +  DP RVG   NPLLS G LST
Sbjct: 23  LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPLLSDGDLST 82

Query: 75  VIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIY 134
           +I K T   S +    S  + +   S  DR ++ AFK I+ M+DR+ L   I DR N ++
Sbjct: 83  MIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLF 142

Query: 135 KKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194
           K+V +QK L+GR  +AI +ACLYIACRQE  PRT KE C+V+   +KKEIGR  + I+K 
Sbjct: 143 KQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSR-ISKKEIGRCFKLILKA 201

Query: 195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI--RRSPISVAA 252
           LE     SV++  I   D++ RFCSNL +  Q   AA    +K+ +LD+   RSPISVAA
Sbjct: 202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAA 255

Query: 253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
           A IY+ +Q S + +  KEI  +  VA+ TI+  Y+ ++P    + P  F  +  +  L
Sbjct: 256 AAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTDFKFDTPVDKL 313

General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Macaca fascicularis (taxid: 9541)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	312
224135681	311	predicted protein [Populus trichocarpa]	0.990	0.993	0.841	1e-147
351724605	313	transcription initiation factor IIB [Gly	0.993	0.990	0.767	1e-142
449465789	312	PREDICTED: transcription initiation fact	0.990	0.990	0.770	1e-142
255544920	312	transcription initiation factor iib, put	0.990	0.990	0.770	1e-142
317106705	312	JHL06B08.6 [Jatropha curcas]	0.990	0.990	0.774	1e-142
225464249	312	PREDICTED: transcription initiation fact	0.990	0.990	0.774	1e-142
225441886	312	PREDICTED: transcription initiation fact	0.990	0.990	0.770	1e-142
225436547	314	PREDICTED: transcription initiation fact	0.993	0.987	0.771	1e-141
297829558	312	transcription initiation factor IIB-2 [A	0.993	0.993	0.755	1e-141
255588003	312	transcription initiation factor iib, put	0.990	0.990	0.770	1e-141

>gi|224135681|ref|XP_002322134.1| predicted protein [Populus trichocarpa] gi|222869130|gb|EEF06261.1| predicted protein [Populus trichocarpa]

 Score =  525 bits (1353), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 261/310 (84%), Positives = 285/310 (91%), Gaps = 1/310 (0%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           M DSYC DCKRLTE+VFDHSAGDTICSECGL+LEA+SVDETSEWR F+NESSDHDP RVG
Sbjct: 1   MEDSYCPDCKRLTEIVFDHSAGDTICSECGLILEAHSVDETSEWRTFSNESSDHDPNRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRL 120
           GPLNPLL+ GGLST I+K T GGS ELLS SLGK Q+R ++PDRN IQAFKSI+AM+DRL
Sbjct: 61  GPLNPLLADGGLSTTISK-TNGGSNELLSCSLGKWQSRGANPDRNRIQAFKSIAAMADRL 119

Query: 121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
           GLVTTIKDRANEIYKKVEDQKPL+GRNQ+AI+AACLYIACRQENK RTVKE CSV NGTT
Sbjct: 120 GLVTTIKDRANEIYKKVEDQKPLKGRNQDAILAACLYIACRQENKARTVKEICSVVNGTT 179

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           KKEIGRAKEFIVKHLE EMG S+EMGTIHA+DYLRRFCSNLGMTNQAVKAA EAVQKSE+
Sbjct: 180 KKEIGRAKEFIVKHLEVEMGHSMEMGTIHAADYLRRFCSNLGMTNQAVKAAHEAVQKSEE 239

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
           LDIRRSPIS+AAAVIYII QLS+D KPLK+IS+VT+VAEGTIKN YKDL PHL++IIP W
Sbjct: 240 LDIRRSPISIAAAVIYIIIQLSDDKKPLKDISVVTQVAEGTIKNSYKDLSPHLSQIIPSW 299

Query: 301 FANEEDIKNL 310
           FA EEDIKNL
Sbjct: 300 FAKEEDIKNL 309

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351724605|ref|NP_001238343.1| transcription initiation factor IIB [Glycine max] gi|1351222|sp|P48513.1|TF2B_SOYBN RecName: Full=Transcription initiation factor IIB; AltName: Full=General transcription factor TFIIB gi|945087|gb|AAB09756.1| transcription factor TFIIB [Glycine max]

 Score =  511 bits (1317), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 238/310 (76%), Positives = 274/310 (88%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           M+D++C+DCKR TEVVFDHSAGDT+CSECGLVLE++S+DETSEWR FANES D+DP RVG
Sbjct: 1   MSDAFCSDCKRQTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPNRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRL 120
           GP NPLL+ GGLSTVIAKP  GG  E LS SLG+ Q R S+PDR LIQAFK+I+ MSDRL
Sbjct: 61  GPSNPLLTDGGLSTVIAKPNGGGGGEFLSSSLGRWQNRGSNPDRALIQAFKTIATMSDRL 120

Query: 121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
           GLV TIKDRANEIYK+VEDQK  RGRNQ+A++AACLYIACRQE+KPRTVKE CSVANG T
Sbjct: 121 GLVATIKDRANEIYKRVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGAT 180

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           KKEIGRAKE+IVK L  E G +VEMGTIHA D++RRFCSNL M NQAVKAAQEAVQKSE+
Sbjct: 181 KKEIGRAKEYIVKQLGLENGNAVEMGTIHAGDFMRRFCSNLCMNNQAVKAAQEAVQKSEE 240

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
            DIRRSPIS+AAAVIYIITQLS+D KPLK+IS+ T VAEGTI+N YKDL+PH+++IIP+W
Sbjct: 241 FDIRRSPISIAAAVIYIITQLSDDKKPLKDISLATGVAEGTIRNSYKDLYPHVSKIIPNW 300

Query: 301 FANEEDIKNL 310
           +A EED+KNL
Sbjct: 301 YAKEEDLKNL 310

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449465789|ref|XP_004150610.1| PREDICTED: transcription initiation factor IIB-2-like [Cucumis sativus] gi|449529834|ref|XP_004171903.1| PREDICTED: transcription initiation factor IIB-2-like [Cucumis sativus]

 Score =  511 bits (1316), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 239/310 (77%), Positives = 275/310 (88%), Gaps = 1/310 (0%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           M+D++C+DCKR TEVVFDHSAGDT+CSECGLVLE++S+DETSEWR FANES D+DPVRVG
Sbjct: 1   MSDAFCSDCKRQTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRL 120
           GP NPLL+ GGLSTVIAKP  G + E LS SLG+ Q R S+PDR LI AFK+I+ MSDRL
Sbjct: 61  GPTNPLLADGGLSTVIAKPN-GTTGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRL 119

Query: 121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
           GLV TIKDRANEIYK+VEDQK  RGRNQ+A++AACLYIACRQE+KPRTVKE CSVANG T
Sbjct: 120 GLVATIKDRANEIYKRVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGAT 179

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           KKEIGRAKE+IVK L  E GQSVEMGTIHA D++RRFCSNLGM NQAVKAAQEAVQKSE+
Sbjct: 180 KKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAVKAAQEAVQKSEE 239

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
            DIRRSPIS+AAAVIYIITQLS+D KPLK+IS+ T VAEGTI+N YKDL+PH+++I+P W
Sbjct: 240 FDIRRSPISIAAAVIYIITQLSDDKKPLKDISVATGVAEGTIRNSYKDLYPHVSKILPGW 299

Query: 301 FANEEDIKNL 310
           +A EED+KNL
Sbjct: 300 YAKEEDLKNL 309

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255544920|ref|XP_002513521.1| transcription initiation factor iib, putative [Ricinus communis] gi|223547429|gb|EEF48924.1| transcription initiation factor iib, putative [Ricinus communis]

 Score =  511 bits (1316), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 239/310 (77%), Positives = 278/310 (89%), Gaps = 1/310 (0%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           MAD+YC DCKR TEVVFDHSAGDT+CSECGLVLE++S+DETSEWR FANES+D+DPVRVG
Sbjct: 1   MADTYCPDCKRPTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESADNDPVRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRL 120
           GP NPLL+ GGLSTVI+KPT G S + L+ SLG+ Q R S+PDR+LIQAFK+I+ MSDRL
Sbjct: 61  GPSNPLLADGGLSTVISKPT-GASGDFLTSSLGRWQNRGSNPDRSLIQAFKTIATMSDRL 119

Query: 121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
           GLV TIKDRANEIYKKVEDQKPLRGRNQ+A++AACLYIACRQE+KPRTVKE CSVANG T
Sbjct: 120 GLVATIKDRANEIYKKVEDQKPLRGRNQDAVLAACLYIACRQEDKPRTVKEICSVANGAT 179

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           KKEIGRAKE+IVK LE E+GQS+EMGTIHA D+LRRFCS+LGM NQAVKAAQEAV+KSE+
Sbjct: 180 KKEIGRAKEYIVKQLEVELGQSMEMGTIHAGDFLRRFCSHLGMNNQAVKAAQEAVKKSEE 239

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
           LDIRRSPIS+AAA+IY+ITQLS + K LK+IS  T VAEGTI+N YKDL+P+ +RI+P W
Sbjct: 240 LDIRRSPISIAAAIIYMITQLSEEKKLLKDISTSTGVAEGTIRNSYKDLYPYASRIVPSW 299

Query: 301 FANEEDIKNL 310
           +A EED+ NL
Sbjct: 300 YAKEEDLINL 309

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|317106705|dbj|BAJ53205.1| JHL06B08.6 [Jatropha curcas]

 Score =  510 bits (1314), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 240/310 (77%), Positives = 273/310 (88%), Gaps = 1/310 (0%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           M D++C+DCKR TEVVFDHSAGDT+CSECGLVLE++S+DETSEWR FANES D+DPVRVG
Sbjct: 1   MGDAFCSDCKRQTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRL 120
           GP NPLL+ GGLSTVIAKP  G S E LS SLG+ Q R S+PDR LI AFK+I+ MSDRL
Sbjct: 61  GPTNPLLADGGLSTVIAKPN-GASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRL 119

Query: 121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
           GLV TIKDRANEIYKKVEDQK  RGRNQ+A++AACLYIACRQE+KPRTVKE CSVANG T
Sbjct: 120 GLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGAT 179

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           KKEIGRAKE+IVK L  E GQSVEMGTIHA D++RRFCSNLGM NQA+KAAQEAVQKSE+
Sbjct: 180 KKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAMKAAQEAVQKSEE 239

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
            DIRRSPIS+AAAVIYII+QLS+D KPL+EIS  T VAEGTI+N YKDL+PH+++IIP W
Sbjct: 240 FDIRRSPISIAAAVIYIISQLSDDKKPLREISQATGVAEGTIRNSYKDLYPHVSKIIPGW 299

Query: 301 FANEEDIKNL 310
           +A EED+KNL
Sbjct: 300 YAKEEDLKNL 309

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225464249|ref|XP_002269045.1| PREDICTED: transcription initiation factor IIB-2 [Vitis vinifera] gi|296088031|emb|CBI35314.3| unnamed protein product [Vitis vinifera]

 Score =  510 bits (1313), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 240/310 (77%), Positives = 275/310 (88%), Gaps = 1/310 (0%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           MAD++C DCK+ TEVVFDHSAGDT+CSECGLVLE++S+DETSEWR FANES D+DPVRVG
Sbjct: 1   MADAFCTDCKKNTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRL 120
           GP NPLL+ GGLSTVIAKP  G S + LS SLG+ Q R S+PDR LI AFK+I+ MSDRL
Sbjct: 61  GPSNPLLTDGGLSTVIAKPN-GVSGDFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRL 119

Query: 121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
           GLV TIKDRANEIYKKVEDQK  RGRNQ+A++AACLYIACRQE+KPRTVKE CSVANG T
Sbjct: 120 GLVATIKDRANEIYKKVEDQKSTRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGAT 179

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           KKEIGRAKE+IVK LEAE GQSVEMGTIHA D++RRFCSNLGMTNQ VKAAQEAVQKSE+
Sbjct: 180 KKEIGRAKEYIVKQLEAEKGQSVEMGTIHAGDFMRRFCSNLGMTNQVVKAAQEAVQKSEE 239

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
            DIRRSP+S+AAAVIYIITQLS++ K L++ISI T VAEGTI+N YKDL+PH++RIIP W
Sbjct: 240 FDIRRSPVSIAAAVIYIITQLSDEKKLLRDISIATGVAEGTIRNSYKDLYPHISRIIPSW 299

Query: 301 FANEEDIKNL 310
           +A EED++NL
Sbjct: 300 YAKEEDLRNL 309

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225441886|ref|XP_002284342.1| PREDICTED: transcription initiation factor IIB-2 [Vitis vinifera] gi|297739630|emb|CBI29812.3| unnamed protein product [Vitis vinifera]

 Score =  508 bits (1309), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 239/310 (77%), Positives = 275/310 (88%), Gaps = 1/310 (0%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           MAD++C DCK+ TEVVFDHSAGDT+CSECGLVLE++S+DETSEWR FANES D+DPVRVG
Sbjct: 1   MADAFCTDCKKNTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRL 120
           GP NPLL+ GGLSTVIAKP  G S + LS SLG+ Q R S+PDR LI AFK+I+ MSDRL
Sbjct: 61  GPSNPLLTDGGLSTVIAKPN-GVSGDFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRL 119

Query: 121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
           GLV TIKDRANEIYKKVEDQK  RGRNQ+A++AACLYIACRQE+KPRTVKE CSVANG T
Sbjct: 120 GLVATIKDRANEIYKKVEDQKSTRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGAT 179

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           KKEIGRAKE+IVK LEAE GQSVEMGTIHA D++RRFCSNLGMTNQ VKAAQEAVQKSE+
Sbjct: 180 KKEIGRAKEYIVKQLEAEKGQSVEMGTIHAGDFMRRFCSNLGMTNQVVKAAQEAVQKSEE 239

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
            DIRRSP+S+AAAVIYIITQLS++ K L++ISI T VAEGTI+N YKDL+PH+++IIP W
Sbjct: 240 FDIRRSPVSIAAAVIYIITQLSDEKKLLRDISIATGVAEGTIRNSYKDLYPHISKIIPSW 299

Query: 301 FANEEDIKNL 310
           +A EED++NL
Sbjct: 300 YAKEEDLRNL 309

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225436547|ref|XP_002277679.1| PREDICTED: transcription initiation factor IIB [Vitis vinifera] gi|297734946|emb|CBI17180.3| unnamed protein product [Vitis vinifera]

 Score =  507 bits (1305), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 240/311 (77%), Positives = 277/311 (89%), Gaps = 1/311 (0%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           M D+YC +CKR TEVV DHSAGDT+CSECGLVLEA+S+DE SEWR FANES+D+DPVRVG
Sbjct: 1   MTDTYCPECKRYTEVVLDHSAGDTVCSECGLVLEAHSIDEASEWRTFANESADNDPVRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGG-STELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDR 119
           GP NPLL+ GGLST+I+KP+ GG S + LS SLG+ Q R S+PDR+LIQAFK+I+ M DR
Sbjct: 61  GPSNPLLADGGLSTLISKPSNGGPSNDFLSSSLGRWQNRGSNPDRSLIQAFKTIATMCDR 120

Query: 120 LGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT 179
           LGLV TIKD ANEIYKKVEDQKPLRGRNQ+AI+AAC+YIACRQE+KPRTVKE CSVANG 
Sbjct: 121 LGLVATIKDLANEIYKKVEDQKPLRGRNQDAILAACIYIACRQEDKPRTVKEICSVANGA 180

Query: 180 TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSE 239
           TKKEIGRAKE+IVK LE EMGQS+EMGTIHA D+LRRFCS+LGMTNQAVKAAQEAVQKSE
Sbjct: 181 TKKEIGRAKEYIVKQLEVEMGQSMEMGTIHAGDFLRRFCSHLGMTNQAVKAAQEAVQKSE 240

Query: 240 DLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPD 299
           +LDIRRSPISVAAAVIY+ITQLS+D K LK+IS+ T VAEGTI+N YKDL+P+ +RIIP 
Sbjct: 241 ELDIRRSPISVAAAVIYMITQLSDDKKLLKDISLATGVAEGTIRNSYKDLYPYASRIIPS 300

Query: 300 WFANEEDIKNL 310
            +A EED++NL
Sbjct: 301 SYAKEEDLRNL 311

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297829558|ref|XP_002882661.1| transcription initiation factor IIB-2 [Arabidopsis lyrata subsp. lyrata] gi|297328501|gb|EFH58920.1| transcription initiation factor IIB-2 [Arabidopsis lyrata subsp. lyrata]

 Score =  507 bits (1305), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 235/311 (75%), Positives = 276/311 (88%), Gaps = 1/311 (0%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           M+D++C+DCKR TEVVFDHSAGDT+CSECGLVLE++S+DETSEWR FANES D+DPVRVG
Sbjct: 1   MSDAFCSDCKRHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRL 120
           GP NPLL+ GGL+TVI+KP  G S + LS SLG+ Q R S+PDR LI AFK+I+ M+DRL
Sbjct: 61  GPTNPLLADGGLTTVISKPN-GSSGDFLSSSLGRWQNRGSNPDRGLIVAFKTIATMADRL 119

Query: 121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
           GLV TIKDRANEIYK+VEDQK  RGRNQ+A++AACLYIACRQE+KPRTVKE CSVANG T
Sbjct: 120 GLVATIKDRANEIYKRVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGAT 179

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           KKEIGRAKE+IVK L  E GQSVEMGTIHA D++RRFCSNLGMTNQ VKAAQE+VQKSE+
Sbjct: 180 KKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMTNQTVKAAQESVQKSEE 239

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
            DIRRSPIS+AAAVIYIITQLS++ KPL++IS+ T VAEGTI+N YKDL+PHL++IIP W
Sbjct: 240 FDIRRSPISIAAAVIYIITQLSDEKKPLRDISVATGVAEGTIRNSYKDLYPHLSKIIPAW 299

Query: 301 FANEEDIKNLK 311
           +A EED+KNL+
Sbjct: 300 YAKEEDLKNLQ 310

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255588003|ref|XP_002534470.1| transcription initiation factor iib, putative [Ricinus communis] gi|223525233|gb|EEF27913.1| transcription initiation factor iib, putative [Ricinus communis]

 Score =  507 bits (1305), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 239/310 (77%), Positives = 272/310 (87%), Gaps = 1/310 (0%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           M D+YC+DCKR TEVVFDHSAGDT+CSECGLVLE++S+DETSEWR FANES D+DPVRVG
Sbjct: 1   MGDAYCSDCKRQTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRL 120
           GP NPLL+ GGLSTVIAKP  G S E LS SLG+ Q R S+PDR LI AFK+I+ MSDRL
Sbjct: 61  GPTNPLLADGGLSTVIAKPN-GASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRL 119

Query: 121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
           GLV TIKDRANEIYKKVEDQK  RGRNQ+A++AACLYIACRQE+KPRTVKE CSVANG T
Sbjct: 120 GLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGAT 179

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           KKEIGRAKE+IVK L  E GQSVEMGTIHA D++RRFCSNLGM NQA+KAAQEAVQKSE+
Sbjct: 180 KKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAMKAAQEAVQKSEE 239

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
            DIRRSPIS+AAAVIYII+QLS+D K L++IS  T VAEGTI+N YKDL+PH+++IIP W
Sbjct: 240 FDIRRSPISIAAAVIYIISQLSDDKKLLRDISHATGVAEGTIRNSYKDLYPHVSKIIPSW 299

Query: 301 FANEEDIKNL 310
           +A EED+KNL
Sbjct: 300 YAKEEDLKNL 309

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	312
TAIR|locus:2076259	312	AT3G10330 [Arabidopsis thalian	0.993	0.993	0.665	4.3e-109
TAIR|locus:2062703	312	TFIIB "transcription factor II	0.990	0.990	0.629	2e-102
TAIR|locus:2093852	336	pBRP2 "plant-specific TFIIB-re	0.980	0.910	0.391	7.2e-52
FB|FBgn0004915	315	TfIIB "Transcription factor II	0.897	0.888	0.418	9.2e-52
ZFIN|ZDB-GENE-030131-3544	316	gtf2b "general transcription f	0.926	0.914	0.399	1.3e-50
UNIPROTKB|F1NXP2	306	GTF2B "Uncharacterized protein	0.926	0.944	0.392	2e-49
MGI|MGI:2385191	316	Gtf2b "general transcription f	0.926	0.914	0.385	4.7e-48
RGD|619735	316	Gtf2b "general transcription f	0.926	0.914	0.385	4.7e-48
UNIPROTKB|F2Z4J6	316	LOC786656 "Uncharacterized pro	0.926	0.914	0.385	6e-48
UNIPROTKB|E2RPG1	316	GTF2B "Uncharacterized protein	0.926	0.914	0.385	6e-48

TAIR|locus:2076259 AT3G10330 [Arabidopsis thaliana (taxid:3702)]

 Score = 1078 (384.5 bits), Expect = 4.3e-109, P = 4.3e-109
 Identities = 207/311 (66%), Positives = 243/311 (78%)

Query:     1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVX 60
             M+D++C+DCKR TEVVFDHSAGDT+CSECGLVLE++S+DETSEWR FANES D+DPVRV 
Sbjct:     1 MSDAFCSDCKRHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query:    61 XXXXXXXXXXXXXTVIAKPTAXXXXXXXXXXXXXXQARSSHPDRNLIQAFKSISAMSDRL 120
                          TVI+KP                Q R S+PDR LI AFK+I+ M+DRL
Sbjct:    61 GPTNPLLADGGLTTVISKPNGSSGDFLSSSLGRW-QNRGSNPDRGLIVAFKTIATMADRL 119

Query:   121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
             GLV TIKDRANEIYK+VEDQK  RGRNQ+A++AACLYIACRQE+KPRTVKE CSVANG T
Sbjct:   120 GLVATIKDRANEIYKRVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGAT 179

Query:   181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSED 240
             KKEIGRAKE+IVK L  E GQ VEMGTIHA D++RRFCSNLGMTN            SE+
Sbjct:   180 KKEIGRAKEYIVKQLGLETGQLVEMGTIHAGDFMRRFCSNLGMTNQTVKAAQESVQKSEE 239

Query:   241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
              DIRRSPIS+AAAVIYIITQLS++ KPL++IS+ T VAEGTI+N YKDL+PHL++IIP W
Sbjct:   240 FDIRRSPISIAAAVIYIITQLSDEKKPLRDISVATGVAEGTIRNSYKDLYPHLSKIIPAW 299

Query:   301 FANEEDIKNLK 311
             +A EED+KNL+
Sbjct:   300 YAKEEDLKNLQ 310

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;ISS

GO:0006413 "translational initiation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA

TAIR|locus:2062703 TFIIB "transcription factor IIB" [Arabidopsis thaliana (taxid:3702)]

 Score = 1015 (362.4 bits), Expect = 2.0e-102, P = 2.0e-102
 Identities = 195/310 (62%), Positives = 234/310 (75%)

Query:     1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVX 60
             M+D+YC DCK+ TE+V DHSAGDT+CSECGLVLE++S+DETSEWR FANESS+ DP RV 
Sbjct:     1 MSDAYCTDCKKETELVVDHSAGDTLCSECGLVLESHSIDETSEWRTFANESSNSDPNRVG 60

Query:    61 XXXXXXXXXXXXXTVIAKPTAXXXXXXXXXXXXXXQARSSHPDRNLIQAFKSISAMSDRL 120
                          TVIAKP                Q R+S+ DR LIQAFK+I+ MS+RL
Sbjct:    61 GPTNPLLADSALTTVIAKPNGSSGDFLSSSLGRW-QNRNSNSDRGLIQAFKTIATMSERL 119

Query:   121 GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT 180
             GLV TIKDRANE+YK++EDQK  RGRNQ+A+ AACLYIACRQE+KPRT+KE C +ANG T
Sbjct:   120 GLVATIKDRANELYKRLEDQKSSRGRNQDALYAACLYIACRQEDKPRTIKEICVIANGAT 179

Query:   181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSED 240
             KKEIGRAK++IVK L  E GQSV++GTIHA D++RRFCSNL M+N            SE+
Sbjct:   180 KKEIGRAKDYIVKTLGLEPGQSVDLGTIHAGDFMRRFCSNLAMSNHAVKAAQEAVQKSEE 239

Query:   241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW 300
              DIRRSPIS+AA VIYIITQLS+D K LK+IS  T VAEGTI+N YKDL+PHL++I P W
Sbjct:   240 FDIRRSPISIAAVVIYIITQLSDDKKTLKDISHATGVAEGTIRNSYKDLYPHLSKIAPSW 299

Query:   301 FANEEDIKNL 310
             +A EED+KNL
Sbjct:   300 YAKEEDLKNL 309

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;ISS

GO:0006413 "translational initiation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA

TAIR|locus:2093852 pBRP2 "plant-specific TFIIB-related protein 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 538 (194.4 bits), Expect = 7.2e-52, P = 7.2e-52
 Identities = 125/319 (39%), Positives = 176/319 (55%)

Query:     1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANES--SDHDPVR 58
             M +  C DCKR T +V DHS+GDTICSECGLVLEA+ ++ + EWR FA++   SD DP R
Sbjct:     1 MEEETCLDCKRPTIMVVDHSSGDTICSECGLVLEAHIIEYSQEWRTFASDDNHSDRDPNR 60

Query:    59 VXXXXXXXXXXXXXXTVIAKPTAXXXXXXXXXXXXXX-QARS---SHPDRNLIQAFKSIS 114
             V              T+I KP                 +A +   +H +  + QAF+ I 
Sbjct:    61 VGAATNPFLKSGDLVTIIEKPKETASSVLSKDDISTLFRAHNQVKNHEEDLIKQAFEEIQ 120

Query:   115 AMSDRLGLVTTIKDRANEIYKKVE---DQKPLRGRNQEAIVAACLYIACRQENKPRTVKE 171
              M+D L L   I  RA EI  K +   + K  RG+   AI AA +  ACR+    RT+KE
Sbjct:   121 RMTDALDLDIVINSRACEIVSKYDGHANTKLRRGKKLNAICAASVSTACRELQLSRTLKE 180

Query:   172 FCSVANGTTKKEIGRAKEFIVKH-LEA-EMGQSVEMGTIHASDYLRRFCSNLGMTNXXXX 229
                VANG  KK+I R +  ++K  LE+ +   S     I+  + +RRFCS L ++     
Sbjct:   181 IAEVANGVDKKDI-RKESLVIKRVLESHQTSVSASQAIINTGELVRRFCSKLDISQREIM 239

Query:   230 XXXXXXXXSEDLDIRRSPISVAAAVIYIITQLSN-DTKPLKEISIVTRVAEGTIKNVYKD 288
                     +E+ DIRR+P SV AA+I++I+ +S  + KP++EI IV  V E TIKN  KD
Sbjct:   240 AIPEAVEKAENFDIRRNPKSVLAAIIFMISHISQTNRKPIREIGIVAEVVENTIKNSVKD 299

Query:   289 LFPHLARIIPDWFANEEDI 307
             ++P+  +IIP+W+A E DI
Sbjct:   300 MYPYALKIIPNWYACESDI 318

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;ISS

GO:0006413 "translational initiation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046686 "response to cadmium ion" evidence=IEP

GO:0000769 "syncytium formation by mitosis without cytokinesis" evidence=IMP

GO:0009960 "endosperm development" evidence=IMP

GO:0010440 "stomatal lineage progression" evidence=RCA

FB|FBgn0004915 TfIIB "Transcription factor IIB" [Drosophila melanogaster (taxid:7227)]

 Score = 537 (194.1 bits), Expect = 9.2e-52, P = 9.2e-52
 Identities = 121/289 (41%), Positives = 166/289 (57%)

Query:    15 VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVXXXXXXXXXXXXXXT 74
             ++ D+ AGD ICSECGLV+    +D  SEWR F+NE S  DP RV              T
Sbjct:    22 LIEDYRAGDMICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPSRVGGPENPLLSGGDLST 81

Query:    75 VIAKPTAXXXXXXXXXXXXXXQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIY 134
             +I   T               +   S  DR+LI AFK IS+M+DR+ L  TI DRAN ++
Sbjct:    82 IIGPGTGSASFDAFGAPKYQNRRTMSSSDRSLISAFKEISSMADRINLPKTIVDRANNLF 141

Query:   135 KKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194
             K+V D K L+GR+ +A  +ACLYIACRQE  PRT KE C+V+   +KKEIGR  +  +K 
Sbjct:   142 KQVHDGKNLKGRSNDAKASACLYIACRQEGVPRTFKEICAVSK-ISKKEIGRCFKLTLKA 200

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI--RRSPISVAA 252
             LE     SV++  I  +D++ RFC+NL + N            + ++DI   RSPISVAA
Sbjct:   201 LET----SVDL--ITTADFMCRFCANLDLPNMVQRAATHIAKKAVEMDIVPGRSPISVAA 254

Query:   253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWF 301
             A IY+ +Q S   +  KEI  +  VA+ TI+  YK ++PH A++ P+ F
Sbjct:   255 AAIYMASQASEHKRSQKEIGDIAGVADVTIRQSYKLMYPHAAKLFPEDF 303

GO:0005634 "nucleus" evidence=NAS;IDA

GO:0001174 "transcriptional start site selection at RNA polymerase II promoter" evidence=IDA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=NAS;IDA

GO:0008134 "transcription factor binding" evidence=IPI

GO:0051101 "regulation of DNA binding" evidence=IDA

GO:0005667 "transcription factor complex" evidence=ISS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

ZFIN|ZDB-GENE-030131-3544 gtf2b "general transcription factor IIB" [Danio rerio (taxid:7955)]

 Score = 526 (190.2 bits), Expect = 1.3e-50, P = 1.3e-50
 Identities = 119/298 (39%), Positives = 166/298 (55%)

Query:    15 VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVXXXXXXXXXXXXXXT 74
             +V D+ AGD IC ECGLV+    +D  SEWR F+NE +  DP RV              T
Sbjct:    23 LVEDYRAGDMICPECGLVVRDRVIDVGSEWRTFSNEKATKDPSRVGDAQNPLLNGGDLTT 82

Query:    75 VIAKPTAXXXXXXXXXXXXXXQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIY 134
             +I+K T               +   S  DR ++ AFK I+ M+DR+ L   I DR N ++
Sbjct:    83 MISKGTGAASFDEFGNSKYQNRRTMSSSDRAMLNAFKEITTMADRINLPRNIIDRTNNLF 142

Query:   135 KKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194
             K+V +QK L+GR+ +AI +ACLYIACRQE  PRT KE C+V+   +KKEIGR  + I+K 
Sbjct:   143 KQVYEQKSLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSR-ISKKEIGRCFKLILKA 201

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI--RRSPISVAA 252
             LE     SV++  I   D++ RFCSNLG+              + +LD+   RSPISVAA
Sbjct:   202 LET----SVDL--ITTGDFMSRFCSNLGLPKQVQMAATYIARKAVELDLVPGRSPISVAA 255

Query:   253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
             A IY+ +Q S + K  KEI  +  VA+ TI+  Y+ ++P  A + P  F  +  +  L
Sbjct:   256 AAIYMASQASAEKKTQKEIGDIAGVADVTIRQSYRLIYPRAADLFPPDFKFDTPVDKL 313

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

UNIPROTKB|F1NXP2 GTF2B "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 117/298 (39%), Positives = 165/298 (55%)

Query:    15 VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVXXXXXXXXXXXXXXT 74
             +V D+ AGD ICSECGLV+    +D  SEWR F+N+ +  DP RV              T
Sbjct:    13 LVEDYRAGDMICSECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDTQNPLLSDGDLST 72

Query:    75 VIAKPTAXXXXXXXXXXXXXXQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIY 134
             +I K T               +   S  DR ++ AFK I+ M+DR+ L   I DR N ++
Sbjct:    73 MIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITNMADRINLPRNIVDRTNNLF 132

Query:   135 KKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194
             K+V +QK L+GR+ +AI +ACLYIACRQE  PRT KE C+V+   +KKEIGR  + I+K 
Sbjct:   133 KQVYEQKSLKGRSNDAIASACLYIACRQEGVPRTFKEICAVSR-ISKKEIGRCFKLILKA 191

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI--RRSPISVAA 252
             LE     SV++  I   D++ RFCSNLG+              + +LD+   RSPISVAA
Sbjct:   192 LET----SVDL--ITTGDFMSRFCSNLGLPKQVQMAATHIARKAVELDLVPGRSPISVAA 245

Query:   253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
             A IY+ +Q S + +  KEI  +  VA+ TI+  Y+ ++P    + P  F  +  +  L
Sbjct:   246 AAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPADFKFDTPVDKL 303

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0046966 "thyroid hormone receptor binding" evidence=IEA

MGI|MGI:2385191 Gtf2b "general transcription factor IIB" [Mus musculus (taxid:10090)]

 Score = 502 (181.8 bits), Expect = 4.7e-48, P = 4.7e-48
 Identities = 115/298 (38%), Positives = 162/298 (54%)

Query:    15 VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVXXXXXXXXXXXXXXT 74
             +V D+ AGD IC ECGLV+    +D  SEWR F+N+ +  DP RV              T
Sbjct:    23 LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPLLSDGDLST 82

Query:    75 VIAKPTAXXXXXXXXXXXXXXQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIY 134
             +I K T               +   S  DR ++ AFK I+ M+DR+ L   I DR N ++
Sbjct:    83 MIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLF 142

Query:   135 KKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194
             K+V +QK L+GR  +AI +ACLYIACRQE  PRT KE C+V+   +KKEIGR  + I+K 
Sbjct:   143 KQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSR-ISKKEIGRCFKLILKA 201

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI--RRSPISVAA 252
             LE     SV++  I   D++ RFCSNL +              + +LD+   RSPISVAA
Sbjct:   202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAA 255

Query:   253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
             A IY+ +Q S + +  KEI  +  VA+ TI+  Y+ ++P    + P  F  +  +  L
Sbjct:   256 AAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPSDFKFDTPVDKL 313

GO:0001047 "core promoter binding" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0008134 "transcription factor binding" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0046966 "thyroid hormone receptor binding" evidence=ISO

RGD|619735 Gtf2b "general transcription factor IIB" [Rattus norvegicus (taxid:10116)]

 Score = 502 (181.8 bits), Expect = 4.7e-48, P = 4.7e-48
 Identities = 115/298 (38%), Positives = 162/298 (54%)

Query:    15 VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVXXXXXXXXXXXXXXT 74
             +V D+ AGD IC ECGLV+    +D  SEWR F+N+ +  DP RV              T
Sbjct:    23 LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPLLSDGDLST 82

Query:    75 VIAKPTAXXXXXXXXXXXXXXQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIY 134
             +I K T               +   S  DR ++ AFK I+ M+DR+ L   I DR N ++
Sbjct:    83 MIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLF 142

Query:   135 KKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194
             K+V +QK L+GR  +AI +ACLYIACRQE  PRT KE C+V+   +KKEIGR  + I+K 
Sbjct:   143 KQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSR-ISKKEIGRCFKLILKA 201

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI--RRSPISVAA 252
             LE     SV++  I   D++ RFCSNL +              + +LD+   RSPISVAA
Sbjct:   202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAA 255

Query:   253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
             A IY+ +Q S + +  KEI  +  VA+ TI+  Y+ ++P    + P  F  +  +  L
Sbjct:   256 AAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPSDFKFDTPVDKL 313

GO:0001047 "core promoter binding" evidence=ISO

GO:0003677 "DNA binding" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0008134 "transcription factor binding" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0046966 "thyroid hormone receptor binding" evidence=IEA;ISO

UNIPROTKB|F2Z4J6 LOC786656 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 501 (181.4 bits), Expect = 6.0e-48, P = 6.0e-48
 Identities = 115/298 (38%), Positives = 162/298 (54%)

Query:    15 VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVXXXXXXXXXXXXXXT 74
             +V D+ AGD IC ECGLV+    +D  SEWR F+N+ +  DP RV              T
Sbjct:    23 LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPLLSDGDLST 82

Query:    75 VIAKPTAXXXXXXXXXXXXXXQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIY 134
             +I K T               +   S  DR ++ AFK I+ M+DR+ L   I DR N ++
Sbjct:    83 MIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLF 142

Query:   135 KKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194
             K+V +QK L+GR  +AI +ACLYIACRQE  PRT KE C+V+   +KKEIGR  + I+K 
Sbjct:   143 KQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSR-ISKKEIGRCFKLILKA 201

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI--RRSPISVAA 252
             LE     SV++  I   D++ RFCSNL +              + +LD+   RSPISVAA
Sbjct:   202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAA 255

Query:   253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
             A IY+ +Q S + +  KEI  +  VA+ TI+  Y+ ++P    + P  F  +  +  L
Sbjct:   256 AAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTDFKFDTPVDKL 313

GO:0046966 "thyroid hormone receptor binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

UNIPROTKB|E2RPG1 GTF2B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 501 (181.4 bits), Expect = 6.0e-48, P = 6.0e-48
 Identities = 115/298 (38%), Positives = 162/298 (54%)

Query:    15 VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVXXXXXXXXXXXXXXT 74
             +V D+ AGD IC ECGLV+    +D  SEWR F+N+ +  DP RV              T
Sbjct:    23 LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPLLSDGDLST 82

Query:    75 VIAKPTAXXXXXXXXXXXXXXQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIY 134
             +I K T               +   S  DR ++ AFK I+ M+DR+ L   I DR N ++
Sbjct:    83 MIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLF 142

Query:   135 KKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194
             K+V +QK L+GR  +AI +ACLYIACRQE  PRT KE C+V+   +KKEIGR  + I+K 
Sbjct:   143 KQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSR-ISKKEIGRCFKLILKA 201

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI--RRSPISVAA 252
             LE     SV++  I   D++ RFCSNL +              + +LD+   RSPISVAA
Sbjct:   202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAA 255

Query:   253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
             A IY+ +Q S + +  KEI  +  VA+ TI+  Y+ ++P    + P  F  +  +  L
Sbjct:   256 AAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTDFKFDTPVDKL 313

GO:0046966 "thyroid hormone receptor binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8W0W3	TF2B_ORYSJ	No assigned EC number	0.7677	0.9903	0.9903	yes	no
Q8TT29	TF2B_METAC	No assigned EC number	0.3355	0.8814	0.8160	yes	no
Q05959	TF2B_KLULA	No assigned EC number	0.3636	0.9198	0.8039	yes	no
Q9SS44	TF2B2_ARATH	No assigned EC number	0.7524	0.9935	0.9935	yes	no
Q8TX21	TF2B_METKA	No assigned EC number	0.3127	0.8846	0.8990	yes	no
O59151	TF2B_PYRHO	No assigned EC number	0.3139	0.8942	0.93	yes	no
P58111	TF2B1_SULSO	No assigned EC number	0.3434	0.8878	0.8964	yes	no
A0B5T8	TF2B_METTP	No assigned EC number	0.3365	0.8942	0.8278	yes	no
Q975S1	TF2B_SULTO	No assigned EC number	0.3355	0.8910	0.9025	yes	no
P62915	TF2B_MOUSE	No assigned EC number	0.4362	0.9262	0.9145	yes	no
P62916	TF2B_RAT	No assigned EC number	0.4362	0.9262	0.9145	yes	no
P61998	TF2B_PYRFU	No assigned EC number	0.31	0.9134	0.95	yes	no
O28970	TF2B_ARCFU	No assigned EC number	0.3388	0.8974	0.8588	yes	no
A8AC96	TF2B_IGNH4	No assigned EC number	0.3172	0.8653	0.8544	yes	no
P0CW15	TF2B_METMA	No assigned EC number	0.3355	0.8814	0.8160	yes	no
P0CW14	TF2B_METMZ	No assigned EC number	0.3355	0.8814	0.8160	yes	no
Q9UWN6	TF2B_SULAC	No assigned EC number	0.3333	0.8878	0.9022	yes	no
Q2KIN8	TF2B_BOVIN	No assigned EC number	0.4328	0.9262	0.9145	yes	no
Q54FD6	TF2B_DICDI	No assigned EC number	0.42	0.9070	0.8707	yes	no
A3CSQ6	TF2B_METMJ	No assigned EC number	0.3300	0.8878	0.8219	yes	no
Q5R886	TF2B_PONAB	No assigned EC number	0.4362	0.9262	0.9145	yes	no
P29052	TF2B_DROME	No assigned EC number	0.4633	0.9326	0.9238	yes	no
P29055	TF2B_YEAST	No assigned EC number	0.3471	0.9358	0.8463	yes	no
A7IAR4	TF2B_METB6	No assigned EC number	0.3224	0.8910	0.8323	yes	no
B8GJQ9	TF2B_METPE	No assigned EC number	0.3257	0.8910	0.8323	yes	no
Q9HJM7	TF2B1_THEAC	No assigned EC number	0.34	0.8942	0.8942	yes	no
Q2NEL6	TF2B_METST	No assigned EC number	0.3267	0.9038	0.9067	yes	no
A5UKA1	TF2B_METS3	No assigned EC number	0.3410	0.9006	0.9064	yes	no
O16991	TF2B_CAEEL	No assigned EC number	0.4329	0.8910	0.9084	yes	no
Q5JGN1	TF2B1_PYRKO	No assigned EC number	0.3322	0.8878	0.9233	yes	no
Q8SRP3	TF2B_ENCCU	No assigned EC number	0.4064	0.9326	0.9326	yes	no
O13749	TF2B_SCHPO	No assigned EC number	0.3817	0.9358	0.8588	yes	no
P48512	TF2B1_ARATH	No assigned EC number	0.7129	0.9903	0.9903	no	no
P48513	TF2B_SOYBN	No assigned EC number	0.7677	0.9935	0.9904	yes	no
Q9HRE6	TF2B2_HALSA	No assigned EC number	0.3133	0.8717	0.8369	yes	no
Q979Q3	TF2B1_THEVO	No assigned EC number	0.3333	0.8942	0.8942	yes	no
Q00403	TF2B_HUMAN	No assigned EC number	0.4362	0.9262	0.9145	yes	no
Q9V0V5	TF2B_PYRAB	No assigned EC number	0.3174	0.8942	0.93	yes	no
O26971	TF2B_METTH	No assigned EC number	0.3234	0.9038	0.9096	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	fgenesh4_pg.C_LG_XV000426	hypothetical protein (311 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	GTF902	global transcription factor group (201 aa)			•		•	•	•		0.839
	GTF901	global transcription factor group (202 aa)			•		•	•	•		0.835
	estExt_Genewise1_v1.C_LG_I4990	hypothetical protein (176 aa)			•		•	•	•		0.635
	gw1.IX.2304.1	hypothetical protein (321 aa)			•		•	•	•		0.633
	gw1.IV.3113.1	hypothetical protein (690 aa)			•		•	•	•		0.530
	estExt_Genewise1_v1.C_LG_IV3101	hypothetical protein (421 aa)			•		•		•		0.504
	grail3.2024000101	hypothetical protein (140 aa)			•						0.451
	estExt_fgenesh4_pg.C_LG_XII1303	RecName- Full=Proteasome subunit alpha type; EC=3.4.25.1;; The proteasome is a multicatalytic p [...] (236 aa)			•						0.441
	estExt_Genewise1_v1.C_LG_XV2760	RecName- Full=Proteasome subunit alpha type; EC=3.4.25.1; (235 aa)			•						0.439
	gw1.I.2689.1	hypothetical protein (1334 aa)			•		•		•		0.436

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	312
COG1405	285	COG1405, SUA7, Transcription initiation factor TFI	8e-71
PRK00423	310	PRK00423, tfb, transcription initiation factor IIB	3e-60
pfam00382	71	pfam00382, TFIIB, Transcription factor TFIIB repea	3e-19
cd00043	88	cd00043, CYCLIN, Cyclin box fold	3e-13
pfam00382	71	pfam00382, TFIIB, Transcription factor TFIIB repea	1e-10
smart00385	83	smart00385, CYCLIN, domain present in cyclins, TFI	3e-10
pfam08271	40	pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding	3e-09
smart00385	83	smart00385, CYCLIN, domain present in cyclins, TFI	5e-08
cd00043	88	cd00043, CYCLIN, Cyclin box fold	4e-07
COG5333	297	COG5333, CCL1, Cdk activating kinase (CAK)/RNA pol	6e-06
pfam00134	127	pfam00134, Cyclin_N, Cyclin, N-terminal domain	0.003

>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]

 Score =  220 bits (563), Expect = 8e-71
 Identities = 106/299 (35%), Positives = 161/299 (53%), Gaps = 22/299 (7%)

Query: 6   CADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNP 65
           C +C   T ++ D+  G+ +C++CGLVLE   +D   EWR F          RVG PL P
Sbjct: 4   CPECGS-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFDERHER----RVGAPLTP 58

Query: 66  LLSGGGLSTVIAKPTAGGSTELLSGSLGKLQAR---SSHPDRNLIQAFKSISAMSDRLGL 122
            +   GLST+I     G   +     L K Q R   SS  +RNLI A + +  ++  LGL
Sbjct: 59  SIHDKGLSTII-----GWGDKDKMYRLRKWQIRIRVSSAKERNLITALEELERIASALGL 113

Query: 123 VTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKK 182
             ++++ A  IY+K  D+  LRGR+ E++ AAC+Y ACR    PRT+ E      G +KK
Sbjct: 114 PESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKAL-GVSKK 172

Query: 183 EIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED-- 240
           EIGR    +V+ L       +++  +  SDY+ RF S LG++++  + A E V+K++   
Sbjct: 173 EIGRTYRLLVREL------KLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAG 226

Query: 241 LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPD 299
           L   +SP  +AAA IY+ + L  + +  KE++ V  V E TI+N YK+L   L   +  
Sbjct: 227 LTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNRYKELADALDIEVTV 285

Length = 285

>gnl|CDD|234758 PRK00423, tfb, transcription initiation factor IIB; Reviewed

 Score =  194 bits (495), Expect = 3e-60
 Identities = 96/293 (32%), Positives = 162/293 (55%), Gaps = 20/293 (6%)

Query: 13  TEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGL 72
            ++++D+  G+ +C++CGLV+E   +D+  EWR F  E  +    RVG P+   +   GL
Sbjct: 20  DKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQRE-KRSRVGAPMTYTIHDKGL 78

Query: 73  STVIA---KPTAGGSTELLSGS----LGKLQAR---SSHPDRNLIQAFKSISAMSDRLGL 122
           ST I    K + G S    + +    L K Q R   S+  +RNL  A   +  ++ +LGL
Sbjct: 79  STDIDWRNKDSYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGL 138

Query: 123 VTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKK 182
             ++++ A  IY+K  ++  +RGR+ E +VAA LY ACR+   PRT+ E   V+   ++K
Sbjct: 139 PRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSR-VSRK 197

Query: 183 EIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD 242
           EIGR   F+++ L      ++++      DY+ RF S LG++ +  K A E +QK+++  
Sbjct: 198 EIGRCYRFLLREL------NLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEKG 251

Query: 243 IR--RSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHL 293
           +   + P  +AAA IYI + L  + +  +E++ V  V E T++N YK+L   L
Sbjct: 252 LTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKL 304

Length = 310

>gnl|CDD|109440 pfam00382, TFIIB, Transcription factor TFIIB repeat

 Score = 80.0 bits (198), Expect = 3e-19
 Identities = 34/72 (47%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEF 172
           I   +D L L   + D ANE+ K   D   L+GR+ E+I AACLYIACR E   RT+KE 
Sbjct: 1   IKRFADALELPKKVADAANELAKLALDDNLLKGRSPESIAAACLYIACRLEEVKRTLKEI 60

Query: 173 CSVANGTTKKEI 184
            SVA   ++K I
Sbjct: 61  SSVAQ-VSEKTI 71

Length = 71

>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold

 Score = 64.2 bits (157), Expect = 3e-13
 Identities = 19/82 (23%), Positives = 33/82 (40%)

Query: 105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN 164
                   +  ++  LGL       A  +  +      + GR+   + AA LY+A + E 
Sbjct: 1   MRPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEE 60

Query: 165 KPRTVKEFCSVANGTTKKEIGR 186
            P  +K+   V    T++EI R
Sbjct: 61  IPPWLKDLVHVTGYATEEEILR 82

Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain. Length = 88

>gnl|CDD|109440 pfam00382, TFIIB, Transcription factor TFIIB repeat

 Score = 56.1 bits (136), Expect = 1e-10
 Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 214 LRRFCSNLGMTNQAVKAAQEAVQKSEDLDIR--RSPISVAAAVIYIITQLSNDTKPLKEI 271
           ++RF   L +  +   AA E  + + D ++   RSP S+AAA +YI  +L    + LKEI
Sbjct: 1   IKRFADALELPKKVADAANELAKLALDDNLLKGRSPESIAAACLYIACRLEEVKRTLKEI 60

Query: 272 SIVTRVAEGTI 282
           S V +V+E TI
Sbjct: 61  SSVAQVSEKTI 71

Length = 71

>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and Retinoblastoma

 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 17/81 (20%), Positives = 31/81 (38%)

Query: 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEF 172
           +  +   L L     + A  +  +          +   I AA LY+A + E  P   KE 
Sbjct: 3   LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTKEL 62

Query: 173 CSVANGTTKKEIGRAKEFIVK 193
                  T++EI R +  +++
Sbjct: 63  VHYTGYFTEEEILRMERLLLE 83

A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control. Length = 83

>gnl|CDD|203895 pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding

 Score = 51.5 bits (124), Expect = 3e-09
 Identities = 20/39 (51%), Positives = 27/39 (69%), Gaps = 1/39 (2%)

Query: 6  CADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEW 44
          C +C   TE+VFD+  G+ +C+ECGLVLE   +DE  EW
Sbjct: 3  CPNCGS-TEIVFDYERGEYVCTECGLVLEDNIIDEGPEW 40

The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure. Length = 40

>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and Retinoblastoma

 Score = 49.1 bits (118), Expect = 5e-08
 Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 3/82 (3%)

Query: 212 DYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRRSPISVAAAVIYIITQLSNDTKPLK 269
           D+LRR C  L +  + +  A   + +       ++ SP  +AAA +Y+ ++        K
Sbjct: 1   DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETPPWTK 60

Query: 270 EISIVTRVA-EGTIKNVYKDLF 290
           E+   T    E  I  + + L 
Sbjct: 61  ELVHYTGYFTEEEILRMERLLL 82

A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control. Length = 83

>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 3/85 (3%)

Query: 208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQK--SEDLDIRRSPISVAAAVIYIITQLSNDT 265
               D+LRR    LG++ + +  A   + +   +   + RSP  VAAA +Y+  ++    
Sbjct: 3   PTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIP 62

Query: 266 KPLKEISIVTRVA-EGTIKNVYKDL 289
             LK++  VT  A E  I  + K L
Sbjct: 63  PWLKDLVHVTGYATEEEILRMEKLL 87

Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain. Length = 88

>gnl|CDD|227640 COG5333, CCL1, Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

 Score = 46.6 bits (111), Expect = 6e-06
 Identities = 34/200 (17%), Positives = 67/200 (33%), Gaps = 25/200 (12%)

Query: 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP 166
           I   K I  +  RL L  T+   A   + +   +  +   +  ++V  C+Y+AC+ E+ P
Sbjct: 46  IYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTP 105

Query: 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ 226
           R +      A     +E   ++E I++  E E+ ++++        Y            +
Sbjct: 106 RDISIESFEARDLWSEEPKSSRERILE-YEFELLEALDFDLHVHHPYKY---------LE 155

Query: 227 AVKAAQEAVQKSEDLDIRRS---------------PISVAAAVIYIITQLSNDTKPLKEI 271
                 +   K + L I                  P  +A A + I  ++          
Sbjct: 156 GFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPIIKLLD 215

Query: 272 SIVTRVAEGTIKNVYKDLFP 291
            +     E  I   YK +  
Sbjct: 216 FVSYETKEEVIALNYKSIVK 235

Length = 297

>gnl|CDD|215740 pfam00134, Cyclin_N, Cyclin, N-terminal domain

 Score = 37.1 bits (87), Expect = 0.003
 Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 2/52 (3%)

Query: 151 IVAACLYIACRQEN-KPRTVKEFCSVANGT-TKKEIGRAKEFIVKHLEAEMG 200
           +   CL IA + E   P +V++F  + +   TK+EI R +  I+  L  ++ 
Sbjct: 76  VGVTCLLIAAKYEEIYPPSVEDFVYITDNAYTKEEILRMELLILSTLNWDLS 127

Cyclins regulate cyclin dependent kinases (CDKs). Human cyclin-O is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain. Length = 127

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	312
KOG1597	308	consensus Transcription initiation factor TFIIB [T	100.0
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	100.0
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	100.0
KOG1598	521	consensus Transcription initiation factor TFIIIB,	100.0
KOG0835	367	consensus Cyclin L [General function prediction on	99.8
PF00382	71	TFIIB: Transcription factor TFIIB repeat; InterPro	99.77
KOG0834	323	consensus CDK9 kinase-activating protein cyclin T	99.74
PF00382	71	TFIIB: Transcription factor TFIIB repeat; InterPro	99.69
TIGR00569	305	ccl1 cyclin ccl1. University).	99.69
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	99.62
COG5333	297	CCL1 Cdk activating kinase (CAK)/RNA polymerase II	99.54
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	99.53
KOG0794	264	consensus CDK8 kinase-activating protein cyclin C	99.39
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	99.3
KOG1597	308	consensus Transcription initiation factor TFIIB [T	99.28
cd00043	88	CYCLIN Cyclin box fold. Protein binding domain fun	99.19
smart00385	83	CYCLIN domain present in cyclins, TFIIB and Retino	99.09
cd00043	88	CYCLIN Cyclin box fold. Protein binding domain fun	99.08
smart00385	83	CYCLIN domain present in cyclins, TFIIB and Retino	99.07
KOG0656	335	consensus G1/S-specific cyclin D [Cell cycle contr	98.98
COG5024	440	Cyclin [Cell division and chromosome partitioning]	98.45
KOG2496	325	consensus Cdk activating kinase (CAK)/RNA polymera	98.36
KOG0653	391	consensus Cyclin B and related kinase-activating p	98.36
PF00134	127	Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR	98.33
KOG1598	521	consensus Transcription initiation factor TFIIIB,	98.21
PF02984	118	Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR	98.1
KOG4557	262	consensus Origin recognition complex, subunit 6 [R	98.08
PF01857	135	RB_B: Retinoblastoma-associated protein B domain;	97.77
KOG0655	408	consensus G1/S-specific cyclin E [Cell cycle contr	97.53
PF11781	36	RRN7: RNA polymerase I-specific transcription init	97.29
PHA00626	59	hypothetical protein	96.77
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	96.75
KOG0835	367	consensus Cyclin L [General function prediction on	96.74
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	96.73
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	96.67
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	96.64
PF02984	118	Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR	96.48
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	96.47
PF13248	26	zf-ribbon_3: zinc-ribbon domain	96.11
smart00778	37	Prim_Zn_Ribbon Zinc-binding domain of primase-heli	96.07
PLN00209	86	ribosomal protein S27; Provisional	96.03
PF01857	135	RB_B: Retinoblastoma-associated protein B domain;	95.99
PRK00420	112	hypothetical protein; Validated	95.98
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	95.92
PTZ00083	85	40S ribosomal protein S27; Provisional	95.92
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	95.87
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	95.8
PF00134	127	Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR	95.75
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	95.71
PRK10220	111	hypothetical protein; Provisional	95.68
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	95.49
PRK00432	50	30S ribosomal protein S27ae; Validated	95.36
KOG0834	323	consensus CDK9 kinase-activating protein cyclin T	95.2
PRK11827	60	hypothetical protein; Provisional	95.18
TIGR00569	305	ccl1 cyclin ccl1. University).	95.01
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	94.9
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	94.87
PF08613	149	Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu	94.82
COG2835	60	Uncharacterized conserved protein [Function unknow	94.71
KOG0654	359	consensus G2/Mitotic-specific cyclin A [Cell cycle	94.66
COG2824	112	PhnA Uncharacterized Zn-ribbon-containing protein	94.6
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	94.52
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	94.45
PF08273	40	Prim_Zn_Ribbon: Zinc-binding domain of primase-hel	94.43
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	94.29
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	94.29
PF03966	68	Trm112p: Trm112p-like protein; InterPro: IPR005651	94.25
smart00661	52	RPOL9 RNA polymerase subunit 9.	94.1
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	94.06
TIGR02300	129	FYDLN_acid conserved hypothetical protein TIGR0230	93.98
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	93.95
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	93.87
KOG4164	497	consensus Cyclin ik3-1/CABLES [Cell cycle control,	93.58
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	93.46
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	93.05
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	93.04
TIGR00686	109	phnA alkylphosphonate utilization operon protein P	92.84
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	92.79
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	92.73
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	92.71
TIGR00244	147	transcriptional regulator NrdR. Members of this al	92.58
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	92.49
PRK14892	99	putative transcription elongation factor Elf1; Pro	92.45
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	92.25
PF13730	55	HTH_36: Helix-turn-helix domain	92.16
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	92.01
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	91.92
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	91.85
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	91.84
PF08613	149	Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu	91.7
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	91.58
KOG1779	84	consensus 40s ribosomal protein S27 [Translation,	91.49
COG4888	104	Uncharacterized Zn ribbon-containing protein [Gene	91.35
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	91.3
KOG4557	262	consensus Origin recognition complex, subunit 6 [R	91.13
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	91.07
PF01780	90	Ribosomal_L37ae: Ribosomal L37ae protein family; I	90.9
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	90.85
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	90.85
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	90.8
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	90.59
PRK12495	226	hypothetical protein; Provisional	90.54
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	90.5
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	90.22
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	90.13
KOG1010	920	consensus Rb (Retinoblastoma tumor suppressor)-rel	90.09
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	89.61
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	89.6
PTZ00255	90	60S ribosomal protein L37a; Provisional	89.38
COG3478	68	Predicted nucleic-acid-binding protein containing	89.36
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	89.25
PF10668	60	Phage_terminase: Phage terminase small subunit; In	89.17
PF05129	81	Elf1: Transcription elongation factor Elf1 like; I	89.01
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	88.84
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	88.72
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	88.61
PRK00135	188	scpB segregation and condensation protein B; Revie	88.49
COG5333	297	CCL1 Cdk activating kinase (CAK)/RNA polymerase II	88.43
PRK12286	57	rpmF 50S ribosomal protein L32; Reviewed	88.4
PF05460	353	ORC6: Origin recognition complex subunit 6 (ORC6);	88.35
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	88.25
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	88.13
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	88.01
PRK05901	509	RNA polymerase sigma factor; Provisional	87.98
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	87.95
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	87.94
TIGR00280	91	L37a ribosomal protein L37a. This model finds euka	87.9
COG5349	126	Uncharacterized protein conserved in bacteria [Fun	87.88
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	87.88
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	87.85
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	87.8
PRK05978	148	hypothetical protein; Provisional	87.77
PRK11169	164	leucine-responsive transcriptional regulator; Prov	87.7
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	87.59
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	87.51
PF05191	36	ADK_lid: Adenylate kinase, active site lid; InterP	87.39
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	87.21
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	87.19
COG4640	465	Predicted membrane protein [Function unknown]	87.19
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	87.02
PRK09678	72	DNA-binding transcriptional regulator; Provisional	87.01
PRK07405	317	RNA polymerase sigma factor SigD; Validated	86.87
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	86.84
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	86.81
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	86.73
COG1725	125	Predicted transcriptional regulators [Transcriptio	86.71
PRK03976	90	rpl37ae 50S ribosomal protein L37Ae; Reviewed	86.7
COG4068	64	Uncharacterized protein containing a Zn-ribbon [Fu	86.46
PF01783	56	Ribosomal_L32p: Ribosomal L32p protein family; Int	86.37
PHA02591	83	hypothetical protein; Provisional	86.34
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	86.33
PRK08402	355	replication factor A; Reviewed	86.18
PF12773	50	DZR: Double zinc ribbon	86.09
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	86.06
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	86.01
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	86.01
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	86.01
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	85.93
KOG2496	325	consensus Cdk activating kinase (CAK)/RNA polymera	85.57
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	85.49
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	85.27
TIGR01031	55	rpmF_bact ribosomal protein L32. This protein desc	85.06
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	84.94
PF14255	52	Cys_rich_CPXG: Cysteine-rich CPXCG	84.57
PRK09710	64	lar restriction alleviation and modification prote	84.54
PRK06266	178	transcription initiation factor E subunit alpha; V	84.49
TIGR02443	59	conserved hypothetical metal-binding protein. Memb	84.46
KOG2906	105	consensus RNA polymerase III subunit C11 [Transcri	84.36
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	84.0
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	83.95
PF04161	208	Arv1: Arv1-like family ; InterPro: IPR007290 Arv1	83.94
PF08646	146	Rep_fac-A_C: Replication factor-A C terminal domai	83.92
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	83.88
PRK04217	110	hypothetical protein; Provisional	83.71
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	83.51
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	83.32
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	83.11
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	83.06
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	82.98
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	82.94
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	82.88
PF08280	59	HTH_Mga: M protein trans-acting positive regulator	82.74
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	82.73
PRK02935	110	hypothetical protein; Provisional	82.68
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	82.26
COG1326	201	Uncharacterized archaeal Zn-finger protein [Genera	82.11
PF14122	87	YokU: YokU-like protein	82.08
COG1522	154	Lrp Transcriptional regulators [Transcription]	82.0
PRK05949	327	RNA polymerase sigma factor; Validated	81.93
COG1327	156	Predicted transcriptional regulator, consists of a	81.49
PF02042	52	RWP-RK: RWP-RK domain; InterPro: IPR003035 This do	81.27
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	81.23
PHA02942	383	putative transposase; Provisional	81.07
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	81.05
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	80.96
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	80.95
PF12773	50	DZR: Double zinc ribbon	80.93
PRK11337	292	DNA-binding transcriptional repressor RpiR; Provis	80.93
TIGR02395	429	rpoN_sigma RNA polymerase sigma-54 factor. A sigma	80.56
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	80.37
PF10058	54	DUF2296: Predicted integral membrane metal-binding	80.13
PRK13130	56	H/ACA RNA-protein complex component Nop10p; Review	80.09
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	80.02

>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]

Probab=100.00  E-value=4.6e-76  Score=507.69  Aligned_cols=301  Identities=58%  Similarity=0.902  Sum_probs=281.3

Q ss_pred             CCCCCCCCCCc-eeeeCCCCceEcCCCcccccCcccccccccccccCCCCCCCCCccCCCCCCcccCCCcceEEecCCCC
Q 021438            4 SYCADCKRLTE-VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG   82 (312)
Q Consensus         4 ~~Cp~Cg~~~~-ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~   82 (312)
                      +.||+|+..+. +++|+.+|++||..||+|+++++||.++|||+|++|+++.||+|||++.||++.++++.|+|+++. +
T Consensus         1 ~~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~Id~~sEwrtfsnd~~~~DPsrvG~~sNPlL~~g~L~T~I~~g~-g   79 (308)
T KOG1597|consen    1 MTCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRIIDEGSEWRTFSNDDSDADPSRVGASSNPLLDGGDLSTFISKGT-G   79 (308)
T ss_pred             CCCCCCCCCCCCeeeeccCCceecccCCeeeccccccccccccccccCCCCCCccccCCCCCCCCCCCCcceeeecCC-C
Confidence            47999998665 999999999999999999999999999999999999989999999999999999999999999987 4


Q ss_pred             CCcccccccchhcccc--CCcchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHH
Q 021438           83 GSTELLSGSLGKLQAR--SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIAC  160 (312)
Q Consensus        83 ~~~~~~~~~l~~~~~~--~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~ac  160 (312)
                      .++.+++ .|.+||++  +++.|+.+..+|..|..||+.++||..+.+.|.++|+++.+.+.++||+.++++|||||+||
T Consensus        80 ~~s~~~s-~l~~~Q~~~sm~~~d~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiAC  158 (308)
T KOG1597|consen   80 TSSSFAS-SLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIAC  158 (308)
T ss_pred             CCHHHHH-HHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHH
Confidence            4444443 38899985  56889999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh
Q 021438          161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED  240 (312)
Q Consensus       161 r~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~  240 (312)
                      |+++.|||++||+.++ +++.++|++.++.|.+.|+..    .+....+..+||+|||+.|+|+.+++..|.++++.+.+
T Consensus       159 Rq~~~pRT~kEI~~~a-nv~kKEIgr~~K~i~~~l~~s----~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~  233 (308)
T KOG1597|consen  159 RQEDVPRTFKEISAVA-NVSKKEIGRCVKLIGEALETS----VDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEE  233 (308)
T ss_pred             HhcCCCchHHHHHHHH-cCCHHHHHHHHHHHHHHHhcc----chhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence            9999999999999999 699999999999999998862    23335568999999999999999999999999999998


Q ss_pred             --ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCCccccccccccccC
Q 021438          241 --LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNLK  311 (312)
Q Consensus       241 --l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p~~~~~~~~~~~l~  311 (312)
                        +..||+|.+||||+|||+++++..+++++||..++||+++|||+.||+||+++..|+|.||.+++++|+||
T Consensus       234 ~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~~~liP~~~a~~~~lk~Lp  306 (308)
T KOG1597|consen  234 MDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLYPHADKLIPSWYANAVPLKNLP  306 (308)
T ss_pred             hccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHHHHhhchhhhChhhhccccchhhcC
Confidence              67899999999999999999999999999999999999999999999999999999999999999999998

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=100.00  E-value=2.6e-72  Score=511.63  Aligned_cols=287  Identities=35%  Similarity=0.628  Sum_probs=266.9

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCcccccccccccccCCCCCCCCCccCCCCCCcccCCCcceEEecCCCC
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG   82 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~   82 (312)
                      ...||+||+ +++++|+.+|++||++||+|++|++||+|||||+|++|+. +|++|+|+|.++++||.|++|.|+++..+
T Consensus        11 ~~~Cp~Cg~-~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~~-~~~~RvG~~~~~~~~~~gl~T~I~~~~~~   88 (310)
T PRK00423         11 KLVCPECGS-DKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQR-EKRSRVGAPMTYTIHDKGLSTDIDWRNKD   88 (310)
T ss_pred             CCcCcCCCC-CCeeEECCCCeEeecccCCcccccccccCCCccCCCcccc-CCccccCCCCCccccCCCCceEeecCCcc
Confidence            357999998 6899999999999999999999999999999999998764 68999999999999999999999976544


Q ss_pred             CCcccccc-------cchhcccc---CCcchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHH
Q 021438           83 GSTELLSG-------SLGKLQAR---SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIV  152 (312)
Q Consensus        83 ~~~~~~~~-------~l~~~~~~---~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~ia  152 (312)
                      ..|..++.       +|++||++   .++.||+|..+++.|+++|+.|+||+.++++|..||+++++.+.++|++.+.++
T Consensus        89 ~~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~  168 (310)
T PRK00423         89 SYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVV  168 (310)
T ss_pred             cccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHH
Confidence            45544432       37889886   367899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHH
Q 021438          153 AACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQ  232 (312)
Q Consensus       153 aAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~  232 (312)
                      |||||+|||++++|+|++||+.++ ++++++|+++|+.|.+.|++      ++++.+|++||+|||+.|++++++.+.|+
T Consensus       169 AAclYiACR~~~~prtl~eI~~~~-~v~~k~i~~~~~~l~k~L~~------~~~~~~p~~~i~r~~~~L~L~~~v~~~A~  241 (310)
T PRK00423        169 AAALYAACRRCKVPRTLDEIAEVS-RVSRKEIGRCYRFLLRELNL------KLPPTDPIDYVPRFASELGLSGEVQKKAI  241 (310)
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHh-CCCHHHHHHHHHHHHHHhCC------CCCCCCHHHHHHHHHHHcCCCHHHHHHHH
Confidence            999999999999999999999999 79999999999999999987      67788999999999999999999999999


Q ss_pred             HHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCC
Q 021438          233 EAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIP  298 (312)
Q Consensus       233 ~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p  298 (312)
                      +|++.+.+  +..||+|.+|||||||+|++++|.++|++|||+++||++.||+++||+|.+.++..+|
T Consensus       242 ~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~~~~~  309 (310)
T PRK00423        242 EILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKLDIKIP  309 (310)
T ss_pred             HHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCcccC
Confidence            99999987  8899999999999999999999999999999999999999999999999999887664

>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]

Probab=100.00  E-value=4.3e-67  Score=465.49  Aligned_cols=279  Identities=38%  Similarity=0.665  Sum_probs=259.8

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCcccccccccccccCCCCCCCCCccCCCCCCcccCCCcceEEecCCCC
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG   82 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~   82 (312)
                      ++.||+||+ +++++|++.|++||.+||+|++|+.||.|||||.|+++   ..+ |+|.|.++.+||.|++|+|+++...
T Consensus         1 ~~~CpeCg~-~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f~e~---~~~-r~g~P~t~~~~d~~l~t~i~~~~~~   75 (285)
T COG1405           1 VMSCPECGS-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFDER---HER-RVGAPLTPSIHDKGLSTIIGWGDKD   75 (285)
T ss_pred             CCCCCCCCC-ccceeeccCCeEEeccCCEEeccccccCCCCccccccc---ccc-cccCCCccccCccchhhhcccchhH
Confidence            368999999 59999999999999999999999999999999999322   334 9999999999999999999987622


Q ss_pred             CCcccccccchhcccc---CCcchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHH
Q 021438           83 GSTELLSGSLGKLQAR---SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIA  159 (312)
Q Consensus        83 ~~~~~~~~~l~~~~~~---~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~a  159 (312)
                           ...+|++||.+   ++.+|+++..++..|+.+++.|+||.++.++|..||+++.+.++++||+.++++|||+|+|
T Consensus        76 -----~~~rlr~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~a  150 (285)
T COG1405          76 -----KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAA  150 (285)
T ss_pred             -----HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHH
Confidence                 12358899975   4578999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhh
Q 021438          160 CRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSE  239 (312)
Q Consensus       160 cr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~  239 (312)
                      ||+++.|+|+.||+.++ +++.++|+++|+.+.+.|++      .+++.+|.+||+|||+.|+|++++.+.|.+|++.+.
T Consensus       151 cR~~~~prtl~eIa~a~-~V~~kei~rtyr~~~~~L~l------~~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~  223 (285)
T COG1405         151 CRINGVPRTLDEIAKAL-GVSKKEIGRTYRLLVRELKL------KIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAK  223 (285)
T ss_pred             HHHcCCCccHHHHHHHH-CCCHHHHHHHHHHHHHhcCC------CCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence            99999999999999999 79999999999999999997      677899999999999999999999999999999999


Q ss_pred             h--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCC
Q 021438          240 D--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIP  298 (312)
Q Consensus       240 ~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p  298 (312)
                      +  +..||+|.++||||||+|+.++|+++||++||.++|||++|||++||||.++++...+
T Consensus       224 ~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnrykel~~~~~i~~~  284 (285)
T COG1405         224 RAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNRYKELADALDIEVT  284 (285)
T ss_pred             HhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHHHHHHHHhhccccC
Confidence            8  8899999999999999999999999999999999999999999999999999876553

>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]

Probab=100.00  E-value=2.1e-43  Score=328.08  Aligned_cols=253  Identities=22%  Similarity=0.387  Sum_probs=224.5

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccCcccccccccccccCCCCCCCCCccCCCCCCcccCCCcceEEecCCCCC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGG   83 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~~   83 (312)
                      +.|++||+ +++..|..+|..+|+.||+|++++.|.  +| .+|.+.                    -.|++|+.++. +
T Consensus         1 ~~C~~C~~-s~fe~d~a~g~~~C~~CG~v~E~~~iv--se-v~F~e~--------------------~~G~~v~~~~~-g   55 (521)
T KOG1598|consen    1 MVCKNCGG-SNFERDEATGNLYCTACGTVLEYNNIV--AE-VTFVEG--------------------AQGQFVRVGQS-G   55 (521)
T ss_pred             CcCCCCCC-CCcccccccCCceeccccceeecccee--EE-eeeecc--------------------cceeEEecccc-C
Confidence            47999999 799999999999999999999999988  44 466632                    13677776552 2


Q ss_pred             CcccccccchhccccCCcchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHh
Q 021438           84 STELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE  163 (312)
Q Consensus        84 ~~~~~~~~l~~~~~~~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~  163 (312)
                      .+.  +         ..++++.++++.+.|..++..|+|++ +++.|..+|+++.+.++.+||+...++|+|+|++||++
T Consensus        56 ~~~--s---------~e~r~~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e  123 (521)
T KOG1598|consen   56 AGS--S---------LESREKTIYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLE  123 (521)
T ss_pred             Ccc--c---------hHHHHHHHHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhh
Confidence            110  0         15678999999999999999999999 99999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCC---HHHHHHHHHHHHHhhh
Q 021438          164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMT---NQAVKAAQEAVQKSED  240 (312)
Q Consensus       164 ~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~---~~v~~~A~~i~~~~~~  240 (312)
                      ++++.+.|++++.+ ++++.||+.|++|.+.|.+..  + .+|.++|..||+||++.|.+.   .++...|.+|+++|++
T Consensus       124 ~t~hlliDfS~~Lq-v~Vy~LG~~~l~l~~~L~i~e--n-~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkr  199 (521)
T KOG1598|consen  124 KTDHLLIDFSSYLQ-VSVYDLGSNFLEVTDSLSIGE--N-VSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKR  199 (521)
T ss_pred             CCceEEEEeccceE-EehhhhhHHHHHHHHHhcccc--c-cccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHH
Confidence            99999999999995 999999999999999999821  1 278999999999999999753   4589999999999998


Q ss_pred             --ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438          241 --LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII  297 (312)
Q Consensus       241 --l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~  297 (312)
                        +.+||+|.+||+||||+||+++|++++..||+.+++|++.||++||+||.+....-+
T Consensus       200 dwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl~Ef~~T~s~~L  258 (521)
T KOG1598|consen  200 DWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRLKEFSDTLSGDL  258 (521)
T ss_pred             HHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHHHHHhccccccc
Confidence              899999999999999999999999999999999999999999999999999865543

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=99.80  E-value=1.7e-18  Score=152.25  Aligned_cols=188  Identities=21%  Similarity=0.273  Sum_probs=160.1

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC-------
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-------  179 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v-------  179 (312)
                      .=+..+|++-|-.|+||+..+.+++.+|++++..+.+.+...+.+++|||.+|++.++.|++++||..+++-+       
T Consensus        24 ~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~~~~  103 (367)
T KOG0835|consen   24 ILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRRESE  103 (367)
T ss_pred             HHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHHhcc
Confidence            4478999999999999999999999999999999999999999999999999999999999999999987611       


Q ss_pred             --C-----------HHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHH--HHHHHHHHHHHhhh--cc
Q 021438          180 --T-----------KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ--AVKAAQEAVQKSED--LD  242 (312)
Q Consensus       180 --~-----------~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~--v~~~A~~i~~~~~~--l~  242 (312)
                        .           +..+.++..++.+.||+      ++...+|+.++..|.+.|++++.  +.+.+|..++++.+  +.
T Consensus       104 ~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF------~~Hv~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~  177 (367)
T KOG0835|consen  104 AAEHLILARLYINLKMQVIRAERRILRELGF------DVHVEHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVF  177 (367)
T ss_pred             CcchhhhhhHHhhhhhHHHHHHHHHHHHhCC------eeeeeccHHHHHHHHHHhcCCCchhHHHHHHHhhhhcccccee
Confidence              0           12344556677888887      77789999999999999999865  58999999999998  88


Q ss_pred             CCCChHHHHHHHHHHHHHhcCCCCC-HHHHHHHhCcchhHHHHHHHHHHhhhcccCCcc
Q 021438          243 IRRSPISVAAAVIYIITQLSNDTKP-LKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW  300 (312)
Q Consensus       243 ~Gr~P~~iaaAaiyla~~~~~~~~~-~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p~~  300 (312)
                      ....|.+||+|+||||++..+++++ +...-.+++++...|..+.-.+.+....-+|.|
T Consensus       178 vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~~~p~~  236 (367)
T KOG0835|consen  178 VRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYRLIPLYKRAKPDE  236 (367)
T ss_pred             eecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHHHHHHHHhcccCH
Confidence            8999999999999999999998876 568888899998888877666655444434433

>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=99.77  E-value=2.9e-18  Score=122.60  Aligned_cols=71  Identities=45%  Similarity=0.849  Sum_probs=65.9

Q ss_pred             HHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHH
Q 021438          113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (312)
Q Consensus       113 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i  184 (312)
                      |+++|+.|+||+++.+.|.++|+++.+.+..+||++..++|||||+|||+++.|+|++||++++ ++++++|
T Consensus         1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~-~Vs~~tI   71 (71)
T PF00382_consen    1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAA-GVSEKTI   71 (71)
T ss_dssp             HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHC-TSSHHHH
T ss_pred             ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHh-CCCCCcC
Confidence            6899999999999999999999999999999999999999999999999999999999999999 7999886

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.

>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]

Probab=99.74  E-value=2.2e-17  Score=149.04  Aligned_cols=187  Identities=19%  Similarity=0.252  Sum_probs=151.8

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC-CH--HH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TK--KE  183 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v-~~--~~  183 (312)
                      .++.++|.++|.+|++|+..+.+|..+|++++-...++...++.+|++|+|+|+|.++.|+.++||..++..+ .+  .+
T Consensus        40 ~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~  119 (323)
T KOG0834|consen   40 QEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLE  119 (323)
T ss_pred             HHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCccccc
Confidence            5789999999999999999999999999999999999999999999999999999999999999999987521 11  23


Q ss_pred             HHHHHHHHHHHH-hhhh----ccccccCCCCHHHHHHHHHhhcCCCHH----HHHHHHHHHHHhhh--ccCCCChHHHHH
Q 021438          184 IGRAKEFIVKHL-EAEM----GQSVEMGTIHASDYLRRFCSNLGMTNQ----AVKAAQEAVQKSED--LDIRRSPISVAA  252 (312)
Q Consensus       184 i~~~~~~l~~~l-~~~~----~~~~~~~~~~p~~~i~r~~~~L~l~~~----v~~~A~~i~~~~~~--l~~Gr~P~~iaa  252 (312)
                      ....|..+++.+ .+|.    +.+|++...+|+.|+.+++..|+....    +.+.||.+++++..  ++....|..||.
T Consensus       120 ~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAv  199 (323)
T KOG0834|consen  120 LEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAV  199 (323)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEe
Confidence            444444433222 1111    234689999999999999999987765    88999999999998  778899999999


Q ss_pred             HHHHHHHHhcCCCCCH---HHHHHHhC--cchhHHHHHHHHHHhhh
Q 021438          253 AVIYIITQLSNDTKPL---KEISIVTR--VAEGTIKNVYKDLFPHL  293 (312)
Q Consensus       253 Aaiyla~~~~~~~~~~---~~Ia~~~~--vs~~ti~~~~kel~~~~  293 (312)
                      |+||||+++.|...+.   +..-+.++  ++..-+....+++....
T Consensus       200 a~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y  245 (323)
T KOG0834|consen  200 ACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEFLDLY  245 (323)
T ss_pred             ehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHHHHHH
Confidence            9999999999876542   12345566  88888888887777654

>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=99.69  E-value=1.8e-16  Score=113.25  Aligned_cols=69  Identities=39%  Similarity=0.578  Sum_probs=63.9

Q ss_pred             HHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHH
Q 021438          214 LRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTI  282 (312)
Q Consensus       214 i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti  282 (312)
                      |+|||+.|+|++++.+.|.++++.+.+  +..||+|.++|||+||+||+.++.++|++||+++++|++.||
T Consensus         1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI   71 (71)
T PF00382_consen    1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI   71 (71)
T ss_dssp             HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred             ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence            689999999999999999999999987  889999999999999999999999999999999999999997

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.

>TIGR00569 ccl1 cyclin ccl1

Probab=99.69  E-value=2.6e-15  Score=135.77  Aligned_cols=160  Identities=13%  Similarity=0.177  Sum_probs=135.6

Q ss_pred             hhhHH-HHHHHHHHHHHhcC--CcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC
Q 021438          103 DRNLI-QAFKSISAMSDRLG--LVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT  179 (312)
Q Consensus       103 e~~l~-~~~~~I~~~~~~L~--Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v  179 (312)
                      |..+. .....|.++|..|+  ||+.++.+|..+|++++-.+.+....+..++++|+|+|||.++.|+++.+++....+.
T Consensus        52 E~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~  131 (305)
T TIGR00569        52 ELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKET  131 (305)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCC
Confidence            44554 46899999999999  9999999999999999998888888999999999999999999999999999866322


Q ss_pred             ---CHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcC-------CCHHHHHHHHHHHHHhhh--ccCCCCh
Q 021438          180 ---TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG-------MTNQAVKAAQEAVQKSED--LDIRRSP  247 (312)
Q Consensus       180 ---~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~-------l~~~v~~~A~~i~~~~~~--l~~Gr~P  247 (312)
                         ....|......|.+.|++      ++.+.+|+.++..|...|+       -.+.+.+.|+.+++++..  +..-..|
T Consensus       132 ~~~~~~~Il~~E~~lL~~L~F------~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~P  205 (305)
T TIGR00569       132 PLKALEQVLEYELLLIQQLNF------HLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTP  205 (305)
T ss_pred             chhhHHHHHHHHHHHHHHCCC------cEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCH
Confidence               237788888889999987      6778889998888876543       234577889999999886  5566999


Q ss_pred             HHHHHHHHHHHHHhcCCCCCH
Q 021438          248 ISVAAAVIYIITQLSNDTKPL  268 (312)
Q Consensus       248 ~~iaaAaiyla~~~~~~~~~~  268 (312)
                      ..||+||||+|++..+.+++-
T Consensus       206 s~IAlAAI~lA~~~~~~~l~~  226 (305)
T TIGR00569       206 SQIALAAILHTASRAGLNMES  226 (305)
T ss_pred             HHHHHHHHHHHHHHhCCCCcc
Confidence            999999999999999987664

University).

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.62  E-value=2.3e-16  Score=100.99  Aligned_cols=43  Identities=47%  Similarity=1.025  Sum_probs=38.8

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccCcccccccccccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIF   47 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f   47 (312)
                      ++||+||+ ..+++|+.+|++||++||.|++|+.++.++|||+|
T Consensus         1 m~Cp~Cg~-~~~~~D~~~g~~vC~~CG~Vl~e~~i~~~~e~r~f   43 (43)
T PF08271_consen    1 MKCPNCGS-KEIVFDPERGELVCPNCGLVLEENIIDEGPEWREF   43 (43)
T ss_dssp             ESBTTTSS-SEEEEETTTTEEEETTT-BBEE-TTBSCCCSCCHC
T ss_pred             CCCcCCcC-CceEEcCCCCeEECCCCCCEeecccccCCcccccC
Confidence            47999999 56999999999999999999999999999999987

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=99.54  E-value=8.3e-14  Score=122.96  Aligned_cols=155  Identities=19%  Similarity=0.285  Sum_probs=132.4

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhc-------CC
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVAN-------GT  179 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~-------~v  179 (312)
                      ...+.+|..+|.+|+||..+.++|..+|++++-+....+.+.+.++++|||+|||.++.|+-+.-.+...+       .-
T Consensus        46 i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~  125 (297)
T COG5333          46 IYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKS  125 (297)
T ss_pred             HHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccc
Confidence            45789999999999999999999999999999988899999999999999999999997655543333221       24


Q ss_pred             CHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCH--HHHHHHHHHHHHhhh--ccCCCChHHHHHHHH
Q 021438          180 TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN--QAVKAAQEAVQKSED--LDIRRSPISVAAAVI  255 (312)
Q Consensus       180 ~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~--~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAai  255 (312)
                      +.+.|-.....+.+.|++      ++-+.+|+.++..|...+.+..  +..+.||.+++++.+  +..-..|..||.|++
T Consensus       126 sr~~Il~~E~~lLEaL~f------d~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~l  199 (297)
T COG5333         126 SRERILEYEFELLEALDF------DLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAAL  199 (297)
T ss_pred             cHHHHHHHHHHHHHHccc------ceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHHH
Confidence            577888888888889986      7888999999999998887654  489999999999998  666788999999999


Q ss_pred             HHHHHhcCCCCC
Q 021438          256 YIITQLSNDTKP  267 (312)
Q Consensus       256 yla~~~~~~~~~  267 (312)
                      ++|+...|.+..
T Consensus       200 ~ia~~~~~~~~~  211 (297)
T COG5333         200 LIACEVLGMPII  211 (297)
T ss_pred             HHHHHhcCCccc
Confidence            999999886643

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=99.53  E-value=8.6e-14  Score=127.25  Aligned_cols=88  Identities=24%  Similarity=0.392  Sum_probs=84.7

Q ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHH
Q 021438          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK  188 (312)
Q Consensus       109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~  188 (312)
                      ...+|.++|+.|+||..+.+.|..+++++.+.++..||+|.++||||||+||+.+|.|+|++||+.++ +++..+|++.|
T Consensus       219 p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~-~Vs~~tI~~~y  297 (310)
T PRK00423        219 PIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVA-GVTEVTVRNRY  297 (310)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHc-CCCHHHHHHHH
Confidence            56899999999999999999999999999999999999999999999999999999999999999999 89999999999


Q ss_pred             HHHHHHHhh
Q 021438          189 EFIVKHLEA  197 (312)
Q Consensus       189 ~~l~~~l~~  197 (312)
                      +.|.+.|++
T Consensus       298 kel~~~l~~  306 (310)
T PRK00423        298 KELAEKLDI  306 (310)
T ss_pred             HHHHHHhCc
Confidence            999999875

>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]

Probab=99.39  E-value=4.2e-12  Score=107.16  Aligned_cols=178  Identities=19%  Similarity=0.315  Sum_probs=132.1

Q ss_pred             HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-HHHHHHHhc---------
Q 021438          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRT-VKEFCSVAN---------  177 (312)
Q Consensus       108 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~t-l~dia~~~~---------  177 (312)
                      ...+.|+.+++.|+|-+.++.+|..+|++++-++.+++..+..+|+.|+|+||+.++.|++ .+-+...+.         
T Consensus        43 ~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~  122 (264)
T KOG0794|consen   43 FMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYW  122 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccc
Confidence            3578899999999999999999999999999999999999999999999999999999822 222222211         


Q ss_pred             ----CCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCC-CHHHHHHHHHHHHHhhh--ccCCCChHHH
Q 021438          178 ----GTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGM-TNQAVKAAQEAVQKSED--LDIRRSPISV  250 (312)
Q Consensus       178 ----~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l-~~~v~~~A~~i~~~~~~--l~~Gr~P~~i  250 (312)
                          ..+.+.|-...-.+.+.|+.      -+-+-+|..-+..+.+.+|+ +.+....+|.|+++..+  ++.-..|.-|
T Consensus       123 ~e~~~~~~~~I~e~Ef~llE~Ld~------~LIVhHPYrsL~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~I  196 (264)
T KOG0794|consen  123 PEKFPYERKDILEMEFYLLEALDC------YLIVHHPYRSLLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQI  196 (264)
T ss_pred             hhhcCCCcCcchhhhhhHHhhhce------eEEEecCCccHHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHH
Confidence                01123333334445555543      23355677778889999998 55588999999999998  7778999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          251 AAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       251 aaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      |-||||+|+...+-..+ +..-....+--.-+.+...+|+..
T Consensus       197 alAcl~Ia~~~~~k~~~-~~w~~el~vD~ekV~~~v~~I~~l  237 (264)
T KOG0794|consen  197 ALACLYIACVIDEKDIP-KAWFAELSVDMEKVKDIVQEILKL  237 (264)
T ss_pred             HHHHHHHHHhhcCCChH-HHHHHHHhccHHHHHHHHHHHHHH
Confidence            99999999998865543 333344455555666666666553

>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]

Probab=99.30  E-value=1.1e-11  Score=110.91  Aligned_cols=89  Identities=27%  Similarity=0.372  Sum_probs=85.7

Q ss_pred             HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHH
Q 021438          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (312)
Q Consensus       108 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~  187 (312)
                      +...+|.++|+.|+||+.+...|.+|.+++.+.+.+.||+|..+||||+|+|+++++.++|.+||+.++ ++++.+|++.
T Consensus       193 ~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~-~vtevTIrnr  271 (285)
T COG1405         193 DPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVA-GVTEVTIRNR  271 (285)
T ss_pred             CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHh-CCeeeHHHHH
Confidence            567899999999999999999999999999999999999999999999999999999999999999999 8999999999


Q ss_pred             HHHHHHHHhh
Q 021438          188 KEFIVKHLEA  197 (312)
Q Consensus       188 ~~~l~~~l~~  197 (312)
                      |+.|.+.+++
T Consensus       272 ykel~~~~~i  281 (285)
T COG1405         272 YKELADALDI  281 (285)
T ss_pred             HHHHHHhhcc
Confidence            9999998876

>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]

Probab=99.28  E-value=2e-11  Score=106.78  Aligned_cols=89  Identities=24%  Similarity=0.343  Sum_probs=84.7

Q ss_pred             HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHH
Q 021438          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (312)
Q Consensus       108 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~  187 (312)
                      ..-.+|.++|+.|+||..+++.|.++.+++.+.+...||+|.++|||+||+++++...+++++||..++ ||.+.+|+..
T Consensus       202 ~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vt-gVaE~TIr~s  280 (308)
T KOG1597|consen  202 STGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVT-GVAEVTIRNS  280 (308)
T ss_pred             hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHh-hhhHHHHHHH
Confidence            366889999999999999999999999999999999999999999999999999999999999999999 8999999999


Q ss_pred             HHHHHHHHhh
Q 021438          188 KEFIVKHLEA  197 (312)
Q Consensus       188 ~~~l~~~l~~  197 (312)
                      |+.|..++..
T Consensus       281 YK~Lyp~~~~  290 (308)
T KOG1597|consen  281 YKDLYPHADK  290 (308)
T ss_pred             HHHHhhchhh
Confidence            9999988763

>cd00043 CYCLIN Cyclin box fold

Probab=99.19  E-value=3e-10  Score=83.36  Aligned_cols=83  Identities=24%  Similarity=0.378  Sum_probs=77.7

Q ss_pred             HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC-CHHHHHH
Q 021438          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGR  186 (312)
Q Consensus       108 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v-~~~~i~~  186 (312)
                      .+..+|.++++.+++|..+...|..+++++...+.+.++++..+++||+|+|||.++.|.+++|+...+ +. +..+|.+
T Consensus         4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~-~~~~~~~i~~   82 (88)
T cd00043           4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVT-GYATEEEILR   82 (88)
T ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHh-CCCCHHHHHH
Confidence            468899999999999999999999999999998888999999999999999999999999999999999 68 9999988


Q ss_pred             HHHHH
Q 021438          187 AKEFI  191 (312)
Q Consensus       187 ~~~~l  191 (312)
                      .++.+
T Consensus        83 ~e~~i   87 (88)
T cd00043          83 MEKLL   87 (88)
T ss_pred             HHHHh
Confidence            87765

Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.

>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma

Probab=99.09  E-value=7.8e-10  Score=80.27  Aligned_cols=80  Identities=23%  Similarity=0.303  Sum_probs=72.3

Q ss_pred             HHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC-CHHHHHHHHHH
Q 021438          112 SISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGRAKEF  190 (312)
Q Consensus       112 ~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v-~~~~i~~~~~~  190 (312)
                      +|.++++.+++|+.+...|..+++++.....+.++++..+++||+|+|||.++.+++..++...+ +. +.++|.+.++.
T Consensus         2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~-~~~~~~~i~~~~~~   80 (83)
T smart00385        2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYT-GYFTEEEILRMEKL   80 (83)
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhh-CCCCHHHHHHHHHH
Confidence            68899999999999999999999999885445559999999999999999999999999999999 78 99999998887


Q ss_pred             HH
Q 021438          191 IV  192 (312)
Q Consensus       191 l~  192 (312)
                      |.
T Consensus        81 il   82 (83)
T smart00385       81 LL   82 (83)
T ss_pred             Hh
Confidence            64

A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.

>cd00043 CYCLIN Cyclin box fold

Probab=99.08  E-value=1.6e-09  Score=79.47  Aligned_cols=83  Identities=28%  Similarity=0.329  Sum_probs=76.9

Q ss_pred             CCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-chhHHHH
Q 021438          208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRV-AEGTIKN  284 (312)
Q Consensus       208 ~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~v-s~~ti~~  284 (312)
                      .++..|+.++++.+++++++...|..++++...  ...+++|..+|+||+|+|+++.+...+.+++...++. +..+|.+
T Consensus         3 ~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~   82 (88)
T cd00043           3 PTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEILR   82 (88)
T ss_pred             chHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHHH
Confidence            457899999999999999999999999999876  5569999999999999999999999999999999999 9999999


Q ss_pred             HHHHHH
Q 021438          285 VYKDLF  290 (312)
Q Consensus       285 ~~kel~  290 (312)
                      .+++|+
T Consensus        83 ~e~~il   88 (88)
T cd00043          83 MEKLLL   88 (88)
T ss_pred             HHHHhC
Confidence            988873

Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.

>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma

Probab=99.07  E-value=1.1e-09  Score=79.39  Aligned_cols=80  Identities=25%  Similarity=0.325  Sum_probs=73.2

Q ss_pred             HHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-chhHHHHHHHH
Q 021438          212 DYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRV-AEGTIKNVYKD  288 (312)
Q Consensus       212 ~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~v-s~~ti~~~~ke  288 (312)
                      +|+.++++.+++++++...|..++++...  -..+++|..+|+||+|+|++..+...+.++++..+++ ++.+|.+.+++
T Consensus         1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~~~   80 (83)
T smart00385        1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRMEKL   80 (83)
T ss_pred             CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHHHH
Confidence            48899999999999999999999999876  3346999999999999999999988899999999999 99999999999


Q ss_pred             HHh
Q 021438          289 LFP  291 (312)
Q Consensus       289 l~~  291 (312)
                      |.+
T Consensus        81 il~   83 (83)
T smart00385       81 LLE   83 (83)
T ss_pred             HhC
Confidence            863

A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.

>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]

Probab=98.98  E-value=3.9e-08  Score=89.32  Aligned_cols=175  Identities=15%  Similarity=0.184  Sum_probs=131.1

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCC---HHHHHHHHHHHHHHHhCC--CCCHHHHHHHh-cCCC
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRN---QEAIVAACLYIACRQENK--PRTVKEFCSVA-NGTT  180 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~---~~~iaaAcly~acr~~~~--p~tl~dia~~~-~~v~  180 (312)
                      ..|+.+|-++|+..+..+.+.=.|..|+.|+..-..+..-+   ...+|+||+.+|+|.+++  |.++.-..... .-..
T Consensus        79 ~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~fe  158 (335)
T KOG0656|consen   79 KQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFE  158 (335)
T ss_pred             HHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcccccccc
Confidence            57999999999999999999999999999997755443333   789999999999999987  55444333321 1367


Q ss_pred             HHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCH----HHHHHHHHHHH-Hhhh-ccCCCChHHHHHHH
Q 021438          181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN----QAVKAAQEAVQ-KSED-LDIRRSPISVAAAV  254 (312)
Q Consensus       181 ~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~----~v~~~A~~i~~-~~~~-l~~Gr~P~~iaaAa  254 (312)
                      .++|.++...+...|+=      .+..++|.+|+..|+.+++...    .+.+.+..++- .+.+ -..+..|+.||||+
T Consensus       159 aktI~rmELLVLstL~W------rl~aVTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~  232 (335)
T KOG0656|consen  159 AKTIQRMELLVLSTLKW------RLRAVTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAA  232 (335)
T ss_pred             HHHHHHHHHHHHhhccc------cccCCCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHH
Confidence            89999999999999986      6778999999999999998743    34444444433 3344 34689999999998


Q ss_pred             HHHHHHhc-CCC--CCHHHHHHHhCcchhHHHHHHH
Q 021438          255 IYIITQLS-NDT--KPLKEISIVTRVAEGTIKNVYK  287 (312)
Q Consensus       255 iyla~~~~-~~~--~~~~~Ia~~~~vs~~ti~~~~k  287 (312)
                      +.+++... +..  ..+..+.....++...++..|.
T Consensus       233 ~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~  268 (335)
T KOG0656|consen  233 ILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYD  268 (335)
T ss_pred             HHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence            87776643 322  2235556667788877777766

>COG5024 Cyclin [Cell division and chromosome partitioning]

Probab=98.45  E-value=2.8e-06  Score=80.16  Aligned_cols=179  Identities=15%  Similarity=0.182  Sum_probs=140.7

Q ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCC-CCHHHHHHHhc-CCCHHHHHH
Q 021438          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP-RTVKEFCSVAN-GTTKKEIGR  186 (312)
Q Consensus       109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p-~tl~dia~~~~-~v~~~~i~~  186 (312)
                      ..++|.++=.+++|-+.+...|..|..++.......=.+...++++|+||||+.+++. .+++++.-++. ..+.++|.+
T Consensus       216 Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~  295 (440)
T COG5024         216 LVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIR  295 (440)
T ss_pred             HHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHH
Confidence            4778888999999988999999999999998877766788899999999999998764 56788887776 478999999


Q ss_pred             HHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhh---hccCCCChHHHHHHHHHHHHHhcC
Q 021438          187 AKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSE---DLDIRRSPISVAAAVIYIITQLSN  263 (312)
Q Consensus       187 ~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~---~l~~Gr~P~~iaaAaiyla~~~~~  263 (312)
                      +++.+...|+.      ++....|..|+.|+...-.-+......+..++..+.   ++...+ |+.+||||-|++-.+.+
T Consensus       296 aE~~ml~~l~f------~is~P~P~sFLRriSka~dyd~~srt~~k~~~e~s~~~~~f~~~~-~S~~~aaa~~~s~~~~~  368 (440)
T COG5024         296 AERYMLEVLDF------NISWPSPMSFLRRISKASDYDIFSRTPAKFSSEISPVDYKFIQIS-PSWCAAAAMYLSRKILS  368 (440)
T ss_pred             HHHHHhhhccc------ccCCCChHHHHHHHHhhcccchhhhhhHhhhCCchHhhhhhccCC-chHHHHHHHHHHHhhhc
Confidence            99999999987      677888999999998888877777777777776644   255566 99999999999999876


Q ss_pred             CCCCHHHHHHHhC-cchhHHHHHHHHHHhhhc
Q 021438          264 DTKPLKEISIVTR-VAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       264 ~~~~~~~Ia~~~~-vs~~ti~~~~kel~~~~~  294 (312)
                      ..-.-....-..| .+...++....++.+++.
T Consensus       369 ~~~w~~~l~~ySg~y~~~~l~~~~~~~~~~l~  400 (440)
T COG5024         369 QNQWDRTLIHYSGNYTNPDLKPLNESNKENLQ  400 (440)
T ss_pred             cCCCCccccccCCCCCchhHHHHHHHHHHHhc
Confidence            3322222222334 566666666666666654

>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]

Probab=98.36  E-value=7.5e-06  Score=72.48  Aligned_cols=146  Identities=16%  Similarity=0.252  Sum_probs=96.2

Q ss_pred             HHHHHHhc--CCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcC---CCHHHHHHH
Q 021438          113 ISAMSDRL--GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG---TTKKEIGRA  187 (312)
Q Consensus       113 I~~~~~~L--~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~---v~~~~i~~~  187 (312)
                      +-++|+++  +||..|+.+|..+|++++-.+....-++..|.++|+|+||+.++..+|+.+|+.-+.|   -+...+-+.
T Consensus        63 l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~~k~~e~vLk~  142 (325)
T KOG2496|consen   63 LVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRKWKTHEIVLKY  142 (325)
T ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhccCcccccHHHHHhc
Confidence            44445554  8899999999999999998888888899999999999999999999999999986521   223333344


Q ss_pred             HHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcC--CCHHH-HH--HHHHHHHHhhh--ccCCCChHHHHHHHHHHHHH
Q 021438          188 KEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG--MTNQA-VK--AAQEAVQKSED--LDIRRSPISVAAAVIYIITQ  260 (312)
Q Consensus       188 ~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~--l~~~v-~~--~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~  260 (312)
                      ...+.+.|++..+  +..|.-..+-|+.-+-..|.  .+++. ..  .....++.+..  ...-..|+-||-|||..++-
T Consensus       143 E~~llqsL~f~L~--vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a~~  220 (325)
T KOG2496|consen  143 EFLLLQSLKFSLT--VHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHAAG  220 (325)
T ss_pred             hHHHHHhhhhhhe--ecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHHhc
Confidence            4456666765322  12233333556555544432  12222 11  11344444443  44568999999999955543

>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.36  E-value=1e-05  Score=76.53  Aligned_cols=165  Identities=15%  Similarity=0.192  Sum_probs=130.6

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHH-HHHHHhCCC-CCHHHHHHHhc-CCCHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLY-IACRQENKP-RTVKEFCSVAN-GTTKKE  183 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly-~acr~~~~p-~tl~dia~~~~-~v~~~~  183 (312)
                      ....+++-++-.+++|..++.-.|..|+.++.....+..+....+..+|++ +|||.+... ..+.|+..+.+ ..+..+
T Consensus       159 ~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~  238 (391)
T KOG0653|consen  159 AILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREE  238 (391)
T ss_pred             HHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHH
Confidence            345899999999999999999999999999988866777888888888866 999975544 44777776665 368899


Q ss_pred             HHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHh
Q 021438          184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQL  261 (312)
Q Consensus       184 i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~  261 (312)
                      |.++.+.+...|+.      ++....|..|+.|+.............+..+++...-  -.....|..+|||+.+++.++
T Consensus       239 il~mE~~il~~L~f------~l~~p~~~~FLrr~~ka~~~d~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~  312 (391)
T KOG0653|consen  239 ILRMEKYILNVLEF------DLSVPTPLSFLRRFLKAADYDIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRM  312 (391)
T ss_pred             HHHHHHHHHhccCe------eecCCchHHHHHHHHHhhhcchhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHH
Confidence            99999999998886      7778899999999999988776777777777776553  235678899999999999998


Q ss_pred             cCCC-CCHHHHHHHhCc
Q 021438          262 SNDT-KPLKEISIVTRV  277 (312)
Q Consensus       262 ~~~~-~~~~~Ia~~~~v  277 (312)
                      .+.+ .....+...+|-
T Consensus       313 ~~~~~~w~~~~~~~sg~  329 (391)
T KOG0653|consen  313 LSKGDVWSPTLEHYSGY  329 (391)
T ss_pred             hccCCccCCCCeeccCC
Confidence            7655 244444444443

>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=98.33  E-value=9.5e-06  Score=64.08  Aligned_cols=93  Identities=20%  Similarity=0.330  Sum_probs=78.9

Q ss_pred             hHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhc-CCCHH
Q 021438          105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN-GTTKK  182 (312)
Q Consensus       105 ~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~-~v~~~  182 (312)
                      ......++|..++..++++..+...|..++.++.........+...+++||+++|||.++. +.++.++..... ..+.+
T Consensus        30 ~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~  109 (127)
T PF00134_consen   30 MRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKK  109 (127)
T ss_dssp             HHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHH
T ss_pred             HHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHH
Confidence            3456899999999999999999999999999998888778888999999999999999987 788999988763 36789


Q ss_pred             HHHHHHHHHHHHHhh
Q 021438          183 EIGRAKEFIVKHLEA  197 (312)
Q Consensus       183 ~i~~~~~~l~~~l~~  197 (312)
                      +|..+.+.+...|+.
T Consensus       110 ~i~~~E~~iL~~L~f  124 (127)
T PF00134_consen  110 DILEMEREILSALNF  124 (127)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHCCC
Confidence            999999999988875

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....

>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]

Probab=98.21  E-value=1.6e-06  Score=82.25  Aligned_cols=91  Identities=19%  Similarity=0.253  Sum_probs=70.9

Q ss_pred             HHHHHHHHHHHHHhcCC-cH--HHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHH
Q 021438          106 LIQAFKSISAMSDRLGL-VT--TIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKK  182 (312)
Q Consensus       106 l~~~~~~I~~~~~~L~L-p~--~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~  182 (312)
                      +.+..-+|.+++..|-. |+  .++.+|..+..+........||+|..+++||||+|||++|+++|+.||+.+.+ |+..
T Consensus       163 lvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvh-V~e~  241 (521)
T KOG1598|consen  163 LVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVH-VCES  241 (521)
T ss_pred             ccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHH-HhHH
Confidence            33444556666666544 33  36666666666655444558999999999999999999999999999999995 9999


Q ss_pred             HHHHHHHHHHHHHhh
Q 021438          183 EIGRAKEFIVKHLEA  197 (312)
Q Consensus       183 ~i~~~~~~l~~~l~~  197 (312)
                      +|.+.|+++.+.+..
T Consensus       242 Tl~kRl~Ef~~T~s~  256 (521)
T KOG1598|consen  242 TLSKRLKEFSDTLSG  256 (521)
T ss_pred             HHHHHHHHHhccccc
Confidence            999999998876653

>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=98.10  E-value=2.1e-05  Score=61.14  Aligned_cols=86  Identities=17%  Similarity=0.162  Sum_probs=70.9

Q ss_pred             CHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHhCcchhHHHHH
Q 021438          209 HASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSND-TKPLKEISIVTRVAEGTIKNV  285 (312)
Q Consensus       209 ~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~-~~~~~~Ia~~~~vs~~ti~~~  285 (312)
                      +|..|+.+|....+.+.++...++.+++.+..  -..+.+|+.|||||+++|....+. +.....+...+|+....++..
T Consensus         2 Tp~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c   81 (118)
T PF02984_consen    2 TPYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKEC   81 (118)
T ss_dssp             -HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHH
T ss_pred             cHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHH
Confidence            58899999966666677899999999998765  457899999999999999999875 455677889999999999999


Q ss_pred             HHHHHhhhc
Q 021438          286 YKDLFPHLA  294 (312)
Q Consensus       286 ~kel~~~~~  294 (312)
                      ++.|.+...
T Consensus        82 ~~~i~~~~~   90 (118)
T PF02984_consen   82 IELIQELLS   90 (118)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999998764

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....

>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]

Probab=98.08  E-value=0.00034  Score=59.05  Aligned_cols=167  Identities=19%  Similarity=0.226  Sum_probs=122.9

Q ss_pred             HHHHHHHhcCCc--HHHHHHHHHHHHHHHhC--CCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHH
Q 021438          112 SISAMSDRLGLV--TTIKDRANEIYKKVEDQ--KPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (312)
Q Consensus       112 ~I~~~~~~L~Lp--~~v~~~A~~i~~~~~~~--~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~  187 (312)
                      .|.+++.+|||.  +.+.+.|.+|.+...-.  +..-|-.-..-|.-|+=+|.-.-+++..-......+ |.+++...+.
T Consensus         2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKLS-Gl~k~~Y~~~   80 (262)
T KOG4557|consen    2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKLS-GLSKKAYSRS   80 (262)
T ss_pred             cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHhc-cccHHHHHHH
Confidence            478999999994  57999999998876432  344555666778888888888889998877777877 9999999999


Q ss_pred             HHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh-------ccCCCChHHHHHHHHHHHHH
Q 021438          188 KEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED-------LDIRRSPISVAAAVIYIITQ  260 (312)
Q Consensus       188 ~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~-------l~~Gr~P~~iaaAaiyla~~  260 (312)
                      ++.+...|+++.    .   .    -|..+|-.+|+.+ +++.|..++..-..       ...-.+-.-.++||+|+||+
T Consensus        81 ~~sfe~llgln~----~---~----~VrdlaVQfgc~e-vi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack  148 (262)
T KOG4557|consen   81 FNSFENLLGLNI----K---L----NVRDLAVQFGCVE-VIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACK  148 (262)
T ss_pred             HHHHHHHhcchh----h---c----CHHHHHHHHhHHH-HHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHH
Confidence            999999998731    1   1    2334455555544 66778887766443       22333444578899999999


Q ss_pred             hcCCCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438          261 LSNDTKPLKEISIVTRVAEGTIKNVYKDLFP  291 (312)
Q Consensus       261 ~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~  291 (312)
                      ....+++...+-.+.|++++......|-+..
T Consensus       149 ~lKlKVdK~kli~~sg~~~s~F~~l~kqler  179 (262)
T KOG4557|consen  149 KLKLKVDKLKLIEVSGTSESEFSCLSKQLER  179 (262)
T ss_pred             HHHHhhhHhhcccccCCCHHHHHHHHHHHHH
Confidence            9988888888888899999877655554443

>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation

Probab=97.77  E-value=0.00012  Score=58.48  Aligned_cols=83  Identities=11%  Similarity=0.250  Sum_probs=63.0

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~--~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i  184 (312)
                      .-|...|+++|++|+|++++.+....+|.-...  ..++++|..+.++.+|+|..||.++.++|++||..... --+..-
T Consensus        12 ~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr-~qpq~~   90 (135)
T PF01857_consen   12 KLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYR-KQPQAS   90 (135)
T ss_dssp             HHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHT-TSTT--
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHH-hccccc
Confidence            347889999999999999998998888877754  35679999999999999999999999999999998773 333333


Q ss_pred             HHHHHH
Q 021438          185 GRAKEF  190 (312)
Q Consensus       185 ~~~~~~  190 (312)
                      ..+|+.
T Consensus        91 ~~Vyr~   96 (135)
T PF01857_consen   91 SHVYRS   96 (135)
T ss_dssp             THHHHS
T ss_pred             ccceEE
Confidence            344443

They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.

>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]

Probab=97.53  E-value=0.0051  Score=55.49  Aligned_cols=172  Identities=17%  Similarity=0.224  Sum_probs=121.4

Q ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCC-CCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhcC-CCHHHHH
Q 021438          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQK-PLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVANG-TTKKEIG  185 (312)
Q Consensus       109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~-~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~~-v~~~~i~  185 (312)
                      .++++-++|+-..|-..+.-.|..+|.++.... ....-....+-.+|+|+|++.+++ |-.+.|||.+++| .+..+|.
T Consensus       148 LlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIl  227 (408)
T KOG0655|consen  148 LLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDIL  227 (408)
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHHHH
Confidence            489999999999999999999999999987643 223345678889999999998875 7899999998874 6889999


Q ss_pred             HHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCH--------HHHHHHHHHH---HHhh-hcc-CCCChHHHHH
Q 021438          186 RAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN--------QAVKAAQEAV---QKSE-DLD-IRRSPISVAA  252 (312)
Q Consensus       186 ~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~--------~v~~~A~~i~---~~~~-~l~-~Gr~P~~iaa  252 (312)
                      .+...|.+.|+-      ++.+++.-..+.-|.+-+++++        -....-..++   ..+. .+. .-..-..+||
T Consensus       228 tmE~iilkal~W------~l~PiTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqiaqlLDlc~ldids~~fsYrilaA  301 (408)
T KOG0655|consen  228 TMELIILKALKW------ELSPITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIAQLLDLCILDIDSLEFSYRILAA  301 (408)
T ss_pred             HHHHHHHHHhcc------cccceehHHHHHHHHHHHhcCCCCceeccccchHHHHHHHHHHHHHHhccccccchHHHHHH
Confidence            999999999987      5667777777777776554331        1112222222   2222 222 3566778888


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438          253 AVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHL  293 (312)
Q Consensus       253 Aaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~  293 (312)
                      ||||.-..       ..-+-+++|.--..|.+..+-+.+..
T Consensus       302 Aal~h~~s-------~e~v~kaSG~~w~~ie~cv~wm~Pf~  335 (408)
T KOG0655|consen  302 AALCHFTS-------IEVVKKASGLEWDSIEECVDWMVPFV  335 (408)
T ss_pred             HHHHHHhH-------HHHHHHcccccHHHHHHHHHHHHHHH
Confidence            88884332       23344556666667777766666653

>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[]

Probab=97.29  E-value=0.0002  Score=43.47  Aligned_cols=27  Identities=30%  Similarity=0.562  Sum_probs=23.3

Q ss_pred             CCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438            5 YCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~   34 (312)
                      .|+.|++ .  .+....|..+|..||.|++
T Consensus        10 ~C~~C~~-~--~~~~~dG~~yC~~cG~~~E   36 (36)
T PF11781_consen   10 PCPVCGS-R--WFYSDDGFYYCDRCGHQSE   36 (36)
T ss_pred             cCCCCCC-e--EeEccCCEEEhhhCceEcC
Confidence            4999998 2  6778899999999999974

>PHA00626 hypothetical protein

Probab=96.77  E-value=0.0013  Score=43.30  Aligned_cols=31  Identities=19%  Similarity=0.538  Sum_probs=23.4

Q ss_pred             CCCCCCCCCCceeee----CCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFD----HSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D----~~~G~~vC~~CG~Vv~e   35 (312)
                      +.||.||+ .+++..    ..+..++|.+||+-...
T Consensus         1 m~CP~CGS-~~Ivrcg~cr~~snrYkCkdCGY~ft~   35 (59)
T PHA00626          1 MSCPKCGS-GNIAKEKTMRGWSDDYVCCDCGYNDSK   35 (59)
T ss_pred             CCCCCCCC-ceeeeeceecccCcceEcCCCCCeech
Confidence            47999999 466642    23689999999997643

>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors []

Probab=96.75  E-value=0.0015  Score=38.81  Aligned_cols=31  Identities=16%  Similarity=0.404  Sum_probs=25.1

Q ss_pred             CCCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      |....|+.||+.  .++....+..+|..||.+.
T Consensus         1 ~~~~~C~~C~~~--~i~~~~~~~~~C~~Cg~~~   31 (33)
T PF08792_consen    1 SNLKKCSKCGGN--GIVNKEDDYEVCIFCGSSF   31 (33)
T ss_pred             CCceEcCCCCCC--eEEEecCCeEEcccCCcEe
Confidence            556789999983  4555778999999999874

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=96.74  E-value=0.011  Score=53.26  Aligned_cols=90  Identities=20%  Similarity=0.246  Sum_probs=67.4

Q ss_pred             HHHHHHHHHHHHHhcCCcHHH--HHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHH-HHHHHhcCCCHH
Q 021438          106 LIQAFKSISAMSDRLGLVTTI--KDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVK-EFCSVANGTTKK  182 (312)
Q Consensus       106 l~~~~~~I~~~~~~L~Lp~~v--~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~-dia~~~~~v~~~  182 (312)
                      +......|-.+...|++|++.  ...+..+........++.-.+++.||+||+|+|.|..++|.... .--.++ +.++.
T Consensus       138 v~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~F-d~~k~  216 (367)
T KOG0835|consen  138 VEHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAF-DTTKR  216 (367)
T ss_pred             eeccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHc-CCcHH
Confidence            344567788889999999754  77777777777767777888999999999999999999886543 444556 68888


Q ss_pred             HHHHHHHHHHHHHh
Q 021438          183 EIGRAKEFIVKHLE  196 (312)
Q Consensus       183 ~i~~~~~~l~~~l~  196 (312)
                      +|......+.....
T Consensus       217 eid~ic~~l~~lY~  230 (367)
T KOG0835|consen  217 EIDEICYRLIPLYK  230 (367)
T ss_pred             HHHHHHHHHHHHHH
Confidence            88776655554443

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=96.73  E-value=0.0012  Score=44.39  Aligned_cols=31  Identities=35%  Similarity=0.745  Sum_probs=28.6

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .+||.|+. ..+++++.+-.+.|..||.++.+
T Consensus        12 VkCp~C~n-~q~vFsha~t~V~C~~Cg~~L~~   42 (59)
T PRK00415         12 VKCPDCGN-EQVVFSHASTVVRCLVCGKTLAE   42 (59)
T ss_pred             EECCCCCC-eEEEEecCCcEEECcccCCCccc
Confidence            57999998 68999999999999999999975

>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]

Probab=96.67  E-value=0.001  Score=45.42  Aligned_cols=31  Identities=35%  Similarity=0.764  Sum_probs=28.4

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .+||+|+. ..+++++.+-.+.|..||.++.+
T Consensus        20 VkCpdC~N-~q~vFshast~V~C~~CG~~l~~   50 (67)
T COG2051          20 VKCPDCGN-EQVVFSHASTVVTCLICGTTLAE   50 (67)
T ss_pred             EECCCCCC-EEEEeccCceEEEecccccEEEe
Confidence            47999998 68999999999999999999875

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=96.64  E-value=0.0015  Score=39.03  Aligned_cols=27  Identities=19%  Similarity=0.652  Sum_probs=15.3

Q ss_pred             CCCCCCCCCceeeeCC----CCceEcCCCcccc
Q 021438            5 YCADCKRLTEVVFDHS----AGDTICSECGLVL   33 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~----~G~~vC~~CG~Vv   33 (312)
                      .||.||+.  +.....    .-..||.+||.|-
T Consensus         2 fC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~Ih   32 (34)
T PF14803_consen    2 FCPQCGGP--LERRIPEGDDRERLVCPACGFIH   32 (34)
T ss_dssp             B-TTT--B---EEE--TT-SS-EEEETTTTEEE
T ss_pred             ccccccCh--hhhhcCCCCCccceECCCCCCEE
Confidence            69999983  444433    3449999999983

>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=96.48  E-value=0.023  Score=43.67  Aligned_cols=87  Identities=14%  Similarity=0.141  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhcCCCHHHHHHH
Q 021438          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVANGTTKKEIGRA  187 (312)
Q Consensus       109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~~v~~~~i~~~  187 (312)
                      .+.+|+.+....+..+.+...|..+.....-...+-+.++..+||||+|+|.+..+. +.--..+...+ |++..+|...
T Consensus         3 p~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t-~~~~~~l~~c   81 (118)
T PF02984_consen    3 PYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLT-GYDKEDLKEC   81 (118)
T ss_dssp             HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHH-TS-HHHHHHH
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhc-CCCHHHHHHH
Confidence            456777775555556677778887777765554467889999999999999999775 43345566667 8999999999


Q ss_pred             HHHHHHHHh
Q 021438          188 KEFIVKHLE  196 (312)
Q Consensus       188 ~~~l~~~l~  196 (312)
                      ++.|.+.+.
T Consensus        82 ~~~i~~~~~   90 (118)
T PF02984_consen   82 IELIQELLS   90 (118)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999887775

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....

>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.47  E-value=0.0016  Score=43.30  Aligned_cols=31  Identities=32%  Similarity=0.687  Sum_probs=23.6

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .+||.|+. ..+|+++.+-.+.|..||.+|.+
T Consensus         8 VkCp~C~~-~q~vFSha~t~V~C~~Cg~~L~~   38 (55)
T PF01667_consen    8 VKCPGCYN-IQTVFSHAQTVVKCVVCGTVLAQ   38 (55)
T ss_dssp             EE-TTT-S-EEEEETT-SS-EE-SSSTSEEEE
T ss_pred             EECCCCCC-eeEEEecCCeEEEcccCCCEecC
Confidence            58999998 68999999999999999999964

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=96.11  E-value=0.0031  Score=35.33  Aligned_cols=22  Identities=23%  Similarity=0.896  Sum_probs=17.9

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGL   31 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~   31 (312)
                      ..||+||..  +    ..+..+|.+||.
T Consensus         3 ~~Cp~Cg~~--~----~~~~~fC~~CG~   24 (26)
T PF13248_consen    3 MFCPNCGAE--I----DPDAKFCPNCGA   24 (26)
T ss_pred             CCCcccCCc--C----CcccccChhhCC
Confidence            789999982  2    357899999996

>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase

Probab=96.07  E-value=0.0056  Score=37.27  Aligned_cols=29  Identities=31%  Similarity=0.715  Sum_probs=22.3

Q ss_pred             CCCCCCCCCCCceeeeC--CCCceEcCCCcc
Q 021438            3 DSYCADCKRLTEVVFDH--SAGDTICSECGL   31 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~--~~G~~vC~~CG~   31 (312)
                      ...||.||+...+-+|.  .+|..+|..||.
T Consensus         3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~   33 (37)
T smart00778        3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA   33 (37)
T ss_pred             ccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence            46799999965555554  459999999984

This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.

>PLN00209 ribosomal protein S27; Provisional

Probab=96.03  E-value=0.0045  Score=44.66  Aligned_cols=31  Identities=32%  Similarity=0.641  Sum_probs=28.5

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .+||.|+. ..+|+++.+-.+.|..||.++.+
T Consensus        37 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~   67 (86)
T PLN00209         37 VKCQGCFN-ITTVFSHSQTVVVCGSCQTVLCQ   67 (86)
T ss_pred             EECCCCCC-eeEEEecCceEEEccccCCEeec
Confidence            57999998 68999999999999999999965

>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation

Probab=95.99  E-value=0.034  Score=44.53  Aligned_cols=77  Identities=19%  Similarity=0.264  Sum_probs=57.9

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh----ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHH
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED----LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVY  286 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~----l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~  286 (312)
                      ..-+..+|++|++++++....|.+.+.+..    |..+|+-.-+...|||..|++.+..++.++|=+.-..-+..-...|
T Consensus        15 ~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~qpq~~~~Vy   94 (135)
T PF01857_consen   15 AVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRKQPQASSHVY   94 (135)
T ss_dssp             HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTTSTT--THHH
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHhcccccccce
Confidence            446677999999999998999999888764    8899999999999999999999988998888766555444444444


Q ss_pred             H
Q 021438          287 K  287 (312)
Q Consensus       287 k  287 (312)
                      +
T Consensus        95 r   95 (135)
T PF01857_consen   95 R   95 (135)
T ss_dssp             H
T ss_pred             E
Confidence            3

They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.

>PRK00420 hypothetical protein; Validated

Probab=95.98  E-value=0.0053  Score=47.19  Aligned_cols=30  Identities=20%  Similarity=0.358  Sum_probs=23.6

Q ss_pred             CCCCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~   34 (312)
                      -...||.||.+  +..+ .+|..+|..||.++.
T Consensus        22 l~~~CP~Cg~p--Lf~l-k~g~~~Cp~Cg~~~~   51 (112)
T PRK00420         22 LSKHCPVCGLP--LFEL-KDGEVVCPVHGKVYI   51 (112)
T ss_pred             ccCCCCCCCCc--ceec-CCCceECCCCCCeee
Confidence            34689999973  4443 789999999999864

>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2

Probab=95.92  E-value=0.0061  Score=36.74  Aligned_cols=31  Identities=19%  Similarity=0.508  Sum_probs=19.2

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~   34 (312)
                      |..||+||+- =+......+...|..||++.+
T Consensus         1 m~FCp~C~nl-L~p~~~~~~~~~C~~C~Y~~~   31 (35)
T PF02150_consen    1 MRFCPECGNL-LYPKEDKEKRVACRTCGYEEP   31 (35)
T ss_dssp             --BETTTTSB-EEEEEETTTTEEESSSS-EEE
T ss_pred             CeeCCCCCcc-ceEcCCCccCcCCCCCCCccC
Confidence            4689999983 333334444458999999853

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=95.92  E-value=0.0057  Score=44.06  Aligned_cols=31  Identities=26%  Similarity=0.624  Sum_probs=28.5

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .+||.|+. ..+|+++.+-.+.|..||.++.+
T Consensus        36 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~   66 (85)
T PTZ00083         36 VKCPGCSQ-ITTVFSHAQTVVLCGGCSSQLCQ   66 (85)
T ss_pred             EECCCCCC-eeEEEecCceEEEccccCCEeec
Confidence            57999998 68999999999999999999964

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=95.87  E-value=0.007  Score=38.92  Aligned_cols=31  Identities=39%  Similarity=0.748  Sum_probs=25.1

Q ss_pred             CCCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      |-...||+||.  .+..|...+.+.|..||.=+
T Consensus         1 ~~~y~C~~CG~--~~~~~~~~~~~~Cp~CG~~~   31 (46)
T PRK00398          1 MAEYKCARCGR--EVELDEYGTGVRCPYCGYRI   31 (46)
T ss_pred             CCEEECCCCCC--EEEECCCCCceECCCCCCeE
Confidence            55689999998  47777777799999999643

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=95.80  E-value=0.0051  Score=33.35  Aligned_cols=22  Identities=27%  Similarity=0.854  Sum_probs=17.0

Q ss_pred             CCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            5 YCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      .||+||..  + .   .+...|..||.-
T Consensus         1 ~Cp~CG~~--~-~---~~~~fC~~CG~~   22 (23)
T PF13240_consen    1 YCPNCGAE--I-E---DDAKFCPNCGTP   22 (23)
T ss_pred             CCcccCCC--C-C---CcCcchhhhCCc
Confidence            59999983  2 2   478889999974

>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=95.75  E-value=0.11  Score=40.49  Aligned_cols=65  Identities=12%  Similarity=0.278  Sum_probs=52.2

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHh
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSND-TKPLKEISIVT  275 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~-~~~~~~Ia~~~  275 (312)
                      .+|+..++..+++++.+...|..++++-..  ......+.-+++||+++|+++... ..+..++....
T Consensus        35 ~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~  102 (127)
T PF00134_consen   35 IDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRIS  102 (127)
T ss_dssp             HHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHT
T ss_pred             HHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHH
Confidence            468888999999999999999999998765  446778999999999999999876 45577777766

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....

>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues

Probab=95.71  E-value=0.0085  Score=34.66  Aligned_cols=27  Identities=26%  Similarity=0.418  Sum_probs=14.6

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      ..+||.|++. ..-.|  ...+||..||.-
T Consensus         2 ~p~Cp~C~se-~~y~D--~~~~vCp~C~~e   28 (30)
T PF08274_consen    2 LPKCPLCGSE-YTYED--GELLVCPECGHE   28 (30)
T ss_dssp             S---TTT------EE---SSSEEETTTTEE
T ss_pred             CCCCCCCCCc-ceecc--CCEEeCCccccc
Confidence            4689999994 33344  778999999974

The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.

>PRK10220 hypothetical protein; Provisional

Probab=95.68  E-value=0.026  Score=42.65  Aligned_cols=29  Identities=31%  Similarity=0.575  Sum_probs=22.5

Q ss_pred             CCCCCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      |+...||.|++ .-.-+|  ...+||..||.=
T Consensus         1 m~lP~CP~C~s-eytY~d--~~~~vCpeC~hE   29 (111)
T PRK10220          1 MSLPHCPKCNS-EYTYED--NGMYICPECAHE   29 (111)
T ss_pred             CCCCcCCCCCC-cceEcC--CCeEECCcccCc
Confidence            78899999999 333343  557999999964

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=95.49  E-value=0.0095  Score=39.57  Aligned_cols=31  Identities=39%  Similarity=0.768  Sum_probs=22.1

Q ss_pred             CCCCCCCCCCCceeeeCCCCc-eEcCCCccccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGD-TICSECGLVLE   34 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~-~vC~~CG~Vv~   34 (312)
                      +..||.||..-. +.|...|+ +.|..||.-++
T Consensus         2 ~~~CP~CG~~ie-v~~~~~GeiV~Cp~CGaele   33 (54)
T TIGR01206         2 QFECPDCGAEIE-LENPELGELVICDECGAELE   33 (54)
T ss_pred             ccCCCCCCCEEe-cCCCccCCEEeCCCCCCEEE
Confidence            468999998323 33444466 67999999875

This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=95.36  E-value=0.012  Score=38.60  Aligned_cols=28  Identities=18%  Similarity=0.610  Sum_probs=21.4

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      ...||.||+ + +..+ ..+...|..||+..
T Consensus        20 ~~fCP~Cg~-~-~m~~-~~~r~~C~~Cgyt~   47 (50)
T PRK00432         20 NKFCPRCGS-G-FMAE-HLDRWHCGKCGYTE   47 (50)
T ss_pred             cCcCcCCCc-c-hhec-cCCcEECCCcCCEE
Confidence            357999998 4 5454 44899999999863

>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]

Probab=95.20  E-value=0.053  Score=49.72  Aligned_cols=83  Identities=16%  Similarity=0.282  Sum_probs=67.2

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHh----CcchhHHHH
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVT----RVAEGTIKN  284 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~----~vs~~ti~~  284 (312)
                      ..||..++.+|+++......|.-+..+-.-  ......|..||++|+|||++..+.++..++|..++    +....+...
T Consensus        43 ~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~~~~  122 (323)
T KOG0834|consen   43 AKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLELEE  122 (323)
T ss_pred             HHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccccHHH
Confidence            568999999999998888788888777554  44677889999999999999999999999998775    333347788


Q ss_pred             HHHHHHhhh
Q 021438          285 VYKDLFPHL  293 (312)
Q Consensus       285 ~~kel~~~~  293 (312)
                      .|.++.+.+
T Consensus       123 ~~~~~~~~I  131 (323)
T KOG0834|consen  123 VYWELKERI  131 (323)
T ss_pred             HHHHHHHHH
Confidence            888887763

>PRK11827 hypothetical protein; Provisional

Probab=95.18  E-value=0.013  Score=39.69  Aligned_cols=29  Identities=17%  Similarity=0.433  Sum_probs=24.8

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      -..||.|++  .+.+|....+++|..||.+.
T Consensus         8 ILaCP~ckg--~L~~~~~~~~Lic~~~~laY   36 (60)
T PRK11827          8 IIACPVCNG--KLWYNQEKQELICKLDNLAF   36 (60)
T ss_pred             heECCCCCC--cCeEcCCCCeEECCccCeec
Confidence            357999997  58888888899999999884

>TIGR00569 ccl1 cyclin ccl1

Probab=95.01  E-value=0.17  Score=46.28  Aligned_cols=68  Identities=12%  Similarity=0.147  Sum_probs=55.7

Q ss_pred             HHHHHHHHhhcC--CCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcc
Q 021438          211 SDYLRRFCSNLG--MTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVA  278 (312)
Q Consensus       211 ~~~i~r~~~~L~--l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs  278 (312)
                      ..+|..+|..|+  ++..+.-.|.-+.++=.-  -..-..|.-|+++|+||||+.-...+++.+++..+.-.
T Consensus        60 ~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~  131 (305)
T TIGR00569        60 EKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKET  131 (305)
T ss_pred             HHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCC
Confidence            357788999999  999999999988877432  23457899999999999999999889999888766543

University).

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=94.90  E-value=0.016  Score=32.37  Aligned_cols=24  Identities=29%  Similarity=0.801  Sum_probs=19.0

Q ss_pred             CCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438            5 YCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~   34 (312)
                      .||+|+..  |    ......|..||++..
T Consensus         2 ~CP~C~~~--V----~~~~~~Cp~CG~~F~   25 (26)
T PF10571_consen    2 TCPECGAE--V----PESAKFCPHCGYDFE   25 (26)
T ss_pred             cCCCCcCC--c----hhhcCcCCCCCCCCc
Confidence            69999983  3    356889999999863

Several members are annotated as putative helicases.

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=94.87  E-value=0.017  Score=44.33  Aligned_cols=31  Identities=19%  Similarity=0.602  Sum_probs=26.4

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      ++.||+||..   .||-..--+||..||.++.-.
T Consensus         9 KR~Cp~CG~k---FYDLnk~PivCP~CG~~~~~~   39 (108)
T PF09538_consen    9 KRTCPSCGAK---FYDLNKDPIVCPKCGTEFPPE   39 (108)
T ss_pred             cccCCCCcch---hccCCCCCccCCCCCCccCcc
Confidence            5789999983   799888889999999998654

The function of members of this family is unknown.

>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=94.82  E-value=0.73  Score=37.47  Aligned_cols=88  Identities=15%  Similarity=0.149  Sum_probs=67.8

Q ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHh---CCC--CCCCCHHHHHHHHHHHHHHH-hCCCCCHHHHHHHhcCCCHH
Q 021438          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVED---QKP--LRGRNQEAIVAACLYIACRQ-ENKPRTVKEFCSVANGTTKK  182 (312)
Q Consensus       109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~---~~~--~~gr~~~~iaaAcly~acr~-~~~p~tl~dia~~~~~v~~~  182 (312)
                      ..+++.++....+++..+.-.|..|..++..   ...  +...+..-+..+|+.+|.|. .....+-+..+.+. |++.+
T Consensus        54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~-gis~~  132 (149)
T PF08613_consen   54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVG-GISLK  132 (149)
T ss_dssp             HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHH-TS-HH
T ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhc-CCCHH
Confidence            5678999999999999999999999999887   222  24567778888999999996 56778899999999 89999


Q ss_pred             HHHHHHHHHHHHHhh
Q 021438          183 EIGRAKEFIVKHLEA  197 (312)
Q Consensus       183 ~i~~~~~~l~~~l~~  197 (312)
                      ++.+..+.+...++.
T Consensus       133 eln~lE~~fL~~l~~  147 (149)
T PF08613_consen  133 ELNELEREFLKLLDY  147 (149)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHCCC
Confidence            999999998888764

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.

>COG2835 Uncharacterized conserved protein [Function unknown]

Probab=94.71  E-value=0.023  Score=38.27  Aligned_cols=31  Identities=29%  Similarity=0.680  Sum_probs=26.9

Q ss_pred             CCCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      |+...||.|++  .+.+|.+.++++|..||...
T Consensus         6 LeiLaCP~~kg--~L~~~~~~~~L~c~~~~~aY   36 (60)
T COG2835           6 LEILACPVCKG--PLVYDEEKQELICPRCKLAY   36 (60)
T ss_pred             heeeeccCcCC--cceEeccCCEEEecccCcee
Confidence            35568999998  39999999999999999874

>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]

Probab=94.66  E-value=0.35  Score=44.98  Aligned_cols=134  Identities=18%  Similarity=0.175  Sum_probs=92.8

Q ss_pred             HHHHHHHHHHHHHHhCC-CCCHHHHHHHhcCCCHHHHHHHHHH---HHHHHhhhhccccccCCCCHHHHHHHHHhhcC-C
Q 021438          149 EAIVAACLYIACRQENK-PRTVKEFCSVANGTTKKEIGRAKEF---IVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG-M  223 (312)
Q Consensus       149 ~~iaaAcly~acr~~~~-p~tl~dia~~~~~v~~~~i~~~~~~---l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~-l  223 (312)
                      ..+--+|-+++.+-+.. +..+.|+...++  .-...++..+.   ++..+.+      .+.......|+.++...-. .
T Consensus       180 ql~g~s~m~I~sk~ee~~~~~~~ef~~itd--~ty~~~qv~~~~~~il~~l~~------~~~~pt~~~~l~~~~~~~~~~  251 (359)
T KOG0654|consen  180 QLVGISAMLIASKYEEIKEPRVEEFCYITD--NTYTYWQVLRMEIDILNALTF------ELVRPTSKTFLRRFLRVAQTP  251 (359)
T ss_pred             HHhCcccceeeccchhhcchHHHHHHhhhh--hhhHHHHHHHHHHHHHHHhHH------HHhCchHHHHHHHHHHhhcch
Confidence            34455667777786544 566788877663  33344444444   4444444      3445567789888865433 4


Q ss_pred             CHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHH
Q 021438          224 TNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLF  290 (312)
Q Consensus       224 ~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~  290 (312)
                      .-++...+..+.+...-  ...-..|+-|||||+++|-...+..-+-..+..-+|++..+++.....|.
T Consensus       252 ~~~~e~~~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~~~pW~~~L~~~T~y~~edl~~~v~~L~  320 (359)
T KOG0654|consen  252 ELQVEPLANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLDFHPWNQTLEDYTGYKAEDLKPCVLDLH  320 (359)
T ss_pred             hHHHHHHHHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhccCCCCchhhHHhhcccHHHHHHHHHHHh
Confidence            45566677777776543  44567899999999999999888666677788889999999998888887

>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]

Probab=94.60  E-value=0.069  Score=40.12  Aligned_cols=32  Identities=28%  Similarity=0.713  Sum_probs=24.5

Q ss_pred             CCCCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      |.+..||.|++  +.+++. .+.++|..|+.=-.+
T Consensus         1 ~~lp~cp~c~s--EytYed-~~~~~cpec~~ew~~   32 (112)
T COG2824           1 MSLPPCPKCNS--EYTYED-GGQLICPECAHEWNE   32 (112)
T ss_pred             CCCCCCCccCC--ceEEec-CceEeCchhcccccc
Confidence            67889999998  355543 459999999976554

>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]

Probab=94.52  E-value=0.035  Score=40.26  Aligned_cols=30  Identities=30%  Similarity=0.560  Sum_probs=25.8

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~   34 (312)
                      ...||.||+ . .+....+|-..|..||.+..
T Consensus        35 ~~~Cp~C~~-~-~VkR~a~GIW~C~kCg~~fA   64 (89)
T COG1997          35 KHVCPFCGR-T-TVKRIATGIWKCRKCGAKFA   64 (89)
T ss_pred             CCcCCCCCC-c-ceeeeccCeEEcCCCCCeec
Confidence            457999998 3 67888999999999999865

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=94.45  E-value=0.02  Score=35.06  Aligned_cols=31  Identities=32%  Similarity=0.629  Sum_probs=20.7

Q ss_pred             CCCCCCCCCCceeee---CCCCceEcCCCccccc
Q 021438            4 SYCADCKRLTEVVFD---HSAGDTICSECGLVLE   34 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D---~~~G~~vC~~CG~Vv~   34 (312)
                      ..||+|+..-.+-.|   ...+.+.|.+||.++.
T Consensus         3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence            579999983222211   1345799999999864

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4

Probab=94.43  E-value=0.034  Score=34.47  Aligned_cols=29  Identities=31%  Similarity=0.620  Sum_probs=16.3

Q ss_pred             CCCCCCCCCCcee-eeC--CCCceEcCCCccc
Q 021438            4 SYCADCKRLTEVV-FDH--SAGDTICSECGLV   32 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii-~D~--~~G~~vC~~CG~V   32 (312)
                      ..||.||+...+- +|.  .+|..+|..|+-+
T Consensus         4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C~~~   35 (40)
T PF08273_consen    4 GPCPICGGKDRFRIFDDKDGRGTWICRQCGGD   35 (40)
T ss_dssp             E--TTTT-TTTEEEETT----S-EEETTTTBE
T ss_pred             CCCCCCcCccccccCcCcccCCCEECCCCCCc
Confidence            4799999954443 543  4699999999433

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.

>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]

Probab=94.29  E-value=0.026  Score=36.21  Aligned_cols=27  Identities=26%  Similarity=0.733  Sum_probs=22.1

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      ..||.||. +.+.-|+.. .+.|..||+.
T Consensus        20 ~~CPrCG~-gvfmA~H~d-R~~CGkCgyT   46 (51)
T COG1998          20 RFCPRCGP-GVFMADHKD-RWACGKCGYT   46 (51)
T ss_pred             ccCCCCCC-cchhhhcCc-eeEeccccce
Confidence            57999996 567777665 8999999986

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=94.29  E-value=0.021  Score=44.95  Aligned_cols=25  Identities=24%  Similarity=0.729  Sum_probs=20.3

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGL   31 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~   31 (312)
                      ...||.||.+  ++.  .+|+++|..||+
T Consensus        28 ~~hCp~Cg~P--LF~--KdG~v~CPvC~~   52 (131)
T COG1645          28 AKHCPKCGTP--LFR--KDGEVFCPVCGY   52 (131)
T ss_pred             HhhCcccCCc--cee--eCCeEECCCCCc
Confidence            3579999983  544  789999999993

>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function

Probab=94.25  E-value=0.046  Score=38.25  Aligned_cols=17  Identities=35%  Similarity=0.806  Sum_probs=15.4

Q ss_pred             eeCCCCceEcCCCcccc
Q 021438           17 FDHSAGDTICSECGLVL   33 (312)
Q Consensus        17 ~D~~~G~~vC~~CG~Vv   33 (312)
                      ++..+|.++|.+||.+.
T Consensus        47 ~~i~eg~L~Cp~c~r~Y   63 (68)
T PF03966_consen   47 VEIVEGELICPECGREY   63 (68)
T ss_dssp             EETTTTEEEETTTTEEE
T ss_pred             ccccCCEEEcCCCCCEE
Confidence            68899999999999884

The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=94.10  E-value=0.042  Score=36.06  Aligned_cols=28  Identities=18%  Similarity=0.689  Sum_probs=19.6

Q ss_pred             CCCCCCCCCceeeeCCC--CceEcCCCccccc
Q 021438            5 YCADCKRLTEVVFDHSA--GDTICSECGLVLE   34 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~--G~~vC~~CG~Vv~   34 (312)
                      .||.||+.  +......  -.++|..||++..
T Consensus         2 FCp~Cg~~--l~~~~~~~~~~~vC~~Cg~~~~   31 (52)
T smart00661        2 FCPKCGNM--LIPKEGKEKRRFVCRKCGYEEP   31 (52)
T ss_pred             CCCCCCCc--cccccCCCCCEEECCcCCCeEE
Confidence            69999982  3333222  3799999998854

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=94.06  E-value=0.061  Score=36.62  Aligned_cols=29  Identities=24%  Similarity=0.634  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCCCceeeeCCCC-------ceEcCCCcc
Q 021438            2 ADSYCADCKRLTEVVFDHSAG-------DTICSECGL   31 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~~G-------~~vC~~CG~   31 (312)
                      ++..||-||+ ..+..+...+       .+.|.+||.
T Consensus         2 ~LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga   37 (61)
T PF14354_consen    2 ELKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA   37 (61)
T ss_pred             CCcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence            4568999987 4565555444       266999999

>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300

Probab=93.98  E-value=0.035  Score=43.27  Aligned_cols=31  Identities=10%  Similarity=0.203  Sum_probs=26.5

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      ++.||.||..   .||-..--+||..||.+....
T Consensus         9 Kr~Cp~cg~k---FYDLnk~p~vcP~cg~~~~~~   39 (129)
T TIGR02300         9 KRICPNTGSK---FYDLNRRPAVSPYTGEQFPPE   39 (129)
T ss_pred             cccCCCcCcc---ccccCCCCccCCCcCCccCcc
Confidence            5689999983   799888999999999998654

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=93.95  E-value=4  Score=35.75  Aligned_cols=33  Identities=15%  Similarity=0.210  Sum_probs=28.3

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARI  296 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~  296 (312)
                      ...|++|||+.+|+|..+|+++.+.....+...
T Consensus       195 ~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~  227 (238)
T TIGR02393       195 RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP  227 (238)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence            568999999999999999999988777766554

This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=93.87  E-value=0.049  Score=44.57  Aligned_cols=30  Identities=27%  Similarity=0.561  Sum_probs=19.7

Q ss_pred             CCCCCCCCCCceeeeCC---CCc-----eEcCCCcccc
Q 021438            4 SYCADCKRLTEVVFDHS---AGD-----TICSECGLVL   33 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~---~G~-----~vC~~CG~Vv   33 (312)
                      ++||+||++..-+.|..   .|.     .-|.+||.-.
T Consensus         1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f   38 (154)
T PRK00464          1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF   38 (154)
T ss_pred             CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence            58999998532455543   454     3488888764

>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]

Probab=93.58  E-value=0.35  Score=44.89  Aligned_cols=60  Identities=13%  Similarity=0.221  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCC
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP  166 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p  166 (312)
                      .-..+++.+++.--+|...++.+|-.||.++.-++++...++..+|+|||++|.+.+...
T Consensus       383 rSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~K  442 (497)
T KOG4164|consen  383 RSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLK  442 (497)
T ss_pred             HHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhh
Confidence            344677788888889988999999999999988888877788999999999999988553

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=93.46  E-value=0.2  Score=31.42  Aligned_cols=28  Identities=14%  Similarity=0.248  Sum_probs=22.7

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHH
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLF  290 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~  290 (312)
                      +-..|..+||+.+|+|+.|+.+|++.|.
T Consensus        15 d~r~s~~~la~~lglS~~~v~~Ri~rL~   42 (42)
T PF13404_consen   15 DGRRSYAELAEELGLSESTVRRRIRRLE   42 (42)
T ss_dssp             -TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             cCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence            4578899999999999999999999873

...

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=93.05  E-value=0.078  Score=35.12  Aligned_cols=31  Identities=23%  Similarity=0.299  Sum_probs=20.5

Q ss_pred             CCCCCCCCCCceee---e--CCCCceEcCCCccccc
Q 021438            4 SYCADCKRLTEVVF---D--HSAGDTICSECGLVLE   34 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~---D--~~~G~~vC~~CG~Vv~   34 (312)
                      ..||.||+....+.   |  ...|...|..||....
T Consensus         2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~   37 (53)
T TIGR03655         2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP   37 (53)
T ss_pred             CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence            57999999533232   3  1334457999999865

Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=93.04  E-value=6.1  Score=35.07  Aligned_cols=34  Identities=15%  Similarity=0.138  Sum_probs=29.1

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII  297 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~  297 (312)
                      ...++++||..+|+|..||+++++.....+...+
T Consensus       218 ~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l  251 (256)
T PRK07408        218 HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLL  251 (256)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            4688999999999999999999988777766544

>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA

Probab=92.84  E-value=0.095  Score=39.65  Aligned_cols=30  Identities=20%  Similarity=0.433  Sum_probs=21.7

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      ...||.|++ .-.-+|  ...+||.+||.--..
T Consensus         2 lp~CP~C~s-eytY~d--g~~~iCpeC~~EW~~   31 (109)
T TIGR00686         2 LPPCPKCNS-EYTYHD--GTQLICPSCLYEWNE   31 (109)
T ss_pred             CCcCCcCCC-cceEec--CCeeECccccccccc
Confidence            468999999 334444  457999999986543

The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).

>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains

Probab=92.79  E-value=0.14  Score=29.99  Aligned_cols=28  Identities=18%  Similarity=0.453  Sum_probs=16.2

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      ...|+.||++  .......-..+|.+||..
T Consensus         3 ~rfC~~CG~~--t~~~~~g~~r~C~~Cg~~   30 (32)
T PF09297_consen    3 HRFCGRCGAP--TKPAPGGWARRCPSCGHE   30 (32)
T ss_dssp             TSB-TTT--B--EEE-SSSS-EEESSSS-E
T ss_pred             CcccCcCCcc--ccCCCCcCEeECCCCcCE
Confidence            4689999984  344445667999999975

; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.

>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

Probab=92.73  E-value=0.091  Score=40.72  Aligned_cols=34  Identities=29%  Similarity=0.611  Sum_probs=24.9

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      |..||.||+---.-.|...+.++|..||+..+-.
T Consensus         2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~   35 (113)
T COG1594           2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS   35 (113)
T ss_pred             ccccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence            6799999983222234467799999999987644

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=92.71  E-value=0.11  Score=32.34  Aligned_cols=25  Identities=32%  Similarity=0.852  Sum_probs=19.7

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECG   30 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG   30 (312)
                      ...||.||.  .+.. ..+|.++|-.|+
T Consensus        17 ~~~Cp~C~~--PL~~-~k~g~~~Cv~C~   41 (41)
T PF06677_consen   17 DEHCPDCGT--PLMR-DKDGKIYCVSCG   41 (41)
T ss_pred             cCccCCCCC--eeEE-ecCCCEECCCCC
Confidence            468999986  3555 468999999996

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

>TIGR00244 transcriptional regulator NrdR

Probab=92.58  E-value=0.12  Score=41.51  Aligned_cols=30  Identities=30%  Similarity=0.633  Sum_probs=22.4

Q ss_pred             CCCCCCCCCCceeeeC---CCCceE-----cCCCcccc
Q 021438            4 SYCADCKRLTEVVFDH---SAGDTI-----CSECGLVL   33 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~---~~G~~v-----C~~CG~Vv   33 (312)
                      |.||.||...+-|.|+   ..|..|     |.+||.=.
T Consensus         1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF   38 (147)
T TIGR00244         1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF   38 (147)
T ss_pred             CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence            5899999966667775   566655     88998653

Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.

>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc

Probab=92.49  E-value=0.17  Score=32.41  Aligned_cols=28  Identities=21%  Similarity=0.424  Sum_probs=21.3

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGL   31 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~   31 (312)
                      ...||.||+ .....-...+..-|.+|+.
T Consensus        18 g~~CP~Cg~-~~~~~~~~~~~~~C~~C~~   45 (46)
T PF12760_consen   18 GFVCPHCGS-TKHYRLKTRGRYRCKACRK   45 (46)
T ss_pred             CCCCCCCCC-eeeEEeCCCCeEECCCCCC
Confidence            457999998 4555545569999999984

It may be a zinc-binding beta ribbon domain that could bind DNA.

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=92.45  E-value=0.066  Score=40.33  Aligned_cols=41  Identities=22%  Similarity=0.467  Sum_probs=28.0

Q ss_pred             CCCCCCCCCCce--eeeCCCCceEcCCCcccccCc------ccccccccc
Q 021438            4 SYCADCKRLTEV--VFDHSAGDTICSECGLVLEAY------SVDETSEWR   45 (312)
Q Consensus         4 ~~Cp~Cg~~~~i--i~D~~~G~~vC~~CG~Vv~e~------~id~~~ewr   45 (312)
                      ..||+||+ ..+  -.|...+..+|..||+.-+..      .||-.++|.
T Consensus        22 f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wi   70 (99)
T PRK14892         22 FECPRCGK-VSISVKIKKNIAIITCGNCGLYTEFEVPSVYDEVDVYNKFI   70 (99)
T ss_pred             eECCCCCC-eEeeeecCCCcceEECCCCCCccCEECCccccchhhHHHHH
Confidence            47999996 333  345567899999999986532      245556663

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=92.25  E-value=0.065  Score=32.69  Aligned_cols=30  Identities=27%  Similarity=0.587  Sum_probs=21.1

Q ss_pred             CCCCCCCCCCceeee---CCCCceEcCCCcccc
Q 021438            4 SYCADCKRLTEVVFD---HSAGDTICSECGLVL   33 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D---~~~G~~vC~~CG~Vv   33 (312)
                      ..||+|+..-.|-.|   ...+.+-|..||.+.
T Consensus         3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence            579999984222222   346779999999885

>PF13730 HTH_36: Helix-turn-helix domain

Probab=92.16  E-value=0.4  Score=31.61  Aligned_cols=26  Identities=15%  Similarity=0.172  Sum_probs=24.2

Q ss_pred             CHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          267 PLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       267 ~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +++.||+.+|+|+.||++..++|.+.
T Consensus        27 S~~~la~~~g~s~~Tv~~~i~~L~~~   52 (55)
T PF13730_consen   27 SQETLAKDLGVSRRTVQRAIKELEEK   52 (55)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            79999999999999999999999873

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=92.01  E-value=0.29  Score=32.29  Aligned_cols=38  Identities=8%  Similarity=0.311  Sum_probs=32.3

Q ss_pred             hcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCC
Q 021438          261 LSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIP  298 (312)
Q Consensus       261 ~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p  298 (312)
                      ......+..++|..+|||++|+.+.++++.+.+...+|
T Consensus        15 ~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l~   52 (53)
T PF13613_consen   15 YLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVLK   52 (53)
T ss_pred             HHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhcC
Confidence            33456789999999999999999999999998877654

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=91.92  E-value=0.24  Score=29.09  Aligned_cols=28  Identities=14%  Similarity=0.167  Sum_probs=22.4

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +++..|||+.+|.|..|+....+.|.+.
T Consensus         2 ~mtr~diA~~lG~t~ETVSR~l~~l~~~   29 (32)
T PF00325_consen    2 PMTRQDIADYLGLTRETVSRILKKLERQ   29 (32)
T ss_dssp             E--HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             CcCHHHHHHHhCCcHHHHHHHHHHHHHc
Confidence            4678999999999999999999988763

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=91.85  E-value=0.12  Score=39.81  Aligned_cols=24  Identities=33%  Similarity=0.660  Sum_probs=19.6

Q ss_pred             CCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            6 CADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         6 Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      ||.||+. -.|+     .+-|.+||+.++-
T Consensus         1 CPvCg~~-l~vt-----~l~C~~C~t~i~G   24 (113)
T PF09862_consen    1 CPVCGGE-LVVT-----RLKCPSCGTEIEG   24 (113)
T ss_pred             CCCCCCc-eEEE-----EEEcCCCCCEEEe
Confidence            9999983 3444     7999999999974

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=91.84  E-value=0.43  Score=30.53  Aligned_cols=30  Identities=20%  Similarity=0.200  Sum_probs=24.8

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +-..|+++||+.+|+|..|++.++++|.+.
T Consensus        15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~~   44 (48)
T PF13412_consen   15 NPRITQKELAEKLGISRSTVNRYLKKLEEK   44 (48)
T ss_dssp             CTTS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             cCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            345899999999999999999999999763

...

>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=91.70  E-value=3.9  Score=33.13  Aligned_cols=89  Identities=10%  Similarity=0.117  Sum_probs=61.0

Q ss_pred             cCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh-------ccCCCChHHHHHHHHHHHHHhcC-CCCCHHHHHHHhC
Q 021438          205 MGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED-------LDIRRSPISVAAAVIYIITQLSN-DTKPLKEISIVTR  276 (312)
Q Consensus       205 ~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~-------l~~Gr~P~~iaaAaiyla~~~~~-~~~~~~~Ia~~~~  276 (312)
                      .|..+-.+|+.|+....+++..+.-.|.-.+++...       ......+.-+-.+|+.+|.+... ...+-+..|++.|
T Consensus        49 ~p~i~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~g  128 (149)
T PF08613_consen   49 VPSISIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGG  128 (149)
T ss_dssp             --SS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHT
T ss_pred             CCCCcHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcC
Confidence            466778899999999999999988777777766543       23466778899999999999875 4577899999999


Q ss_pred             cchhHHHHHHHHHHhhh
Q 021438          277 VAEGTIKNVYKDLFPHL  293 (312)
Q Consensus       277 vs~~ti~~~~kel~~~~  293 (312)
                      ++...+..-=.+++..+
T Consensus       129 is~~eln~lE~~fL~~l  145 (149)
T PF08613_consen  129 ISLKELNELEREFLKLL  145 (149)
T ss_dssp             S-HHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHC
Confidence            98777765544554443

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=91.58  E-value=0.5  Score=30.56  Aligned_cols=31  Identities=19%  Similarity=0.300  Sum_probs=26.3

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPHL  293 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~  293 (312)
                      ....|+.|||+..|+|..||+++.+...+.+
T Consensus        18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL   48 (50)
T PF04545_consen   18 FEGLTLEEIAERLGISRSTVRRILKRALKKL   48 (50)
T ss_dssp             TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence            5678999999999999999999998776654

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]

Probab=91.49  E-value=0.08  Score=37.41  Aligned_cols=30  Identities=27%  Similarity=0.683  Sum_probs=26.8

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~   34 (312)
                      .+||.|-. ...++.+.+..++|.+|++|+=
T Consensus        35 VkC~gc~~-iT~vfSHaqtvVvc~~c~~il~   64 (84)
T KOG1779|consen   35 VKCPGCFK-ITTVFSHAQTVVVCEGCSTILC   64 (84)
T ss_pred             EEcCCceE-EEEEeecCceEEEcCCCceEEE
Confidence            57999998 5789999999999999999973

>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]

Probab=91.35  E-value=0.13  Score=38.28  Aligned_cols=30  Identities=30%  Similarity=0.746  Sum_probs=22.5

Q ss_pred             CCCCCCCCCCcee---ee--CCCCceEcCCCccccc
Q 021438            4 SYCADCKRLTEVV---FD--HSAGDTICSECGLVLE   34 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii---~D--~~~G~~vC~~CG~Vv~   34 (312)
                      ..||.||.. .++   .|  ...|..+|.+||.-.+
T Consensus        23 FtCp~Cghe-~vs~ctvkk~~~~g~~~Cg~CGls~e   57 (104)
T COG4888          23 FTCPRCGHE-KVSSCTVKKTVNIGTAVCGNCGLSFE   57 (104)
T ss_pred             EecCccCCe-eeeEEEEEecCceeEEEcccCcceEE
Confidence            479999984 454   44  3568899999998754

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=91.30  E-value=0.5  Score=31.10  Aligned_cols=31  Identities=23%  Similarity=0.163  Sum_probs=26.7

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPHL  293 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~  293 (312)
                      +..+|.+++|+.++||..||++.+++|.+..
T Consensus        13 ~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen   13 KEPITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             TTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            4458999999999999999999999998765

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]

Probab=91.13  E-value=1.1  Score=38.26  Aligned_cols=82  Identities=15%  Similarity=0.319  Sum_probs=58.5

Q ss_pred             HHHHHHhcCCcHHHHHHHHHHHHHHHhC-----CCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHH
Q 021438          113 ISAMSDRLGLVTTIKDRANEIYKKVEDQ-----KPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (312)
Q Consensus       113 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~-----~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~  187 (312)
                      |+++|=.||+- .++..|.+++..+.+.     ..--..+.....+|++|.|||..+...+-..+..++ |+++..+...
T Consensus        96 VrdlaVQfgc~-evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~~s-g~~~s~F~~l  173 (262)
T KOG4557|consen   96 VRDLAVQFGCV-EVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIEVS-GTSESEFSCL  173 (262)
T ss_pred             HHHHHHHHhHH-HHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhccccc-CCCHHHHHHH
Confidence            55666666664 3677788888776442     111234566889999999999999887777777777 8999888777


Q ss_pred             HHHHHHHHh
Q 021438          188 KEFIVKHLE  196 (312)
Q Consensus       188 ~~~l~~~l~  196 (312)
                      .+.+.+...
T Consensus       174 ~kqler~~~  182 (262)
T KOG4557|consen  174 SKQLERNYK  182 (262)
T ss_pred             HHHHHHHHH
Confidence            777666554

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=91.07  E-value=0.62  Score=31.65  Aligned_cols=38  Identities=21%  Similarity=0.277  Sum_probs=30.7

Q ss_pred             HHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          254 VIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       254 aiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +||.... .+..++..+||+.++|+.+|+....+.|.+.
T Consensus        12 ~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~   49 (60)
T PF01325_consen   12 AIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEK   49 (60)
T ss_dssp             HHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHC
Confidence            4565555 5677889999999999999999999998873

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=90.90  E-value=0.13  Score=37.75  Aligned_cols=31  Identities=26%  Similarity=0.497  Sum_probs=24.9

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      ...||.||. .. +.-...|-.-|..||.++..
T Consensus        35 ky~Cp~Cgk-~~-vkR~a~GIW~C~~C~~~~AG   65 (90)
T PF01780_consen   35 KYTCPFCGK-TS-VKRVATGIWKCKKCGKKFAG   65 (90)
T ss_dssp             -BEESSSSS-SE-EEEEETTEEEETTTTEEEE-
T ss_pred             CCcCCCCCC-ce-eEEeeeEEeecCCCCCEEeC
Confidence            357999998 34 67788999999999999764

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=90.85  E-value=13  Score=34.29  Aligned_cols=34  Identities=9%  Similarity=0.305  Sum_probs=28.9

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII  297 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~  297 (312)
                      ...|+++||+.+|+|..||+++.+.-...+...+
T Consensus       281 e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l  314 (325)
T PRK05657        281 EAATLEDVAREIGLTRERVRQIQVEALRRLREIL  314 (325)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999887777666544

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=90.85  E-value=0.12  Score=31.89  Aligned_cols=31  Identities=32%  Similarity=0.513  Sum_probs=20.7

Q ss_pred             CCCCCCCCCCCCceeeeCC-CCceEcCCCccc
Q 021438            2 ADSYCADCKRLTEVVFDHS-AGDTICSECGLV   32 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~-~G~~vC~~CG~V   32 (312)
                      ...+|++||..-++..... .....|..||.-
T Consensus         4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~   35 (41)
T smart00834        4 YEYRCEDCGHTFEVLQKISDDPLATCPECGGD   35 (41)
T ss_pred             EEEEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence            3468999998333444333 456789999984

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=90.80  E-value=15  Score=34.65  Aligned_cols=31  Identities=23%  Similarity=0.330  Sum_probs=25.9

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~  294 (312)
                      ...|+++||+.+|+|...||+..+.-...+.
T Consensus       324 ~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr  354 (367)
T PRK09210        324 RTRTLEEVGKVFGVTRERIRQIEAKALRKLR  354 (367)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            5699999999999999999998776555443

>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins

Probab=90.59  E-value=0.18  Score=35.21  Aligned_cols=29  Identities=21%  Similarity=0.509  Sum_probs=21.5

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~   34 (312)
                      ..||.||..  ...+.......|..||...+
T Consensus        29 q~C~~CG~~--~~~~~~~r~~~C~~Cg~~~~   57 (69)
T PF07282_consen   29 QTCPRCGHR--NKKRRSGRVFTCPNCGFEMD   57 (69)
T ss_pred             cCccCcccc--cccccccceEEcCCCCCEEC
Confidence            579999983  22245667899999999865

More information about these proteins can be found at Protein of the Month: Transposase [].

>PRK12495 hypothetical protein; Provisional

Probab=90.54  E-value=0.18  Score=43.22  Aligned_cols=32  Identities=22%  Similarity=0.668  Sum_probs=25.7

Q ss_pred             CCCCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      |....|+.||.+  | + ...|.++|..|+.++.+.
T Consensus        40 msa~hC~~CG~P--I-p-a~pG~~~Cp~CQ~~~~~~   71 (226)
T PRK12495         40 MTNAHCDECGDP--I-F-RHDGQEFCPTCQQPVTED   71 (226)
T ss_pred             cchhhcccccCc--c-c-CCCCeeECCCCCCccccc
Confidence            566789999983  3 3 458999999999998753

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=90.50  E-value=0.45  Score=30.10  Aligned_cols=29  Identities=17%  Similarity=0.189  Sum_probs=19.1

Q ss_pred             HHhcCCCCCHHHHHHHhCcchhHHHHHHH
Q 021438          259 TQLSNDTKPLKEISIVTRVAEGTIKNVYK  287 (312)
Q Consensus       259 ~~~~~~~~~~~~Ia~~~~vs~~ti~~~~k  287 (312)
                      ..+.....++++||+.+|++.+||.+-+|
T Consensus        14 ~~l~~~G~s~~~IA~~lg~s~sTV~relk   42 (44)
T PF13936_consen   14 EALLEQGMSIREIAKRLGRSRSTVSRELK   42 (44)
T ss_dssp             HHHHCS---HHHHHHHTT--HHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence            34556678999999999999999996554

>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=90.22  E-value=0.26  Score=30.37  Aligned_cols=28  Identities=25%  Similarity=0.591  Sum_probs=15.3

Q ss_pred             CCCCCCCCCceeeeC-----CCC---ceEcCCCccc
Q 021438            5 YCADCKRLTEVVFDH-----SAG---DTICSECGLV   32 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~-----~~G---~~vC~~CG~V   32 (312)
                      .||.||+...+.+..     +++   .++|.+||..
T Consensus         2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~   37 (39)
T PF01096_consen    2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR   37 (39)
T ss_dssp             --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred             CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence            699999854333321     222   3789999964

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=90.13  E-value=0.2  Score=38.06  Aligned_cols=27  Identities=30%  Similarity=0.817  Sum_probs=21.1

Q ss_pred             CCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            5 YCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .||.||+.  +  .+..+.++|..||.+...
T Consensus         2 fC~~Cg~~--l--~~~~~~~~C~~C~~~~~~   28 (104)
T TIGR01384         2 FCPKCGSL--M--TPKNGVYVCPSCGYEKEK   28 (104)
T ss_pred             CCcccCcc--c--ccCCCeEECcCCCCcccc
Confidence            79999983  3  345689999999998653

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]

Probab=90.09  E-value=0.61  Score=47.48  Aligned_cols=82  Identities=12%  Similarity=0.252  Sum_probs=67.3

Q ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHH
Q 021438          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGR  186 (312)
Q Consensus       109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~--~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~  186 (312)
                      |...|+.+|++|.|.+.+.+....+|.-...  ..+++.|..+.+.-+|+|+.+|..+..+++.+|....+ --......
T Consensus       680 AavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR-~QPqa~~~  758 (920)
T KOG1010|consen  680 AAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYR-RQPQAVSL  758 (920)
T ss_pred             HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHh-cCchhhhh
Confidence            6788999999999999888887777755433  35668899999999999999999999999999998774 55555666


Q ss_pred             HHHHH
Q 021438          187 AKEFI  191 (312)
Q Consensus       187 ~~~~l  191 (312)
                      +|+.+
T Consensus       759 vyRsV  763 (920)
T KOG1010|consen  759 VYRSV  763 (920)
T ss_pred             hhhhe
Confidence            67654

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=89.61  E-value=0.55  Score=30.22  Aligned_cols=27  Identities=19%  Similarity=0.108  Sum_probs=18.9

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDLFP  291 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~  291 (312)
                      ..|.++||+.+|+|..||.+..+...+
T Consensus        17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~   43 (50)
T PF13384_consen   17 GWSIREIAKRLGVSRSTVYRWIKRYRE   43 (50)
T ss_dssp             T--HHHHHHHHTS-HHHHHHHHT----
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHccc
Confidence            678999999999999999998877654

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=89.60  E-value=0.3  Score=30.30  Aligned_cols=27  Identities=26%  Similarity=0.643  Sum_probs=18.3

Q ss_pred             CCCCCCCCCceee------eCCCC---ceEcCCCccc
Q 021438            5 YCADCKRLTEVVF------DHSAG---DTICSECGLV   32 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~------D~~~G---~~vC~~CG~V   32 (312)
                      .||.||.. +.++      ..++|   .++|.+||..
T Consensus         2 ~Cp~C~~~-~a~~~q~Q~RsaDE~mT~fy~C~~C~~~   37 (40)
T smart00440        2 PCPKCGNR-EATFFQLQTRSADEPMTVFYVCTKCGHR   37 (40)
T ss_pred             cCCCCCCC-eEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence            69999984 4433      12333   5899999964

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

>PTZ00255 60S ribosomal protein L37a; Provisional

Probab=89.38  E-value=0.27  Score=36.15  Aligned_cols=31  Identities=19%  Similarity=0.477  Sum_probs=25.2

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      ...||.||. .. +.-...|-..|..||.++.-
T Consensus        36 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AG   66 (90)
T PTZ00255         36 KYFCPFCGK-HA-VKRQAVGIWRCKGCKKTVAG   66 (90)
T ss_pred             CccCCCCCC-Cc-eeeeeeEEEEcCCCCCEEeC
Confidence            457999998 44 45577899999999999864

>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]

Probab=89.36  E-value=0.25  Score=33.60  Aligned_cols=28  Identities=21%  Similarity=0.545  Sum_probs=17.5

Q ss_pred             CCCCCCCCCCceeeeC--------------CCCc---eEcCCCccc
Q 021438            4 SYCADCKRLTEVVFDH--------------SAGD---TICSECGLV   32 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~--------------~~G~---~vC~~CG~V   32 (312)
                      .+||.||. ++..+++              +.-.   +.|.+||+-
T Consensus         5 ~kCpKCgn-~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYt   49 (68)
T COG3478           5 FKCPKCGN-TNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYT   49 (68)
T ss_pred             ccCCCcCC-cchhhceeeccCCCcceeEEecccEEEEEEeccCCch
Confidence            35999997 4554443              2221   569999874

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=89.25  E-value=16  Score=32.88  Aligned_cols=34  Identities=15%  Similarity=0.376  Sum_probs=27.7

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII  297 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~  297 (312)
                      ...|++|||+.+|+|+.||+++.+.-.+.+...+
T Consensus       241 e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l  274 (285)
T TIGR02394       241 EPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL  274 (285)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999998876666555444

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=89.17  E-value=0.97  Score=30.70  Aligned_cols=38  Identities=39%  Similarity=0.362  Sum_probs=28.5

Q ss_pred             CChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHH
Q 021438          245 RSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNV  285 (312)
Q Consensus       245 r~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~  285 (312)
                      |+|.-=-|=-+|+.   ++-.+++++||+.+||++.||++.
T Consensus         5 Rsp~rdkA~e~y~~---~~g~i~lkdIA~~Lgvs~~tIr~W   42 (60)
T PF10668_consen    5 RSPNRDKAFEIYKE---SNGKIKLKDIAEKLGVSESTIRKW   42 (60)
T ss_pred             CCcCHHHHHHHHHH---hCCCccHHHHHHHHCCCHHHHHHH
Confidence            44544445556643   566789999999999999999965

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines

Probab=89.01  E-value=0.13  Score=37.25  Aligned_cols=33  Identities=24%  Similarity=0.459  Sum_probs=17.5

Q ss_pred             CCCCCCCCCCce--eeeC--CCCceEcCCCcccccCc
Q 021438            4 SYCADCKRLTEV--VFDH--SAGDTICSECGLVLEAY   36 (312)
Q Consensus         4 ~~Cp~Cg~~~~i--i~D~--~~G~~vC~~CG~Vv~e~   36 (312)
                      ..||.|+....+  ..|.  ..|.+.|..||...+-.
T Consensus        23 F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~   59 (81)
T PF05129_consen   23 FDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK   59 (81)
T ss_dssp             ---TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred             EcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence            579999953444  3443  56789999999887543

; PDB: 1WII_A.

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=88.84  E-value=0.29  Score=32.84  Aligned_cols=26  Identities=35%  Similarity=0.742  Sum_probs=13.7

Q ss_pred             CCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            5 YCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      .|..||.  .|--++.--...|.+||.+
T Consensus        11 ~CtSCg~--~i~p~e~~v~F~CPnCGe~   36 (61)
T COG2888          11 VCTSCGR--EIAPGETAVKFPCPNCGEV   36 (61)
T ss_pred             eeccCCC--EeccCCceeEeeCCCCCce
Confidence            5666665  2323333344667777733

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=88.72  E-value=0.53  Score=30.17  Aligned_cols=20  Identities=25%  Similarity=0.413  Sum_probs=17.8

Q ss_pred             CHHHHHHHhCcchhHHHHHH
Q 021438          267 PLKEISIVTRVAEGTIKNVY  286 (312)
Q Consensus       267 ~~~~Ia~~~~vs~~ti~~~~  286 (312)
                      |++|||+.+|||..|+.+.+
T Consensus         1 Ti~dIA~~agvS~~TVSr~l   20 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVL   20 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHH
Confidence            57899999999999999665

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=88.61  E-value=0.38  Score=30.53  Aligned_cols=27  Identities=30%  Similarity=0.645  Sum_probs=20.0

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      ..|.+||..  +..+ ..+.+-|.+||.=+
T Consensus         3 Y~C~~Cg~~--~~~~-~~~~irC~~CG~rI   29 (44)
T smart00659        3 YICGECGRE--NEIK-SKDVVRCRECGYRI   29 (44)
T ss_pred             EECCCCCCE--eecC-CCCceECCCCCceE
Confidence            579999983  3333 56889999999744

present in RNA polymerase I, II and III

>PRK00135 scpB segregation and condensation protein B; Reviewed

Probab=88.49  E-value=5.7  Score=33.66  Aligned_cols=122  Identities=13%  Similarity=0.190  Sum_probs=70.4

Q ss_pred             HHHHHHHHHHHHHHHhCCC-CCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHH
Q 021438          148 QEAIVAACLYIACRQENKP-RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ  226 (312)
Q Consensus       148 ~~~iaaAcly~acr~~~~p-~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~  226 (312)
                      ...++=|+||+    .+-| +++.+++.++ +++..++..++..|...+..... .+.+-.+ ...|      +|...++
T Consensus         5 ~~~~iEA~LF~----sg~pgls~~~La~~l-~~~~~~v~~~l~~L~~~y~~~~~-gi~i~~~-~~~y------~l~tk~e   71 (188)
T PRK00135          5 YKSIIEALLFV----SGEEGLSLEQLAEIL-ELEPTEVQQLLEELQEKYEGDDR-GLKLIEF-NDVY------KLVTKEE   71 (188)
T ss_pred             HHHHHHHHHHH----cCCCCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHhhCCC-CEEEEEE-CCEE------EEEEcHH
Confidence            45667788886    5777 9999999999 79999999999998887753210 0011000 0001      1222333


Q ss_pred             HHHHHHHHHHHhhhccCCCChHHHHHHHH-HHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          227 AVKAAQEAVQKSEDLDIRRSPISVAAAVI-YIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       227 v~~~A~~i~~~~~~l~~Gr~P~~iaaAai-yla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .......+..       .+.|..+.-|++ -||.-.++-++|..+|++..|++.   ....++|.+.
T Consensus        72 ~~~~v~~~~~-------~~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv~~---~~ii~~L~~~  128 (188)
T PRK00135         72 NADYLQKLVK-------TPIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGVNS---DGALQTLLAK  128 (188)
T ss_pred             HHHHHHHHhc-------ccccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCH---HHHHHHHHHC
Confidence            3222222221       112222332333 233344567899999999999996   5556666654

>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=88.43  E-value=1.2  Score=40.12  Aligned_cols=53  Identities=13%  Similarity=0.178  Sum_probs=46.7

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcC
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSN  263 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~  263 (312)
                      ..+|.++|.+|+++..+...|.-+.++-.-  -..+..|..||+++|||||+..+
T Consensus        49 ~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed  103 (297)
T COG5333          49 LKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVED  103 (297)
T ss_pred             HHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeeccc
Confidence            468999999999999999999988888554  45789999999999999999877

>PRK12286 rpmF 50S ribosomal protein L32; Reviewed

Probab=88.40  E-value=0.36  Score=32.47  Aligned_cols=28  Identities=21%  Similarity=0.546  Sum_probs=20.1

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccCccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSV   38 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~i   38 (312)
                      ..||+||+. .      .--.+|.+||+--+..++
T Consensus        28 ~~C~~CG~~-~------~~H~vC~~CG~Y~gr~v~   55 (57)
T PRK12286         28 VECPNCGEP-K------LPHRVCPSCGYYKGREVV   55 (57)
T ss_pred             eECCCCCCc-c------CCeEECCCCCcCCCEEee
Confidence            469999983 2      357899999987654443

>PF05460 ORC6: Origin recognition complex subunit 6 (ORC6); InterPro: IPR008721 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []

Probab=88.35  E-value=0.14  Score=47.84  Aligned_cols=77  Identities=16%  Similarity=0.214  Sum_probs=0.0

Q ss_pred             CCcHHHHHHHHHHHHHHH-hCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhh
Q 021438          121 GLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE  198 (312)
Q Consensus       121 ~Lp~~v~~~A~~i~~~~~-~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~  198 (312)
                      ++|+.++..|..||+... ....+++..-.+-+.+|+|+||...+.+..+....... +++++...+.|..+.+.|+..
T Consensus        11 ~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~-pl~pk~y~~l~~~~~~~L~~~   88 (353)
T PF05460_consen   11 GLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRS-PLPPKVYKKLLNTFENLLGNS   88 (353)
T ss_dssp             -------------------------------------------------------------------------------
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCC-CCCHHHHHHHHHHHHHHHhCC
Confidence            346789999999999887 34555776667889999999999999999888877777 799999888888888888763

ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 6, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; interacts with Spp1 and with trimethylated histone H3; phosphorylated by Cdc28 [, ]. In Saccharomyces cerevisiae (Baker's yeast), both ends of the Orc6 interact with Cdt1 [] and the N terminus mediates an interaction with the S-phase cyclin Clb5 []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex; PDB: 3M03_B.

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=88.25  E-value=0.74  Score=30.78  Aligned_cols=32  Identities=22%  Similarity=0.238  Sum_probs=26.9

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ...+.++||+..++|+.||+.+.+.|.+.++.
T Consensus        17 ~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~   48 (58)
T PF00196_consen   17 QGMSNKEIAEELGISEKTVKSHRRRIMKKLGV   48 (58)
T ss_dssp             TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred             hcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence            35679999999999999999999999987653

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=88.13  E-value=0.46  Score=27.00  Aligned_cols=22  Identities=23%  Similarity=0.533  Sum_probs=11.8

Q ss_pred             CCCCCCCCCceeeeCCCCceEcCC
Q 021438            5 YCADCKRLTEVVFDHSAGDTICSE   28 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~G~~vC~~   28 (312)
                      .||.||+  .++.+..+-.+.|.+
T Consensus         1 ~CP~C~s--~l~~~~~ev~~~C~N   22 (28)
T PF03119_consen    1 TCPVCGS--KLVREEGEVDIRCPN   22 (28)
T ss_dssp             B-TTT----BEEE-CCTTCEEE--
T ss_pred             CcCCCCC--EeEcCCCCEeEECCC
Confidence            5999998  477766666777764

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.

>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A

Probab=88.01  E-value=1.1  Score=31.40  Aligned_cols=29  Identities=21%  Similarity=0.168  Sum_probs=26.4

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .++++++||+.+|+|..|+.+.+++|.+.
T Consensus        27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~   55 (76)
T PF13545_consen   27 LPLTQEEIADMLGVSRETVSRILKRLKDE   55 (76)
T ss_dssp             EESSHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            45789999999999999999999999885

...

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=87.98  E-value=29  Score=34.20  Aligned_cols=31  Identities=26%  Similarity=0.335  Sum_probs=26.4

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~  294 (312)
                      ...|+++||..+|||..-||+.-+.....+.
T Consensus       466 e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR  496 (509)
T PRK05901        466 QPKTLDEIGQVYGVTRERIRQIESKTLRKLR  496 (509)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            5799999999999999999988876666554

>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family

Probab=87.95  E-value=1.9  Score=29.22  Aligned_cols=29  Identities=17%  Similarity=0.103  Sum_probs=26.5

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      ..+++.+||+.+|++..|+.+.++.|.+.
T Consensus        24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~   52 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTLKELEEE   52 (67)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            56889999999999999999999999884

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=87.94  E-value=0.88  Score=29.55  Aligned_cols=30  Identities=23%  Similarity=0.265  Sum_probs=26.6

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~  294 (312)
                      ..+.++||+.+|+|..|++++.+.+.+.+.
T Consensus        18 g~s~~eia~~l~is~~tv~~~~~~~~~kl~   47 (58)
T smart00421       18 GLTNKEIAERLGISEKTVKTHLSNIMRKLG   47 (58)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence            368999999999999999999998877664

lux regulon (activates the bioluminescence operon

>TIGR00280 L37a ribosomal protein L37a

Probab=87.90  E-value=0.36  Score=35.57  Aligned_cols=31  Identities=26%  Similarity=0.517  Sum_probs=25.4

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      ...||.||. .. +.-...|-..|..||.++.-
T Consensus        35 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AG   65 (91)
T TIGR00280        35 KYVCPFCGK-KT-VKRGSTGIWTCRKCGAKFAG   65 (91)
T ss_pred             CccCCCCCC-Cc-eEEEeeEEEEcCCCCCEEeC
Confidence            457999997 44 56678999999999999764

This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.

>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=87.88  E-value=0.25  Score=38.20  Aligned_cols=32  Identities=19%  Similarity=0.367  Sum_probs=23.2

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      -.||+||+ ..+..-+-.=.-.|..||.=...+
T Consensus        22 grCP~CGe-GrLF~gFLK~~p~C~aCG~dyg~~   53 (126)
T COG5349          22 GRCPRCGE-GRLFRGFLKVVPACEACGLDYGFA   53 (126)
T ss_pred             CCCCCCCC-chhhhhhcccCchhhhccccccCC
Confidence            47999998 666554555567899999866543

>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=87.88  E-value=0.31  Score=28.62  Aligned_cols=25  Identities=28%  Similarity=0.589  Sum_probs=17.2

Q ss_pred             CCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            5 YCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      .|.+||..   +.+.....+-|..||.=
T Consensus         2 ~C~~Cg~~---~~~~~~~~irC~~CG~R   26 (32)
T PF03604_consen    2 ICGECGAE---VELKPGDPIRCPECGHR   26 (32)
T ss_dssp             BESSSSSS---E-BSTSSTSSBSSSS-S
T ss_pred             CCCcCCCe---eEcCCCCcEECCcCCCe
Confidence            58899983   23455667899999963

Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....

>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression

Probab=87.85  E-value=0.94  Score=33.29  Aligned_cols=31  Identities=32%  Similarity=0.275  Sum_probs=26.9

Q ss_pred             hcCCCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438          261 LSNDTKPLKEISIVTRVAEGTIKNVYKDLFP  291 (312)
Q Consensus       261 ~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~  291 (312)
                      ++....|+++|++.+|+|..||.+.-+.|..
T Consensus        45 lL~~g~syreIa~~tgvS~aTItRvsr~Lk~   75 (87)
T PF01371_consen   45 LLDEGKSYREIAEETGVSIATITRVSRCLKY   75 (87)
T ss_dssp             HHHTTSSHHHHHHHHTSTHHHHHHHHHHHHH
T ss_pred             HHHCCCCHHHHHHHhCCCHHHHHHHHHHHHc
Confidence            6667799999999999999999987777764

The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=87.80  E-value=2.3  Score=29.76  Aligned_cols=71  Identities=15%  Similarity=0.232  Sum_probs=42.5

Q ss_pred             HHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC-CHHHHHHHHHHH
Q 021438          113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGRAKEFI  191 (312)
Q Consensus       113 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v-~~~~i~~~~~~l  191 (312)
                      |.+++..++++.....   .+|+.........-....-+.-|+-|+.    ..+.++.|++..+ |. +...+.+.+++.
T Consensus         4 ~~~la~~~~~s~~~l~---~~f~~~~~~s~~~~~~~~r~~~a~~~l~----~~~~~~~~ia~~~-g~~s~~~f~r~Fk~~   75 (84)
T smart00342        4 LEDLAEALGMSPRHLQ---RLFKKETGTTPKQYLRDRRLERARRLLR----DTDLSVTEIALRV-GFSSQSYFSRAFKKL   75 (84)
T ss_pred             HHHHHHHhCCCHHHHH---HHHHHHhCcCHHHHHHHHHHHHHHHHHH----cCCCCHHHHHHHh-CCCChHHHHHHHHHH
Confidence            6788899999876433   3444432211100011122333334432    2289999999999 89 999998888664

>PRK05978 hypothetical protein; Provisional

Probab=87.77  E-value=0.41  Score=38.84  Aligned_cols=31  Identities=16%  Similarity=0.390  Sum_probs=23.2

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .+||.||. ..+..-+-.=..-|..||.-.+-
T Consensus        34 grCP~CG~-G~LF~g~Lkv~~~C~~CG~~~~~   64 (148)
T PRK05978         34 GRCPACGE-GKLFRAFLKPVDHCAACGEDFTH   64 (148)
T ss_pred             CcCCCCCC-CcccccccccCCCccccCCcccc
Confidence            58999998 67755455555789999987653

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=87.70  E-value=0.95  Score=37.40  Aligned_cols=30  Identities=10%  Similarity=-0.020  Sum_probs=27.7

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +-+.+..+||+.+|+|+.|+++|++.|.+.
T Consensus        26 d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~   55 (164)
T PRK11169         26 DGRISNVELSKRVGLSPTPCLERVRRLERQ   55 (164)
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            456889999999999999999999999986

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=87.59  E-value=0.36  Score=30.68  Aligned_cols=29  Identities=21%  Similarity=0.237  Sum_probs=20.1

Q ss_pred             HHHhcCCCCCHHHHHHHhCcchhHHHHHH
Q 021438          258 ITQLSNDTKPLKEISIVTRVAEGTIKNVY  286 (312)
Q Consensus       258 a~~~~~~~~~~~~Ia~~~~vs~~ti~~~~  286 (312)
                      +.+++....|..+||+.+|||..||.+..
T Consensus        14 i~~l~~~G~si~~IA~~~gvsr~TvyR~l   42 (45)
T PF02796_consen   14 IKELYAEGMSIAEIAKQFGVSRSTVYRYL   42 (45)
T ss_dssp             HHHHHHTT--HHHHHHHTTS-HHHHHHHH
T ss_pred             HHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence            33455455889999999999999998654

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=87.51  E-value=26  Score=33.13  Aligned_cols=32  Identities=22%  Similarity=0.321  Sum_probs=27.4

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ...|+++||..+|+|..+||+..+.-...+..
T Consensus       330 ~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~  361 (373)
T PRK07406        330 RMKTLEEIGQIFNVTRERIRQIEAKALRKLRH  361 (373)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            46899999999999999999998877766544

>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2

Probab=87.39  E-value=0.084  Score=31.97  Aligned_cols=30  Identities=27%  Similarity=0.747  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      ..||.||..=++.+++..-+-+|..||.-+
T Consensus         2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L   31 (36)
T PF05191_consen    2 RICPKCGRIYHIEFNPPKVEGVCDNCGGEL   31 (36)
T ss_dssp             EEETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred             cCcCCCCCccccccCCCCCCCccCCCCCee
Confidence            368899974466777777788898888743

7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=87.21  E-value=0.96  Score=28.48  Aligned_cols=30  Identities=17%  Similarity=0.113  Sum_probs=26.6

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .++.++.+||+.+|++..|+.+.++.|.+.
T Consensus         6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~   35 (48)
T smart00419        6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE   35 (48)
T ss_pred             EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            356889999999999999999999998874

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=87.19  E-value=2.3  Score=28.13  Aligned_cols=27  Identities=11%  Similarity=0.140  Sum_probs=23.4

Q ss_pred             CCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          266 KPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       266 ~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .++.|||+.+|||.+|+..+.+.-...
T Consensus        24 ~tl~elA~~lgis~st~~~~LRrae~k   50 (53)
T PF04967_consen   24 ITLEELAEELGISKSTVSEHLRRAERK   50 (53)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            679999999999999999988765544

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>COG4640 Predicted membrane protein [Function unknown]

Probab=87.19  E-value=0.34  Score=44.99  Aligned_cols=28  Identities=21%  Similarity=0.699  Sum_probs=21.2

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      |..||.||+. .     .++++-|+.||.=+..+
T Consensus         1 M~fC~kcG~q-k-----~Ed~~qC~qCG~~~t~~   28 (465)
T COG4640           1 MKFCPKCGSQ-K-----AEDDVQCTQCGHKFTSR   28 (465)
T ss_pred             CCcccccccc-c-----ccccccccccCCcCCch
Confidence            6789999983 2     25677799999887653

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=87.02  E-value=1.3  Score=28.27  Aligned_cols=32  Identities=19%  Similarity=0.220  Sum_probs=26.7

Q ss_pred             hcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          261 LSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       261 ~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +..-+.+..||++.++++.+||+...+.|.+.
T Consensus        11 L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~   42 (47)
T PF01022_consen   11 LSEGPLTVSELAEELGLSQSTVSHHLKKLREA   42 (47)
T ss_dssp             HTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHhCCCchhhHHHhccccchHHHHHHHHHHHC
Confidence            44466889999999999999999999998874

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=87.01  E-value=0.7  Score=32.65  Aligned_cols=31  Identities=13%  Similarity=0.252  Sum_probs=21.8

Q ss_pred             CCCCCCCCCCCceeeeCC-------CCceEcC--CCccccc
Q 021438            3 DSYCADCKRLTEVVFDHS-------AGDTICS--ECGLVLE   34 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~-------~G~~vC~--~CG~Vv~   34 (312)
                      |+.||.||+. ..|.+..       +-...|+  +||.-.-
T Consensus         1 mm~CP~Cg~~-a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~   40 (72)
T PRK09678          1 MFHCPLCQHA-AHARTSRYITDTTKERYHQCQNVNCSATFI   40 (72)
T ss_pred             CccCCCCCCc-cEEEEChhcChhhheeeeecCCCCCCCEEE
Confidence            6899999984 5666642       2236788  8998764

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=86.87  E-value=25  Score=32.32  Aligned_cols=31  Identities=10%  Similarity=0.266  Sum_probs=25.4

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPHL  293 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~  293 (312)
                      +.+.|++|||..+|+|..+||++.+.-...+
T Consensus       274 ~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kL  304 (317)
T PRK07405        274 GQPLTLAKIGERLNISRERVRQIEREALSKL  304 (317)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            3679999999999999999998876554443

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=86.84  E-value=1.2  Score=29.42  Aligned_cols=30  Identities=17%  Similarity=0.224  Sum_probs=26.2

Q ss_pred             CCCC-CHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTK-PLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~-~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +..+ +.+++|+.+++|..|+++.++.|.+.
T Consensus        17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~   47 (60)
T smart00345       17 GDKLPSERELAAQLGVSRTTVREALSRLEAE   47 (60)
T ss_pred             CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            3345 79999999999999999999999874

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=86.81  E-value=1.2  Score=36.33  Aligned_cols=30  Identities=23%  Similarity=0.267  Sum_probs=27.7

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +-..|..+||+.+|+|+.|+++|++.|.+.
T Consensus        21 d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~   50 (153)
T PRK11179         21 NARTPYAELAKQFGVSPGTIHVRVEKMKQA   50 (153)
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            456889999999999999999999999996

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=86.73  E-value=0.53  Score=33.36  Aligned_cols=28  Identities=25%  Similarity=0.140  Sum_probs=23.9

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFP  291 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~  291 (312)
                      ...|++|||+.+|+|+.||+++++.+..
T Consensus        31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~   58 (73)
T TIGR03879        31 AGKTASEIAEELGRTEQTVRNHLKGETK   58 (73)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence            3578999999999999999999886544

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=86.71  E-value=1  Score=35.51  Aligned_cols=30  Identities=23%  Similarity=0.418  Sum_probs=27.0

Q ss_pred             CCCCC-HHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKP-LKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~-~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      |.++| .++.|..++|.+.|+++.|++|.+.
T Consensus        32 GdkLPSvRelA~~~~VNpnTv~raY~eLE~e   62 (125)
T COG1725          32 GDKLPSVRELAKDLGVNPNTVQRAYQELERE   62 (125)
T ss_pred             CCCCCcHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            66765 8999999999999999999999884

>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed

Probab=86.70  E-value=0.45  Score=35.01  Aligned_cols=32  Identities=25%  Similarity=0.481  Sum_probs=25.5

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      ...||.||. .. +.-...|-.-|..||.++.-.
T Consensus        36 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGG   67 (90)
T PRK03976         36 KHVCPVCGR-PK-VKRVGTGIWECRKCGAKFAGG   67 (90)
T ss_pred             CccCCCCCC-Cc-eEEEEEEEEEcCCCCCEEeCC
Confidence            457999997 34 456788999999999998653

>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]

Probab=86.46  E-value=0.16  Score=33.88  Aligned_cols=26  Identities=31%  Similarity=0.883  Sum_probs=20.0

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCC-Cccccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSE-CGLVLE   34 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~-CG~Vv~   34 (312)
                      +..|+.||..  |    ..|+.+|++ ||.+++
T Consensus         8 H~HC~VCg~a--I----p~de~~CSe~C~eil~   34 (64)
T COG4068           8 HRHCVVCGKA--I----PPDEQVCSEECGEILN   34 (64)
T ss_pred             CccccccCCc--C----CCccchHHHHHHHHHH
Confidence            4689999983  3    257889986 998875

>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=86.37  E-value=0.45  Score=31.86  Aligned_cols=27  Identities=19%  Similarity=0.530  Sum_probs=18.9

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccCcc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~   37 (312)
                      ..||+||..       ...-.+|.+||+.=.-.+
T Consensus        27 ~~c~~cg~~-------~~~H~vc~~cG~y~~r~v   53 (56)
T PF01783_consen   27 VKCPNCGEP-------KLPHRVCPSCGYYKGRQV   53 (56)
T ss_dssp             EESSSSSSE-------ESTTSBCTTTBBSSSSSS
T ss_pred             eeeccCCCE-------ecccEeeCCCCeECCEEE
Confidence            479999972       246789999997644333

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....

>PHA02591 hypothetical protein; Provisional

Probab=86.34  E-value=1.1  Score=31.86  Aligned_cols=32  Identities=9%  Similarity=0.195  Sum_probs=25.3

Q ss_pred             HHHHHhcCCCCCHHHHHHHhCcchhHHHHHHH
Q 021438          256 YIITQLSNDTKPLKEISIVTRVAEGTIKNVYK  287 (312)
Q Consensus       256 yla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~k  287 (312)
                      -+|-++.....|+.+||+.+|++..++++..+
T Consensus        50 ~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         50 SVTHELARKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            34455555678899999999999999997654

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=86.33  E-value=23  Score=31.39  Aligned_cols=32  Identities=22%  Similarity=0.295  Sum_probs=27.2

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ..+|++|||..+|+|..||+++.+.....+..
T Consensus       220 e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~  251 (257)
T PRK05911        220 EELVLKEIGKILGVSESRVSQIHSKALLKLRA  251 (257)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            56899999999999999999998776666544

>PRK08402 replication factor A; Reviewed

Probab=86.18  E-value=0.6  Score=43.65  Aligned_cols=27  Identities=37%  Similarity=0.812  Sum_probs=23.1

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      ..||.|+.  .++.|...|...|..||.|
T Consensus       213 ~aCp~CnK--kv~~~~~~~~~~Ce~~~~v  239 (355)
T PRK08402        213 DACPECRR--KVDYDPATDTWICPEHGEV  239 (355)
T ss_pred             ecCCCCCe--EEEEecCCCCEeCCCCCCc
Confidence            47999997  4666888999999999975

>PF12773 DZR: Double zinc ribbon

Probab=86.09  E-value=0.44  Score=30.88  Aligned_cols=28  Identities=21%  Similarity=0.633  Sum_probs=12.9

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~   34 (312)
                      ..||+||..  +. .......+|..||..++
T Consensus        13 ~fC~~CG~~--l~-~~~~~~~~C~~Cg~~~~   40 (50)
T PF12773_consen   13 KFCPHCGTP--LP-PPDQSKKICPNCGAENP   40 (50)
T ss_pred             cCChhhcCC--hh-hccCCCCCCcCCcCCCc
Confidence            345555542  21 22233455666665543

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=86.06  E-value=6.7  Score=28.81  Aligned_cols=71  Identities=15%  Similarity=0.236  Sum_probs=48.7

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhhccCCCC-hHHHH-HHHHHHHHHhcCCCCCHHHHHHHhC-cchhHHHHHHH
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRRS-PISVA-AAVIYIITQLSNDTKPLKEISIVTR-VAEGTIKNVYK  287 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~l~~Gr~-P~~ia-aAaiyla~~~~~~~~~~~~Ia~~~~-vs~~ti~~~~k  287 (312)
                      +..+..+|..+|++.+..            ...+|. +.+.| .-+.|++-+..|  .|..+|++.+| .+.+||...++
T Consensus         2 ~~Ii~~Va~~~~v~~~~i------------~~~~R~~~~~~aR~ia~yl~~~~~~--~s~~~Ig~~fg~r~hStV~~a~~   67 (90)
T cd06571           2 ELIIEAVAEYFGISVEDL------------RSKSRKKEIALARQIAMYLARELTG--LSLPEIGRAFGGRDHSTVLHAVR   67 (90)
T ss_pred             HHHHHHHHHHhCCCHHHH------------hcCCCCcCcchHHHHHHHHHHHHhC--CCHHHHHHHhCCCCHhHHHHHHH
Confidence            345666666666665321            112222 33334 567888888875  56899999999 99999999999


Q ss_pred             HHHhhhcc
Q 021438          288 DLFPHLAR  295 (312)
Q Consensus       288 el~~~~~~  295 (312)
                      .+.+.+..
T Consensus        68 ri~~~~~~   75 (90)
T cd06571          68 KIEELLEE   75 (90)
T ss_pred             HHHHHHHh
Confidence            88886643

The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=86.01  E-value=1.2  Score=29.12  Aligned_cols=28  Identities=18%  Similarity=0.215  Sum_probs=21.0

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFP  291 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~  291 (312)
                      ...|.+|||+..|+|+.|+++++..-.+
T Consensus        25 ~g~s~~eIa~~l~~s~~~v~~~l~ra~~   52 (54)
T PF08281_consen   25 QGMSYAEIAEILGISESTVKRRLRRARK   52 (54)
T ss_dssp             S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred             HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            4577999999999999999999876554

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins

Probab=86.01  E-value=0.52  Score=32.48  Aligned_cols=27  Identities=30%  Similarity=0.715  Sum_probs=17.5

Q ss_pred             CCCCCCCCCcee--------------eeCCCCc---eEcCCCccc
Q 021438            5 YCADCKRLTEVV--------------FDHSAGD---TICSECGLV   32 (312)
Q Consensus         5 ~Cp~Cg~~~~ii--------------~D~~~G~---~vC~~CG~V   32 (312)
                      .||.||+. +..              +|-++..   ++|++||+.
T Consensus         2 ~C~KCg~~-~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT   45 (64)
T PF09855_consen    2 KCPKCGNE-EYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT   45 (64)
T ss_pred             CCCCCCCc-ceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence            69999973 332              3322222   689999987

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=86.01  E-value=1.6  Score=28.30  Aligned_cols=24  Identities=13%  Similarity=0.386  Sum_probs=21.7

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHH
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKD  288 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~ke  288 (312)
                      ..|+++||+..|+|..||++.+++
T Consensus        27 ~~s~~~vA~~~~vs~~TV~ri~~~   50 (52)
T PF13542_consen   27 SRSFKDVARELGVSWSTVRRIFDR   50 (52)
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHh
Confidence            379999999999999999988765

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=85.93  E-value=0.35  Score=29.25  Aligned_cols=29  Identities=28%  Similarity=0.603  Sum_probs=19.6

Q ss_pred             CCCCCCCCCCceeee----CCCCceEcCCCcccc
Q 021438            4 SYCADCKRLTEVVFD----HSAGDTICSECGLVL   33 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D----~~~G~~vC~~CG~Vv   33 (312)
                      ..||+|+.. --+.|    .....+-|+.||.+.
T Consensus         3 i~Cp~C~~~-y~i~d~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    3 ITCPNCQAK-YEIDDEKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             EECCCCCCE-EeCCHHHCCCCCcEEECCCCCCEe
Confidence            579999983 22233    234458899999874

>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]

Probab=85.57  E-value=3.2  Score=37.48  Aligned_cols=66  Identities=14%  Similarity=0.129  Sum_probs=54.8

Q ss_pred             HHHHHHHHhhc--CCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhC
Q 021438          211 SDYLRRFCSNL--GMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTR  276 (312)
Q Consensus       211 ~~~i~r~~~~L--~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~  276 (312)
                      +..+..|++++  .++..|+..|....++..-  ....-+|-.|.++++||||+...+-+|..++++-..
T Consensus        60 E~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~  129 (325)
T KOG2496|consen   60 ELSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN  129 (325)
T ss_pred             HHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc
Confidence            44566677665  5899999999998888764  456789999999999999999999999999988765

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=85.49  E-value=1  Score=30.14  Aligned_cols=29  Identities=24%  Similarity=0.195  Sum_probs=25.2

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      -.++.+++|+.++||+.|||+-+.+|.+.
T Consensus        13 ~~~s~~ela~~~~VS~~TiRRDl~~L~~~   41 (57)
T PF08220_consen   13 GKVSVKELAEEFGVSEMTIRRDLNKLEKQ   41 (57)
T ss_pred             CCEEHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            46889999999999999999888877664

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=85.27  E-value=1.6  Score=28.34  Aligned_cols=31  Identities=26%  Similarity=0.363  Sum_probs=27.0

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ..+.++||+.+++|+.||+.+.+.+.+.+..
T Consensus        15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~   45 (57)
T cd06170          15 GKTNKEIADILGISEKTVKTHLRNIMRKLGV   45 (57)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            4689999999999999999999988776543

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>TIGR01031 rpmF_bact ribosomal protein L32

Probab=85.06  E-value=0.64  Score=31.02  Aligned_cols=25  Identities=20%  Similarity=0.679  Sum_probs=17.8

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      ..||+||+.       ..---||..||+--+.
T Consensus        27 ~~C~~cG~~-------~~~H~vc~~cG~Y~gr   51 (55)
T TIGR01031        27 VVCPNCGEF-------KLPHRVCPSCGYYKGR   51 (55)
T ss_pred             eECCCCCCc-------ccCeeECCccCeECCE
Confidence            469999972       2356899999976543

This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=84.94  E-value=7.6  Score=32.26  Aligned_cols=29  Identities=17%  Similarity=0.053  Sum_probs=26.8

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .++|+++||+.+|+|..|+.+..++|.+.
T Consensus       142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~  170 (193)
T TIGR03697       142 LRLSHQAIAEAIGSTRVTITRLLGDLRKK  170 (193)
T ss_pred             CCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence            56899999999999999999999999885

Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.

>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG

Probab=84.57  E-value=0.68  Score=30.50  Aligned_cols=29  Identities=34%  Similarity=0.672  Sum_probs=21.2

Q ss_pred             CCCCCCCCCceeeeCCCCc----eEcCCCcccc
Q 021438            5 YCADCKRLTEVVFDHSAGD----TICSECGLVL   33 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~G~----~vC~~CG~Vv   33 (312)
                      .||+||....+..|.+.|.    -=|.-|..=+
T Consensus         2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI   34 (52)
T PF14255_consen    2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPI   34 (52)
T ss_pred             CCCCCCCeeEEEEecCCCCeeEEeehhhcCCcc
Confidence            6999999778888988885    2366665544

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=84.54  E-value=1.2  Score=30.47  Aligned_cols=29  Identities=21%  Similarity=0.306  Sum_probs=19.5

Q ss_pred             CCCCCCCCCCCceeeeCCCCc--eEcCCCccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGD--TICSECGLV   32 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~--~vC~~CG~V   32 (312)
                      ...||.||.....+.+ ..|-  .+|..||..
T Consensus         6 lKPCPFCG~~~~~v~~-~~g~~~v~C~~CgA~   36 (64)
T PRK09710          6 VKPCPFCGCPSVTVKA-ISGYYRAKCNGCESR   36 (64)
T ss_pred             ccCCCCCCCceeEEEe-cCceEEEEcCCCCcC
Confidence            3579999984333333 3333  689999985

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=84.49  E-value=0.28  Score=41.28  Aligned_cols=31  Identities=23%  Similarity=0.491  Sum_probs=22.6

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      ..||.|+.. =-..|.-+....|..||.++.+
T Consensus       118 Y~Cp~C~~r-ytf~eA~~~~F~Cp~Cg~~L~~  148 (178)
T PRK06266        118 FFCPNCHIR-FTFDEAMEYGFRCPQCGEMLEE  148 (178)
T ss_pred             EECCCCCcE-EeHHHHhhcCCcCCCCCCCCee
Confidence            469999973 2233445678999999999875

>TIGR02443 conserved hypothetical metal-binding protein

Probab=84.46  E-value=0.99  Score=30.37  Aligned_cols=30  Identities=20%  Similarity=0.491  Sum_probs=20.3

Q ss_pred             CCCCCCCCCCCceeeeCCCC--ceEcCCCccc
Q 021438            3 DSYCADCKRLTEVVFDHSAG--DTICSECGLV   32 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G--~~vC~~CG~V   32 (312)
                      .-.||.|+.-..+..=.++|  ..-|-.||+-
T Consensus         9 GA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~   40 (59)
T TIGR02443         9 GAVCPACSAQDTLAMWKENNIELVECVECGYQ   40 (59)
T ss_pred             cccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence            35799999854443322333  3789999987

Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.

>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]

Probab=84.36  E-value=0.81  Score=33.96  Aligned_cols=31  Identities=19%  Similarity=0.470  Sum_probs=21.3

Q ss_pred             CCCCCCCCCCCceeeeCC-CCceEcCCCccccc
Q 021438            3 DSYCADCKRLTEVVFDHS-AGDTICSECGLVLE   34 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~-~G~~vC~~CG~Vv~   34 (312)
                      |..||.||. .=+++.-. -....|..|++|..
T Consensus         1 m~FCP~Cgn-~Live~g~~~~rf~C~tCpY~~~   32 (105)
T KOG2906|consen    1 MLFCPTCGN-MLIVESGESCNRFSCRTCPYVFP   32 (105)
T ss_pred             CcccCCCCC-EEEEecCCeEeeEEcCCCCceee
Confidence            468999998 33333222 25678999999963

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=84.00  E-value=1.6  Score=25.58  Aligned_cols=27  Identities=19%  Similarity=0.356  Sum_probs=21.6

Q ss_pred             CCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 021438          166 PRTVKEFCSVANGTTKKEIGRAKEFIVK  193 (312)
Q Consensus       166 p~tl~dia~~~~~v~~~~i~~~~~~l~~  193 (312)
                      |.|-.||++.. |.+.+++.|.++++.+
T Consensus         2 ~mtr~diA~~l-G~t~ETVSR~l~~l~~   28 (32)
T PF00325_consen    2 PMTRQDIADYL-GLTRETVSRILKKLER   28 (32)
T ss_dssp             E--HHHHHHHH-TS-HHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHh-CCcHHHHHHHHHHHHH
Confidence            67889999999 8999999999988764

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=83.95  E-value=0.53  Score=30.76  Aligned_cols=30  Identities=27%  Similarity=0.506  Sum_probs=18.7

Q ss_pred             CCCCCCCCCCCCceeee-CCCCceEcCCCcc
Q 021438            2 ADSYCADCKRLTEVVFD-HSAGDTICSECGL   31 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D-~~~G~~vC~~CG~   31 (312)
                      +..+|++||..-++... .+.....|..||.
T Consensus         4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~   34 (52)
T TIGR02605         4 YEYRCTACGHRFEVLQKMSDDPLATCPECGG   34 (52)
T ss_pred             EEEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence            34679999973233322 2245678999997

This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.

>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis

Probab=83.94  E-value=0.55  Score=40.53  Aligned_cols=34  Identities=29%  Similarity=0.662  Sum_probs=25.8

Q ss_pred             CCCCCCCCC-CceeeeCCCCc---eEcCCCcccccCcc
Q 021438            4 SYCADCKRL-TEVVFDHSAGD---TICSECGLVLEAYS   37 (312)
Q Consensus         4 ~~Cp~Cg~~-~~ii~D~~~G~---~vC~~CG~Vv~e~~   37 (312)
                      +.|-+||.+ ..+..+++.|.   ..|.+||.|.|..+
T Consensus         1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDkYi   38 (208)
T PF04161_consen    1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADKYI   38 (208)
T ss_pred             CEeccCCCcchhhhhccCCCcEEEeeccccCCccccee
Confidence            479999984 34567777664   89999999987543

Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].

>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing

Probab=83.92  E-value=0.86  Score=36.81  Aligned_cols=28  Identities=25%  Similarity=0.699  Sum_probs=20.4

Q ss_pred             CCC--CCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            5 YCA--DCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         5 ~Cp--~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .||  .|++  .+..+ .+|.+.|..||..+++
T Consensus        20 aC~~~~C~k--Kv~~~-~~~~y~C~~C~~~~~~   49 (146)
T PF08646_consen   20 ACPNEKCNK--KVTEN-GDGSYRCEKCNKTVEN   49 (146)
T ss_dssp             E-TSTTTS---B-EEE-TTTEEEETTTTEEESS
T ss_pred             CCCCccCCC--EeecC-CCcEEECCCCCCcCCC
Confidence            599  9998  46665 7799999999988753

It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=83.88  E-value=12  Score=25.95  Aligned_cols=26  Identities=19%  Similarity=0.404  Sum_probs=22.9

Q ss_pred             CCCHHHHHHHhCc-chhHHHHHHHHHH
Q 021438          265 TKPLKEISIVTRV-AEGTIKNVYKDLF  290 (312)
Q Consensus       265 ~~~~~~Ia~~~~v-s~~ti~~~~kel~  290 (312)
                      +.++.+||..+|. +...+.+.+|+..
T Consensus        50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~   76 (84)
T smart00342       50 DLSVTEIALRVGFSSQSYFSRAFKKLF   76 (84)
T ss_pred             CCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence            6889999999999 9999998887764

>PRK04217 hypothetical protein; Provisional

Probab=83.71  E-value=1.4  Score=33.90  Aligned_cols=32  Identities=16%  Similarity=0.133  Sum_probs=27.1

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ..+++++||+.+|+|..||+++++...+.+..
T Consensus        57 eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre   88 (110)
T PRK04217         57 EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQ   88 (110)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            45689999999999999999998877776654

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=83.51  E-value=1.4  Score=32.80  Aligned_cols=31  Identities=26%  Similarity=0.203  Sum_probs=25.3

Q ss_pred             HhcCCCCCHHHHHHHhCcchhHHHHHHHHHH
Q 021438          260 QLSNDTKPLKEISIVTRVAEGTIKNVYKDLF  290 (312)
Q Consensus       260 ~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~  290 (312)
                      .+..-.+||+|||+.+|||..||.+.-+.+.
T Consensus        50 ~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk   80 (94)
T TIGR01321        50 ELLNGNMSQREIASKLGVSIATITRGSNNLK   80 (94)
T ss_pred             HHHhCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence            3444679999999999999999997766655

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center

Probab=83.32  E-value=0.93  Score=26.73  Aligned_cols=23  Identities=26%  Similarity=0.788  Sum_probs=14.5

Q ss_pred             CCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438            5 YCADCKRLTEVVFDHSAGDTICSECGL   31 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~   31 (312)
                      .|+.||-    ++|.......|..||.
T Consensus         3 ~C~~CGy----~y~~~~~~~~CP~Cg~   25 (33)
T cd00350           3 VCPVCGY----IYDGEEAPWVCPVCGA   25 (33)
T ss_pred             ECCCCCC----EECCCcCCCcCcCCCC
Confidence            5777774    4555556667777765

The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities

Probab=83.11  E-value=1.6  Score=29.77  Aligned_cols=30  Identities=17%  Similarity=0.216  Sum_probs=25.1

Q ss_pred             CCCC-CHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTK-PLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~-~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      |..+ +..++|+..+||..|+++.++.|.+.
T Consensus        21 g~~lps~~~la~~~~vsr~tvr~al~~L~~~   51 (64)
T PF00392_consen   21 GDRLPSERELAERYGVSRTTVREALRRLEAE   51 (64)
T ss_dssp             TSBE--HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             CCEeCCHHHHHHHhccCCcHHHHHHHHHHHC
Confidence            5667 79999999999999999999998774

The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=83.06  E-value=7.6  Score=28.87  Aligned_cols=31  Identities=16%  Similarity=0.198  Sum_probs=27.3

Q ss_pred             cCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          262 SNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       262 ~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      ....+++.|||+.+|++..|+.+..++|.+.
T Consensus        44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~   74 (95)
T TIGR01610        44 KQDRVTATVIAELTGLSRTHVSDAIKSLARR   74 (95)
T ss_pred             cCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            3467899999999999999999999998874

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria

Probab=82.98  E-value=0.63  Score=29.14  Aligned_cols=30  Identities=30%  Similarity=0.599  Sum_probs=19.2

Q ss_pred             CCCCCCCCCCCceeeeCC-CCceEcCCCccc
Q 021438            3 DSYCADCKRLTEVVFDHS-AGDTICSECGLV   32 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~-~G~~vC~~CG~V   32 (312)
                      ...|+.||..-++..... .....|..||..
T Consensus         5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~   35 (42)
T PF09723_consen    5 EYRCEECGHEFEVLQSISEDDPVPCPECGST   35 (42)
T ss_pred             EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCC
Confidence            457899996333333333 367889999873

The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]

Probab=82.94  E-value=0.49  Score=30.66  Aligned_cols=27  Identities=37%  Similarity=0.714  Sum_probs=21.2

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      ..|-.||.  .+..|.....+-|..||.=
T Consensus         7 Y~C~~Cg~--~~~~~~~~~~irCp~Cg~r   33 (49)
T COG1996           7 YKCARCGR--EVELDQETRGIRCPYCGSR   33 (49)
T ss_pred             EEhhhcCC--eeehhhccCceeCCCCCcE
Confidence            47999998  3545777888999999964

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=82.88  E-value=2.9  Score=28.94  Aligned_cols=32  Identities=6%  Similarity=0.092  Sum_probs=27.2

Q ss_pred             hcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          261 LSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       261 ~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +.+-..+.+++|+.+|+|..||+++.+.|.+.
T Consensus         9 L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~   40 (69)
T TIGR00122         9 LADNPFSGEKLGEALGMSRTAVNKHIQTLREW   40 (69)
T ss_pred             HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            33445779999999999999999999999764

This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.

>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=82.74  E-value=1.8  Score=29.13  Aligned_cols=31  Identities=29%  Similarity=0.299  Sum_probs=24.6

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~  294 (312)
                      -..+.+++|+.+|+|+.||++...+|.+.+.
T Consensus        18 ~~~~~~ela~~l~~S~rti~~~i~~L~~~f~   48 (59)
T PF08280_consen   18 KWITLKELAKKLNISERTIKNDINELNEFFP   48 (59)
T ss_dssp             TSBBHHHHHHHCTS-HHHHHHHHHHHHTT--
T ss_pred             CCCcHHHHHHHHCCCHHHHHHHHHHHHHHhh
Confidence            4578999999999999999999888877543

; PDB: 2WTE_A 3SQN_A.

>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ]

Probab=82.73  E-value=0.39  Score=31.21  Aligned_cols=32  Identities=16%  Similarity=0.397  Sum_probs=23.2

Q ss_pred             CCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      ...+|++|+..-.-..+..+.++-|.-||++-
T Consensus         3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN   34 (51)
T PF10122_consen    3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTIN   34 (51)
T ss_pred             cceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence            45789999973111135667899999999993

>PRK02935 hypothetical protein; Provisional

Probab=82.68  E-value=0.93  Score=34.15  Aligned_cols=38  Identities=24%  Similarity=0.502  Sum_probs=24.1

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccCccccccccccccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFA   48 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~   48 (312)
                      ..||+|++.+.+.=+    ...|-.|+.-+.   +|.+.|-..|+
T Consensus        71 V~CP~C~K~TKmLGr----vD~CM~C~~PLT---Ld~~legkefd  108 (110)
T PRK02935         71 VICPSCEKPTKMLGR----VDACMHCNQPLT---LDRSLEGKEFD  108 (110)
T ss_pred             eECCCCCchhhhccc----eeecCcCCCcCC---cCccccccCcC
Confidence            479999986554322    358999998874   35444433343

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp

Probab=82.26  E-value=2  Score=31.04  Aligned_cols=39  Identities=13%  Similarity=0.250  Sum_probs=29.2

Q ss_pred             HHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          254 VIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       254 aiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .+|+|..-.+.+.+.++||+..++++..+++..+.|.+.
T Consensus        14 l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~   52 (83)
T PF02082_consen   14 LLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA   52 (83)
T ss_dssp             HHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC
Confidence            344444333344899999999999999999999999884

(strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.

>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]

Probab=82.11  E-value=0.52  Score=39.61  Aligned_cols=29  Identities=38%  Similarity=0.690  Sum_probs=20.0

Q ss_pred             CCCCCCCCCCce----eeeCCCC---ceEcCCCcccccC
Q 021438            4 SYCADCKRLTEV----VFDHSAG---DTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~i----i~D~~~G---~~vC~~CG~Vv~e   35 (312)
                      ..||.||+ .++    +.  ..|   .+-|.+||+|-.+
T Consensus         7 ~~Cp~Cg~-eev~hEVik--~~g~~~lvrC~eCG~V~~~   42 (201)
T COG1326           7 IECPSCGS-EEVSHEVIK--ERGREPLVRCEECGTVHPA   42 (201)
T ss_pred             EECCCCCc-chhhHHHHH--hcCCceEEEccCCCcEeec
Confidence            47999995 333    22  123   4789999999854

>PF14122 YokU: YokU-like protein

Probab=82.08  E-value=0.87  Score=32.98  Aligned_cols=39  Identities=31%  Similarity=0.599  Sum_probs=25.6

Q ss_pred             CCCCCCCC------CceeeeCCCCc----------eEcCCCcccccCcccccccc
Q 021438            5 YCADCKRL------TEVVFDHSAGD----------TICSECGLVLEAYSVDETSE   43 (312)
Q Consensus         5 ~Cp~Cg~~------~~ii~D~~~G~----------~vC~~CG~Vv~e~~id~~~e   43 (312)
                      +|--||+.      +++-++-..|.          ++|++||.|-.+..+...-|
T Consensus         1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~d~vi~EIE   55 (87)
T PF14122_consen    1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQDDEVIKEIE   55 (87)
T ss_pred             CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEehhHHHHHHh
Confidence            36667752      34555555555          89999999987766554444

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=82.00  E-value=2.4  Score=34.22  Aligned_cols=30  Identities=13%  Similarity=0.060  Sum_probs=27.4

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +-+.|+.+||+.+|+|+.|+++|.+.|.+.
T Consensus        20 d~r~~~~eia~~lglS~~~v~~Ri~~L~~~   49 (154)
T COG1522          20 DARISNAELAERVGLSPSTVLRRIKRLEEE   49 (154)
T ss_pred             hCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            445899999999999999999999999985

>PRK05949 RNA polymerase sigma factor; Validated

Probab=81.93  E-value=43  Score=30.97  Aligned_cols=30  Identities=10%  Similarity=0.244  Sum_probs=24.9

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHL  293 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~  293 (312)
                      ...|++|||+.+|+|..+|+++...-.+.+
T Consensus       285 e~~Tl~EIa~~lgiS~erVrq~~~rAl~kL  314 (327)
T PRK05949        285 KELSLAKVGERLNLSRERVRQLEHQALAHL  314 (327)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            579999999999999999998876544444

>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]

Probab=81.49  E-value=1.2  Score=35.98  Aligned_cols=29  Identities=31%  Similarity=0.593  Sum_probs=19.3

Q ss_pred             CCCCCCCCCCceeeeC---CCCc-----eEcCCCccc
Q 021438            4 SYCADCKRLTEVVFDH---SAGD-----TICSECGLV   32 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~---~~G~-----~vC~~CG~V   32 (312)
                      |.||.|++..+-+.|+   +.|.     -.|.+||.=
T Consensus         1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~R   37 (156)
T COG1327           1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGER   37 (156)
T ss_pred             CCCCCCCCCCCeeeecccccccchhhhhhcccccccc
Confidence            5899999865556664   3343     358888754

>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain

Probab=81.27  E-value=2.1  Score=28.18  Aligned_cols=26  Identities=27%  Similarity=0.239  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHH
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDL  289 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel  289 (312)
                      +.+|++|.|+.+||+..+++++++++
T Consensus        14 fhlp~~eAA~~Lgv~~T~LKr~CR~~   39 (52)
T PF02042_consen   14 FHLPIKEAAKELGVSVTTLKRRCRRL   39 (52)
T ss_pred             hCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence            56899999999999999999998754

The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=81.23  E-value=2.4  Score=29.28  Aligned_cols=31  Identities=16%  Similarity=0.140  Sum_probs=24.8

Q ss_pred             hcCCCCCHHHHHHHhCcc-hhHHHHHHHHHHh
Q 021438          261 LSNDTKPLKEISIVTRVA-EGTIKNVYKDLFP  291 (312)
Q Consensus       261 ~~~~~~~~~~Ia~~~~vs-~~ti~~~~kel~~  291 (312)
                      -+|++-|.+|||+.+|++ .+|+....+.|.+
T Consensus        21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~   52 (65)
T PF01726_consen   21 ENGYPPTVREIAEALGLKSTSTVQRHLKALER   52 (65)
T ss_dssp             HHSS---HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred             HcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence            368889999999999986 9999999998876

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>PHA02942 putative transposase; Provisional

Probab=81.07  E-value=1  Score=42.63  Aligned_cols=29  Identities=17%  Similarity=0.436  Sum_probs=21.3

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      ..||.||...   .+.......|.+||+..+-
T Consensus       326 q~Cs~CG~~~---~~l~~r~f~C~~CG~~~dr  354 (383)
T PHA02942        326 VSCPKCGHKM---VEIAHRYFHCPSCGYENDR  354 (383)
T ss_pred             ccCCCCCCcc---CcCCCCEEECCCCCCEeCc
Confidence            5799999732   2344567999999999754

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=81.05  E-value=0.88  Score=45.30  Aligned_cols=43  Identities=19%  Similarity=0.516  Sum_probs=29.5

Q ss_pred             CCCCCCCCCCce-----eee----CCCCceEcCCCcccccCcc---ccccccccc
Q 021438            4 SYCADCKRLTEV-----VFD----HSAGDTICSECGLVLEAYS---VDETSEWRI   46 (312)
Q Consensus         4 ~~Cp~Cg~~~~i-----i~D----~~~G~~vC~~CG~Vv~e~~---id~~~ewr~   46 (312)
                      ..||+||....+     .+|    +.+-.++|..||..++|+.   ....-+|+.
T Consensus       201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~~~G~Wv~  255 (557)
T PF05876_consen  201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMVRRGRWVA  255 (557)
T ss_pred             ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhccCCeEEEe
Confidence            579999975333     332    4456799999999999863   223466764

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family

Probab=80.96  E-value=35  Score=29.34  Aligned_cols=31  Identities=23%  Similarity=0.318  Sum_probs=25.9

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~  294 (312)
                      ...|.+|||+.+|+|..||+++++.-.+.+.
T Consensus       190 ~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr  220 (224)
T TIGR02479       190 EELNLKEIGEVLGLTESRVSQIHSQALKKLR  220 (224)
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence            4578999999999999999998876666554

Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.

>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]

Probab=80.95  E-value=40  Score=29.92  Aligned_cols=170  Identities=15%  Similarity=0.184  Sum_probs=88.2

Q ss_pred             hHHHHHHHHHHHHHhc--CCc---HHHHHH-HHHHHHHHHhCCCCCCCCHHHHHHHHHHHH----HHHhC---CCCCHHH
Q 021438          105 NLIQAFKSISAMSDRL--GLV---TTIKDR-ANEIYKKVEDQKPLRGRNQEAIVAACLYIA----CRQEN---KPRTVKE  171 (312)
Q Consensus       105 ~l~~~~~~I~~~~~~L--~Lp---~~v~~~-A~~i~~~~~~~~~~~gr~~~~iaaAcly~a----cr~~~---~p~tl~d  171 (312)
                      -+.+....+..++.++  ++|   ++.+.. ...+.+-+......+|.++.+.|.=||==+    +|.++   .||++++
T Consensus        28 Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~~v~vpR~~~~  107 (247)
T COG1191          28 LIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKNDSVKVPRSLRE  107 (247)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCCCccCcHHHHH
Confidence            3456677778887777  455   233333 344666666667778888887776654333    45444   5677666


Q ss_pred             HHHHhcCCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh-------c--c
Q 021438          172 FCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED-------L--D  242 (312)
Q Consensus       172 ia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~-------l--~  242 (312)
                      ...-        +..+...+...++-           +|  ....++..||++.+-+..+....+...-       .  .
T Consensus       108 ~~~~--------i~~~~~~l~~el~r-----------~p--t~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~  166 (247)
T COG1191         108 LGRR--------IEEAIDELEQELGR-----------EP--TDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDD  166 (247)
T ss_pred             HHHH--------HHHHHHHHHHHhCC-----------CC--cHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhcccc
Confidence            6442        22333334433331           01  1123455555554433333322221110       0  0


Q ss_pred             CCC------ChH-----HHHHHHHHHHHH------------hcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          243 IRR------SPI-----SVAAAVIYIITQ------------LSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       243 ~Gr------~P~-----~iaaAaiyla~~------------~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      .|.      .|.     ..--..++=+..            .+...+|++||++++|||++.|.+..+.....+..
T Consensus       167 d~~~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~eelt~kEI~~~LgISes~VSql~kkai~kLr~  242 (247)
T COG1191         167 DDDVDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYKEELTQKEIAEVLGISESRVSRLHKKAIKKLRK  242 (247)
T ss_pred             ccchhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence            010      010     001111111111            12346999999999999999999888877776544

>PF12773 DZR: Double zinc ribbon

Probab=80.93  E-value=1.2  Score=28.73  Aligned_cols=22  Identities=23%  Similarity=0.832  Sum_probs=16.4

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECG   30 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG   30 (312)
                      ...||.||..      ...+..+|..||
T Consensus        29 ~~~C~~Cg~~------~~~~~~fC~~CG   50 (50)
T PF12773_consen   29 KKICPNCGAE------NPPNAKFCPNCG   50 (50)
T ss_pred             CCCCcCCcCC------CcCCcCccCccc
Confidence            4579999973      235788899888

>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional

Probab=80.93  E-value=6.6  Score=35.45  Aligned_cols=63  Identities=14%  Similarity=0.051  Sum_probs=48.8

Q ss_pred             ccCCCCHHHHHHHHHhhcC-CCHHHHHHHHHHHHHhhhccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHH
Q 021438          204 EMGTIHASDYLRRFCSNLG-MTNQAVKAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTI  282 (312)
Q Consensus       204 ~~~~~~p~~~i~r~~~~L~-l~~~v~~~A~~i~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti  282 (312)
                      +.....|..++.++-+.+. |++.-.+.|..|++.         |.-++             ..+..+||+.++||+.||
T Consensus         6 ~~~~~~~~~i~~~i~~~~~~Lt~~e~~Ia~yil~~---------~~~v~-------------~~si~~lA~~~~vS~aTi   63 (292)
T PRK11337          6 DSALPNGIGLGPYIRMKQEGLTPLESRVVEWLLKP---------GDLSE-------------ATALKDIAEALAVSEAMI   63 (292)
T ss_pred             cccccCchhHHHHHHHHHhhcCHHHHHHHHHHHhC---------HHHHH-------------hcCHHHHHHHhCCChHHH
Confidence            4445678899999998886 999888888888854         44433             356789999999999999


Q ss_pred             HHHHHH
Q 021438          283 KNVYKD  288 (312)
Q Consensus       283 ~~~~ke  288 (312)
                      -+-+|.
T Consensus        64 ~Rf~kk   69 (292)
T PRK11337         64 VKVAKK   69 (292)
T ss_pred             HHHHHH
Confidence            876543

>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor

Probab=80.56  E-value=12  Score=36.06  Aligned_cols=163  Identities=13%  Similarity=0.213  Sum_probs=0.0

Q ss_pred             HHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCC------------------CHHHHHH
Q 021438          113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPR------------------TVKEFCS  174 (312)
Q Consensus       113 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~------------------tl~dia~  174 (312)
                      +..++..++++...++.|..+.+.+.-.|+...-     ..=|+.+=.+..+..-                  .+..|+.
T Consensus       116 ~~eia~~l~~~~~~ve~~l~~iq~leP~GIgAr~-----L~EcLllQl~~~~~~~~~~a~~il~~~le~l~~~~~~~i~~  190 (429)
T TIGR02395       116 LEEIADELEVSEEEVEKVLELIQRLDPAGVGARD-----LQECLLLQLERLDIDDPELAYNILLEHLELLAEKDFRRLAK  190 (429)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHhcCCCCccCcCC-----HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHhccHHHHHH


Q ss_pred             HhcCCCHHHHHHHHHHHHHHHhhhhcccc----ccCCCCHHHHHHHHHh------------hcCCCHHHH----------
Q 021438          175 VANGTTKKEIGRAKEFIVKHLEAEMGQSV----EMGTIHASDYLRRFCS------------NLGMTNQAV----------  228 (312)
Q Consensus       175 ~~~~v~~~~i~~~~~~l~~~l~~~~~~~~----~~~~~~p~~~i~r~~~------------~L~l~~~v~----------  228 (312)
                      .. +++..++..++..|+ .|+-..+..+    ....+.|..+|.+.-.            +|.+++...          
T Consensus       191 ~l-~is~~~v~~~~~~I~-~L~P~Pg~~~~~~~~~~yi~PDv~V~~~~~~~~v~ln~~~~P~l~i~~~y~~~~~~~~~~~  268 (429)
T TIGR02395       191 KL-GLSEEELKEALDLIK-SLSPKPGKEFADPEEVEYVIPDVIVTKKNGEWVVELNGRSLPELRINEEYFKLLKDAEKEA  268 (429)
T ss_pred             HH-CcCHHHHHHHHHHHh-CCCCCCcccccCCCCCCccCCCEEEEEECCEEEEEEcCCCCceEEECHHHHHHHHhccchH


Q ss_pred             ---------HHHHHHHHHhhhccCCCChHHHHHHHHHHHHHhcCC---------CCCHHHHHHHhCcchhHHHHHHH
Q 021438          229 ---------KAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLSND---------TKPLKEISIVTRVAEGTIKNVYK  287 (312)
Q Consensus       229 ---------~~A~~i~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~---------~~~~~~Ia~~~~vs~~ti~~~~k  287 (312)
                               +.|..+++...     ++-.++--.+-.++-+-.++         ++++++||+.+|++++||++..+
T Consensus       269 ~~~ylk~k~~~A~~li~~i~-----~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~  340 (429)
T TIGR02395       269 AAQYLKQKLKEARWLIKALE-----QREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAIN  340 (429)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhc

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=80.37  E-value=3.4  Score=31.22  Aligned_cols=29  Identities=21%  Similarity=0.194  Sum_probs=26.8

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      -..|..+||+.+|+++.|++++++.|.+.
T Consensus        16 ~~~~~~~la~~l~~s~~tv~~~l~~L~~~   44 (108)
T smart00344       16 ARISLAELAKKVGLSPSTVHNRVKRLEEE   44 (108)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            46889999999999999999999999885

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function []

Probab=80.13  E-value=0.95  Score=30.09  Aligned_cols=30  Identities=17%  Similarity=0.408  Sum_probs=22.0

Q ss_pred             CCCCCCCCCCCcee--eeCCCCceEcCCCccc
Q 021438            3 DSYCADCKRLTEVV--FDHSAGDTICSECGLV   32 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii--~D~~~G~~vC~~CG~V   32 (312)
                      ...|++|.+.+-+.  ++.+.-.++|..||..
T Consensus        22 aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~   53 (54)
T PF10058_consen   22 ALICSKCFSHNGLAPKEEFEEIQYRCPYCGAL   53 (54)
T ss_pred             eEECcccchhhcccccccCCceEEEcCCCCCc
Confidence            35799999754343  6677778999999963

>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed

Probab=80.09  E-value=0.91  Score=30.36  Aligned_cols=25  Identities=24%  Similarity=0.538  Sum_probs=19.2

Q ss_pred             CCCCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~   34 (312)
                      -+..|+.||. -.+       ..+|..||....
T Consensus         4 ~mr~C~~Cgv-YTL-------k~~CP~CG~~t~   28 (56)
T PRK13130          4 KIRKCPKCGV-YTL-------KEICPVCGGKTK   28 (56)
T ss_pred             cceECCCCCC-EEc-------cccCcCCCCCCC
Confidence            4678999997 333       678999998754

>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []

Probab=80.02  E-value=6.8  Score=24.81  Aligned_cols=29  Identities=7%  Similarity=0.108  Sum_probs=21.3

Q ss_pred             cCCCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438          262 SNDTKPLKEISIVTRVAEGTIKNVYKDLFP  291 (312)
Q Consensus       262 ~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~  291 (312)
                      +|. +++++.|+..||...|+..+++...+
T Consensus        14 ~g~-~S~r~AA~~ygVp~sTL~~r~~g~~~   42 (45)
T PF05225_consen   14 NGK-MSIRKAAKKYGVPRSTLRRRLRGKPS   42 (45)
T ss_dssp             TTS-S-HHHHHHHHT--HHHHHHHHHHTTT
T ss_pred             hCC-CCHHHHHHHHCcCHHHHHHHHcCCCC
Confidence            444 99999999999999999988876443

In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	312
1c9b_A	207	Crystal Structure Of A Human Tbp Core Domain-Human		5e-38
2phg_A	206	Model For Vp16 Binding To Tfiib Length = 206		2e-37
1tfb_A	208	Nmr Studies Of Human General Transcription Factor T		3e-37
1vol_A	204	Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEME		3e-35
3k7a_M	345	Crystal Structure Of An Rna Polymerase Ii-Tfiib Com		2e-26
1d3u_B	201	Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+T		1e-19
1ais_B	200	Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-		1e-19
1rly_A	60	Rdc-Derived Models Of The Zinc Ribbon Domain Of Hum		9e-05
1dl6_A	58	Solution Structure Of Human Tfiib N-Terminal Domain		1e-04
3k1f_M	197	Crystal Structure Of Rna Polymerase Ii In Complex W		2e-04

>pdb|1C9B|A Chain A, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib Core Domain Complex Bound To An Extended, Modified Adenoviral Major Late Promoter (Admlp) Length = 207

Iteration: 1
 Score =  154 bits (390), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 87/210 (41%), Positives = 125/210 (59%), Gaps = 9/210 (4%)
Query: 103 DRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQ 162
           DR ++ AFK I+ M+DR+ L   I DR N ++K+V +QK L+GR  +AI +ACLYIACRQ
Sbjct: 2   DRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQ 61
Query: 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG 222
           E  PRT KE C+V+   +KKEIGR  + I+K LE     SV++  I   D++ RFCSNL 
Sbjct: 62  EGVPRTFKEICAVSR-ISKKEIGRCFKLILKALET----SVDL--ITTGDFMSRFCSNLC 114
Query: 223 MTNXXXXXXXXXXXXSEDLDI--RRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEG 280
           +              + +LD+   RSPISVAAA IY+ +Q S + +  KEI  +  VA+ 
Sbjct: 115 LPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV 174
Query: 281 TIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
           TI+  Y+ ++P    + P  F  +  +  L
Sbjct: 175 TIRQSYRLIYPRAPDLFPTDFKFDTPVDKL 204

>pdb|2PHG|A Chain A, Model For Vp16 Binding To Tfiib Length = 206

Iteration: 1
 Score =  152 bits (384), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 86/209 (41%), Positives = 124/209 (59%), Gaps = 9/209 (4%)
Query: 104 RNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE 163
           R ++ AFK I+ M+DR+ L   I DR N ++K+V +QK L+GR  +AI +ACLYIACRQE
Sbjct: 2   RAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQE 61
Query: 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGM 223
             PRT KE C+V+   +KKEIGR  + I+K LE     SV++  I   D++ RFCSNL +
Sbjct: 62  GVPRTFKEICAVSR-ISKKEIGRCFKLILKALET----SVDL--ITTGDFMSRFCSNLCL 114
Query: 224 TNXXXXXXXXXXXXSEDLDI--RRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGT 281
                         + +LD+   RSPISVAAA IY+ +Q S + +  KEI  +  VA+ T
Sbjct: 115 PKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVT 174
Query: 282 IKNVYKDLFPHLARIIPDWFANEEDIKNL 310
           I+  Y+ ++P    + P  F  +  +  L
Sbjct: 175 IRQSYRLIYPRAPDLFPTDFKFDTPVDKL 203

>pdb|1TFB|A Chain A, Nmr Studies Of Human General Transcription Factor Tfiib: Dynamics And Interaction With Vp16 Activation Domain, 20 Structures Length = 208

Iteration: 1
 Score =  152 bits (384), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 86/209 (41%), Positives = 124/209 (59%), Gaps = 9/209 (4%)
Query: 104 RNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE 163
           R ++ AFK I+ M+DR+ L   I DR N ++K+V +QK L+GR  +AI +ACLYIACRQE
Sbjct: 4   RAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQE 63
Query: 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGM 223
             PRT KE C+V+   +KKEIGR  + I+K LE     SV++  I   D++ RFCSNL +
Sbjct: 64  GVPRTFKEICAVSR-ISKKEIGRCFKLILKALET----SVDL--ITTGDFMSRFCSNLCL 116
Query: 224 TNXXXXXXXXXXXXSEDLDI--RRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGT 281
                         + +LD+   RSPISVAAA IY+ +Q S + +  KEI  +  VA+ T
Sbjct: 117 PKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVT 176
Query: 282 IKNVYKDLFPHLARIIPDWFANEEDIKNL 310
           I+  Y+ ++P    + P  F  +  +  L
Sbjct: 177 IRQSYRLIYPRAPDLFPTDFKFDTPVDKL 205

>pdb|1VOL|A Chain A, Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEMENT Ternary Complex Length = 204

Iteration: 1
 Score =  145 bits (365), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 82/207 (39%), Positives = 121/207 (58%), Gaps = 9/207 (4%)
Query: 106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK 165
           ++ AFK I+ M+DR+ L     DR N ++++  +QK L+GR  +AI +ACLYIACRQE  
Sbjct: 2   MMNAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGV 61
Query: 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN 225
           PRT KE C+V+   +KKEIGR  + I+K LE     SV++  I   D++ RFCSNL +  
Sbjct: 62  PRTFKEICAVSR-ISKKEIGRCFKLILKALET----SVDL--ITTGDFMSRFCSNLCLPK 114
Query: 226 XXXXXXXXXXXXSEDLDI--RRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIK 283
                       + +LD+   RSPISVAAA IY+ +Q S + +  KEI  +  VA+ TI+
Sbjct: 115 QVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIR 174
Query: 284 NVYKDLFPHLARIIPDWFANEEDIKNL 310
             Y+ ++P    + P  F  +  +  L
Sbjct: 175 QSYRLIYPRAPDLFPTDFKFDTPVDKL 201

>pdb|3K7A|M Chain M, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex Length = 345

Iteration: 1
 Score =  115 bits (289), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 93/311 (29%), Positives = 138/311 (44%), Gaps = 16/311 (5%)
Query: 6   CADCKRLT-EVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDH---DPVRVXX 61
           C +CK    ++V   S GD +C+ CGLVL    VD  SEWR F+N+  DH   DP RV  
Sbjct: 24  CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSND--DHNGDDPSRVGE 81
Query: 62  XXXXXXXXXXXXTVIAKPTAXXXXXXXXXXXXXXQARSSHPDRNLIQAFKSISAMSDRLG 121
                       T I K                 +      D  +  AF  I+ + D   
Sbjct: 82  ASNPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAE 141
Query: 122 LVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTK 181
           L   +KD A E YK   D+K L+G++ E+I+AA + I CR+    RT KE  S+ +  T 
Sbjct: 142 LPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLIHVKT- 200
Query: 182 KEIGRAKEFIVKHL--EAEMG----QSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXX 235
           KE G+    +   L  ++E G     +  M       Y+ RFCS+LG+            
Sbjct: 201 KEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSAEYTA 260
Query: 236 XXSEDLD--IRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHL 293
              +++     +SPI++A   IY+   L        ++    +V EGTIK+ YK L+ H 
Sbjct: 261 KKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTIKSGYKILYEHR 320
Query: 294 ARII-PDWFAN 303
            +++ P   AN
Sbjct: 321 DKLVDPQLIAN 331

>pdb|1D3U|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+TATA- Box Complex From Pyrococcus Woesei Length = 201

Iteration: 1
 Score = 93.6 bits (231), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 59/202 (29%), Positives = 104/202 (51%), Gaps = 7/202 (3%)
Query: 99  SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI 158
           S   +RNL  A   +  ++ +L L   +++ A  +Y++   +  +RGR+ E+++AAC+Y 
Sbjct: 3   SDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYA 62
Query: 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFC 218
           ACR    PRT+ E   +A    KKEIGR+  FI ++L      + +   +  +DY+ +F 
Sbjct: 63  ACRLLKVPRTLDEIADIAR-VDKKEIGRSYRFIARNL----NLTPKKLFVKPTDYVNKFA 117
Query: 219 SNLGMTNXXXXXXXXXXXXS--EDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTR 276
             LG++             +    L   +SP  + AA +YI + L  + +  +E++ V R
Sbjct: 118 DELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVAR 177
Query: 277 VAEGTIKNVYKDLFPHLARIIP 298
           V E T++N YK+L   L   +P
Sbjct: 178 VTEVTVRNRYKELVEKLKIKVP 199

>pdb|1AIS|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-Box Complex From Pyrococcus Woesei Length = 200

Iteration: 1
 Score = 93.6 bits (231), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 59/202 (29%), Positives = 104/202 (51%), Gaps = 7/202 (3%)
Query: 99  SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI 158
           S   +RNL  A   +  ++ +L L   +++ A  +Y++   +  +RGR+ E+++AAC+Y 
Sbjct: 2   SDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYA 61
Query: 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFC 218
           ACR    PRT+ E   +A    KKEIGR+  FI ++L      + +   +  +DY+ +F 
Sbjct: 62  ACRLLKVPRTLDEIADIAR-VDKKEIGRSYRFIARNL----NLTPKKLFVKPTDYVNKFA 116
Query: 219 SNLGMTNXXXXXXXXXXXXS--EDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTR 276
             LG++             +    L   +SP  + AA +YI + L  + +  +E++ V R
Sbjct: 117 DELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVAR 176
Query: 277 VAEGTIKNVYKDLFPHLARIIP 298
           V E T++N YK+L   L   +P
Sbjct: 177 VTEVTVRNRYKELVEKLKIKVP 198

>pdb|1RLY|A Chain A, Rdc-Derived Models Of The Zinc Ribbon Domain Of Human General Transcription Tfiib (Zinc Bound Structures) Length = 60

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 19/38 (50%), Positives = 26/38 (68%)
Query: 15 VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESS 52
          +V D+ AGD IC ECGLV+    +D  SEWR F+N+ +
Sbjct: 23 LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKA 60

>pdb|1DL6|A Chain A, Solution Structure Of Human Tfiib N-Terminal Domain Length = 58

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/36 (52%), Positives = 25/36 (69%)
Query: 15 VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE 50
          +V D+ AGD IC ECGLV+    +D  SEWR F+N+
Sbjct: 22 LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND 57

>pdb|3K1F|M Chain M, Crystal Structure Of Rna Polymerase Ii In Complex With Tfiib Length = 197

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/45 (46%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 6  CADCKRLT-EVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFAN 49
          C +CK    ++V   S GD +C+ CGLVL    VD  SEWR F+N
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSN 68

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	312
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	5e-73
1c9b_A	207	General transcription factor IIB; protein-DNA comp	1e-58
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	4e-55
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	7e-11
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	8e-06
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	8e-24
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	9e-13
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	6e-12
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	6e-07
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	9e-07
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	2e-06
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	2e-05
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	4e-05
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	8e-05
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	8e-04

>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae} Length = 345

 Score =  227 bits (580), Expect = 5e-73
 Identities = 98/317 (30%), Positives = 148/317 (46%), Gaps = 13/317 (4%)

Query: 6   CADCKRL-TEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE-SSDHDPVRVGGPL 63
           C +CK    ++V   S GD +C+ CGLVL    VD  SEWR F+N+  +  DP RVG   
Sbjct: 24  CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEAS 83

Query: 64  NPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLV 123
           NPLL G  LST I K            +  + +      D  +  AF  I+ + D   L 
Sbjct: 84  NPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAELP 143

Query: 124 TTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKE 183
             +KD A E YK   D+K L+G++ E+I+AA + I CR+    RT KE  S+ +    KE
Sbjct: 144 KIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLIH-VKTKE 202

Query: 184 IGRAKEFIVKHLE------AEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQK 237
            G+    +   L            +  M       Y+ RFCS+LG+  Q   +A+   +K
Sbjct: 203 FGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSAEYTAKK 262

Query: 238 SEDLDI--RRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR 295
            +++     +SPI++A   IY+   L        ++    +V EGTIK+ YK L+ H  +
Sbjct: 263 CKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTIKSGYKILYEHRDK 322

Query: 296 IIPDWFANEE--DIKNL 310
           ++           + NL
Sbjct: 323 LVDPQLIANGVVSLDNL 339

>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A* Length = 207

 Score =  186 bits (473), Expect = 1e-58
 Identities = 87/210 (41%), Positives = 125/210 (59%), Gaps = 9/210 (4%)

Query: 103 DRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQ 162
           DR ++ AFK I+ M+DR+ L   I DR N ++K+V +QK L+GR  +AI +ACLYIACRQ
Sbjct: 2   DRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQ 61

Query: 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG 222
           E  PRT KE C+V+   +KKEIGR  + I+K           +  I   D++ RFCSNL 
Sbjct: 62  EGVPRTFKEICAVSR-ISKKEIGRCFKLILKA------LETSVDLITTGDFMSRFCSNLC 114

Query: 223 MTNQAVKAAQEAVQKSEDLDI--RRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEG 280
           +  Q   AA    +K+ +LD+   RSPISVAAA IY+ +Q S + +  KEI  +  VA+ 
Sbjct: 115 LPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV 174

Query: 281 TIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
           TI+  Y+ ++P    + P  F  +  +  L
Sbjct: 175 TIRQSYRLIYPRAPDLFPTDFKFDTPVDKL 204

>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B* Length = 200

 Score =  177 bits (449), Expect = 4e-55
 Identities = 57/202 (28%), Positives = 108/202 (53%), Gaps = 7/202 (3%)

Query: 99  SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI 158
           S   +RNL  A   +  ++ +L L   +++ A  +Y++   +  +RGR+ E+++AAC+Y 
Sbjct: 2   SDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYA 61

Query: 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFC 218
           ACR    PRT+ E   +A    KKEIGR+     + +   +  + +   +  +DY+ +F 
Sbjct: 62  ACRLLKVPRTLDEIADIAR-VDKKEIGRS----YRFIARNLNLTPKKLFVKPTDYVNKFA 116

Query: 219 SNLGMTNQAVKAAQEAVQKSEDLDI--RRSPISVAAAVIYIITQLSNDTKPLKEISIVTR 276
             LG++ +  + A E + ++    +   +SP  + AA +YI + L  + +  +E++ V R
Sbjct: 117 DELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVAR 176

Query: 277 VAEGTIKNVYKDLFPHLARIIP 298
           V E T++N YK+L   L   +P
Sbjct: 177 VTEVTVRNRYKELVEKLKIKVP 198

>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B* Length = 200

 Score = 59.6 bits (144), Expect = 7e-11
 Identities = 29/124 (23%), Positives = 55/124 (44%), Gaps = 1/124 (0%)

Query: 76  IAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYK 135
           IA        E+        +  +  P +  ++    ++  +D LGL   ++ RA EI  
Sbjct: 75  IADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLSEKVRRRAIEILD 134

Query: 136 KVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195
           +   +    G++   +VAA LYIA   E + RT +E   VA   T+  +    + +V+ L
Sbjct: 135 EAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVA-RVTEVTVRNRYKELVEKL 193

Query: 196 EAEM 199
           + ++
Sbjct: 194 KIKV 197

>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B* Length = 200

 Score = 45.0 bits (106), Expect = 8e-06
 Identities = 24/108 (22%), Positives = 41/108 (37%), Gaps = 2/108 (1%)

Query: 202 SVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIR--RSPISVAAAVIYIIT 259
           + E     A   L R  + L +     + A    +++    +   RS  SV AA +Y   
Sbjct: 4   AAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAAC 63

Query: 260 QLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDI 307
           +L    + L EI+ + RV +  I   Y+ +  +L       F    D 
Sbjct: 64  RLLKVPRTLDEIADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDY 111

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197

 Score = 95.5 bits (237), Expect = 8e-24
 Identities = 21/45 (46%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 6  CADCK-RLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFAN 49
          C +CK    ++V   S GD +C+ CGLVL    VD  SEWR F+N
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSN 68

>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A Length = 58

 Score = 61.1 bits (148), Expect = 9e-13
 Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 6  CADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE 50
          C +      +V D+ AGD IC ECGLV+    +D  SEWR F+N+
Sbjct: 14 CPNHPD-AILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND 57

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1 Length = 50

 Score = 58.6 bits (142), Expect = 6e-12
 Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 6  CADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIF 47
          C  C+   E+++D   G+ +C++CG V+E   +D   EWR F
Sbjct: 8  CPACES-AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAF 48

>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} Length = 235

 Score = 48.5 bits (115), Expect = 6e-07
 Identities = 36/166 (21%), Positives = 72/166 (43%), Gaps = 6/166 (3%)

Query: 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQK-PLRGRNQEAIVAACLYIACRQENK 165
           I  +K +    DRL L   +   A  + ++   +K   +G + EA+VA C+Y++C+ E  
Sbjct: 29  IYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKGFSLEALVATCIYLSCKVEEC 88

Query: 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSV--EMGTIHASDYLRRFCSNLGM 223
           P  ++  C+ AN     ++  ++  I + +E E+   +   +   H    L +   +  +
Sbjct: 89  PVHIRTICNEANDLWSLKVKLSRSNISE-IEFEIISVLDAFLIVHHPYTSLEQAFHDGII 147

Query: 224 TNQAVKAAQEAVQKS--EDLDIRRSPISVAAAVIYIITQLSNDTKP 267
             + ++ A   V  S    L +   P  +A A + I      +T P
Sbjct: 148 NQKQLEFAWSIVNDSYASSLCLMAHPHQLAYAALLISCCNDENTIP 193

>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 Length = 258

 Score = 48.4 bits (115), Expect = 9e-07
 Identities = 32/177 (18%), Positives = 63/177 (35%), Gaps = 14/177 (7%)

Query: 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP 166
            +  + I  +  RLGL           + +       +   +    A CL++A + E  P
Sbjct: 42  REGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETP 101

Query: 167 RTVKEFCSVANGTT-----KKEIGRAKEFIVKHLEAEMGQSV--EMGTIHASDYLRRFCS 219
           +  K+    A          +     KE ++  LE  + Q++  ++   H   +L ++  
Sbjct: 102 KKCKDIIKTARSLLNDVQFGQFGDDPKEEVMV-LERILLQTIKFDLQVEHPYQFLLKYAK 160

Query: 220 NLG----MTNQAVKAAQEAVQKS--EDLDIRRSPISVAAAVIYIITQLSNDTKPLKE 270
            L        + V+ A   V  S    L ++  P  +A AV+Y+  +L         
Sbjct: 161 QLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWT 217

>2ivx_A Cyclin-T2; transcription regulation, cell division, phosphorylation, NU protein, cell cycle, transcription; 1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A 3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B* 3lq5_B* 3my1_B* 3tn8_B* Length = 257

 Score = 47.4 bits (112), Expect = 2e-06
 Identities = 28/178 (15%), Positives = 57/178 (32%), Gaps = 14/178 (7%)

Query: 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP 166
            QA   I  M  RL +     + A     +          N+  I +  L++A + E + 
Sbjct: 32  QQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQA 91

Query: 167 RTVKEFCSVANGTTKKEIGRAKEFI---------VKHLEAEMGQSV--EMGTIHASDYLR 215
           R ++    VA+                       +  LE  M Q++  E+   H    + 
Sbjct: 92  RKLEHVIKVAHACLHPLEPLLDTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDVV 151

Query: 216 RFCSNLGMTNQAVKAAQEAVQKS---EDLDIRRSPISVAAAVIYIITQLSNDTKPLKE 270
           +    +  +    + +      S       ++  P  +A   I++  + SN   P+  
Sbjct: 152 KCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVST 209

>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Length = 269

 Score = 44.3 bits (105), Expect = 2e-05
 Identities = 25/149 (16%), Positives = 58/149 (38%), Gaps = 12/149 (8%)

Query: 153 AACLYIACR-QENKPRTVKEFCSVANGT-TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHA 210
              ++IA + +E  P  + +F  V + T TK +I + +  I++ L         +G    
Sbjct: 85  VTAMFIASKYEEMYPPEIGDFAFVTDNTYTKHQIRQMEMKILRALN------FGLGRPLP 138

Query: 211 SDYLRRFCSNLGMTNQAVKAAQ---EAVQKSEDLDIRRSPISVAAAVIYIITQLSNDTKP 267
             +LRR      +  +    A+   E      D+ +   P  +AA    +  ++ ++ + 
Sbjct: 139 LHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDM-VHFPPSQIAAGAFSLALKILDNGEW 197

Query: 268 LKEISIVTRVAEGTIKNVYKDLFPHLARI 296
              +       E ++  V + L  ++  +
Sbjct: 198 TPTLQHYLSYTEESLLPVMQHLAKNVVMV 226

>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C Length = 358

 Score = 43.7 bits (102), Expect = 4e-05
 Identities = 24/178 (13%), Positives = 57/178 (32%), Gaps = 14/178 (7%)

Query: 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP 166
            QA   +  M  RL +     + A     +    +        ++  A L++A + E +P
Sbjct: 39  QQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEEQP 98

Query: 167 RTVKEFCSVANGTTKKEIGRAKEFIVKH-------LEAEMGQSVEMG----TIHASDYLR 215
           + ++    VA+     +          +       +  E      +G      H   ++ 
Sbjct: 99  KKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVV 158

Query: 216 RFCSNLGMTNQAVKAAQEAVQKSE---DLDIRRSPISVAAAVIYIITQLSNDTKPLKE 270
           +    +  +    + +      S       ++ +P  VA   I++  + SN   P+  
Sbjct: 159 KCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVST 216

>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division), ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B* 1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B* 2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B* 2x1n_B* 1vyw_B* ... Length = 260

 Score = 42.3 bits (100), Expect = 8e-05
 Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 8/69 (11%)

Query: 153 AACLYIACR-QENKPRTVKEFCSVANGT-TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHA 210
            A + +A + +E  P  V EF  + + T TKK++ R +  ++K L        ++     
Sbjct: 86  TAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLKVLT------FDLAAPTV 139

Query: 211 SDYLRRFCS 219
           + +L ++  
Sbjct: 140 NQFLTQYFL 148

>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens} Length = 306

 Score = 39.4 bits (92), Expect = 8e-04
 Identities = 12/76 (15%), Positives = 32/76 (42%), Gaps = 8/76 (10%)

Query: 153 AACLYIACRQ-ENKPRTVKEFCSVANGT-TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHA 210
           A C+ +A +  E  P T+++ C   +   + +++   +  ++  L+       ++  + A
Sbjct: 118 AVCMLLASKLRETTPLTIEKLCIYTDHAVSPRQLRDWEVLVLGKLK------WDLAAVIA 171

Query: 211 SDYLRRFCSNLGMTNQ 226
            D+L      L +   
Sbjct: 172 HDFLAFILHRLSLPRD 187

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	312
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	100.0
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	100.0
1c9b_A	207	General transcription factor IIB; protein-DNA comp	100.0
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	100.0
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	99.94
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	99.92
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	99.92
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	99.91
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	99.9
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	99.89
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	99.88
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	99.88
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	99.85
1g3n_C	257	V-cyclin; cyclin-dependent kinase, INK4 inhibitor,	99.85
2f2c_A	254	Cyclin homolog, V-cyclin; small molecule inhibitor	99.84
1w98_B	283	Cyclin E, G1/S-specific cyclin E1; cell cycle, tra	99.81
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	99.79
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	99.79
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	99.73
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	99.58
1f5q_B	252	Gamma herpesvirus cyclin; herpesviral cyclin, cycl	99.52
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	99.51
1c9b_A	207	General transcription factor IIB; protein-DNA comp	99.32
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	99.0
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	98.89
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	98.1
3h4c_A	260	Transcription factor TFIIB-like; cyclin, transcrip	97.81
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	97.56
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	97.53
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	97.52
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	97.48
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	97.46
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	97.44
3m03_A	95	ORC6, origin recognition complex subunit 6; helix	97.28
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	97.14
2f2c_A	254	Cyclin homolog, V-cyclin; small molecule inhibitor	97.0
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	96.98
1g3n_C	257	V-cyclin; cyclin-dependent kinase, INK4 inhibitor,	96.89
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	96.87
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	96.8
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	96.77
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	96.65
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	96.64
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	96.6
1w98_B	283	Cyclin E, G1/S-specific cyclin E1; cell cycle, tra	96.55
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	96.54
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	96.48
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	96.21
2r7g_A	347	PP110, retinoblastoma-associated protein, P105-RB,	96.13
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	96.12
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	96.12
4ell_A	411	Retinoblastoma-associated protein; cyclin fold, tu	96.12
2akl_A	138	PHNA-like protein PA0128; two domains, Zn binding	95.94
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	95.87
2qdj_A	304	Retinoblastoma-associated protein; cyclin fold, cy	95.82
3m03_A	95	ORC6, origin recognition complex subunit 6; helix	95.74
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	95.64
4elj_A	656	Retinoblastoma-associated protein; cyclin fold, tu	95.53
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	95.11
2kpi_A	56	Uncharacterized protein SCO3027; zinc finger, PSI-	94.39
2r7g_A	347	PP110, retinoblastoma-associated protein, P105-RB,	93.42
4elj_A	656	Retinoblastoma-associated protein; cyclin fold, tu	93.22
2k5r_A	97	Uncharacterized protein XF2673; solution structure	93.03
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	93.0
2pmi_B	293	PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de	92.9
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	92.34
1k81_A	36	EIF-2-beta, probable translation initiation factor	92.26
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	92.26
6rxn_A	46	Rubredoxin; electron transfer(iron-sulfur protein)	91.59
1nui_A	255	DNA primase/helicase; zinc-biding domain, toprim f	91.53
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	91.16
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	90.92
3j21_i	83	50S ribosomal protein L37AE; archaea, archaeal, KI	90.68
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	90.58
4rxn_A	54	Rubredoxin; electron transfer(iron-sulfur protein)	90.45
3jyw_9	72	60S ribosomal protein L43; eukaryotic ribosome, RA	90.42
3h4c_A	260	Transcription factor TFIIB-like; cyclin, transcrip	90.3
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	90.06
1e8j_A	52	Rubredoxin; iron-sulfur-protein, zinc-substitution	90.05
1t6s_A	162	Conserved hypothetical protein; A winged helix-tur	90.0
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	89.91
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	89.86
3iz5_m	92	60S ribosomal protein L43 (L37AE); eukaryotic ribo	89.85
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	89.84
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	89.79
1ffk_W	73	Ribosomal protein L37AE; ribosome assembly, RNA-RN	89.79
3cc2_Z	116	50S ribosomal protein L37AE, 50S ribosomal protein	89.78
3izc_m	92	60S ribosomal protein RPL43 (L37AE); eukaryotic ri	89.47
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	89.16
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	89.03
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	88.91
4a17_Y	103	RPL37A, 60S ribosomal protein L32; eukaryotic ribo	88.63
1f5q_B	252	Gamma herpesvirus cyclin; herpesviral cyclin, cycl	88.58
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	88.44
2qdj_A	304	Retinoblastoma-associated protein; cyclin fold, cy	88.22
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	87.97
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	87.68
3u50_C	172	Telomerase-associated protein 82; TEB1, processivi	87.61
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	87.4
4ell_A	411	Retinoblastoma-associated protein; cyclin fold, tu	87.19
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	87.19
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	87.18
2pmi_B	293	PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de	87.14
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	87.05
3c57_A	95	Two component transcriptional regulatory protein;	86.74
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	86.01
1gnf_A	46	Transcription factor GATA-1; zinc finger, transcri	85.59
1dxg_A	36	Desulforedoxin; non-heme iron protein, rubredoxin	85.26
3ga8_A	78	HTH-type transcriptional regulator MQSA (YGIT/B30;	84.94
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	84.83
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	84.57
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	84.54
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	84.48
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	84.25
2v3b_B	55	Rubredoxin 2, rubredoxin; alkane degradation, iron	84.1
1tfi_A	50	Transcriptional elongation factor SII; transcripti	83.95
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	83.51
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	83.05
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	82.9
1j1v_A	94	Chromosomal replication initiator protein DNAA, 5'	82.81
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	82.32
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	82.16
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	81.71
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	81.63
1dx8_A	70	Rubredoxin; electron transport, zinc-substitution;	81.56
2vut_I	43	AREA, nitrogen regulatory protein AREA; transcript	81.49
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	81.07
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	80.98
2apo_B	60	Ribosome biogenesis protein NOP10; protein-protein	80.59
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	80.52
2kn9_A	81	Rubredoxin; metalloprotein, ssgcid, structural gen	80.5
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	80.1
2e9h_A	157	EIF-5, eukaryotic translation initiation factor 5;	80.09

>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M

Probab=100.00  E-value=9.9e-77  Score=546.87  Aligned_cols=307  Identities=34%  Similarity=0.533  Sum_probs=174.4

Q ss_pred             CCCCCCCCC-CCceeeeCCCCceEcCCCcccccCcccccccccccccCCC-CCCCCCccCCCCCCcccCCCcceEEecCC
Q 021438            3 DSYCADCKR-LTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANES-SDHDPVRVGGPLNPLLSGGGLSTVIAKPT   80 (312)
Q Consensus         3 ~~~Cp~Cg~-~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~~~-~~~~~~r~G~~~~~~~~~~~~~t~i~~~~   80 (312)
                      ...||+||+ .+++++|+.+|++||++||+|++|++||+|||||+|++|+ ++.|++|+|+|.|+++||+|++|.|+++.
T Consensus        21 ~~~Cp~C~~~~~~lv~D~~~G~~vC~~CGlVl~e~~iD~g~EWR~f~~d~~~~~d~sRvG~~~~~~~~~~glsT~I~~~~  100 (345)
T 4bbr_M           21 VLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEASNPLLDGNNLSTRIGKGE  100 (345)
T ss_dssp             -CCCSSCCCSSCCEEEEGGGTEEEETTTCBEEESCCBCHHHHHTTTSCSCSSSCCSSCCEEEECHHHHCSCCCCEEECCS
T ss_pred             CCcCCCCCCCCCceeEECCCCcEEeCCCCCCccCcccccCccccCCCcccccCCCcCCCCCCCCccccCCCcceeecCCC
Confidence            458999997 4589999999999999999999999999999999999775 36889999999999999999999999765


Q ss_pred             CCCCcccccccchhcccc--CCcchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHH
Q 021438           81 AGGSTELLSGSLGKLQAR--SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI  158 (312)
Q Consensus        81 ~~~~~~~~~~~l~~~~~~--~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~  158 (312)
                       ++++. .+..|++||++  .+++|++|.+|+..|+++|++|+||+.+.++|..||+++++.++++||+.+.++|||||+
T Consensus       101 -~~~~~-~~~~L~r~q~r~~~~~~er~L~~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~a~~~~~~rGrs~e~vaAAclYi  178 (345)
T 4bbr_M          101 -TTDMR-FTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILI  178 (345)
T ss_dssp             -SCCHH-HHHHHHHHHHHTCCCCSSSSTTHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTCTTTTTCCHHHHHHHHHHH
T ss_pred             -Ccchh-hHHHHHHHHHhhhcChHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHH
Confidence             33311 23458899987  578999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhcc------ccccCCCCHHHHHHHHHhhcCCCHHHHHHHH
Q 021438          159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQ------SVEMGTIHASDYLRRFCSNLGMTNQAVKAAQ  232 (312)
Q Consensus       159 acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~------~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~  232 (312)
                      |||+++.|+|++||++++ ++++++|+++|+.|.+.|++....      ++.+++.+|++||+|||++|+|++++.+.|+
T Consensus       179 ACR~~~~prtl~eI~~~~-~v~~keigr~~k~l~~~L~l~~~~~~~~~~~~~~~~~~p~~~i~Rf~s~L~l~~~v~~~A~  257 (345)
T 4bbr_M          179 GCRRAEVARTFKEIQSLI-HVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSAE  257 (345)
T ss_dssp             HHHHTCCBCCHHHHHHHH-TCCTTHHHHHHHHHHHCC-------------------------------------------
T ss_pred             HHHhcCCCccHHHHHHHh-CCCHHHHHHHHHHHHHHhCccccccccccccccCCCCCHHHHHHHHHHHcCCcHHHHHHHH
Confidence            999999999999999999 799999999999999999974211      1236788999999999999999999999999


Q ss_pred             HHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCCccc-cc-ccccc
Q 021438          233 EAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWF-AN-EEDIK  308 (312)
Q Consensus       233 ~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p~~~-~~-~~~~~  308 (312)
                      +|++.+.+  +..||+|.+|||||||+|++++|.++|++|||+++|||++|||++||||+++++.|+|+|| .+ .++++
T Consensus       258 ~i~~~~~~~~i~~GR~P~~IAAAaIylAa~l~g~~~t~~eIa~v~~Vse~TIr~rykel~~~~~~l~~~~~~~~~~~~~~  337 (345)
T 4bbr_M          258 YTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTIKSGYKILYEHRDKLVDPQLIANGVVSLD  337 (345)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHhcccccCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcCHHHhhcccCchh
Confidence            99999998  8899999999999999999999999999999999999999999999999999999996665 43 48999


Q ss_pred             ccCC
Q 021438          309 NLKL  312 (312)
Q Consensus       309 ~l~~  312 (312)
                      +||.
T Consensus       338 ~l~~  341 (345)
T 4bbr_M          338 NLPG  341 (345)
T ss_dssp             ----
T ss_pred             hCCC
Confidence            9994

>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.3e-72  Score=521.13  Aligned_cols=306  Identities=33%  Similarity=0.525  Sum_probs=163.6

Q ss_pred             CCCCCCCCCCC-ceeeeCCCCceEcCCCcccccCcccccccccccccCCC-CCCCCCccCCCCCCcccCCCcceEEecCC
Q 021438            3 DSYCADCKRLT-EVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANES-SDHDPVRVGGPLNPLLSGGGLSTVIAKPT   80 (312)
Q Consensus         3 ~~~Cp~Cg~~~-~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~~~-~~~~~~r~G~~~~~~~~~~~~~t~i~~~~   80 (312)
                      .+.||+||+.+ ++++|+.+|++||++||+|++|++||+|||||+|++++ ++.|++|+|+|.+|++||.|++|.|+++.
T Consensus        21 ~~~Cp~Cg~~~~~iv~D~~~G~~vC~~CG~Vl~e~~id~~~EwR~F~~~~~~~~~~srvG~~~~~~~~~~~l~T~I~~~~  100 (345)
T 3k7a_M           21 VLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEASNPLLDGNNLSTRIGKGE  100 (345)
T ss_dssp             CCCCSTTCCSCCCCCCCSSSCSCCCSSSCCCCCCCCCCTTCCCCCC--------------CCCCCSSSCCCCCCCCCCTT
T ss_pred             CCcCcCCCCCCCceEEECCCCCEecCCCCeEcccccccCCccccccccccccCCCCCccCCCCCccccCCCCceeeccCC
Confidence            46899999832 79999999999999999999999999999999999764 36789999999999999999999999752


Q ss_pred             -CCCCcccccccchhcccc--CCcchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHH
Q 021438           81 -AGGSTELLSGSLGKLQAR--SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLY  157 (312)
Q Consensus        81 -~~~~~~~~~~~l~~~~~~--~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly  157 (312)
                       .+++|   .+.|++||++  .+++|++|.+++.+|+++|+.|+||+.++++|..||+++++.+.++|++.+.++|||||
T Consensus       101 ~~~~~~---~r~l~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~~~~~~~~kgr~~~~vaaAcly  177 (345)
T 3k7a_M          101 TTDMRF---TKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASIL  177 (345)
T ss_dssp             SCCHHH---HHHHHHHHHHHTTSSCCTTHHHHHHHHHHHHHHTTCCHHHHTHHHHHHHHHSSSCSSCCCCSHHHHTTTTT
T ss_pred             CCCchh---hhhhhhhcccccCCHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCcHHHHHHHHHH
Confidence             12222   2248899876  58899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhh------ccccccCCCCHHHHHHHHHhhcCCCHHHHHHH
Q 021438          158 IACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM------GQSVEMGTIHASDYLRRFCSNLGMTNQAVKAA  231 (312)
Q Consensus       158 ~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~------~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A  231 (312)
                      +|||++++|++++||+.++ +++.++|+++|+.|.+.|+...      +..+.+++.+|+.||+|||+.|++++++.+.|
T Consensus       178 iAcR~e~~prtl~ei~~~~-~v~~keIgr~~~~l~~~L~~~~~~~~~~~~~~~~~~~~p~~~i~Rf~~~L~l~~~v~~~A  256 (345)
T 3k7a_M          178 IGCRRAEVARTFKEIQSLI-HVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSA  256 (345)
T ss_dssp             TTSBTTBSSCCHHHHHHSS-SCCSHHHHHHHHHHHHHHTCC---------------------------------------
T ss_pred             HHHHHcCCCccHHHHHHHH-CCCHHHHHHHHHHHHHHHhhhhccccccccccccCCCCHHHHHHHHHHHcCCCHHHHHHH
Confidence            9999999999999999999 6999999999999999998210      00136778999999999999999999999999


Q ss_pred             HHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCCcccc-cc-ccc
Q 021438          232 QEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFA-NE-EDI  307 (312)
Q Consensus       232 ~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p~~~~-~~-~~~  307 (312)
                      ++|++++.+  +..||+|.+|||||||||++++|.++|+++|++++||+++||+++||||++++..++|+||. ++ +++
T Consensus       257 ~~i~~~~~~~~l~~Gr~P~~IAaAaIylAa~~~~~~~t~~eIa~~~~Vse~TIr~~ykel~~~~~~l~~~~~~~~~~~~~  336 (345)
T 3k7a_M          257 EYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTIKSGYKILYEHRDKLVDPQLIANGVVSL  336 (345)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHhchhcCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCHHHhhcccCCH
Confidence            999999998  88999999999999999999999999999999999999999999999999999999977766 55 899


Q ss_pred             cccCC
Q 021438          308 KNLKL  312 (312)
Q Consensus       308 ~~l~~  312 (312)
                      ++||.
T Consensus       337 ~~lp~  341 (345)
T 3k7a_M          337 DNLPG  341 (345)
T ss_dssp             -----
T ss_pred             hhCCC
Confidence            99994

>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A*

Probab=100.00  E-value=9.5e-45  Score=312.80  Aligned_cols=204  Identities=43%  Similarity=0.713  Sum_probs=198.2

Q ss_pred             chhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCH
Q 021438          102 PDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTK  181 (312)
Q Consensus       102 ~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~  181 (312)
                      +||++.+++++|+++|.+|+||+.++++|..+|+++++.+.++|++++.++|||+|+|||.++.|++++||+.++ +++.
T Consensus         1 ~er~l~~a~~~I~~~~~~L~L~~~v~~~A~~~~~r~~~~~~~~~~~~~~v~aaclylAcK~ee~p~~l~di~~~~-~~~~   79 (207)
T 1c9b_A            1 SDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVS-RISK   79 (207)
T ss_dssp             CGGGHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTCSTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHTS-SSCH
T ss_pred             CchHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHH-CCCH
Confidence            488999999999999999999999999999999999999999999999999999999999999999999999999 6999


Q ss_pred             HHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHH
Q 021438          182 KEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIIT  259 (312)
Q Consensus       182 ~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~  259 (312)
                      ++|+++|+.|.+.|++      ++++.+|+.|+.||++.|++++++.+.|+.+++.+.+  +..|++|.+|||||||+|+
T Consensus        80 ~~i~~~~~~ll~~L~~------~l~~~~p~~~l~r~~~~l~l~~~~~~~A~~i~~~~~~~~l~~g~~P~~IAaAaiylA~  153 (207)
T 1c9b_A           80 KEIGRCFKLILKALET------SVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMAS  153 (207)
T ss_dssp             HHHHHHHHHHHHHTTC------CCCCCCTHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCC------CcCcCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHH
Confidence            9999999999999997      7888999999999999999999999999999999987  8899999999999999999


Q ss_pred             HhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCCccccccccccccCC
Q 021438          260 QLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNLKL  312 (312)
Q Consensus       260 ~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p~~~~~~~~~~~l~~  312 (312)
                      +++|.++++++|++++||++.||+++|++|.+.++.++|+||.+++++++||.
T Consensus       154 ~~~~~~~~~~~i~~~~~v~~~tI~~~~~~l~~~l~~~~p~~~~~~~~~~~l~~  206 (207)
T 1c9b_A          154 QASAEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTDFKFDTPVDKLPQ  206 (207)
T ss_dssp             HTSSSCCCHHHHHHHHTCCHHHHHHHHHHHGGGHHHHSCSSCCCSSCSTTSCC
T ss_pred             HHHCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHhChHHHcccCCHhhCCC
Confidence            99999999999999999999999999999999999999999999999999994

>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B*

Probab=100.00  E-value=3.1e-43  Score=301.78  Aligned_cols=192  Identities=31%  Similarity=0.588  Sum_probs=181.4

Q ss_pred             CcchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC
Q 021438          100 SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT  179 (312)
Q Consensus       100 ~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v  179 (312)
                      +++|+++.+++++|.++|++|+||+.+.++|..+|+++++.+.++|++++.++|||||+|||+++.|++++||++++ ++
T Consensus         3 ~~~er~l~~a~~~I~~~~~~L~L~~~v~~~A~~l~~~~~~~~~~~gr~~~~vaaAclylAcr~~~~p~~l~di~~~~-~v   81 (200)
T 1ais_B            3 DAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIA-RV   81 (200)
T ss_dssp             -----CHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTTTTTTCCHHHHHHHHHHHHHHHHTCCCCHHHHHHHT-TS
T ss_pred             ChHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHHH-CC
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999 79


Q ss_pred             CHHHHHHHHHHHHHHHhhhhccccccCC--CCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHH
Q 021438          180 TKKEIGRAKEFIVKHLEAEMGQSVEMGT--IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVI  255 (312)
Q Consensus       180 ~~~~i~~~~~~l~~~l~~~~~~~~~~~~--~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAai  255 (312)
                      +.++|+++|+.|.+.|++      ++++  .+|+.||.||++.|++++++.+.|++|++++.+  +..||+|.+||||||
T Consensus        82 ~~~~i~~~~~~l~~~L~~------~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~~~~gr~P~~iAaAal  155 (200)
T 1ais_B           82 DKKEIGRSYRFIARNLNL------TPKKLFVKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAAL  155 (200)
T ss_dssp             CHHHHHHHHHHHHHHTTC------CTTTTCCCGGGGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhcc------cCCcCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHH
Confidence            999999999999999997      6777  899999999999999999999999999999997  889999999999999


Q ss_pred             HHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCC
Q 021438          256 YIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIP  298 (312)
Q Consensus       256 yla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p  298 (312)
                      |+|++++|.++|+++|+.++||++.||+++|++|.+.++..+|
T Consensus       156 y~A~~~~~~~~t~~ei~~~~~vs~~ti~~~~~~l~~~l~~~~~  198 (200)
T 1ais_B          156 YIASLLEGEKRTQREVAEVARVTEVTVRNRYKELVEKLKIKVP  198 (200)
T ss_dssp             HHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             HHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCC
Confidence            9999999999999999999999999999999999999986654

>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe}

Probab=99.94  E-value=4.1e-26  Score=199.95  Aligned_cols=182  Identities=20%  Similarity=0.266  Sum_probs=165.3

Q ss_pred             HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCC-CCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhc-------
Q 021438          106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRG-RNQEAIVAACLYIACRQENKPRTVKEFCSVAN-------  177 (312)
Q Consensus       106 l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~g-r~~~~iaaAcly~acr~~~~p~tl~dia~~~~-------  177 (312)
                      ...+.++|.+++.+|+||+.+..+|..+|++++..+.+++ +++..+++||+|+|||.++.|++++||+.+++       
T Consensus        28 R~~~~~~i~~v~~~l~L~~~t~~~A~~~~~Rf~~~~~~~~~~~~~lv~~acL~lA~K~Ee~~~~l~d~~~~~~~~~~~~~  107 (235)
T 1zp2_A           28 TIYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKGFSLEALVATCIYLSCKVEECPVHIRTICNEANDLWSLKV  107 (235)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCSCCCCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHTTCCCSS
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccccCHHHHHHHHHHHHhccccCcccHHHHHHHHHHHccchh
Confidence            5678999999999999999999999999999999988888 99999999999999999999999999998763       


Q ss_pred             CCCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHH
Q 021438          178 GTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVI  255 (312)
Q Consensus       178 ~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAai  255 (312)
                      ..+.++|.++++.|.+.|++      ++.+.+|..|+.+|++.+++++++.+.|+.+++++..  +..|+.|+.||||||
T Consensus       108 ~~~~~~I~~~E~~iL~~L~f------~l~~~~P~~~l~~~~~~~~~~~~~~~~A~~~l~~s~~~~~~l~~~Ps~IAaAai  181 (235)
T 1zp2_A          108 KLSRSNISEIEFEIISVLDA------FLIVHHPYTSLEQAFHDGIINQKQLEFAWSIVNDSYASSLCLMAHPHQLAYAAL  181 (235)
T ss_dssp             CCCHHHHHHHHHHHHHHTTT------CCCCCCTHHHHHHHHHTTSSCHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHH
T ss_pred             hccHHHHHHHHHHHHHHCCC------cEEecChHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCCchhccCHHHHHHHHH
Confidence            36899999999999999997      7888999999999999999999999999999999987  788999999999999


Q ss_pred             HHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438          256 YIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       256 yla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~  294 (312)
                      |+|+++.|.+.+ .+.+...|+++.+|++++++|.+...
T Consensus       182 ~lA~~~~~~~~~-~~~~~~~~~~~~~i~~~~~~i~~ly~  219 (235)
T 1zp2_A          182 LISCCNDENTIP-KLLDLIKSTDAFKVILCVQRIISIYY  219 (235)
T ss_dssp             HHHHTSCTTHHH-HHHHHCCHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhcCCCCC-CCcchhhcCCHHHHHHHHHHHHHHHh
Confidence            999999886543 23444459999999999999998643

>2ivx_A Cyclin-T2; transcription regulation, cell division, phosphorylation, NU protein, cell cycle, transcription; 1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A 3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B* 3lq5_B* 3my1_B* 3tn8_B*

Probab=99.92  E-value=2.4e-23  Score=184.71  Aligned_cols=182  Identities=16%  Similarity=0.186  Sum_probs=161.5

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcC--------
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG--------  178 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~--------  178 (312)
                      ..+.++|.+++.+|+||+.+..+|..||++++..+.++++++..+++||+|+|||.++.|++++||+.+++.        
T Consensus        32 ~~~~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~qlv~~acL~lA~K~EE~p~~l~d~~~~~~~~~~~~~~~  111 (257)
T 2ivx_A           32 QQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHACLHPLEPL  111 (257)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHCTTSCC
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhCChhhhCHHHHHHHHHHHHhccccCCcCHHHHHHHHHHHhccCCCC
Confidence            357999999999999999999999999999999999999999999999999999999999999999877521        


Q ss_pred             --CC-------HHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhh-h--ccCCCC
Q 021438          179 --TT-------KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSE-D--LDIRRS  246 (312)
Q Consensus       179 --v~-------~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~-~--l~~Gr~  246 (312)
                        ++       .++|.++++.|.+.|++      ++...+|+.|+.+|++.++.++++.+.|+.+++.+. .  +..+..
T Consensus       112 ~~~~~~~y~~~~~~I~~~E~~iL~~L~f------~l~~~~P~~fl~~~~~~l~~~~~~~~~A~~~~~~sl~~~~~~l~~~  185 (257)
T 2ivx_A          112 LDTKCDAYLQQTRELVILETIMLQTLGF------EITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYK  185 (257)
T ss_dssp             CCTTSHHHHHHHHHHHHHHHHHHHHTTT------CCCCCCHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCGGGTSC
T ss_pred             CCcchHHHHHHHHHHHHHHHHHHHHccc------ceEeeCcHHHHHHHHHHhCCCcHHHHHHHHHHHhhhhcccHHHcCC
Confidence              11       67899999999999997      788899999999999999999999999999998876 3  678999


Q ss_pred             hHHHHHHHHHHHHHhcCCCCCHH----HHHHH--hCcchhHHHHHHHHHHhhhc
Q 021438          247 PISVAAAVIYIITQLSNDTKPLK----EISIV--TRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       247 P~~iaaAaiyla~~~~~~~~~~~----~Ia~~--~~vs~~ti~~~~kel~~~~~  294 (312)
                      |+.||+||||+|++++|.++++.    .....  .++++.+|++++++|.+...
T Consensus       186 Ps~IAaAai~lA~~~~~~~~p~~~~~~~W~~~~~~~~~~~~l~~~~~~i~~~~~  239 (257)
T 2ivx_A          186 PTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLELLDELTHEFLQILE  239 (257)
T ss_dssp             HHHHHHHHHHHHHHHHTCCCCCCTTCCCGGGGTCSSCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCCCCCchHHHHhCCCCCHHHHHHHHHHHHHHHH
Confidence            99999999999999999876642    24443  37999999999999998654

>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1

Probab=99.92  E-value=2.1e-23  Score=185.25  Aligned_cols=182  Identities=16%  Similarity=0.238  Sum_probs=161.0

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcC-C------
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG-T------  179 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~-v------  179 (312)
                      ..+.++|.+++.+|+||+.+..+|..||++++..+.+++++...+++||+|+|||.++.|++++||..++.. +      
T Consensus        42 ~~~~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~qlv~~acL~lA~K~eE~~~~l~d~~~~~~~~~~~~~~~  121 (258)
T 2i53_A           42 REGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFG  121 (258)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHSCHHHHG
T ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCChhhcCHHHHHHHHHHHHHccccccccHHHHHHHHHHHhchhhhh
Confidence            357999999999999999999999999999999999999999999999999999999999999999976421 1      


Q ss_pred             -----CHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCH----HHHHHHHHHHHHhhh--ccCCCChH
Q 021438          180 -----TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN----QAVKAAQEAVQKSED--LDIRRSPI  248 (312)
Q Consensus       180 -----~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~----~v~~~A~~i~~~~~~--l~~Gr~P~  248 (312)
                           +.++|.++++.|.+.|++      ++...+|+.|+.+|++.|+.+.    ++.+.|+.+++.+..  +..++.|+
T Consensus       122 ~~~~~~~~~i~~~E~~iL~~L~f------~l~~~~P~~fl~~~~~~l~~~~~~~~~~~~~A~~l~~~s~~~~~~l~~~Ps  195 (258)
T 2i53_A          122 QFGDDPKEEVMVLERILLQTIKF------DLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPE  195 (258)
T ss_dssp             GGCSCHHHHHHHHHHHHHHHTTT------CCCCCCHHHHHHHHHHTBCSCHHHHHHHHHHHHHHHHHHTTTTGGGTSCHH
T ss_pred             hhhhhHHHHHHHHHHHHHHHCCC------ceeccChHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHHHcCCchhccChH
Confidence                 357899999999999997      7888999999999999999987    688999999999876  77899999


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHH-------HH--hCcchhHHHHHHHHHHhhhc
Q 021438          249 SVAAAVIYIITQLSNDTKPLKEIS-------IV--TRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       249 ~iaaAaiyla~~~~~~~~~~~~Ia-------~~--~~vs~~ti~~~~kel~~~~~  294 (312)
                      .||+||||+|++++|.++++.+..       ..  .|+++.+|++++++|.+...
T Consensus       196 ~IAaAai~lA~~~~~~~~~~~~~~~~~~~W~~~~~~~~~~~~l~~~~~~il~ly~  250 (258)
T 2i53_A          196 IIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQDVPVDVLEDICHQILDLYS  250 (258)
T ss_dssp             HHHHHHHHHHHHHHTCCGGGGBSSCCSSCGGGGTSSSCCHHHHHHHHHHHHTTTS
T ss_pred             HHHHHHHHHHHHHhCCCCCccccCCCcccHHHHhccCCCHHHHHHHHHHHHHHHh
Confidence            999999999999999877654332       22  49999999999999998644

>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B*

Probab=99.91  E-value=9.4e-23  Score=181.99  Aligned_cols=182  Identities=13%  Similarity=0.156  Sum_probs=169.4

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhc-CCCHHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN-GTTKKEI  184 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~-~v~~~~i  184 (312)
                      ....++|.+++..++|++.+...|..+++++.....+.+++...+++||+|+|||.++. |++++|+..+++ ..+.++|
T Consensus        39 ~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfl~~~~v~~~~lqlv~~acL~iA~K~eE~~~p~~~d~~~~~~~~~~~~eI  118 (269)
T 2b9r_A           39 AILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQNNSVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKHQI  118 (269)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHTTSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTCSSSCHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcCCCCcHHHhhHHHHHHHHHHHhcccccCccHHHHHHHhcCCCCHHHH
Confidence            45789999999999999999999999999999998889999999999999999999988 899999999874 3799999


Q ss_pred             HHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhc
Q 021438          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLS  262 (312)
Q Consensus       185 ~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~  262 (312)
                      .++++.|.+.|+.      ++...+|..|+.+|++.++++.++...|+.+++.+..  ...++.|+.|||||||+|..+.
T Consensus       119 ~~mE~~IL~~L~f------~l~~~tp~~fl~~~~~~~~~~~~~~~~a~~l~e~sl~~~~~~~~~Ps~iAaAai~lA~~~l  192 (269)
T 2b9r_A          119 RQMEMKILRALNF------GLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFPPSQIAAGAFSLALKIL  192 (269)
T ss_dssp             HHHHHHHHHHTTS------CCCCCCHHHHHHHHHHSSCCCHHHHHHHHHHHHHGGGCGGGSSSCTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCC------ccCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhhhcCCHHHHHHHHHHHHHHHh
Confidence            9999999999997      7888999999999999999999999999999999875  5689999999999999999999


Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~  294 (312)
                      |.+.+.++++..+|+++.+|+.++++|.+...
T Consensus       193 ~~~~w~~~l~~~tg~~~~~l~~~~~~l~~~~~  224 (269)
T 2b9r_A          193 DNGEWTPTLQHYLSYTEESLLPVMQHLAKNVV  224 (269)
T ss_dssp             TCCCSCTTHHHHSCCCSSTTTTHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            98888999999999999999999999988653

>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens}

Probab=99.90  E-value=1.5e-22  Score=182.04  Aligned_cols=183  Identities=13%  Similarity=0.186  Sum_probs=164.0

Q ss_pred             hhhHH-HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCC-CHHHHHHHhcC--
Q 021438          103 DRNLI-QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPR-TVKEFCSVANG--  178 (312)
Q Consensus       103 e~~l~-~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~-tl~dia~~~~~--  178 (312)
                      ++.+. .+.++|.+++.+|+||+.+..+|..||++++..+.++++++..+++||+|+|||.++.|+ +++||..++..  
T Consensus        39 e~~~R~~~~~~I~~v~~~l~L~~~t~~tA~~~~~RF~~~~s~~~~~~~lva~acLfLA~K~EE~~~~~~~di~~~~~~~~  118 (285)
T 3rgf_B           39 YWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVL  118 (285)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHSCTTTSCHHHHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhCCchhcCHHHHHHHHHHHHHhhhccccccHHHHHHHHHHHH
Confidence            44443 479999999999999999999999999999999999999999999999999999999997 78998875421  


Q ss_pred             -------------CCHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccC
Q 021438          179 -------------TTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDI  243 (312)
Q Consensus       179 -------------v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~  243 (312)
                                   .+.++|.++++.|.+.|++      ++...+|+.|+.+|+..|+.+.++.+.|+.+++++..  +..
T Consensus       119 k~~~~~~~~~~~~~~~~~Il~~E~~iL~~L~f------~l~v~~P~~fL~~~~~~l~~~~~~~~~A~~~l~~sl~t~~~l  192 (285)
T 3rgf_B          119 KTRFSYAFPKEFPYRMNHILECEFYLLELMDC------CLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCL  192 (285)
T ss_dssp             HHHCTTTCCSCCCCCHHHHHHHHHHHHHHTTT------CCCCCCSHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSHHH
T ss_pred             cccccccCchhhHHHHHHHHHHHHHHHHHcCC------CeEeCChHHHHHHHHHHhCCCHHHHHHHHHHHHHHHccChhh
Confidence                         3678999999999999997      7888899999999999999999999999999999887  778


Q ss_pred             CCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhh
Q 021438          244 RRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHL  293 (312)
Q Consensus       244 Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~  293 (312)
                      +..|..||+||||+|+++.+.+.  ...-..++++...|...+++|.+..
T Consensus       193 ~~~Ps~IAaAaiylA~~~~~~~~--~~W~~~~~~~~~~l~~~~~~il~ly  240 (285)
T 3rgf_B          193 LYPPFMIALACLHVACVVQQKDA--RQWFAELSVDMEKILEIIRVILKLY  240 (285)
T ss_dssp             HSCHHHHHHHHHHHHHHHTTCCC--HHHHHTSCSCHHHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHHcCCCh--hhHHHHHCCCHHHHHHHHHHHHHHH
Confidence            99999999999999999998654  4667789999999999999998763

>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division), ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B* 1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B* 2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B* 2x1n_B* 1vyw_B* ...

Probab=99.89  E-value=5.7e-22  Score=176.10  Aligned_cols=182  Identities=14%  Similarity=0.121  Sum_probs=167.2

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhc-CCCHHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN-GTTKKEI  184 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~-~v~~~~i  184 (312)
                      ..+.++|.+++..++|+..+.-.|..+++++.....+..++...+++||+|+|||.++. |++++|+..+++ ..+.++|
T Consensus        40 ~~lvdwl~~v~~~~~l~~~tl~lAv~~lDRfls~~~v~~~~lqlv~~acl~iA~K~ee~~~~~~~d~~~i~~~~~~~~~i  119 (260)
T 2cch_B           40 AILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQV  119 (260)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTSSSCHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccCCCCHHHHhHHHHHHHHHHHHhcccCCCCHHHHHHHHcCCcCHHHH
Confidence            45789999999999999999999999999999888788888999999999999999998 999999998874 3789999


Q ss_pred             HHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCH-HHHHHHHHHHHHhhh--c-cCCCChHHHHHHHHHHHHH
Q 021438          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN-QAVKAAQEAVQKSED--L-DIRRSPISVAAAVIYIITQ  260 (312)
Q Consensus       185 ~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~-~v~~~A~~i~~~~~~--l-~~Gr~P~~iaaAaiyla~~  260 (312)
                      .++++.|.+.|+.      ++...+|..|+.+|++.++++. ++...|+.+++.+..  - ..+..|+.|||||||+|..
T Consensus       120 ~~mE~~iL~~L~~------~l~~~tp~~fl~~~~~~l~~~~~~~~~~a~~l~e~sl~~~~~~~~~~Ps~iAaAai~lA~~  193 (260)
T 2cch_B          120 LRMEHLVLKVLTF------DLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALY  193 (260)
T ss_dssp             HHHHHHHHHHTTT------CCCCCCHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCC------ccCCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHhHHHHhCCCHHHHHHHHHHHHHH
Confidence            9999999999997      7788899999999999999876 888999999998763  3 7899999999999999999


Q ss_pred             hcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438          261 LSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       261 ~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~  294 (312)
                      ..+.+.+.++++..+|+++.+|+.++++|.+...
T Consensus       194 ~~~~~~w~~~l~~~~g~~~~~i~~~~~~l~~~~~  227 (260)
T 2cch_B          194 TVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYL  227 (260)
T ss_dssp             HHHSCCSCHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_pred             HhCCCcchHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence            9988888999999999999999999999998653

>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase, chromosomal rearrangement, ATP-binding, transferase, polymorphism, cell division; 2.30A {Homo sapiens} PDB: 2w99_A 2w9f_A 2w9z_A

Probab=99.88  E-value=2.9e-21  Score=172.60  Aligned_cols=188  Identities=15%  Similarity=0.204  Sum_probs=165.2

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhc-CCCHHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN-GTTKKEI  184 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~-~v~~~~i  184 (312)
                      ....++|.+++..+++++.+.-.|..+++++.....+..++...+++||+|+|||.++. |++++|++.+++ ..+.++|
T Consensus        58 ~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~v~~~~lqlv~~acL~iAsK~EE~~p~~~~~~~~~~~~~~~~~eI  137 (271)
T 2w96_A           58 KIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRPEEL  137 (271)
T ss_dssp             HHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHTTSCCCTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTTSSCHHHH
T ss_pred             HHHHHHHHHHHHHHCCchhHHHHHHHHHHHhCCcCCcCHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCHHHH
Confidence            45789999999999999999999999999999988888899999999999999999998 999999998864 3799999


Q ss_pred             HHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHH----HHHHHHHHHHhhh--ccCCCChHHHHHHHHHHH
Q 021438          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQA----VKAAQEAVQKSED--LDIRRSPISVAAAVIYII  258 (312)
Q Consensus       185 ~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v----~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla  258 (312)
                      .++++.|.+.|++      ++...+|..|+.+|++.++++.+.    .+.|+.+++.+..  ...+..|+.|||||||+|
T Consensus       138 ~~mE~~IL~~L~~------~l~~~tp~~fl~~~~~~l~~~~~~~~~~~~~a~~~l~~~~~d~~~~~~~PS~iAaAai~lA  211 (271)
T 2w96_A          138 LQMELLLVNKLKW------NLAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISNPPSMVAAGSVVAA  211 (271)
T ss_dssp             HHHHHHHHHHTTT------CCCCCCHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHTSTHHHHSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCC------ccCCCCHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHHHhhhhhhccCHHHHHHHHHHHH
Confidence            9999999999997      788899999999999999998765    3567888877653  446899999999999999


Q ss_pred             HHhcCC---------CCCHHHHHHHhCcchhHHHHHHHHHHhhhcccCCcc
Q 021438          259 TQLSND---------TKPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDW  300 (312)
Q Consensus       259 ~~~~~~---------~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~p~~  300 (312)
                      ....+.         ..++++++.++|+++.+|++++++|.+.+..-+..+
T Consensus       212 ~~~l~~~~~~~~~w~~~~~~~l~~~~~v~~~~l~~c~~~i~~l~~~~~~~~  262 (271)
T 2w96_A          212 VQGLNLRSPNNFLSYYRLTRFLSRVIKCDPDCLRACQEQIEALLESSLRQA  262 (271)
T ss_dssp             HHHHHHHSTTSCGGGTTHHHHHHHHHTSCHHHHHHHHHHHHHHHTTTTTSS
T ss_pred             HHHhCcCCCCCCCcHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            987753         123678999999999999999999999887766544

>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C

Probab=99.88  E-value=1.6e-22  Score=187.06  Aligned_cols=182  Identities=15%  Similarity=0.182  Sum_probs=160.1

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcC--------
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG--------  178 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~--------  178 (312)
                      ..+.++|.+++.+|+||+.+..+|..||++++....++++++..+++||||+|||.++.|++++||..+++.        
T Consensus        39 ~~~v~wI~ev~~~l~L~~~t~~tAv~~~dRFl~~~sv~~~~~qlva~acLfLA~K~EE~p~~l~d~v~v~~~~~~~~~~~  118 (358)
T 2pk2_A           39 QQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESL  118 (358)
T ss_dssp             HHHHHHHHHHHTTTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHTTHHHHHCSSSCC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHhhccCCCCHHHHHHHHHHHhcccccc
Confidence            357999999999999999999999999999999999999999999999999999999999999999865420        


Q ss_pred             --C-------CHHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhh-h--ccCCCC
Q 021438          179 --T-------TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSE-D--LDIRRS  246 (312)
Q Consensus       179 --v-------~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~-~--l~~Gr~  246 (312)
                        +       ..++|.++++.|.+.|++      ++.+.+|+.||.+|+..++.+.++.+.|+.+++++. .  +..+..
T Consensus       119 ~~~~~~~y~~~~~~Il~~E~~IL~~L~f------~L~v~~P~~fL~~~~~~l~~~~~l~~~A~~ll~~sl~~t~l~l~y~  192 (358)
T 2pk2_A          119 PDTRSEAYLQQVQDLVILESIILQTLGF------ELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYT  192 (358)
T ss_dssp             CCTTSHHHHGGGTGGGTHHHHHHHHTTT------CCCCCCTTHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCGGGTSC
T ss_pred             ccccchhhhHHHHHHHHHHHHHHHHcCC------ceeCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhccC
Confidence              1       256788889999999997      788899999999999999999999999999998876 2  678999


Q ss_pred             hHHHHHHHHHHHHHhcCCCCCHH----HHHHH--hCcchhHHHHHHHHHHhhhc
Q 021438          247 PISVAAAVIYIITQLSNDTKPLK----EISIV--TRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       247 P~~iaaAaiyla~~~~~~~~~~~----~Ia~~--~~vs~~ti~~~~kel~~~~~  294 (312)
                      |..|||||||+|+++++.++++.    .+...  +++++.+|++++++|.+...
T Consensus       193 Ps~IAaAAI~lA~~~l~~~~p~~~~~~~W~~~~~~~vt~~~l~~i~~~il~~y~  246 (358)
T 2pk2_A          193 PPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILE  246 (358)
T ss_dssp             HHHHTTTTTTTHHHHTTCCCCCCSSSCCTTTTSCSSCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCCccccchHHHHhccCCHHHHHHHHHHHHHHHH
Confidence            99999999999999999776642    24444  37899999999999998654

>1jkw_A Cyclin H; cell cycle, cell division, nuclear protein; 2.60A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1kxu_A

Probab=99.85  E-value=5.4e-20  Score=168.01  Aligned_cols=185  Identities=12%  Similarity=0.140  Sum_probs=153.3

Q ss_pred             chhhHH-HHHHHHHHHHHhcC--CcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcC
Q 021438          102 PDRNLI-QAFKSISAMSDRLG--LVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG  178 (312)
Q Consensus       102 ~e~~l~-~~~~~I~~~~~~L~--Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~  178 (312)
                      .|..+. .+..+|.++|.+|+  ||+.+..+|..||++++..+.+++.++..+++||+|+|||.++.|++++||+..+ .
T Consensus        52 eE~~lr~~~~~~I~ev~~~l~~~Lp~~t~~tA~~~~~RF~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~d~v~~~-~  130 (323)
T 1jkw_A           52 EEMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNL-R  130 (323)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHGGGS-S
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhhCChhhcCHHHHHHHHHHHHHhhhcCCCCHHHHHHHh-c
Confidence            355554 46799999999999  9999999999999999999999999999999999999999999999999998766 3


Q ss_pred             CC-------HHHHHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhc-------CCCHHHHHHHHHHHHHhhh--cc
Q 021438          179 TT-------KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNL-------GMTNQAVKAAQEAVQKSED--LD  242 (312)
Q Consensus       179 v~-------~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L-------~l~~~v~~~A~~i~~~~~~--l~  242 (312)
                      .+       .++|.++++.|.+.|++      ++.+.+|+.|+.+|+..|       +.++.+.+.|+.+++.+..  +.
T Consensus       131 ~~p~~~~~~~~~Il~~E~~iL~~L~f------~l~v~~P~~~L~~~l~~l~~~~~~~~~~~~l~~~A~~~l~~sl~t~~~  204 (323)
T 1jkw_A          131 ESPLGQEKALEQILEYELLLIQQLNF------HLIVHNPYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAY  204 (323)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHHTTT------CCCCCCSHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHTTSTHH
T ss_pred             cChhhhHHHHHHHHHHHHHHHHHCCC------cEEcCChHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHhccHH
Confidence            45       57899999999999997      788899999999999776       3345688999999999876  66


Q ss_pred             CCCChHHHHHHHHHHHHHhcCCCCCH--HHHHH--HhCcchhHHHHHHHHHHhhh
Q 021438          243 IRRSPISVAAAVIYIITQLSNDTKPL--KEISI--VTRVAEGTIKNVYKDLFPHL  293 (312)
Q Consensus       243 ~Gr~P~~iaaAaiyla~~~~~~~~~~--~~Ia~--~~~vs~~ti~~~~kel~~~~  293 (312)
                      .+..|..||+||||+|++..|.+++.  .++-.  ..+.+..-+....++|....
T Consensus       205 l~~~Ps~IAaAai~lA~~~~~~~~~~w~~~l~~~~~~~~~~~~l~~~~~~i~~l~  259 (323)
T 1jkw_A          205 LLYTPSQIALTAILSSASRAGITMESYLSESLMLKENRTCLSQLLDIMKSMRNLV  259 (323)
T ss_dssp             HHSCHHHHHHHHHHHHHHHHSCCCTTHHHHHTTSCSSSCCTHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHHcCCChHHHHHHHhccccccccHHHHHHHHHHHHHHH
Confidence            78999999999999999999876552  22211  13445566666666665543

>1g3n_C V-cyclin; cyclin-dependent kinase, INK4 inhibitor, viral cyclin, cell cycle, signaling protein; 2.90A {Human herpesvirus 8} SCOP: a.74.1.1 a.74.1.1

Probab=99.85  E-value=4.3e-20  Score=163.68  Aligned_cols=183  Identities=11%  Similarity=0.107  Sum_probs=162.0

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhc-CCCHHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN-GTTKKEI  184 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~-~v~~~~i  184 (312)
                      ....++|.+++..++|+..+.-.|..|++++.....+++++...+++||+|+|||.++. |++++|+..+++ ..+.++|
T Consensus        52 ~~lvdwl~ev~~~~~l~~etl~lAv~~~DRfls~~~v~~~~lqLv~~acl~iA~K~eE~~~p~~~d~~~~~~~~~~~~~i  131 (257)
T 1g3n_C           52 KLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAADSFSRQEL  131 (257)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTTCSCHHHH
T ss_pred             HHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHccccCCCHHHHHHHHCCCCCHHHH
Confidence            45789999999999999999999999999999988888889999999999999998876 999999998864 3789999


Q ss_pred             HHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHH----HHHHHHHHHHhhh--ccCCCChHHHHHHHHHHH
Q 021438          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQA----VKAAQEAVQKSED--LDIRRSPISVAAAVIYII  258 (312)
Q Consensus       185 ~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v----~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla  258 (312)
                      .++.+.|.+.|+.      ++...+|..|+.+|++.++++.+.    .+.|+.+++.+..  ...+.+|+.|||||||+|
T Consensus       132 ~~mE~~iL~~L~~------~l~~~tp~~fl~~~~~~~~~~~~~~~~~~~~a~~~le~~l~d~~~~~~~PS~iAaAai~lA  205 (257)
T 1g3n_C          132 IDQEKELLEKLAW------RTEAVLATDVTSFLLLKLVGGSQHLDFWHHEVNTLITKALVDPLTGSLPASIISAAGCALL  205 (257)
T ss_dssp             HHHHHHHHHHTTT------CCCCCCHHHHHHHHHHHHSCSSTTHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCC------cCCCCCHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhCcchhCcCHHHHHHHHHHHH
Confidence            9999999999997      778899999999999999987543    5668888877664  457999999999999999


Q ss_pred             HHhcCC------CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          259 TQLSND------TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       259 ~~~~~~------~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ....+.      +.+.++++..+|+++.+|+.++++|.+.+..
T Consensus       206 ~~~l~~~~~~~~~~w~~~l~~~t~~~~~~l~~c~~~i~~l~~~  248 (257)
T 1g3n_C          206 VPANVIPQDTHSGGVVPQLASILGCDVSVLQAAVEQILTSVSD  248 (257)
T ss_dssp             CCGGGSCC-----CHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCcccchhhHHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            998874      3457899999999999999999999987643

>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between N-terminal and C-TERM domain of kinase, cell cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A* 1xo2_A* 1bu2_A

Probab=99.84  E-value=1.4e-19  Score=160.12  Aligned_cols=182  Identities=18%  Similarity=0.241  Sum_probs=159.9

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhC-CCCCHHHHHHHhc-CCCHHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVAN-GTTKKEI  184 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~-~p~tl~dia~~~~-~v~~~~i  184 (312)
                      ....++|.+++..++|+..+.-.|..|+.++.....+++++...+++||+|+|||.++ .|++++|+..+.+ ..+.++|
T Consensus        53 ~~lvdwl~~v~~~~~l~~etl~lAv~~~DRfls~~~v~~~~lqLv~~acl~iA~K~eE~~~p~~~d~~~~~~~~~~~~~i  132 (254)
T 2f2c_A           53 TILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSCDCFTNLEL  132 (254)
T ss_dssp             HHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTSCCCTTTHHHHHHHHHHHHHHHHCSSCCCHHHHSTTC---CCHHHH
T ss_pred             HHHHHHHHHHHHHHCCCchHHHHHHHHHHHHHccCCcCHHHccHHHHHHHHHHHHhcccCCCCHHHHHHHhCCCCCHHHH
Confidence            4578999999999999999999999999999998888999999999999999999977 5999999987653 3789999


Q ss_pred             HHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHHH----HHHHHHHHHHhhh--ccCCCChHHHHHHHHHHH
Q 021438          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQA----VKAAQEAVQKSED--LDIRRSPISVAAAVIYII  258 (312)
Q Consensus       185 ~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v----~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla  258 (312)
                      .++.+.|.+.|+.      ++...+|..|+.+|+..++++.+.    .+.|+.+++.+..  ...+.+|+.|||||||+|
T Consensus       133 ~~mE~~IL~~L~~------~l~~~tp~~fl~~~~~~~~~~~~~~~~~~~~a~~ll~~~l~d~~~~~~~PS~iAaAai~la  206 (254)
T 2f2c_A          133 INQEKDILEALKW------DTEAVLATDFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPNIALLSPGLICAGGLLTT  206 (254)
T ss_dssp             HHHHHHHHHHTTT------CCCCCCGGGSHHHHHHHTTCCGGGHHHHHHHHHHHHHHHTTSGGGTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCC------cCCCCCHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHHHcCcchhccCHHHHHHHHHHHH
Confidence            9999999999997      778899999999999999988653    4568888876654  457999999999999999


Q ss_pred             HHhcC-CCCC----HHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438          259 TQLSN-DTKP----LKEISIVTRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       259 ~~~~~-~~~~----~~~Ia~~~~vs~~ti~~~~kel~~~~~  294 (312)
                      .+..+ .+.+    +++++..+|+++.+|+.+++.|.+.+.
T Consensus       207 ~~~~~~~~~~w~~~~~~l~~~tg~~~~~l~~c~~~i~~~~~  247 (254)
T 2f2c_A          207 IETDNTNCRPWTCYLEDLSSILNFSTNTVRTVKDQVSEAFS  247 (254)
T ss_dssp             HHTTCCSSCCTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             HHhcCCCCCChHHHHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            99863 4455    789999999999999999999988653

>1w98_B Cyclin E, G1/S-specific cyclin E1; cell cycle, transferase; HET: TPO; 2.15A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1

Probab=99.81  E-value=1.9e-18  Score=155.17  Aligned_cols=176  Identities=14%  Similarity=0.129  Sum_probs=152.2

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhC-CCCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhc-CCCHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQ-KPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN-GTTKKE  183 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~-~~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~-~v~~~~  183 (312)
                      ....++|.+++..+++++.+.-.|..+++++... +.+++++...+++||+|+|||.++. |++++|+..+++ ..+.++
T Consensus        51 ~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~~v~~~~lqlv~~acL~iA~K~eE~~~p~l~~~~~i~~~~~~~~e  130 (283)
T 1w98_B           51 AILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDE  130 (283)
T ss_dssp             HHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTTSSCHHH
T ss_pred             HHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcccCCCcHHHHHHHHcCCCCHHH
Confidence            4578999999999999999999999999999986 5778899999999999999999987 899999998774 378999


Q ss_pred             HHHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHH-----------HHHHHHHHHHHhhh--ccCCCChHHH
Q 021438          184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ-----------AVKAAQEAVQKSED--LDIRRSPISV  250 (312)
Q Consensus       184 i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~-----------v~~~A~~i~~~~~~--l~~Gr~P~~i  250 (312)
                      |.++++.|.+.|+.      ++...+|..|+.+|++.+++++.           ....+.++++.+..  -..+..|+.|
T Consensus       131 i~~mE~~IL~~L~~------~l~~~tp~~fL~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~llelsl~d~~~l~~~PS~i  204 (283)
T 1w98_B          131 ILTMELMIMKALKW------RLSPLTIVSWLNVYMQVAYLNDLHEVLLPQYPQQIFIQIAELLDLCVLDVDCLEFPYGIL  204 (283)
T ss_dssp             HHHHHHHHHHHTTT------CCCCCCHHHHHHHHHHHHTCCSSCCSSSCCSCHHHHHHHHHHHHHHHHSGGGGGSCHHHH
T ss_pred             HHHHHHHHHHHcCC------cCCCCCHHHHHHHHHHHhccCchhhHHHHhhhHHHHHHHHHHHHHHHhhhhhhcCCHHHH
Confidence            99999999999997      77889999999999998876532           22345566666553  4579999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          251 AAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       251 aaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ||||||+|+       .++.+...+|+++.+|+.++++|.+....
T Consensus       205 AaAai~la~-------~~~~l~~~tg~~~~~i~~c~~~l~~~~~~  242 (283)
T 1w98_B          205 AASALYHFS-------SSELMQKVSGYQWCDIENCVKWMVPFAMV  242 (283)
T ss_dssp             HHHHHHHTS-------CHHHHHHHSCCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH-------ChHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            999999985       37889999999999999999999887554

>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens}

Probab=99.79  E-value=6.8e-18  Score=152.99  Aligned_cols=185  Identities=12%  Similarity=0.149  Sum_probs=160.0

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhC-CCCCHHHHHHHhc-CCCHHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVAN-GTTKKEI  184 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~-~p~tl~dia~~~~-~v~~~~i  184 (312)
                      ..+.++|.+++..++|++.+...|..|+++++....+.......++++|+|+|||.++ .|.++.++..+.+ ..+.++|
T Consensus        72 ~~lvdwl~ev~~~~~l~~~t~~lAv~~lDRfls~~~v~~~~lqLv~~tcL~lAsK~eE~~p~~~~~l~~~~~~~~~~~~i  151 (306)
T 3g33_B           72 KMLAYWMLEVCEEQRCEEEVFPLAMNYLDRYLSCVPTRKAQLQLLGAVCMLLASKLRETTPLTIEKLCIYTDHAVSPRQL  151 (306)
T ss_dssp             HHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHCCCCGGGHHHHHHHHHHHHHHHHCSSCCCTTHHHHHTTTSSCHHHH
T ss_pred             HHHHHHHHHHHHHhCCcHhHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHhccCccHHHH
Confidence            4579999999999999999999999999999998888889999999999999999865 5789999998764 3789999


Q ss_pred             HHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHH----HHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHH
Q 021438          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ----AVKAAQEAVQKSED--LDIRRSPISVAAAVIYII  258 (312)
Q Consensus       185 ~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~----v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla  258 (312)
                      .++.+.|.+.|+.      ++...+|..|+.+|+..++++.+    +.+.|+.+++.+..  ...+..|+.|||||||+|
T Consensus       152 ~~mE~~IL~~L~f------~l~~~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~lsl~d~~~l~~~PS~IAaAai~lA  225 (306)
T 3g33_B          152 RDWEVLVLGKLKW------DLAAVIAHDFLAFILHRLSLPRDRQALVKKHAQTFLALCATDYTFAMYPPSMIATGSIGAA  225 (306)
T ss_dssp             HHHHHHHHHHTTT------CCCCCCGGGGHHHHHHTSSCCTTTHHHHHHHHHHHHHHHHHCGGGTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCC------ccCCCCHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhhhhhccCCHHHHHHHHHHHH
Confidence            9999999999997      78889999999999999988743    45678888887654  567999999999999999


Q ss_pred             HHhcCCCCC-----HHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438          259 TQLSNDTKP-----LKEISIVTRVAEGTIKNVYKDLFPHLARII  297 (312)
Q Consensus       259 ~~~~~~~~~-----~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~  297 (312)
                      ....+....     ...++..+|+++.+|+.+++.|.+.+..-+
T Consensus       226 ~~~l~~~~~w~~~w~~~L~~~tg~~~~~l~~c~~~I~~l~~~~l  269 (306)
T 3g33_B          226 VQGLGACSMSGDELTELLAGITGTEVDCLRACQEQIEAALRESL  269 (306)
T ss_dssp             HHTCC---CCHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTC-
T ss_pred             HHHhcCCCCchhhHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            999875432     367889999999999999999999876543

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae}

Probab=99.79  E-value=3.5e-20  Score=148.44  Aligned_cols=66  Identities=32%  Similarity=0.617  Sum_probs=58.7

Q ss_pred             CCCCCCCCCC-CceeeeCCCCceEcCCCcccccCcccccccccccccCCC-CCCCCCccCCCCCCccc
Q 021438            3 DSYCADCKRL-TEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANES-SDHDPVRVGGPLNPLLS   68 (312)
Q Consensus         3 ~~~Cp~Cg~~-~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~~~-~~~~~~r~G~~~~~~~~   68 (312)
                      ...||+||+. +++++|+.+|++||.+||+|++|++||.|||||+|++++ ++.|++|+|+|.+++..
T Consensus        21 ~~~CPECGs~~t~IV~D~erGE~VCsdCGLVLEEriID~GPEWRAFsnDD~~~dDpSRVGAPs~~~~~   88 (197)
T 3k1f_M           21 VLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNXXXXXXXXXXXXXXXXXXXX   88 (197)
T ss_dssp             CCCCTTTCCSSCCEEEEGGGTEEEETTTCBBCCCCCBCHHHHHHHHHCCCTTTTCSCCCBCCBCCHHH
T ss_pred             CeECcCCCCcCCeEEEeCCCCEEEEcCCCCCcCCceeECCCCCcCcCCcccccccccccccccccccc
Confidence            4589999982 479999999999999999999999999999999999765 36789999999987654

>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A

Probab=99.73  E-value=1.9e-18  Score=116.41  Aligned_cols=47  Identities=43%  Similarity=0.777  Sum_probs=43.8

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCcccccccccccccCC
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE   50 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~~   50 (312)
                      ...||+||+ ..+++|+.+|++||..||+|++|++||.|||||+|+++
T Consensus        11 ~~~Cp~C~~-~~lv~D~~~ge~vC~~CGlVl~e~~iD~gpEWR~F~~~   57 (58)
T 1dl6_A           11 RVTCPNHPD-AILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND   57 (58)
T ss_dssp             CCSBTTBSS-SCCEECSSSCCEECTTTCCEECCSCCCCCCSCCCSCCC
T ss_pred             cccCcCCCC-CceeEeCCCCeEEeCCCCCEEeccccccCCcccccCCC
Confidence            458999998 57999999999999999999999999999999999865

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=99.58  E-value=1e-15  Score=100.44  Aligned_cols=44  Identities=34%  Similarity=0.940  Sum_probs=41.9

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccCccccccccccccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFA   48 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~   48 (312)
                      ..||+||+ ..+++|+.+|++||..||+|++++.||.|||||+|+
T Consensus         6 ~~CP~C~~-~~l~~d~~~gelvC~~CG~v~~e~~id~~~ewr~f~   49 (50)
T 1pft_A            6 KVCPACES-AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAFD   49 (50)
T ss_dssp             CSCTTTSC-CCEEEETTTTEEEESSSCCBCCCCCCCCCSSSSCCC
T ss_pred             EeCcCCCC-cceEEcCCCCeEECcccCCcccccccccCCcccccC
Confidence            57999998 589999999999999999999999999999999997

>1f5q_B Gamma herpesvirus cyclin; herpesviral cyclin, cyclin dependent kinase. protein/protein complex, transferase; 2.50A {Murid herpesvirus 4} SCOP: a.74.1.1 a.74.1.1

Probab=99.52  E-value=1.8e-12  Score=114.05  Aligned_cols=180  Identities=8%  Similarity=0.030  Sum_probs=148.6

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhc-CCCHHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN-GTTKKEI  184 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~-~v~~~~i  184 (312)
                      ....++|-+++..++|++.+.-.|..++.++.....+.......++++|+|+|+|.++. |.++.++...++ ..+.++|
T Consensus        50 ~~lvdWl~ev~~~~~l~~eT~~lAv~~lDRfLs~~~v~~~~lqLvg~tcl~iAsK~eE~~p~~~~~l~~~~~~~yt~~~i  129 (252)
T 1f5q_B           50 KVLTTWMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAYMPIKATQLAYLCGGATTADKL  129 (252)
T ss_dssp             HHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHCTTCCHHHH
T ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCCCHHHH
Confidence            35689999999999999999999999999999887777778999999999999998775 889999988765 4789999


Q ss_pred             HHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHH----HHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHH
Q 021438          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ----AVKAAQEAVQKSED--LDIRRSPISVAAAVIYII  258 (312)
Q Consensus       185 ~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~----v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla  258 (312)
                      .++.+.|.+.|+.      ++..++|..|+.+|...++.+.+    +.+.|..++..+.-  -....+|+.|||||+.++
T Consensus       130 ~~mE~~IL~~L~w------~l~~pTp~~FL~~~l~~~~~~~~~~~~~~~~a~~~l~~~l~d~~~l~~~PS~iAaaa~~~~  203 (252)
T 1f5q_B          130 LTLEVKSLDTLSW------VADRCLSTDLICYILHIMHAPREDYLNIYNLCRPKIFCALCDGRSAMKRPVLITLACMHLT  203 (252)
T ss_dssp             HHHHHHHHHHTTT------CCCCCCHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCC------ccCCCCHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHHHhchhhhccCHHHHHHHHHHHH
Confidence            9999999999997      78889999999999999998865    34566776666543  235789999999996544


Q ss_pred             HHhcCCCCC----HHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438          259 TQLSNDTKP----LKEISIVTRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       259 ~~~~~~~~~----~~~Ia~~~~vs~~ti~~~~kel~~~~~  294 (312)
                      .  .+...+    ...++..+|++...++..++.|.+.+.
T Consensus       204 l--~~~~~~~~~~~~~L~~~t~~~~~~l~~C~~~i~~~l~  241 (252)
T 1f5q_B          204 M--NQKYDYYENRIDGVCKSLYITKEELHQCCDLVDIAIV  241 (252)
T ss_dssp             H--TTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHH
T ss_pred             h--ccCCCchhhHHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            3  222222    346788899999999999999888764

>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B*

Probab=99.51  E-value=1.2e-13  Score=117.49  Aligned_cols=89  Identities=28%  Similarity=0.401  Sum_probs=85.5

Q ss_pred             HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHH
Q 021438          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (312)
Q Consensus       108 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~  187 (312)
                      ....+|.++|+.|+||+.+.+.|..+++.+.+.+...|++|..+||||||+||+.+|.|++++||+.++ |+++.+|++.
T Consensus       107 ~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~~~~gr~P~~iAaAaly~A~~~~~~~~t~~ei~~~~-~vs~~ti~~~  185 (200)
T 1ais_B          107 KPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVA-RVTEVTVRNR  185 (200)
T ss_dssp             CGGGGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHH-TCCHHHHHHH
T ss_pred             CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHh-CCCHHHHHHH
Confidence            356889999999999999999999999999999999999999999999999999999999999999999 8999999999


Q ss_pred             HHHHHHHHhh
Q 021438          188 KEFIVKHLEA  197 (312)
Q Consensus       188 ~~~l~~~l~~  197 (312)
                      |+.|.+.|++
T Consensus       186 ~~~l~~~l~~  195 (200)
T 1ais_B          186 YKELVEKLKI  195 (200)
T ss_dssp             HHHHHHHHTC
T ss_pred             HHHHHHHcCC
Confidence            9999999987

>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like fold, helix-turn-helix, transcription/DNA complex; 2.65A {Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A 2phg_A 1vol_A*

Probab=99.32  E-value=1e-11  Score=106.13  Aligned_cols=89  Identities=22%  Similarity=0.305  Sum_probs=85.1

Q ss_pred             HHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHH
Q 021438          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (312)
Q Consensus       108 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~  187 (312)
                      ....+|.++++.|++|+.+.+.|..+++.+.+.+...|++|..+||||||+||+..|.+++++||+.++ ++++.+|++.
T Consensus       101 ~p~~~l~r~~~~l~l~~~~~~~A~~i~~~~~~~~l~~g~~P~~IAaAaiylA~~~~~~~~~~~~i~~~~-~v~~~tI~~~  179 (207)
T 1c9b_A          101 TTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIA-GVADVTIRQS  179 (207)
T ss_dssp             CTHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHHHHHHHTSSSCCCHHHHHHHH-TCCHHHHHHH
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHh-CCCHHHHHHH
Confidence            457889999999999999999999999999999999999999999999999999999999999999999 8999999999


Q ss_pred             HHHHHHHHhh
Q 021438          188 KEFIVKHLEA  197 (312)
Q Consensus       188 ~~~l~~~l~~  197 (312)
                      |+.|.+.++.
T Consensus       180 ~~~l~~~l~~  189 (207)
T 1c9b_A          180 YRLIYPRAPD  189 (207)
T ss_dssp             HHHHGGGHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999886

>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M

Probab=99.00  E-value=1.6e-09  Score=99.26  Aligned_cols=89  Identities=19%  Similarity=0.142  Sum_probs=82.6

Q ss_pred             CCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHH
Q 021438          207 TIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKN  284 (312)
Q Consensus       207 ~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~  284 (312)
                      .......|.++|+.|+||+.+...|..+.+.+..  +..||+..++||||||+||+..+.+++++||+++++++...|.+
T Consensus       126 L~~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~a~~~~~~rGrs~e~vaAAclYiACR~~~~prtl~eI~~~~~v~~keigr  205 (345)
T 4bbr_M          126 VQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLIHVKTKEFGK  205 (345)
T ss_dssp             TTHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTCTTTTTCCHHHHHHHHHHHHHHHTCCBCCHHHHHHHHTCCTTHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHH
Confidence            4556789999999999999999999999999986  88999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhcc
Q 021438          285 VYKDLFPHLAR  295 (312)
Q Consensus       285 ~~kel~~~~~~  295 (312)
                      .|+.|.+.+..
T Consensus       206 ~~k~l~~~L~l  216 (345)
T 4bbr_M          206 TLNIMKNILRG  216 (345)
T ss_dssp             HHHHHHHCC--
T ss_pred             HHHHHHHHhCc
Confidence            99999998875

>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae}

Probab=98.89  E-value=1.7e-10  Score=106.07  Aligned_cols=87  Identities=18%  Similarity=0.262  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHH
Q 021438          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK  188 (312)
Q Consensus       109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~  188 (312)
                      ...+|.++|+.|+|+..+...|..|.+.+.+.++..||+|..+||||||+|++..+.+++.++|+.++ ++++.+|+..|
T Consensus       235 p~~~i~Rf~~~L~l~~~v~~~A~~i~~~~~~~~l~~Gr~P~~IAaAaIylAa~~~~~~~t~~eIa~~~-~Vse~TIr~~y  313 (345)
T 3k7a_M          235 NLTYIPRFCSHLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTL-QVTEGTIKSGY  313 (345)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhchhcCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHH-CCCHHHHHHHH
Confidence            45678899999999999999999999999988888999999999999999999999999999999999 89999999999


Q ss_pred             HHHHHHHh
Q 021438          189 EFIVKHLE  196 (312)
Q Consensus       189 ~~l~~~l~  196 (312)
                      +.|.+.+.
T Consensus       314 kel~~~~~  321 (345)
T 3k7a_M          314 KILYEHRD  321 (345)
T ss_dssp             --------
T ss_pred             HHHHHHHH
Confidence            99998775

>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe}

Probab=98.10  E-value=2.7e-05  Score=67.33  Aligned_cols=85  Identities=12%  Similarity=0.172  Sum_probs=75.3

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCC-CChHHHHHHHHHHHHHhcCCCCCHHHHHHHh--------Ccch
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIR-RSPISVAAAVIYIITQLSNDTKPLKEISIVT--------RVAE  279 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~G-r~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~--------~vs~  279 (312)
                      .++|.+++..|+++..+...|..+.++...  ...+ ++|..|++||+|+||+..+.++++++|+.++        ..+.
T Consensus        32 ~~~i~~v~~~l~L~~~t~~~A~~~~~Rf~~~~~~~~~~~~~lv~~acL~lA~K~Ee~~~~l~d~~~~~~~~~~~~~~~~~  111 (235)
T 1zp2_A           32 WKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKGFSLEALVATCIYLSCKVEECPVHIRTICNEANDLWSLKVKLSR  111 (235)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCSCCCCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHTTCCCSSCCCH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccccCHHHHHHHHHHHHhccccCcccHHHHHHHHHHHccchhhccH
Confidence            468999999999999999999999998765  4455 9999999999999999999999999999876        5788


Q ss_pred             hHHHHHHHHHHhhhcc
Q 021438          280 GTIKNVYKDLFPHLAR  295 (312)
Q Consensus       280 ~ti~~~~kel~~~~~~  295 (312)
                      ..|.+..+.|.+.++-
T Consensus       112 ~~I~~~E~~iL~~L~f  127 (235)
T 1zp2_A          112 SNISEIEFEIISVLDA  127 (235)
T ss_dssp             HHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHCCC
Confidence            8999999999988764

>3h4c_A Transcription factor TFIIB-like; cyclin, transcription factor TFIIB repeat; 2.30A {Trypanosoma brucei brucei}

Probab=97.81  E-value=0.00052  Score=56.54  Aligned_cols=115  Identities=20%  Similarity=0.353  Sum_probs=79.0

Q ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCC---CCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHH
Q 021438          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRG---RNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIG  185 (312)
Q Consensus       109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~g---r~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~  185 (312)
                      ..+.|..+..+-.+|+.+.+.|.++.+.+...+--+|   .+...++|||+.+|....+.|+++.|+--.-  -+..++.
T Consensus        15 M~nclr~L~kKs~~~eaVL~~AieLar~fvg~rR~rgqRvE~q~dVAAAc~miAae~~~~PiplaE~r~lD--~sL~Dve   92 (260)
T 3h4c_A           15 MLNCMRGLHKKAVLPEPVLDRGIELARAFVGGRRARGQRVERQPDVAAACLMIAAEEAQQPLPLAEVRCLD--SSLGDVE   92 (260)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHC--TTCCCHH
T ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHHHhhhhhhhcccccccHHHHHHHHHHHHHHcCCCccHHHHHHHh--hhhhHHH
Confidence            4567788899999999999999999998865433333   4677999999999999999999999997643  2222333


Q ss_pred             HHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhcCCCHH
Q 021438          186 RAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ  226 (312)
Q Consensus       186 ~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~  226 (312)
                      -..-+|.+.++++.... .+...-...++..|..+|+|+-.
T Consensus        93 lrr~Eiv~~l~l~e~e~-rl~~~~~~NLl~~Yv~kL~Lq~s  132 (260)
T 3h4c_A           93 LRRADIVRELHLEDSER-RLRDTFADNLLVKYILKLGLQVS  132 (260)
T ss_dssp             HHHHHHHHHTTCHHHHH-HHHHHHHHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHccCCHHHH-HHHHHhhhhHHHHHHHHhccchh
Confidence            33336666666531100 01111134577788888888743

>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division), ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B* 1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B* 2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B* 2x1n_B* 1vyw_B* ...

Probab=97.56  E-value=0.00024  Score=62.31  Aligned_cols=89  Identities=7%  Similarity=-0.109  Sum_probs=74.7

Q ss_pred             HHHHHHHHHHHhcCCcH-HHHHHHHHHHHHHHhCCC-CCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHH
Q 021438          108 QAFKSISAMSDRLGLVT-TIKDRANEIYKKVEDQKP-LRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIG  185 (312)
Q Consensus       108 ~~~~~I~~~~~~L~Lp~-~v~~~A~~i~~~~~~~~~-~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~  185 (312)
                      ....++..++..++++. .+...|..+......... +-+.++..+||||+|+|++..+.+....++..++ |++..+|.
T Consensus       138 tp~~fl~~~~~~l~~~~~~~~~~a~~l~e~sl~~~~~~~~~~Ps~iAaAai~lA~~~~~~~~w~~~l~~~~-g~~~~~i~  216 (260)
T 2cch_B          138 TVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRKT-GYTLESLK  216 (260)
T ss_dssp             CHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHHHHHHHHHHHHSCCSCHHHHHHH-CCCHHHHH
T ss_pred             CHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHhHHHHhCCCHHHHHHHHHHHHHHHhCCCcchHHHHHHh-CcCHHHHH
Confidence            35788999999999986 777888877777543332 5789999999999999999888888888999888 89999999


Q ss_pred             HHHHHHHHHHhh
Q 021438          186 RAKEFIVKHLEA  197 (312)
Q Consensus       186 ~~~~~l~~~l~~  197 (312)
                      ..++.|.+.+..
T Consensus       217 ~~~~~l~~~~~~  228 (260)
T 2cch_B          217 PCLMDLHQTYLK  228 (260)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999999987754

>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B*

Probab=97.53  E-value=0.00012  Score=64.51  Aligned_cols=87  Identities=8%  Similarity=-0.021  Sum_probs=76.0

Q ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHH
Q 021438          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK  188 (312)
Q Consensus       109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~  188 (312)
                      ...++.+++..++++..+...|..+.........+-+.+|..+||||+|+|++..+.+....++...+ |++..+|...+
T Consensus       138 p~~fl~~~~~~~~~~~~~~~~a~~l~e~sl~~~~~~~~~Ps~iAaAai~lA~~~l~~~~w~~~l~~~t-g~~~~~l~~~~  216 (269)
T 2b9r_A          138 PLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFPPSQIAAGAFSLALKILDNGEWTPTLQHYL-SYTEESLLPVM  216 (269)
T ss_dssp             HHHHHHHHHHSSCCCHHHHHHHHHHHHHGGGCGGGSSSCTTHHHHHHHHHHHHHHTCCCSCTTHHHHS-CCCSSTTTTHH
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhhhcCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHH-CCCHHHHHHHH
Confidence            46788999999999998888898888887766667789999999999999999998887777888888 89999999999


Q ss_pred             HHHHHHHh
Q 021438          189 EFIVKHLE  196 (312)
Q Consensus       189 ~~l~~~l~  196 (312)
                      +.|.+.+.
T Consensus       217 ~~l~~~~~  224 (269)
T 2b9r_A          217 QHLAKNVV  224 (269)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99987764

>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive transcription elongation factor, P-TEFB; 1.50A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1

Probab=97.52  E-value=0.00048  Score=60.11  Aligned_cols=84  Identities=10%  Similarity=0.123  Sum_probs=68.1

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCc--c--------
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRV--A--------  278 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~v--s--------  278 (312)
                      .++|.+++.+|+++.++...|..++++...  ...++++.-|++||+|+||+....++++++|+.++..  +        
T Consensus        45 ~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~qlv~~acL~lA~K~eE~~~~l~d~~~~~~~~~~~~~~~~~~  124 (258)
T 2i53_A           45 ARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFG  124 (258)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHSCHHHHGGGC
T ss_pred             HHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCChhhcCHHHHHHHHHHHHHccccccccHHHHHHHHHHHhchhhhhhhh
Confidence            468899999999999999999999998764  5578999999999999999999988999999876542  2        


Q ss_pred             ---hhHHHHHHHHHHhhhc
Q 021438          279 ---EGTIKNVYKDLFPHLA  294 (312)
Q Consensus       279 ---~~ti~~~~kel~~~~~  294 (312)
                         ...|.+..+.|++.++
T Consensus       125 ~~~~~~i~~~E~~iL~~L~  143 (258)
T 2i53_A          125 DDPKEEVMVLERILLQTIK  143 (258)
T ss_dssp             SCHHHHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHHHHHHHHHCC
Confidence               3455555566666554

>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens}

Probab=97.48  E-value=0.00056  Score=60.76  Aligned_cols=86  Identities=16%  Similarity=0.179  Sum_probs=73.5

Q ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHH
Q 021438          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK  188 (312)
Q Consensus       109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~  188 (312)
                      .+.+|.+++..|++++.+...|..+.........+-+..+..+||||||+|++..+.+.  ..-...+ +++..+|...+
T Consensus       157 P~~fL~~~~~~l~~~~~~~~~A~~~l~~sl~t~~~l~~~Ps~IAaAaiylA~~~~~~~~--~~W~~~~-~~~~~~l~~~~  233 (285)
T 3rgf_B          157 PYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDA--RQWFAEL-SVDMEKILEII  233 (285)
T ss_dssp             SHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSHHHHSCHHHHHHHHHHHHHHHTTCCC--HHHHHTS-CSCHHHHHHHH
T ss_pred             hHHHHHHHHHHhCCCHHHHHHHHHHHHHHHccChhhccCHHHHHHHHHHHHHHHcCCCh--hhHHHHH-CCCHHHHHHHH
Confidence            46788999999999999999999999988766666789999999999999999988754  4566667 79999999999


Q ss_pred             HHHHHHHhh
Q 021438          189 EFIVKHLEA  197 (312)
Q Consensus       189 ~~l~~~l~~  197 (312)
                      +.|......
T Consensus       234 ~~il~ly~~  242 (285)
T 3rgf_B          234 RVILKLYEQ  242 (285)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            998877754

>2ivx_A Cyclin-T2; transcription regulation, cell division, phosphorylation, NU protein, cell cycle, transcription; 1.8A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_A 3mi9_B* 3mia_B* 3tnh_B* 3tni_B* 3blh_B* 3blq_B* 3blr_B* 3lq5_B* 3my1_B* 3tn8_B*

Probab=97.46  E-value=0.00067  Score=59.20  Aligned_cols=66  Identities=6%  Similarity=0.179  Sum_probs=59.1

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhC
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTR  276 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~  276 (312)
                      .++|.+++.+|+++.++...|..++++-..  ...+++|.-|++||+|+||+....++++++|+.++.
T Consensus        35 ~~~i~~v~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~qlv~~acL~lA~K~EE~p~~l~d~~~~~~  102 (257)
T 2ivx_A           35 ANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAH  102 (257)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhCChhhhCHHHHHHHHHHHHhccccCCcCHHHHHHHHH
Confidence            478999999999999999999999998765  557899999999999999999998999999987763

>1jkw_A Cyclin H; cell cycle, cell division, nuclear protein; 2.60A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1kxu_A

Probab=97.44  E-value=0.00095  Score=60.36  Aligned_cols=84  Identities=14%  Similarity=0.065  Sum_probs=68.9

Q ss_pred             HHHHHHHhhcC--CCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcc-------hh
Q 021438          212 DYLRRFCSNLG--MTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVA-------EG  280 (312)
Q Consensus       212 ~~i~r~~~~L~--l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs-------~~  280 (312)
                      .+|.+++..|+  ++..+...|..++++-..  ...+++|..|++||+||||+....++++++++..+...       ..
T Consensus        62 ~~I~ev~~~l~~~Lp~~t~~tA~~~~~RF~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~d~v~~~~~~p~~~~~~~~  141 (323)
T 1jkw_A           62 KRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLGQEKALE  141 (323)
T ss_dssp             HHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHGGGSSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhhCChhhcCHHHHHHHHHHHHHhhhcCCCCHHHHHHHhccChhhhHHHHH
Confidence            57888999999  999999999999998765  55789999999999999999999999999998776544       24


Q ss_pred             HHHHHHHHHHhhhcc
Q 021438          281 TIKNVYKDLFPHLAR  295 (312)
Q Consensus       281 ti~~~~kel~~~~~~  295 (312)
                      .|.+....|.+.++-
T Consensus       142 ~Il~~E~~iL~~L~f  156 (323)
T 1jkw_A          142 QILEYELLLIQQLNF  156 (323)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHCCC
Confidence            566666666666553

>3m03_A ORC6, origin recognition complex subunit 6; helix turn helix, DNA binding protein, origin recognition CO DNA replication; HET: MES; 2.50A {Homo sapiens}

Probab=97.28  E-value=0.0015  Score=47.64  Aligned_cols=80  Identities=16%  Similarity=0.179  Sum_probs=64.9

Q ss_pred             HHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCC------CCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHH
Q 021438          113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLR------GRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGR  186 (312)
Q Consensus       113 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~------gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~  186 (312)
                      |+++|-.||.++ +++.|.+++.++... +..      ..+....+||++|.+||..+...+-..+.+.+ |+++.++.+
T Consensus         6 v~dLcVqfgc~e-~~~~a~~lL~~Yk~~-l~~~~~~~~D~s~P~f~aaA~~~acr~~K~kVdK~KL~~~s-~lk~~~f~~   82 (95)
T 3m03_A            6 IRDLAVQFSCIE-AVNMASKILKSYESS-LPQTQQVDLDLSRPLFTSAALLSACKILKLKVDKNKMVATS-GVKKAIFDR   82 (95)
T ss_dssp             HHHHHHHHTCGG-GHHHHHHHHHHHHTT-SCHHHHHHCCTTSHHHHHHHHHHHHHHTTCCCCHHHHHHTT-CBCHHHHHH
T ss_pred             HHHHHHHhCCHH-HHHHHHHHHHHHHHH-hHHHhhccccccccHHHHHHHHHHHHHHccCCCHHHHHHHH-CCCHHHHHH
Confidence            788999999997 888899998887533 211      23455789999999999999999999999988 899999888


Q ss_pred             HHHHHHHHH
Q 021438          187 AKEFIVKHL  195 (312)
Q Consensus       187 ~~~~l~~~l  195 (312)
                      ....+.+..
T Consensus        83 l~~~~e~~~   91 (95)
T 3m03_A           83 LCKQLEKIG   91 (95)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            877776554

>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P- TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 2w2h_C

Probab=97.14  E-value=0.0011  Score=60.93  Aligned_cols=65  Identities=17%  Similarity=0.218  Sum_probs=58.4

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHh
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVT  275 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~  275 (312)
                      .++|.+++..|+|+.++...|..++++...  ...+++|.-|++||+||||+....++++++|..++
T Consensus        42 v~wI~ev~~~l~L~~~t~~tAv~~~dRFl~~~sv~~~~~qlva~acLfLA~K~EE~p~~l~d~v~v~  108 (358)
T 2pk2_A           42 ANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFPGNSVAPAALFLAAKVEEQPKKLEHVIKVA  108 (358)
T ss_dssp             HHHHHHHHTTTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHTTH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHhhccCCCCHHHHHHHH
Confidence            578999999999999999999999998765  55789999999999999999999988999998665

>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between N-terminal and C-TERM domain of kinase, cell cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A* 1xo2_A* 1bu2_A

Probab=97.00  E-value=0.0023  Score=55.66  Aligned_cols=86  Identities=12%  Similarity=0.140  Sum_probs=66.5

Q ss_pred             HHHHHHHHHhcCCcHHH----HHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHh-CCCCC----HHHHHHHhcCCC
Q 021438          110 FKSISAMSDRLGLVTTI----KDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE-NKPRT----VKEFCSVANGTT  180 (312)
Q Consensus       110 ~~~I~~~~~~L~Lp~~v----~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~-~~p~t----l~dia~~~~~v~  180 (312)
                      +.++..++..++++...    ...|..+.........+-+.++..+||||+|+|.+.. +.|.+    ..++..++ |++
T Consensus       153 ~~fl~~~~~~~~~~~~~~~~~~~~a~~ll~~~l~d~~~~~~~PS~iAaAai~la~~~~~~~~~~w~~~~~~l~~~t-g~~  231 (254)
T 2f2c_A          153 TDFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPNIALLSPGLICAGGLLTTIETDNTNCRPWTCYLEDLSSIL-NFS  231 (254)
T ss_dssp             GGSHHHHHHHTTCCGGGHHHHHHHHHHHHHHHTTSGGGTTSCHHHHHHHHHHHHHHTTCCSSCCTHHHHHHHHHHH-TCC
T ss_pred             HHHHHHHHHHcCCChhhHHHHHHHHHHHHHHHHcCcchhccCHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHH-CcC
Confidence            45778888888887643    3456666655544444568899999999999999986 44556    78888888 899


Q ss_pred             HHHHHHHHHHHHHHHh
Q 021438          181 KKEIGRAKEFIVKHLE  196 (312)
Q Consensus       181 ~~~i~~~~~~l~~~l~  196 (312)
                      ..+|...++.|.+.+.
T Consensus       232 ~~~l~~c~~~i~~~~~  247 (254)
T 2f2c_A          232 TNTVRTVKDQVSEAFS  247 (254)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999988775

>2w96_A G1/S-specific cyclin-D1; serine/threonine-protein kinase, chromosomal rearrangement, ATP-binding, transferase, polymorphism, cell division; 2.30A {Homo sapiens} PDB: 2w99_A 2w9f_A 2w9z_A

Probab=96.98  E-value=0.0046  Score=54.33  Aligned_cols=85  Identities=8%  Similarity=0.142  Sum_probs=72.3

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHhC--cchhHHHHH
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSND-TKPLKEISIVTR--VAEGTIKNV  285 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~-~~~~~~Ia~~~~--vs~~ti~~~  285 (312)
                      .+++.+++.+++++.++...|..++++-..  -...+++.-+++||+|+|++..+. +.+.++++..++  .+...|.+.
T Consensus        61 v~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~v~~~~lqlv~~acL~iAsK~EE~~p~~~~~~~~~~~~~~~~~eI~~m  140 (271)
T 2w96_A           61 ATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRPEELLQM  140 (271)
T ss_dssp             HHHHHHHHHHTTCCTTHHHHHHHHHHHHHTTSCCCTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTTSSCHHHHHHH
T ss_pred             HHHHHHHHHHHCCchhHHHHHHHHHHHhCCcCCcCHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCHHHHHHH
Confidence            357778888899999898899999888665  346788999999999999999986 788999998864  788999999


Q ss_pred             HHHHHhhhcc
Q 021438          286 YKDLFPHLAR  295 (312)
Q Consensus       286 ~kel~~~~~~  295 (312)
                      .+.|.+.++-
T Consensus       141 E~~IL~~L~~  150 (271)
T 2w96_A          141 ELLLVNKLKW  150 (271)
T ss_dssp             HHHHHHHTTT
T ss_pred             HHHHHHHCCC
Confidence            9999998764

>1g3n_C V-cyclin; cyclin-dependent kinase, INK4 inhibitor, viral cyclin, cell cycle, signaling protein; 2.90A {Human herpesvirus 8} SCOP: a.74.1.1 a.74.1.1

Probab=96.89  E-value=0.0024  Score=55.68  Aligned_cols=88  Identities=16%  Similarity=0.035  Sum_probs=68.9

Q ss_pred             HHHHHHHHHHhcCCcHHH----HHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCC------CCCHHHHHHHhcC
Q 021438          109 AFKSISAMSDRLGLVTTI----KDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK------PRTVKEFCSVANG  178 (312)
Q Consensus       109 ~~~~I~~~~~~L~Lp~~v----~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~------p~tl~dia~~~~~  178 (312)
                      .+.++..++..++++...    ...|..+.........+-+.++..+||||+|+|.+..+.      +....++...+ |
T Consensus       151 p~~fl~~~~~~~~~~~~~~~~~~~~a~~~le~~l~d~~~~~~~PS~iAaAai~lA~~~l~~~~~~~~~~w~~~l~~~t-~  229 (257)
T 1g3n_C          151 ATDVTSFLLLKLVGGSQHLDFWHHEVNTLITKALVDPLTGSLPASIISAAGCALLVPANVIPQDTHSGGVVPQLASIL-G  229 (257)
T ss_dssp             HHHHHHHHHHHHSCSSTTHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHCCGGGSCC-----CHHHHHHHHH-T
T ss_pred             HHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhCcchhCcCHHHHHHHHHHHHHHHhCCCcccchhhHHHHHHHHH-C
Confidence            567888899999887543    455666666555445567899999999999999988875      34567888888 8


Q ss_pred             CCHHHHHHHHHHHHHHHhh
Q 021438          179 TTKKEIGRAKEFIVKHLEA  197 (312)
Q Consensus       179 v~~~~i~~~~~~l~~~l~~  197 (312)
                      ++..+|...++.|.+.+..
T Consensus       230 ~~~~~l~~c~~~i~~l~~~  248 (257)
T 1g3n_C          230 CDVSVLQAAVEQILTSVSD  248 (257)
T ss_dssp             CCHHHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHHHH
Confidence            9999999999999988764

>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}

Probab=96.87  E-value=0.00079  Score=46.39  Aligned_cols=30  Identities=20%  Similarity=0.493  Sum_probs=26.5

Q ss_pred             CCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      +...||.|++  .+.++..+|.++|..||...
T Consensus         7 ~iL~CP~ck~--~L~~~~~~~~LiC~~cg~~Y   36 (70)
T 2js4_A            7 DILVCPVCKG--RLEFQRAQAELVCNADRLAF   36 (70)
T ss_dssp             CCCBCTTTCC--BEEEETTTTEEEETTTTEEE
T ss_pred             hheECCCCCC--cCEEeCCCCEEEcCCCCcee
Confidence            4568999998  58999999999999999885

>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}

Probab=96.80  E-value=0.0009  Score=45.83  Aligned_cols=30  Identities=10%  Similarity=0.159  Sum_probs=26.4

Q ss_pred             CCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      +...||.|++  .+.++...|.++|..||...
T Consensus         7 ~iL~CP~ck~--~L~~~~~~~~LiC~~cg~~Y   36 (68)
T 2jr6_A            7 DILVCPVTKG--RLEYHQDKQELWSRQAKLAY   36 (68)
T ss_dssp             CCCBCSSSCC--BCEEETTTTEEEETTTTEEE
T ss_pred             hheECCCCCC--cCeEeCCCCEEEcCCCCcEe
Confidence            4568999997  58899899999999999885

>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1

Probab=96.77  E-value=0.00098  Score=45.47  Aligned_cols=30  Identities=13%  Similarity=0.066  Sum_probs=26.2

Q ss_pred             CCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      +...||.|++  .+.+|..+|.++|..||...
T Consensus         9 eiL~CP~ck~--~L~~~~~~g~LvC~~c~~~Y   38 (67)
T 2jny_A            9 EVLACPKDKG--PLRYLESEQLLVNERLNLAY   38 (67)
T ss_dssp             CCCBCTTTCC--BCEEETTTTEEEETTTTEEE
T ss_pred             HHhCCCCCCC--cCeEeCCCCEEEcCCCCccc
Confidence            4458999998  58999999999999999875

>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1

Probab=96.65  E-value=0.00092  Score=45.93  Aligned_cols=30  Identities=20%  Similarity=0.330  Sum_probs=26.0

Q ss_pred             CCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      +...||.|++  .+.++..+|.++|..||...
T Consensus         7 eiL~CP~ck~--~L~~~~~~~~LiC~~cg~~Y   36 (69)
T 2pk7_A            7 DILACPICKG--PLKLSADKTELISKGAGLAY   36 (69)
T ss_dssp             GTCCCTTTCC--CCEECTTSSEEEETTTTEEE
T ss_pred             hheeCCCCCC--cCeEeCCCCEEEcCCCCcEe
Confidence            3468999998  58888889999999999885

>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4

Probab=96.64  E-value=0.00093  Score=44.79  Aligned_cols=31  Identities=32%  Similarity=0.771  Sum_probs=28.5

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .+||.|+. ..+|++..+-.+.|..||.++.+
T Consensus         8 VKCp~C~n-iq~VFShA~tvV~C~~Cg~~L~~   38 (66)
T 1qxf_A            8 VKCPDCEH-EQVIFDHPSTIVKCIICGRTVAE   38 (66)
T ss_dssp             EECTTTCC-EEEEESSCSSCEECSSSCCEEEE
T ss_pred             EECCCCCC-ceEEEecCceEEEcccCCCEEee
Confidence            58999998 68999999999999999999964

>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1

Probab=96.60  E-value=0.00082  Score=46.04  Aligned_cols=29  Identities=34%  Similarity=0.592  Sum_probs=25.6

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      ...||.|++  .+.++..+|.++|..||...
T Consensus         8 iL~CP~ck~--~L~~~~~~~~LiC~~cg~~Y   36 (68)
T 2hf1_A            8 ILVCPLCKG--PLVFDKSKDELICKGDRLAF   36 (68)
T ss_dssp             ECBCTTTCC--BCEEETTTTEEEETTTTEEE
T ss_pred             heECCCCCC--cCeEeCCCCEEEcCCCCcEe
Confidence            458999997  58899899999999999885

>1w98_B Cyclin E, G1/S-specific cyclin E1; cell cycle, transferase; HET: TPO; 2.15A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1

Probab=96.55  E-value=0.016  Score=51.24  Aligned_cols=85  Identities=14%  Similarity=0.187  Sum_probs=72.7

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh---ccCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHhC--cchhHHHH
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED---LDIRRSPISVAAAVIYIITQLSND-TKPLKEISIVTR--VAEGTIKN  284 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~---l~~Gr~P~~iaaAaiyla~~~~~~-~~~~~~Ia~~~~--vs~~ti~~  284 (312)
                      .++|..++.+++++.++...|..++++...   ...++.+.-+++||+|+|++.... ..+.++++.+++  .+...|.+
T Consensus        54 v~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~~v~~~~lqlv~~acL~iA~K~eE~~~p~l~~~~~i~~~~~~~~ei~~  133 (283)
T 1w98_B           54 LDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDEILT  133 (283)
T ss_dssp             HHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTTSSCHHHHHH
T ss_pred             HHHHHHHHHHhCCCccHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcccCCCcHHHHHHHHcCCCCHHHHHH
Confidence            367888999999999999999999998664   346889999999999999999875 677999998874  78889999


Q ss_pred             HHHHHHhhhcc
Q 021438          285 VYKDLFPHLAR  295 (312)
Q Consensus       285 ~~kel~~~~~~  295 (312)
                      ..+.|.+.++-
T Consensus       134 mE~~IL~~L~~  144 (283)
T 1w98_B          134 MELMIMKALKW  144 (283)
T ss_dssp             HHHHHHHHTTT
T ss_pred             HHHHHHHHcCC
Confidence            99999988764

>3j20_W 30S ribosomal protein S27E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=96.54  E-value=0.0012  Score=43.91  Aligned_cols=31  Identities=35%  Similarity=0.754  Sum_probs=28.5

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .+||.|+. ..+|+++.+-.+.|..||.++.+
T Consensus        16 VkCp~C~~-~q~VFSha~t~V~C~~Cgt~L~~   46 (63)
T 3j20_W           16 VKCIDCGN-EQIVFSHPATKVRCLICGATLVE   46 (63)
T ss_dssp             EECSSSCC-EEEEESSCSSCEECSSSCCEEEE
T ss_pred             EECCCCCC-eeEEEecCCeEEEccCcCCEEec
Confidence            47999998 68999999999999999999975

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=96.48  E-value=0.001  Score=47.37  Aligned_cols=30  Identities=23%  Similarity=0.496  Sum_probs=26.7

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      ..||.||+  +.++|...|.+.|..||.++..
T Consensus        28 y~Cp~CG~--~~v~r~atGiW~C~~Cg~~~ag   57 (83)
T 1vq8_Z           28 HACPNCGE--DRVDRQGTGIWQCSYCDYKFTG   57 (83)
T ss_dssp             EECSSSCC--EEEEEEETTEEEETTTCCEEEC
T ss_pred             CcCCCCCC--cceeccCCCeEECCCCCCEecC
Confidence            47999997  5889999999999999998764

>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6

Probab=96.21  E-value=0.0022  Score=44.86  Aligned_cols=31  Identities=26%  Similarity=0.769  Sum_probs=28.4

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .+||.|+. ..+|+++.+-.+.|..||.|+-+
T Consensus        33 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~   63 (81)
T 2xzm_6           33 VKCAQCQN-IQMIFSNAQSTIICEKCSAILCK   63 (81)
T ss_dssp             EECSSSCC-EEEEETTCSSCEECSSSCCEEEE
T ss_pred             eECCCCCC-eeEEEecCccEEEccCCCCEEee
Confidence            47999998 68999999999999999999964

>2r7g_A PP110, retinoblastoma-associated protein, P105-RB, RB; retinoblastoma protein, E2F displacement, transcription repressor; 1.67A {Homo sapiens} SCOP: a.74.1.3 a.74.1.3 PDB: 1n4m_A 3pom_A 1gh6_B 1gux_A 1o9k_A 1ad6_A 1gux_B 1o9k_B

Probab=96.13  E-value=0.015  Score=52.58  Aligned_cols=71  Identities=14%  Similarity=0.253  Sum_probs=59.4

Q ss_pred             HHHHHHHHHHHHhcCCcH-HHHHHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhc
Q 021438          107 IQAFKSISAMSDRLGLVT-TIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVAN  177 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~-~v~~~A~~i~~~~~~--~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~  177 (312)
                      .-|...|+.+|+.|+++. .+.+.+..+|..+..  ..++++|..+.++.+|+|..||..+...++++|.....
T Consensus       216 ~La~~Rl~~LC~~L~~~~~~~~~~iWt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~tF~~Ii~~Yr  289 (347)
T 2r7g_A          216 RLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYK  289 (347)
T ss_dssp             HHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHhChHhhcCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence            347888999999998875 566677777766644  36779999999999999999999999999999998764

>3u5c_b RP61, YS20, 40S ribosomal protein S27-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_X 3u5g_b

Probab=96.12  E-value=0.0025  Score=44.60  Aligned_cols=31  Identities=26%  Similarity=0.654  Sum_probs=28.5

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .+||.|+. ..+|+++.+-.+.|..||.|+.+
T Consensus        35 VkCp~C~~-~q~VFSha~t~V~C~~Cg~~L~~   65 (82)
T 3u5c_b           35 VKCPGCLN-ITTVFSHAQTAVTCESCSTILCT   65 (82)
T ss_dssp             EECTTSCS-CEEEESBCSSCCCCSSSCCCCEE
T ss_pred             EECCCCCC-eeEEEecCCeEEEccccCCEEec
Confidence            47999998 68999999999999999999975

>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens}

Probab=96.12  E-value=0.017  Score=51.62  Aligned_cols=87  Identities=14%  Similarity=0.125  Sum_probs=64.2

Q ss_pred             HHHHHHHHHhcCCcHH----HHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-----HHHHHHHhcCCC
Q 021438          110 FKSISAMSDRLGLVTT----IKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRT-----VKEFCSVANGTT  180 (312)
Q Consensus       110 ~~~I~~~~~~L~Lp~~----v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~t-----l~dia~~~~~v~  180 (312)
                      +.+|..+...++++..    +...|..+.........+-+.++..+||||||+|.+..+....     ...+..++ |++
T Consensus       172 ~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~lsl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~w~~~w~~~L~~~t-g~~  250 (306)
T 3g33_B          172 HDFLAFILHRLSLPRDRQALVKKHAQTFLALCATDYTFAMYPPSMIATGSIGAAVQGLGACSMSGDELTELLAGIT-GTE  250 (306)
T ss_dssp             GGGHHHHHHTSSCCTTTHHHHHHHHHHHHHHHHHCGGGTTSCHHHHHHHHHHHHHHTCC---CCHHHHHHHHHHHH-TCC
T ss_pred             HHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhhhhhccCCHHHHHHHHHHHHHHHhcCCCCchhhHHHHHHHHH-CCC
Confidence            4577888888888643    4456666666554444566899999999999999997764322     25667778 899


Q ss_pred             HHHHHHHHHHHHHHHhh
Q 021438          181 KKEIGRAKEFIVKHLEA  197 (312)
Q Consensus       181 ~~~i~~~~~~l~~~l~~  197 (312)
                      ..+|...++.|.+.+..
T Consensus       251 ~~~l~~c~~~I~~l~~~  267 (306)
T 3g33_B          251 VDCLRACQEQIEAALRE  267 (306)
T ss_dssp             HHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999988864

>4ell_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor, cell cycle; 1.98A {Homo sapiens}

Probab=96.12  E-value=0.014  Score=54.03  Aligned_cols=70  Identities=14%  Similarity=0.268  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHHhcCCcH-HHHHHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhc
Q 021438          108 QAFKSISAMSDRLGLVT-TIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVAN  177 (312)
Q Consensus       108 ~~~~~I~~~~~~L~Lp~-~v~~~A~~i~~~~~~--~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~  177 (312)
                      -|...|+.+|++|++++ .+.+....+|.-...  ..++++|..+.++.+|+|..||..+..++++||....+
T Consensus       281 LAa~Rl~~LC~~L~~~~~~l~~~IWt~fe~~l~~~teLm~dRHLDQiiLCsiY~i~Kv~~~~~tFk~Ii~~Yr  353 (411)
T 4ell_A          281 LAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYK  353 (411)
T ss_dssp             HHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHhhhHhhccccHHHHHHHHHHHHHhhccCCCCHHHHHHHHH
Confidence            47889999999999875 566676666666543  46779999999999999999999999999999998764

>2akl_A PHNA-like protein PA0128; two domains, Zn binding protein, beta-strand protein, structural genomics, PSI; NMR {Pseudomonas aeruginosa PAO1} SCOP: b.34.11.2 g.41.3.5

Probab=95.94  E-value=0.014  Score=44.50  Aligned_cols=29  Identities=21%  Similarity=0.431  Sum_probs=21.4

Q ss_pred             CCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      +...||.|++ .-.-+|  ...+||.+||.--
T Consensus        26 ~lP~CP~C~s-eytYeD--g~l~vCPeC~hEW   54 (138)
T 2akl_A           26 TLPPCPQCNS-EYTYED--GALLVCPECAHEW   54 (138)
T ss_dssp             CSCCCTTTCC-CCCEEC--SSSEEETTTTEEE
T ss_pred             cCCCCCCCCC-cceEec--CCeEECCcccccc
Confidence            4678999999 334444  5579999999754

>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=95.87  E-value=0.0034  Score=44.35  Aligned_cols=31  Identities=32%  Similarity=0.630  Sum_probs=28.6

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .+||.|+. ..+|+++.+-.+.|..||.|+-+
T Consensus        37 VkCp~C~~-~~~VFShA~t~V~C~~CgtvL~~   67 (86)
T 3iz6_X           37 VKCQGCFN-ITTVFSHSQTVVVCPGCQTVLCQ   67 (86)
T ss_dssp             EECTTTCC-EEEEETTCSSCCCCSSSCCCCSC
T ss_pred             EECCCCCC-eeEEEecCCcEEEccCCCCEeec
Confidence            57999998 68999999999999999999975

>2qdj_A Retinoblastoma-associated protein; cyclin fold, cyclin wedge, antitumor protein; 2.00A {Homo sapiens}

Probab=95.82  E-value=0.044  Score=48.74  Aligned_cols=71  Identities=15%  Similarity=0.287  Sum_probs=53.3

Q ss_pred             HHHHHHHhcCCcHHHHHHHHHHHHHHHhC-C---CCCCCCHHHHHHHHHHHHHH-HhCCCCCHHHHHHHhcCCCHHHH
Q 021438          112 SISAMSDRLGLVTTIKDRANEIYKKVEDQ-K---PLRGRNQEAIVAACLYIACR-QENKPRTVKEFCSVANGTTKKEI  184 (312)
Q Consensus       112 ~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~-~---~~~gr~~~~iaaAcly~acr-~~~~p~tl~dia~~~~~v~~~~i  184 (312)
                      ....+|+.|+|++.+.+.|..+|+.+... +   ...+. ....-.||||+||. .++...||-.+.+.+ +++..++
T Consensus         5 rF~~lC~~Lnld~~~~~~Aw~~~~~~~~~~~~~~~~~~~-~~~~w~acLY~a~~~~~~n~vsLt~LLr~~-~lsi~~F   80 (304)
T 2qdj_A            5 DFTALCQKLKIPDHVRERAWLTWEKVSSVDGVLGGYIQK-KKELWGICIFIAAVDLDEMSFTFTELQKNI-EISVHKF   80 (304)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHC----------C-HHHHHHHHHHHHHHHHTCCCSCHHHHHHHH-TCCHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCCccc-hHHHHHHhHHHHhhccCCCcCcHHHHHHHc-CCCHHHH
Confidence            45688999999999999999999998764 2   22333 44455556999997 467789999999998 6887665

>3m03_A ORC6, origin recognition complex subunit 6; helix turn helix, DNA binding protein, origin recognition CO DNA replication; HET: MES; 2.50A {Homo sapiens}

Probab=95.74  E-value=0.056  Score=39.24  Aligned_cols=79  Identities=14%  Similarity=0.166  Sum_probs=59.4

Q ss_pred             HHHHHhhcCCCHHHHHHHHHHHHHhhh-cc-------CCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHH
Q 021438          214 LRRFCSNLGMTNQAVKAAQEAVQKSED-LD-------IRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNV  285 (312)
Q Consensus       214 i~r~~~~L~l~~~v~~~A~~i~~~~~~-l~-------~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~  285 (312)
                      |..+|-.||.++ +.+.|.+|++.-+. +.       ...+|. .++||+|.+|+.+..+++...+...+|+++.-..+-
T Consensus         6 v~dLcVqfgc~e-~~~~a~~lL~~Yk~~l~~~~~~~~D~s~P~-f~aaA~~~acr~~K~kVdK~KL~~~s~lk~~~f~~l   83 (95)
T 3m03_A            6 IRDLAVQFSCIE-AVNMASKILKSYESSLPQTQQVDLDLSRPL-FTSAALLSACKILKLKVDKNKMVATSGVKKAIFDRL   83 (95)
T ss_dssp             HHHHHHHHTCGG-GHHHHHHHHHHHHTTSCHHHHHHCCTTSHH-HHHHHHHHHHHHTTCCCCHHHHHHTTCBCHHHHHHH
T ss_pred             HHHHHHHhCCHH-HHHHHHHHHHHHHHHhHHHhhccccccccH-HHHHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHH
Confidence            345666777776 66777777776443 21       223454 567999999999999999999999999999999888


Q ss_pred             HHHHHhhhc
Q 021438          286 YKDLFPHLA  294 (312)
Q Consensus       286 ~kel~~~~~  294 (312)
                      .+.+.....
T Consensus        84 ~~~~e~~~~   92 (95)
T 3m03_A           84 CKQLEKIGQ   92 (95)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHH
Confidence            887766543

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=95.64  E-value=0.0069  Score=38.73  Aligned_cols=28  Identities=21%  Similarity=0.614  Sum_probs=21.4

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      ..||.||+ +-+..+ ......|..||.+.
T Consensus        20 k~CP~CG~-~~fm~~-~~~R~~C~kCG~t~   47 (50)
T 3j20_Y           20 KFCPRCGP-GVFMAD-HGDRWACGKCGYTE   47 (50)
T ss_dssp             EECSSSCS-SCEEEE-CSSEEECSSSCCEE
T ss_pred             ccCCCCCC-ceEEec-CCCeEECCCCCCEE
Confidence            57999998 444444 45889999999873

>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens}

Probab=95.53  E-value=0.044  Score=53.55  Aligned_cols=71  Identities=14%  Similarity=0.255  Sum_probs=59.9

Q ss_pred             HHHHHHHHHHHHhcCCc-HHHHHHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhc
Q 021438          107 IQAFKSISAMSDRLGLV-TTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVAN  177 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp-~~v~~~A~~i~~~~~~--~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~  177 (312)
                      .-|..+|+.+|+.|+++ +.+.+.+..+|.....  ..++++|..+.++.+|+|..||..+..+++++|.....
T Consensus       525 ~LAa~Rl~~LC~~L~~~~~~i~~~IWt~fe~~l~~~t~L~~dRHLDQiilCsiY~icKv~~~~ltFk~Ii~~Yr  598 (656)
T 4elj_A          525 RLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYK  598 (656)
T ss_dssp             HHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHHHHHCGGGSTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhccCCcCHHHHHHHHH
Confidence            34789999999999887 4677777777766644  36779999999999999999999999999999998654

>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8

Probab=95.11  E-value=0.012  Score=38.43  Aligned_cols=28  Identities=21%  Similarity=0.646  Sum_probs=21.4

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      +..||.||+ .-+ .....+...|..||+.
T Consensus        18 ~~fCPkCG~-~~~-ma~~~dr~~C~kCgyt   45 (55)
T 2k4x_A           18 HRFCPRCGP-GVF-LAEHADRYSCGRCGYT   45 (55)
T ss_dssp             SCCCTTTTT-TCC-CEECSSEEECTTTCCC
T ss_pred             cccCcCCCC-cee-EeccCCEEECCCCCCE
Confidence            568999998 333 3344579999999997

>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}

Probab=94.39  E-value=0.034  Score=36.36  Aligned_cols=28  Identities=25%  Similarity=0.647  Sum_probs=22.8

Q ss_pred             CCCCCCCCCCCCceeeeCCCCceEcC--CCcccc
Q 021438            2 ADSYCADCKRLTEVVFDHSAGDTICS--ECGLVL   33 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~--~CG~Vv   33 (312)
                      +...||.|++  .+..+.  |+++|.  +||...
T Consensus         9 ~iL~CP~c~~--~L~~~~--~~L~C~~~~c~~~Y   38 (56)
T 2kpi_A            9 EILACPACHA--PLEERD--AELICTGQDCGLAY   38 (56)
T ss_dssp             TSCCCSSSCS--CEEEET--TEEEECSSSCCCEE
T ss_pred             hheeCCCCCC--cceecC--CEEEcCCcCCCcEE
Confidence            3458999998  477764  999999  999874

>2r7g_A PP110, retinoblastoma-associated protein, P105-RB, RB; retinoblastoma protein, E2F displacement, transcription repressor; 1.67A {Homo sapiens} SCOP: a.74.1.3 a.74.1.3 PDB: 1n4m_A 3pom_A 1gh6_B 1gux_A 1o9k_A 1ad6_A 1gux_B 1o9k_B

Probab=93.42  E-value=1.4  Score=39.66  Aligned_cols=127  Identities=17%  Similarity=0.117  Sum_probs=85.7

Q ss_pred             HHHHHHHHHHHHHHh----------CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH-----------Hhh-h-hc-----
Q 021438          149 EAIVAACLYIACRQE----------NKPRTVKEFCSVANGTTKKEIGRAKEFIVKH-----------LEA-E-MG-----  200 (312)
Q Consensus       149 ~~iaaAcly~acr~~----------~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~-----------l~~-~-~~-----  200 (312)
                      .++.|.|+=++..-+          ...+++--|.+++ +++..++.+++..+.++           |+. + ..     
T Consensus       105 ~sLlACc~EiVl~ay~~~~~~~~~~~~~~~FP~il~~~-~i~afdf~KVIE~fVr~e~~LprelvkHL~~iEe~iLesla  183 (347)
T 2r7g_A          105 MSLLACALEVVMATYSRSTSQNLDSGTDLSFPWILNVL-NLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESLA  183 (347)
T ss_dssp             HHHHHHHHHHHHHHHHHHC------CCCCCTTHHHHHH-TCCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHTGG
T ss_pred             HHHHHHHHHHHHHHhcccccccccccccCCCcHHHHhc-CCChHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHH
Confidence            467777776655433          3367888899999 79999999987655443           321 0 00     


Q ss_pred             ---cc--cc-c----C----CCC-----------HHHHHHHHHhhcCCCH-HHHHHHHHHHHHhhh----ccCCCChHHH
Q 021438          201 ---QS--VE-M----G----TIH-----------ASDYLRRFCSNLGMTN-QAVKAAQEAVQKSED----LDIRRSPISV  250 (312)
Q Consensus       201 ---~~--~~-~----~----~~~-----------p~~~i~r~~~~L~l~~-~v~~~A~~i~~~~~~----l~~Gr~P~~i  250 (312)
                         .+  ++ +    +    ...           ...=+..+|++|+++. ++.+.+|.+.+.+..    |..+|+-.-|
T Consensus       184 W~~~S~L~~~l~~~~~~~g~~~sl~~f~rKvy~La~~Rl~~LC~~L~~~~~~~~~~iWt~fe~~l~~~t~L~~dRHLDQi  263 (347)
T 2r7g_A          184 WLSDSPLFDLIKQSKDREGKSTSLSLFYKKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQI  263 (347)
T ss_dssp             GSTTCTHHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCGGGGTTSCHHHH
T ss_pred             hccCCHHHHHHHhccccCCcccHHHHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHhChHhhcCCcHHHH
Confidence               00  00 0    0    000           1122566788887654 567778887777653    8899999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHhC
Q 021438          251 AAAVIYIITQLSNDTKPLKEISIVTR  276 (312)
Q Consensus       251 aaAaiyla~~~~~~~~~~~~Ia~~~~  276 (312)
                      .-.|||..|+..+..++.++|=+.-.
T Consensus       264 ilCaiY~i~Kv~~~~~tF~~Ii~~Yr  289 (347)
T 2r7g_A          264 MMCSMYGICKVKNIDLKFKIIVTAYK  289 (347)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHT
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence            99999999999998899998876543

>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens}

Probab=93.22  E-value=0.53  Score=45.99  Aligned_cols=72  Identities=14%  Similarity=0.188  Sum_probs=56.3

Q ss_pred             HHHHHHHHhcCCcHHHHHHHHHHHHHHHh-CCC----CCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHH
Q 021438          111 KSISAMSDRLGLVTTIKDRANEIYKKVED-QKP----LRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (312)
Q Consensus       111 ~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~-~~~----~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i  184 (312)
                      .....+|..|++++.+.++|.+.|..+.. .+.    +.| ....+.|+.+|.||+.+|...||-.+.+.+ +++..++
T Consensus         6 ~~f~~lC~~Ln~d~~~~~~Aw~~~~~~~~~~~~l~~tleg-~~~~W~aC~ly~~~~~~gn~vsLt~lLr~~-~lsl~~F   82 (656)
T 4elj_A            6 PDFTALCQKLKIPDHVRERAWLTWEKVSSVDGVLGGYIQK-KKELWGICIFIAAVDLDEMSFTFTELQKNI-EISVHKF   82 (656)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCSCC-----C-CHHHHHHHHHHHHHHTTCCCSCHHHHHHHH-TCCHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHHHhccccccCCccc-chHHhhhhhheeeeeccCCeeeHHHHHHHh-cCCHHHH
Confidence            34678899999999999999999999974 222    233 455667777888888899999999999988 6886544

>2k5r_A Uncharacterized protein XF2673; solution structure, structural genomics, PSI-2, protein structure initiative; NMR {Xylella fastidiosa TEMECULA1}

Probab=93.03  E-value=0.045  Score=39.93  Aligned_cols=31  Identities=13%  Similarity=0.093  Sum_probs=24.0

Q ss_pred             CCCCCCCCCCCCCceeeeCC---------------------------CCceEcCCCcccc
Q 021438            1 MADSYCADCKRLTEVVFDHS---------------------------AGDTICSECGLVL   33 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D~~---------------------------~G~~vC~~CG~Vv   33 (312)
                      |+...||.|+.  .+..+..                           +|.++|..||...
T Consensus         6 LdILaCP~cK~--pL~l~~~~~~~~~~ca~~~~~~~~~~~~~~~e~~~~~LvC~~c~~~Y   63 (97)
T 2k5r_A            6 LHLLCSPDTRQ--PLSLLESKGLEALNKAIVSGTVQRADGSIQNQSLHEALITRDRKQVF   63 (97)
T ss_dssp             CSSCCCCTTSS--CCEECCHHHHHHHHHHHHHTCCBCTTSCBCCCCCSEEEECTTSCEEE
T ss_pred             hhheECCCCCC--cccccccchhhhhhhhhhccccccccccccccccCCeEEcCCCCCCc
Confidence            45678999997  3555544                           7899999999874

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...

Probab=93.00  E-value=0.054  Score=41.48  Aligned_cols=34  Identities=24%  Similarity=0.392  Sum_probs=24.4

Q ss_pred             CCCCCCCCCCCCCceeee--CCCCceEcCCCccccc
Q 021438            1 MADSYCADCKRLTEVVFD--HSAGDTICSECGLVLE   34 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D--~~~G~~vC~~CG~Vv~   34 (312)
                      |.+..||+||+--.+..|  ...+.+.|..||+...
T Consensus         2 ~~~~FCp~CgnlL~~~~~~~~~~~~~~C~~C~y~~~   37 (122)
T 1twf_I            2 TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEE   37 (122)
T ss_dssp             CCCCBCSSSCCBCEEEEETTTTEEEEECSSSSCEEE
T ss_pred             CCCCcccccCccCcccccCcCCCCEEECCcCCCeee
Confidence            567899999983233334  3456799999999764

>2pmi_B PHO85 cyclin PHO80, aminoglycoside anti; cyclin-dependent kinase, signaling protein,transfera cycle complex; HET: MES AGS; 2.90A {Saccharomyces cerevisiae} PDB: 2pk9_B*

Probab=92.90  E-value=2.7  Score=36.91  Aligned_cols=105  Identities=9%  Similarity=0.035  Sum_probs=79.8

Q ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhC--CC-CCCCCHHHHHHHHHHHHHHH-hCCCCCHHHHHHHhcCCCHHHH
Q 021438          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQ--KP-LRGRNQEAIVAACLYIACRQ-ENKPRTVKEFCSVANGTTKKEI  184 (312)
Q Consensus       109 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~--~~-~~gr~~~~iaaAcly~acr~-~~~p~tl~dia~~~~~v~~~~i  184 (312)
                      ..++|.++...-+++..+.-.|..|..++...  +. +...+..-+..+|+.+|.|. .....+-+..+.+. |++.+++
T Consensus        77 I~~Yl~RI~k~t~ls~~~ll~ALvYLdRL~~~~p~~~l~~~nvHRLlLtALmlAsK~ldD~~ysN~~wAkVg-Gisl~EL  155 (293)
T 2pmi_B           77 IFNYFIRLTKFSSLEHCVLMTSLYYIDLLQTVYPDFTLNSLTAHRFLLTATTVATKGLCDSFSTNAHYAKVG-GVRCHEL  155 (293)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHCTTCCCSTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHH-TSCHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhCCCCccCCchHHHHHHHHHHHHHHhccccccChhHhhhcc-CcCHHHH
Confidence            45778888888899998888888888888663  22 23456777888889999996 45668889999998 8999999


Q ss_pred             HHHHHHHHHHHhhhhccccccCCCCHHHHHHHHHhhc
Q 021438          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNL  221 (312)
Q Consensus       185 ~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L  221 (312)
                      .+..+.+...++.      ++ .+++++|...+.+.+
T Consensus       156 N~LE~eFL~lLdf------~L-~V~~ee~~~cy~E~~  185 (293)
T 2pmi_B          156 NILENDFLKRVNY------RI-IPRDHNITLCSIEQK  185 (293)
T ss_dssp             HHHHHHHHHTTTT------CC-SCCTTHHHHHHHHSC
T ss_pred             HHHHHHHHHHcCC------ce-eeCHHHHHHHHHHHh
Confidence            9999999988876      33 244566665555443

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=92.34  E-value=0.11  Score=36.39  Aligned_cols=30  Identities=7%  Similarity=0.049  Sum_probs=27.5

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      |.+.+.+|||+.+|+|+.||+...+.|.+.
T Consensus        22 g~~psv~EIa~~lgvS~~TVrr~L~~Le~k   51 (77)
T 2jt1_A           22 GAPVKTRDIADAAGLSIYQVRLYLEQLHDV   51 (77)
T ss_dssp             TSCEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            688999999999999999999998888774

>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1

Probab=92.26  E-value=0.06  Score=31.76  Aligned_cols=28  Identities=21%  Similarity=0.629  Sum_probs=20.3

Q ss_pred             CCCCCCCC-CceeeeCCCCceEcCCCccc
Q 021438            5 YCADCKRL-TEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         5 ~Cp~Cg~~-~~ii~D~~~G~~vC~~CG~V   32 (312)
                      .||.|+++ +.++.+...-.+-|..||..
T Consensus         2 lC~~C~~peT~l~~~~~~~~l~C~aCG~~   30 (36)
T 1k81_A            2 ICRECGKPDTKIIKEGRVHLLKCMACGAI   30 (36)
T ss_dssp             CCSSSCSCEEEEEEETTEEEEEEETTTEE
T ss_pred             CCcCCCCCCcEEEEeCCcEEEEhhcCCCc
Confidence            69999995 34555544445779999986

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=92.26  E-value=0.1  Score=39.37  Aligned_cols=31  Identities=16%  Similarity=0.439  Sum_probs=21.9

Q ss_pred             CCCCCCCCCCCCceeeeCCCC----ceEcCCCccccc
Q 021438            2 ADSYCADCKRLTEVVFDHSAG----DTICSECGLVLE   34 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~~G----~~vC~~CG~Vv~   34 (312)
                      .|..||+||+-  +......|    .++|..||++..
T Consensus         3 ~m~FCp~Cgn~--L~~~~~~~~~~~~~~C~~C~y~~~   37 (113)
T 3h0g_I            3 NFQYCIECNNM--LYPREDKVDRVLRLACRNCDYSEI   37 (113)
T ss_dssp             CCCCCSSSCCC--CEECCCTTTCCCCEECSSSCCEEC
T ss_pred             cceeCcCCCCE--eeEcccCCCCeeEEECCCCCCeEE
Confidence            46799999983  33333322    699999999853

>6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1

Probab=91.59  E-value=0.055  Score=33.77  Aligned_cols=27  Identities=30%  Similarity=0.679  Sum_probs=16.0

Q ss_pred             CCCCCCCCCCCCCceeeeCCCCc----------eEcCCCcc
Q 021438            1 MADSYCADCKRLTEVVFDHSAGD----------TICSECGL   31 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D~~~G~----------~vC~~CG~   31 (312)
                      |....|+.||-    ++|++.|+          .+|..||.
T Consensus         2 m~~y~C~vCGy----vyd~~~Gd~t~f~~lP~dw~CP~Cg~   38 (46)
T 6rxn_A            2 MQKYVCNVCGY----EYDPAEHDNVPFDQLPDDWCCPVCGV   38 (46)
T ss_dssp             CCCEEETTTCC----EECGGGGTTCCGGGSCTTCBCTTTCC
T ss_pred             CCEEECCCCCe----EEeCCcCCCcchhhCCCCCcCcCCCC
Confidence            44556777774    56655553          36666664

>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2

Probab=91.53  E-value=0.11  Score=44.83  Aligned_cols=28  Identities=25%  Similarity=0.432  Sum_probs=21.9

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      ..||.||+...+..+ ..|...|.+||.-
T Consensus        15 ~~CP~Cg~~d~~~~~-~dg~~~C~~Cg~~   42 (255)
T 1nui_A           15 IPCDNCGSSDGNSLF-SDGHTFCYVCEKW   42 (255)
T ss_dssp             ECCSSSCCSSCEEEE-TTSCEEETTTCCE
T ss_pred             CcCCCCCCCCCceEe-CCCCeecccCCCc
Confidence            579999984455555 4688999999975

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=91.16  E-value=0.21  Score=32.53  Aligned_cols=31  Identities=13%  Similarity=0.060  Sum_probs=27.6

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ..+.+|||+.+|+|+.||+.+.+.+.+.+..
T Consensus        13 g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~   43 (61)
T 2jpc_A           13 GYTNHGISEKLHISIKTVETHRMNMMRKLQV   43 (61)
T ss_dssp             SCCSHHHHHHTCSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHCC
Confidence            4689999999999999999999999887654

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1

Probab=90.92  E-value=0.16  Score=33.10  Aligned_cols=31  Identities=16%  Similarity=0.416  Sum_probs=21.2

Q ss_pred             CCCCCCCCCCceeeeC------CCC---ceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDH------SAG---DTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~------~~G---~~vC~~CG~Vv~e   35 (312)
                      ..||.||. ....+..      +++   .++|.+||....+
T Consensus        16 ~~Cp~Cg~-~~~~~~q~Q~rsadep~T~fy~C~~Cg~~w~~   55 (57)
T 1qyp_A           16 ITCPKCGN-DTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS   55 (57)
T ss_dssp             CCCTTTCC-SEEEEEEECCSSSSCSSEEEEEESSSCCEEEC
T ss_pred             eECCCCCC-CEEEEEEeecccCCCCCcEEEEcCCCCCEecc
Confidence            47999998 5554432      233   3899999987543

>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=90.68  E-value=0.14  Score=36.13  Aligned_cols=32  Identities=28%  Similarity=0.507  Sum_probs=25.7

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      ...||.||+ .. +.....|-.-|..||.++...
T Consensus        35 ky~CpfCGk-~~-vkR~a~GIW~C~kCg~~~AGG   66 (83)
T 3j21_i           35 KHTCPVCGR-KA-VKRISTGIWQCQKCGATFAGG   66 (83)
T ss_dssp             CBCCSSSCS-SC-EEEEETTEEEETTTCCEEECC
T ss_pred             ccCCCCCCC-ce-eEecCcCeEEcCCCCCEEeCC
Confidence            457999998 45 455678999999999998654

>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ...

Probab=90.58  E-value=0.11  Score=35.53  Aligned_cols=28  Identities=25%  Similarity=0.697  Sum_probs=18.1

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcc-ccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGL-VLE   34 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~-Vv~   34 (312)
                      ..|++||..  +.. .....+.|..||. ||-
T Consensus        29 Y~C~~CG~~--~e~-~~~d~irCp~CG~RILy   57 (70)
T 1twf_L           29 YICAECSSK--LSL-SRTDAVRCKDCGHRILL   57 (70)
T ss_dssp             EECSSSCCE--ECC-CTTSTTCCSSSCCCCCB
T ss_pred             EECCCCCCc--cee-CCCCCccCCCCCceEeE
Confidence            479999973  222 2344567999998 653

>4rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.20A {Clostridium pasteurianum} SCOP: g.41.5.1 PDB: 5rxn_A 1bfy_A 1fhh_A 1fhm_A 1irn_A 1iro_A 1r0f_A 1r0g_A 1r0h_A 1r0i_A 1r0j_A 1t9q_A 1c09_A 1b2j_A 1b13_A 1smm_A 1smu_A 1smw_A 1be7_A 1t9o_A ...

Probab=90.45  E-value=0.12  Score=33.43  Aligned_cols=18  Identities=28%  Similarity=0.680  Sum_probs=10.7

Q ss_pred             CCCCCCCCCCCCCceeeeCCCC
Q 021438            1 MADSYCADCKRLTEVVFDHSAG   22 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D~~~G   22 (312)
                      |....|+.||-    |+|+..|
T Consensus         1 m~~y~C~vCGy----vYd~~~G   18 (54)
T 4rxn_A            1 MKKYTCTVCGY----IYDPEDG   18 (54)
T ss_dssp             CCCEEETTTCC----EECTTTC
T ss_pred             CCceECCCCCe----EECCCcC
Confidence            45556666664    5666555

>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}

Probab=90.42  E-value=0.16  Score=34.77  Aligned_cols=32  Identities=25%  Similarity=0.357  Sum_probs=25.6

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      ...||.||. .. +.....|-.-|..||.++...
T Consensus        26 ky~C~fCgk-~~-vkR~a~GIW~C~~C~~~~AGG   57 (72)
T 3jyw_9           26 RYDCSFCGK-KT-VKRGAAGIWTCSCCKKTVAGG   57 (72)
T ss_dssp             CBCCSSCCS-SC-BSBCSSSCBCCSSSCCCCCCS
T ss_pred             CccCCCCCC-ce-eEecCCCeEECCCCCCEEeCC
Confidence            457999998 44 455778999999999998653

>3h4c_A Transcription factor TFIIB-like; cyclin, transcription factor TFIIB repeat; 2.30A {Trypanosoma brucei brucei}

Probab=90.30  E-value=2.8  Score=34.55  Aligned_cols=79  Identities=15%  Similarity=0.173  Sum_probs=54.4

Q ss_pred             HHHHHHHhhcCCCHHHHHHHHHHHHHhh--h--c-cCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHH
Q 021438          212 DYLRRFCSNLGMTNQAVKAAQEAVQKSE--D--L-DIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVY  286 (312)
Q Consensus       212 ~~i~r~~~~L~l~~~v~~~A~~i~~~~~--~--l-~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~  286 (312)
                      .-+.++-.+-.+++.+...|.++++.--  +  . .-=.+|.-+||||+.+|++-.+.++|+.|+- ...-+-.-|.-|-
T Consensus        17 nclr~L~kKs~~~eaVL~~AieLar~fvg~rR~rgqRvE~q~dVAAAc~miAae~~~~PiplaE~r-~lD~sL~Dvelrr   95 (260)
T 3h4c_A           17 NCMRGLHKKAVLPEPVLDRGIELARAFVGGRRARGQRVERQPDVAAACLMIAAEEAQQPLPLAEVR-CLDSSLGDVELRR   95 (260)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHHHTTCCCCHHHHH-HHCTTCCCHHHHH
T ss_pred             HHHHHHHhhccCcHHHHHHHHHHHHHHhhhhhhhcccccccHHHHHHHHHHHHHHcCCCccHHHHH-HHhhhhhHHHHHH
Confidence            4566777777899999999999988632  1  1 1124699999999999999999999986652 2223333444444


Q ss_pred             HHHHh
Q 021438          287 KDLFP  291 (312)
Q Consensus       287 kel~~  291 (312)
                      -||.+
T Consensus        96 ~Eiv~  100 (260)
T 3h4c_A           96 ADIVR  100 (260)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44444

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=90.06  E-value=0.15  Score=37.51  Aligned_cols=34  Identities=9%  Similarity=0.002  Sum_probs=25.7

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII  297 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~  297 (312)
                      +-..||+|||+.+|+|.+||.+. +.....+..-+
T Consensus        56 ~ge~TQREIA~~lGiS~stISRi-~r~L~~l~~~~   89 (101)
T 1jhg_A           56 RGEMSQRELKNELGAGIATITRG-SNSLKAAPVEL   89 (101)
T ss_dssp             HCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSCHHH
T ss_pred             cCCcCHHHHHHHHCCChhhhhHH-HHHHHHccHHH
Confidence            34599999999999999999977 54445444433

>1e8j_A Rubredoxin; iron-sulfur-protein, zinc-substitution, thermostability; NMR {Desulfovibrio gigas} SCOP: g.41.5.1 PDB: 1rdg_A 2dsx_A 1spw_A

Probab=90.05  E-value=0.12  Score=33.16  Aligned_cols=10  Identities=30%  Similarity=0.561  Sum_probs=4.8

Q ss_pred             CCCCCCCCCC
Q 021438            1 MADSYCADCK   10 (312)
Q Consensus         1 ~~~~~Cp~Cg   10 (312)
                      |....|+.||
T Consensus         1 m~~y~C~~CG   10 (52)
T 1e8j_A            1 MDIYVCTVCG   10 (52)
T ss_dssp             CCCEECSSSC
T ss_pred             CCcEEeCCCC
Confidence            3344455555

>1t6s_A Conserved hypothetical protein; A winged helix-turn-helix, structural genomics, BSGC structu by NIH, protein structure initiative, PSI; 1.95A {Chlorobium tepidum tls} SCOP: a.4.5.60 a.4.5.60

Probab=90.00  E-value=1.5  Score=35.15  Aligned_cols=111  Identities=11%  Similarity=0.139  Sum_probs=70.1

Q ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhcC--CCHHHHHHHHHHHHHHHhhhh-c-------cccccC-CCCHHHHHHHHH
Q 021438          150 AIVAACLYIACRQENKPRTVKEFCSVANG--TTKKEIGRAKEFIVKHLEAEM-G-------QSVEMG-TIHASDYLRRFC  218 (312)
Q Consensus       150 ~iaaAcly~acr~~~~p~tl~dia~~~~~--v~~~~i~~~~~~l~~~l~~~~-~-------~~~~~~-~~~p~~~i~r~~  218 (312)
                      .++=|.||++    +.|.++.+++.++ +  ++..++...+..|...+.... +       ....+. ..+-..++.++.
T Consensus        10 ~~iEAlLf~~----~~pvs~~~La~~~-~~~~~~~~v~~~l~~L~~~y~~~~rg~~l~~v~~gy~l~t~~~~~~~v~~~~   84 (162)
T 1t6s_A           10 RSLEALIFSS----EEPVNLQTLSQIT-AHKFTPSELQEAVDELNRDYEATGRTFRIHAIAGGYRFLTEPEFADLVRQLL   84 (162)
T ss_dssp             HHHHHHHHHC----SSCBCHHHHHHHT-TCCCCHHHHHHHHHHHHHHHHHHTCSEEEEEETTEEEEEECGGGHHHHHHHH
T ss_pred             HHHHHHHHHc----CCCCCHHHHHHHh-CcCCCHHHHHHHHHHHHHHhhhCCCCEEEEEECCEEEEEEcHHHHHHHHHHh
Confidence            4566777765    7899999999999 8  999999999999988775211 0       000000 112233444433


Q ss_pred             hhcCCCHHHHHHHHHHHHHhhhccCCCChHHHHHHHH-HHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          219 SNLGMTNQAVKAAQEAVQKSEDLDIRRSPISVAAAVI-YIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       219 ~~L~l~~~v~~~A~~i~~~~~~l~~Gr~P~~iaaAai-yla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .                        .+.|..+.-|++ -||.-.+..++|..||+++.|++   +.+..++|.+.
T Consensus        85 ~------------------------~~~~~~LS~aaLEtLaiIay~qPiTR~eI~~irGv~---~~~~v~~L~e~  132 (162)
T 1t6s_A           85 A------------------------PVIQRRLSRSMLEVLAVVAWHQPVTKGEIQQIRGAS---PDYSIDRLLAR  132 (162)
T ss_dssp             S------------------------CHHHHHHHHHHHHHHHHHHHHCSEEHHHHHHHHTCC---CCSHHHHHHHT
T ss_pred             c------------------------ccccCccCHHHHHHHHHHHHcCCcCHHHHHHHHCCC---HHHHHHHHHHC
Confidence            2                        112333444443 34444556789999999999998   44566677664

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=89.91  E-value=0.66  Score=34.07  Aligned_cols=39  Identities=13%  Similarity=0.303  Sum_probs=30.6

Q ss_pred             cCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhc-ccCCcc
Q 021438          262 SNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLA-RIIPDW  300 (312)
Q Consensus       262 ~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~-~~~p~~  300 (312)
                      +-..++|.|||+.+|+|..+|.+..++-.+... ..+|+.
T Consensus        31 Yv~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~~~~~~~P~g   70 (101)
T 2w7n_A           31 LVDGKPQATFATSLGLTRGAVSQAVHRVWAAFEDKNLPEG   70 (101)
T ss_dssp             HTTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTCCCTT
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCCCC
Confidence            456789999999999999999988887776643 245543

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=89.86  E-value=0.47  Score=33.16  Aligned_cols=32  Identities=22%  Similarity=0.235  Sum_probs=28.3

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ...+.+|||+.+|+|+.||+++.+.+++.+..
T Consensus        35 ~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~   66 (82)
T 1je8_A           35 QGLPNKMIARRLDITESTVKVHVKHMLKKMKL   66 (82)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTC
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            34789999999999999999999999887754

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=89.84  E-value=0.45  Score=31.80  Aligned_cols=34  Identities=15%  Similarity=0.155  Sum_probs=30.1

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII  297 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~  297 (312)
                      ...|.+|||+..|+|+.||+++.....+.+...+
T Consensus        24 ~g~s~~eIA~~lgis~~tV~~~~~ra~~kLr~~~   57 (68)
T 2p7v_B           24 TDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPS   57 (68)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCC
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999998888877654

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=89.79  E-value=0.49  Score=32.72  Aligned_cols=42  Identities=12%  Similarity=0.196  Sum_probs=37.5

Q ss_pred             HHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHHhh
Q 021438          155 CLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEA  197 (312)
Q Consensus       155 cly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~  197 (312)
                      -|+-+.+..|-|....||+..+ |++.+++.++++.|++.-.+
T Consensus        23 kVLe~LkeaG~PlkageIae~~-GvdKKeVdKaik~LKkEgkI   64 (80)
T 2lnb_A           23 RILQVLTEAGSPVKLAQLVKEC-QAPKRELNQVLYRMKKELKV   64 (80)
T ss_dssp             HHHHHHHHHTSCEEHHHHHHHH-TSCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHcCCCCCHHHHHHHH-CCCHHHHHHHHHHHHHcCCc
Confidence            4667889999999999999999 89999999999999987654

>1ffk_W Ribosomal protein L37AE; ribosome assembly, RNA-RNA, protein-RNA, protein-protein; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1jj2_Y 1k73_1* 1k8a_1* 1k9m_1* 1kc8_1* 1kd1_1* 1kqs_Y* 1m1k_1* 1m90_1* 1n8r_1* 1nji_1* 1q7y_1* 1q81_1* 1q82_1* 1q86_1* 1qvf_Y 1qvg_Y 1w2b_Y 3cxc_Y*

Probab=89.79  E-value=0.15  Score=35.02  Aligned_cols=32  Identities=19%  Similarity=0.400  Sum_probs=25.1

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      ...||.||. ..+ .-...|-..|..||.++.-.
T Consensus        27 ky~C~fCgk-~~v-kR~a~GIW~C~~C~~~~AGG   58 (73)
T 1ffk_W           27 KYKCPVCGF-PKL-KRASTSIWVCGHCGYKIAGG   58 (73)
T ss_pred             CccCCCCCC-cee-EEEEeEEEECCCCCcEEECC
Confidence            457999998 444 44568999999999998654

>3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic sequnece for R-proteins, ribonucleoprotein, ribosoma protein, RNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z* 3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z* 3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3i55_Z* 3i56_Z* 3cpw_Y* 4adx_Z

Probab=89.78  E-value=0.15  Score=38.25  Aligned_cols=32  Identities=25%  Similarity=0.470  Sum_probs=24.9

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      ...||.||. ..+ .-...|-.-|..||.++.-.
T Consensus        60 kytCPfCGk-~~v-KR~avGIW~C~~Cgk~fAGG   91 (116)
T 3cc2_Z           60 DHACPNCGE-DRV-DRQGTGIWQCSYCDYKFTGG   91 (116)
T ss_dssp             CEECSSSCC-EEE-EEEETTEEEETTTCCEEECC
T ss_pred             CCcCCCCCC-cee-EecCceeEECCCCCCEEECC
Confidence            357999998 444 44568999999999997643

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=89.16  E-value=0.41  Score=34.29  Aligned_cols=31  Identities=16%  Similarity=0.192  Sum_probs=27.9

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ..+.+|||+.+|+|+.||+.+.+.+++.++.
T Consensus        44 G~s~~eIA~~L~iS~~TV~~~~~~i~~Klgv   74 (90)
T 3ulq_B           44 GFTNQEIADALHLSKRSIEYSLTSIFNKLNV   74 (90)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            4679999999999999999999999987753

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=89.03  E-value=0.61  Score=31.36  Aligned_cols=31  Identities=26%  Similarity=0.296  Sum_probs=27.7

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ..+.++||+.+|+|+.||+.+.+.+.+.+..
T Consensus        26 g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~   56 (74)
T 1fse_A           26 DKTTKEIASELFISEKTVRNHISNAMQKLGV   56 (74)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence            4589999999999999999999999887654

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=88.91  E-value=0.19  Score=30.69  Aligned_cols=25  Identities=24%  Similarity=0.186  Sum_probs=21.8

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHH
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDL  289 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel  289 (312)
                      ..+.++||+.+|+|..||.+.++..
T Consensus        21 g~s~~~IA~~lgis~~Tv~~~~~~~   45 (51)
T 1tc3_C           21 NVSLHEMSRKISRSRHCIRVYLKDP   45 (51)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHCS
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHhhH
Confidence            4689999999999999999887654

>4a17_Y RPL37A, 60S ribosomal protein L32; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_Y 4a1c_Y 4a1e_Y

Probab=88.63  E-value=0.21  Score=36.53  Aligned_cols=31  Identities=19%  Similarity=0.412  Sum_probs=24.8

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      ...||.||. .. +.....|-.-|..||.++..
T Consensus        36 ky~CpfCgk-~~-vKR~a~GIW~C~kCg~~~AG   66 (103)
T 4a17_Y           36 KYGCPFCGK-VA-VKRAAVGIWKCKPCKKIIAG   66 (103)
T ss_dssp             CEECTTTCC-EE-EEEEETTEEEETTTTEEEEC
T ss_pred             CCCCCCCCC-ce-eeecCcceEEcCCCCCEEeC
Confidence            357999998 44 55567899999999999764

>1f5q_B Gamma herpesvirus cyclin; herpesviral cyclin, cyclin dependent kinase. protein/protein complex, transferase; 2.50A {Murid herpesvirus 4} SCOP: a.74.1.1 a.74.1.1

Probab=88.58  E-value=3.1  Score=35.69  Aligned_cols=84  Identities=12%  Similarity=0.089  Sum_probs=64.1

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHhC--cchhHHHHH
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSND-TKPLKEISIVTR--VAEGTIKNV  285 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~-~~~~~~Ia~~~~--vs~~ti~~~  285 (312)
                      .+++..++.++++++++.-.|..++++-..  -.......-++++|+++|++.... +.+.++++..++  .+...|.+-
T Consensus        53 vdWl~ev~~~~~l~~eT~~lAv~~lDRfLs~~~v~~~~lqLvg~tcl~iAsK~eE~~p~~~~~l~~~~~~~yt~~~i~~m  132 (252)
T 1f5q_B           53 TTWMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAYMPIKATQLAYLCGGATTADKLLTL  132 (252)
T ss_dssp             HHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHCTTCCHHHHHHH
T ss_pred             HHHHHHHHHHcCCChHHHHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCCCHHHHHHH
Confidence            467888888999999999999999888554  334567888999999999998764 566888877654  566677766


Q ss_pred             HHHHHhhhc
Q 021438          286 YKDLFPHLA  294 (312)
Q Consensus       286 ~kel~~~~~  294 (312)
                      =+.|+..++
T Consensus       133 E~~IL~~L~  141 (252)
T 1f5q_B          133 EVKSLDTLS  141 (252)
T ss_dssp             HHHHHHHTT
T ss_pred             HHHHHHHCC
Confidence            666666654

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=88.44  E-value=0.53  Score=31.28  Aligned_cols=34  Identities=15%  Similarity=0.002  Sum_probs=28.7

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII  297 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~  297 (312)
                      ...+.++||+..|+|+.||+++.+...+.+...+
T Consensus        30 ~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l   63 (70)
T 2o8x_A           30 LGLSYADAAAVCGCPVGTIRSRVARARDALLADA   63 (70)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC--
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            3578999999999999999999998888877655

>2qdj_A Retinoblastoma-associated protein; cyclin fold, cyclin wedge, antitumor protein; 2.00A {Homo sapiens}

Probab=88.22  E-value=2.3  Score=37.65  Aligned_cols=68  Identities=10%  Similarity=0.121  Sum_probs=50.1

Q ss_pred             HHHHhhcCCCHHHHHHHHHHHHHhhhc-----cCCCChHHHHHHHHHHHHHhc-CCCCCHHHHHHHhCcchhHH
Q 021438          215 RRFCSNLGMTNQAVKAAQEAVQKSEDL-----DIRRSPISVAAAVIYIITQLS-NDTKPLKEISIVTRVAEGTI  282 (312)
Q Consensus       215 ~r~~~~L~l~~~v~~~A~~i~~~~~~l-----~~Gr~P~~iaaAaiyla~~~~-~~~~~~~~Ia~~~~vs~~ti  282 (312)
                      ..+|..|++++.+...||++.+.+..+     .+--...-.-.||||.|+.-. |..+++.+|-+.++++....
T Consensus         7 ~~lC~~Lnld~~~~~~Aw~~~~~~~~~~~~~~~~~~~~~~~w~acLY~a~~~~~~n~vsLt~LLr~~~lsi~~F   80 (304)
T 2qdj_A            7 TALCQKLKIPDHVRERAWLTWEKVSSVDGVLGGYIQKKKELWGICIFIAAVDLDEMSFTFTELQKNIEISVHKF   80 (304)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHC----------CHHHHHHHHHHHHHHHHTCCCSCHHHHHHHHTCCHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHHHhccccccCCCccchHHHHHHhHHHHhhccCCCcCcHHHHHHHcCCCHHHH
Confidence            568999999999999999999998763     122224444555699999754 56789999999888876543

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=87.97  E-value=0.77  Score=31.36  Aligned_cols=32  Identities=13%  Similarity=0.167  Sum_probs=28.3

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ...+.+|||+.+|+|+.||+.+.+.+.+.+..
T Consensus        30 ~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~~   61 (79)
T 1x3u_A           30 AGLPNKSIAYDLDISPRTVEVHRANVMAKMKA   61 (79)
T ss_dssp             TTCCHHHHHHHTTSCHHHHHHHHHHHHHHTTC
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            45789999999999999999999999887654

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=87.68  E-value=0.31  Score=37.76  Aligned_cols=32  Identities=22%  Similarity=0.379  Sum_probs=20.6

Q ss_pred             CCCCCCCCCCCCceeeeC--CCCceEcCCCcccc
Q 021438            2 ADSYCADCKRLTEVVFDH--SAGDTICSECGLVL   33 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~--~~G~~vC~~CG~Vv   33 (312)
                      .+..||+||+---+..|.  ....++|..||++.
T Consensus        23 ~~~FCPeCgNmL~pked~~~~~l~~~CrtCgY~~   56 (133)
T 3qt1_I           23 TFRFCRDCNNMLYPREDKENNRLLFECRTCSYVE   56 (133)
T ss_dssp             CCCBCTTTCCBCBCCBCTTTCCBCCBCSSSCCBC
T ss_pred             CCeeCCCCCCEeeECccCCCceeEEECCCCCCcE
Confidence            357899999821112222  12359999999975

>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4

Probab=87.40  E-value=0.17  Score=36.01  Aligned_cols=32  Identities=22%  Similarity=0.467  Sum_probs=22.9

Q ss_pred             CCCCCCCCCC--ceeeeC--CCCceEcCCCcccccC
Q 021438            4 SYCADCKRLT--EVVFDH--SAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~--~ii~D~--~~G~~vC~~CG~Vv~e   35 (312)
                      ..||.|+...  .+..|.  ..|.+.|..||.-.+.
T Consensus        24 F~CPfCnh~~sV~vkidk~~~~g~l~C~~Cg~~~~~   59 (85)
T 1wii_A           24 FTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQT   59 (85)
T ss_dssp             CCCTTTCCSSCEEEEEETTTTEEEEEESSSCCEEEE
T ss_pred             EcCCCCCCCCeEEEEEEccCCEEEEEcccCCCeEEe
Confidence            5799999853  334443  4678999999976543

>4ell_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor, cell cycle; 1.98A {Homo sapiens}

Probab=87.19  E-value=1.4  Score=40.57  Aligned_cols=70  Identities=16%  Similarity=0.131  Sum_probs=54.3

Q ss_pred             HHHHHhhcCCCH-HHHHHHHHHHHHhhh----ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHH
Q 021438          214 LRRFCSNLGMTN-QAVKAAQEAVQKSED----LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIK  283 (312)
Q Consensus       214 i~r~~~~L~l~~-~v~~~A~~i~~~~~~----l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~  283 (312)
                      |..+|++|+++. ++....|.+.+.+..    |..+|+-.-|.-.|||..|++.+..++.++|-..-..-+.+-+
T Consensus       286 l~~LC~~L~~~~~~l~~~IWt~fe~~l~~~teLm~dRHLDQiiLCsiY~i~Kv~~~~~tFk~Ii~~Yr~qPqa~~  360 (411)
T 4ell_A          286 LNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQ  360 (411)
T ss_dssp             HHHHHHHHCTTSTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHTTSTTCCT
T ss_pred             HHHHHHHhCCCcHHHHHHHHHHHHHHHHhhhHhhccccHHHHHHHHHHHHHhhccCCCCHHHHHHHHHhCcCCCC
Confidence            456788898764 677778887777653    8889999999999999999999999999998775444433333

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=87.19  E-value=0.78  Score=32.35  Aligned_cols=34  Identities=18%  Similarity=0.212  Sum_probs=29.8

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII  297 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~  297 (312)
                      ...|.+|||..+|+|+.||+++.......+...+
T Consensus        37 ~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~~l   70 (87)
T 1tty_A           37 KPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPS   70 (87)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTB
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            5689999999999999999999988888776654

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=87.18  E-value=0.45  Score=33.94  Aligned_cols=34  Identities=21%  Similarity=0.165  Sum_probs=28.5

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcccC
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARII  297 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~~  297 (312)
                      ...+.+|||+.+|+|+.||++++......+...+
T Consensus        52 ~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l   85 (92)
T 3hug_A           52 RGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTL   85 (92)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            3578999999999999999999988777765543

>2pmi_B PHO85 cyclin PHO80, aminoglycoside anti; cyclin-dependent kinase, signaling protein,transfera cycle complex; HET: MES AGS; 2.90A {Saccharomyces cerevisiae} PDB: 2pk9_B*

Probab=87.14  E-value=10  Score=33.20  Aligned_cols=91  Identities=9%  Similarity=-0.003  Sum_probs=71.7

Q ss_pred             ccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh----c-cCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHhCc
Q 021438          204 EMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED----L-DIRRSPISVAAAVIYIITQLSND-TKPLKEISIVTRV  277 (312)
Q Consensus       204 ~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~----l-~~Gr~P~~iaaAaiyla~~~~~~-~~~~~~Ia~~~~v  277 (312)
                      ..|.+.-.+|+.|+...-+++..+.-.|.-.+++...    + .......-+-.+|+.+|++..++ ..+-+..|++.|+
T Consensus        71 ~~P~ISI~~Yl~RI~k~t~ls~~~ll~ALvYLdRL~~~~p~~~l~~~nvHRLlLtALmlAsK~ldD~~ysN~~wAkVgGi  150 (293)
T 2pmi_B           71 IPPNISIFNYFIRLTKFSSLEHCVLMTSLYYIDLLQTVYPDFTLNSLTAHRFLLTATTVATKGLCDSFSTNAHYAKVGGV  150 (293)
T ss_dssp             SCCSSCHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHCTTCCCSTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHTS
T ss_pred             CCCCCcHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhCCCCccCCchHHHHHHHHHHHHHHhccccccChhHhhhccCc
Confidence            3566677899999999989998887777666666553    2 24567888899999999998764 4668999999999


Q ss_pred             chhHHHHHHHHHHhhhc
Q 021438          278 AEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       278 s~~ti~~~~kel~~~~~  294 (312)
                      +...+..-=++++..++
T Consensus       151 sl~ELN~LE~eFL~lLd  167 (293)
T 2pmi_B          151 RCHELNILENDFLKRVN  167 (293)
T ss_dssp             CHHHHHHHHHHHHHTTT
T ss_pred             CHHHHHHHHHHHHHHcC
Confidence            99998877778777655

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=87.05  E-value=0.81  Score=30.95  Aligned_cols=34  Identities=15%  Similarity=0.200  Sum_probs=29.2

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhc-ccC
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLA-RII  297 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~-~~~  297 (312)
                      ...|.+|||+.+|+|+.||+++.....+.+. ..+
T Consensus        29 ~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~~~   63 (73)
T 1ku3_A           29 REHTLEEVGAYFGVTRERIRQIENKALRKLKYHES   63 (73)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHh
Confidence            5789999999999999999999888877776 443

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=86.74  E-value=0.69  Score=33.28  Aligned_cols=31  Identities=29%  Similarity=0.226  Sum_probs=27.8

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ..+.+|||+.+|+|+.||+++.+.+++.+..
T Consensus        42 g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~   72 (95)
T 3c57_A           42 GLTNKQIADRMFLAEKTVKNYVSRLLAKLGM   72 (95)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            4679999999999999999999999988754

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=86.01  E-value=0.68  Score=32.93  Aligned_cols=31  Identities=16%  Similarity=0.228  Sum_probs=27.7

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ..+.+|||+.+|+|+.||+++.+.+++.+..
T Consensus        44 g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~   74 (91)
T 2rnj_A           44 GYSNQEIASASHITIKTVKTHVSNILSKLEV   74 (91)
T ss_dssp             TCCTTHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            4778999999999999999999999887654

>1gnf_A Transcription factor GATA-1; zinc finger, transcription regulation; NMR {Mus musculus} SCOP: g.39.1.1 PDB: 1y0j_A 2l6y_A 2l6z_A

Probab=85.59  E-value=0.25  Score=30.72  Aligned_cols=32  Identities=22%  Similarity=0.575  Sum_probs=21.1

Q ss_pred             CCCCCCCCCCCC-ceeeeCCCCceEcCCCcccc
Q 021438            2 ADSYCADCKRLT-EVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         2 ~~~~Cp~Cg~~~-~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      +...|.+|+... ..-..-.+|.++|..||+-.
T Consensus         3 ~~~~C~~C~tt~Tp~WR~gp~G~~LCNaCGl~~   35 (46)
T 1gnf_A            3 EARECVNCGATATPLWRRDRTGHYLCNACGLYH   35 (46)
T ss_dssp             CSCCCTTTCCCCCSSCBCCTTCCCBCSHHHHHH
T ss_pred             CCCCCCCcCCCCCCcCccCCCCCccchHHHHHH
Confidence            346788998742 23333456788899998753

>1dxg_A Desulforedoxin; non-heme iron protein, rubredoxin type metal center, electron transport; 1.80A {Desulfovibrio gigas} SCOP: g.41.5.2 PDB: 1dcd_A 1dhg_A 1cfw_A 2lk5_A 2lk6_A

Probab=85.26  E-value=0.48  Score=27.72  Aligned_cols=26  Identities=27%  Similarity=0.770  Sum_probs=13.7

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGL   31 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~   31 (312)
                      -.+|+.||..-. +.....|+++|  ||.
T Consensus         6 fY~C~~CGnive-v~~~g~~~l~C--CG~   31 (36)
T 1dxg_A            6 VYKCELCGQVVK-VLEEGGGTLVC--CGE   31 (36)
T ss_dssp             EEECTTTCCEEE-EEECCSSCEEE--TTE
T ss_pred             EEEcCCCCcEEE-EEeCCCcCEEe--CCc
Confidence            346777775211 22245566676  553

>3ga8_A HTH-type transcriptional regulator MQSA (YGIT/B30; helix-turn-helix, Zn-binding protein, DNA-binding, transcrip transcription regulation; HET: PE4; 1.70A {Escherichia coli k-12} PDB: 3hi2_A

Probab=84.94  E-value=0.53  Score=32.72  Aligned_cols=31  Identities=23%  Similarity=0.447  Sum_probs=19.1

Q ss_pred             CCCCCCCCCCCceeeeC------CCCc---------eEcCCCccccc
Q 021438            3 DSYCADCKRLTEVVFDH------SAGD---------TICSECGLVLE   34 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~------~~G~---------~vC~~CG~Vv~   34 (312)
                      .++||.||+ ..++.+.      -.|.         .+|..||.++-
T Consensus         2 ~m~Cp~Cg~-~~l~~~~~~~~~~~~G~~~~I~~Vp~~~C~~CGE~~~   47 (78)
T 3ga8_A            2 HMKCPVCHQ-GEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIM   47 (78)
T ss_dssp             -CBCTTTSS-SBEEEEEEEEEEEETTEEEEEEEEEEEEETTTCCEEC
T ss_pred             ceECCCCCC-CeeEeEEEEEEEEECCEEEEEcCceeEECCCCCCEEE
Confidence            478999997 3343221      1232         67999998753

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=84.83  E-value=0.64  Score=29.44  Aligned_cols=23  Identities=13%  Similarity=0.225  Sum_probs=20.4

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHH
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYK  287 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~k  287 (312)
                      ..++++||+.+|+|..||+++.+
T Consensus        31 g~s~~eIA~~lgis~~TV~~~l~   53 (55)
T 2x48_A           31 GYTVQQIANALGVSERKVRRYLE   53 (55)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH
Confidence            46899999999999999998764

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=84.57  E-value=0.96  Score=32.96  Aligned_cols=31  Identities=19%  Similarity=0.036  Sum_probs=27.5

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ..+.+|||+.+++|+.||+.+.+.+++.++.
T Consensus        49 G~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv   79 (99)
T 1p4w_A           49 GFLVTEIAKKLNRSIKTISSQKKSAMMKLGV   79 (99)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            4678999999999999999999999887654

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=84.54  E-value=0.78  Score=30.67  Aligned_cols=22  Identities=27%  Similarity=0.273  Sum_probs=19.2

Q ss_pred             CCHHHHHHHhCcchhHHHHHHH
Q 021438          266 KPLKEISIVTRVAEGTIKNVYK  287 (312)
Q Consensus       266 ~~~~~Ia~~~~vs~~ti~~~~k  287 (312)
                      +|++|||+.+|||..||.+.+.
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLn   22 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVIN   22 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHc
Confidence            4789999999999999997764

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=84.48  E-value=1.1  Score=31.33  Aligned_cols=30  Identities=13%  Similarity=0.104  Sum_probs=26.8

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      |..++..+||+.+|++..||+++...|.+.
T Consensus        25 g~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~   54 (81)
T 1qbj_A           25 GKATTAHDLSGKLGTPKKEINRVLYSLAKK   54 (81)
T ss_dssp             TCCBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            357899999999999999999999999774

>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1

Probab=84.25  E-value=0.5  Score=32.30  Aligned_cols=28  Identities=25%  Similarity=0.561  Sum_probs=22.3

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      ..|| ||..  .+.|...-..-|. ||.++.-
T Consensus         5 v~C~-C~~~--~~~~~~~kT~~C~-CG~~~~~   32 (71)
T 1gh9_A            5 FRCD-CGRA--LYSREGAKTRKCV-CGRTVNV   32 (71)
T ss_dssp             EEET-TSCC--EEEETTCSEEEET-TTEEEEC
T ss_pred             EECC-CCCE--EEEcCCCcEEECC-CCCeeee
Confidence            4699 9983  5667777889998 9999864

>2v3b_B Rubredoxin 2, rubredoxin; alkane degradation, iron-sulfur protein, oxidoreductase, ELE transfer, electron transport, FAD, NAD, iron; HET: FAD; 2.45A {Pseudomonas aeruginosa}

Probab=84.10  E-value=0.37  Score=31.19  Aligned_cols=19  Identities=26%  Similarity=0.543  Sum_probs=9.2

Q ss_pred             CCCCCCCCCCCCCceeeeCCCCc
Q 021438            1 MADSYCADCKRLTEVVFDHSAGD   23 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D~~~G~   23 (312)
                      |....|+.||-    ++|...|+
T Consensus         1 m~~y~C~~CGy----vYd~~~Gd   19 (55)
T 2v3b_B            1 MRKWQCVVCGF----IYDEALGL   19 (55)
T ss_dssp             CCEEEETTTCC----EEETTTCB
T ss_pred             CCcEEeCCCCe----EECCCcCC
Confidence            34445555553    35554443

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=83.95  E-value=0.85  Score=28.85  Aligned_cols=30  Identities=23%  Similarity=0.432  Sum_probs=19.2

Q ss_pred             CCCCCCCCCCCceeeeC-----CCC---ceEcCCCccc
Q 021438            3 DSYCADCKRLTEVVFDH-----SAG---DTICSECGLV   32 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~-----~~G---~~vC~~CG~V   32 (312)
                      ...||.||....+.+..     ++|   .++|.+||..
T Consensus         9 ~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~   46 (50)
T 1tfi_A            9 LFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNR   46 (50)
T ss_dssp             CSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCE
T ss_pred             ccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCCe
Confidence            45899999854333321     223   3799999963

>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=83.51  E-value=0.3  Score=31.08  Aligned_cols=23  Identities=26%  Similarity=0.677  Sum_probs=19.2

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      ..||.|++.      ...|-.-|..||+.
T Consensus        15 ~iCpkC~a~------~~~gaw~CrKCG~~   37 (51)
T 3j21_g           15 YVCLRCGAT------NPWGAKKCRKCGYK   37 (51)
T ss_dssp             EECTTTCCE------ECTTCSSCSSSSSC
T ss_pred             ccCCCCCCc------CCCCceecCCCCCc
Confidence            579999982      45799999999998

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=83.05  E-value=1.3  Score=30.59  Aligned_cols=29  Identities=14%  Similarity=0.103  Sum_probs=26.2

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      ...|..+||+.+|++..||+++.+.|.+.
T Consensus        30 ~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~   58 (77)
T 1qgp_A           30 KATTAHDLSGKLGTPKKEINRVLYSLAKK   58 (77)
T ss_dssp             SCEEHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            46889999999999999999999999764

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=82.90  E-value=1.7  Score=34.50  Aligned_cols=30  Identities=3%  Similarity=0.027  Sum_probs=27.5

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +-+.|..+||+.+|+|+.|++++++.|.+.
T Consensus        15 ~~~~s~~~la~~lg~s~~tv~~rl~~L~~~   44 (162)
T 3i4p_A           15 DSTLAVADLAKKVGLSTTPCWRRIQKMEED   44 (162)
T ss_dssp             CSCSCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            456899999999999999999999999885

>1j1v_A Chromosomal replication initiator protein DNAA, 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3'; protein-DNA complex; 2.10A {Escherichia coli} SCOP: a.4.12.2

Probab=82.81  E-value=11  Score=26.97  Aligned_cols=71  Identities=15%  Similarity=0.136  Sum_probs=49.8

Q ss_pred             CHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhccCCCChHHHH---HHHHHHHHHhcCCCCCHHHHHHHh-CcchhHHHH
Q 021438          209 HASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRRSPISVA---AAVIYIITQLSNDTKPLKEISIVT-RVAEGTIKN  284 (312)
Q Consensus       209 ~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~l~~Gr~P~~ia---aAaiyla~~~~~~~~~~~~Ia~~~-~vs~~ti~~  284 (312)
                      +++..+..+|+.+|++.+-             |...++...++   --|.||+-.+.+  .|+.+|++.+ |....|+..
T Consensus         2 t~~~I~~~Va~~f~i~~~d-------------l~s~~R~~~i~~aRqiamyL~r~~t~--~Sl~~IG~~fggrdHsTV~h   66 (94)
T 1j1v_A            2 TIDNIQKTVAEYYKIKVAD-------------LLSKRRSRSVARPRQMAMALAKELTN--HSLPEIGDAFGGRDHTTVLH   66 (94)
T ss_dssp             CHHHHHHHHHHHTTCCHHH-------------HHSCCCCHHHHHHHHHHHHHHHHHSC--CCHHHHHHHTTSCCHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCHHH-------------HhCCCCCchhHHHHHHHHHHHHHHHC--cCHHHHHHHhCCCCHHHHHH
Confidence            4566677777777777532             11222222333   467899888865  5699999999 899999999


Q ss_pred             HHHHHHhhhc
Q 021438          285 VYKDLFPHLA  294 (312)
Q Consensus       285 ~~kel~~~~~  294 (312)
                      .++.+.+.+.
T Consensus        67 a~~ki~~~~~   76 (94)
T 1j1v_A           67 ACRKIEQLRE   76 (94)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9998887653

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=82.32  E-value=1.8  Score=28.94  Aligned_cols=31  Identities=13%  Similarity=0.131  Sum_probs=27.6

Q ss_pred             cCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          262 SNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       262 ~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .+.+++..+||+.+|++..||.+..+.|.+.
T Consensus        22 ~~~~~s~~eLA~~lglsr~tv~~~l~~L~~~   52 (67)
T 2heo_A           22 DGGPVAIFQLVKKCQVPKKTLNQVLYRLKKE   52 (67)
T ss_dssp             HCSCEEHHHHHHHHCSCHHHHHHHHHHHHHT
T ss_pred             cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            4456889999999999999999999999875

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=82.16  E-value=2.2  Score=29.40  Aligned_cols=29  Identities=14%  Similarity=-0.036  Sum_probs=26.4

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      -+.+..|||+.+|+|..|+++..+.|.+.
T Consensus        13 ~~~s~~eLa~~lgvs~~tv~r~L~~L~~~   41 (81)
T 2htj_A           13 NGGKTAEIAEALAVTDYQARYYLLLLEKA   41 (81)
T ss_dssp             CCCCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            35899999999999999999999999875

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=81.71  E-value=1  Score=34.54  Aligned_cols=30  Identities=17%  Similarity=0.327  Sum_probs=26.7

Q ss_pred             CCCC-CHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTK-PLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~-~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      |.++ +.+++|+.+|||..|||++|+.|...
T Consensus        35 G~~LPser~La~~~gVSr~tVReAl~~L~~e   65 (134)
T 4ham_A           35 GEKILSIREFASRIGVNPNTVSKAYQELERQ   65 (134)
T ss_dssp             TCEECCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCCccHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            5667 58899999999999999999999774

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=81.63  E-value=1.4  Score=33.46  Aligned_cols=30  Identities=23%  Similarity=0.459  Sum_probs=26.7

Q ss_pred             CCCCC-HHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKP-LKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~-~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      |.+++ .+++|+.+|||..|+++.|+.|...
T Consensus        34 g~~Lps~~~La~~~~vSr~tvr~Al~~L~~~   64 (125)
T 3neu_A           34 EDKLPSVREMGVKLAVNPNTVSRAYQELERA   64 (125)
T ss_dssp             TCBCCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            45675 9999999999999999999999874

>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A

Probab=81.56  E-value=0.56  Score=31.97  Aligned_cols=11  Identities=36%  Similarity=0.966  Sum_probs=5.1

Q ss_pred             eEcCCCccccc
Q 021438           24 TICSECGLVLE   34 (312)
Q Consensus        24 ~vC~~CG~Vv~   34 (312)
                      .+|..||+|.+
T Consensus         8 y~C~vCGyiYd   18 (70)
T 1dx8_A            8 YECEACGYIYE   18 (70)
T ss_dssp             EEETTTCCEEC
T ss_pred             EEeCCCCEEEc
Confidence            44444444443

>2vut_I AREA, nitrogen regulatory protein AREA; transcription regulation, protein-protein interactions, metal-binding, nitrate assimilation; HET: NAD; 2.3A {Emericella nidulans} SCOP: g.39.1.1 PDB: 2vus_I* 2vuu_I*

Probab=81.49  E-value=0.49  Score=28.96  Aligned_cols=30  Identities=30%  Similarity=0.762  Sum_probs=20.8

Q ss_pred             CCCCCCCCCC-ceeeeCCCCceEcCCCcccc
Q 021438            4 SYCADCKRLT-EVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         4 ~~Cp~Cg~~~-~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      ..|-+|+... ..-..-.+|..+|..||.-.
T Consensus         2 ~~C~~C~tt~Tp~WR~gp~G~~LCNaCGl~~   32 (43)
T 2vut_I            2 TTCTNCFTQTTPLWRRNPEGQPLCNACGLFL   32 (43)
T ss_dssp             CCCSSSCCCCCSCCEECTTSCEECHHHHHHH
T ss_pred             CcCCccCCCCCCccccCCCCCcccHHHHHHH
Confidence            4688999743 23344457889999999764

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=81.07  E-value=1.7  Score=30.48  Aligned_cols=39  Identities=15%  Similarity=0.323  Sum_probs=31.2

Q ss_pred             CCHHHHHHHhCcchhHHHHHHHHHHhh--hcc---cCCcccccc
Q 021438          266 KPLKEISIVTRVAEGTIKNVYKDLFPH--LAR---IIPDWFANE  304 (312)
Q Consensus       266 ~~~~~Ia~~~~vs~~ti~~~~kel~~~--~~~---~~p~~~~~~  304 (312)
                      .+..+||+.+|+|..+|+++.+.|.+.  +..   --|.|+...
T Consensus        31 ~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~~~~PP~W~~~~   74 (82)
T 1oyi_A           31 ATAAQLTRQLNMEKREVNKALYDLQRSAMVYSSDDIPPRWFMTT   74 (82)
T ss_dssp             EEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEECSSSSCEEESCC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCcceecc
Confidence            889999999999999999999999774  211   237887754

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=80.98  E-value=2.3  Score=31.03  Aligned_cols=31  Identities=10%  Similarity=0.039  Sum_probs=28.2

Q ss_pred             cCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          262 SNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       262 ~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .|.+++..+||+.+|+|.+|++++++.|.+.
T Consensus        30 ~g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~   60 (110)
T 1q1h_A           30 KGTEMTDEEIANQLNIKVNDVRKKLNLLEEQ   60 (110)
T ss_dssp             HCSCBCHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            4667899999999999999999999999874

>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A

Probab=80.59  E-value=0.64  Score=30.60  Aligned_cols=25  Identities=24%  Similarity=0.569  Sum_probs=19.1

Q ss_pred             CCCCCCCCCCCCceeeeCCCCceEcCCCccccc
Q 021438            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~   34 (312)
                      -+..||.||. -++       ..+|..||....
T Consensus         5 ~mr~C~~Cgv-YTL-------k~~CP~CG~~T~   29 (60)
T 2apo_B            5 RMKKCPKCGL-YTL-------KEICPKCGEKTV   29 (60)
T ss_dssp             CCEECTTTCC-EES-------SSBCSSSCSBCB
T ss_pred             hceeCCCCCC-Eec-------cccCcCCCCcCC
Confidence            4678999997 333       567999998854

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=80.52  E-value=5.7  Score=29.32  Aligned_cols=54  Identities=15%  Similarity=0.154  Sum_probs=37.1

Q ss_pred             HHHHHHhhc-CCCHHHHHHHHHHHHHhhhccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHH
Q 021438          213 YLRRFCSNL-GMTNQAVKAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKD  288 (312)
Q Consensus       213 ~i~r~~~~L-~l~~~v~~~A~~i~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~ke  288 (312)
                      ++.++-..+ +|++.-.+.|..|++.         |..++             ..+..+||+.+|||+.||-+-+|.
T Consensus         8 i~~~i~~~~~~ls~~e~~ia~yil~~---------~~~~~-------------~~si~elA~~~~vS~aTv~Rf~kk   62 (111)
T 2o3f_A            8 GLAIIQSMXHXLPPSERKLADYILAH---------PHXAI-------------ESTVNEISALANSSDAAVIRLCXS   62 (111)
T ss_dssp             HHHHHHHHGGGSCHHHHHHHHHHHHC---------HHHHH-------------TCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHhccCCHHHHHHHHHHHHC---------hHHHH-------------hcCHHHHHHHHCCCHHHHHHHHHH
Confidence            344444333 4777777777777754         44333             478999999999999999976543

>2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle structural genomics center for infectious electron transport, iron; NMR {Mycobacterium tuberculosis}

Probab=80.50  E-value=0.59  Score=32.76  Aligned_cols=16  Identities=19%  Similarity=0.380  Sum_probs=12.3

Q ss_pred             CCceEcCCCcccccCc
Q 021438           21 AGDTICSECGLVLEAY   36 (312)
Q Consensus        21 ~G~~vC~~CG~Vv~e~   36 (312)
                      ...++|..||+|.++.
T Consensus        25 m~~y~C~vCGyvYD~~   40 (81)
T 2kn9_A           25 YKLFRCIQCGFEYDEA   40 (81)
T ss_dssp             CCEEEETTTCCEEETT
T ss_pred             cceEEeCCCCEEEcCC
Confidence            3468999999998763

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=80.10  E-value=2.5  Score=32.93  Aligned_cols=30  Identities=17%  Similarity=0.104  Sum_probs=27.4

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +-..+..+||+.+|+|+.|++++.+.|.+.
T Consensus        20 ~~~~s~~ela~~lg~s~~tv~~~l~~L~~~   49 (152)
T 2cg4_A           20 NARTAYAELAKQFGVSPETIHVRVEKMKQA   49 (152)
T ss_dssp             CTTSCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence            356899999999999999999999999885

>2e9h_A EIF-5, eukaryotic translation initiation factor 5; zinc binding, C4 type zinc finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=80.09  E-value=1.4  Score=35.02  Aligned_cols=29  Identities=21%  Similarity=0.599  Sum_probs=20.8

Q ss_pred             CCCCCCCCC-CceeeeCCC--CceEcCCCccc
Q 021438            4 SYCADCKRL-TEVVFDHSA--GDTICSECGLV   32 (312)
Q Consensus         4 ~~Cp~Cg~~-~~ii~D~~~--G~~vC~~CG~V   32 (312)
                      ..|+.|+++ +.++.|...  =.+.|..||..
T Consensus       104 VlC~~C~sPdT~L~~~~~~r~~~l~C~ACGa~  135 (157)
T 2e9h_A          104 VLCPECENPETDLHVNPKKQTIGNSCKACGYR  135 (157)
T ss_dssp             TSCTTTCCSCCEEEEETTTTEEEEECSSSCCE
T ss_pred             EECCCCCCCccEEEEecCCCEEEEEccCCCCC
Confidence            479999995 455554333  34789999987

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	312
d1vola2	109	a.74.1.2 (A:208-316) Transcription factor IIB (TFI	7e-29
d1vola2	109	a.74.1.2 (A:208-316) Transcription factor IIB (TFI	9e-20
d1aisb1	98	a.74.1.2 (B:1108-1205) Transcription factor IIB (T	3e-24
d1aisb1	98	a.74.1.2 (B:1108-1205) Transcription factor IIB (T	3e-15
d1vola1	95	a.74.1.2 (A:113-207) Transcription factor IIB (TFI	2e-22
d1vola1	95	a.74.1.2 (A:113-207) Transcription factor IIB (TFI	2e-13
d1aisb2	95	a.74.1.2 (B:1206-1300) Transcription factor IIB (T	2e-18
d1aisb2	95	a.74.1.2 (B:1206-1300) Transcription factor IIB (T	2e-18
d1dl6a_	58	g.41.3.1 (A:) Transcription initiation factor TFII	1e-12
d1pfta_	50	g.41.3.1 (A:) Transcription initiation factor TFII	2e-11
d2cchb1	128	a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [T	8e-04
d1jkwa1	151	a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo s	8e-04
d2ivxa1	143	a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens)	0.001
d1g3nc1	132	a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma	0.001
d1w98b2	140	a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human	0.002
d2i53a1	144	a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens)	0.002

>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  104 bits (262), Expect = 7e-29
 Identities = 39/105 (37%), Positives = 59/105 (56%), Gaps = 2/105 (1%)

Query: 208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIR--RSPISVAAAVIYIITQLSNDT 265
           I   D++ RFCSNL +  Q   AA    +K+ +LD+   RSPISVAAA IY+ +Q S + 
Sbjct: 2   ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEK 61

Query: 266 KPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWFANEEDIKNL 310
           +  KEI  +  VA+ TI+  Y+ ++P    + P  F  +  +  L
Sbjct: 62  RTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTDFKFDTPVDKL 106

>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 80.6 bits (199), Expect = 9e-20
 Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 1/91 (1%)

Query: 106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK 165
           LI     +S     L L   ++  A  I +K  +   + GR+  ++ AA +Y+A +   +
Sbjct: 1   LITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAE 60

Query: 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196
            RT KE   +A G     I ++   I     
Sbjct: 61  KRTQKEIGDIA-GVADVTIRQSYRLIYPRAP 90

>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 98

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

 Score = 92.6 bits (230), Expect = 3e-24
 Identities = 32/92 (34%), Positives = 54/92 (58%), Gaps = 1/92 (1%)

Query: 105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN 164
           NL  A   +  ++ +L L   +++ A  +Y++   +  +RGR+ E+++AAC+Y ACR   
Sbjct: 1   NLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLK 60

Query: 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196
            PRT+ E   +A    KKEIGR+  FI ++L 
Sbjct: 61  VPRTLDEIADIAR-VDKKEIGRSYRFIARNLN 91

>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 98

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

 Score = 68.0 bits (166), Expect = 3e-15
 Identities = 22/96 (22%), Positives = 39/96 (40%), Gaps = 3/96 (3%)

Query: 208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRR--SPISVAAAVIYIITQLSNDT 265
             A   L R  + L +     + A    +++    + R  S  SV AA +Y   +L    
Sbjct: 3   AFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVP 62

Query: 266 KPLKEISIVTRVAEGTIKNVYKDLFPHLARIIPDWF 301
           + L EI+ + RV +  I   Y+ +  +L  + P   
Sbjct: 63  RTLDEIADIARVDKKEIGRSYRFIARNL-NLTPKKL 97

>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 87.3 bits (216), Expect = 2e-22
 Identities = 45/94 (47%), Positives = 64/94 (68%), Gaps = 1/94 (1%)

Query: 106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK 165
           ++ AFK I+ M+DR+ L     DR N ++++  +QK L+GR  +AI +ACLYIACRQE  
Sbjct: 2   MMNAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGV 61

Query: 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM 199
           PRT KE C+V+   +KKEIGR  + I+K LE  +
Sbjct: 62  PRTFKEICAVSR-ISKKEIGRCFKLILKALETSV 94

>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.0 bits (153), Expect = 2e-13
 Identities = 14/88 (15%), Positives = 37/88 (42%), Gaps = 2/88 (2%)

Query: 208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRR--SPISVAAAVIYIITQLSNDT 265
           ++A   +      + +    V       +++ +    +  +  ++A+A +YI  +     
Sbjct: 3   MNAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGVP 62

Query: 266 KPLKEISIVTRVAEGTIKNVYKDLFPHL 293
           +  KEI  V+R+++  I   +K +   L
Sbjct: 63  RTFKEICAVSRISKKEIGRCFKLILKAL 90

>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 95

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

 Score = 76.8 bits (189), Expect = 2e-18
 Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 1/87 (1%)

Query: 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEF 172
           ++  +D LGL   ++ RA EI  +   +    G++   +VAA LYIA   E + RT +E 
Sbjct: 7   VNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREV 66

Query: 173 CSVANGTTKKEIGRAKEFIVKHLEAEM 199
             VA   T+  +    + +V+ L+ ++
Sbjct: 67  AEVAR-VTEVTVRNRYKELVEKLKIKV 92

>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 95

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

 Score = 76.8 bits (189), Expect = 2e-18
 Identities = 26/93 (27%), Positives = 51/93 (54%), Gaps = 2/93 (2%)

Query: 208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIR--RSPISVAAAVIYIITQLSNDT 265
           +  +DY+ +F   LG++ +  + A E + ++    +   +SP  + AA +YI + L  + 
Sbjct: 1   VKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEK 60

Query: 266 KPLKEISIVTRVAEGTIKNVYKDLFPHLARIIP 298
           +  +E++ V RV E T++N YK+L   L   +P
Sbjct: 61  RTQREVAEVARVTEVTVRNRYKELVEKLKIKVP 93

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.8 bits (145), Expect = 1e-12
 Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 6  CADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE 50
          C +      +V D+ AGD IC ECGLV+    +D  SEWR F+N+
Sbjct: 14 CPNHPD-AILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND 57

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 50

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 55.9 bits (135), Expect = 2e-11
 Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 6  CADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIF 47
          C  C+   E+++D   G+ +C++CG V+E   +D   EWR F
Sbjct: 8  CPACES-AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAF 48

>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Length = 128

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin A
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 36.9 bits (85), Expect = 8e-04
 Identities = 21/96 (21%), Positives = 40/96 (41%), Gaps = 9/96 (9%)

Query: 106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN- 164
           L++  +     ++ L L     DR       +  +  L G        A + +A + E  
Sbjct: 38  LVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVG-------TAAMLLASKFEEI 90

Query: 165 KPRTVKEFCSVANGT-TKKEIGRAKEFIVKHLEAEM 199
            P  V EF  + + T TKK++ R +  ++K L  ++
Sbjct: 91  YPPEVAEFVYITDDTYTKKQVLRMEHLVLKVLTFDL 126

>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]} Length = 151

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin H (mcs2)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 8e-04
 Identities = 9/87 (10%), Positives = 32/87 (36%), Gaps = 6/87 (6%)

Query: 119 RLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG 178
           +  +  ++   A   +K+      +   +   I+  C ++AC+ +    +  +F      
Sbjct: 62  KPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRE 121

Query: 179 T------TKKEIGRAKEFIVKHLEAEM 199
           +        ++I   +  +++ L   +
Sbjct: 122 SPLGQEKALEQILEYELLLIQQLNFHL 148

>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Length = 143

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin-T2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 13/71 (18%), Positives = 25/71 (35%)

Query: 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEF 172
           I  M  RL +     + A     +          N+  I +  L++A + E + R ++  
Sbjct: 38  IQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHV 97

Query: 173 CSVANGTTKKE 183
             VA+      
Sbjct: 98  IKVAHACLHPL 108

>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]} Length = 132

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 10/66 (15%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 133 IYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVANGT-TKKEIGRAKEF 190
           +  ++   K +   + +   +ACL +A +  +  P +    C  A  + +++E+   ++ 
Sbjct: 63  LLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAADSFSRQELIDQEKE 122

Query: 191 IVKHLE 196
           +++ L 
Sbjct: 123 LLEKLA 128

>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]} Length = 140

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: G1/S-specific cyclin-E1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 151 IVAACLYIACRQEN-KPRTVKEFCSVANGT-TKKEIGRAKEFIVKHLEAEM 199
           I  + L+IA + E   P  + +F  V +G  +  EI   +  I+K L+  +
Sbjct: 89  IGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDEILTMELMIMKALKWRL 139

>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Length = 144

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin K
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 15/96 (15%), Positives = 33/96 (34%), Gaps = 12/96 (12%)

Query: 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEF 172
           I  +  RLGL           + +       +   +    A CL++A + E  P+  K+ 
Sbjct: 44  IFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDI 103

Query: 173 CSVA------------NGTTKKEIGRAKEFIVKHLE 196
              A                K+E+   +  +++ ++
Sbjct: 104 IKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIK 139

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	312
d1vola2	109	Transcription factor IIB (TFIIB), core domain {Hum	99.92
d1aisb2	95	Transcription factor IIB (TFIIB), core domain {Arc	99.88
d1vola1	95	Transcription factor IIB (TFIIB), core domain {Hum	99.87
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	99.87
d1aisb2	95	Transcription factor IIB (TFIIB), core domain {Arc	99.82
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	99.8
d1vola2	109	Transcription factor IIB (TFIIB), core domain {Hum	99.8
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	99.78
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	99.73
d1vola1	95	Transcription factor IIB (TFIIB), core domain {Hum	99.72
d2i53a1	144	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	98.96
d2ivxa1	143	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	98.9
d1jkwa1	151	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	98.76
d2ivxa2	113	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	98.62
d2i53a2	110	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	98.43
d2cchb1	128	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	98.26
d1bu2a1	127	Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}	98.25
d1g3nc1	132	Viral cyclin {Kaposi's sarcoma-associated herpesvi	98.2
d1f5qb1	141	Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]	98.1
d1w98b2	140	G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax	98.08
d2cchb2	124	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	97.7
d2ivxa2	113	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	97.11
d2ivxa1	143	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	97.11
d2i53a1	144	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	97.07
d2r7ga2	142	Retinoblastoma tumor suppressor domains {Human (Ho	96.84
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	96.73
d1jkwa1	151	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	96.67
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	96.31
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	96.23
d2i53a2	110	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	96.2
d2pk7a1	59	Uncharacterized protein PFL1779 {Pseudomonas fluor	96.02
d2hf1a1	59	Hypothetical protein CV3345 {Chromobacterium viola	95.76
d1jkwa2	126	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	95.57
d2cchb1	128	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	94.95
d1vd4a_	62	Transcription initiation factor TFIIE-alpha {Human	94.88
d1bu2a1	127	Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}	94.86
d1f5qb1	141	Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]	94.68
d1w98b2	140	G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax	94.16
d2r7ga2	142	Retinoblastoma tumor suppressor domains {Human (Ho	93.99
d1g3nc1	132	Viral cyclin {Kaposi's sarcoma-associated herpesvi	93.97
d1neea2	37	Zinc-binding domain of translation initiation fact	93.88
d1k81a_	36	Zinc-binding domain of translation initiation fact	93.46
d1nuia2	54	Zinc-binding domain of primase-helicase {Bacteriop	93.18
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	93.15
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	93.02
d1y0ja1	39	Erythroid transcription factor GATA-1 {Mouse (Mus	92.56
d1jkwa2	126	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	92.32
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	92.07
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	91.67
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	91.54
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	91.33
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	91.19
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	90.76
d1jj2y_	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	90.57
d2cchb2	124	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	90.31
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	90.29
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	90.18
d1vqoz1	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	90.16
d1u5ka2	157	Recombinational repair protein RecO, C-terminal do	89.92
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	89.75
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	89.48
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	89.02
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	88.89
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	88.88
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	88.83
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	88.09
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	88.04
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	87.98
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	87.68
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	87.64
d2vuti1	42	Erythroid transcription factor GATA-1 {Emericella	87.6
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	87.4
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	87.27
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	87.19
d2dsxa1	52	Rubredoxin {Desulfovibrio gigas [TaxId: 879]}	87.03
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	87.0
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	86.5
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	86.38
d1rqga3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro	86.37
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	86.04
d2ak3a2	37	Microbial and mitochondrial ADK, insert "zinc fing	86.02
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	85.98
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	85.41
d1iroa_	53	Rubredoxin {Clostridium pasteurianum [TaxId: 1501]	85.32
d2j0151	59	Ribosomal protein L32p {Thermus thermophilus [TaxI	85.27
d3gata_	66	Erythroid transcription factor GATA-1 {Chicken (Ga	85.05
d1l1oc_	178	Replication protein A 70 KDa subunit (RPA70) {Huma	84.74
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	84.68
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	84.67
d1zina2	35	Microbial and mitochondrial ADK, insert "zinc fing	84.27
d1zyba1	73	Probable transcription regulator BT4300, C-termina	83.8
d1s3ga2	35	Microbial and mitochondrial ADK, insert "zinc fing	83.29
d2j9ub1	47	Vacuolar protein-sorting-associated protein 36, VP	83.28
d1akya2	38	Microbial and mitochondrial ADK, insert "zinc fing	83.09
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	82.98
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	82.39
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	82.31
d1e4va2	35	Microbial and mitochondrial ADK, insert "zinc fing	82.2
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	82.12
d1z0xa1	68	Transcriptional regulator EF0787 {Enterococcus fae	82.07
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	81.92
d6rxna_	45	Rubredoxin {Desulfovibrio desulfuricans, strain 27	81.64
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	81.14
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	81.09
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	80.82
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	80.47
d1hlva1	66	DNA-binding domain of centromere binding protein B	80.22
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	80.01

>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=1.4e-25  Score=171.20  Aligned_cols=105  Identities=36%  Similarity=0.565  Sum_probs=101.9

Q ss_pred             CCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHH
Q 021438          208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNV  285 (312)
Q Consensus       208 ~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~  285 (312)
                      ++|.+||+|||++|+|++++.+.|.++++.+.+  +..||+|.++|||+||+||+.+|.+++++|||+++||++.||+++
T Consensus         2 i~~~d~i~Rf~s~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~iaAa~iY~a~r~~~~~~t~~eIa~~~~vs~~tI~k~   81 (109)
T d1vola2           2 ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQS   81 (109)
T ss_dssp             CCGGGTHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHHHHHHHTSSSCCCHHHHHHHHTCCHHHHHHH
T ss_pred             CCHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHH
Confidence            578999999999999999999999999999987  889999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhcccCCccccccccccccCC
Q 021438          286 YKDLFPHLARIIPDWFANEEDIKNLKL  312 (312)
Q Consensus       286 ~kel~~~~~~~~p~~~~~~~~~~~l~~  312 (312)
                      ||+|++++..++|.|+..+.+++.||.
T Consensus        82 yk~l~~~~~~lip~~~~~~~~~~~lP~  108 (109)
T d1vola2          82 YRLIYPRAPDLFPTDFKFDTPVDKLPQ  108 (109)
T ss_dssp             HHHHGGGHHHHSCSSCCCSSCGGGSCC
T ss_pred             HHHHHHHHHHhCChhhcccCCHHHcCC
Confidence            999999999999999999999999994

>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=99.88  E-value=1.4e-22  Score=150.54  Aligned_cols=91  Identities=30%  Similarity=0.573  Sum_probs=88.1

Q ss_pred             CCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHH
Q 021438          208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNV  285 (312)
Q Consensus       208 ~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~  285 (312)
                      ++|++||+|||+.|+|++++.+.|.++++.+.+  +..||+|.++|||+||+||+++|.+++++|||+++|+|+.||+++
T Consensus         1 i~P~d~I~R~~~~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~vaAA~iY~a~r~~~~~~t~~eIa~~~~vs~~tI~~~   80 (95)
T d1aisb2           1 VKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTVRNR   80 (95)
T ss_dssp             CCGGGGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHH
T ss_pred             CCHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCcHHhHHHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHH
Confidence            469999999999999999999999999999987  889999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhcccCC
Q 021438          286 YKDLFPHLARIIP  298 (312)
Q Consensus       286 ~kel~~~~~~~~p  298 (312)
                      ||+|.+.++..+|
T Consensus        81 yk~l~~~l~~~~p   93 (95)
T d1aisb2          81 YKELVEKLKIKVP   93 (95)
T ss_dssp             HHHHHHHHTCCCC
T ss_pred             HHHHHHHhCCCCC
Confidence            9999999998887

>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=3.8e-22  Score=148.20  Aligned_cols=91  Identities=49%  Similarity=0.874  Sum_probs=88.5

Q ss_pred             HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHH
Q 021438          106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIG  185 (312)
Q Consensus       106 l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~  185 (312)
                      |.++++.|+++|+.|+||+.+.++|..+|+++.+.+..+|+++..++|||||+|||+++.|+|++||++++ ++++++|+
T Consensus         2 L~~a~~~I~~~~~~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~~~~i~AA~iY~acr~~~~p~t~~eIa~~~-~i~~~~i~   80 (95)
T d1vola1           2 MMNAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVS-RISKKEIG   80 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTCCCTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHTTT-CSCHHHHH
T ss_pred             hHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHh-CCCHHHHH
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999 79999999


Q ss_pred             HHHHHHHHHHhh
Q 021438          186 RAKEFIVKHLEA  197 (312)
Q Consensus       186 ~~~~~l~~~l~~  197 (312)
                      +.|+.|.+.|++
T Consensus        81 k~~k~i~~~L~~   92 (95)
T d1vola1          81 RCFKLILKALET   92 (95)
T ss_dssp             HHHHHHHHHTTC
T ss_pred             HHHHHHHHHHCC
Confidence            999999999986

>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=99.87  E-value=6.6e-22  Score=147.76  Aligned_cols=92  Identities=35%  Similarity=0.646  Sum_probs=89.2

Q ss_pred             hHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHH
Q 021438          105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (312)
Q Consensus       105 ~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i  184 (312)
                      +|..|++.|+++|+.|+||+.+.++|..||+++.+.+..+|+++..++|||||+|||+++.|++++||++++ ++++++|
T Consensus         1 nL~~a~~~I~~~~~~L~L~~~i~~~A~~i~k~~~~~~~~~g~~~~~iaaA~iY~Acr~~~~~~t~~eIa~~~-~is~~ti   79 (98)
T d1aisb1           1 NLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIA-RVDKKEI   79 (98)
T ss_dssp             CHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTTTTTTCCHHHHHHHHHHHHHHHHTCCCCHHHHHHHT-TSCHHHH
T ss_pred             CHHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHHH-CCCHHHH
Confidence            467899999999999999999999999999999999999999999999999999999999999999999999 7999999


Q ss_pred             HHHHHHHHHHHhh
Q 021438          185 GRAKEFIVKHLEA  197 (312)
Q Consensus       185 ~~~~~~l~~~l~~  197 (312)
                      +++|+.|.+.|++
T Consensus        80 ~k~yk~i~~~L~l   92 (98)
T d1aisb1          80 GRSYRFIARNLNL   92 (98)
T ss_dssp             HHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCC
Confidence            9999999999986

>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=99.82  E-value=6.7e-20  Score=135.83  Aligned_cols=86  Identities=29%  Similarity=0.417  Sum_probs=84.0

Q ss_pred             HHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHH
Q 021438          111 KSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEF  190 (312)
Q Consensus       111 ~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~  190 (312)
                      ++|.++|++|+||+.+.++|..+|+++.+.+..+||++..++|||||+|||++|.|++++||++++ |+++.+|++.|+.
T Consensus         5 d~I~R~~~~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~vaAA~iY~a~r~~~~~~t~~eIa~~~-~vs~~tI~~~yk~   83 (95)
T d1aisb2           5 DYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVA-RVTEVTVRNRYKE   83 (95)
T ss_dssp             GGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHH-TCCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCcHHhHHHHHHHHHHHHcCCCcCHHHHHHHH-CCCHHHHHHHHHH
Confidence            689999999999999999999999999999999999999999999999999999999999999999 8999999999999


Q ss_pred             HHHHHhh
Q 021438          191 IVKHLEA  197 (312)
Q Consensus       191 l~~~l~~  197 (312)
                      |.+.|++
T Consensus        84 l~~~l~~   90 (95)
T d1aisb2          84 LVEKLKI   90 (95)
T ss_dssp             HHHHHTC
T ss_pred             HHHHhCC
Confidence            9999986

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.3e-20  Score=124.45  Aligned_cols=49  Identities=41%  Similarity=0.767  Sum_probs=45.9

Q ss_pred             CCCCCCCCCCCCCceeeeCCCCceEcCCCcccccCcccccccccccccCC
Q 021438            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE   50 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~~~   50 (312)
                      |+..+||+||+ .++++|+.+|++||.+||+|++|++||.|||||+|+++
T Consensus         9 ~~~~~Cp~Cgs-~~ii~D~~~Ge~vC~~CG~Vlee~~ID~g~EWR~f~~d   57 (58)
T d1dl6a_           9 LPRVTCPNHPD-AILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND   57 (58)
T ss_dssp             CSCCSBTTBSS-SCCEECSSSCCEECTTTCCEECCSCCCCCCSCCCSCCC
T ss_pred             ccccCCCCCCC-CCEEEECCCCcEecccCCCEeccccccCCCcccccCCC
Confidence            56789999999 68999999999999999999999999999999999865

>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=5.6e-20  Score=139.68  Aligned_cols=87  Identities=23%  Similarity=0.309  Sum_probs=83.9

Q ss_pred             HHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHH
Q 021438          110 FKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKE  189 (312)
Q Consensus       110 ~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~  189 (312)
                      .++|.++|++|+||+.+.+.|..+|+++.+.+..+||++.+++|||||+|||++|.|+|++||++++ |+++.+|++.|+
T Consensus         5 ~d~i~Rf~s~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~iaAa~iY~a~r~~~~~~t~~eIa~~~-~vs~~tI~k~yk   83 (109)
T d1vola2           5 GDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIA-GVADVTIRQSYR   83 (109)
T ss_dssp             GGTHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHHHHHHHTSSSCCCHHHHHHHH-TCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHHH-CCCHHHHHHHHH
Confidence            4789999999999999999999999999999999999999999999999999999999999999999 899999999999


Q ss_pred             HHHHHHhh
Q 021438          190 FIVKHLEA  197 (312)
Q Consensus       190 ~l~~~l~~  197 (312)
                      .|.++++.
T Consensus        84 ~l~~~~~~   91 (109)
T d1vola2          84 LIYPRAPD   91 (109)
T ss_dssp             HHGGGHHH
T ss_pred             HHHHHHHH
Confidence            99888874

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.78  E-value=7.1e-20  Score=117.38  Aligned_cols=45  Identities=33%  Similarity=0.926  Sum_probs=42.6

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCccccccccccccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFA   48 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr~f~   48 (312)
                      ...||+||+ +++++|+.+|++||++||+|++|++||.|||||+|+
T Consensus         5 ~~~Cp~Cgs-~~iv~D~~~Ge~vC~~CG~Viee~~iD~gpEWR~f~   49 (50)
T d1pfta_           5 QKVCPACES-AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAFD   49 (50)
T ss_dssp             CCSCTTTSC-CCEEEETTTTEEEESSSCCBCCCCCCCCCSSSSCCC
T ss_pred             cccCcCCCC-CcEEEECCCCeEecccCCcEeccccccCCCcccccC
Confidence            357999998 689999999999999999999999999999999996

>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=99.73  E-value=1.5e-17  Score=123.65  Aligned_cols=91  Identities=25%  Similarity=0.298  Sum_probs=84.7

Q ss_pred             HHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHH
Q 021438          210 ASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYK  287 (312)
Q Consensus       210 p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~k  287 (312)
                      ....|.++|+.|+||+.+.+.|..+.+.+.+  +..|++|.++|||+||+||+.+|.+++++|||+++++++.||+++||
T Consensus         5 a~~~I~~~~~~L~L~~~i~~~A~~i~k~~~~~~~~~g~~~~~iaaA~iY~Acr~~~~~~t~~eIa~~~~is~~ti~k~yk   84 (98)
T d1aisb1           5 ALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVDKKEIGRSYR   84 (98)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTTTTTTCCHHHHHHHHHHHHHHHHTCCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4567999999999999999999999999987  77999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhcccCCccc
Q 021438          288 DLFPHLARIIPDWF  301 (312)
Q Consensus       288 el~~~~~~~~p~~~  301 (312)
                      +|.+.++ +.|+|+
T Consensus        85 ~i~~~L~-l~~~~~   97 (98)
T d1aisb1          85 FIARNLN-LTPKKL   97 (98)
T ss_dssp             HHHHHTT-CCTTTT
T ss_pred             HHHHHcC-CCcccc
Confidence            9999875 567664

>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=2.8e-17  Score=121.52  Aligned_cols=88  Identities=17%  Similarity=0.288  Sum_probs=83.3

Q ss_pred             HHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHH
Q 021438          210 ASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYK  287 (312)
Q Consensus       210 p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~k  287 (312)
                      +...|.++|+.|+||+.+.+.|.++.+.+.+  +..||+|.+++||+||+||+.++.+++++|||+++++++.||++.||
T Consensus         5 a~~~I~~~~~~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~~~~i~AA~iY~acr~~~~p~t~~eIa~~~~i~~~~i~k~~k   84 (95)
T d1vola1           5 AFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFK   84 (95)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTCCCTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHTTTCSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            5678999999999999999999999999987  88999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhcccC
Q 021438          288 DLFPHLARII  297 (312)
Q Consensus       288 el~~~~~~~~  297 (312)
                      +|.+.++..+
T Consensus        85 ~i~~~L~~~v   94 (95)
T d1vola1          85 LILKALETSV   94 (95)
T ss_dssp             HHHHHTTCCC
T ss_pred             HHHHHHCCcC
Confidence            9999887543

>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin K
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.96  E-value=2.8e-09  Score=83.65  Aligned_cols=91  Identities=16%  Similarity=0.250  Sum_probs=77.1

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC-------
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-------  179 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v-------  179 (312)
                      ..+.++|.+++.+|+||..+..+|..+|++++....+...++..+++||+|+|||.++.|+.+++|..+...+       
T Consensus        38 ~~~~~~i~~~~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~~lva~acl~LA~K~eE~~~~l~~vi~~~~~~~~~~~~~  117 (144)
T d2i53a1          38 REGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFG  117 (144)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHSCHHHHG
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhhCcccchhHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHhhhhhhh
Confidence            3579999999999999999999999999999998888889999999999999999999999999998765311       


Q ss_pred             -----CHHHHHHHHHHHHHHHhh
Q 021438          180 -----TKKEIGRAKEFIVKHLEA  197 (312)
Q Consensus       180 -----~~~~i~~~~~~l~~~l~~  197 (312)
                           ..++|-.+...|.+.|++
T Consensus       118 ~~~~~~~~~i~~~E~~iL~~L~F  140 (144)
T d2i53a1         118 QFGDDPKEEVMVLERILLQTIKF  140 (144)
T ss_dssp             GGCSCHHHHHHHHHHHHHHHTTT
T ss_pred             hhchhhHHHHHHHHHHHHHHCCC
Confidence                 234566666666666665

>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin-T2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.90  E-value=6.8e-09  Score=81.26  Aligned_cols=95  Identities=18%  Similarity=0.247  Sum_probs=77.9

Q ss_pred             hhhH-HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcC---
Q 021438          103 DRNL-IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG---  178 (312)
Q Consensus       103 e~~l-~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~---  178 (312)
                      |..+ ..+.++|.++|..|+||..+..+|..+|++++....+...++..+++||+|+|||.++.|+.++++..++..   
T Consensus        27 E~~~R~~~~~~i~~~~~~l~l~~~t~~~A~~l~~Rf~~~~s~~~~~~~~va~acl~LA~K~eE~~~~~~~ii~~~~~~~~  106 (143)
T d2ivxa1          27 ELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHACLH  106 (143)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHhccccccHHHHHHHHHHHhc
Confidence            4444 357899999999999999999999999999999888888899999999999999999999999999876530   


Q ss_pred             ---C-----------CHHHHHHHHHHHHHHHhh
Q 021438          179 ---T-----------TKKEIGRAKEFIVKHLEA  197 (312)
Q Consensus       179 ---v-----------~~~~i~~~~~~l~~~l~~  197 (312)
                         .           ..++|-.+...|.+.|++
T Consensus       107 ~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~F  139 (143)
T d2ivxa1         107 PLEPLLDTKCDAYLQQTRELVILETIMLQTLGF  139 (143)
T ss_dssp             TTSCCCCTTSHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             ccchhhhhchhhhHHHHHHHHHHHHHHHHHcCC
Confidence               0           124555566666666665

>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin H (mcs2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.76  E-value=4.5e-08  Score=77.18  Aligned_cols=95  Identities=12%  Similarity=0.219  Sum_probs=77.8

Q ss_pred             hhhHH-HHHHHHHHHHHhc--CCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCC
Q 021438          103 DRNLI-QAFKSISAMSDRL--GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT  179 (312)
Q Consensus       103 e~~l~-~~~~~I~~~~~~L--~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v  179 (312)
                      +..+. ....+|.++|..+  +||+.+..+|..+|++++....+.-.++..+++||+|+|||.++.|++++++.......
T Consensus        43 e~~l~~~~~~~l~~~~~~~k~~l~~~~~~tA~~~~~RF~~~~s~~~~~~~li~~acl~LA~K~ee~~~~~~~~~~~~~~~  122 (151)
T d1jkwa1          43 EMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRES  122 (151)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHGGGSSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHhhcCccccccHHHHHHHHHHHHHHHcccCCCHHHHHHHHHhh
Confidence            33443 4678999999976  49999999999999999999888889999999999999999999999999998765311


Q ss_pred             ------CHHHHHHHHHHHHHHHhh
Q 021438          180 ------TKKEIGRAKEFIVKHLEA  197 (312)
Q Consensus       180 ------~~~~i~~~~~~l~~~l~~  197 (312)
                            +.++|......+.+.|++
T Consensus       123 ~~~~~~~~~~i~~~E~~iL~~L~f  146 (151)
T d1jkwa1         123 PLGQEKALEQILEYELLLIQQLNF  146 (151)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             cccccccHHHHHHHHHHHHHHcCC
Confidence                  345666666677777765

>d2ivxa2 a.74.1.1 (A:150-262) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin-T2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.62  E-value=1.1e-07  Score=70.76  Aligned_cols=84  Identities=11%  Similarity=0.108  Sum_probs=69.8

Q ss_pred             CHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh---ccCCCChHHHHHHHHHHHHHhcCCCCCHH----HHHHHh--Ccch
Q 021438          209 HASDYLRRFCSNLGMTNQAVKAAQEAVQKSED---LDIRRSPISVAAAVIYIITQLSNDTKPLK----EISIVT--RVAE  279 (312)
Q Consensus       209 ~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~---l~~Gr~P~~iaaAaiyla~~~~~~~~~~~----~Ia~~~--~vs~  279 (312)
                      +|+.|+..++..|+.+.++.+.|+.+++++.+   ++.-..|..||+||||||+++.|.+++..    ..-+.+  +++.
T Consensus         2 HPhk~ll~~~k~l~~~~~l~q~AW~~lnDs~r~T~lcL~~~P~~IA~a~I~LA~~~~~~~~p~~~~~~~Ww~~fd~~vt~   81 (113)
T d2ivxa2           2 HPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTL   81 (113)
T ss_dssp             CHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCGGGTSCHHHHHHHHHHHHHHHHTCCCCCCTTCCCGGGGTCSSCCH
T ss_pred             CCcHHHHHHHHHhCCChHHHHHHHHHHHHHhccCCeeeecCcHHHHHHHHHHHHHHhCCCCCCCCCCCcHHHHHccCCCH
Confidence            79999999999999999999999999999875   67889999999999999999999876532    233344  5777


Q ss_pred             hHHHHHHHHHHhh
Q 021438          280 GTIKNVYKDLFPH  292 (312)
Q Consensus       280 ~ti~~~~kel~~~  292 (312)
                      .-|.+...+|.+.
T Consensus        82 e~i~~i~~~il~l   94 (113)
T d2ivxa2          82 ELLDELTHEFLQI   94 (113)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            7777777766654

>d2i53a2 a.74.1.1 (A:158-267) Cyclin K {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin K
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.43  E-value=4.7e-07  Score=67.24  Aligned_cols=84  Identities=18%  Similarity=0.238  Sum_probs=69.6

Q ss_pred             CHHHHHHHHHhhcCCCH----HHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCH-------HHHHHHh
Q 021438          209 HASDYLRRFCSNLGMTN----QAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPL-------KEISIVT  275 (312)
Q Consensus       209 ~p~~~i~r~~~~L~l~~----~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~-------~~Ia~~~  275 (312)
                      +|+.|+..++..|+...    ++.+.||.+++++.+  ++.-..|..||+||||||+++.+.+++.       +.--..+
T Consensus         2 HP~~~L~~~~~~l~~~~~~~~~l~q~AW~~lNDs~rT~lcL~~~P~~IA~a~I~lA~~~~~~~ip~~~~~~~~~~W~~~f   81 (110)
T d2i53a2           2 HPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQF   81 (110)
T ss_dssp             CHHHHHHHHHHTBCSCHHHHHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHHHHTCCGGGGBSSCCSSCGGGGT
T ss_pred             CCcHHHHHHHHHhcCccccchHHHHHHHHHHHHHhcCCchhccCcHHHHHHHHHHHHHHhCCCCCCcccCcccccHHHHH
Confidence            69999999999999875    578999999999998  8889999999999999999999877542       1233334


Q ss_pred             --CcchhHHHHHHHHHHhh
Q 021438          276 --RVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       276 --~vs~~ti~~~~kel~~~  292 (312)
                        +++..-|.+...+|.+.
T Consensus        82 ~~dvt~e~i~~i~~~il~l  100 (110)
T d2i53a2          82 VQDVPVDVLEDICHQILDL  100 (110)
T ss_dssp             SSSCCHHHHHHHHHHHHTT
T ss_pred             HccCCHHHHHHHHHHHHHH
Confidence              78888888888887764

>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin A
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.26  E-value=5.9e-06  Score=62.76  Aligned_cols=91  Identities=16%  Similarity=0.201  Sum_probs=80.2

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhc-CCCHHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN-GTTKKEI  184 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~-~v~~~~i  184 (312)
                      ....++|-+++..++++..+.-.|..++.++.....+.......+++||+|+|+|.++. |.++.++...++ ..+..+|
T Consensus        32 ~~li~W~~~v~~~~~l~~~t~~lAv~llDr~l~~~~i~~~~~qLi~~~cl~iAsK~ee~~~~~l~~l~~~~~~~~t~~~i  111 (128)
T d2cchb1          32 AILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQV  111 (128)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTSSSCHHHH
T ss_pred             HHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcccCCchHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHcCCCCHHHH
Confidence            45789999999999999999999999999998877666667889999999999998765 679999988764 3689999


Q ss_pred             HHHHHHHHHHHhh
Q 021438          185 GRAKEFIVKHLEA  197 (312)
Q Consensus       185 ~~~~~~l~~~l~~  197 (312)
                      .++.+.|...|+.
T Consensus       112 ~~mE~~IL~~L~~  124 (128)
T d2cchb1         112 LRMEHLVLKVLTF  124 (128)
T ss_dssp             HHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHCCC
Confidence            9999999999986

>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Herpesvirus saimiri [TaxId: 10381]

Probab=98.25  E-value=8.3e-06  Score=61.82  Aligned_cols=91  Identities=16%  Similarity=0.167  Sum_probs=81.2

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhc-CCCHHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN-GTTKKEI  184 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~-p~tl~dia~~~~-~v~~~~i  184 (312)
                      ....+++-+++..++++..+.-.|..++.++.....+.......+++||+++|+|.++. |.++.++...++ ..+..+|
T Consensus        32 ~~lidWl~~v~~~~~l~~eTl~lAv~llDryl~~~~i~~~~lqLi~~tcL~IAsK~ee~~~~~l~~l~~~~~~~~t~~ei  111 (127)
T d1bu2a1          32 TILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSCDCFTNLEL  111 (127)
T ss_dssp             HHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTSCCCTTTHHHHHHHHHHHHHHHSSSSCCCHHHHHHTTTTSSCHHHH
T ss_pred             HHHHHHHHHHHHHHCCChHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHcCCCCHHHH
Confidence            45689999999999999999999999999998887777788999999999999998765 789999988764 3689999


Q ss_pred             HHHHHHHHHHHhh
Q 021438          185 GRAKEFIVKHLEA  197 (312)
Q Consensus       185 ~~~~~~l~~~l~~  197 (312)
                      .++...|.+.|+.
T Consensus       112 ~~mE~~IL~~L~~  124 (127)
T d1bu2a1         112 INQEKDILEALKW  124 (127)
T ss_dssp             HHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHcCC
Confidence            9999999999876

>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]

Probab=98.20  E-value=1e-05  Score=61.77  Aligned_cols=91  Identities=13%  Similarity=0.186  Sum_probs=79.7

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhC-CCCCHHHHHHHhc-CCCHHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVAN-GTTKKEI  184 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~-~p~tl~dia~~~~-~v~~~~i  184 (312)
                      ....+++-+++..++++..+.-.|..++.++.....+.......++++|+++|+|.++ .|.++.++....+ ..+..+|
T Consensus        37 ~~lidWl~~v~~~~~l~~et~~lAv~llDrfls~~~v~~~~lqLia~tcl~iAsK~ee~~~~~~~~l~~~~~~~~t~~ei  116 (132)
T d1g3nc1          37 KLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAADSFSRQEL  116 (132)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTTCSCHHHH
T ss_pred             HHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCcccCcHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHcCCCCHHHH
Confidence            4578999999999999999999999999999887666656678999999999999875 5789999988765 4689999


Q ss_pred             HHHHHHHHHHHhh
Q 021438          185 GRAKEFIVKHLEA  197 (312)
Q Consensus       185 ~~~~~~l~~~l~~  197 (312)
                      .++...|...|+.
T Consensus       117 ~~mE~~IL~~L~w  129 (132)
T d1g3nc1         117 IDQEKELLEKLAW  129 (132)
T ss_dssp             HHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHcCC
Confidence            9999999999875

>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Murine herpesvirus 68 [TaxId: 33708]

Probab=98.10  E-value=1.4e-05  Score=61.70  Aligned_cols=91  Identities=12%  Similarity=0.049  Sum_probs=80.5

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhC-CCCCHHHHHHHhc-CCCHHHH
Q 021438          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVAN-GTTKKEI  184 (312)
Q Consensus       107 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~-~p~tl~dia~~~~-~v~~~~i  184 (312)
                      ....+++-+++..++|+..+.-.|..++.++.....+.......++++|+++|+|.++ .|.++.++...+. ..+..+|
T Consensus        45 ~~lvdWm~~v~~~~~l~~etl~lAv~llDrfls~~~i~~~~lqL~a~tcL~IAsK~ee~~~~~~~~l~~~~~~~yt~~ei  124 (141)
T d1f5qb1          45 KVLTTWMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAYMPIKATQLAYLCGGATTADKL  124 (141)
T ss_dssp             HHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHCTTCCHHHH
T ss_pred             HHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHhcCCCCHHHH
Confidence            4578999999999999999999999999999887777777899999999999999875 5789999998875 3689999


Q ss_pred             HHHHHHHHHHHhh
Q 021438          185 GRAKEFIVKHLEA  197 (312)
Q Consensus       185 ~~~~~~l~~~l~~  197 (312)
                      .++...|...|+-
T Consensus       125 ~~mE~~IL~~L~w  137 (141)
T d1f5qb1         125 LTLEVKSLDTLSW  137 (141)
T ss_dssp             HHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHCCc
Confidence            9999999888864

>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: G1/S-specific cyclin-E1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.08  E-value=3.7e-05  Score=59.10  Aligned_cols=92  Identities=16%  Similarity=0.174  Sum_probs=78.1

Q ss_pred             HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhC-CCCCCCCHHHHHHHHHHHHHHHh-CCCCCHHHHHHHhc-CCCHH
Q 021438          106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQ-KPLRGRNQEAIVAACLYIACRQE-NKPRTVKEFCSVAN-GTTKK  182 (312)
Q Consensus       106 l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~-~~~~gr~~~~iaaAcly~acr~~-~~p~tl~dia~~~~-~v~~~  182 (312)
                      -....+++-+++..++|+..+.-.|..++.++... ..........+++||+|+|+|.+ ..|.++.++...++ ..+..
T Consensus        43 R~~lidW~~~v~~~~~l~~et~~lAv~llDryl~~~~~v~~~~lqL~a~acL~IAsK~ee~~~~~~~~l~~~~~~~~t~~  122 (140)
T d1w98b2          43 RAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGD  122 (140)
T ss_dssp             HHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTTSSCHH
T ss_pred             HHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhccccccHHHHhHHHHHHHHHHHHHcccCCCCHHHHHHHHcCCCCHH
Confidence            34578999999999999999999999999998763 33444567899999999999986 46899999988764 46899


Q ss_pred             HHHHHHHHHHHHHhh
Q 021438          183 EIGRAKEFIVKHLEA  197 (312)
Q Consensus       183 ~i~~~~~~l~~~l~~  197 (312)
                      +|.++...|.+.|+.
T Consensus       123 ei~~mE~~IL~~L~~  137 (140)
T d1w98b2         123 EILTMELMIMKALKW  137 (140)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHCCC
Confidence            999999999999875

>d2cchb2 a.74.1.1 (B:309-432) Cyclin A {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin A
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.70  E-value=0.00014  Score=54.57  Aligned_cols=84  Identities=12%  Similarity=0.027  Sum_probs=71.9

Q ss_pred             CHHHHHHHHH-hhcCCCHHHHHHHHHHHHHhhh---ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHH
Q 021438          209 HASDYLRRFC-SNLGMTNQAVKAAQEAVQKSED---LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKN  284 (312)
Q Consensus       209 ~p~~~i~r~~-~~L~l~~~v~~~A~~i~~~~~~---l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~  284 (312)
                      .+..|+.||. ..-+.+.++...|..+++.+.-   ...+..|+-+||||||+|-.+.+..-+-.++...+|.++..++.
T Consensus         2 T~~~FL~ry~~~~~~~d~~~~~la~Yl~ElsLl~~~~~l~~~PS~lAaaai~lar~~l~~~~W~~~L~~~t~y~~~~l~~   81 (124)
T d2cchb2           2 TVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKP   81 (124)
T ss_dssp             CHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHHHHHHHHHHHHSCCSCHHHHHHHCCCHHHHHH
T ss_pred             chhHHHHHHHHHHccCcHHHHHHHHHHHHHHHHhHHHHHccChHHHHHHHHHHHHHHhCCCCchHHHHHHhCCCHHHHHH
Confidence            4788999876 4556788889999999999763   34688999999999999999888776788899999999999999


Q ss_pred             HHHHHHhh
Q 021438          285 VYKDLFPH  292 (312)
Q Consensus       285 ~~kel~~~  292 (312)
                      ..++|.+.
T Consensus        82 c~~~L~~~   89 (124)
T d2cchb2          82 CLMDLHQT   89 (124)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999875

>d2ivxa2 a.74.1.1 (A:150-262) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin-T2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.11  E-value=0.0019  Score=47.21  Aligned_cols=87  Identities=10%  Similarity=0.125  Sum_probs=66.8

Q ss_pred             HHHHHHHHHhcCCcHHHHHHHHHHHHHHHh-CCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHH----HHHHhc-CCCHHH
Q 021438          110 FKSISAMSDRLGLVTTIKDRANEIYKKVED-QKPLRGRNQEAIVAACLYIACRQENKPRTVKE----FCSVAN-GTTKKE  183 (312)
Q Consensus       110 ~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~-~~~~~gr~~~~iaaAcly~acr~~~~p~tl~d----ia~~~~-~v~~~~  183 (312)
                      .++|-.++..|+.++++...|-.+....+. ..+.--..+..||+||||+|+|..|.+.....    --++++ +++.+.
T Consensus         4 hk~ll~~~k~l~~~~~l~q~AW~~lnDs~r~T~lcL~~~P~~IA~a~I~LA~~~~~~~~p~~~~~~~Ww~~fd~~vt~e~   83 (113)
T d2ivxa2           4 HTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLEL   83 (113)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCGGGTSCHHHHHHHHHHHHHHHHTCCCCCCTTCCCGGGGTCSSCCHHH
T ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHHHhccCCeeeecCcHHHHHHHHHHHHHHhCCCCCCCCCCCcHHHHHccCCCHHH
Confidence            467778888999999999999999998765 55545688999999999999999998764321    222332 588888


Q ss_pred             HHHHHHHHHHHHh
Q 021438          184 IGRAKEFIVKHLE  196 (312)
Q Consensus       184 i~~~~~~l~~~l~  196 (312)
                      |......+.+...
T Consensus        84 i~~i~~~il~lYe   96 (113)
T d2ivxa2          84 LDELTHEFLQILE   96 (113)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            8888877776664

>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin-T2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.11  E-value=0.0012  Score=50.34  Aligned_cols=65  Identities=6%  Similarity=0.179  Sum_probs=56.5

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHh
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVT  275 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~  275 (312)
                      ..||..++..|+++..+...|..++++-..  -.....|.-||+||+|||+++....++.++|..++
T Consensus        35 ~~~i~~~~~~l~l~~~t~~~A~~l~~Rf~~~~s~~~~~~~~va~acl~LA~K~eE~~~~~~~ii~~~  101 (143)
T d2ivxa1          35 ANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVA  101 (143)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHhccccccHHHHHHHH
Confidence            468999999999999999999999998654  34567899999999999999999889998887764

>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin K
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.07  E-value=0.0013  Score=50.16  Aligned_cols=65  Identities=9%  Similarity=0.111  Sum_probs=56.0

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHh
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVT  275 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~  275 (312)
                      .+||..++.+|+++..+.-.|..++++-..  -.....|.-||+||+|+|+++....+++++|..++
T Consensus        41 ~~~i~~~~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~~lva~acl~LA~K~eE~~~~l~~vi~~~  107 (144)
T d2i53a1          41 ARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTA  107 (144)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHHHhhCcccchhHHHHHHHHHHHHHHhhcccccHHHHHHHH
Confidence            478999999999999999999999988654  34567899999999999999998888888887654

>d2r7ga2 a.74.1.3 (A:644-785) Retinoblastoma tumor suppressor domains {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Retinoblastoma tumor suppressor domains
domain: Retinoblastoma tumor suppressor domains
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.84  E-value=0.0021  Score=48.50  Aligned_cols=69  Identities=14%  Similarity=0.280  Sum_probs=57.6

Q ss_pred             HHHHHHHHHHhcCCcH-HHHHHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhc
Q 021438          109 AFKSISAMSDRLGLVT-TIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVAN  177 (312)
Q Consensus       109 ~~~~I~~~~~~L~Lp~-~v~~~A~~i~~~~~~--~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~  177 (312)
                      |...|+.+|++|++++ .+.+....+|.-...  ..++++|..+.++-+|+|..||..+..++++||....+
T Consensus        15 a~~Rl~~LC~~L~~~~~~l~~~Iw~~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~~F~~Ii~~Yr   86 (142)
T d2r7ga2          15 AYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYK   86 (142)
T ss_dssp             HHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHCcCcHHHHHHHHHHHHHHHHHhHHHHhccchhHHHHHHHHHHHHhccCCCCHHHHHHHHH
Confidence            7788999999998764 566666777765543  46779999999999999999999999999999998764

>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27e
domain: Ribosomal protein S27e
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.73  E-value=0.00036  Score=44.18  Aligned_cols=31  Identities=32%  Similarity=0.771  Sum_probs=28.6

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .+||.|+. ..+++++.+-.+.|..||.++.+
T Consensus         8 VkC~~C~n-~~ivFsha~t~V~C~~Cg~~L~~   38 (58)
T d1qxfa_           8 VKCPDCEH-EQVIFDHPSTIVKCIICGRTVAE   38 (58)
T ss_dssp             EECTTTCC-EEEEESSCSSCEECSSSCCEEEE
T ss_pred             eECCCCCC-eEEEEecCceEEEccccCCEEec
Confidence            57999998 68999999999999999999975

>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin H (mcs2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.67  E-value=0.0096  Score=45.50  Aligned_cols=67  Identities=13%  Similarity=0.110  Sum_probs=54.0

Q ss_pred             HHHHHHHhhc--CCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcc
Q 021438          212 DYLRRFCSNL--GMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVA  278 (312)
Q Consensus       212 ~~i~r~~~~L--~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs  278 (312)
                      .+|.++|..+  +++..+.-.|..+.++-.-  ...-..|.-+|+||+|||+++....++.+++.......
T Consensus        52 ~~l~~~~~~~k~~l~~~~~~tA~~~~~RF~~~~s~~~~~~~li~~acl~LA~K~ee~~~~~~~~~~~~~~~  122 (151)
T d1jkwa1          52 KRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRES  122 (151)
T ss_dssp             HHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHGGGSSSC
T ss_pred             HHHHHHHHHHccCCCHHHHHHHHHHHHHHhhcCccccccHHHHHHHHHHHHHHHcccCCCHHHHHHHHHhh
Confidence            4667788865  4899999999998887443  44567899999999999999998888888887765543

>d2jnya1 b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405/cg1592 {Corynebacterium glutamicum [TaxId: 1718]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein Cgl1405/cg1592
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=96.31  E-value=0.0014  Score=41.87  Aligned_cols=29  Identities=14%  Similarity=0.068  Sum_probs=25.6

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      ...||.|++  .+.+|...+.++|..||.+.
T Consensus        10 iL~CP~ck~--~L~~~~~~~~Lvc~~~~~~Y   38 (59)
T d2jnya1          10 VLACPKDKG--PLRYLESEQLLVNERLNLAY   38 (59)
T ss_dssp             CCBCTTTCC--BCEEETTTTEEEETTTTEEE
T ss_pred             HhcCCCCCC--EeEEeCCCCEEEcCccCccc
Confidence            457999997  68999999999999999874

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: PhnA zinc-binding domain
domain: Hypothetical protein PA0128, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=96.23  E-value=0.0018  Score=36.99  Aligned_cols=27  Identities=22%  Similarity=0.431  Sum_probs=20.5

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      ...||.|++. -.-.|  .+.+||.+||.-
T Consensus         3 lP~CP~C~se-ytYed--g~l~vCPeC~hE   29 (38)
T d2akla2           3 LPPCPQCNSE-YTYED--GALLVCPECAHE   29 (38)
T ss_dssp             SCCCTTTCCC-CCEEC--SSSEEETTTTEE
T ss_pred             CCcCCCCCCc-ceEcC--CCEEECCcccCc
Confidence            5689999993 33343  678999999974

>d2i53a2 a.74.1.1 (A:158-267) Cyclin K {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin K
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.20  E-value=0.01  Score=42.82  Aligned_cols=87  Identities=10%  Similarity=-0.006  Sum_probs=60.3

Q ss_pred             HHHHHHHHHhcCCcH----HHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHH-------HHHHHh-c
Q 021438          110 FKSISAMSDRLGLVT----TIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVK-------EFCSVA-N  177 (312)
Q Consensus       110 ~~~I~~~~~~L~Lp~----~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~-------dia~~~-~  177 (312)
                      .+++-.+...|+...    .+.+.|-.+....+...+.--..+..||+||||+|+|..+.++.-.       .=-..+ .
T Consensus         4 ~~~L~~~~~~l~~~~~~~~~l~q~AW~~lNDs~rT~lcL~~~P~~IA~a~I~lA~~~~~~~ip~~~~~~~~~~W~~~f~~   83 (110)
T d2i53a2           4 YQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQ   83 (110)
T ss_dssp             HHHHHHHHHTBCSCHHHHHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHHHHTCCGGGGBSSCCSSCGGGGTSS
T ss_pred             cHHHHHHHHHhcCccccchHHHHHHHHHHHHHhcCCchhccCcHHHHHHHHHHHHHHhCCCCCCcccCcccccHHHHHHc
Confidence            456777777887764    4677777777777655555668899999999999999998865211       011112 1


Q ss_pred             CCCHHHHHHHHHHHHHHHh
Q 021438          178 GTTKKEIGRAKEFIVKHLE  196 (312)
Q Consensus       178 ~v~~~~i~~~~~~l~~~l~  196 (312)
                      +++..+|......|.+...
T Consensus        84 dvt~e~i~~i~~~il~lY~  102 (110)
T d2i53a2          84 DVPVDVLEDICHQILDLYS  102 (110)
T ss_dssp             SCCHHHHHHHHHHHHTTTS
T ss_pred             cCCHHHHHHHHHHHHHHHc
Confidence            5888888887777665543

>d2pk7a1 b.171.1.1 (A:3-61) Uncharacterized protein PFL1779 {Pseudomonas fluorescens [TaxId: 294]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein PFL1779
species: Pseudomonas fluorescens [TaxId: 294]

Probab=96.02  E-value=0.0017  Score=41.44  Aligned_cols=30  Identities=20%  Similarity=0.330  Sum_probs=26.0

Q ss_pred             CCCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         2 ~~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      +...||.|++  .+.+|..++++||..||...
T Consensus         5 ~iL~CP~ck~--~L~~~~~~~~Lvc~~~~laY   34 (59)
T d2pk7a1           5 DILACPICKG--PLKLSADKTELISKGAGLAY   34 (59)
T ss_dssp             GTCCCTTTCC--CCEECTTSSEEEETTTTEEE
T ss_pred             hheECCCCCC--cceEeCCCCEEecCCcCccc
Confidence            3468999998  58999999999999999874

>d2hf1a1 b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromobacterium violaceum [TaxId: 536]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Hypothetical protein CV3345
species: Chromobacterium violaceum [TaxId: 536]

Probab=95.76  E-value=0.0028  Score=40.39  Aligned_cols=29  Identities=34%  Similarity=0.592  Sum_probs=25.5

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      ...||.|++  .+.+|...+++||..||...
T Consensus         7 iL~CP~ck~--~L~~~~~~~~Lvc~~~~l~Y   35 (59)
T d2hf1a1           7 ILVCPLCKG--PLVFDKSKDELICKGDRLAF   35 (59)
T ss_dssp             ECBCTTTCC--BCEEETTTTEEEETTTTEEE
T ss_pred             hhcCCCCCC--eeeEeCCCCEEecCCcCccc
Confidence            357999998  68999999999999999874

>d1jkwa2 a.74.1.1 (A:162-287) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin H (mcs2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.57  E-value=0.022  Score=42.08  Aligned_cols=72  Identities=14%  Similarity=0.099  Sum_probs=50.9

Q ss_pred             CHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCCCCC--HHHHH--HHhCcchhHHHHHHHHHHhhhcc
Q 021438          224 TNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSNDTKP--LKEIS--IVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       224 ~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~~~~--~~~Ia--~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      .+++.+.||.+++++..  +..-..|..||.||||+|++..+..++  +.++.  .........+....++|......
T Consensus        23 ~~~l~~~a~~~lnds~~Td~~l~y~P~qIalaal~~a~~~~~~~l~~y~~~~~~~~~~~~~~~~l~~~i~~i~~l~~~  100 (126)
T d1jkwa2          23 PEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKENRTCLSQLLDIMKSMRNLVKK  100 (126)
T ss_dssp             HHHHHHHHHHHHHHHTTSTHHHHSCHHHHHHHHHHHHHHHHSCCCTTHHHHHTTSCSSSCCTHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHcCCeeeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccccchhhHHHHHHHHHHHHHHHHc
Confidence            35678899999999887  666789999999999999999987654  23332  12233444566666666665544

>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin A
species: Cow (Bos taurus) [TaxId: 9913]

Probab=94.95  E-value=0.1  Score=38.16  Aligned_cols=83  Identities=12%  Similarity=0.165  Sum_probs=63.8

Q ss_pred             HHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHhC--cchhHHHHHH
Q 021438          212 DYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSND-TKPLKEISIVTR--VAEGTIKNVY  286 (312)
Q Consensus       212 ~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~-~~~~~~Ia~~~~--vs~~ti~~~~  286 (312)
                      +++.+++..++++.++...|..++++-..  -.......-++++|+++|++.... ..+.+++...++  .+...|.+.=
T Consensus        36 ~W~~~v~~~~~l~~~t~~lAv~llDr~l~~~~i~~~~~qLi~~~cl~iAsK~ee~~~~~l~~l~~~~~~~~t~~~i~~mE  115 (128)
T d2cchb1          36 DWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRME  115 (128)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTSSSCHHHHHHHH
T ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHHhcccCCchHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHcCCCCHHHHHHHH
Confidence            68889999999999999999999988665  223446778899999999999864 456888877654  4566677666


Q ss_pred             HHHHhhhc
Q 021438          287 KDLFPHLA  294 (312)
Q Consensus       287 kel~~~~~  294 (312)
                      .+|...++
T Consensus       116 ~~IL~~L~  123 (128)
T d2cchb1         116 HLVLKVLT  123 (128)
T ss_dssp             HHHHHHTT
T ss_pred             HHHHHHCC
Confidence            66666554

>d1vd4a_ g.41.3.1 (A:) Transcription initiation factor TFIIE-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIE-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.88  E-value=0.0031  Score=40.47  Aligned_cols=32  Identities=28%  Similarity=0.532  Sum_probs=26.0

Q ss_pred             CCCCCCCCC-C----ceeeeCCCCceEcCCCcccccC
Q 021438            4 SYCADCKRL-T----EVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~-~----~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .+||.|++. +    .-..|+.+|...|..|+..|.|
T Consensus        15 y~Cp~C~~~ys~Lda~~L~d~~~~~F~C~~C~~el~e   51 (62)
T d1vd4a_          15 FKCPVCSSTFTDLEANQLFDPMTGTFRCTFCHTEVEE   51 (62)
T ss_dssp             EECSSSCCEEEHHHHHHHEETTTTEEBCSSSCCBCEE
T ss_pred             eECCCCCCCcchhhHHHhcCcCCCeEEecCCCCEEec
Confidence            579999973 1    1258899999999999999876

>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Herpesvirus saimiri [TaxId: 10381]

Probab=94.86  E-value=0.13  Score=37.63  Aligned_cols=83  Identities=10%  Similarity=0.211  Sum_probs=63.5

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcCC-CCCHHHHHHHhC--cchhHHHHH
Q 021438          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSND-TKPLKEISIVTR--VAEGTIKNV  285 (312)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~~-~~~~~~Ia~~~~--vs~~ti~~~  285 (312)
                      .+++..++..++++.++...|..++++...  -.....-.-+++||+++|+++... +.+.+++...++  .+...|.+.
T Consensus        35 idWl~~v~~~~~l~~eTl~lAv~llDryl~~~~i~~~~lqLi~~tcL~IAsK~ee~~~~~l~~l~~~~~~~~t~~ei~~m  114 (127)
T d1bu2a1          35 LTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSCDCFTNLELINQ  114 (127)
T ss_dssp             HHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTSCCCTTTHHHHHHHHHHHHHHHSSSSCCCHHHHHHTTTTSSCHHHHHHH
T ss_pred             HHHHHHHHHHHCCChHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHcCCCCHHHHHHH
Confidence            378889999999999999999999998654  234566788999999999999864 466888887765  356666655


Q ss_pred             HHHHHhhh
Q 021438          286 YKDLFPHL  293 (312)
Q Consensus       286 ~kel~~~~  293 (312)
                      =..|...+
T Consensus       115 E~~IL~~L  122 (127)
T d1bu2a1         115 EKDILEAL  122 (127)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHc
Confidence            55555544

>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Murine herpesvirus 68 [TaxId: 33708]

Probab=94.68  E-value=0.13  Score=38.34  Aligned_cols=85  Identities=12%  Similarity=0.083  Sum_probs=64.6

Q ss_pred             HHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh--ccCCCChHHHHHHHHHHHHHhcC-CCCCHHHHHHHhC--cchhHHHH
Q 021438          210 ASDYLRRFCSNLGMTNQAVKAAQEAVQKSED--LDIRRSPISVAAAVIYIITQLSN-DTKPLKEISIVTR--VAEGTIKN  284 (312)
Q Consensus       210 p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~--l~~Gr~P~~iaaAaiyla~~~~~-~~~~~~~Ia~~~~--vs~~ti~~  284 (312)
                      ..+++..++..++++.++...|..++++-..  -.......-+|++|+++|+++.. .+.+..+++..++  .+...|.+
T Consensus        47 lvdWm~~v~~~~~l~~etl~lAv~llDrfls~~~i~~~~lqL~a~tcL~IAsK~ee~~~~~~~~l~~~~~~~yt~~ei~~  126 (141)
T d1f5qb1          47 LTTWMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAYMPIKATQLAYLCGGATTADKLLT  126 (141)
T ss_dssp             HHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHCTTCCHHHHHH
T ss_pred             HHHHHHHHHHHHCCChHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHhcCCCCHHHHHH
Confidence            3578899999999999999999999998664  33455678899999999999985 4566888888776  45555555


Q ss_pred             HHHHHHhhhc
Q 021438          285 VYKDLFPHLA  294 (312)
Q Consensus       285 ~~kel~~~~~  294 (312)
                      -=.+|...++
T Consensus       127 mE~~IL~~L~  136 (141)
T d1f5qb1         127 LEVKSLDTLS  136 (141)
T ss_dssp             HHHHHHHHTT
T ss_pred             HHHHHHHHCC
Confidence            5455555443

>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: G1/S-specific cyclin-E1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.16  E-value=0.26  Score=36.57  Aligned_cols=82  Identities=15%  Similarity=0.214  Sum_probs=60.3

Q ss_pred             HHHHHHHhhcCCCHHHHHHHHHHHHHhhh---ccCCCChHHHHHHHHHHHHHhcC-CCCCHHHHHHHhC--cchhHHHHH
Q 021438          212 DYLRRFCSNLGMTNQAVKAAQEAVQKSED---LDIRRSPISVAAAVIYIITQLSN-DTKPLKEISIVTR--VAEGTIKNV  285 (312)
Q Consensus       212 ~~i~r~~~~L~l~~~v~~~A~~i~~~~~~---l~~Gr~P~~iaaAaiyla~~~~~-~~~~~~~Ia~~~~--vs~~ti~~~  285 (312)
                      +++.+++..++++.++...|..++++-..   ......-.-+|+||+++|++... ...+.++++..++  .+...|.+.
T Consensus        48 dW~~~v~~~~~l~~et~~lAv~llDryl~~~~~v~~~~lqL~a~acL~IAsK~ee~~~~~~~~l~~~~~~~~t~~ei~~m  127 (140)
T d1w98b2          48 DWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDEILTM  127 (140)
T ss_dssp             HHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTTSSCHHHHHHH
T ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHHHhccccccHHHHhHHHHHHHHHHHHHcccCCCCHHHHHHHHcCCCCHHHHHHH
Confidence            67889999999999999999999987543   23344567899999999999975 4566888887654  345555544


Q ss_pred             HHHHHhhh
Q 021438          286 YKDLFPHL  293 (312)
Q Consensus       286 ~kel~~~~  293 (312)
                      =.+|...+
T Consensus       128 E~~IL~~L  135 (140)
T d1w98b2         128 ELMIMKAL  135 (140)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHC
Confidence            44554443

>d2r7ga2 a.74.1.3 (A:644-785) Retinoblastoma tumor suppressor domains {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Retinoblastoma tumor suppressor domains
domain: Retinoblastoma tumor suppressor domains
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.99  E-value=0.072  Score=39.80  Aligned_cols=77  Identities=16%  Similarity=0.117  Sum_probs=60.3

Q ss_pred             HHHHHHHHhhcCCC-HHHHHHHHHHHHHhhh----ccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHH
Q 021438          211 SDYLRRFCSNLGMT-NQAVKAAQEAVQKSED----LDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNV  285 (312)
Q Consensus       211 ~~~i~r~~~~L~l~-~~v~~~A~~i~~~~~~----l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~  285 (312)
                      ..-+..+|++|+++ +++.+..|.+.+.+..    |..+|+-.-+.-.|+|..|+..+..++.++|-+.-.-.+.+-...
T Consensus        16 ~~Rl~~LC~~L~~~~~~l~~~Iw~~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~~F~~Ii~~Yr~qPq~~~~v   95 (142)
T d2r7ga2          16 YLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQET   95 (142)
T ss_dssp             HHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHTTSTTCCTHH
T ss_pred             HHHHHHHHHHHCcCcHHHHHHHHHHHHHHHHHhHHHHhccchhHHHHHHHHHHHHhccCCCCHHHHHHHHHhCCccchhH
Confidence            34567788898765 4677778888887654    788999999999999999999999999999977765555554444


Q ss_pred             HH
Q 021438          286 YK  287 (312)
Q Consensus       286 ~k  287 (312)
                      |+
T Consensus        96 yR   97 (142)
T d2r7ga2          96 FK   97 (142)
T ss_dssp             HH
T ss_pred             hh
Confidence            44

>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Viral cyclin
species: Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]

Probab=93.97  E-value=0.21  Score=36.65  Aligned_cols=82  Identities=10%  Similarity=0.165  Sum_probs=60.1

Q ss_pred             HHHHHHHhhcCCCHHHHHHHHHHHHHhhh-c-cCCCChHHHHHHHHHHHHHhcC-CCCCHHHHHHHhC--cchhHHHHHH
Q 021438          212 DYLRRFCSNLGMTNQAVKAAQEAVQKSED-L-DIRRSPISVAAAVIYIITQLSN-DTKPLKEISIVTR--VAEGTIKNVY  286 (312)
Q Consensus       212 ~~i~r~~~~L~l~~~v~~~A~~i~~~~~~-l-~~Gr~P~~iaaAaiyla~~~~~-~~~~~~~Ia~~~~--vs~~ti~~~~  286 (312)
                      +++.+++..++++.++...|..++++... . ..-..-.-+|++|+++|+++.. .+.+.+++...++  .+...|.+.=
T Consensus        41 dWl~~v~~~~~l~~et~~lAv~llDrfls~~~v~~~~lqLia~tcl~iAsK~ee~~~~~~~~l~~~~~~~~t~~ei~~mE  120 (132)
T d1g3nc1          41 TWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAADSFSRQELIDQE  120 (132)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHTTTCSCHHHHHHHH
T ss_pred             HHHHHHHHHhCCCcchHHHHHHHHHHHcCcccCcHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHcCCCCHHHHHHHH
Confidence            68889999999999999999999998664 1 1122345688999999999975 4566788887763  5556666555


Q ss_pred             HHHHhhh
Q 021438          287 KDLFPHL  293 (312)
Q Consensus       287 kel~~~~  293 (312)
                      ..|...+
T Consensus       121 ~~IL~~L  127 (132)
T d1g3nc1         121 KELLEKL  127 (132)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHc
Confidence            5555544

>d1neea2 g.59.1.1 (A:99-135) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Small proteins
fold: Zinc-binding domain of translation initiation factor 2 beta
superfamily: Zinc-binding domain of translation initiation factor 2 beta
family: Zinc-binding domain of translation initiation factor 2 beta
domain: Zinc-binding domain of translation initiation factor 2 beta
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=93.88  E-value=0.017  Score=32.77  Aligned_cols=28  Identities=25%  Similarity=0.637  Sum_probs=23.4

Q ss_pred             CCCCCCCC-CceeeeCCCCceEcCCCccc
Q 021438            5 YCADCKRL-TEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         5 ~Cp~Cg~~-~~ii~D~~~G~~vC~~CG~V   32 (312)
                      .|+.|+++ +.++.|...-.+.|..||.-
T Consensus         3 ~C~~C~spDT~l~ke~R~~~l~C~aCGa~   31 (37)
T d1neea2           3 ICHECNRPDTRIIREGRISLLKCEACGAK   31 (37)
T ss_dssp             HHTCCSSCSSCCEEETTTTEEECSTTSCC
T ss_pred             ECCCCCCCCCEEEEcCCEEEEEeccCCCC
Confidence            59999995 57788877788999999963

>d1k81a_ g.59.1.1 (A:) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Small proteins
fold: Zinc-binding domain of translation initiation factor 2 beta
superfamily: Zinc-binding domain of translation initiation factor 2 beta
family: Zinc-binding domain of translation initiation factor 2 beta
domain: Zinc-binding domain of translation initiation factor 2 beta
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.46  E-value=0.015  Score=32.73  Aligned_cols=28  Identities=21%  Similarity=0.629  Sum_probs=22.1

Q ss_pred             CCCCCCCC-CceeeeCCCCceEcCCCccc
Q 021438            5 YCADCKRL-TEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         5 ~Cp~Cg~~-~~ii~D~~~G~~vC~~CG~V   32 (312)
                      .|+.||++ +.++.|...-.+.|..||.-
T Consensus         2 ~C~~C~spDT~l~ke~R~~~l~C~aCGa~   30 (36)
T d1k81a_           2 ICRECGKPDTKIIKEGRVHLLKCMACGAI   30 (36)
T ss_dssp             CCSSSCSCEEEEEEETTEEEEEEETTTEE
T ss_pred             CCCCCCCCCCEEEEcCCEEEEEeccCCCC
Confidence            69999995 46677766667899999963

>d1nuia2 g.41.3.2 (A:10-63) Zinc-binding domain of primase-helicase {Bacteriophage T7 [TaxId: 10760]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: DNA primase zinc finger
domain: Zinc-binding domain of primase-helicase
species: Bacteriophage T7 [TaxId: 10760]

Probab=93.18  E-value=0.029  Score=34.68  Aligned_cols=32  Identities=22%  Similarity=0.339  Sum_probs=23.4

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      +..||.||+...+ -=++.|-..|-.|+.-...
T Consensus         5 H~pCp~CgSSDa~-a~y~DGh~~CFsC~~~~~~   36 (54)
T d1nuia2           5 HIPCDNCGSSDGN-SLFSDGHTFCYVCEKWTAG   36 (54)
T ss_dssp             EECCSSSCCSSCE-EEETTSCEEETTTCCEEC-
T ss_pred             ccCCCCCCCCCCC-eEccCCCeEeeeCCCCcCC
Confidence            3579999995333 3356899999999987643

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=93.15  E-value=0.073  Score=33.62  Aligned_cols=30  Identities=20%  Similarity=0.313  Sum_probs=27.7

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +-.+|..+||+.+|+|+.|+..|++.|.+.
T Consensus        15 n~r~s~~~lA~~~gls~~~v~~Ri~~L~~~   44 (60)
T d1i1ga1          15 DARTPFTEIAKKLGISETAVRKRVKALEEK   44 (60)
T ss_dssp             CTTCCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            457899999999999999999999999986

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=93.02  E-value=0.074  Score=33.95  Aligned_cols=30  Identities=7%  Similarity=0.206  Sum_probs=27.6

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +-+.|..+||+.+|+|+.|+..|++.|.+.
T Consensus        17 n~r~s~~~iA~~lgis~~tv~~Ri~~L~~~   46 (63)
T d2cfxa1          17 DSRLSMRELGRKIKLSPPSVTERVRQLESF   46 (63)
T ss_dssp             CSCCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            457899999999999999999999999885

>d1y0ja1 g.39.1.1 (A:200-238) Erythroid transcription factor GATA-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Erythroid transcription factor GATA-1
domain: Erythroid transcription factor GATA-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.56  E-value=0.039  Score=31.54  Aligned_cols=31  Identities=23%  Similarity=0.613  Sum_probs=21.9

Q ss_pred             CCCCCCCCCCCC-ceeeeCCCCceEcCCCccc
Q 021438            2 ADSYCADCKRLT-EVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         2 ~~~~Cp~Cg~~~-~ii~D~~~G~~vC~~CG~V   32 (312)
                      +...|.+||... ..-.....|...|..||+-
T Consensus         1 e~r~C~~Cgtt~Tp~WR~gp~G~~LCNACGl~   32 (39)
T d1y0ja1           1 EARECVNCGATATPLWRRDRTGHYLCNACGLY   32 (39)
T ss_dssp             CCCCCSSSCCCCCSCCEECTTSCEECSSHHHH
T ss_pred             CcCCCCCCCCCCCcccccCCCCCEeeHHhHHH
Confidence            356899999742 3333446788999999975

>d1jkwa2 a.74.1.1 (A:162-287) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin H (mcs2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.32  E-value=0.31  Score=35.54  Aligned_cols=91  Identities=5%  Similarity=0.005  Sum_probs=58.9

Q ss_pred             hHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHhCCCC--CHHHHHHH--hcCCC
Q 021438          105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPR--TVKEFCSV--ANGTT  180 (312)
Q Consensus       105 ~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaaAcly~acr~~~~p~--tl~dia~~--~~~v~  180 (312)
                      .|...+..|+..+..+.=++.+...|..+....+-....--..+..||.||||+|++..+.+.  .+.++...  . ..+
T Consensus         5 pl~g~l~dl~~~~~~~~~~~~l~~~a~~~lnds~~Td~~l~y~P~qIalaal~~a~~~~~~~l~~y~~~~~~~~~~-~~~   83 (126)
T d1jkwa2           5 PFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKEN-RTC   83 (126)
T ss_dssp             HHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHTTSTHHHHSCHHHHHHHHHHHHHHHHSCCCTTHHHHHTTSCSS-SCC
T ss_pred             cHHHHHHHHHHhccCcCCHHHHHHHHHHHHHHHHcCCeeeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccccc-hhh
Confidence            444444445544444555678888999999887655443446899999999999999998754  34454321  1 234


Q ss_pred             HHHHHHHHHHHHHHHh
Q 021438          181 KKEIGRAKEFIVKHLE  196 (312)
Q Consensus       181 ~~~i~~~~~~l~~~l~  196 (312)
                      ..++....+++...++
T Consensus        84 ~~~l~~~i~~i~~l~~   99 (126)
T d1jkwa2          84 LSQLLDIMKSMRNLVK   99 (126)
T ss_dssp             THHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4556666666665554

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=92.07  E-value=0.12  Score=32.45  Aligned_cols=30  Identities=37%  Similarity=0.505  Sum_probs=27.7

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +-..|..+||+.+|+|+.|+..|++.|.+.
T Consensus        15 n~r~s~~eiA~~l~ls~~~v~~Ri~~L~~~   44 (60)
T d2cyya1          15 DGKAPLREISKITGLAESTIHERIRKLRES   44 (60)
T ss_dssp             CTTCCHHHHHHHHCSCHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            457899999999999999999999999886

>d1hw1a1 a.4.5.6 (A:5-78) Fatty acid responsive transcription factor FadR, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Fatty acid responsive transcription factor FadR, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.67  E-value=0.27  Score=32.24  Aligned_cols=30  Identities=20%  Similarity=0.246  Sum_probs=26.9

Q ss_pred             CCCC-CHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTK-PLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~-~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      |.++ +.+++|+.++||..|+++.|+.|.+.
T Consensus        24 G~~LPs~~eLa~~~~vSr~tvr~Al~~L~~~   54 (74)
T d1hw1a1          24 GTILPAERELSELIGVTRTTLREVLQRLARD   54 (74)
T ss_dssp             TSBCCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCccHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            5667 58999999999999999999999875

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=91.54  E-value=0.14  Score=32.75  Aligned_cols=35  Identities=14%  Similarity=0.167  Sum_probs=30.1

Q ss_pred             hcCCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          261 LSNDTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       261 ~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      +.....+-+|||+.+++|+.|++.+.+.+++.++.
T Consensus        15 l~~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   49 (65)
T d1l3la1          15 WIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDV   49 (65)
T ss_dssp             HHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             HHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            33456889999999999999999999999998753

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=91.33  E-value=0.15  Score=32.78  Aligned_cols=33  Identities=24%  Similarity=0.265  Sum_probs=28.9

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ....+.+|||...|+|+.||+++.+.+++.++.
T Consensus        17 ~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v   49 (67)
T d1fsea_          17 VQDKTTKEIASELFISEKTVRNHISNAMQKLGV   49 (67)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             HccCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            345789999999999999999999999987653

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=91.19  E-value=0.17  Score=32.08  Aligned_cols=30  Identities=17%  Similarity=0.104  Sum_probs=27.5

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +-..|..+||+.+|+|+.|++.|++.|.+.
T Consensus        17 ~~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~   46 (63)
T d2cg4a1          17 NARTAYAELAKQFGVSPETIHVRVEKMKQA   46 (63)
T ss_dssp             CTTSCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            456889999999999999999999999986

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.76  E-value=0.18  Score=31.96  Aligned_cols=29  Identities=7%  Similarity=0.086  Sum_probs=26.4

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFP  291 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~  291 (312)
                      +..+|..++|+.+|||..||++..++|.+
T Consensus        17 ~~~~s~~eLa~~l~vS~~ti~r~i~~L~~   45 (63)
T d1biaa1          17 GEFHSGEQLGETLGMSRAAINKHIQTLRD   45 (63)
T ss_dssp             SSCBCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            45688999999999999999999999877

>d1jj2y_ g.41.8.1 (Y:) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=90.57  E-value=0.073  Score=34.84  Aligned_cols=32  Identities=19%  Similarity=0.457  Sum_probs=25.8

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      ...||.||. .. +.-...|-.-|..||..+.-.
T Consensus        27 ky~Cp~Cgk-~~-vkR~a~GIW~C~kC~~~~AGg   58 (73)
T d1jj2y_          27 KHKCPVCGF-KK-LKRAGTGIWMCGHCGYKIAGG   58 (73)
T ss_dssp             CBCCSSSCC-SC-EEEEETTEEEETTTCCEEECC
T ss_pred             CccCCCCCC-Cc-eEEEEEEEEECCCCCCEEeCc
Confidence            458999998 33 566789999999999998653

>d2cchb2 a.74.1.1 (B:309-432) Cyclin A {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin A
species: Cow (Bos taurus) [TaxId: 9913]

Probab=90.31  E-value=1.1  Score=32.25  Aligned_cols=85  Identities=9%  Similarity=-0.026  Sum_probs=56.7

Q ss_pred             HHHHHHH-HhcCCcHHHHHHHHHHHHHHH-hCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHH
Q 021438          111 KSISAMS-DRLGLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK  188 (312)
Q Consensus       111 ~~I~~~~-~~L~Lp~~v~~~A~~i~~~~~-~~~~~~gr~~~~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~  188 (312)
                      .++.++. ..-+....+...|.-+..... +...+-+.++-.+||||+|+|-+..+.+-=-.++...+ |.+..+|....
T Consensus         5 ~FL~ry~~~~~~~d~~~~~la~Yl~ElsLl~~~~~l~~~PS~lAaaai~lar~~l~~~~W~~~L~~~t-~y~~~~l~~c~   83 (124)
T d2cchb2           5 QFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRKT-GYTLESLKPCL   83 (124)
T ss_dssp             HHHHHHHTTCSSCCHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHHHHHHHHHHHHSCCSCHHHHHHH-CCCHHHHHHHH
T ss_pred             HHHHHHHHHHccCcHHHHHHHHHHHHHHHHhHHHHHccChHHHHHHHHHHHHHHhCCCCchHHHHHHh-CCCHHHHHHHH
Confidence            4555543 233444555556666666543 22334467888999999999977766543335566667 89999999999


Q ss_pred             HHHHHHHh
Q 021438          189 EFIVKHLE  196 (312)
Q Consensus       189 ~~l~~~l~  196 (312)
                      +.|.+.+.
T Consensus        84 ~~L~~~~~   91 (124)
T d2cchb2          84 MDLHQTYL   91 (124)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88877653

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=90.29  E-value=0.21  Score=32.40  Aligned_cols=32  Identities=22%  Similarity=0.109  Sum_probs=28.3

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ...+.++||...|+|+.||++..+.++..++.
T Consensus        26 ~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   57 (70)
T d1yioa1          26 RGLMNKQIAGELGIAEVTVKVHRHNIMQKLNV   57 (70)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            45678999999999999999999999987653

>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27a
domain: Ribosomal protein S27ae
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=90.18  E-value=0.11  Score=31.85  Aligned_cols=27  Identities=22%  Similarity=0.726  Sum_probs=20.8

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      ..||.||. .-+.-++. ....|..||+-
T Consensus        19 k~CP~CG~-GvFmA~H~-dR~~CGKCgyT   45 (55)
T d2k4xa1          19 RFCPRCGP-GVFLAEHA-DRYSCGRCGYT   45 (55)
T ss_dssp             CCCTTTTT-TCCCEECS-SEEECTTTCCC
T ss_pred             CcCcCCCC-cEEeeecC-CCccccCCccc
Confidence            46999997 55555554 68999999986

>d1vqoz1 g.41.8.1 (Z:10-82) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=90.16  E-value=0.081  Score=34.61  Aligned_cols=32  Identities=25%  Similarity=0.470  Sum_probs=25.8

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      ...||.||. .. +.-...|-..|..||..+.-.
T Consensus        27 ky~Cp~Cgk-~~-vkR~a~GIW~C~kC~~~~AGG   58 (73)
T d1vqoz1          27 DHACPNCGE-DR-VDRQGTGIWQCSYCDYKFTGG   58 (73)
T ss_dssp             CBCCSSSSC-SC-EEEEETTEEEETTTCCEEECC
T ss_pred             CccCCCCCC-ce-eEEEEEEEEECCCCCCEEeCC
Confidence            357999998 34 566789999999999998643

>d1u5ka2 g.45.1.2 (A:81-237) Recombinational repair protein RecO, C-terminal domain {Deinococcus radiodurans [TaxId: 1299]}

class: Small proteins
fold: ArfGap/RecO-like zinc finger
superfamily: ArfGap/RecO-like zinc finger
family: RecO C-terminal domain-like
domain: Recombinational repair protein RecO, C-terminal domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=89.92  E-value=0.097  Score=39.79  Aligned_cols=29  Identities=28%  Similarity=0.563  Sum_probs=25.0

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGL   31 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~   31 (312)
                      ...|..||......+|...|..+|.+|+.
T Consensus        70 l~~C~~cg~~~~~~f~~~~Gg~~C~~c~~   98 (157)
T d1u5ka2          70 TARCARCGAPDPEHPDPLGGQLLCSKCAA   98 (157)
T ss_dssp             CSBCTTTCCBSCCEECTTTSSEECTTTCS
T ss_pred             hhhHhcCCCCCCCcccccCCeeECCCCCC
Confidence            45799999877778899999999999974

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=89.75  E-value=0.18  Score=32.38  Aligned_cols=31  Identities=23%  Similarity=0.233  Sum_probs=27.9

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ..+.++||+..++|+.|++++.+.+++.++.
T Consensus        21 G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   51 (67)
T d1a04a1          21 GLPNKMIARRLDITESTVKVHVKHMLKKMKL   51 (67)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            5678999999999999999999999998753

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=89.48  E-value=0.47  Score=31.27  Aligned_cols=29  Identities=3%  Similarity=0.045  Sum_probs=26.7

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .++|+.|||+.+|+|..|+.+..++|.+.
T Consensus        28 ~~lt~~eLA~~~G~sretvsr~L~~l~~~   56 (81)
T d2gaua1          28 IYLSREELATLSNMTVSNAIRTLSTFVSE   56 (81)
T ss_dssp             CCCCHHHHHHHTTSCHHHHHHHHHHHHHT
T ss_pred             ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            46889999999999999999999999885

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=89.02  E-value=0.61  Score=30.68  Aligned_cols=29  Identities=24%  Similarity=0.150  Sum_probs=26.7

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .++|+.+||+.+|+|..|+.+.+++|.+.
T Consensus        29 ~~lt~~elA~~~g~sretvsr~l~~l~~~   57 (80)
T d3e5ua1          29 MPLSQKSIGEITGVHHVTVSRVLASLKRE   57 (80)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             eCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            46889999999999999999999999885

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=88.89  E-value=0.17  Score=32.43  Aligned_cols=33  Identities=15%  Similarity=0.165  Sum_probs=26.8

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhccc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLARI  296 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~~  296 (312)
                      ...+.+|||...|+|+.|++.++..-...+...
T Consensus        33 ~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~   65 (68)
T d1or7a1          33 DGLSYEEIAAIMDCPVGTVRSRIFRAREAIDNK   65 (68)
T ss_dssp             TCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            347799999999999999999987766655443

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=88.88  E-value=0.15  Score=32.84  Aligned_cols=32  Identities=13%  Similarity=0.270  Sum_probs=26.8

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhhhcc
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPHLAR  295 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~~  295 (312)
                      ...|.+|||..+|+|+.|+++++....+.+..
T Consensus        36 ~~~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~   67 (71)
T d1rp3a2          36 EELPAKEVAKILETSVSRVSQLKAKALERLRE   67 (71)
T ss_dssp             SCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            45889999999999999999998776666543

>d1efaa1 a.35.1.5 (A:2-60) Lac repressor (LacR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Lac repressor (LacR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=88.83  E-value=0.15  Score=32.06  Aligned_cols=22  Identities=18%  Similarity=0.187  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHhCcchhHHHHHH
Q 021438          265 TKPLKEISIVTRVAEGTIKNVY  286 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~  286 (312)
                      ++|++|||+.+|||..|+...+
T Consensus         2 ~~Ti~diA~~agvS~sTVSr~l   23 (59)
T d1efaa1           2 PVTLYDVAEYAGVSYQTVSRVV   23 (59)
T ss_dssp             CCCHHHHHHTTTSCHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHH
Confidence            5789999999999999999765

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=88.09  E-value=0.5  Score=29.93  Aligned_cols=30  Identities=10%  Similarity=-0.037  Sum_probs=26.0

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      ...++..++|+.++||+.||++-+++|.+.
T Consensus        20 ~~~vs~~~La~~l~VS~~TI~rdi~~L~~~   49 (65)
T d1j5ya1          20 KEPVSGAQLAEELSVSRQVIVQDIAYLRSL   49 (65)
T ss_dssp             SSCBCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            345899999999999999999999888653

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=88.04  E-value=0.2  Score=32.41  Aligned_cols=30  Identities=13%  Similarity=0.242  Sum_probs=27.2

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      |.+++.+++|+.+|+|..|+++.++.|...
T Consensus        23 G~~l~~~~La~~~~vSr~tvr~Al~~L~~~   52 (69)
T d2hs5a1          23 GARLSEPDICAALDVSRNTVREAFQILIED   52 (69)
T ss_dssp             TCEECHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            667889999999999999999999999864

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=87.98  E-value=0.5  Score=30.39  Aligned_cols=38  Identities=13%  Similarity=0.258  Sum_probs=30.5

Q ss_pred             HHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          254 VIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       254 aiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .|+-..+.++ ++|..|||+.+|+|..|++...++|.+.
T Consensus        10 ~Il~~l~~~g-~~sr~eLa~~~glS~~Tv~~~l~~L~~~   47 (71)
T d1z05a1          10 RVYKLIDQKG-PISRIDLSKESELAPASITKITRELIDA   47 (71)
T ss_dssp             HHHHHHHHHC-SBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            3443334444 7999999999999999999999999885

>d2hsga1 a.35.1.5 (A:2-58) Glucose-resistance amylase regulator CcpA, N-terminal domain {Bacillus megaterium [TaxId: 1404]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Glucose-resistance amylase regulator CcpA, N-terminal domain
species: Bacillus megaterium [TaxId: 1404]

Probab=87.68  E-value=0.18  Score=31.37  Aligned_cols=22  Identities=14%  Similarity=0.217  Sum_probs=19.5

Q ss_pred             CCHHHHHHHhCcchhHHHHHHH
Q 021438          266 KPLKEISIVTRVAEGTIKNVYK  287 (312)
Q Consensus       266 ~~~~~Ia~~~~vs~~ti~~~~k  287 (312)
                      +|++|||+.+|||..|+.+.+.
T Consensus         2 vTi~dvA~~agvS~~TVSr~Ln   23 (57)
T d2hsga1           2 VTIYDVAREASVSMATVSRVVN   23 (57)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHT
T ss_pred             cCHHHHHHHHCcCHHHHHHHhC
Confidence            6899999999999999997653

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=87.64  E-value=0.52  Score=29.55  Aligned_cols=38  Identities=13%  Similarity=0.235  Sum_probs=29.8

Q ss_pred             HHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          254 VIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       254 aiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +||....- +...+..+||+.+||+.+|+.+..|.|.+.
T Consensus        11 ~I~~l~~~-~~~v~~~~iA~~L~vs~~SVs~mikrL~~~   48 (61)
T d2ev0a1          11 QIYMLIEE-KGYARVSDIAEALAVHPSSVTKMVQKLDKD   48 (61)
T ss_dssp             HHHHHHHH-HSSCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHhc-CCCccHHHHHHHhCCCchhHHHHHHHHHHC
Confidence            34444433 346788999999999999999999999874

>d2vuti1 g.39.1.1 (I:671-712) Erythroid transcription factor GATA-1 {Emericella nidulans [TaxId: 162425]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Erythroid transcription factor GATA-1
domain: Erythroid transcription factor GATA-1
species: Emericella nidulans [TaxId: 162425]

Probab=87.60  E-value=0.084  Score=30.59  Aligned_cols=29  Identities=31%  Similarity=0.771  Sum_probs=20.4

Q ss_pred             CCCCCCCC-CceeeeCCCCceEcCCCcccc
Q 021438            5 YCADCKRL-TEVVFDHSAGDTICSECGLVL   33 (312)
Q Consensus         5 ~Cp~Cg~~-~~ii~D~~~G~~vC~~CG~Vv   33 (312)
                      .|.+||.. +.+-..-..|..+|..||+-.
T Consensus         2 ~C~nC~tt~Tp~WRr~~~G~~lCNACGl~~   31 (42)
T d2vuti1           2 TCTNCFTQTTPLWRRNPEGQPLCNACGLFL   31 (42)
T ss_dssp             CCSSSCCCCCSCCEECTTSCEECHHHHHHH
T ss_pred             cCCCCCCCCCccceeCCCCCCchhhhhHHH
Confidence            68899974 233344567889999999853

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.40  E-value=0.24  Score=31.90  Aligned_cols=29  Identities=17%  Similarity=0.131  Sum_probs=26.3

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .++|+.|||+.+|+|..|+.+..++|.+.
T Consensus        28 l~lt~~~lA~~~G~sRetvsr~L~~l~~~   56 (69)
T d1i5za1          28 IKITRQEIGQIVGCSRETVGRILKMLEDQ   56 (69)
T ss_dssp             EECCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            35889999999999999999999999874

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=87.27  E-value=1.1  Score=29.81  Aligned_cols=54  Identities=19%  Similarity=0.212  Sum_probs=37.3

Q ss_pred             HHHHHhhc-CCCHHHHHHHHHHHHHhhhccCCCChHHHHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHH
Q 021438          214 LRRFCSNL-GMTNQAVKAAQEAVQKSEDLDIRRSPISVAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDL  289 (312)
Q Consensus       214 i~r~~~~L-~l~~~v~~~A~~i~~~~~~l~~Gr~P~~iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel  289 (312)
                      +.++-+.+ +|++...+.|..|++.         |..++             ..+.++||+.++||++||-+-+|.|
T Consensus         6 l~~i~~~~~~Ls~~e~~ia~yil~~---------~~~~~-------------~~si~~lA~~~~vS~sTi~Rf~kkl   60 (83)
T d2o3fa1           6 LAIIQSMKHKLPPSERKLADYILAH---------PHKAI-------------ESTVNEISALANSSDAAVIRLCKSL   60 (83)
T ss_dssp             HHHHHHHGGGSCHHHHHHHHHHHHC---------HHHHH-------------TCCHHHHHHHTTCCHHHHHHHHHHT
T ss_pred             HHHHHHHHhhCCHHHHHHHHHHHcC---------HHHHH-------------HccHHHHHHHHCCCHHHHHHHHHHh
Confidence            44444444 4677666677766654         33333             5789999999999999999876654

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional regulator YydK
species: Bacillus subtilis [TaxId: 1423]

Probab=87.19  E-value=0.3  Score=32.24  Aligned_cols=30  Identities=20%  Similarity=0.157  Sum_probs=26.9

Q ss_pred             CCCC-CHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTK-PLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~-~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      |.++ +.+++|+.++||..||++.++.|...
T Consensus        19 G~~LPse~~La~~~~vSr~tvr~Al~~L~~~   49 (78)
T d3bwga1          19 GDKLPVLETLMAQFEVSKSTITKSLELLEQK   49 (78)
T ss_dssp             TCBCCCHHHHHHHTTCCHHHHHHHHHHHHHT
T ss_pred             cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            5677 68999999999999999999999874

>d2dsxa1 g.41.5.1 (A:1-52) Rubredoxin {Desulfovibrio gigas [TaxId: 879]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio gigas [TaxId: 879]

Probab=87.03  E-value=0.13  Score=31.40  Aligned_cols=19  Identities=32%  Similarity=0.593  Sum_probs=9.8

Q ss_pred             CCCCCCCCCCCCCceeeeCCCCc
Q 021438            1 MADSYCADCKRLTEVVFDHSAGD   23 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D~~~G~   23 (312)
                      |....|+.||-    ++|+..|+
T Consensus         1 M~~y~C~~Cgy----iYdp~~Gd   19 (52)
T d2dsxa1           1 MDIYVCTVCGY----EYDPAKGD   19 (52)
T ss_dssp             CCCEEETTTCC----EECTTTCB
T ss_pred             CCeEEeCCCCe----EECcccCC
Confidence            44555555553    45555544

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.00  E-value=0.21  Score=31.29  Aligned_cols=22  Identities=27%  Similarity=0.273  Sum_probs=19.4

Q ss_pred             CCHHHHHHHhCcchhHHHHHHH
Q 021438          266 KPLKEISIVTRVAEGTIKNVYK  287 (312)
Q Consensus       266 ~~~~~Ia~~~~vs~~ti~~~~k  287 (312)
                      +|++|||+.+|||..|+...+.
T Consensus         1 vTl~diA~~agvS~sTVSrvLn   22 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVIN   22 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHc
Confidence            5789999999999999997764

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=86.50  E-value=0.37  Score=31.29  Aligned_cols=32  Identities=13%  Similarity=0.024  Sum_probs=28.2

Q ss_pred             hcCCCCCHHHHHHHhCc-chhHHHHHHHHHHhh
Q 021438          261 LSNDTKPLKEISIVTRV-AEGTIKNVYKDLFPH  292 (312)
Q Consensus       261 ~~~~~~~~~~Ia~~~~v-s~~ti~~~~kel~~~  292 (312)
                      -+|++.|.+||++.+|+ |.+|+....+.|.+.
T Consensus        20 ~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~k   52 (71)
T d1jhfa1          20 QTGMPPTRAEIAQRLGFRSPNAAEEHLKALARK   52 (71)
T ss_dssp             HHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHT
T ss_pred             HhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHC
Confidence            35889999999999998 899999999988774

>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Purine repressor (PurR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=86.38  E-value=0.27  Score=30.56  Aligned_cols=21  Identities=19%  Similarity=0.374  Sum_probs=18.5

Q ss_pred             CHHHHHHHhCcchhHHHHHHH
Q 021438          267 PLKEISIVTRVAEGTIKNVYK  287 (312)
Q Consensus       267 ~~~~Ia~~~~vs~~ti~~~~k  287 (312)
                      |++|||+.+|||..|+.+.+.
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln   22 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVIN   22 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHC
Confidence            689999999999999997664

>d1rqga3 g.41.1.1 (A:139-173) Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyrococcus abyssi [TaxId: 29292]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Pyrococcus abyssi [TaxId: 29292]

Probab=86.37  E-value=0.23  Score=27.47  Aligned_cols=26  Identities=31%  Similarity=0.635  Sum_probs=18.9

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccCc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~   36 (312)
                      ..||.||..      ...|+ -|..||..++..
T Consensus         3 G~CP~C~~~------~a~GD-qCe~CG~~~~p~   28 (35)
T d1rqga3           3 GTCPYCGAE------DQKGD-QCEVCGRPLTPE   28 (35)
T ss_dssp             SBCSSSCCS------CCCTT-TCSSSCCCCCTT
T ss_pred             EECCCCCCC------cccCc-chhhcCCccCHH
Confidence            579999983      12454 599999998653

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.04  E-value=0.46  Score=30.92  Aligned_cols=32  Identities=19%  Similarity=0.567  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCceeeeCC-----CC---ceEcCCCcccccC
Q 021438            4 SYCADCKRLTEVVFDHS-----AG---DTICSECGLVLEA   35 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~-----~G---~~vC~~CG~Vv~e   35 (312)
                      ..||.||....+.+...     +|   .++|.+||.--.+
T Consensus        24 ~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~C~h~Wr~   63 (72)
T d1twfi2          24 RECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTS   63 (72)
T ss_dssp             CCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEEC
T ss_pred             CCCCCCCCCeEEEEEeecCccCCCceEEEEcCCCCCCccc
Confidence            58999998544443322     22   3899999987433

>d2ak3a2 g.41.2.1 (A:125-161) Microbial and mitochondrial ADK, insert "zinc finger" domain {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=86.02  E-value=0.035  Score=31.49  Aligned_cols=29  Identities=14%  Similarity=0.045  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~V   32 (312)
                      ..||.||..=.+.+.+..=+-+|-.||.-
T Consensus         3 ~vc~~cG~~Yh~~~~pPk~~g~CD~cg~~   31 (37)
T d2ak3a2           3 WIHPGSGRVYNIEFNPPKTMGIDDLTGEP   31 (37)
T ss_dssp             EEETTTTEEEETTTBCCSSTTBCTTTCCB
T ss_pred             eeeCCcCChhhhccCCccccCCccCCCCc
Confidence            46888887446667777777888888853

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=85.98  E-value=0.37  Score=31.83  Aligned_cols=29  Identities=14%  Similarity=0.131  Sum_probs=26.5

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .++|+++||+.+|+|..|+.+.+++|.+.
T Consensus        29 ~~~t~~eiA~~lG~sretvsr~l~~l~~~   57 (80)
T d1ft9a1          29 VDFTVEEIANLIGSSRQTTSTALNSLIKE   57 (80)
T ss_dssp             ECCCHHHHHHHHCSCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            36789999999999999999999999885

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=85.41  E-value=0.87  Score=28.68  Aligned_cols=30  Identities=10%  Similarity=-0.059  Sum_probs=26.6

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +...+..+||+.+||+.+|+.+..|.|.+.
T Consensus        21 ~~~v~~~~iA~~L~vs~~SVt~mvkrL~~~   50 (63)
T d2isya1          21 GVTPLRARIAERLDQSGPTVSQTVSRMERD   50 (63)
T ss_dssp             TCCCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCCcHHHHHHHhCCCchhHHHHHHHHHHC
Confidence            446788999999999999999999999874

>d1iroa_ g.41.5.1 (A:) Rubredoxin {Clostridium pasteurianum [TaxId: 1501]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Clostridium pasteurianum [TaxId: 1501]

Probab=85.32  E-value=0.18  Score=30.89  Aligned_cols=19  Identities=26%  Similarity=0.683  Sum_probs=9.7

Q ss_pred             CCCCCCCCCCCCCceeeeCCCCc
Q 021438            1 MADSYCADCKRLTEVVFDHSAGD   23 (312)
Q Consensus         1 ~~~~~Cp~Cg~~~~ii~D~~~G~   23 (312)
                      |....|+.||-    |+|+..|+
T Consensus         1 M~ky~C~~Cgy----iYd~~~Gd   19 (53)
T d1iroa_           1 MKKYTCTVCGY----IYNPEDGD   19 (53)
T ss_dssp             CCCEEETTTCC----EECTTTCB
T ss_pred             CCCeEcCCCCc----EECcccCC
Confidence            44455555553    45555444

>d2j0151 g.41.8.5 (5:2-60) Ribosomal protein L32p {Thermus thermophilus [TaxId: 274]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L32p
domain: Ribosomal protein L32p
species: Thermus thermophilus [TaxId: 274]

Probab=85.27  E-value=0.26  Score=30.82  Aligned_cols=26  Identities=31%  Similarity=0.758  Sum_probs=18.4

Q ss_pred             CCCCCCCCCCCceeeeCCCCceEcCCCcccccC
Q 021438            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         3 ~~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      ...||+||.. .      .--.||.+||+-=+-
T Consensus        29 l~~C~~CG~~-~------~pHrvC~~CG~YkGr   54 (59)
T d2j0151          29 LVPCPECKAM-K------PPHTVCPECGYYAGR   54 (59)
T ss_dssp             CBCCSSSSSC-B------CTTCBCTTTCCSSSC
T ss_pred             eeECCCCCCc-c------cceeECCCCCeECCE
Confidence            4579999983 2      345689999986443

>d3gata_ g.39.1.1 (A:) Erythroid transcription factor GATA-1 {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Erythroid transcription factor GATA-1
domain: Erythroid transcription factor GATA-1
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=85.05  E-value=0.15  Score=32.75  Aligned_cols=33  Identities=27%  Similarity=0.722  Sum_probs=23.6

Q ss_pred             CCCCCCCCCC-CceeeeCCCCceEcCCCcccccC
Q 021438            3 DSYCADCKRL-TEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         3 ~~~Cp~Cg~~-~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      ...|-+||.. +.+=.....|..+|..||+-..-
T Consensus         4 g~~C~nCgt~~Tp~WRr~~~G~~lCNACGl~~~~   37 (66)
T d3gata_           4 GTVCSNCQTSTTTLWRRSPMGDPVCNACGLYYKL   37 (66)
T ss_dssp             TCCCTTTCCCCCSSEEECTTSCEEEHHHHHHHHH
T ss_pred             CCCCCCCCCCCCcccccCCCCCcccchhHHHHHH
Confidence            4579999974 23344456788999999988643

>d1l1oc_ b.40.4.3 (C:) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 70 KDa subunit (RPA70)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.74  E-value=0.22  Score=38.73  Aligned_cols=28  Identities=25%  Similarity=0.676  Sum_probs=22.1

Q ss_pred             CCCC--CCCCCceeeeCCCCceEcCCCcccccC
Q 021438            5 YCAD--CKRLTEVVFDHSAGDTICSECGLVLEA   35 (312)
Q Consensus         5 ~Cp~--Cg~~~~ii~D~~~G~~vC~~CG~Vv~e   35 (312)
                      .||.  |+.  . +.|..+|...|..||.+.++
T Consensus        42 aCp~~~C~K--K-v~~~~~g~~~C~kC~~~~~~   71 (178)
T d1l1oc_          42 ACPTQDCNK--K-VIDQQNGLYRCEKCDTEFPN   71 (178)
T ss_dssp             BCCSTTCCC--B-CEEETTTEEEETTTTEEESS
T ss_pred             CCCCcccCC--c-cccCCCCcEECCCCCCcCCC
Confidence            6997  776  3 46678899999999988754

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.68  E-value=0.3  Score=31.85  Aligned_cols=37  Identities=19%  Similarity=0.646  Sum_probs=27.5

Q ss_pred             CCCCCCCCCCceeeeCCCCceEcCCCcccccCcccccccccc
Q 021438            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWR   45 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~D~~~G~~vC~~CG~Vv~e~~id~~~ewr   45 (312)
                      ..||.|+.  .++.|...-.+.|..||...=   ..=+.+|+
T Consensus        19 k~CP~C~~--~~~~~~~~~~~~C~~C~~~fC---~~C~~~w~   55 (73)
T d2ct7a1          19 LWCAQCSF--GFIYEREQLEATCPQCHQTFC---VRCKRQWE   55 (73)
T ss_dssp             ECCSSSCC--CEECCCSCSCEECTTTCCEEC---SSSCSBCC
T ss_pred             CCCCCCCC--EeEECCCCCEEEcCCCCCeEC---cccCcchh
Confidence            57999998  477887777799999999863   33445564

>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: MarA
species: Escherichia coli [TaxId: 562]

Probab=84.67  E-value=0.86  Score=27.39  Aligned_cols=41  Identities=12%  Similarity=0.191  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438          250 VAAAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFP  291 (312)
Q Consensus       250 iaaAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~  291 (312)
                      |..+.-|+-... ..+++++++|+.+|+|+.++.+.+|+...
T Consensus         5 i~~v~~yI~~~~-~~~~tl~~lA~~~~~s~~~l~r~Fk~~~g   45 (54)
T d1bl0a1           5 IHSILDWIEDNL-ESPLSLEKVSERSGYSKWHLQRMFKKETG   45 (54)
T ss_dssp             HHHHHHHHHTTT-TSCCCCHHHHHHSSSCHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHhcc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHC
Confidence            444445555444 56899999999999999999999887653

>d1zina2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=84.27  E-value=0.066  Score=29.89  Aligned_cols=27  Identities=26%  Similarity=0.747  Sum_probs=13.9

Q ss_pred             CCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438            5 YCADCKRLTEVVFDHSAGDTICSECGL   31 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~   31 (312)
                      .||.||..=.+.+.+..=+-+|..||.
T Consensus         4 ~C~~CG~~Yh~~~~pPk~~g~CD~cG~   30 (35)
T d1zina2           4 ICRNCGATYHLIFHPPAKPGVCDKCGG   30 (35)
T ss_dssp             EETTTCCEEETTTBCCSSTTBCTTTCC
T ss_pred             CCcCcCchhccccCCCCCCCcCCCCCC
Confidence            456666532344445555555555553

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=83.80  E-value=0.45  Score=30.97  Aligned_cols=29  Identities=7%  Similarity=0.045  Sum_probs=26.5

Q ss_pred             CCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          264 DTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       264 ~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .++++++||+.+|+|..|+.+..++|.+.
T Consensus        26 i~lt~~elA~~lg~sr~tvsr~l~~l~~~   54 (73)
T d1zyba1          26 FKVKMDDLARCLDDTRLNISKTLNELQDN   54 (73)
T ss_dssp             EECCHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             eecCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            46899999999999999999999999885

>d1s3ga2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus globisporus [TaxId: 1459]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus globisporus [TaxId: 1459]

Probab=83.29  E-value=0.073  Score=29.71  Aligned_cols=27  Identities=19%  Similarity=0.426  Sum_probs=13.9

Q ss_pred             CCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438            5 YCADCKRLTEVVFDHSAGDTICSECGL   31 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~   31 (312)
                      .||.||..=++.+.+..=+-+|..||.
T Consensus         4 ~C~~CG~~Yh~~~~pPk~~g~CD~cg~   30 (35)
T d1s3ga2           4 ICKVCGTSYHLLFNPPQVEGKCDKDGG   30 (35)
T ss_dssp             EETTTCCEEETTTBCCSBTTBCTTTCC
T ss_pred             CCcCcCchhccccCCCCCCCccCCCCC
Confidence            455666532344445555555555553

>d2j9ub1 g.41.11.1 (B:115-161) Vacuolar protein-sorting-associated protein 36, VPS36 {Saccharomyces cerevisiae [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Ran binding protein zinc finger-like
family: Ran binding protein zinc finger-like
domain: Vacuolar protein-sorting-associated protein 36, VPS36
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=83.28  E-value=0.22  Score=29.03  Aligned_cols=31  Identities=19%  Similarity=0.409  Sum_probs=20.1

Q ss_pred             CCCCCCCCCceeeeC----CCCceEcCCCcccccCc
Q 021438            5 YCADCKRLTEVVFDH----SAGDTICSECGLVLEAY   36 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~----~~G~~vC~~CG~Vv~e~   36 (312)
                      .||-|+-. +-+.-+    ..-..+|.+||...+-.
T Consensus         5 ~CPICm~~-Ne~~~e~~~n~~~~p~C~nCGV~~D~e   39 (47)
T d2j9ub1           5 VCPICMVS-NETQGEFTKDTLPTPICINCGVPADYE   39 (47)
T ss_dssp             ECTTTCCE-EEESSCCCTTCSSCCBCTTTCCBCCHH
T ss_pred             ecceeeee-ccceeeeccCCCCCCcccccCCccCHH
Confidence            69999973 322222    12357999999997643

>d1akya2 g.41.2.1 (A:131-168) Microbial and mitochondrial ADK, insert "zinc finger" domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.09  E-value=0.1  Score=29.61  Aligned_cols=27  Identities=15%  Similarity=0.095  Sum_probs=15.7

Q ss_pred             CCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438            5 YCADCKRLTEVVFDHSAGDTICSECGL   31 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~   31 (312)
                      .||.||..=.+.+.+..=.-+|-.||.
T Consensus         4 ~C~~cG~~Yh~~~~ppk~~g~CD~cg~   30 (38)
T d1akya2           4 IHPASGRSYHKIFNPPKEDMKDDVTGE   30 (38)
T ss_dssp             ECTTTCCEEETTTBCCSSTTBCTTTCC
T ss_pred             CCcCccchhhhhccCcCcCCccCCCCC
Confidence            566676633445555555556666664

>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: MarA
species: Escherichia coli [TaxId: 562]

Probab=82.98  E-value=2.2  Score=25.42  Aligned_cols=40  Identities=15%  Similarity=0.140  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhcCCCHHHHHHHHHHH
Q 021438          150 AIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI  191 (312)
Q Consensus       150 ~iaaAcly~acr~~~~p~tl~dia~~~~~v~~~~i~~~~~~l  191 (312)
                      .+-.++-|+--.. ..|+++.|+|..+ |++...+.+.+++.
T Consensus         4 ~i~~v~~yI~~~~-~~~~tl~~lA~~~-~~s~~~l~r~Fk~~   43 (54)
T d1bl0a1           4 TIHSILDWIEDNL-ESPLSLEKVSERS-GYSKWHLQRMFKKE   43 (54)
T ss_dssp             HHHHHHHHHHTTT-TSCCCCHHHHHHS-SSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcc-CCCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence            4555666666444 5789999999999 89999998887664

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=82.39  E-value=2.7  Score=27.23  Aligned_cols=44  Identities=14%  Similarity=0.298  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHHhC----------CCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 021438          150 AIVAACLYIACRQEN----------KPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (312)
Q Consensus       150 ~iaaAcly~acr~~~----------~p~tl~dia~~~~~v~~~~i~~~~~~l~~~  194 (312)
                      .-.|..++.-|+..|          .|.|..|+|+.+ |++..++.++++.+.+.
T Consensus         4 ~Rla~~L~~L~~~~g~~~~~~~~i~~~lt~~elA~~~-g~sretvsr~l~~l~~~   57 (80)
T d3e5ua1           4 IRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEIT-GVHHVTVSRVLASLKRE   57 (80)
T ss_dssp             HHHHHHHHHHHHHHCEEETTEEECCSCCCHHHHHHHH-TCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhCCCCCCCeEEeeCCCHHHHHHHH-CCCHHHHHHHHHHHHHC
Confidence            334455555555554          578999999999 89999999999998864

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=82.31  E-value=0.74  Score=28.83  Aligned_cols=28  Identities=11%  Similarity=0.095  Sum_probs=26.4

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      +++..|||+.+|.|..||.+..++|.+.
T Consensus        12 pisr~eLa~~~gls~~TVs~~v~~L~~~   39 (62)
T d2hoea1          12 PVSRVELAEELGLTKTTVGEIAKIFLEK   39 (62)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            6899999999999999999999999885

>d1e4va2 g.41.2.1 (A:122-156) Microbial and mitochondrial ADK, insert "zinc finger" domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Escherichia coli [TaxId: 562]

Probab=82.20  E-value=0.068  Score=29.86  Aligned_cols=27  Identities=19%  Similarity=0.101  Sum_probs=14.0

Q ss_pred             CCCCCCCCCceeeeCCCCceEcCCCcc
Q 021438            5 YCADCKRLTEVVFDHSAGDTICSECGL   31 (312)
Q Consensus         5 ~Cp~Cg~~~~ii~D~~~G~~vC~~CG~   31 (312)
                      .||.||..=.+.+++..=+-+|..||.
T Consensus         4 ~c~~cG~~Yh~~~~PPk~~g~CD~cg~   30 (35)
T d1e4va2           4 VHAPSGRVYHVKFNPPKVEGKDDVTGE   30 (35)
T ss_dssp             EETTTTEEEETTTBCCSSTTBCTTTCC
T ss_pred             CCcCcCChhhhccCccccCCcccCCCC
Confidence            456666533444455455555665554

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=82.12  E-value=0.53  Score=31.74  Aligned_cols=30  Identities=20%  Similarity=0.059  Sum_probs=27.1

Q ss_pred             CCCHHHHHHHhCcchhHHHHHHHHHHhhhc
Q 021438          265 TKPLKEISIVTRVAEGTIKNVYKDLFPHLA  294 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~~kel~~~~~  294 (312)
                      ..+.++||+..++|+.||+.+.+.+++.++
T Consensus        37 G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~   66 (87)
T d1p4wa_          37 GFLVTEIAKKLNRSIKTISSQKKSAMMKLG   66 (87)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            467899999999999999999999998765

>d1z0xa1 a.4.1.9 (A:4-71) Transcriptional regulator EF0787 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator EF0787
species: Enterococcus faecalis [TaxId: 1351]

Probab=82.07  E-value=0.24  Score=31.77  Aligned_cols=44  Identities=11%  Similarity=0.113  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHhcCC-CCCHHHHHHHhCcchhHHHHHHHHHHh
Q 021438          248 ISVAAAVIYIITQLSND-TKPLKEISIVTRVAEGTIKNVYKDLFP  291 (312)
Q Consensus       248 ~~iaaAaiyla~~~~~~-~~~~~~Ia~~~~vs~~ti~~~~kel~~  291 (312)
                      ..|..|++-+..+..|+ ..|.++||+.+|+|..||-.+|+.-.+
T Consensus         5 ~~Ii~aa~~l~~e~~G~~~~t~~~Ia~~agvs~~~iy~hF~~K~~   49 (68)
T d1z0xa1           5 DTIIAAAFSLLEKSPTLEQLSMRKVAKQLGVQAPAIYWYFKNKQA   49 (68)
T ss_dssp             HHHHHHHHHHHHHSCCGGGCCHHHHHHHHTSCHHHHHTTCSSHHH
T ss_pred             HHHHHHHHHHHHHcCCccccCHHHHHHHHCcchhHHHHhcCCHHH
Confidence            45777888888877775 489999999999999999888754333

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: Rob transcription factor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=81.92  E-value=1.3  Score=26.50  Aligned_cols=29  Identities=10%  Similarity=0.252  Sum_probs=25.4

Q ss_pred             cCCCCCHHHHHHHhCcchhHHHHHHHHHH
Q 021438          262 SNDTKPLKEISIVTRVAEGTIKNVYKDLF  290 (312)
Q Consensus       262 ~~~~~~~~~Ia~~~~vs~~ti~~~~kel~  290 (312)
                      ...++++.++|+.+|+|+.++.+.+|+..
T Consensus        16 ~~~~itl~~lA~~~~~S~~~l~r~Fk~~~   44 (54)
T d1d5ya1          16 LDQPLSLDNVAAKAGYSKWHLQRMFKDVT   44 (54)
T ss_dssp             SSSSCCCHHHHTTTSSCHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            35679999999999999999999888764

>d6rxna_ g.41.5.1 (A:) Rubredoxin {Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]

Probab=81.64  E-value=0.2  Score=29.51  Aligned_cols=12  Identities=25%  Similarity=0.858  Sum_probs=6.5

Q ss_pred             eEcCCCcccccC
Q 021438           24 TICSECGLVLEA   35 (312)
Q Consensus        24 ~vC~~CG~Vv~e   35 (312)
                      .+|..||+|.++
T Consensus         4 y~C~~CgyiYd~   15 (45)
T d6rxna_           4 YVCNVCGYEYDP   15 (45)
T ss_dssp             EEETTTCCEECG
T ss_pred             eEeCCCCeEECc
Confidence            455555555544

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=81.14  E-value=1  Score=33.04  Aligned_cols=41  Identities=20%  Similarity=0.308  Sum_probs=34.1

Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          252 AAVIYIITQLSNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       252 aAaiyla~~~~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      .+-||......+.++|+.|||+.+|++.+++....+.|.+.
T Consensus        28 ~~~i~~~L~~~~~plt~~ela~~l~vsk~~vs~~l~~L~~~   68 (151)
T d1ku9a_          28 VGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEEL   68 (151)
T ss_dssp             HHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCCCCcCHHHHHHHhCCCcchHHHHHHHHHHC
Confidence            45555555567778999999999999999999999999884

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=81.09  E-value=1.9  Score=27.44  Aligned_cols=31  Identities=10%  Similarity=0.221  Sum_probs=28.0

Q ss_pred             cCCCCCHHHHHHHhCcchhHHHHHHHHHHhh
Q 021438          262 SNDTKPLKEISIVTRVAEGTIKNVYKDLFPH  292 (312)
Q Consensus       262 ~~~~~~~~~Ia~~~~vs~~ti~~~~kel~~~  292 (312)
                      ..-++|..|||+.+|+|.+||.+...+|.+.
T Consensus        16 ~~g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~   46 (70)
T d1z6ra1          16 QLGPVSRIDLSRLAQLAPASITKIVHEMLEA   46 (70)
T ss_dssp             SSCSCCHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            3557899999999999999999999999885

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

Probab=80.82  E-value=0.53  Score=29.11  Aligned_cols=28  Identities=18%  Similarity=0.535  Sum_probs=18.6

Q ss_pred             CCCCCCCCCCceee-e-----CCCCc---eEcCCCccc
Q 021438            4 SYCADCKRLTEVVF-D-----HSAGD---TICSECGLV   32 (312)
Q Consensus         4 ~~Cp~Cg~~~~ii~-D-----~~~G~---~vC~~CG~V   32 (312)
                      ..||.||+. +.++ .     .++|.   ++|.+||.-
T Consensus        16 ~~CpkC~~~-~a~~~~~QtRsaDE~~T~fy~C~~Cg~~   52 (57)
T d1qypa_          16 ITCPKCGND-TAYWWEMQTRAGDEPSTIFYKCTKCGHT   52 (57)
T ss_dssp             CCCTTTCCS-EEEEEEECCSSSSCSSEEEEEESSSCCE
T ss_pred             CCCCCCCCC-ceEEEEeecccccCCCeEEEEeCCCCCc
Confidence            479999984 4433 1     12333   789999975

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=80.47  E-value=0.51  Score=27.96  Aligned_cols=21  Identities=14%  Similarity=0.325  Sum_probs=18.4

Q ss_pred             CCCHHHHHHHhCcchhHHHHH
Q 021438          265 TKPLKEISIVTRVAEGTIKNV  285 (312)
Q Consensus       265 ~~~~~~Ia~~~~vs~~ti~~~  285 (312)
                      ..+..+||+.+|||..||-++
T Consensus        21 G~s~~~iA~~~gVSr~TiYry   41 (47)
T d1ijwc_          21 GHPRQQLAIIFGIGVSTLYRY   41 (47)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHhh
Confidence            468999999999999999754

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.22  E-value=0.84  Score=29.07  Aligned_cols=25  Identities=20%  Similarity=0.199  Sum_probs=21.8

Q ss_pred             CCCCCHHHHHHHhCcchhHHHHHHH
Q 021438          263 NDTKPLKEISIVTRVAEGTIKNVYK  287 (312)
Q Consensus       263 ~~~~~~~~Ia~~~~vs~~ti~~~~k  287 (312)
                      |-+.++.|||+.+||..+||++.+|
T Consensus        23 g~k~sq~eIA~~fGv~~STvs~IlK   47 (66)
T d1hlva1          23 NPDLRKGEIARRFNIPPSTLSTILK   47 (66)
T ss_dssp             CTTSCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCcchHHHHHHHhCCChhHHHHHHH
Confidence            4557899999999999999998875