Citrus Sinensis ID: 025357

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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----
Protein Sequence
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVLDFSSCMIFCSLWPYLSNPMHPFT
Secondary Structure (PSIPRED)
ccccccccccccccEEEEcccccEEcccccEEEccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccEEEccccccEEcHHccEEEcccEccccccHEEccccccccccccccccccccccccccEEEEcccccccccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHccccHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHccccHHHHccccHHHHHHHccccHHccccccccc
Coil and Loop (DISEMBL)
MADSYCADCKRLTEVvfdhsagdticseCGLVLEaysvdetsewrifanessdhdpvrvggplnpllsggglstviakptaggstellsgslgklqarsshpdrNLIQAFKSISAMSDRLGLVTTIKDRANEIYKkvedqkplrgrnQEAIVAACLYIACrqenkprtvKEFCSVANGTTKKEIGRAKEFIVKHLEAemgqsvemgtiHASDYLVIFLLNIFKNFFFLFVLDFsscmifcslwpylsnpmhpft
Flexible Loop (DISEMBL)
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFAnessdhdpvrVGGPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKsisamsdrlGLVTTIKDRANEIykkvedqkplrgrnQEAIVAACLYIACrqenkprtvKEFCSvangttkkeigRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVLDFSSCMIFCSLWPYLSNPMHPFT
Low Complexity Region (SEG)
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVggplnpllsggglsTVIAKPTAggstellsgslgklQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYlvifllnifknffflfvldfSSCMIFCSLWPYLSNPMHPFT
Disordered region (IsUnstruct)
****YCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFAN**********************L*TV*******************************IQAFKSISAMSDRLGLVTTIKDRANEIYKKV*******GRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVLDFSSCMIFCSLWPYLS*******
Disordered Region (DISOPRED)
**DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWR*******************PLLSGGGLS*******************************NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVLDFSSCMIFCSLWPY**NP*****
Disordered Region (DISEMBL)
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGGSTELLSGSL*********PDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVLDFSSCMIFCSLWPYLSNPMHPFT
Disordered Region (DISPRO)
****YCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE************LNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVLDFSSCMIFCSLWPYLSNP*****
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVLDFSSCMIFCSLWPYLSNPMHPFT
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	254	2.2.26 [Sep-21-2011]
P48513	313	Transcription initiation	yes	no	0.881	0.715	0.741	8e-97
Q8W0W3	312	Transcription initiation	yes	no	0.850	0.692	0.769	2e-96
Q9SS44	312	Transcription initiation	yes	no	0.866	0.705	0.733	6e-94
P48512	312	Transcription initiation	no	no	0.866	0.705	0.683	9e-88
P29052	315	Transcription initiation	yes	no	0.795	0.641	0.483	8e-47
P29054	316	Transcription initiation	N/A	no	0.787	0.632	0.458	7e-44
Q5R886	316	Transcription initiation	yes	no	0.787	0.632	0.458	5e-43
Q4R3J5	316	Transcription initiation	N/A	no	0.787	0.632	0.458	5e-43
Q00403	316	Transcription initiation	yes	no	0.787	0.632	0.458	5e-43
Q2KIN8	316	Transcription initiation	yes	no	0.787	0.632	0.458	6e-43

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

 Score =  353 bits (905), Expect = 8e-97,   Method: Compositional matrix adjust.
 Identities = 166/224 (74%), Positives = 190/224 (84%)

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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKN 224
           KKEIGRAKE+IVK L  E G +VEMGTIHA D++  F  N+  N
Sbjct: 181 KKEIGRAKEYIVKQLGLENGNAVEMGTIHAGDFMRRFCSNLCMN 224

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 =  352 bits (902), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 167/217 (76%), Positives = 189/217 (87%), Gaps = 1/217 (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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIF 217
           KKEIGRAKEFIVK LE EMGQS+EMGTIHA D+L  F
Sbjct: 180 KKEIGRAKEFIVKQLEVEMGQSMEMGTIHAGDFLRRF 216

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 =  343 bits (880), Expect = 6e-94,   Method: Compositional matrix adjust.
 Identities = 162/221 (73%), Positives = 189/221 (85%), Gaps = 1/221 (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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI 221
           KKEIGRAKE+IVK L  E GQ VEMGTIHA D++  F  N+
Sbjct: 180 KKEIGRAKEYIVKQLGLETGQLVEMGTIHAGDFMRRFCSNL 220

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 =  323 bits (827), Expect = 9e-88,   Method: Compositional matrix adjust.
 Identities = 151/221 (68%), Positives = 184/221 (83%), Gaps = 1/221 (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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI 221
           KKEIGRAK++IVK L  E GQSV++GTIHA D++  F  N+
Sbjct: 180 KKEIGRAKDYIVKTLGLEPGQSVDLGTIHAGDFMRRFCSNL 220

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 =  187 bits (474), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 101/209 (48%), Positives = 134/209 (64%), Gaps = 7/209 (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 KHLEAEMGQSVEMGTIHASDYLVIFLLNI 221
           K LE     SV++  I  +D++  F  N+
Sbjct: 199 KALET----SVDL--ITTADFMCRFCANL 221

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 =  177 bits (449), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 95/207 (45%), Positives = 128/207 (61%), Gaps = 7/207 (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 LEAEMGQSVEMGTIHASDYLVIFLLNI 221
           LE        +  I   D++  F  N+
Sbjct: 202 LE------TNVDLITTGDFMSRFCSNL 222

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

Xenopus laevis (taxid: 8355)

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

 Score =  174 bits (441), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 95/207 (45%), Positives = 128/207 (61%), Gaps = 7/207 (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 LEAEMGQSVEMGTIHASDYLVIFLLNI 221
           LE     SV++  I   D++  F  N+
Sbjct: 202 LET----SVDL--ITTGDFMSRFCSNL 222

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 =  174 bits (441), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 95/207 (45%), Positives = 128/207 (61%), Gaps = 7/207 (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 LEAEMGQSVEMGTIHASDYLVIFLLNI 221
           LE     SV++  I   D++  F  N+
Sbjct: 202 LET----SVDL--ITTGDFMSRFCSNL 222

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

Macaca fascicularis (taxid: 9541)

>sp|Q00403|TF2B_HUMAN Transcription initiation factor IIB OS=Homo sapiens GN=GTF2B PE=1 SV=1

 Score =  174 bits (441), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 95/207 (45%), Positives = 128/207 (61%), Gaps = 7/207 (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 LEAEMGQSVEMGTIHASDYLVIFLLNI 221
           LE     SV++  I   D++  F  N+
Sbjct: 202 LET----SVDL--ITTGDFMSRFCSNL 222

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

Homo sapiens (taxid: 9606)

>sp|Q2KIN8|TF2B_BOVIN Transcription initiation factor IIB OS=Bos taurus GN=GTF2B PE=2 SV=1

 Score =  174 bits (441), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 95/207 (45%), Positives = 128/207 (61%), Gaps = 7/207 (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 LEAEMGQSVEMGTIHASDYLVIFLLNI 221
           LE     SV++  I   D++  F  N+
Sbjct: 202 LET----SVDL--ITTGDFMSRFCSNL 222

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

Bos taurus (taxid: 9913)

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	254
224135681	311	predicted protein [Populus trichocarpa]	0.866	0.707	0.823	1e-103
255544920	312	transcription initiation factor iib, put	0.877	0.714	0.767	1e-98
225436547	314	PREDICTED: transcription initiation fact	0.854	0.691	0.766	7e-96
255588003	312	transcription initiation factor iib, put	0.877	0.714	0.758	1e-95
225464249	312	PREDICTED: transcription initiation fact	0.866	0.705	0.764	3e-95
225441886	312	PREDICTED: transcription initiation fact	0.866	0.705	0.764	3e-95
351724605	313	transcription initiation factor IIB [Gly	0.881	0.715	0.741	5e-95
317106705	312	JHL06B08.6 [Jatropha curcas]	0.877	0.714	0.754	6e-95
224138070	312	predicted protein [Populus trichocarpa]	0.866	0.705	0.760	8e-95
115480363	312	Os09g0534800 [Oryza sativa Japonica Grou	0.850	0.692	0.769	1e-94

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

 Score =  380 bits (977), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 182/221 (82%), Positives = 199/221 (90%), Gaps = 1/221 (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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI 221
           KKEIGRAKEFIVKHLE EMG S+EMGTIHA+DYL  F  N+
Sbjct: 180 KKEIGRAKEFIVKHLEVEMGHSMEMGTIHAADYLRRFCSNL 220

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  365 bits (937), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 172/224 (76%), Positives = 198/224 (88%), Gaps = 1/224 (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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKN 224
           KKEIGRAKE+IVK LE E+GQS+EMGTIHA D+L  F  ++  N
Sbjct: 180 KKEIGRAKEYIVKQLEVELGQSMEMGTIHAGDFLRRFCSHLGMN 223

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  355 bits (912), Expect = 7e-96,   Method: Compositional matrix adjust.
 Identities = 167/218 (76%), Positives = 191/218 (87%), Gaps = 1/218 (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 TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIF 217
           TKKEIGRAKE+IVK LE EMGQS+EMGTIHA D+L  F
Sbjct: 181 TKKEIGRAKEYIVKQLEVEMGQSMEMGTIHAGDFLRRF 218

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  355 bits (910), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 170/224 (75%), Positives = 190/224 (84%), Gaps = 1/224 (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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKN 224
           KKEIGRAKE+IVK L  E GQSVEMGTIHA D++  F  N+  N
Sbjct: 180 KKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMN 223

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

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 =  353 bits (907), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 169/221 (76%), Positives = 191/221 (86%), Gaps = 1/221 (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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI 221
           KKEIGRAKE+IVK LEAE GQSVEMGTIHA D++  F  N+
Sbjct: 180 KKEIGRAKEYIVKQLEAEKGQSVEMGTIHAGDFMRRFCSNL 220

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 =  353 bits (907), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 169/221 (76%), Positives = 191/221 (86%), Gaps = 1/221 (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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI 221
           KKEIGRAKE+IVK LEAE GQSVEMGTIHA D++  F  N+
Sbjct: 180 KKEIGRAKEYIVKQLEAEKGQSVEMGTIHAGDFMRRFCSNL 220

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  353 bits (905), Expect = 5e-95,   Method: Compositional matrix adjust.
 Identities = 166/224 (74%), Positives = 190/224 (84%)

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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKN 224
           KKEIGRAKE+IVK L  E G +VEMGTIHA D++  F  N+  N
Sbjct: 181 KKEIGRAKEYIVKQLGLENGNAVEMGTIHAGDFMRRFCSNLCMN 224

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  352 bits (904), Expect = 6e-95,   Method: Compositional matrix adjust.
 Identities = 169/224 (75%), Positives = 190/224 (84%), Gaps = 1/224 (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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKN 224
           KKEIGRAKE+IVK L  E GQSVEMGTIHA D++  F  N+  N
Sbjct: 180 KKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMN 223

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224138070|ref|XP_002322722.1| predicted protein [Populus trichocarpa] gi|222867352|gb|EEF04483.1| predicted protein [Populus trichocarpa]

 Score =  352 bits (903), Expect = 8e-95,   Method: Compositional matrix adjust.
 Identities = 168/221 (76%), Positives = 189/221 (85%), Gaps = 1/221 (0%)

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

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

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

Query: 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI 221
           KKEIGRAKE+IVK L  E GQSVEMGTIHA D++  F  N+
Sbjct: 180 KKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNL 220

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115480363|ref|NP_001063775.1| Os09g0534800 [Oryza sativa Japonica Group] gi|21362998|sp|Q8W0W3.1|TF2B_ORYSJ RecName: Full=Transcription initiation factor IIB; AltName: Full=General transcription factor TFIIB gi|18481632|gb|AAL73491.1|AF464908_1 general transcription factor TFIIB [Oryza sativa] gi|50725809|dbj|BAD33339.1| Transcription initiation factor IIB [Oryza sativa Japonica Group] gi|50726577|dbj|BAD34211.1| Transcription initiation factor IIB [Oryza sativa Japonica Group] gi|113632008|dbj|BAF25689.1| Os09g0534800 [Oryza sativa Japonica Group] gi|125564497|gb|EAZ09877.1| hypothetical protein OsI_32170 [Oryza sativa Indica Group] gi|125606444|gb|EAZ45480.1| hypothetical protein OsJ_30135 [Oryza sativa Japonica Group] gi|347737122|gb|AEP20532.1| transcription factor [Oryza sativa Japonica Group]

 Score =  352 bits (902), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 167/217 (76%), Positives = 189/217 (87%), Gaps = 1/217 (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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIF 217
           KKEIGRAKEFIVK LE EMGQS+EMGTIHA D+L  F
Sbjct: 180 KKEIGRAKEFIVKQLEVEMGQSMEMGTIHAGDFLRRF 216

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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	254
TAIR|locus:2076259	312	AT3G10330 [Arabidopsis thalian	0.834	0.679	0.671	9.6e-73
TAIR|locus:2062703	312	TFIIB "transcription factor II	0.834	0.679	0.629	1e-68
FB|FBgn0004915	315	TfIIB "Transcription factor II	0.724	0.584	0.443	3.1e-35
ZFIN|ZDB-GENE-030131-3544	316	gtf2b "general transcription f	0.724	0.582	0.427	8.3e-35
UNIPROTKB|F1NXP2	306	GTF2B "Uncharacterized protein	0.724	0.601	0.427	1.3e-34
UNIPROTKB|F2Z4J6	316	LOC786656 "Uncharacterized pro	0.724	0.582	0.421	5.8e-34
UNIPROTKB|Q2KIN8	316	GTF2B "Transcription initiatio	0.724	0.582	0.421	5.8e-34
UNIPROTKB|E2RPG1	316	GTF2B "Uncharacterized protein	0.724	0.582	0.421	5.8e-34
UNIPROTKB|B1APE1	224	GTF2B "Transcription initiatio	0.724	0.821	0.421	5.8e-34
UNIPROTKB|Q00403	316	GTF2B "Transcription initiatio	0.724	0.582	0.421	5.8e-34

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

 Score = 735 (263.8 bits), Expect = 9.6e-73, P = 9.6e-73
 Identities = 143/213 (67%), Positives = 164/213 (76%)

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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDY 213
             KKEIGRAKE+IVK L  E GQ VEMGTIHA D+
Sbjct:   180 KKEIGRAKEYIVKQLGLETGQLVEMGTIHAGDF 212

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 = 697 (250.4 bits), Expect = 1.0e-68, P = 1.0e-68
 Identities = 134/213 (62%), Positives = 161/213 (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 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDY 213
             KKEIGRAK++IVK L  E GQSV++GTIHA D+
Sbjct:   180 KKEIGRAKDYIVKTLGLEPGQSVDLGTIHAGDF 212

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

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

 Score = 381 (139.2 bits), Expect = 3.1e-35, P = 3.1e-35
 Identities = 82/185 (44%), Positives = 107/185 (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 LEAEM 199
             LE  +
Sbjct:   201 LETSV 205

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 = 377 (137.8 bits), Expect = 8.3e-35, P = 8.3e-35
 Identities = 79/185 (42%), Positives = 107/185 (57%)

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 LEAEM 199
             LE  +
Sbjct:   202 LETSV 206

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 = 375 (137.1 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 79/185 (42%), Positives = 107/185 (57%)

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 LEAEM 199
             LE  +
Sbjct:   192 LETSV 196

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

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

 Score = 369 (135.0 bits), Expect = 5.8e-34, P = 5.8e-34
 Identities = 78/185 (42%), Positives = 105/185 (56%)

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 LEAEM 199
             LE  +
Sbjct:   202 LETSV 206

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|Q2KIN8 GTF2B "Transcription initiation factor IIB" [Bos taurus (taxid:9913)]

 Score = 369 (135.0 bits), Expect = 5.8e-34, P = 5.8e-34
 Identities = 78/185 (42%), Positives = 105/185 (56%)

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 LEAEM 199
             LE  +
Sbjct:   202 LETSV 206

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

 Score = 369 (135.0 bits), Expect = 5.8e-34, P = 5.8e-34
 Identities = 78/185 (42%), Positives = 105/185 (56%)

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 LEAEM 199
             LE  +
Sbjct:   202 LETSV 206

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|B1APE1 GTF2B "Transcription initiation factor IIB" [Homo sapiens (taxid:9606)]

 Score = 369 (135.0 bits), Expect = 5.8e-34, P = 5.8e-34
 Identities = 78/185 (42%), Positives = 105/185 (56%)

Query:    15 VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVXXXXXXXXXXXXXXT 74
             +V D+ AGD IC ECGLV+    +D  SEWR F+N+ +  DP RV              T
Sbjct:    22 LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKATKDPSRVGDSQNPLLSDGDLST 81

Query:    75 VIAKPTAXXXXXXXXXXXXXXQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIY 134
             +I K T               +   S  DR ++ AFK I+ M+DR+ L   I DR N ++
Sbjct:    82 MIGKGTGAASFDEFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINLPRNIVDRTNNLF 141

Query:   135 KKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194
             K+V +QK L+GR  +AI +ACLYIACRQE  PRT KE C+V+   +KKEIGR  + I+K 
Sbjct:   142 KQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSR-ISKKEIGRCFKLILKA 200

Query:   195 LEAEM 199
             LE  +
Sbjct:   201 LETSV 205

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

UNIPROTKB|Q00403 GTF2B "Transcription initiation factor IIB" [Homo sapiens (taxid:9606)]

 Score = 369 (135.0 bits), Expect = 5.8e-34, P = 5.8e-34
 Identities = 78/185 (42%), Positives = 105/185 (56%)

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 LEAEM 199
             LE  +
Sbjct:   202 LETSV 206

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0019048 "virus-host interaction" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

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

GO:0008134 "transcription factor binding" evidence=IPI

GO:0005654 "nucleoplasm" evidence=TAS

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

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

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

---

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	0.7695	0.8503	0.6923	yes	no
Q9SS44	TF2B2_ARATH	No assigned EC number	0.7330	0.8661	0.7051	yes	no
P48513	TF2B_SOYBN	No assigned EC number	0.7410	0.8818	0.7156	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	254
COG1405	285	COG1405, SUA7, Transcription initiation factor TFI	6e-49
PRK00423	310	PRK00423, tfb, transcription initiation factor IIB	1e-42
pfam00382	71	pfam00382, TFIIB, Transcription factor TFIIB repea	4e-21
cd00043	88	cd00043, CYCLIN, Cyclin box fold	2e-13
smart00385	83	smart00385, CYCLIN, domain present in cyclins, TFI	3e-10
pfam08271	40	pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding	7e-09
COG1405	285	COG1405, SUA7, Transcription initiation factor TFI	2e-08
COG5333	297	COG5333, CCL1, Cdk activating kinase (CAK)/RNA pol	3e-06
PRK00423	310	PRK00423, tfb, transcription initiation factor IIB	2e-05
pfam00134	127	pfam00134, Cyclin_N, Cyclin, N-terminal domain	0.002

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

 Score =  162 bits (412), Expect = 6e-49
 Identities = 73/193 (37%), Positives = 104/193 (53%), Gaps = 14/193 (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 EIGRAKEFIVKHL 195
           EIGR    +V+ L
Sbjct: 173 EIGRTYRLLVREL 185

Length = 285

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

 Score =  147 bits (372), Expect = 1e-42
 Identities = 66/193 (34%), Positives = 108/193 (55%), Gaps = 12/193 (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 EIGRAKEFIVKHL 195
           EIGR   F+++ L
Sbjct: 198 EIGRCYRFLLREL 210

Length = 310

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

 Score = 83.9 bits (208), Expect = 4e-21
 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 = 63.8 bits (156), Expect = 2e-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|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and Retinoblastoma

 Score = 54.9 bits (133), 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 = 50.0 bits (120), Expect = 7e-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|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]

 Score = 53.1 bits (128), Expect = 2e-08
 Identities = 21/67 (31%), Positives = 33/67 (49%)

Query: 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEF 172
           I   + +LGL   ++ +A EI KK +      G++   + AA +Y+A     + RT KE 
Sbjct: 198 IPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEV 257

Query: 173 CSVANGT 179
             VA  T
Sbjct: 258 AKVAGVT 264

Length = 285

>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 = 47.0 bits (112), Expect = 3e-06
 Identities = 25/126 (19%), Positives = 50/126 (39%), Gaps = 7/126 (5%)

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

Query: 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFF 226
           R +      A     +E   ++E I++  E E+ ++++       D  V       + F 
Sbjct: 106 RDISIESFEARDLWSEEPKSSRERILE-YEFELLEALD------FDLHVHHPYKYLEGFL 158

Query: 227 FLFVLD 232
                 
Sbjct: 159 KDLQEK 164

Length = 297

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

 Score = 44.6 bits (106), Expect = 2e-05
 Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 3/84 (3%)

Query: 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEF 172
           +   +  LGL   ++ +A EI +K +++    G+    + AA +YIA     + RT +E 
Sbjct: 223 VPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREV 282

Query: 173 CSVANGTTKKEI-GRAKEFIVKHL 195
             VA G T+  +  R KE + + L
Sbjct: 283 AEVA-GVTEVTVRNRYKE-LAEKL 304

Length = 310

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

 Score = 36.8 bits (86), Expect = 0.002
 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	254
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	100.0
KOG1597	308	consensus Transcription initiation factor TFIIB [T	100.0
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	100.0
KOG1598	521	consensus Transcription initiation factor TFIIIB,	99.94
PF00382	71	TFIIB: Transcription factor TFIIB repeat; InterPro	99.81
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	99.64
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	99.61
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	99.52
KOG1597	308	consensus Transcription initiation factor TFIIB [T	99.51
cd00043	88	CYCLIN Cyclin box fold. Protein binding domain fun	99.18
smart00385	83	CYCLIN domain present in cyclins, TFIIB and Retino	99.07
KOG0834	323	consensus CDK9 kinase-activating protein cyclin T	98.72
KOG1598	521	consensus Transcription initiation factor TFIIIB,	98.58
TIGR00569	305	ccl1 cyclin ccl1. University).	98.55
COG5333	297	CCL1 Cdk activating kinase (CAK)/RNA polymerase II	98.06
KOG0835	367	consensus Cyclin L [General function prediction on	98.05
PF00134	127	Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR	97.88
PF01857	135	RB_B: Retinoblastoma-associated protein B domain;	97.54
KOG0656	335	consensus G1/S-specific cyclin D [Cell cycle contr	97.24
KOG0794	264	consensus CDK8 kinase-activating protein cyclin C	97.2
KOG0835	367	consensus Cyclin L [General function prediction on	97.02
PF11781	36	RRN7: RNA polymerase I-specific transcription init	96.94
PF02984	118	Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR	96.81
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	96.78
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	96.75
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	96.73
COG5024	440	Cyclin [Cell division and chromosome partitioning]	96.59
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	96.56
PLN00209	86	ribosomal protein S27; Provisional	96.27
PTZ00083	85	40S ribosomal protein S27; Provisional	96.26
PHA00626	59	hypothetical protein	96.21
PRK00420	112	hypothetical protein; Validated	96.11
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	95.98
KOG2496	325	consensus Cdk activating kinase (CAK)/RNA polymera	95.92
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	95.92
PF13248	26	zf-ribbon_3: zinc-ribbon domain	95.79
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	95.74
PRK11827	60	hypothetical protein; Provisional	95.45
smart00778	37	Prim_Zn_Ribbon Zinc-binding domain of primase-heli	95.45
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	95.44
PRK00432	50	30S ribosomal protein S27ae; Validated	95.43
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	95.19
COG2835	60	Uncharacterized conserved protein [Function unknow	95.06
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	95.03
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	94.99
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	94.99
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	94.93
KOG0653	391	consensus Cyclin B and related kinase-activating p	94.87
PF03966	68	Trm112p: Trm112p-like protein; InterPro: IPR005651	94.84
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	94.83
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	94.25
smart00661	52	RPOL9 RNA polymerase subunit 9.	94.23
PRK10220	111	hypothetical protein; Provisional	94.11
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	94.01
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	94.01
KOG1779	84	consensus 40s ribosomal protein S27 [Translation,	93.71
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	93.63
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	93.58
PF08273	40	Prim_Zn_Ribbon: Zinc-binding domain of primase-hel	93.44
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	93.41
KOG4164	497	consensus Cyclin ik3-1/CABLES [Cell cycle control,	92.97
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	92.69
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	92.55
COG2824	112	PhnA Uncharacterized Zn-ribbon-containing protein	92.48
COG4888	104	Uncharacterized Zn ribbon-containing protein [Gene	92.25
KOG0655	408	consensus G1/S-specific cyclin E [Cell cycle contr	92.22
PF05129	81	Elf1: Transcription elongation factor Elf1 like; I	91.9
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	91.83
TIGR02300	129	FYDLN_acid conserved hypothetical protein TIGR0230	91.75
PRK14892	99	putative transcription elongation factor Elf1; Pro	91.69
PF01780	90	Ribosomal_L37ae: Ribosomal L37ae protein family; I	91.68
PF08613	149	Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu	91.53
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	91.29
TIGR00686	109	phnA alkylphosphonate utilization operon protein P	91.15
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	91.1
PF05460	353	ORC6: Origin recognition complex subunit 6 (ORC6);	91.0
TIGR00244	147	transcriptional regulator NrdR. Members of this al	90.98
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	90.79
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	90.29
KOG4557	262	consensus Origin recognition complex, subunit 6 [R	89.97
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	89.89
PTZ00255	90	60S ribosomal protein L37a; Provisional	89.74
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	89.58
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	89.37
TIGR00280	91	L37a ribosomal protein L37a. This model finds euka	88.78
KOG4557	262	consensus Origin recognition complex, subunit 6 [R	88.51
PRK12495	226	hypothetical protein; Provisional	88.33
PRK03976	90	rpl37ae 50S ribosomal protein L37Ae; Reviewed	87.63
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	87.41
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	87.31
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	87.29
PRK09710	64	lar restriction alleviation and modification prote	87.28
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	86.92
COG5349	126	Uncharacterized protein conserved in bacteria [Fun	86.78
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	86.54
PRK05978	148	hypothetical protein; Provisional	86.33
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	86.26
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	86.11
COG4640	465	Predicted membrane protein [Function unknown]	85.81
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	85.24
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	85.23
PRK12286	57	rpmF 50S ribosomal protein L32; Reviewed	85.08
PF14255	52	Cys_rich_CPXG: Cysteine-rich CPXCG	84.95
TIGR02443	59	conserved hypothetical metal-binding protein. Memb	84.5
TIGR00569	305	ccl1 cyclin ccl1. University).	84.12
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	84.1
PF12773	50	DZR: Double zinc ribbon	83.71
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	83.66
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	83.58
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	83.29
PF05191	36	ADK_lid: Adenylate kinase, active site lid; InterP	82.8
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	82.78
COG3877	122	Uncharacterized protein conserved in bacteria [Fun	81.87
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	81.8
PF01783	56	Ribosomal_L32p: Ribosomal L32p protein family; Int	81.65
KOG0794	264	consensus CDK8 kinase-activating protein cyclin C	81.44
PRK09678	72	DNA-binding transcriptional regulator; Provisional	81.43
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	81.29
TIGR01031	55	rpmF_bact ribosomal protein L32. This protein desc	81.05
PHA02942	383	putative transposase; Provisional	80.98
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	80.7
PRK12336	201	translation initiation factor IF-2 subunit beta; P	80.69
PF15616	131	TerY-C: TerY-C metal binding domain	80.16

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=100.00  E-value=8.6e-56  Score=396.88  Aligned_cols=219  Identities=32%  Similarity=0.569  Sum_probs=202.4

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccccccCcccccccCCCCCCCCcccCCCCCccccCCCcceEEecCCCCC
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGG   83 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~d~~r~G~~~~~~~~~~~~~t~i~~~~~~~   83 (254)
                      ..||+||+ +++|+|+++|++||++||+|++|++||+|||||+|++++ .+|++|+|+|.++++||.|++|.|++++.++
T Consensus        12 ~~Cp~Cg~-~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~-~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~~   89 (310)
T PRK00423         12 LVCPECGS-DKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTYTIHDKGLSTDIDWRNKDS   89 (310)
T ss_pred             CcCcCCCC-CCeeEECCCCeEeecccCCcccccccccCCCccCCCccc-cCCccccCCCCCccccCCCCceEeecCCccc
Confidence            57999998 789999999999999999999999999999999999754 4689999999999999999999999877666


Q ss_pred             Ccccccc-------ccccccccC---CCchhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHH
Q 025357           84 STELLSG-------SLGKLQARS---SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVA  153 (254)
Q Consensus        84 ~~~~l~~-------~l~~~~~~~---~~~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaA  153 (254)
                      +|+.++.       +|++||++.   +++||+|..++++|+++|+.|+||+.++++|..||+++.+.++++||++++++|
T Consensus        90 ~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~A  169 (310)
T PRK00423         90 YGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVA  169 (310)
T ss_pred             ccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHH
Confidence            6655542       478898865   567999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhhee
Q 025357          154 ACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVL  231 (254)
Q Consensus       154 AclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v~  231 (254)
                      ||||+|||++++|+|++||+++ +++++++|+++|+.|.+.|+++      +++.+|++||+|||++|+|++++...|
T Consensus       170 AclYiACR~~~~prtl~eI~~~-~~v~~k~i~~~~~~l~k~L~~~------~~~~~p~~~i~r~~~~L~L~~~v~~~A  240 (310)
T PRK00423        170 AALYAACRRCKVPRTLDEIAEV-SRVSRKEIGRCYRFLLRELNLK------LPPTDPIDYVPRFASELGLSGEVQKKA  240 (310)
T ss_pred             HHHHHHHHHcCCCcCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC------CCCCCHHHHHHHHHHHcCCCHHHHHHH
Confidence            9999999999999999999995 8999999999999999999987      788999999999999999999887743

>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]

Probab=100.00  E-value=1.7e-52  Score=359.98  Aligned_cols=220  Identities=55%  Similarity=0.815  Sum_probs=200.8

Q ss_pred             CCCCCCCCCCc-eEEecCCCceEcCcCceeecccccccCcccccccCCCCCCCCcccCCCCCccccCCCcceEEecCCCC
Q 025357            4 SYCADCKRLTE-VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG   82 (254)
Q Consensus         4 ~~Cp~Cg~~~~-lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~d~~r~G~~~~~~~~~~~~~t~i~~~~~~   82 (254)
                      ++|++|+..+. +|+|+.+|++||..||+|+++++||.++|||+|++++++.|++|||++.+|++.+++++|+|+++. +
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            47999998765 999999999999999999999999999999999998889999999999999999999999999987 4


Q ss_pred             CCccccccccccccccC--CCchhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHH
Q 025357           83 GSTELLSGSLGKLQARS--SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIAC  160 (254)
Q Consensus        83 ~~~~~l~~~l~~~~~~~--~~~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~Ac  160 (254)
                      .++..+ ..|.++|++.  ++.|+.+..++..|..+++.++||..+.++|.++|+++.+.+.++||+.++++|||||+||
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 TSSSFA-SSLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIAC  158 (308)
T ss_pred             CCHHHH-HHHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHH
Confidence            444333 3488899743  6789999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhhe
Q 025357          161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFV  230 (254)
Q Consensus       161 R~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v  230 (254)
                      |+++.|||++||+.+ ++|+.++|+|++|.|.+.|+...+    ...++..+||+|||+.|+|++.+++-
T Consensus       159 Rq~~~pRT~kEI~~~-anv~kKEIgr~~K~i~~~l~~s~~----~~s~~t~~~m~RFCs~L~L~~~~q~a  223 (308)
T KOG1597|consen  159 RQEDVPRTFKEISAV-ANVSKKEIGRCVKLIGEALETSVD----LISISTGDFMPRFCSNLGLPKSAQEA  223 (308)
T ss_pred             HhcCCCchHHHHHHH-HcCCHHHHHHHHHHHHHHHhccch----hhhhhHHHHHHHHHHhcCCCHHHHHH
Confidence            999999999999996 789999999999999999987732    33567999999999999999999874

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

Probab=100.00  E-value=7.2e-51  Score=357.85  Aligned_cols=210  Identities=37%  Similarity=0.645  Sum_probs=194.1

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccccccCcccccccCCCCCCCCcccCCCCCccccCCCcceEEecCCCCC
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGG   83 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~d~~r~G~~~~~~~~~~~~~t~i~~~~~~~   83 (254)
                      +.||+||+ +++++|++.|++||.+||+|++|+.||.|||||.|+ +  ...+ |+|.|.++.+||.|++|.|+++..+ 
T Consensus         2 ~~CpeCg~-~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f~-e--~~~~-r~g~P~t~~~~d~~l~t~i~~~~~~-   75 (285)
T COG1405           2 MSCPECGS-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFD-E--RHER-RVGAPLTPSIHDKGLSTIIGWGDKD-   75 (285)
T ss_pred             CCCCCCCC-ccceeeccCCeEEeccCCEEeccccccCCCCccccc-c--cccc-cccCCCccccCccchhhhcccchhH-
Confidence            68999999 799999999999999999999999999999999993 2  2334 9999999999999999999987632 


Q ss_pred             CccccccccccccccC---CCchhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHH
Q 025357           84 STELLSGSLGKLQARS---SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIAC  160 (254)
Q Consensus        84 ~~~~l~~~l~~~~~~~---~~~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~Ac  160 (254)
                          ...+|++||.+.   +.+++++..++.+|.++++.|+||.++.++|..||+++.++++++||+.++++|||+|+||
T Consensus        76 ----~~~rlr~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~ac  151 (285)
T COG1405          76 ----KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAAC  151 (285)
T ss_pred             ----HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHH
Confidence                234588998653   4689999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhhe
Q 025357          161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFV  230 (254)
Q Consensus       161 R~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v  230 (254)
                      |+++.|+|+.||++ ++++++++|+++|+.+.+.|++.      +++.+|.+||+|||++|+|+++|...
T Consensus       152 R~~~~prtl~eIa~-a~~V~~kei~rtyr~~~~~L~l~------~~~~~p~~yi~rf~s~L~l~~~v~~~  214 (285)
T COG1405         152 RINGVPRTLDEIAK-ALGVSKKEIGRTYRLLVRELKLK------IPPVDPSDYIPRFASKLGLSDEVRRK  214 (285)
T ss_pred             HHcCCCccHHHHHH-HHCCCHHHHHHHHHHHHHhcCCC------CCCCCHHHHHHHHHHHcCCCHHHHHH
Confidence            99999999999999 48999999999999999999998      78899999999999999999999884

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

Probab=99.94  E-value=5.6e-27  Score=216.70  Aligned_cols=190  Identities=22%  Similarity=0.358  Sum_probs=164.0

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccccccCcccccccCCCCCCCCcccCCCCCccccCCCcceEEecCCCCC
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGG   83 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~d~~r~G~~~~~~~~~~~~~t~i~~~~~~~   83 (254)
                      +.|++||+ +++-.|..+|..+|+.||.|++++.|..  | .+|.+.           +         -|+.|+....++
T Consensus         1 ~~C~~C~~-s~fe~d~a~g~~~C~~CG~v~E~~~ivs--e-v~F~e~-----------~---------~G~~v~~~~~g~   56 (521)
T KOG1598|consen    1 MVCKNCGG-SNFERDEATGNLYCTACGTVLEYNNIVA--E-VTFVEG-----------A---------QGQFVRVGQSGA   56 (521)
T ss_pred             CcCCCCCC-CCcccccccCCceeccccceeeccceeE--E-eeeecc-----------c---------ceeEEeccccCC
Confidence            47999999 7899999999999999999999999884  4 567632           1         134555433222


Q ss_pred             CccccccccccccccCCCchhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhc
Q 025357           84 STELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE  163 (254)
Q Consensus        84 ~~~~l~~~l~~~~~~~~~~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~  163 (254)
                      ..            ...++++++.++.+.|..++..|+|++ +++.|..+|+.+.+.++.+||+...++|+|+|++||++
T Consensus        57 ~~------------s~e~r~~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e  123 (521)
T KOG1598|consen   57 GS------------SLESREKTIYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLE  123 (521)
T ss_pred             cc------------chHHHHHHHHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhh
Confidence            10            114578999999999999999999999 99999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhheeeCc
Q 025357          164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVLDFS  234 (254)
Q Consensus       164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v~~~~  234 (254)
                      +.++.+.|++++ ++|+.+.|++.|++|.+.|.+...  + .|.+||.-||+||+..|.+.+...+|+.++
T Consensus       124 ~t~hlliDfS~~-Lqv~Vy~LG~~~l~l~~~L~i~en--~-~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a  190 (521)
T KOG1598|consen  124 KTDHLLIDFSSY-LQVSVYDLGSNFLEVTDSLSIGEN--V-SPLVDPSLYIVRFSCRLLFGDKTEDVAKTA  190 (521)
T ss_pred             CCceEEEEeccc-eEEehhhhhHHHHHHHHHhccccc--c-ccccCcceeeechhHhhhcCCchHHHHHHH
Confidence            999999999996 999999999999999999998743  2 688999999999999999888888888776

>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=99.81  E-value=2e-19  Score=127.48  Aligned_cols=71  Identities=44%  Similarity=0.836  Sum_probs=65.9

Q ss_pred             HHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHH
Q 025357          113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (254)
Q Consensus       113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i  184 (254)
                      |+++|+.|+||+.+.+.|.++|+++.+.++.+||+|.+++|||||+|||+++.|+|++||+++ ++|++++|
T Consensus         1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~-~~Vs~~tI   71 (71)
T PF00382_consen    1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEA-AGVSEKTI   71 (71)
T ss_dssp             HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHH-CTSSHHHH
T ss_pred             ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHH-hCCCCCcC
Confidence            689999999999999999999999999999999999999999999999999999999999995 99999986

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.

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=99.64  E-value=1.5e-15  Score=136.68  Aligned_cols=90  Identities=22%  Similarity=0.381  Sum_probs=86.0

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~  187 (254)
                      +...+|.++|+.|+||..+.+.|.+|++++.+.+++.||+|.++||||||+||+.+|.|+|++||+++ ++|++.+|++.
T Consensus       218 ~p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v-~~Vs~~tI~~~  296 (310)
T PRK00423        218 DPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEV-AGVTEVTVRNR  296 (310)
T ss_pred             CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHH-cCCCHHHHHHH
Confidence            35789999999999999999999999999999999999999999999999999999999999999995 99999999999


Q ss_pred             HHHHHHHhchh
Q 025357          188 KEFIVKHLEAE  198 (254)
Q Consensus       188 ~k~l~~~l~~~  198 (254)
                      |++|.+.|++.
T Consensus       297 ykel~~~l~~~  307 (310)
T PRK00423        297 YKELAEKLDIK  307 (310)
T ss_pred             HHHHHHHhCcc
Confidence            99999999865

>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=99.61  E-value=3.2e-16  Score=100.14  Aligned_cols=43  Identities=47%  Similarity=1.025  Sum_probs=38.8

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccccccCcccccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIF   47 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f   47 (254)
                      ++||+||+ +.+++|+.+|++||++||+|++|+.++.++|||+|
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 67999999999999999999999999999999987

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.

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

Probab=99.52  E-value=4.5e-14  Score=124.84  Aligned_cols=90  Identities=27%  Similarity=0.371  Sum_probs=87.0

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~  187 (254)
                      +...+|.+||+.|+||+.+...|.+|.+++.+.|++.||+|.++||||+|+|+++++.++|++||+.+ ++|++.+|++.
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 DPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKV-AGVTEVTIRNR  271 (285)
T ss_pred             CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHH-hCCeeeHHHHH
Confidence            66789999999999999999999999999999999999999999999999999999999999999996 99999999999


Q ss_pred             HHHHHHHhchh
Q 025357          188 KEFIVKHLEAE  198 (254)
Q Consensus       188 ~k~l~~~l~~~  198 (254)
                      |++|.+.+++.
T Consensus       272 ykel~~~~~i~  282 (285)
T COG1405         272 YKELADALDIE  282 (285)
T ss_pred             HHHHHHhhccc
Confidence            99999999876

>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]

Probab=99.51  E-value=8.3e-14  Score=120.97  Aligned_cols=89  Identities=24%  Similarity=0.342  Sum_probs=85.0

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~  187 (254)
                      +...+|.+||+.|+||.++++.|.++.+++.+.....||+|.++|||+||+++++...++|++||.++ +||.+.+|+..
T Consensus       202 ~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~v-tgVaE~TIr~s  280 (308)
T KOG1597|consen  202 STGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEV-TGVAEVTIRNS  280 (308)
T ss_pred             hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHH-hhhhHHHHHHH
Confidence            46789999999999999999999999999999999999999999999999999999999999999995 99999999999


Q ss_pred             HHHHHHHhch
Q 025357          188 KEFIVKHLEA  197 (254)
Q Consensus       188 ~k~l~~~l~~  197 (254)
                      ||.|..++.-
T Consensus       281 YK~Lyp~~~~  290 (308)
T KOG1597|consen  281 YKDLYPHADK  290 (308)
T ss_pred             HHHHhhchhh
Confidence            9999988753

>cd00043 CYCLIN Cyclin box fold

Probab=99.18  E-value=3.5e-10  Score=81.21  Aligned_cols=83  Identities=24%  Similarity=0.378  Sum_probs=77.6

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCC-CHHHHHH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGR  186 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v-~~~~i~~  186 (254)
                      .+.++|.++++.+++|..+...|..+++++...+.+.++++..+|+||+|+||+.++.|.+++|+... .+. +..+|.+
T Consensus         4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~-~~~~~~~~i~~   82 (88)
T cd00043           4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHV-TGYATEEEILR   82 (88)
T ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHH-hCCCCHHHHHH
Confidence            46789999999999999999999999999999888889999999999999999999999999999995 889 9999998


Q ss_pred             HHHHH
Q 025357          187 AKEFI  191 (254)
Q Consensus       187 ~~k~l  191 (254)
                      .++.+
T Consensus        83 ~e~~i   87 (88)
T cd00043          83 MEKLL   87 (88)
T ss_pred             HHHHh
Confidence            88765

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=9e-10  Score=78.30  Aligned_cols=80  Identities=23%  Similarity=0.303  Sum_probs=71.6

Q ss_pred             HHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCC-CHHHHHHHHHH
Q 025357          112 SISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGRAKEF  190 (254)
Q Consensus       112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v-~~~~i~~~~k~  190 (254)
                      +|.++++.+++|..+...|..+++++.....+.++++..+|+||+|+||+.++.+++..++... ++. ++.+|.+.++.
T Consensus         2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~-~~~~~~~~i~~~~~~   80 (83)
T smart00385        2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHY-TGYFTEEEILRMEKL   80 (83)
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHh-hCCCCHHHHHHHHHH
Confidence            6889999999999999999999999987433445999999999999999999999999999995 888 99999999887


Q ss_pred             HH
Q 025357          191 IV  192 (254)
Q Consensus       191 l~  192 (254)
                      |.
T Consensus        81 il   82 (83)
T smart00385       81 LL   82 (83)
T ss_pred             Hh
Confidence            74

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

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

Probab=98.72  E-value=3.2e-08  Score=88.90  Aligned_cols=116  Identities=17%  Similarity=0.245  Sum_probs=95.0

Q ss_pred             HHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcC-CCH--H
Q 025357          106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG-TTK--K  182 (254)
Q Consensus       106 l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~-v~~--~  182 (254)
                      -.++.++|.+++.+|++|...+.+|..+|.+..-...++.-.+..+|++|+|+|++.++.|+.++||..++.. ..+  .
T Consensus        39 r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~  118 (323)
T KOG0834|consen   39 RQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDL  118 (323)
T ss_pred             HHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccc
Confidence            4688999999999999999999999999999988888888888999999999999999999999999886422 222  2


Q ss_pred             HHHHHHHHHHH-----------HhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357          183 EIGRAKEFIVK-----------HLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF  227 (254)
Q Consensus       183 ~i~~~~k~l~~-----------~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v  227 (254)
                      +....|.++++           .|+++      +....|..||-+|+.+|+.....
T Consensus       119 ~~~~~~~~~~~~Iv~~E~~lL~tl~Fd------l~v~hPy~~ll~~~k~l~~~~~~  168 (323)
T KOG0834|consen  119 ELEEVYWELKERIVQLELLLLETLGFD------LNVEHPYKYLLKYLKKLKADENL  168 (323)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHccCc------eeccCchHHHHHHHHHhhhhhhc
Confidence            45555554443           34444      66778999999999999888764

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

Probab=98.58  E-value=3.6e-08  Score=92.38  Aligned_cols=90  Identities=18%  Similarity=0.221  Sum_probs=74.8

Q ss_pred             HHHHHHHHHHhccCC-CH--HHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHH
Q 025357          108 QAFKSISAMSDRLGL-VT--TIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (254)
Q Consensus       108 ~a~~~I~~i~~~L~L-p~--~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i  184 (254)
                      +..-+|.+++..|-. |.  .++.+|..+..++..-.+..||+|..+++||||+|||.+|+++|..||+.+ ..|++.+|
T Consensus       165 DpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~v-vhV~e~Tl  243 (521)
T KOG1598|consen  165 DPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKV-VHVCESTL  243 (521)
T ss_pred             CcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHH-HHHhHHHH
Confidence            344567777766644 33  478888888888777777789999999999999999999999999999996 89999999


Q ss_pred             HHHHHHHHHHhchh
Q 025357          185 GRAKEFIVKHLEAE  198 (254)
Q Consensus       185 ~~~~k~l~~~l~~~  198 (254)
                      ++.|+++.+.+...
T Consensus       244 ~kRl~Ef~~T~s~~  257 (521)
T KOG1598|consen  244 SKRLKEFSDTLSGD  257 (521)
T ss_pred             HHHHHHHhcccccc
Confidence            99999998866433

>TIGR00569 ccl1 cyclin ccl1

Probab=98.55  E-value=5.7e-07  Score=80.69  Aligned_cols=108  Identities=15%  Similarity=0.230  Sum_probs=92.5

Q ss_pred             HHHHHHHHHHHhccC--CCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCC----
Q 025357          107 IQAFKSISAMSDRLG--LVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT----  180 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~--Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~----  180 (254)
                      ......|.++|..|+  ||..++-+|..+|++.+-.+.+.--.+..++++|+|+||+.+..|+++.+++.. ..-+    
T Consensus        57 ~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~-~~~~~~~~  135 (305)
T TIGR00569        57 KYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGN-LKETPLKA  135 (305)
T ss_pred             HHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhh-ccCCchhh
Confidence            466789999999999  999999999999999988887777789999999999999999999999999874 3333    


Q ss_pred             HHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhc
Q 025357          181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI  221 (254)
Q Consensus       181 ~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L  221 (254)
                      ...|...-..|.+.|++.      +....|..++..|...|
T Consensus       136 ~~~Il~~E~~lL~~L~F~------L~V~hPyr~L~~~l~dl  170 (305)
T TIGR00569       136 LEQVLEYELLLIQQLNFH------LIVHNPYRPLEGFLIDI  170 (305)
T ss_pred             HHHHHHHHHHHHHHCCCc------EEeeCccHHHHHHHHHH
Confidence            367777778888899887      66678888888888655

University).

>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=98.06  E-value=1.2e-05  Score=70.97  Aligned_cols=114  Identities=21%  Similarity=0.306  Sum_probs=93.7

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHh-------cCC
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVA-------NGT  179 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~-------~~v  179 (254)
                      ......|..+|.+|+||..+..+|..+|++..-+....+.++..++++|||+||+.+..|+-+.-..-.+       .--
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            4567999999999999999999999999999998889999999999999999999999765544332221       123


Q ss_pred             CHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcc
Q 025357          180 TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFF  226 (254)
Q Consensus       180 ~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~  226 (254)
                      +.+.|-..-.++.+.|+..      .-...|..++..|...+.+...
T Consensus       126 sr~~Il~~E~~lLEaL~fd------~~V~hPy~~l~~f~~~~q~~~~  166 (297)
T COG5333         126 SRERILEYEFELLEALDFD------LHVHHPYKYLEGFLKDLQEKDK  166 (297)
T ss_pred             cHHHHHHHHHHHHHHcccc------eEeccccHHHHHHHHHHHhccH
Confidence            5677777778888888877      5667899999999988877655

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=98.05  E-value=3e-05  Score=69.02  Aligned_cols=118  Identities=18%  Similarity=0.265  Sum_probs=97.9

Q ss_pred             hhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCC----
Q 025357          104 RNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT----  179 (254)
Q Consensus       104 r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v----  179 (254)
                      ....-+..+|++-|=.|+||....-++.-+|++.....-+.+-..+.++.|||.+|++.+..|++++||..|+-.+    
T Consensus        21 el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~  100 (367)
T KOG0835|consen   21 ELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRR  100 (367)
T ss_pred             HHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHH
Confidence            3345678999999999999999999999999999888888889999999999999999999999999998652111    


Q ss_pred             -----C-----------HHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357          180 -----T-----------KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF  227 (254)
Q Consensus       180 -----~-----------~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v  227 (254)
                           .           +..+.++..++.+.||+.      +-..+|..+|--|..-|++++..
T Consensus       101 ~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~------~Hv~hPhklii~YLqtL~~~~~~  158 (367)
T KOG0835|consen  101 ESEAAEHLILARLYINLKMQVIRAERRILRELGFD------VHVEHPHKLIIMYLQTLQLPPNL  158 (367)
T ss_pred             hccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCe------eeeeccHHHHHHHHHHhcCCCch
Confidence                 0           123345566778888877      55678999999999999998876

>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=97.88  E-value=0.00019  Score=55.39  Aligned_cols=93  Identities=20%  Similarity=0.331  Sum_probs=76.3

Q ss_pred             hHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHhc--CCCH
Q 025357          105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN--GTTK  181 (254)
Q Consensus       105 ~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~~--~v~~  181 (254)
                      .-....++|..++..++++..+.-.|..++.+..........+...++++|+++||+.+.. +.++.++... .  ..+.
T Consensus        30 ~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~-~~~~~~~  108 (127)
T PF00134_consen   30 MRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRI-SDNTFTK  108 (127)
T ss_dssp             HHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHH-TTTSSHH
T ss_pred             HHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHH-HcCCCCH
Confidence            3457789999999999999999999999999998888778888999999999999999877 7888998875 4  3578


Q ss_pred             HHHHHHHHHHHHHhchh
Q 025357          182 KEIGRAKEFIVKHLEAE  198 (254)
Q Consensus       182 ~~i~~~~k~l~~~l~~~  198 (254)
                      ++|...-+.+...|+.+
T Consensus       109 ~~i~~~E~~iL~~L~f~  125 (127)
T PF00134_consen  109 KDILEMEREILSALNFD  125 (127)
T ss_dssp             HHHHHHHHHHHHHTTT-
T ss_pred             HHHHHHHHHHHHHCCCC
Confidence            88888888888887754

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 ....

>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=97.54  E-value=0.00041  Score=55.04  Aligned_cols=84  Identities=11%  Similarity=0.247  Sum_probs=63.0

Q ss_pred             hHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhh--CCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHH
Q 025357          105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKK  182 (254)
Q Consensus       105 ~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~--~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~  182 (254)
                      ...-|...|+.+|++|+|++.+.+..-.+++.+..  ..++++|-.+.+.-.|+|..||..+.++|.+||-.. ..--+.
T Consensus        10 vy~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~-Yr~qpq   88 (135)
T PF01857_consen   10 VYKLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKA-YRKQPQ   88 (135)
T ss_dssp             HHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHH-HTTSTT
T ss_pred             HHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHH-HHhccc
Confidence            44568889999999999999998998888888754  457899999999999999999999999999999883 543333


Q ss_pred             HHHHHHH
Q 025357          183 EIGRAKE  189 (254)
Q Consensus       183 ~i~~~~k  189 (254)
                      .-...|+
T Consensus        89 ~~~~Vyr   95 (135)
T PF01857_consen   89 ASSHVYR   95 (135)
T ss_dssp             --THHHH
T ss_pred             ccccceE
Confidence            3333333

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.

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

Probab=97.24  E-value=0.0046  Score=56.02  Aligned_cols=115  Identities=17%  Similarity=0.191  Sum_probs=92.3

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCC-CCC--CHHHHHHHHHHHHHHhcCC--CCCHHHHHHH-hcCCC
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPL-RGR--NQEAIVAACLYIACRQENK--PRTVKEFCSV-ANGTT  180 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~-~Gr--~~~~iaAAclY~AcR~~~~--p~tl~eIa~~-~~~v~  180 (254)
                      .+|+.+|-++|...+....+.=.|..++.+.....-+ +++  -...+|+||+.+|++.+..  |.++.-.... ..-+.
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            4799999999999999999999999999998664433 333  2689999999999998876  6555433221 13457


Q ss_pred             HHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357          181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF  227 (254)
Q Consensus       181 ~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v  227 (254)
                      .++|.|.-..+...|+=.      +..++|.+|+.-|+++++.....
T Consensus       159 aktI~rmELLVLstL~Wr------l~aVTP~sF~~~fl~ki~~~~~~  199 (335)
T KOG0656|consen  159 AKTIQRMELLVLSTLKWR------LRAVTPFSFIDHFLSKISQKDHN  199 (335)
T ss_pred             HHHHHHHHHHHHhhcccc------ccCCCchHHHHHHHHHcCcccch
Confidence            899999998889999876      77899999999999999886443

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

Probab=97.20  E-value=0.00044  Score=58.93  Aligned_cols=59  Identities=22%  Similarity=0.406  Sum_probs=55.9

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCC
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP  166 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p  166 (254)
                      .....|+.+++.|+|.+.++.+|.-++++.+-+..+++-.|..+|+.|+|+||+.+..|
T Consensus        43 ~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~  101 (264)
T KOG0794|consen   43 FMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECP  101 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcc
Confidence            56789999999999999999999999999988888999999999999999999999988

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=97.02  E-value=0.0039  Score=55.79  Aligned_cols=129  Identities=18%  Similarity=0.149  Sum_probs=81.8

Q ss_pred             HHHHHHHHHHHhccCCCHHH-HHHHH-HHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHH-HHHHHhcCCCHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTI-KDRAN-EIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVK-EFCSVANGTTKKE  183 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v-~e~A~-~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~-eIa~~~~~v~~~~  183 (254)
                      .+..+.|-.+...|++|++. +.++. .+......-.+..--+|+++|+||+|+|+|..++|.+.. .--. +.+.++.+
T Consensus       139 ~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~-~Fd~~k~e  217 (367)
T KOG0835|consen  139 EHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFK-AFDTTKRE  217 (367)
T ss_pred             eccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHH-HcCCcHHH
Confidence            35677888889999999765 33333 333333333344445899999999999999999886554 3434 58889999


Q ss_pred             HHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCC-----CcchhheeeCcceeeehhhcccccCCCC
Q 025357          184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFK-----NFFFLFVLDFSSCMIFCSLWPYLSNPMH  251 (254)
Q Consensus       184 i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l-----~~~v~~v~~~~~~~~~~~~~~~~~~~~~  251 (254)
                      |-.....+.......      .|.   ..+|.-|++++..     +++.+.+.|.      +|+|.-+..-.|
T Consensus       218 id~ic~~l~~lY~~~------~p~---~~li~~~vd~~k~~~~da~~k~~~~~ds------~~~l~g~~~a~~  275 (367)
T KOG0835|consen  218 IDEICYRLIPLYKRA------KPD---ETLIEAFVDRLKRKFSDASGKAKGANDS------ASLLGGFAPAVD  275 (367)
T ss_pred             HHHHHHHHHHHHHhc------ccC---HHHHHHHHHHhhHHHHhccCCccchhhH------HHhhcccccccC
Confidence            887776666665542      121   4566666666543     4444444442      356655544333

>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=96.94  E-value=0.00066  Score=41.30  Aligned_cols=27  Identities=30%  Similarity=0.562  Sum_probs=23.4

Q ss_pred             CCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            5 YCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      .|+.|++ .  .+....|..+|..||.|++
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 3  6788899999999999974

>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=96.81  E-value=0.0074  Score=45.59  Aligned_cols=87  Identities=14%  Similarity=0.129  Sum_probs=63.9

Q ss_pred             HHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHhcCCCHHHHHHH
Q 025357          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVANGTTKKEIGRA  187 (254)
Q Consensus       109 a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~~~v~~~~i~~~  187 (254)
                      .+.+|+++....+....+...|..+.....-...+-+-+|..+||||+|+|.+..+. +.--..+.. ..|++..+|..+
T Consensus         3 p~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~-~t~~~~~~l~~c   81 (118)
T PF02984_consen    3 PYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEK-LTGYDKEDLKEC   81 (118)
T ss_dssp             HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHH-HHTS-HHHHHHH
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchh-hcCCCHHHHHHH
Confidence            466788886655566678888888888754443355678999999999999998765 333444556 378999999999


Q ss_pred             HHHHHHHhc
Q 025357          188 KEFIVKHLE  196 (254)
Q Consensus       188 ~k~l~~~l~  196 (254)
                      ++.|.+.+.
T Consensus        82 ~~~i~~~~~   90 (118)
T PF02984_consen   82 IELIQELLS   90 (118)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999988775

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 ....

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

Probab=96.78  E-value=0.0015  Score=38.89  Aligned_cols=31  Identities=16%  Similarity=0.446  Sum_probs=25.1

Q ss_pred             CCCCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      |....|+.||+  +.++..+.+..+|.+||.+.
T Consensus         1 ~~~~~C~~C~~--~~i~~~~~~~~~C~~Cg~~~   31 (33)
T PF08792_consen    1 SNLKKCSKCGG--NGIVNKEDDYEVCIFCGSSF   31 (33)
T ss_pred             CCceEcCCCCC--CeEEEecCCeEEcccCCcEe
Confidence            45678999998  34555779999999999985

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

Probab=96.75  E-value=0.0005  Score=45.72  Aligned_cols=31  Identities=35%  Similarity=0.740  Sum_probs=23.6

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      +.+||.|+. ..+|+++.+-.+.|..||.+|.
T Consensus         7 ~VkCp~C~~-~q~vFSha~t~V~C~~Cg~~L~   37 (55)
T PF01667_consen    7 DVKCPGCYN-IQTVFSHAQTVVKCVVCGTVLA   37 (55)
T ss_dssp             EEE-TTT-S-EEEEETT-SS-EE-SSSTSEEE
T ss_pred             EEECCCCCC-eeEEEecCCeEEEcccCCCEec
Confidence            368999998 7899999999999999999995

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.

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=96.73  E-value=0.00073  Score=45.46  Aligned_cols=31  Identities=35%  Similarity=0.751  Sum_probs=28.5

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      +.+||.|+. ..+|+++.+-.+.|..||.+|.
T Consensus        11 ~VkCp~C~n-~q~vFsha~t~V~C~~Cg~~L~   41 (59)
T PRK00415         11 KVKCPDCGN-EQVVFSHASTVVRCLVCGKTLA   41 (59)
T ss_pred             EEECCCCCC-eEEEEecCCcEEECcccCCCcc
Confidence            367999998 6899999999999999999995

>COG5024 Cyclin [Cell division and chromosome partitioning]

Probab=96.59  E-value=0.014  Score=54.92  Aligned_cols=120  Identities=15%  Similarity=0.183  Sum_probs=100.1

Q ss_pred             HHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHh-cCCCHHHHHH
Q 025357          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVA-NGTTKKEIGR  186 (254)
Q Consensus       109 a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~-~~v~~~~i~~  186 (254)
                      ...+|.++-.+++|-+.....|..|..+....+.+.=.+...+++.|+||||+-+.+ +.++++++-+. -..+.+.|.+
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            467888889999999999999999999998888776677889999999999998865 45677876642 3568999999


Q ss_pred             HHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhheeeCc
Q 025357          187 AKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVLDFS  234 (254)
Q Consensus       187 ~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v~~~~  234 (254)
                      +.+.+...|+..      +.-..|..|+.|+.....-+.+...++.+.
T Consensus       296 aE~~ml~~l~f~------is~P~P~sFLRriSka~dyd~~srt~~k~~  337 (440)
T COG5024         296 AERYMLEVLDFN------ISWPSPMSFLRRISKASDYDIFSRTPAKFS  337 (440)
T ss_pred             HHHHHhhhcccc------cCCCChHHHHHHHHhhcccchhhhhhHhhh
Confidence            999999999987      667789999999988888887777666655

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

Probab=96.56  E-value=0.0016  Score=44.66  Aligned_cols=30  Identities=37%  Similarity=0.790  Sum_probs=27.9

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      .+||.||. ..+++++.+-.+.|..||.+|-
T Consensus        20 VkCpdC~N-~q~vFshast~V~C~~CG~~l~   49 (67)
T COG2051          20 VKCPDCGN-EQVVFSHASTVVTCLICGTTLA   49 (67)
T ss_pred             EECCCCCC-EEEEeccCceEEEecccccEEE
Confidence            57999998 7899999999999999999985

>PLN00209 ribosomal protein S27; Provisional

Probab=96.27  E-value=0.0022  Score=46.32  Aligned_cols=31  Identities=35%  Similarity=0.694  Sum_probs=28.5

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      +.+||.|+. ..+|+++.+-.+.|..||.+|.
T Consensus        36 ~VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~   66 (86)
T PLN00209         36 DVKCQGCFN-ITTVFSHSQTVVVCGSCQTVLC   66 (86)
T ss_pred             EEECCCCCC-eeEEEecCceEEEccccCCEee
Confidence            367999998 7899999999999999999995

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=96.26  E-value=0.0023  Score=46.05  Aligned_cols=31  Identities=29%  Similarity=0.677  Sum_probs=28.5

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      +.+||.|+. ..+|+++.+-.+.|..||.+|.
T Consensus        35 ~VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~   65 (85)
T PTZ00083         35 DVKCPGCSQ-ITTVFSHAQTVVLCGGCSSQLC   65 (85)
T ss_pred             EEECCCCCC-eeEEEecCceEEEccccCCEee
Confidence            367999998 7899999999999999999995

>PHA00626 hypothetical protein

Probab=96.21  E-value=0.0044  Score=41.01  Aligned_cols=33  Identities=18%  Similarity=0.489  Sum_probs=24.6

Q ss_pred             CCCCCCCCCCceEEe----cCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFD----HSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D----~~~G~~vC~~CG~Vl~e~~   37 (254)
                      +.||.||+ .+++.-    ......+|.+||+-.....
T Consensus         1 m~CP~CGS-~~Ivrcg~cr~~snrYkCkdCGY~ft~~~   37 (59)
T PHA00626          1 MSCPKCGS-GNIAKEKTMRGWSDDYVCCDCGYNDSKDA   37 (59)
T ss_pred             CCCCCCCC-ceeeeeceecccCcceEcCCCCCeechhh
Confidence            47999998 566653    2378999999999875433

>PRK00420 hypothetical protein; Validated

Probab=96.11  E-value=0.0045  Score=47.38  Aligned_cols=31  Identities=26%  Similarity=0.560  Sum_probs=24.0

Q ss_pred             CCCCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      |-...||.||.+  + +-...|..+|..||.++.
T Consensus        21 ml~~~CP~Cg~p--L-f~lk~g~~~Cp~Cg~~~~   51 (112)
T PRK00420         21 MLSKHCPVCGLP--L-FELKDGEVVCPVHGKVYI   51 (112)
T ss_pred             HccCCCCCCCCc--c-eecCCCceECCCCCCeee
Confidence            334789999973  4 333799999999999874

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

Probab=95.98  E-value=0.0053  Score=39.32  Aligned_cols=31  Identities=39%  Similarity=0.748  Sum_probs=25.4

Q ss_pred             CCCCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      |....|+.||.  .+.+|+..+.+.|..||.-+
T Consensus         1 ~~~y~C~~CG~--~~~~~~~~~~~~Cp~CG~~~   31 (46)
T PRK00398          1 MAEYKCARCGR--EVELDEYGTGVRCPYCGYRI   31 (46)
T ss_pred             CCEEECCCCCC--EEEECCCCCceECCCCCCeE
Confidence            56688999997  47778777799999999644

>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=95.92  E-value=0.026  Score=50.18  Aligned_cols=63  Identities=19%  Similarity=0.405  Sum_probs=53.9

Q ss_pred             HHHHHhcc--CCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 025357          113 ISAMSDRL--GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSV  175 (254)
Q Consensus       113 I~~i~~~L--~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~  175 (254)
                      +-.+++++  .||..|+-+|..+|+++.=.+...--.|..+.++|+|+||+.+..-+++.+|+.-
T Consensus        63 l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn  127 (325)
T KOG2496|consen   63 LVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKN  127 (325)
T ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhh
Confidence            33444444  7899999999999999987777767789999999999999999999999999884

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

Probab=95.92  E-value=0.0027  Score=38.09  Aligned_cols=27  Identities=19%  Similarity=0.685  Sum_probs=16.0

Q ss_pred             CCCCCCCCCceEEe----cCCCceEcCcCceee
Q 025357            5 YCADCKRLTEVVFD----HSAGDTICSECGLVL   33 (254)
Q Consensus         5 ~Cp~Cg~~~~lv~D----~~~G~~vC~~CG~Vl   33 (254)
                      .||.||+.  +...    ...-..||..||.|-
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            69999984  3333    456678999999984

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=95.79  E-value=0.0049  Score=34.60  Aligned_cols=23  Identities=22%  Similarity=0.936  Sum_probs=18.4

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCce
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGL   31 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~   31 (254)
                      ...||+||. . +    ..+..+|..||.
T Consensus         2 ~~~Cp~Cg~-~-~----~~~~~fC~~CG~   24 (26)
T PF13248_consen    2 EMFCPNCGA-E-I----DPDAKFCPNCGA   24 (26)
T ss_pred             cCCCcccCC-c-C----CcccccChhhCC
Confidence            489999997 2 1    367899999996

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

Probab=95.74  E-value=0.01  Score=35.79  Aligned_cols=31  Identities=16%  Similarity=0.452  Sum_probs=19.7

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      +..||+||+ --+......+...|..||++.+
T Consensus         1 m~FCp~C~n-lL~p~~~~~~~~~C~~C~Y~~~   31 (35)
T PF02150_consen    1 MRFCPECGN-LLYPKEDKEKRVACRTCGYEEP   31 (35)
T ss_dssp             --BETTTTS-BEEEEEETTTTEEESSSS-EEE
T ss_pred             CeeCCCCCc-cceEcCCCccCcCCCCCCCccC
Confidence            367999997 3334444555557999999864

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 ....

>PRK11827 hypothetical protein; Provisional

Probab=95.45  E-value=0.01  Score=40.31  Aligned_cols=28  Identities=18%  Similarity=0.494  Sum_probs=24.6

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      ..||.|++  .+.+|....+++|..||++.
T Consensus         9 LaCP~ckg--~L~~~~~~~~Lic~~~~laY   36 (60)
T PRK11827          9 IACPVCNG--KLWYNQEKQELICKLDNLAF   36 (60)
T ss_pred             eECCCCCC--cCeEcCCCCeEECCccCeec
Confidence            57999987  58888888899999999985

>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase

Probab=95.45  E-value=0.013  Score=35.82  Aligned_cols=28  Identities=32%  Similarity=0.736  Sum_probs=21.5

Q ss_pred             CCCCCCCCCCceEEec--CCCceEcCcCce
Q 025357            4 SYCADCKRLTEVVFDH--SAGDTICSECGL   31 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~--~~G~~vC~~CG~   31 (254)
                      ..||.||+....-+|.  ..|..+|..||.
T Consensus         4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~   33 (37)
T smart00778        4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA   33 (37)
T ss_pred             cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence            5799999854444554  569999999984

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.

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=95.44  E-value=0.0089  Score=36.53  Aligned_cols=29  Identities=28%  Similarity=0.607  Sum_probs=21.0

Q ss_pred             CCCCCCCCCCceEEe-----cCCCceEcCcCceeec
Q 025357            4 SYCADCKRLTEVVFD-----HSAGDTICSECGLVLE   34 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D-----~~~G~~vC~~CG~Vl~   34 (254)
                      ..||+|+..  ...+     ...+.+.|..||.++.
T Consensus         3 ~~CP~C~~~--~~v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         3 IQCPNCKTS--FRVVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             EECCCCCCE--EEeCHHHcCCCCCEEECCCCCCEEE
Confidence            689999983  2233     2345799999999874

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.

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=95.43  E-value=0.011  Score=38.63  Aligned_cols=27  Identities=22%  Similarity=0.682  Sum_probs=21.3

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      ..||.||+ + +..++ .+...|..||+..
T Consensus        21 ~fCP~Cg~-~-~m~~~-~~r~~C~~Cgyt~   47 (50)
T PRK00432         21 KFCPRCGS-G-FMAEH-LDRWHCGKCGYTE   47 (50)
T ss_pred             CcCcCCCc-c-hhecc-CCcEECCCcCCEE
Confidence            57999998 5 55544 5899999999874

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=95.19  E-value=0.0091  Score=32.55  Aligned_cols=22  Identities=27%  Similarity=0.916  Sum_probs=17.0

Q ss_pred             CCCCCCCCCceEEecCCCceEcCcCcee
Q 025357            5 YCADCKRLTEVVFDHSAGDTICSECGLV   32 (254)
Q Consensus         5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V   32 (254)
                      .||+||.+  +    ..+..+|..||.-
T Consensus         1 ~Cp~CG~~--~----~~~~~fC~~CG~~   22 (23)
T PF13240_consen    1 YCPNCGAE--I----EDDAKFCPNCGTP   22 (23)
T ss_pred             CCcccCCC--C----CCcCcchhhhCCc
Confidence            59999983  2    2578899999964

>COG2835 Uncharacterized conserved protein [Function unknown]

Probab=95.06  E-value=0.017  Score=38.96  Aligned_cols=30  Identities=30%  Similarity=0.671  Sum_probs=26.6

Q ss_pred             CCCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         2 ~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      +...||.|++  .+.+|.+.++++|..||...
T Consensus         7 eiLaCP~~kg--~L~~~~~~~~L~c~~~~~aY   36 (60)
T COG2835           7 EILACPVCKG--PLVYDEEKQELICPRCKLAY   36 (60)
T ss_pred             eeeeccCcCC--cceEeccCCEEEecccCcee
Confidence            4567999997  39999999999999999985

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=95.03  E-value=0.014  Score=38.77  Aligned_cols=31  Identities=39%  Similarity=0.768  Sum_probs=21.4

Q ss_pred             CCCCCCCCCCCceEEecCCCc-eEcCcCceeec
Q 025357            3 DSYCADCKRLTEVVFDHSAGD-TICSECGLVLE   34 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~-~vC~~CG~Vl~   34 (254)
                      +..||+||..-. +.|...|+ +.|..||.-++
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            468999998322 23434455 56999999884

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.

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=94.99  E-value=0.028  Score=38.01  Aligned_cols=29  Identities=24%  Similarity=0.634  Sum_probs=21.2

Q ss_pred             CCCCCCCCCCCCceEEecCCC-------ceEcCcCce
Q 025357            2 ADSYCADCKRLTEVVFDHSAG-------DTICSECGL   31 (254)
Q Consensus         2 ~~~~Cp~Cg~~~~lv~D~~~G-------~~vC~~CG~   31 (254)
                      ++..||.||+ ..+..+...+       .+.|.+||.
T Consensus         2 ~LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga   37 (61)
T PF14354_consen    2 ELKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA   37 (61)
T ss_pred             CCcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence            3567999987 5666665554       366999999

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

Probab=94.99  E-value=0.014  Score=45.78  Aligned_cols=27  Identities=22%  Similarity=0.683  Sum_probs=21.1

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCc-eee
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECG-LVL   33 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG-~Vl   33 (254)
                      ...||.||.+  ++ - .+|+++|..|| .+.
T Consensus        28 ~~hCp~Cg~P--LF-~-KdG~v~CPvC~~~~~   55 (131)
T COG1645          28 AKHCPKCGTP--LF-R-KDGEVFCPVCGYREV   55 (131)
T ss_pred             HhhCcccCCc--ce-e-eCCeEECCCCCceEE
Confidence            3579999983  43 3 89999999999 443

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

Probab=94.93  E-value=0.021  Score=41.43  Aligned_cols=29  Identities=31%  Similarity=0.573  Sum_probs=25.2

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      -.||.||+ + .|.-..+|-+.|..||.++.
T Consensus        36 ~~Cp~C~~-~-~VkR~a~GIW~C~kCg~~fA   64 (89)
T COG1997          36 HVCPFCGR-T-TVKRIATGIWKCRKCGAKFA   64 (89)
T ss_pred             CcCCCCCC-c-ceeeeccCeEEcCCCCCeec
Confidence            46999998 4 67788999999999999975

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

Probab=94.87  E-value=0.17  Score=47.19  Aligned_cols=114  Identities=16%  Similarity=0.238  Sum_probs=89.8

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHH-HHHHhcCC-CCCHHHHHHHh-cCCCHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLY-IACRQENK-PRTVKEFCSVA-NGTTKKE  183 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY-~AcR~~~~-p~tl~eIa~~~-~~v~~~~  183 (254)
                      ..-.+++-++-.+++|...+.-.|..|+.+......+..+....+..+|++ |||+.+.. +-.+.|+.-+. -..+..+
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            345788999999999999999999999999988766777777777777756 99996544 33366665431 2368999


Q ss_pred             HHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcc
Q 025357          184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFF  226 (254)
Q Consensus       184 i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~  226 (254)
                      |.+.-+.+...|+..      +....|..|+.||........+
T Consensus       239 il~mE~~il~~L~f~------l~~p~~~~FLrr~~ka~~~d~~  275 (391)
T KOG0653|consen  239 ILRMEKYILNVLEFD------LSVPTPLSFLRRFLKAADYDIK  275 (391)
T ss_pred             HHHHHHHHHhccCee------ecCCchHHHHHHHHHhhhcchh
Confidence            999999999998877      6677899999999999885444

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

Probab=94.84  E-value=0.034  Score=38.66  Aligned_cols=17  Identities=35%  Similarity=0.806  Sum_probs=15.8

Q ss_pred             EecCCCceEcCcCceee
Q 025357           17 FDHSAGDTICSECGLVL   33 (254)
Q Consensus        17 ~D~~~G~~vC~~CG~Vl   33 (254)
                      ++..+|.++|.+||.+.
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            68999999999999986

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.

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

Probab=94.83  E-value=0.03  Score=32.57  Aligned_cols=27  Identities=26%  Similarity=0.459  Sum_probs=14.8

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      -+||.|++. ..-.|  ...+||.+||.-.
T Consensus         3 p~Cp~C~se-~~y~D--~~~~vCp~C~~ew   29 (30)
T PF08274_consen    3 PKCPLCGSE-YTYED--GELLVCPECGHEW   29 (30)
T ss_dssp             ---TTT------EE---SSSEEETTTTEEE
T ss_pred             CCCCCCCCc-ceecc--CCEEeCCcccccC
Confidence            479999994 33344  7889999999753

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.

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

Probab=94.25  E-value=0.026  Score=36.41  Aligned_cols=27  Identities=26%  Similarity=0.733  Sum_probs=22.3

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V   32 (254)
                      ..||.||. ..+..|+.. .+.|..||+.
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            46999996 567777766 8999999987

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=94.23  E-value=0.034  Score=36.18  Aligned_cols=28  Identities=18%  Similarity=0.632  Sum_probs=19.6

Q ss_pred             CCCCCCCCCceEEecCC--CceEcCcCceeec
Q 025357            5 YCADCKRLTEVVFDHSA--GDTICSECGLVLE   34 (254)
Q Consensus         5 ~Cp~Cg~~~~lv~D~~~--G~~vC~~CG~Vl~   34 (254)
                      .||.||+  .+......  -..+|..||.+..
T Consensus         2 FCp~Cg~--~l~~~~~~~~~~~vC~~Cg~~~~   31 (52)
T smart00661        2 FCPKCGN--MLIPKEGKEKRRFVCRKCGYEEP   31 (52)
T ss_pred             CCCCCCC--ccccccCCCCCEEECCcCCCeEE
Confidence            6999997  33333222  3799999998854

>PRK10220 hypothetical protein; Provisional

Probab=94.11  E-value=0.15  Score=38.50  Aligned_cols=30  Identities=30%  Similarity=0.548  Sum_probs=22.4

Q ss_pred             CCCCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      |..-.||.|++ ...-.|  ...+||.+||.--
T Consensus         1 m~lP~CP~C~s-eytY~d--~~~~vCpeC~hEW   30 (111)
T PRK10220          1 MSLPHCPKCNS-EYTYED--NGMYICPECAHEW   30 (111)
T ss_pred             CCCCcCCCCCC-cceEcC--CCeEECCcccCcC
Confidence            67778999998 344444  5679999999753

>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=94.01  E-value=0.027  Score=31.62  Aligned_cols=25  Identities=28%  Similarity=0.771  Sum_probs=19.1

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      ..||+|+..  |    ......|..||++..
T Consensus         1 K~CP~C~~~--V----~~~~~~Cp~CG~~F~   25 (26)
T PF10571_consen    1 KTCPECGAE--V----PESAKFCPHCGYDFE   25 (26)
T ss_pred             CcCCCCcCC--c----hhhcCcCCCCCCCCc
Confidence            369999983  2    356789999999863

Several members are annotated as putative helicases.

>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=94.01  E-value=0.074  Score=31.23  Aligned_cols=28  Identities=18%  Similarity=0.426  Sum_probs=16.9

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      ..|+.||++  .+.....-..+|.+||...
T Consensus         4 rfC~~CG~~--t~~~~~g~~r~C~~Cg~~~   31 (32)
T PF09297_consen    4 RFCGRCGAP--TKPAPGGWARRCPSCGHEH   31 (32)
T ss_dssp             SB-TTT--B--EEE-SSSS-EEESSSS-EE
T ss_pred             cccCcCCcc--ccCCCCcCEeECCCCcCEe
Confidence            579999983  4456667889999999763

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

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

Probab=93.71  E-value=0.031  Score=39.57  Aligned_cols=30  Identities=30%  Similarity=0.769  Sum_probs=27.2

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      +.+||.|-. ...++.+++..++|.+|+.|+
T Consensus        34 ~VkC~gc~~-iT~vfSHaqtvVvc~~c~~il   63 (84)
T KOG1779|consen   34 DVKCPGCFK-ITTVFSHAQTVVVCEGCSTIL   63 (84)
T ss_pred             EEEcCCceE-EEEEeecCceEEEcCCCceEE
Confidence            468999987 678999999999999999997

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=93.63  E-value=0.063  Score=35.39  Aligned_cols=32  Identities=22%  Similarity=0.248  Sum_probs=21.1

Q ss_pred             CCCCCCCCCCCceEE---e--cCCCceEcCcCceeec
Q 025357            3 DSYCADCKRLTEVVF---D--HSAGDTICSECGLVLE   34 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~---D--~~~G~~vC~~CG~Vl~   34 (254)
                      +..||.||+....+.   |  ...|...|..||....
T Consensus         1 LkPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~   37 (53)
T TIGR03655         1 LKPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP   37 (53)
T ss_pred             CCCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence            357999999433132   3  2344557999999864

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.

>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=93.58  E-value=0.071  Score=33.33  Aligned_cols=26  Identities=31%  Similarity=0.804  Sum_probs=20.1

Q ss_pred             CCCCCCCCCCCCceEEecCCCceEcCcCc
Q 025357            2 ADSYCADCKRLTEVVFDHSAGDTICSECG   30 (254)
Q Consensus         2 ~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG   30 (254)
                      -...||.||.  .+.. ..+|.++|..|+
T Consensus        16 L~~~Cp~C~~--PL~~-~k~g~~~Cv~C~   41 (41)
T PF06677_consen   16 LDEHCPDCGT--PLMR-DKDGKIYCVSCG   41 (41)
T ss_pred             hcCccCCCCC--eeEE-ecCCCEECCCCC
Confidence            3468999986  3544 579999999996

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

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

Probab=93.44  E-value=0.074  Score=33.07  Aligned_cols=29  Identities=31%  Similarity=0.620  Sum_probs=16.0

Q ss_pred             CCCCCCCCCCceE-Eec--CCCceEcCcCcee
Q 025357            4 SYCADCKRLTEVV-FDH--SAGDTICSECGLV   32 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv-~D~--~~G~~vC~~CG~V   32 (254)
                      ..||.||+....- ++.  .+|..+|..|+-+
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            4699999854433 553  5699999999434

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.

>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=93.41  E-value=0.045  Score=41.74  Aligned_cols=31  Identities=19%  Similarity=0.602  Sum_probs=25.6

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeeccc
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~   36 (254)
                      .+.||.||..   .+|-..--+||..||.++.-.
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            3679999983   688778889999999998644

The function of members of this family is unknown.

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

Probab=92.97  E-value=0.49  Score=43.68  Aligned_cols=59  Identities=14%  Similarity=0.228  Sum_probs=51.0

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK  165 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~  165 (254)
                      ....++|++++.--+|...++.+|.-+|.++.=+|++.-.++..+|+|||.+|++.+..
T Consensus       383 rSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~  441 (497)
T KOG4164|consen  383 RSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDL  441 (497)
T ss_pred             HHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhh
Confidence            34467788888888999999999999999998888888788999999999999997764

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=92.69  E-value=0.096  Score=42.49  Aligned_cols=30  Identities=30%  Similarity=0.644  Sum_probs=19.8

Q ss_pred             CCCCCCCCCCceEEecC---CCceE-----cCcCceee
Q 025357            4 SYCADCKRLTEVVFDHS---AGDTI-----CSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~---~G~~v-----C~~CG~Vl   33 (254)
                      ++||+||++..-+.|..   .|..|     |.+||.-.
T Consensus         1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f   38 (154)
T PRK00464          1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF   38 (154)
T ss_pred             CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence            57999998532455533   45444     99999765

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=92.55  E-value=0.049  Score=33.19  Aligned_cols=30  Identities=27%  Similarity=0.527  Sum_probs=21.6

Q ss_pred             CCCCCCCCCCCceEEe----cCCCceEcCcCceee
Q 025357            3 DSYCADCKRLTEVVFD----HSAGDTICSECGLVL   33 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D----~~~G~~vC~~CG~Vl   33 (254)
                      ...||+|+.. --+-|    ...+.+-|..||.+.
T Consensus         2 ~i~CP~C~~~-f~v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    2 IITCPNCQTR-FRVPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             EEECCCCCce-EEcCHHHcccCCcEEECCCCCcEe
Confidence            3689999973 22222    357789999999886

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

Probab=92.48  E-value=0.34  Score=36.45  Aligned_cols=32  Identities=28%  Similarity=0.714  Sum_probs=23.6

Q ss_pred             CCCCCCCCCCCCCceEEecCCCceEcCcCceeecc
Q 025357            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (254)
Q Consensus         1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e   35 (254)
                      |.+..||.|.+  .-+++ ..+.++|.+|+.--.+
T Consensus         1 ~~lp~cp~c~s--EytYe-d~~~~~cpec~~ew~~   32 (112)
T COG2824           1 MSLPPCPKCNS--EYTYE-DGGQLICPECAHEWNE   32 (112)
T ss_pred             CCCCCCCccCC--ceEEe-cCceEeCchhcccccc
Confidence            56778999998  34454 3569999999976543

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

Probab=92.25  E-value=0.092  Score=39.09  Aligned_cols=29  Identities=31%  Similarity=0.834  Sum_probs=22.6

Q ss_pred             CCCCCCCCCceE---Ee--cCCCceEcCcCceeec
Q 025357            5 YCADCKRLTEVV---FD--HSAGDTICSECGLVLE   34 (254)
Q Consensus         5 ~Cp~Cg~~~~lv---~D--~~~G~~vC~~CG~Vl~   34 (254)
                      .||.||+ ..++   .+  ...|.++|..||+-.+
T Consensus        24 tCp~Cgh-e~vs~ctvkk~~~~g~~~Cg~CGls~e   57 (104)
T COG4888          24 TCPRCGH-EKVSSCTVKKTVNIGTAVCGNCGLSFE   57 (104)
T ss_pred             ecCccCC-eeeeEEEEEecCceeEEEcccCcceEE
Confidence            5999998 4555   44  4678999999999764

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

Probab=92.22  E-value=0.54  Score=42.52  Aligned_cols=112  Identities=19%  Similarity=0.217  Sum_probs=87.5

Q ss_pred             HHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCC-CCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHh-cCCCHHHHH
Q 025357          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQK-PLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVA-NGTTKKEIG  185 (254)
Q Consensus       109 a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~-~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~-~~v~~~~i~  185 (254)
                      .++++-++|+...|-..+.-.|..+|.+...-. -...-....+--+|||+|++.+.+ |-.+.|+|.++ ..++..+|.
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            478999999999999999999999999875532 112223456677899999998875 88889998763 356899999


Q ss_pred             HHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcc
Q 025357          186 RAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFF  226 (254)
Q Consensus       186 ~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~  226 (254)
                      +.-..|.+.|+-+      +.|++....+.-|..-++++..
T Consensus       228 tmE~iilkal~W~------l~PiTii~WL~vylQv~~~n~~  262 (408)
T KOG0655|consen  228 TMELIILKALKWE------LSPITIISWLNVYLQVDALNDA  262 (408)
T ss_pred             HHHHHHHHHhccc------ccceehHHHHHHHHHHHhcCCC
Confidence            9999999999887      6777777777777766665543

>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=91.90  E-value=0.072  Score=38.47  Aligned_cols=32  Identities=25%  Similarity=0.500  Sum_probs=18.1

Q ss_pred             CCCCCCCCCce--EEe--cCCCceEcCcCceeeccc
Q 025357            5 YCADCKRLTEV--VFD--HSAGDTICSECGLVLEAY   36 (254)
Q Consensus         5 ~Cp~Cg~~~~l--v~D--~~~G~~vC~~CG~Vl~e~   36 (254)
                      .||.|+...+|  ..|  ...|.+.|..||...+-.
T Consensus        24 ~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~   59 (81)
T PF05129_consen   24 DCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK   59 (81)
T ss_dssp             --TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred             cCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence            59999954444  444  357899999999987543

; PDB: 1WII_A.

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

Probab=91.83  E-value=0.15  Score=39.14  Aligned_cols=25  Identities=32%  Similarity=0.634  Sum_probs=19.8

Q ss_pred             CCCCCCCCceEEecCCCceEcCcCceeeccc
Q 025357            6 CADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (254)
Q Consensus         6 Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~   36 (254)
                      ||.||+ .-+|+-     +-|.+||+.++.+
T Consensus         1 CPvCg~-~l~vt~-----l~C~~C~t~i~G~   25 (113)
T PF09862_consen    1 CPVCGG-ELVVTR-----LKCPSCGTEIEGE   25 (113)
T ss_pred             CCCCCC-ceEEEE-----EEcCCCCCEEEee
Confidence            999998 445544     9999999999633

>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300

Probab=91.75  E-value=0.1  Score=40.57  Aligned_cols=31  Identities=10%  Similarity=0.203  Sum_probs=25.8

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeeccc
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~   36 (254)
                      .+.||.||..   .+|-..--+||..||.++...
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            3679999983   688888899999999998644

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.

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=91.69  E-value=0.093  Score=39.33  Aligned_cols=41  Identities=22%  Similarity=0.467  Sum_probs=28.5

Q ss_pred             CCCCCCCCCCce--EEecCCCceEcCcCceeeccc------ccccCcccc
Q 025357            4 SYCADCKRLTEV--VFDHSAGDTICSECGLVLEAY------SVDETSEWR   45 (254)
Q Consensus         4 ~~Cp~Cg~~~~l--v~D~~~G~~vC~~CG~Vl~e~------~id~~~ewr   45 (254)
                      ..||+||+ ..+  -.|...+.++|..||+.-+-.      .||-..+|.
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            35999996 333  356678899999999986432      245556674

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

Probab=91.68  E-value=0.15  Score=37.44  Aligned_cols=32  Identities=25%  Similarity=0.446  Sum_probs=25.7

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      -.||.||. .. +.-...|-+-|..||.++....
T Consensus        36 y~Cp~Cgk-~~-vkR~a~GIW~C~~C~~~~AGGA   67 (90)
T PF01780_consen   36 YTCPFCGK-TS-VKRVATGIWKCKKCGKKFAGGA   67 (90)
T ss_dssp             BEESSSSS-SE-EEEEETTEEEETTTTEEEE-BS
T ss_pred             CcCCCCCC-ce-eEEeeeEEeecCCCCCEEeCCC
Confidence            46999998 45 6677999999999999986443

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 ....

>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=91.53  E-value=4.6  Score=32.27  Aligned_cols=90  Identities=14%  Similarity=0.129  Sum_probs=65.7

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhh---CCC--CCCCCHHHHHHHHHHHHHHhc-CCCCCHHHHHHHhcCCCH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVED---QKP--LRGRNQEAIVAACLYIACRQE-NKPRTVKEFCSVANGTTK  181 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~---~~~--~~Gr~~~~iaAAclY~AcR~~-~~p~tl~eIa~~~~~v~~  181 (254)
                      ...+++.++....+++..+.-.|..+..++..   ...  +...+..-+..+|+-+|.+.. ....+.+..+.+ .|++.
T Consensus        53 ~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v-~gis~  131 (149)
T PF08613_consen   53 SIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKV-GGISL  131 (149)
T ss_dssp             -HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHH-HTS-H
T ss_pred             cHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhh-cCCCH
Confidence            35778999999999999999999999998877   222  334567778888888888854 678889999996 89999


Q ss_pred             HHHHHHHHHHHHHhchh
Q 025357          182 KEIGRAKEFIVKHLEAE  198 (254)
Q Consensus       182 ~~i~~~~k~l~~~l~~~  198 (254)
                      ++|.+.-+.+...++.+
T Consensus       132 ~eln~lE~~fL~~l~~~  148 (149)
T PF08613_consen  132 KELNELEREFLKLLDYN  148 (149)
T ss_dssp             HHHHHHHHHHHHHTTT-
T ss_pred             HHHHHHHHHHHHHCCCc
Confidence            99999988888877653

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.

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=91.29  E-value=0.92  Score=31.30  Aligned_cols=71  Identities=17%  Similarity=0.218  Sum_probs=43.0

Q ss_pred             HHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCC-CHHHHHHHHHHH
Q 025357          113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGRAKEFI  191 (254)
Q Consensus       113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v-~~~~i~~~~k~l  191 (254)
                      |..++..++++.....+   +++.........-....-+.-|.-|+..   + +.++.|||.. .|. +...+.+.|++.
T Consensus         4 ~~~la~~~~~s~~~l~~---~f~~~~~~s~~~~~~~~r~~~a~~~l~~---~-~~~~~~ia~~-~g~~s~~~f~r~Fk~~   75 (84)
T smart00342        4 LEDLAEALGMSPRHLQR---LFKKETGTTPKQYLRDRRLERARRLLRD---T-DLSVTEIALR-VGFSSQSYFSRAFKKL   75 (84)
T ss_pred             HHHHHHHhCCCHHHHHH---HHHHHhCcCHHHHHHHHHHHHHHHHHHc---C-CCCHHHHHHH-hCCCChHHHHHHHHHH
Confidence            67788888998755444   3443322211110112223344444432   2 8999999995 999 999999988764

>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA

Probab=91.15  E-value=0.6  Score=35.34  Aligned_cols=28  Identities=21%  Similarity=0.511  Sum_probs=20.7

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      -.||.|++ .-.-.|  ...+||.+||.--.
T Consensus         3 p~CP~C~s-eytY~d--g~~~iCpeC~~EW~   30 (109)
T TIGR00686         3 PPCPKCNS-EYTYHD--GTQLICPSCLYEWN   30 (109)
T ss_pred             CcCCcCCC-cceEec--CCeeECcccccccc
Confidence            47999998 344444  45799999998654

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).

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=91.10  E-value=1.1  Score=32.63  Aligned_cols=46  Identities=17%  Similarity=0.175  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHhcC-CCHHHHHHHHHHHHHHhchh
Q 025357          150 AIVAACLYIACRQENKPRTVKEFCSVANG-TTKKEIGRAKEFIVKHLEAE  198 (254)
Q Consensus       150 ~iaAAclY~AcR~~~~p~tl~eIa~~~~~-v~~~~i~~~~k~l~~~l~~~  198 (254)
                      ..=..++|++-+..|  .|+.+|+.. +| .+..++..+++++.+.+..+
T Consensus        30 ~aR~ia~yl~~~~~~--~s~~~Ig~~-fg~r~hStV~~a~~ri~~~~~~d   76 (90)
T cd06571          30 LARQIAMYLARELTG--LSLPEIGRA-FGGRDHSTVLHAVRKIEELLEED   76 (90)
T ss_pred             hHHHHHHHHHHHHhC--CCHHHHHHH-hCCCCHhHHHHHHHHHHHHHHhC
Confidence            333466788766655  789999995 77 99999999999999988643

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.

>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=91.00  E-value=0.066  Score=49.25  Aligned_cols=78  Identities=15%  Similarity=0.204  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHHHHh-hCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhc
Q 025357          121 GLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM  199 (254)
Q Consensus       121 ~Lp~~v~e~A~~i~k~~~-~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~  199 (254)
                      ++|+.++..|..+|+... ....+++..-.+-+.+|+|+||...+.+..+...... .++.++...+.|+.|.+.|+...
T Consensus        11 ~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~-~pl~pk~y~~l~~~~~~~L~~~s   89 (353)
T PF05460_consen   11 GLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKR-SPLPPKVYKKLLNTFENLLGNSS   89 (353)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCC-CCCCHHHHHHHHHHHHHHHhCCC
Confidence            456789999999999987 4566777777788999999999999999988887774 89999999999999999998774

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.

>TIGR00244 transcriptional regulator NrdR

Probab=90.98  E-value=0.23  Score=39.71  Aligned_cols=30  Identities=30%  Similarity=0.633  Sum_probs=22.5

Q ss_pred             CCCCCCCCCCceEEec---CCCceE-----cCcCceee
Q 025357            4 SYCADCKRLTEVVFDH---SAGDTI-----CSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~---~~G~~v-----C~~CG~Vl   33 (254)
                      +.||.||...+-|.|.   +.|..|     |..||.=.
T Consensus         1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF   38 (147)
T TIGR00244         1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF   38 (147)
T ss_pred             CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence            5799999865667784   567666     89998653

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.

>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=90.79  E-value=0.16  Score=35.15  Aligned_cols=29  Identities=21%  Similarity=0.544  Sum_probs=21.9

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      +.||.||.. . .........+|..||...+
T Consensus        29 q~C~~CG~~-~-~~~~~~r~~~C~~Cg~~~~   57 (69)
T PF07282_consen   29 QTCPRCGHR-N-KKRRSGRVFTCPNCGFEMD   57 (69)
T ss_pred             cCccCcccc-c-ccccccceEEcCCCCCEEC
Confidence            679999973 2 2246778899999999875

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

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=90.29  E-value=0.17  Score=37.99  Aligned_cols=27  Identities=26%  Similarity=0.733  Sum_probs=21.3

Q ss_pred             CCCCCCCCCceEEecCCCceEcCcCceeecc
Q 025357            5 YCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (254)
Q Consensus         5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e   35 (254)
                      .||.||+  .+  .+..+.++|..||.+...
T Consensus         2 fC~~Cg~--~l--~~~~~~~~C~~C~~~~~~   28 (104)
T TIGR01384         2 FCPKCGS--LM--TPKNGVYVCPSCGYEKEK   28 (104)
T ss_pred             CCcccCc--cc--ccCCCeEECcCCCCcccc
Confidence            6999997  23  456789999999998653

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.

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

Probab=89.97  E-value=7.1  Score=33.38  Aligned_cols=88  Identities=20%  Similarity=0.247  Sum_probs=71.0

Q ss_pred             HHHHHHhccCCC--HHHHHHHHHHHHHHhhC--CCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357          112 SISAMSDRLGLV--TTIKDRANEIYKKVEDQ--KPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (254)
Q Consensus       112 ~I~~i~~~L~Lp--~~v~e~A~~i~k~~~~~--~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~  187 (254)
                      .|.+++.+|||.  +.+.+.|.+|.+...-.  +..-|-.-..-|.-|+=+|+-.-++|..-...... +|.++++-.+.
T Consensus         2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKL-SGl~k~~Y~~~   80 (262)
T KOG4557|consen    2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKL-SGLSKKAYSRS   80 (262)
T ss_pred             cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHh-ccccHHHHHHH
Confidence            478899999994  57999999998876432  33445556677888898888888998887777785 99999999999


Q ss_pred             HHHHHHHhchhcc
Q 025357          188 KEFIVKHLEAEMG  200 (254)
Q Consensus       188 ~k~l~~~l~~~~~  200 (254)
                      ++.+...||+...
T Consensus        81 ~~sfe~llgln~~   93 (262)
T KOG4557|consen   81 FNSFENLLGLNIK   93 (262)
T ss_pred             HHHHHHHhcchhh
Confidence            9999999998743

>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=89.89  E-value=0.36  Score=30.76  Aligned_cols=27  Identities=22%  Similarity=0.438  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCce
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGL   31 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~   31 (254)
                      ..||.||+ ..+..-...+..-|.+|+.
T Consensus        19 ~~CP~Cg~-~~~~~~~~~~~~~C~~C~~   45 (46)
T PF12760_consen   19 FVCPHCGS-TKHYRLKTRGRYRCKACRK   45 (46)
T ss_pred             CCCCCCCC-eeeEEeCCCCeEECCCCCC
Confidence            46999998 4555555579999999974

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

>PTZ00255 60S ribosomal protein L37a; Provisional

Probab=89.74  E-value=0.24  Score=36.35  Aligned_cols=32  Identities=19%  Similarity=0.427  Sum_probs=25.7

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      -.||.||. .. +.-...|-+.|..||.++....
T Consensus        37 y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGGA   68 (90)
T PTZ00255         37 YFCPFCGK-HA-VKRQAVGIWRCKGCKKTVAGGA   68 (90)
T ss_pred             ccCCCCCC-Cc-eeeeeeEEEEcCCCCCEEeCCc
Confidence            57999997 55 4566889999999999986444

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

Probab=89.58  E-value=0.49  Score=27.89  Aligned_cols=27  Identities=19%  Similarity=0.334  Sum_probs=21.8

Q ss_pred             CCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357          166 PRTVKEFCSVANGTTKKEIGRAKEFIVK  193 (254)
Q Consensus       166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~  193 (254)
                      |.|-.|||+. .|.+..++.|.++++.+
T Consensus         2 ~mtr~diA~~-lG~t~ETVSR~l~~l~~   28 (32)
T PF00325_consen    2 PMTRQDIADY-LGLTRETVSRILKKLER   28 (32)
T ss_dssp             E--HHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred             CcCHHHHHHH-hCCcHHHHHHHHHHHHH
Confidence            6788999995 99999999999999875

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 ....

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

Probab=89.37  E-value=0.29  Score=37.60  Aligned_cols=32  Identities=28%  Similarity=0.659  Sum_probs=24.1

Q ss_pred             CCCCCCCCCCCceEE--ecCCCceEcCcCceeeccc
Q 025357            3 DSYCADCKRLTEVVF--DHSAGDTICSECGLVLEAY   36 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~--D~~~G~~vC~~CG~Vl~e~   36 (254)
                      |..||.||+  -++.  |...+.++|..||...+-.
T Consensus         2 m~FCp~Cgs--ll~p~~~~~~~~l~C~kCgye~~~~   35 (113)
T COG1594           2 MRFCPKCGS--LLYPKKDDEGGKLVCRKCGYEEEAS   35 (113)
T ss_pred             ccccCCccC--eeEEeEcCCCcEEECCCCCcchhcc
Confidence            588999998  2333  3367799999999987544

>TIGR00280 L37a ribosomal protein L37a

Probab=88.78  E-value=0.3  Score=35.93  Aligned_cols=32  Identities=25%  Similarity=0.466  Sum_probs=25.9

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      -.||.||. .. +.-...|-+.|..||.++....
T Consensus        36 y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGGA   67 (91)
T TIGR00280        36 YVCPFCGK-KT-VKRGSTGIWTCRKCGAKFAGGA   67 (91)
T ss_pred             ccCCCCCC-Cc-eEEEeeEEEEcCCCCCEEeCCc
Confidence            57999997 45 5667899999999999986443

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

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

Probab=88.51  E-value=1.6  Score=37.13  Aligned_cols=80  Identities=14%  Similarity=0.289  Sum_probs=53.6

Q ss_pred             HHHHHhccCCCHHHHHHHHHHHHHHhhCCCC------CCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHH
Q 025357          113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPL------RGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGR  186 (254)
Q Consensus       113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~------~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~  186 (254)
                      |+++|=.||+-+ ++..|.++.+...+. +-      .--+....++|++|.|||..+..+.--.+.. ++|+++..+..
T Consensus        96 VrdlaVQfgc~e-vi~~a~~vl~syk~~-lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~-~sg~~~s~F~~  172 (262)
T KOG4557|consen   96 VRDLAVQFGCVE-VIKSAQNVLSSYKER-LPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIE-VSGTSESEFSC  172 (262)
T ss_pred             HHHHHHHHhHHH-HHHHHHHHHHHHHhc-CchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhccc-ccCCCHHHHHH
Confidence            455555555543 666677766665441 11      1235567899999999999988777666667 48999988877


Q ss_pred             HHHHHHHHh
Q 025357          187 AKEFIVKHL  195 (254)
Q Consensus       187 ~~k~l~~~l  195 (254)
                      .-+.+.+..
T Consensus       173 l~kqler~~  181 (262)
T KOG4557|consen  173 LSKQLERNY  181 (262)
T ss_pred             HHHHHHHHH
Confidence            776666544

>PRK12495 hypothetical protein; Provisional

Probab=88.33  E-value=0.29  Score=41.71  Aligned_cols=32  Identities=22%  Similarity=0.668  Sum_probs=25.0

Q ss_pred             CCCCCCCCCCCCCceEEecCCCceEcCcCceeeccc
Q 025357            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (254)
Q Consensus         1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~   36 (254)
                      |....|+.||.+   ++ ...|.++|..|+.++.+.
T Consensus        40 msa~hC~~CG~P---Ip-a~pG~~~Cp~CQ~~~~~~   71 (226)
T PRK12495         40 MTNAHCDECGDP---IF-RHDGQEFCPTCQQPVTED   71 (226)
T ss_pred             cchhhcccccCc---cc-CCCCeeECCCCCCccccc
Confidence            445789999983   33 458999999999998653

>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed

Probab=87.63  E-value=0.38  Score=35.32  Aligned_cols=32  Identities=25%  Similarity=0.487  Sum_probs=25.8

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      -.||.||. .. +.-...|-+-|..||.++....
T Consensus        37 y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGGA   68 (90)
T PRK03976         37 HVCPVCGR-PK-VKRVGTGIWECRKCGAKFAGGA   68 (90)
T ss_pred             ccCCCCCC-Cc-eEEEEEEEEEcCCCCCEEeCCc
Confidence            57999987 44 4567899999999999986444

>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=87.41  E-value=0.56  Score=26.73  Aligned_cols=22  Identities=23%  Similarity=0.533  Sum_probs=12.3

Q ss_pred             CCCCCCCCCceEEecCCCceEcCc
Q 025357            5 YCADCKRLTEVVFDHSAGDTICSE   28 (254)
Q Consensus         5 ~Cp~Cg~~~~lv~D~~~G~~vC~~   28 (254)
                      .||.||+  .++.++.+-.+.|.+
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  477777777778864

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.

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=87.31  E-value=0.39  Score=29.37  Aligned_cols=30  Identities=33%  Similarity=0.544  Sum_probs=19.3

Q ss_pred             CCCCCCCCCCceEEecC-CCceEcCcCceee
Q 025357            4 SYCADCKRLTEVVFDHS-AGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~-~G~~vC~~CG~Vl   33 (254)
                      -.|++||..-.+..... ...+.|..||.-+
T Consensus         6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~   36 (41)
T smart00834        6 YRCEDCGHTFEVLQKISDDPLATCPECGGDV   36 (41)
T ss_pred             EEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence            46999997323333322 5577899999844

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.

>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=87.29  E-value=0.37  Score=28.41  Aligned_cols=25  Identities=28%  Similarity=0.589  Sum_probs=17.4

Q ss_pred             CCCCCCCCCceEEecCCCceEcCcCcee
Q 025357            5 YCADCKRLTEVVFDHSAGDTICSECGLV   32 (254)
Q Consensus         5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V   32 (254)
                      .|.+||..   +.+.....+-|..||.=
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            58899973   23556777899999963

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 ....

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=87.28  E-value=0.68  Score=31.69  Aligned_cols=30  Identities=20%  Similarity=0.353  Sum_probs=20.1

Q ss_pred             CCCCCCCCCCCceEEecCCC--ceEcCcCceee
Q 025357            3 DSYCADCKRLTEVVFDHSAG--DTICSECGLVL   33 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G--~~vC~~CG~Vl   33 (254)
                      ...||.||.. .+..-...|  ..+|..||...
T Consensus         6 lKPCPFCG~~-~~~v~~~~g~~~v~C~~CgA~~   37 (64)
T PRK09710          6 VKPCPFCGCP-SVTVKAISGYYRAKCNGCESRT   37 (64)
T ss_pred             ccCCCCCCCc-eeEEEecCceEEEEcCCCCcCc
Confidence            3679999984 443333343  36899999853

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=86.92  E-value=0.51  Score=29.94  Aligned_cols=27  Identities=30%  Similarity=0.645  Sum_probs=19.9

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      -.|.+||..  +..+ ..+.+-|.+||.=+
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 57889999999744

present in RNA polymerase I, II and III

>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=86.78  E-value=0.3  Score=37.71  Aligned_cols=38  Identities=18%  Similarity=0.373  Sum_probs=24.8

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccccccCc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETS   42 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~   42 (254)
                      ..||+||. ..+.--.-.=.-.|..||+=+...--|++|
T Consensus        22 grCP~CGe-GrLF~gFLK~~p~C~aCG~dyg~~~a~DgP   59 (126)
T COG5349          22 GRCPRCGE-GRLFRGFLKVVPACEACGLDYGFADADDGP   59 (126)
T ss_pred             CCCCCCCC-chhhhhhcccCchhhhccccccCCcccCCC
Confidence            57999998 566433444456899999877544434333

>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=86.54  E-value=2.2  Score=27.66  Aligned_cols=33  Identities=21%  Similarity=0.296  Sum_probs=27.9

Q ss_pred             hcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357          162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL  195 (254)
Q Consensus       162 ~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l  195 (254)
                      .++.|+|..++|+. ++||..+|.+.++.|.+.+
T Consensus        11 ~~~~~it~~eLa~~-l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen   11 ESKEPITAKELAEE-LGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HTTTSBEHHHHHHH-CTS-HHHHHHHHHHHHHTT
T ss_pred             HcCCCcCHHHHHHH-hCCCHHHHHHHHHHHHHCC
Confidence            45667999999995 9999999999999997765

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 ....

>PRK05978 hypothetical protein; Provisional

Probab=86.33  E-value=0.5  Score=38.04  Aligned_cols=30  Identities=17%  Similarity=0.412  Sum_probs=22.1

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      .+||+||. ..+..-+-.=..-|..||.-++
T Consensus        34 grCP~CG~-G~LF~g~Lkv~~~C~~CG~~~~   63 (148)
T PRK05978         34 GRCPACGE-GKLFRAFLKPVDHCAACGEDFT   63 (148)
T ss_pred             CcCCCCCC-CcccccccccCCCccccCCccc
Confidence            58999998 5664434444567999999875

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=86.26  E-value=0.72  Score=28.55  Aligned_cols=27  Identities=26%  Similarity=0.566  Sum_probs=18.7

Q ss_pred             CCCCCCCCCceEEe---------cCCCceEcCcCcee
Q 025357            5 YCADCKRLTEVVFD---------HSAGDTICSECGLV   32 (254)
Q Consensus         5 ~Cp~Cg~~~~lv~D---------~~~G~~vC~~CG~V   32 (254)
                      .||.||. ...++-         +.+-..+|.+||..
T Consensus         2 ~Cp~C~~-~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~   37 (40)
T smart00440        2 PCPKCGN-REATFFQLQTRSADEPMTVFYVCTKCGHR   37 (40)
T ss_pred             cCCCCCC-CeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence            6999998 454432         23447899999964

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

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=86.11  E-value=0.29  Score=29.61  Aligned_cols=29  Identities=28%  Similarity=0.603  Sum_probs=20.2

Q ss_pred             CCCCCCCCCCceEEe----cCCCceEcCcCceee
Q 025357            4 SYCADCKRLTEVVFD----HSAGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D----~~~G~~vC~~CG~Vl   33 (254)
                      ..||+|+.. --+-|    .....+-|+.||.+.
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            689999973 22222    345678899999874

>COG4640 Predicted membrane protein [Function unknown]

Probab=85.81  E-value=0.4  Score=44.22  Aligned_cols=29  Identities=21%  Similarity=0.670  Sum_probs=21.8

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      |..||.||+.      ..+++.-|+.||.-+..+.
T Consensus         1 M~fC~kcG~q------k~Ed~~qC~qCG~~~t~~~   29 (465)
T COG4640           1 MKFCPKCGSQ------KAEDDVQCTQCGHKFTSRQ   29 (465)
T ss_pred             CCcccccccc------cccccccccccCCcCCchh
Confidence            5789999983      3466777999998876443

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=85.24  E-value=4.1  Score=33.18  Aligned_cols=29  Identities=17%  Similarity=0.116  Sum_probs=26.7

Q ss_pred             CCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357          165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (254)
Q Consensus       165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~  194 (254)
                      .|.|..|||+. .|++..++.|.+++|.+.
T Consensus       142 ~~~t~~~iA~~-lG~tretvsR~l~~l~~~  170 (193)
T TIGR03697       142 LRLSHQAIAEA-IGSTRVTITRLLGDLRKK  170 (193)
T ss_pred             CCCCHHHHHHH-hCCcHHHHHHHHHHHHHC
Confidence            68999999995 999999999999999876

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.

>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=85.23  E-value=1.4  Score=31.48  Aligned_cols=45  Identities=20%  Similarity=0.279  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357          149 EAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (254)
Q Consensus       149 ~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~  194 (254)
                      +.-.-+.+|+|-...+.|.+.+|||+. .++++..+++..+.|.+.
T Consensus         8 ~~Al~~l~~la~~~~~~~~s~~eiA~~-~~i~~~~l~kil~~L~~~   52 (83)
T PF02082_consen    8 DYALRILLYLARHPDGKPVSSKEIAER-LGISPSYLRKILQKLKKA   52 (83)
T ss_dssp             HHHHHHHHHHHCTTTSC-BEHHHHHHH-HTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCCCCCCCHHHHHHH-HCcCHHHHHHHHHHHhhC
Confidence            344556678877766778999999995 999999999999999874

(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.

>PRK12286 rpmF 50S ribosomal protein L32; Reviewed

Probab=85.08  E-value=0.62  Score=31.26  Aligned_cols=28  Identities=21%  Similarity=0.533  Sum_probs=19.9

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeeccccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSV   38 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~i   38 (254)
                      ..||+||+.       ..--.||..||+--+..++
T Consensus        28 ~~C~~CG~~-------~~~H~vC~~CG~Y~gr~v~   55 (57)
T PRK12286         28 VECPNCGEP-------KLPHRVCPSCGYYKGREVV   55 (57)
T ss_pred             eECCCCCCc-------cCCeEECCCCCcCCCEEee
Confidence            569999972       2346899999987654443

>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG

Probab=84.95  E-value=0.7  Score=30.41  Aligned_cols=28  Identities=36%  Similarity=0.663  Sum_probs=20.0

Q ss_pred             CCCCCCCCCceEEecCCCce----EcCcCcee
Q 025357            5 YCADCKRLTEVVFDHSAGDT----ICSECGLV   32 (254)
Q Consensus         5 ~Cp~Cg~~~~lv~D~~~G~~----vC~~CG~V   32 (254)
                      .||+||....+..|.+.|.-    =|.-|..=
T Consensus         2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~P   33 (52)
T PF14255_consen    2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRP   33 (52)
T ss_pred             CCCCCCCeeEEEEecCCCCeeEEeehhhcCCc
Confidence            69999987778889888852    25555543

>TIGR02443 conserved hypothetical metal-binding protein

Probab=84.50  E-value=0.99  Score=30.39  Aligned_cols=29  Identities=21%  Similarity=0.509  Sum_probs=20.2

Q ss_pred             CCCCCCCCCCceEEecCCCc--eEcCcCcee
Q 025357            4 SYCADCKRLTEVVFDHSAGD--TICSECGLV   32 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~--~vC~~CG~V   32 (254)
                      -.||.|+.-..|++=.+.|.  +-|..||+-
T Consensus        10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~   40 (59)
T TIGR02443        10 AVCPACSAQDTLAMWKENNIELVECVECGYQ   40 (59)
T ss_pred             ccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence            47999998545544333443  779999987

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.

>TIGR00569 ccl1 cyclin ccl1

Probab=84.12  E-value=22  Score=32.10  Aligned_cols=71  Identities=6%  Similarity=-0.001  Sum_probs=43.4

Q ss_pred             HHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCC--CHHHHHHHHHHHHHHhc
Q 025357          124 TTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT--TKKEIGRAKEFIVKHLE  196 (254)
Q Consensus       124 ~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v--~~~~i~~~~k~l~~~l~  196 (254)
                      +.+...|-.+...+.--...---.|..+|+||||+|+|..++...-.+- ++ ..+  +...+...+..+++...
T Consensus       181 ~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA~~~~~~~l~~~~~-e~-~~~~~~~~~~~~l~~~~~~~~~  253 (305)
T TIGR00569       181 EYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNMESYLT-EQ-LSVPGNREELPQLIDIMRELRI  253 (305)
T ss_pred             HHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHHHHHHhCCCCcccch-hh-hcccccHHHHHHHHHHHHHHHH
Confidence            4455666665555433222222679999999999999999875443322 32 344  66776666655555443

University).

>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=84.10  E-value=2.7  Score=29.03  Aligned_cols=44  Identities=18%  Similarity=0.200  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHhcC----------CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357          151 IVAACLYIACRQEN----------KPRTVKEFCSVANGTTKKEIGRAKEFIVKHL  195 (254)
Q Consensus       151 iaAAclY~AcR~~~----------~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l  195 (254)
                      +|...++++-+...          .|.|..+||+. +|++..++.+.+++|.+.=
T Consensus         3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~-~g~sr~tv~r~l~~l~~~g   56 (76)
T PF13545_consen    3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADM-LGVSRETVSRILKRLKDEG   56 (76)
T ss_dssp             HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHH-HTSCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHH-HCCCHHHHHHHHHHHHHCC
Confidence            45555666655442          57899999995 9999999999999998753

...

>PF12773 DZR: Double zinc ribbon

Probab=83.71  E-value=0.54  Score=30.19  Aligned_cols=27  Identities=22%  Similarity=0.662  Sum_probs=12.1

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      ..||.||..  +. .......+|..||..+
T Consensus        13 ~fC~~CG~~--l~-~~~~~~~~C~~Cg~~~   39 (50)
T PF12773_consen   13 KFCPHCGTP--LP-PPDQSKKICPNCGAEN   39 (50)
T ss_pred             cCChhhcCC--hh-hccCCCCCCcCCcCCC
Confidence            345555542  11 2223345555555544

>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]

Probab=83.66  E-value=0.37  Score=31.25  Aligned_cols=27  Identities=37%  Similarity=0.714  Sum_probs=21.1

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V   32 (254)
                      -.|-.||.  .+..|.....+.|..||.=
T Consensus         7 Y~C~~Cg~--~~~~~~~~~~irCp~Cg~r   33 (49)
T COG1996           7 YKCARCGR--EVELDQETRGIRCPYCGSR   33 (49)
T ss_pred             EEhhhcCC--eeehhhccCceeCCCCCcE
Confidence            56999997  3444778889999999964

>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=83.58  E-value=4  Score=27.44  Aligned_cols=38  Identities=13%  Similarity=0.245  Sum_probs=30.8

Q ss_pred             HHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357          155 CLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (254)
Q Consensus       155 clY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~  194 (254)
                      +||.... .+.+.+..+||+. ++|++.++..++++|.+.
T Consensus        12 ~Iy~l~~-~~~~v~~~~iA~~-L~vs~~tvt~ml~~L~~~   49 (60)
T PF01325_consen   12 AIYELSE-EGGPVRTKDIAER-LGVSPPTVTEMLKRLAEK   49 (60)
T ss_dssp             HHHHHHH-CTSSBBHHHHHHH-HTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHc-CCCCccHHHHHHH-HCCChHHHHHHHHHHHHC
Confidence            3565555 7889999999994 999999999999998753

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 ....

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=83.29  E-value=3.3  Score=32.45  Aligned_cols=46  Identities=20%  Similarity=0.174  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357          148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (254)
Q Consensus       148 ~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~  194 (254)
                      .+.-..+++|+|-+..+.|.+..||++. .+++...+.+....|.+.
T Consensus         7 ~~YAl~~l~~La~~~~~~~~s~~~ia~~-~~ip~~~l~kil~~L~~~   52 (135)
T TIGR02010         7 GRYAVTAMLDLALNAETGPVTLADISER-QGISLSYLEQLFAKLRKA   52 (135)
T ss_pred             HHHHHHHHHHHHhCCCCCcCcHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence            4455667888887766678999999995 999999999999999874

This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.

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

Probab=82.80  E-value=0.23  Score=30.13  Aligned_cols=29  Identities=28%  Similarity=0.775  Sum_probs=19.4

Q ss_pred             CCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            5 YCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      .||.||..=++.+++-.-+.+|..||.-|
T Consensus         3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L   31 (36)
T PF05191_consen    3 ICPKCGRIYHIEFNPPKVEGVCDNCGGEL   31 (36)
T ss_dssp             EETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred             CcCCCCCccccccCCCCCCCccCCCCCee
Confidence            58888874356677777778888888744

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 ....

>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=82.78  E-value=1.1  Score=27.53  Aligned_cols=28  Identities=25%  Similarity=0.555  Sum_probs=15.3

Q ss_pred             CCCCCCCCCceEEe--------cCCCceEcCcCcee
Q 025357            5 YCADCKRLTEVVFD--------HSAGDTICSECGLV   32 (254)
Q Consensus         5 ~Cp~Cg~~~~lv~D--------~~~G~~vC~~CG~V   32 (254)
                      .||.||+...+.+.        +.+-..+|.+||..
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            69999984333332        12334689999964

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 ....

>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=81.87  E-value=1.5  Score=33.02  Aligned_cols=26  Identities=27%  Similarity=0.650  Sum_probs=22.0

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e   35 (254)
                      ..||.||. ..||+.     +-|.+||+-+..
T Consensus         7 ~~cPvcg~-~~iVTe-----L~c~~~etTVrg   32 (122)
T COG3877           7 NRCPVCGR-KLIVTE-----LKCSNCETTVRG   32 (122)
T ss_pred             CCCCcccc-cceeEE-----EecCCCCceEec
Confidence            67999998 577775     999999999863

>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center

Probab=81.80  E-value=1.1  Score=26.46  Aligned_cols=23  Identities=26%  Similarity=0.788  Sum_probs=14.9

Q ss_pred             CCCCCCCCCceEEecCCCceEcCcCce
Q 025357            5 YCADCKRLTEVVFDHSAGDTICSECGL   31 (254)
Q Consensus         5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~   31 (254)
                      .|+.||-    +.|.......|..||.
T Consensus         3 ~C~~CGy----~y~~~~~~~~CP~Cg~   25 (33)
T cd00350           3 VCPVCGY----IYDGEEAPWVCPVCGA   25 (33)
T ss_pred             ECCCCCC----EECCCcCCCcCcCCCC
Confidence            4777774    3555556677777775

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.

>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=81.65  E-value=0.83  Score=30.46  Aligned_cols=27  Identities=19%  Similarity=0.560  Sum_probs=18.5

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      ..||.||. -      ...-.||.+||+.=...+
T Consensus        27 ~~c~~cg~-~------~~~H~vc~~cG~y~~r~v   53 (56)
T PF01783_consen   27 VKCPNCGE-P------KLPHRVCPSCGYYKGRQV   53 (56)
T ss_dssp             EESSSSSS-E------ESTTSBCTTTBBSSSSSS
T ss_pred             eeeccCCC-E------ecccEeeCCCCeECCEEE
Confidence            46999996 1      245689999997644333

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 ....

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

Probab=81.44  E-value=11  Score=32.61  Aligned_cols=99  Identities=18%  Similarity=0.159  Sum_probs=62.0

Q ss_pred             HHHhccCC-CHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357          115 AMSDRLGL-VTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK  193 (254)
Q Consensus       115 ~i~~~L~L-p~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~  193 (254)
                      ++-..+|+ +.+..+-+-.|...-+...+.-=--|..+|-||+|+||-..+.+.+-.=+++  ..++...+..+.++|.+
T Consensus       159 q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~~~~w~~e--l~vD~ekV~~~v~~I~~  236 (264)
T KOG0794|consen  159 QFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDIPKAWFAE--LSVDMEKVKDIVQEILK  236 (264)
T ss_pred             HHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCChHHHHHHH--HhccHHHHHHHHHHHHH
Confidence            33334444 3334455544544443333322346889999999999998887765444555  46899999999988888


Q ss_pred             HhchhcccccccCCCCHHHHHHHHHhhcCC
Q 025357          194 HLEAEMGQSVEMGTIHASDYLVIFLLNIFK  223 (254)
Q Consensus       194 ~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l  223 (254)
                      ....-.       ..+ +.-|....++|-+
T Consensus       237 lYe~wk-------~~~-E~~v~~ll~kl~~  258 (264)
T KOG0794|consen  237 LYELWK-------IFD-EKKVKKLLSKLPK  258 (264)
T ss_pred             HHHHHh-------hhh-HHHHHHHHHhccc
Confidence            776542       122 3337777777644

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=81.43  E-value=1.7  Score=30.61  Aligned_cols=31  Identities=13%  Similarity=0.275  Sum_probs=21.5

Q ss_pred             CCCCCCCCCCCceEEec-------CCCceEcC--cCceeec
Q 025357            3 DSYCADCKRLTEVVFDH-------SAGDTICS--ECGLVLE   34 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~-------~~G~~vC~--~CG~Vl~   34 (254)
                      |+.||.||+ ...|.+.       .+-.-.|+  +||....
T Consensus         1 mm~CP~Cg~-~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~   40 (72)
T PRK09678          1 MFHCPLCQH-AAHARTSRYITDTTKERYHQCQNVNCSATFI   40 (72)
T ss_pred             CccCCCCCC-ccEEEEChhcChhhheeeeecCCCCCCCEEE
Confidence            479999998 4566653       22345688  8998764

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=81.29  E-value=0.99  Score=29.90  Aligned_cols=27  Identities=26%  Similarity=0.695  Sum_probs=20.3

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      .+|+.||..    +-+..--+||..||.+.=
T Consensus         6 ~~C~~Cg~~----~~~~dDiVvCp~CgapyH   32 (54)
T PF14446_consen    6 CKCPVCGKK----FKDGDDIVVCPECGAPYH   32 (54)
T ss_pred             ccChhhCCc----ccCCCCEEECCCCCCccc
Confidence            679999972    223456799999999873

>TIGR01031 rpmF_bact ribosomal protein L32

Probab=81.05  E-value=1.2  Score=29.59  Aligned_cols=27  Identities=19%  Similarity=0.596  Sum_probs=18.5

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      ..||+||+.       ..---||..||+--+..+
T Consensus        27 ~~C~~cG~~-------~~~H~vc~~cG~Y~gr~v   53 (55)
T TIGR01031        27 VVCPNCGEF-------KLPHRVCPSCGYYKGRQV   53 (55)
T ss_pred             eECCCCCCc-------ccCeeECCccCeECCEEc
Confidence            469999972       234589999997654433

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.

>PHA02942 putative transposase; Provisional

Probab=80.98  E-value=0.92  Score=42.25  Aligned_cols=31  Identities=16%  Similarity=0.352  Sum_probs=22.3

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      +.||.||.. .  .+.......|..||.+.+..+
T Consensus       326 q~Cs~CG~~-~--~~l~~r~f~C~~CG~~~drD~  356 (383)
T PHA02942        326 VSCPKCGHK-M--VEIAHRYFHCPSCGYENDRDV  356 (383)
T ss_pred             ccCCCCCCc-c--CcCCCCEEECCCCCCEeCcHH
Confidence            679999972 2  244456799999999985433

>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=80.70  E-value=7.3  Score=25.86  Aligned_cols=30  Identities=20%  Similarity=0.286  Sum_probs=26.5

Q ss_pred             CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357          164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (254)
Q Consensus       164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~  194 (254)
                      ..+.+..||++. .|++..++.+.++.|.+.
T Consensus        23 ~~~~s~~ela~~-~g~s~~tv~r~l~~L~~~   52 (67)
T cd00092          23 QLPLTRQEIADY-LGLTRETVSRTLKELEEE   52 (67)
T ss_pred             cCCcCHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence            467999999994 999999999999998874

>PRK12336 translation initiation factor IF-2 subunit beta; Provisional

Probab=80.69  E-value=1.1  Score=37.95  Aligned_cols=30  Identities=23%  Similarity=0.455  Sum_probs=22.7

Q ss_pred             CCCCCCCCC-CceEEecCCCceEcCcCceee
Q 025357            4 SYCADCKRL-TEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~-~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      ..|+.|+++ +.++.+...=.+.|..||..-
T Consensus        99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~  129 (201)
T PRK12336         99 VICSECGLPDTRLVKEDRVLMLRCDACGAHR  129 (201)
T ss_pred             EECCCCCCCCcEEEEcCCeEEEEcccCCCCc
Confidence            359999996 567766555567899999873

>PF15616 TerY-C: TerY-C metal binding domain

Probab=80.16  E-value=1.1  Score=35.35  Aligned_cols=21  Identities=24%  Similarity=0.725  Sum_probs=12.7

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      --||+||..        .+..+| +||.|.
T Consensus        78 PgCP~CGn~--------~~fa~C-~CGkl~   98 (131)
T PF15616_consen   78 PGCPHCGNQ--------YAFAVC-GCGKLF   98 (131)
T ss_pred             CCCCCCcCh--------hcEEEe-cCCCEE
Confidence            359999973        244555 455553

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	254
1c9b_A	207	Crystal Structure Of A Human Tbp Core Domain-Human		9e-23
1tfb_A	208	Nmr Studies Of Human General Transcription Factor T		4e-22
2phg_A	206	Model For Vp16 Binding To Tfiib Length = 206		5e-22
1vol_A	204	Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEME		7e-20
3k7a_M	345	Crystal Structure Of An Rna Polymerase Ii-Tfiib Com		9e-18
1d3u_B	201	Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+T		1e-10
1ais_B	200	Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-		2e-10
1rly_A	60	Rdc-Derived Models Of The Zinc Ribbon Domain Of Hum		4e-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 =  103 bits (257), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 50/94 (53%), Positives = 67/94 (71%), Gaps = 1/94 (1%)
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 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196
           E  PRT KE C+V+   +KKEIGR  + I+K LE
Sbjct: 62  EGVPRTFKEICAVSR-ISKKEIGRCFKLILKALE 94

>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 =  101 bits (251), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 49/93 (52%), Positives = 66/93 (70%), Gaps = 1/93 (1%)
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 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196
             PRT KE C+V+   +KKEIGR  + I+K LE
Sbjct: 64  GVPRTFKEICAVSR-ISKKEIGRCFKLILKALE 95

>pdb|2PHG|A Chain A, Model For Vp16 Binding To Tfiib Length = 206

Iteration: 1
 Score =  101 bits (251), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 49/93 (52%), Positives = 66/93 (70%), Gaps = 1/93 (1%)
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 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196
             PRT KE C+V+   +KKEIGR  + I+K LE
Sbjct: 62  GVPRTFKEICAVSR-ISKKEIGRCFKLILKALE 93

>pdb|1VOL|A Chain A, Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEMENT Ternary Complex Length = 204

Iteration: 1
 Score = 94.0 bits (232), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 45/91 (49%), Positives = 63/91 (69%), Gaps = 1/91 (1%)
Query: 106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK 165
           ++ AFK I+ M+DR+ L     DR N ++++  +QK L+GR  +AI +ACLYIACRQE  
Sbjct: 2   MMNAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGV 61
Query: 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196
           PRT KE C+V+   +KKEIGR  + I+K LE
Sbjct: 62  PRTFKEICAVSR-ISKKEIGRCFKLILKALE 91

>pdb|3K7A|M Chain M, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex Length = 345

Iteration: 1
 Score = 87.0 bits (214), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 62/185 (33%), Positives = 85/185 (45%), Gaps = 7/185 (3%)
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 KEIGR 186
           KE G+
Sbjct: 201 KEFGK 205

>pdb|1D3U|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+TATA- Box Complex From Pyrococcus Woesei Length = 201

Iteration: 1
 Score = 63.2 bits (152), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 34/97 (35%), Positives = 57/97 (58%), Gaps = 1/97 (1%)
Query: 99  SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI 158
           S   +RNL  A   +  ++ +L L   +++ A  +Y++   +  +RGR+ E+++AAC+Y 
Sbjct: 3   SDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYA 62
Query: 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195
           ACR    PRT+ E   +A    KKEIGR+  FI ++L
Sbjct: 63  ACRLLKVPRTLDEIADIAR-VDKKEIGRSYRFIARNL 98

>pdb|1AIS|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-Box Complex From Pyrococcus Woesei Length = 200

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/97 (35%), Positives = 57/97 (58%), Gaps = 1/97 (1%)
Query: 99  SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI 158
           S   +RNL  A   +  ++ +L L   +++ A  +Y++   +  +RGR+ E+++AAC+Y 
Sbjct: 2   SDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYA 61
Query: 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195
           ACR    PRT+ E   +A    KKEIGR+  FI ++L
Sbjct: 62  ACRLLKVPRTLDEIADIAR-VDKKEIGRSYRFIARNL 97

>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 = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 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 = 43.5 bits (101), 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 = 42.7 bits (99), 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	254
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	4e-44
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	3e-10
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	1e-30
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	5e-12
1c9b_A	207	General transcription factor IIB; protein-DNA comp	5e-30
1c9b_A	207	General transcription factor IIB; protein-DNA comp	6e-10
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	3e-23
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	6e-13
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	8e-12

>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 =  151 bits (381), Expect = 4e-44
 Identities = 68/205 (33%), Positives = 96/205 (46%), Gaps = 3/205 (1%)

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 IGRAKEFIVKHLEAEMGQSVEMGTI 208
            G+    +   L  +          
Sbjct: 203 FGKTLNIMKNILRGKSEDGFLKIDT 227

>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 = 58.8 bits (141), Expect = 3e-10
 Identities = 19/111 (17%), Positives = 37/111 (33%), Gaps = 1/111 (0%)

Query: 86  ELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRG 145
            +L G       +    + +  Q    I      LGL   +   A    KK ++ K + G
Sbjct: 212 NILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSAEYTAKKCKEIKEIAG 271

Query: 146 RNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196
           ++   I    +Y+       P T  +        T+  I    + + +H +
Sbjct: 272 KSPITIAVVSIYLNILLFQIPITAAKVGQTL-QVTEGTIKSGYKILYEHRD 321

>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 =  112 bits (280), Expect = 1e-30
 Identities = 33/116 (28%), Positives = 62/116 (53%), Gaps = 5/116 (4%)

Query: 99  SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI 158
           S   +RNL  A   +  ++ +L L   +++ A  +Y++   +  +RGR+ E+++AAC+Y 
Sbjct: 2   SDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYA 61

Query: 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYL 214
           ACR    PRT+ E   +A    KKEIGR+     + +   +  + +   +  +DY+
Sbjct: 62  ACRLLKVPRTLDEIADIAR-VDKKEIGRS----YRFIARNLNLTPKKLFVKPTDYV 112

>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 = 62.3 bits (151), Expect = 5e-12
 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

>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 =  110 bits (276), Expect = 5e-30
 Identities = 46/85 (54%), Positives = 61/85 (71%), Gaps = 1/85 (1%)

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 ENKPRTVKEFCSVANGTTKKEIGRA 187
           E  PRT KE C+V+   +KKEIGR 
Sbjct: 62  EGVPRTFKEICAVSR-ISKKEIGRC 85

>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 = 56.6 bits (136), Expect = 6e-10
 Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 1/89 (1%)

Query: 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPR 167
                +S     L L   ++  A  I +K  +   + GR+  ++ AA +Y+A +   + R
Sbjct: 101 TTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKR 160

Query: 168 TVKEFCSVANGTTKKEIGRAKEFIVKHLE 196
           T KE   +A G     I ++   I     
Sbjct: 161 TQKEIGDIA-GVADVTIRQSYRLIYPRAP 188

>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 = 92.4 bits (229), Expect = 3e-23
 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 = 6e-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 = 57.9 bits (140), Expect = 8e-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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	254
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	100.0
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	100.0
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	99.93
1c9b_A	207	General transcription factor IIB; protein-DNA comp	99.9
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	99.78
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	99.73
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	99.63
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	99.61
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	99.6
1c9b_A	207	General transcription factor IIB; protein-DNA comp	99.48
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	99.42
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	99.38
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	99.37
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	99.32
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	99.28
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	99.28
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	99.24
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	99.2
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	99.18
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	99.15
1g3n_C	257	V-cyclin; cyclin-dependent kinase, INK4 inhibitor,	99.09
1w98_B	283	Cyclin E, G1/S-specific cyclin E1; cell cycle, tra	99.08
2f2c_A	254	Cyclin homolog, V-cyclin; small molecule inhibitor	98.98
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	98.79
3h4c_A	260	Transcription factor TFIIB-like; cyclin, transcrip	98.4
1f5q_B	252	Gamma herpesvirus cyclin; herpesviral cyclin, cycl	98.38
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	97.9
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	97.9
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	97.88
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	97.7
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	97.68
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	97.57
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	97.47
2f2c_A	254	Cyclin homolog, V-cyclin; small molecule inhibitor	97.47
1g3n_C	257	V-cyclin; cyclin-dependent kinase, INK4 inhibitor,	97.37
3m03_A	95	ORC6, origin recognition complex subunit 6; helix	97.11
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	97.04
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	96.97
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	96.97
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	96.86
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	96.83
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	96.78
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	96.74
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	96.71
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	96.69
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	96.68
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	96.57
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	96.38
1w98_B	283	Cyclin E, G1/S-specific cyclin E1; cell cycle, tra	96.19
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	96.11
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	95.87
2qdj_A	304	Retinoblastoma-associated protein; cyclin fold, cy	95.78
2r7g_A	347	PP110, retinoblastoma-associated protein, P105-RB,	95.53
4ell_A	411	Retinoblastoma-associated protein; cyclin fold, tu	95.3
4elj_A	656	Retinoblastoma-associated protein; cyclin fold, tu	94.85
2kpi_A	56	Uncharacterized protein SCO3027; zinc finger, PSI-	94.79
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	94.75
2akl_A	138	PHNA-like protein PA0128; two domains, Zn binding	94.67
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	94.49
2k5r_A	97	Uncharacterized protein XF2673; solution structure	94.04
4elj_A	656	Retinoblastoma-associated protein; cyclin fold, tu	93.5
1k81_A	36	EIF-2-beta, probable translation initiation factor	93.01
3j21_i	83	50S ribosomal protein L37AE; archaea, archaeal, KI	91.62
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	91.2
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	91.12
1nui_A	255	DNA primase/helicase; zinc-biding domain, toprim f	91.05
1ffk_W	73	Ribosomal protein L37AE; ribosome assembly, RNA-RN	91.03
3iz5_m	92	60S ribosomal protein L43 (L37AE); eukaryotic ribo	90.8
4a17_Y	103	RPL37A, 60S ribosomal protein L32; eukaryotic ribo	90.77
3cc2_Z	116	50S ribosomal protein L37AE, 50S ribosomal protein	90.67
3jyw_9	72	60S ribosomal protein L43; eukaryotic ribosome, RA	90.39
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	90.16
3izc_m	92	60S ribosomal protein RPL43 (L37AE); eukaryotic ri	90.14
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	89.81
6rxn_A	46	Rubredoxin; electron transfer(iron-sulfur protein)	89.78
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	89.64
1f5q_B	252	Gamma herpesvirus cyclin; herpesviral cyclin, cycl	88.03
4rxn_A	54	Rubredoxin; electron transfer(iron-sulfur protein)	87.85
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	87.82
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	86.99
1e8j_A	52	Rubredoxin; iron-sulfur-protein, zinc-substitution	86.01
1j1v_A	94	Chromosomal replication initiator protein DNAA, 5'	85.51
2pmi_B	293	PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de	85.07
1dxg_A	36	Desulforedoxin; non-heme iron protein, rubredoxin	84.21
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	83.63
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	83.59
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	83.48
1tfi_A	50	Transcriptional elongation factor SII; transcripti	83.37
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	82.8
3u50_C	172	Telomerase-associated protein 82; TEB1, processivi	82.12
3pvv_A	101	Chromosomal replication initiator protein DNAA; he	81.6
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	80.96
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	80.94
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	80.73
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	80.22

>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M

Probab=100.00  E-value=2.1e-56  Score=404.86  Aligned_cols=225  Identities=33%  Similarity=0.519  Sum_probs=173.3

Q ss_pred             CCCCCCCCC-CCceEEecCCCceEcCcCceeecccccccCcccccccCCC-CCCCCcccCCCCCccccCCCcceEEecCC
Q 025357            3 DSYCADCKR-LTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANES-SDHDPVRVGGPLNPLLSGGGLSTVIAKPT   80 (254)
Q Consensus         3 ~~~Cp~Cg~-~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~-~~~d~~r~G~~~~~~~~~~~~~t~i~~~~   80 (254)
                      ...||+||+ ++++++|+++|++||++||+|++|++||.|||||+|++++ ++.|++|+|+|.++++||.|++|.|++++
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            468999996 3689999999999999999999999999999999999655 46889999999999999999999999764


Q ss_pred             CCCCccccccccccccccC--CCchhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHH
Q 025357           81 AGGSTELLSGSLGKLQARS--SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI  158 (254)
Q Consensus        81 ~~~~~~~l~~~l~~~~~~~--~~~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~  158 (254)
                       ++++ ....+|++||+++  +++||+|.+|+++|.++|+.|+||+.+.++|..||+++.+.++++||+.++++|||||+
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 -TTDM-RFTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILI  178 (345)
T ss_dssp             -SCCH-HHHHHHHHHHHHTCCCCSSSSTTHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTCTTTTTCCHHHHHHHHHHH
T ss_pred             -Ccch-hhHHHHHHHHHhhhcChHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHH
Confidence             2221 1234588899875  77899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhccccc------ccCCCCHHHHHHHHHhhcCCCcchhhe
Q 025357          159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSV------EMGTIHASDYLVIFLLNIFKNFFFLFV  230 (254)
Q Consensus       159 AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~------~~~~~~p~~~i~r~~~~L~l~~~v~~v  230 (254)
                      |||+++.|+|++||+++ +++++++|+++|+.|.+.|++...+.+      .+++++|++||+|||++|+|+.+|...
T Consensus       179 ACR~~~~prtl~eI~~~-~~v~~keigr~~k~l~~~L~l~~~~~~~~~~~~~~~~~~p~~~i~Rf~s~L~l~~~v~~~  255 (345)
T 4bbr_M          179 GCRRAEVARTFKEIQSL-IHVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTS  255 (345)
T ss_dssp             HHHHTCCBCCHHHHHHH-HTCCTTHHHHHHHHHHHCC-----------------------------------------
T ss_pred             HHHhcCCCccHHHHHHH-hCCCHHHHHHHHHHHHHHhCccccccccccccccCCCCCHHHHHHHHHHHcCCcHHHHHH
Confidence            99999999999999995 899999999999999999998632221      267889999999999999999998873

>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=5e-52  Score=376.79  Aligned_cols=223  Identities=33%  Similarity=0.522  Sum_probs=163.3

Q ss_pred             CCCCCCCCCCC-ceEEecCCCceEcCcCceeecccccccCcccccccCCC-CCCCCcccCCCCCccccCCCcceEEecCC
Q 025357            3 DSYCADCKRLT-EVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANES-SDHDPVRVGGPLNPLLSGGGLSTVIAKPT   80 (254)
Q Consensus         3 ~~~Cp~Cg~~~-~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~-~~~d~~r~G~~~~~~~~~~~~~t~i~~~~   80 (254)
                      ...||+||+.+ ++++|+.+|++||++||+|++|++||.+||||+|++++ ++.+++|+|+|.++++||.|++|.|++++
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 79999999999999999999999999999999999653 46789999999999999999999998753


Q ss_pred             -CCCCccccccccccccccC--CCchhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHH
Q 025357           81 -AGGSTELLSGSLGKLQARS--SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLY  157 (254)
Q Consensus        81 -~~~~~~~l~~~l~~~~~~~--~~~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY  157 (254)
                       .++++   .++|++||++.  +++||+|.+|+++|+++|+.|+||+.++++|..||+++.+.++++||+.+.++|||||
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             23333   23588888753  7889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcc------cccccCCCCHHHHHHHHHhhcCCCcchhh
Q 025357          158 IACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMG------QSVEMGTIHASDYLVIFLLNIFKNFFFLF  229 (254)
Q Consensus       158 ~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~------~~~~~~~~~p~~~i~r~~~~L~l~~~v~~  229 (254)
                      +|||+++.|++++||+.+ +++++++|+++|+.|.+.|+....      ..+.+++.+|.+||+|||++|+|+.++..
T Consensus       178 iAcR~e~~prtl~ei~~~-~~v~~keIgr~~~~l~~~L~~~~~~~~~~~~~~~~~~~~p~~~i~Rf~~~L~l~~~v~~  254 (345)
T 3k7a_M          178 IGCRRAEVARTFKEIQSL-IHVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTT  254 (345)
T ss_dssp             TTSBTTBSSCCHHHHHHS-SSCCSHHHHHHHHHHHHHHTCC-------------------------------------
T ss_pred             HHHHHcCCCccHHHHHHH-HCCCHHHHHHHHHHHHHHHhhhhccccccccccccCCCCHHHHHHHHHHHcCCCHHHHH
Confidence            999999999999999995 899999999999999999982100      00227889999999999999999988866

>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=99.93  E-value=4.7e-26  Score=191.04  Aligned_cols=123  Identities=28%  Similarity=0.493  Sum_probs=114.3

Q ss_pred             CCchhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCC
Q 025357          100 SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT  179 (254)
Q Consensus       100 ~~~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v  179 (254)
                      +++||+|.+|+++|.++|++|+||+.+.++|..+|+++.+.++++|++++.++|||||+|||+++.|++++||+++ +++
T Consensus         3 ~~~er~l~~a~~~I~~~~~~L~L~~~v~~~A~~l~~~~~~~~~~~gr~~~~vaaAclylAcr~~~~p~~l~di~~~-~~v   81 (200)
T 1ais_B            3 DAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADI-ARV   81 (200)
T ss_dssp             -----CHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTTTTTTCCHHHHHHHHHHHHHHHHTCCCCHHHHHHH-TTS
T ss_pred             ChHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHH-HCC
Confidence            4578999999999999999999999999999999999999999999999999999999999999999999999995 899


Q ss_pred             CHHHHHHHHHHHHHHhchhcccccccCC--CCHHHHHHHHHhhcCCCcchhh
Q 025357          180 TKKEIGRAKEFIVKHLEAEMGQSVEMGT--IHASDYLVIFLLNIFKNFFFLF  229 (254)
Q Consensus       180 ~~~~i~~~~k~l~~~l~~~~~~~~~~~~--~~p~~~i~r~~~~L~l~~~v~~  229 (254)
                      ++++|+++|+.|.+.|++.      +++  .+|.+||+|||++|++++++..
T Consensus        82 ~~~~i~~~~~~l~~~L~~~------~~~~~~~p~~~i~r~~~~L~l~~~v~~  127 (200)
T 1ais_B           82 DKKEIGRSYRFIARNLNLT------PKKLFVKPTDYVNKFADELGLSEKVRR  127 (200)
T ss_dssp             CHHHHHHHHHHHHHHTTCC------TTTTCCCGGGGHHHHHHHHTCCHHHHH
T ss_pred             CHHHHHHHHHHHHHHhccc------CCcCCCCHHHHHHHHHHHcCCCHHHHH
Confidence            9999999999999999987      788  9999999999999999988765

>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=99.90  E-value=2.8e-23  Score=175.07  Aligned_cols=122  Identities=44%  Similarity=0.745  Sum_probs=116.8

Q ss_pred             chhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCH
Q 025357          102 PDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTK  181 (254)
Q Consensus       102 ~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~  181 (254)
                      +||++.+|+++|.++|.+|+||+.+.++|..+|+++.+.+.++|+++..++|||+|+|||.++.|++++||+.+ ++++.
T Consensus         1 ~er~l~~a~~~I~~~~~~L~L~~~v~~~A~~~~~r~~~~~~~~~~~~~~v~aaclylAcK~ee~p~~l~di~~~-~~~~~   79 (207)
T 1c9b_A            1 SDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAV-SRISK   79 (207)
T ss_dssp             CGGGHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTCSTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHT-SSSCH
T ss_pred             CchHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHH-HCCCH
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999995 89999


Q ss_pred             HHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhhe
Q 025357          182 KEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFV  230 (254)
Q Consensus       182 ~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v  230 (254)
                      ++|+++|+.|.+.|+++      +++.+|..||.||++.|+++.++...
T Consensus        80 ~~i~~~~~~ll~~L~~~------l~~~~p~~~l~r~~~~l~l~~~~~~~  122 (207)
T 1c9b_A           80 KEIGRCFKLILKALETS------VDLITTGDFMSRFCSNLCLPKQVQMA  122 (207)
T ss_dssp             HHHHHHHHHHHHHTTCC------CCCCCTHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCC------cCcCCHHHHHHHHHHHCCCCHHHHHH
Confidence            99999999999999987      78899999999999999999887664

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae}

Probab=99.78  E-value=6.4e-20  Score=146.86  Aligned_cols=65  Identities=32%  Similarity=0.623  Sum_probs=57.6

Q ss_pred             CCCCCCCCCC-CceEEecCCCceEcCcCceeecccccccCcccccccCCC-CCCCCcccCCCCCccc
Q 025357            3 DSYCADCKRL-TEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANES-SDHDPVRVGGPLNPLL   67 (254)
Q Consensus         3 ~~~Cp~Cg~~-~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~-~~~d~~r~G~~~~~~~   67 (254)
                      ...||+||+. +++++|+++|++||.+||+|++|++||.|||||+|++++ ++.+++|+|+|.++..
T Consensus        21 ~~~CPECGs~~t~IV~D~erGE~VCsdCGLVLEEriID~GPEWRAFsnDD~~~dDpSRVGAPs~~~~   87 (197)
T 3k1f_M           21 VLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNXXXXXXXXXXXXXXXXXXX   87 (197)
T ss_dssp             CCCCTTTCCSSCCEEEEGGGTEEEETTTCBBCCCCCBCHHHHHHHHHCCCTTTTCSCCCBCCBCCHH
T ss_pred             CeECcCCCCcCCeEEEeCCCCEEEEcCCCCCcCCceeECCCCCcCcCCccccccccccccccccccc
Confidence            4579999982 479999999999999999999999999999999999754 4678999999988654

>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=1.8e-18  Score=116.45  Aligned_cols=47  Identities=43%  Similarity=0.777  Sum_probs=43.7

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeecccccccCcccccccCC
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE   50 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~   50 (254)
                      .+.||+||+ ..+++|+.+|++||.+||+|++|++||.|||||+|+++
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 67999999999999999999999999999999999854

>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=99.63  E-value=1.8e-15  Score=126.45  Aligned_cols=90  Identities=27%  Similarity=0.391  Sum_probs=86.4

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~  187 (254)
                      +...+|.++++.|+||+.+.+.|..|++.+.+.++..||+|.++||||||+|||..|.|+|++||+.+ +++++.+|+++
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 KPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEV-ARVTEVTVRNR  185 (200)
T ss_dssp             CGGGGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHH-HTCCHHHHHHH
T ss_pred             CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHH-hCCCHHHHHHH
Confidence            45679999999999999999999999999999999999999999999999999999999999999995 89999999999


Q ss_pred             HHHHHHHhchh
Q 025357          188 KEFIVKHLEAE  198 (254)
Q Consensus       188 ~k~l~~~l~~~  198 (254)
                      |++|.+.|+++
T Consensus       186 ~~~l~~~l~~~  196 (200)
T 1ais_B          186 YKELVEKLKIK  196 (200)
T ss_dssp             HHHHHHHHTCC
T ss_pred             HHHHHHHcCCC
Confidence            99999999987

>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe}

Probab=99.61  E-value=8.9e-15  Score=125.28  Aligned_cols=118  Identities=24%  Similarity=0.301  Sum_probs=108.9

Q ss_pred             HHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCC-CCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhc-------
Q 025357          106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRG-RNQEAIVAACLYIACRQENKPRTVKEFCSVAN-------  177 (254)
Q Consensus       106 l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~G-r~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~-------  177 (254)
                      ...+.++|.+++..|+||..+..+|..+|+++...+.+++ +++..+++||+|+|||.++.|++++||+.++.       
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            5678899999999999999999999999999999888888 99999999999999999999999999988632       


Q ss_pred             CCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhh
Q 025357          178 GTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLF  229 (254)
Q Consensus       178 ~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~  229 (254)
                      ..+.++|.++.+.|.+.|+.+      +...+|..||.+|++++++++++..
T Consensus       108 ~~~~~~I~~~E~~iL~~L~f~------l~~~~P~~~l~~~~~~~~~~~~~~~  153 (235)
T 1zp2_A          108 KLSRSNISEIEFEIISVLDAF------LIVHHPYTSLEQAFHDGIINQKQLE  153 (235)
T ss_dssp             CCCHHHHHHHHHHHHHHTTTC------CCCCCTHHHHHHHHHTTSSCHHHHH
T ss_pred             hccHHHHHHHHHHHHHHCCCc------EEecChHHHHHHHHHHcCCCHHHHH
Confidence            578999999999999999988      7788999999999999999887654

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=99.60  E-value=6.3e-16  Score=101.08  Aligned_cols=44  Identities=34%  Similarity=0.940  Sum_probs=42.0

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccccccCccccccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFA   48 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~   48 (254)
                      ..||+||+ ..|++|+.+|++||..||+|++++.||.+||||+|+
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 689999999999999999999999999999999997

>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=99.48  E-value=1.7e-13  Score=114.95  Aligned_cols=90  Identities=21%  Similarity=0.281  Sum_probs=86.1

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~  187 (254)
                      +...+|.++++.|++|+.+.+.|..+++.+.+.++..|++|..+||||||+||+..|.+++++||+++ ++|++.+|+++
T Consensus       101 ~p~~~l~r~~~~l~l~~~~~~~A~~i~~~~~~~~l~~g~~P~~IAaAaiylA~~~~~~~~~~~~i~~~-~~v~~~tI~~~  179 (207)
T 1c9b_A          101 TTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDI-AGVADVTIRQS  179 (207)
T ss_dssp             CTHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHHHHHHHTSSSCCCHHHHHHH-HTCCHHHHHHH
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHH-hCCCHHHHHHH
Confidence            56789999999999999999999999999999999999999999999999999999999999999995 89999999999


Q ss_pred             HHHHHHHhchh
Q 025357          188 KEFIVKHLEAE  198 (254)
Q Consensus       188 ~k~l~~~l~~~  198 (254)
                      |+.|.+.++..
T Consensus       180 ~~~l~~~l~~~  190 (207)
T 1c9b_A          180 YRLIYPRAPDL  190 (207)
T ss_dssp             HHHHGGGHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99999999876

>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=99.42  E-value=3.6e-12  Score=110.29  Aligned_cols=117  Identities=18%  Similarity=0.185  Sum_probs=105.4

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhc---------
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVAN---------  177 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~---------  177 (254)
                      ..+.++|.+++..|+||..+..+|..+|++....+.++++++..+++||+|+||+.++.|++++||..++.         
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            46789999999999999999999999999999999999999999999999999999999999999987521         


Q ss_pred             -CCC-------HHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhh
Q 025357          178 -GTT-------KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLF  229 (254)
Q Consensus       178 -~v~-------~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~  229 (254)
                       .++       .++|.+..+.|.+.|+.+      +...+|..||.+|+..++.+.++..
T Consensus       112 ~~~~~~~y~~~~~~I~~~E~~iL~~L~f~------l~~~~P~~fl~~~~~~l~~~~~~~~  165 (257)
T 2ivx_A          112 LDTKCDAYLQQTRELVILETIMLQTLGFE------ITIEHPHTDVVKCTQLVRASKDLAQ  165 (257)
T ss_dssp             CCTTSHHHHHHHHHHHHHHHHHHHHTTTC------CCCCCHHHHHHHHHHHTTCCHHHHH
T ss_pred             CCcchHHHHHHHHHHHHHHHHHHHHcccc------eEeeCcHHHHHHHHHHhCCCcHHHH
Confidence             122       678999999999999988      7788999999999999999887755

>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=99.38  E-value=4.6e-12  Score=109.59  Aligned_cols=113  Identities=15%  Similarity=0.248  Sum_probs=102.0

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcC-C------
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG-T------  179 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~-v------  179 (254)
                      ..+.++|.+++..|+||..+...|..+|++....+.++++++..+++||+|+||+.++.|++++||..++.. +      
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            467899999999999999999999999999999999999999999999999999999999999999874211 1      


Q ss_pred             -----CHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCc
Q 025357          180 -----TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNF  225 (254)
Q Consensus       180 -----~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~  225 (254)
                           +.++|.+..+.|.+.|+.+      +...+|..||.+|+..|+.+.
T Consensus       122 ~~~~~~~~~i~~~E~~iL~~L~f~------l~~~~P~~fl~~~~~~l~~~~  166 (258)
T 2i53_A          122 QFGDDPKEEVMVLERILLQTIKFD------LQVEHPYQFLLKYAKQLKGDK  166 (258)
T ss_dssp             GGCSCHHHHHHHHHHHHHHHTTTC------CCCCCHHHHHHHHHHTBCSCH
T ss_pred             hhhhhHHHHHHHHHHHHHHHCCCc------eeccChHHHHHHHHHHhCCCc
Confidence                 3678999999999999987      778899999999999999886

>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens}

Probab=99.37  E-value=4.2e-12  Score=111.71  Aligned_cols=117  Identities=14%  Similarity=0.209  Sum_probs=105.0

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCC-CHHHHHHHhc--------
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPR-TVKEFCSVAN--------  177 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~-tl~eIa~~~~--------  177 (254)
                      ..+.++|.+++.+|+||..+..+|..+|++....+.+++.++..+++||+|+||+.++.|+ +++||..++.        
T Consensus        44 ~~~~~~I~~v~~~l~L~~~t~~tA~~~~~RF~~~~s~~~~~~~lva~acLfLA~K~EE~~~~~~~di~~~~~~~~k~~~~  123 (285)
T 3rgf_B           44 IFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFS  123 (285)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHSCTTTSCHHHHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhCCchhcCHHHHHHHHHHHHHhhhccccccHHHHHHHHHHHHccccc
Confidence            4678999999999999999999999999999999999999999999999999999999987 7889876421        


Q ss_pred             -------CCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhh
Q 025357          178 -------GTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLF  229 (254)
Q Consensus       178 -------~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~  229 (254)
                             ..+.++|.+..+.|.+.|+.+      +...+|..||.+|+..|+++.++..
T Consensus       124 ~~~~~~~~~~~~~Il~~E~~iL~~L~f~------l~v~~P~~fL~~~~~~l~~~~~~~~  176 (285)
T 3rgf_B          124 YAFPKEFPYRMNHILECEFYLLELMDCC------LIVYHPYRPLLQYVQDMGQEDMLLP  176 (285)
T ss_dssp             TTCCSCCCCCHHHHHHHHHHHHHHTTTC------CCCCCSHHHHHHHHHHHTCHHHHHH
T ss_pred             ccCchhhHHHHHHHHHHHHHHHHHcCCC------eEeCChHHHHHHHHHHhCCCHHHHH
Confidence                   146799999999999999988      7778999999999999998877655

>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M

Probab=99.32  E-value=1.5e-13  Score=124.09  Aligned_cols=90  Identities=19%  Similarity=0.245  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~  187 (254)
                      +...+|.++|+.|+|+..+...|.+|.+++.+.+++.||+|.++||||||+|++.++.++|++||+++ ++|++.+|++.
T Consensus       234 ~p~~~i~Rf~s~L~l~~~v~~~A~~i~~~~~~~~i~~GR~P~~IAAAaIylAa~l~g~~~t~~eIa~v-~~Vse~TIr~r  312 (345)
T 4bbr_M          234 QNLTYIPRFCSHLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQT-LQVTEGTIKSG  312 (345)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcccccCCChHHHHHHHHHHHHHHhCCCCCHHHHHHH-HCCCHHHHHHH
Confidence            56679999999999999999999999999999999999999999999999999999999999999995 99999999999


Q ss_pred             HHHHHHHhchh
Q 025357          188 KEFIVKHLEAE  198 (254)
Q Consensus       188 ~k~l~~~l~~~  198 (254)
                      |++|.+.++.-
T Consensus       313 ykel~~~~~~l  323 (345)
T 4bbr_M          313 YKILYEHRDKL  323 (345)
T ss_dssp             -----------
T ss_pred             HHHHHHHHHhh
Confidence            99999998754

>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=99.28  E-value=1.3e-11  Score=111.96  Aligned_cols=117  Identities=16%  Similarity=0.172  Sum_probs=103.7

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhc---------
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVAN---------  177 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~---------  177 (254)
                      ..+.++|.+++..|+||..+..+|..||+++.....+++.++..+++||||+||+.+..|++++||..++.         
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            46799999999999999999999999999999999999999999999999999999999999999986421         


Q ss_pred             -CC-------CHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhh
Q 025357          178 -GT-------TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLF  229 (254)
Q Consensus       178 -~v-------~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~  229 (254)
                       .+       ..++|.++.+.|.+.|+.+      +...+|..||.+|+..|+++.++..
T Consensus       119 ~~~~~~~y~~~~~~Il~~E~~IL~~L~f~------L~v~~P~~fL~~~~~~l~~~~~l~~  172 (358)
T 2pk2_A          119 PDTRSEAYLQQVQDLVILESIILQTLGFE------LTIDHPHTHVVKCTQLVRASKDLAQ  172 (358)
T ss_dssp             CCTTSHHHHGGGTGGGTHHHHHHHHTTTC------CCCCCTTHHHHHHHHHTTCCHHHHH
T ss_pred             ccccchhhhHHHHHHHHHHHHHHHHcCCc------eeCCCHHHHHHHHHHHcCCCHHHHH
Confidence             11       1567888889999999987      7788999999999999999887755

>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B*

Probab=99.28  E-value=5.9e-11  Score=103.51  Aligned_cols=116  Identities=13%  Similarity=0.108  Sum_probs=106.4

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHhc--CCCHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN--GTTKKE  183 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~~--~v~~~~  183 (254)
                      ....++|.+++..++|+..+...|..++.+......+.+++...+++||+|+||+.++. |++++|+..+ +  ..+.++
T Consensus        39 ~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfl~~~~v~~~~lqlv~~acL~iA~K~eE~~~p~~~d~~~~-~~~~~~~~e  117 (269)
T 2b9r_A           39 AILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQNNSVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFV-TDNTYTKHQ  117 (269)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHTTSCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHH-TCSSSCHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcCCCCcHHHhhHHHHHHHHHHHhcccccCccHHHHHHH-hcCCCCHHH
Confidence            45788999999999999999999999999999988889999999999999999999887 8999999985 4  378999


Q ss_pred             HHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhh
Q 025357          184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLF  229 (254)
Q Consensus       184 i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~  229 (254)
                      |.+..+.|.+.|+.+      +...+|.+||.||+..++++.++..
T Consensus       118 I~~mE~~IL~~L~f~------l~~~tp~~fl~~~~~~~~~~~~~~~  157 (269)
T 2b9r_A          118 IRQMEMKILRALNFG------LGRPLPLHFLRRASKIGEVDVEQHT  157 (269)
T ss_dssp             HHHHHHHHHHHTTSC------CCCCCHHHHHHHHHHSSCCCHHHHH
T ss_pred             HHHHHHHHHHHcCCc------cCCCCHHHHHHHHHHhcCCCHHHHH
Confidence            999999999999987      7788999999999999999877654

>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=99.24  E-value=9.2e-11  Score=104.93  Aligned_cols=108  Identities=11%  Similarity=0.181  Sum_probs=98.6

Q ss_pred             HHHHHHHHHHHhccC--CCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCC----
Q 025357          107 IQAFKSISAMSDRLG--LVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT----  180 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~--Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~----  180 (254)
                      ..+..+|.++|..|+  ||..+..+|..+|++....+.+.+.++..+++||+|+||+.++.|++++||+.+ ...+    
T Consensus        58 ~~~~~~I~ev~~~l~~~Lp~~t~~tA~~~~~RF~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~d~v~~-~~~~p~~~  136 (323)
T 1jkw_A           58 KYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGN-LRESPLGQ  136 (323)
T ss_dssp             HHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHGGG-SSSCHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhhCChhhcCHHHHHHHHHHHHHhhhcCCCCHHHHHHH-hccChhhh
Confidence            466799999999999  999999999999999999999999999999999999999999999999999874 4444    


Q ss_pred             ---HHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhc
Q 025357          181 ---KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI  221 (254)
Q Consensus       181 ---~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L  221 (254)
                         .++|.+..+.|.+.|+..      +.+.+|..||.+|+..|
T Consensus       137 ~~~~~~Il~~E~~iL~~L~f~------l~v~~P~~~L~~~l~~l  174 (323)
T 1jkw_A          137 EKALEQILEYELLLIQQLNFH------LIVHNPYRPFEGFLIDL  174 (323)
T ss_dssp             HHHHHHHHHHHHHHHHHTTTC------CCCCCSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHCCCc------EEcCChHHHHHHHHHHH
Confidence               578999999999999988      77889999999999876

>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=99.20  E-value=1.5e-10  Score=100.42  Aligned_cols=116  Identities=15%  Similarity=0.174  Sum_probs=105.1

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHhc--CCCHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN--GTTKKE  183 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~~--~v~~~~  183 (254)
                      ..+.++|.+++..++|+..+.-.|..++.+......+..++...+++||+|+||+.++. |++++|+..+ +  ..+.++
T Consensus        40 ~~lvdwl~~v~~~~~l~~~tl~lAv~~lDRfls~~~v~~~~lqlv~~acl~iA~K~ee~~~~~~~d~~~i-~~~~~~~~~  118 (260)
T 2cch_B           40 AILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYI-TDDTYTKKQ  118 (260)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHH-TTSSSCHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccCCCCHHHHhHHHHHHHHHHHHhcccCCCCHHHHHHH-HcCCcCHHH
Confidence            46789999999999999999999999999998887777788999999999999999998 9999999885 4  378999


Q ss_pred             HHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCc-chhh
Q 025357          184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNF-FFLF  229 (254)
Q Consensus       184 i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~-~v~~  229 (254)
                      |.+..+.|.+.|+.+      +.+.+|.+||.+|+..++++. ++..
T Consensus       119 i~~mE~~iL~~L~~~------l~~~tp~~fl~~~~~~l~~~~~~~~~  159 (260)
T 2cch_B          119 VLRMEHLVLKVLTFD------LAAPTVNQFLTQYFLHQQPANCKVES  159 (260)
T ss_dssp             HHHHHHHHHHHTTTC------CCCCCHHHHHHHHHTTCSSCCHHHHH
T ss_pred             HHHHHHHHHHHcCCc------cCCCCHHHHHHHHHHHcCCChHHHHH
Confidence            999999999999988      778899999999999999876 5544

>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=99.18  E-value=3.6e-10  Score=98.56  Aligned_cols=115  Identities=13%  Similarity=0.236  Sum_probs=104.9

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHh-cCCCHHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVA-NGTTKKEI  184 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~-~~v~~~~i  184 (254)
                      ....++|.+++..++++..+.-.|..++.+......+..++...+++||+|+||+.++. |++++|++.+. ...+.++|
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            46788999999999999999999999999999888888889999999999999999998 99999998852 23789999


Q ss_pred             HHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF  227 (254)
Q Consensus       185 ~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v  227 (254)
                      .+..+.|.+.|+..      +.+.+|..||.+|+..|+++.+.
T Consensus       138 ~~mE~~IL~~L~~~------l~~~tp~~fl~~~~~~l~~~~~~  174 (271)
T 2w96_A          138 LQMELLLVNKLKWN------LAAMTPHDFIEHFLSKMPEAEEN  174 (271)
T ss_dssp             HHHHHHHHHHTTTC------CCCCCHHHHHHHHHHTSCCCHHH
T ss_pred             HHHHHHHHHHCCCc------cCCCCHHHHHHHHHHHcCCCchH
Confidence            99999999999988      78889999999999999998765

>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae}

Probab=99.15  E-value=3.5e-12  Score=115.17  Aligned_cols=88  Identities=19%  Similarity=0.262  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~  187 (254)
                      +...+|.++|+.|+|+..+...|.+|.+.+.+.++..||+|.++||||||+|++..+.+++++||+++ ++|++.+|++.
T Consensus       234 ~p~~~i~Rf~~~L~l~~~v~~~A~~i~~~~~~~~l~~Gr~P~~IAaAaIylAa~~~~~~~t~~eIa~~-~~Vse~TIr~~  312 (345)
T 3k7a_M          234 QNLTYIPRFCSHLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQT-LQVTEGTIKSG  312 (345)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhchhcCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHH-HCCCHHHHHHH
Confidence            45678889999999999999999999999999999999999999999999999999999999999995 89999999999


Q ss_pred             HHHHHHHhc
Q 025357          188 KEFIVKHLE  196 (254)
Q Consensus       188 ~k~l~~~l~  196 (254)
                      |++|.+.+.
T Consensus       313 ykel~~~~~  321 (345)
T 3k7a_M          313 YKILYEHRD  321 (345)
T ss_dssp             ---------
T ss_pred             HHHHHHHHH
Confidence            999998875

>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=99.09  E-value=1.4e-09  Score=94.05  Aligned_cols=115  Identities=14%  Similarity=0.191  Sum_probs=104.1

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHh-cCCCHHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVA-NGTTKKEI  184 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~-~~v~~~~i  184 (254)
                      ....++|.+++..++|+..+.-.|..++.+......+++++...+++||+|+||+.+.. |.+++|++.+. ...+.++|
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            45689999999999999999999999999999988888889999999999999997765 99999998852 23789999


Q ss_pred             HHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF  227 (254)
Q Consensus       185 ~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v  227 (254)
                      .+..+.|.+.|+..      +...+|..|+.+|+..++++.+.
T Consensus       132 ~~mE~~iL~~L~~~------l~~~tp~~fl~~~~~~~~~~~~~  168 (257)
T 1g3n_C          132 IDQEKELLEKLAWR------TEAVLATDVTSFLLLKLVGGSQH  168 (257)
T ss_dssp             HHHHHHHHHHTTTC------CCCCCHHHHHHHHHHHHSCSSTT
T ss_pred             HHHHHHHHHHCCCc------CCCCCHHHHHHHHHHHcCCChhH
Confidence            99999999999988      77889999999999999998764

>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=99.08  E-value=1.6e-09  Score=95.03  Aligned_cols=114  Identities=15%  Similarity=0.213  Sum_probs=103.1

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhC-CCCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHhc--CCCHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQ-KPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN--GTTKK  182 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~-~~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~~--~v~~~  182 (254)
                      ....++|.+++..++++..+.-.|..++.+.... ..+++++...+++||+|+||+.++. |.+++|++.+ +  ..+.+
T Consensus        51 ~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~~v~~~~lqlv~~acL~iA~K~eE~~~p~l~~~~~i-~~~~~~~~  129 (283)
T 1w98_B           51 AILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYV-TDGACSGD  129 (283)
T ss_dssp             HHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHT-TTTSSCHH
T ss_pred             HHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcccCCCcHHHHHHH-HcCCCCHH
Confidence            4568899999999999999999999999999886 5788899999999999999999976 8999999885 4  47899


Q ss_pred             HHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357          183 EIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF  227 (254)
Q Consensus       183 ~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v  227 (254)
                      +|.+..+.|.+.|+..      +.+++|.+||.+|+..++++...
T Consensus       130 ei~~mE~~IL~~L~~~------l~~~tp~~fL~~f~~~~~~~~~~  168 (283)
T 1w98_B          130 EILTMELMIMKALKWR------LSPLTIVSWLNVYMQVAYLNDLH  168 (283)
T ss_dssp             HHHHHHHHHHHHTTTC------CCCCCHHHHHHHHHHHHTCCSSC
T ss_pred             HHHHHHHHHHHHcCCc------CCCCCHHHHHHHHHHHhccCchh
Confidence            9999999999999988      77889999999999999987654

>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=98.98  E-value=3.4e-09  Score=91.43  Aligned_cols=115  Identities=17%  Similarity=0.184  Sum_probs=103.1

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcC-CCCCHHHHHHHh-cCCCHHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVA-NGTTKKEI  184 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~-~p~tl~eIa~~~-~~v~~~~i  184 (254)
                      ....++|.+++..++|+..+.-.|..++.+......+++++...+++||+|+||+.+. .|.+++|++.+. ...+.++|
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            4568899999999999999999999999999998888999999999999999999976 599999997641 23689999


Q ss_pred             HHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF  227 (254)
Q Consensus       185 ~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v  227 (254)
                      .+..+.|.+.|+.+      +..++|.+|+.+|+..++++.+.
T Consensus       133 ~~mE~~IL~~L~~~------l~~~tp~~fl~~~~~~~~~~~~~  169 (254)
T 2f2c_A          133 INQEKDILEALKWD------TEAVLATDFLIPLCNALKIPEDL  169 (254)
T ss_dssp             HHHHHHHHHHTTTC------CCCCCGGGSHHHHHHHTTCCGGG
T ss_pred             HHHHHHHHHHCCCc------CCCCCHHHHHHHHHHHcCCChhh
Confidence            99999999999988      77889999999999999998764

>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens}

Probab=98.79  E-value=3.9e-08  Score=87.15  Aligned_cols=115  Identities=12%  Similarity=0.186  Sum_probs=102.7

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhc-CCCCCHHHHHHHh-cCCCHHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE-NKPRTVKEFCSVA-NGTTKKEI  184 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~-~~p~tl~eIa~~~-~~v~~~~i  184 (254)
                      ..+.++|.+++..++|+..+.-.|..++.+......+.......++++|+|+||+.+ ..|.++.++..+. ...+..+|
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            467899999999999999999999999999998888888899999999999999975 4688999998752 23689999


Q ss_pred             HHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF  227 (254)
Q Consensus       185 ~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v  227 (254)
                      .+.-+.|.+.|+..      +...+|..||.+|+..++++.+.
T Consensus       152 ~~mE~~IL~~L~f~------l~~~tp~~fl~~~l~~l~~~~~~  188 (306)
T 3g33_B          152 RDWEVLVLGKLKWD------LAAVIAHDFLAFILHRLSLPRDR  188 (306)
T ss_dssp             HHHHHHHHHHTTTC------CCCCCGGGGHHHHHHTSSCCTTT
T ss_pred             HHHHHHHHHHcCCc------cCCCCHHHHHHHHHHHcCCChhH
Confidence            99999999999988      77889999999999999987653

>3h4c_A Transcription factor TFIIB-like; cyclin, transcription factor TFIIB repeat; 2.30A {Trypanosoma brucei brucei}

Probab=98.40  E-value=7.3e-07  Score=73.21  Aligned_cols=114  Identities=23%  Similarity=0.358  Sum_probs=86.4

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCC---CCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRG---RNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~G---r~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i  184 (254)
                      .+...|.++..+-++|+.+.+.|.++.+......--+|   -++..+||||+.+|+.+.+.|+++.|+-.....+...++
T Consensus        14 ~M~nclr~L~kKs~~~eaVL~~AieLar~fvg~rR~rgqRvE~q~dVAAAc~miAae~~~~PiplaE~r~lD~sL~Dvel   93 (260)
T 3h4c_A           14 TMLNCMRGLHKKAVLPEPVLDRGIELARAFVGGRRARGQRVERQPDVAAACLMIAAEEAQQPLPLAEVRCLDSSLGDVEL   93 (260)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHCTTCCCHHH
T ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHHHhhhhhhhcccccccHHHHHHHHHHHHHHcCCCccHHHHHHHhhhhhHHHH
Confidence            35677899999999999999999999999876443344   367899999999999999999999999665334444445


Q ss_pred             HHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCC
Q 025357          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKN  224 (254)
Q Consensus       185 ~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~  224 (254)
                      ++.  +|.+.++++.... ++...-..++|..|+.+|+|.
T Consensus        94 rr~--Eiv~~l~l~e~e~-rl~~~~~~NLl~~Yv~kL~Lq  130 (260)
T 3h4c_A           94 RRA--DIVRELHLEDSER-RLRDTFADNLLVKYILKLGLQ  130 (260)
T ss_dssp             HHH--HHHHHTTCHHHHH-HHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHH--HHHHHccCCHHHH-HHHHHhhhhHHHHHHHHhccc
Confidence            444  8888888764211 122334578899999999885

>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=98.38  E-value=5.6e-06  Score=71.29  Aligned_cols=115  Identities=11%  Similarity=0.021  Sum_probs=100.7

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcC-CCCCHHHHHHHh-cCCCHHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVA-NGTTKKEI  184 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~-~p~tl~eIa~~~-~~v~~~~i  184 (254)
                      ....++|-+++..++|+..+.-.|..++.+......+.......++++|+|+|++.+. .|.++.++.... ...+..+|
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            3568899999999999999999999999999887777777889999999999999765 488999998752 34689999


Q ss_pred             HHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF  227 (254)
Q Consensus       185 ~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v  227 (254)
                      .+.-+.|.+.|+.+      +..++|..|+.+|...++.+.+.
T Consensus       130 ~~mE~~IL~~L~w~------l~~pTp~~FL~~~l~~~~~~~~~  166 (252)
T 1f5q_B          130 LTLEVKSLDTLSWV------ADRCLSTDLICYILHIMHAPRED  166 (252)
T ss_dssp             HHHHHHHHHHTTTC------CCCCCHHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHCCCc------cCCCCHHHHHHHHHHHcCCCcch
Confidence            99999999999988      77889999999999999987654

>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe}

Probab=97.90  E-value=1.8e-05  Score=67.06  Aligned_cols=89  Identities=12%  Similarity=0.039  Sum_probs=75.1

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~  187 (254)
                      ...++|.+++..+++++.+...|..+...+......-|.+|..+||||||+|++..+.+.+ .+.... .++++.+|..+
T Consensus       133 ~P~~~l~~~~~~~~~~~~~~~~A~~~l~~s~~~~~~l~~~Ps~IAaAai~lA~~~~~~~~~-~~~~~~-~~~~~~~i~~~  210 (235)
T 1zp2_A          133 HPYTSLEQAFHDGIINQKQLEFAWSIVNDSYASSLCLMAHPHQLAYAALLISCCNDENTIP-KLLDLI-KSTDAFKVILC  210 (235)
T ss_dssp             CTHHHHHHHHHTTSSCHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHTSCTTHHH-HHHHHC-CHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCCchhccCHHHHHHHHHHHHHHhcCCCCC-CCcchh-hcCCHHHHHHH
Confidence            3567899999999999999999999999998877788999999999999999999886543 345453 47899999999


Q ss_pred             HHHHHHHhchh
Q 025357          188 KEFIVKHLEAE  198 (254)
Q Consensus       188 ~k~l~~~l~~~  198 (254)
                      ++.|.+.....
T Consensus       211 ~~~i~~ly~~~  221 (235)
T 1zp2_A          211 VQRIISIYYFE  221 (235)
T ss_dssp             HHHHHHHHTSS
T ss_pred             HHHHHHHHhhC
Confidence            99999876543

>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=97.90  E-value=3e-05  Score=66.77  Aligned_cols=89  Identities=9%  Similarity=-0.047  Sum_probs=75.3

Q ss_pred             HHHHHHHHHHhccCCCH-HHHHHHHHHHHHHh-hCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHH
Q 025357          108 QAFKSISAMSDRLGLVT-TIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIG  185 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~-~v~e~A~~i~k~~~-~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~  185 (254)
                      ...++|.+++..++++. .+...|..+..... +...+-+.+|..+||||+|+|++..+.+....+++.+ +|+++.+|.
T Consensus       138 tp~~fl~~~~~~l~~~~~~~~~~a~~l~e~sl~~~~~~~~~~Ps~iAaAai~lA~~~~~~~~w~~~l~~~-~g~~~~~i~  216 (260)
T 2cch_B          138 TVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRK-TGYTLESLK  216 (260)
T ss_dssp             CHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHHHHHHHHHHHHSCCSCHHHHHH-HCCCHHHHH
T ss_pred             CHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHhHHHHhCCCHHHHHHHHHHHHHHHhCCCcchHHHHHH-hCcCHHHHH
Confidence            46789999999999986 78888888887754 4432567899999999999999988878888889885 899999999


Q ss_pred             HHHHHHHHHhch
Q 025357          186 RAKEFIVKHLEA  197 (254)
Q Consensus       186 ~~~k~l~~~l~~  197 (254)
                      .+++.|.+.+..
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=97.88  E-value=1.5e-05  Score=69.11  Aligned_cols=88  Identities=8%  Similarity=-0.034  Sum_probs=77.0

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~  187 (254)
                      ...++|.+++..++++..+...|..+...+.....+-+.+|..+||||+|+|++..+.+....++..+ +|+++.+|..+
T Consensus       137 tp~~fl~~~~~~~~~~~~~~~~a~~l~e~sl~~~~~~~~~Ps~iAaAai~lA~~~l~~~~w~~~l~~~-tg~~~~~l~~~  215 (269)
T 2b9r_A          137 LPLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFPPSQIAAGAFSLALKILDNGEWTPTLQHY-LSYTEESLLPV  215 (269)
T ss_dssp             CHHHHHHHHHHSSCCCHHHHHHHHHHHHHGGGCGGGSSSCTTHHHHHHHHHHHHHHTCCCSCTTHHHH-SCCCSSTTTTH
T ss_pred             CHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhhhcCCHHHHHHHHHHHHHHHhCCCCCCHHHHHH-HCCCHHHHHHH
Confidence            45688999999999999999999999888776566678999999999999999999887777788885 89999999999


Q ss_pred             HHHHHHHhc
Q 025357          188 KEFIVKHLE  196 (254)
Q Consensus       188 ~k~l~~~l~  196 (254)
                      ++.|.+.+.
T Consensus       216 ~~~l~~~~~  224 (269)
T 2b9r_A          216 MQHLAKNVV  224 (269)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999988764

>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=97.70  E-value=0.00011  Score=63.57  Aligned_cols=90  Identities=13%  Similarity=0.073  Sum_probs=69.9

Q ss_pred             HHHHHHHHHHhccCCCHHHH----HHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC---------CCCHHHHHH
Q 025357          108 QAFKSISAMSDRLGLVTTIK----DRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK---------PRTVKEFCS  174 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~----e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~---------p~tl~eIa~  174 (254)
                      ..+++|.++...++++....    ..|..+...+.....+-+.+|..+||||||+|++..+.         +.+..+++.
T Consensus       156 tp~~fl~~~~~~l~~~~~~~~~~~~~a~~~l~~~~~d~~~~~~~PS~iAaAai~lA~~~l~~~~~~~~~w~~~~~~~l~~  235 (271)
T 2w96_A          156 TPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISNPPSMVAAGSVVAAVQGLNLRSPNNFLSYYRLTRFLSR  235 (271)
T ss_dssp             CHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHTSTHHHHSCHHHHHHHHHHHHHHHHHHHSTTSCGGGTTHHHHHHH
T ss_pred             CHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHHHhhhhhhccCHHHHHHHHHHHHHHHhCcCCCCCCCcHHHHHHHHHH
Confidence            46788999999999987653    45666666554333345789999999999999986542         234678888


Q ss_pred             HhcCCCHHHHHHHHHHHHHHhchh
Q 025357          175 VANGTTKKEIGRAKEFIVKHLEAE  198 (254)
Q Consensus       175 ~~~~v~~~~i~~~~k~l~~~l~~~  198 (254)
                      + +|+++.+|+.+++.|.+.++..
T Consensus       236 ~-~~v~~~~l~~c~~~i~~l~~~~  258 (271)
T 2w96_A          236 V-IKCDPDCLRACQEQIEALLESS  258 (271)
T ss_dssp             H-HTSCHHHHHHHHHHHHHHHTTT
T ss_pred             H-HCcCHHHHHHHHHHHHHHHHHH
Confidence            5 8999999999999999998866

>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens}

Probab=97.68  E-value=0.00023  Score=62.04  Aligned_cols=104  Identities=14%  Similarity=0.155  Sum_probs=81.8

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~  187 (254)
                      +.+++|.+++..|+++..+...|..+..........-+..|..+||||||+|++..+.+.  ...... ++++..+|..+
T Consensus       156 ~P~~fL~~~~~~l~~~~~~~~~A~~~l~~sl~t~~~l~~~Ps~IAaAaiylA~~~~~~~~--~~W~~~-~~~~~~~l~~~  232 (285)
T 3rgf_B          156 HPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDA--RQWFAE-LSVDMEKILEI  232 (285)
T ss_dssp             CSHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSHHHHSCHHHHHHHHHHHHHHHTTCCC--HHHHHT-SCSCHHHHHHH
T ss_pred             ChHHHHHHHHHHhCCCHHHHHHHHHHHHHHHccChhhccCHHHHHHHHHHHHHHHcCCCh--hhHHHH-HCCCHHHHHHH
Confidence            346789999999999999999999999988776666788999999999999999988754  456664 89999999999


Q ss_pred             HHHHHHHhchhcccccccCCCCHHHHHHHHHhhc
Q 025357          188 KEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI  221 (254)
Q Consensus       188 ~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L  221 (254)
                      ++.|.......       +..+...=|+++..++
T Consensus       233 ~~~il~ly~~~-------~~~~~~~~~~~~~~k~  259 (285)
T 3rgf_B          233 IRVILKLYEQW-------KNFDERKEMATILSKM  259 (285)
T ss_dssp             HHHHHHHHHHH-------HHCCHHHHHHHHHHHS
T ss_pred             HHHHHHHHHhc-------ccCchhhhHHHHHHhC
Confidence            99998877653       1123334455555554

>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=97.57  E-value=0.00015  Score=62.11  Aligned_cols=91  Identities=10%  Similarity=-0.027  Sum_probs=73.0

Q ss_pred             HHHHHHHHHHhccCCCH----HHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHH-------HH-
Q 025357          108 QAFKSISAMSDRLGLVT----TIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFC-------SV-  175 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~----~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa-------~~-  175 (254)
                      ....+|.+++..|+.+.    .+...|..+...+......-+.+|..+||||||+|++..|.+++..+..       .. 
T Consensus       150 ~P~~fl~~~~~~l~~~~~~~~~~~~~A~~l~~~s~~~~~~l~~~Ps~IAaAai~lA~~~~~~~~~~~~~~~~~~~W~~~~  229 (258)
T 2i53_A          150 HPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQF  229 (258)
T ss_dssp             CHHHHHHHHHHTBCSCHHHHHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHHHHTCCGGGGBSSCCSSCGGGGT
T ss_pred             ChHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHHHcCCchhccChHHHHHHHHHHHHHHhCCCCCccccCCCcccHHHHh
Confidence            45778999999999987    5788888888888777777789999999999999999998765543221       21 


Q ss_pred             hcCCCHHHHHHHHHHHHHHhchh
Q 025357          176 ANGTTKKEIGRAKEFIVKHLEAE  198 (254)
Q Consensus       176 ~~~v~~~~i~~~~k~l~~~l~~~  198 (254)
                      ..++++.+|...++.|.+.+...
T Consensus       230 ~~~~~~~~l~~~~~~il~ly~~~  252 (258)
T 2i53_A          230 VQDVPVDVLEDICHQILDLYSQG  252 (258)
T ss_dssp             SSSCCHHHHHHHHHHHHTTTSSS
T ss_pred             ccCCCHHHHHHHHHHHHHHHhcc
Confidence            14899999999999998877643

>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=97.47  E-value=0.00037  Score=59.61  Aligned_cols=89  Identities=10%  Similarity=0.100  Sum_probs=71.2

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHh-hCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHH----HHHHH-hcCCCH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVK----EFCSV-ANGTTK  181 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~-~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~----eIa~~-~~~v~~  181 (254)
                      +.+.+|.+++..++.+..+...|..+..... ...+.-+..|..+||||+|+|++..|.+++..    ..... ..++++
T Consensus       145 ~P~~fl~~~~~~l~~~~~~~~~A~~~~~~sl~~~~~~l~~~Ps~IAaAai~lA~~~~~~~~p~~~~~~~W~~~~~~~~~~  224 (257)
T 2ivx_A          145 HPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTL  224 (257)
T ss_dssp             CHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCGGGTSCHHHHHHHHHHHHHHHHTCCCCCCTTCCCGGGGTCSSCCH
T ss_pred             CcHHHHHHHHHHhCCCcHHHHHHHHHHHhhhhcccHHHcCCHHHHHHHHHHHHHHHhCCCCCCCCCCchHHHHhCCCCCH
Confidence            4578899999999999999999999887765 45656789999999999999999988654431    12221 137899


Q ss_pred             HHHHHHHHHHHHHhc
Q 025357          182 KEIGRAKEFIVKHLE  196 (254)
Q Consensus       182 ~~i~~~~k~l~~~l~  196 (254)
                      .+|...++.|.+.+.
T Consensus       225 ~~l~~~~~~i~~~~~  239 (257)
T 2ivx_A          225 ELLDELTHEFLQILE  239 (257)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999988774

>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=97.47  E-value=0.00039  Score=59.48  Aligned_cols=87  Identities=13%  Similarity=0.140  Sum_probs=66.6

Q ss_pred             HHHHHHHHHhccCCCHHH----HHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhc-CCCCC----HHHHHHHhcCC
Q 025357          109 AFKSISAMSDRLGLVTTI----KDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE-NKPRT----VKEFCSVANGT  179 (254)
Q Consensus       109 a~~~I~~i~~~L~Lp~~v----~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~-~~p~t----l~eIa~~~~~v  179 (254)
                      ..+++.++...++++...    ...|..+.....-...+-+.+|..+||||+|+|.+.. +.|.+    ..+++.+ +|+
T Consensus       152 p~~fl~~~~~~~~~~~~~~~~~~~~a~~ll~~~l~d~~~~~~~PS~iAaAai~la~~~~~~~~~~w~~~~~~l~~~-tg~  230 (254)
T 2f2c_A          152 ATDFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPNIALLSPGLICAGGLLTTIETDNTNCRPWTCYLEDLSSI-LNF  230 (254)
T ss_dssp             GGGSHHHHHHHTTCCGGGHHHHHHHHHHHHHHHTTSGGGTTSCHHHHHHHHHHHHHHTTCCSSCCTHHHHHHHHHH-HTC
T ss_pred             HHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHHHcCcchhccCHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHH-HCc
Confidence            356788888889888653    3456666655543333467899999999999999986 44555    7888885 899


Q ss_pred             CHHHHHHHHHHHHHHhc
Q 025357          180 TKKEIGRAKEFIVKHLE  196 (254)
Q Consensus       180 ~~~~i~~~~k~l~~~l~  196 (254)
                      ++.+|..+++.|.+.+.
T Consensus       231 ~~~~l~~c~~~i~~~~~  247 (254)
T 2f2c_A          231 STNTVRTVKDQVSEAFS  247 (254)
T ss_dssp             CHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHH
Confidence            99999999999988764

>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=97.37  E-value=0.00047  Score=59.08  Aligned_cols=89  Identities=16%  Similarity=0.022  Sum_probs=69.3

Q ss_pred             HHHHHHHHHHhccCCCHHH----HHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC------CCCHHHHHHHhc
Q 025357          108 QAFKSISAMSDRLGLVTTI----KDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK------PRTVKEFCSVAN  177 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v----~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~------p~tl~eIa~~~~  177 (254)
                      ...+++.++...++++...    ...|..+.....-...+-+.+|..+||||+|+|.+..+.      +....+++.+ +
T Consensus       150 tp~~fl~~~~~~~~~~~~~~~~~~~~a~~~le~~l~d~~~~~~~PS~iAaAai~lA~~~l~~~~~~~~~~w~~~l~~~-t  228 (257)
T 1g3n_C          150 LATDVTSFLLLKLVGGSQHLDFWHHEVNTLITKALVDPLTGSLPASIISAAGCALLVPANVIPQDTHSGGVVPQLASI-L  228 (257)
T ss_dssp             CHHHHHHHHHHHHSCSSTTHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHCCGGGSCC-----CHHHHHHHH-H
T ss_pred             CHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhCcchhCcCHHHHHHHHHHHHHHHhCCCcccchhhHHHHHHHH-H
Confidence            4677899999999887643    455666666554444456789999999999999988874      3557788885 8


Q ss_pred             CCCHHHHHHHHHHHHHHhch
Q 025357          178 GTTKKEIGRAKEFIVKHLEA  197 (254)
Q Consensus       178 ~v~~~~i~~~~k~l~~~l~~  197 (254)
                      |+++.+|..+++.|.+.+.-
T Consensus       229 ~~~~~~l~~c~~~i~~l~~~  248 (257)
T 1g3n_C          229 GCDVSVLQAAVEQILTSVSD  248 (257)
T ss_dssp             TCCHHHHHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHH
Confidence            99999999999999988753

>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=97.11  E-value=0.0028  Score=46.00  Aligned_cols=80  Identities=16%  Similarity=0.175  Sum_probs=63.7

Q ss_pred             HHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCC------CCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHH
Q 025357          113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRG------RNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGR  186 (254)
Q Consensus       113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~G------r~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~  186 (254)
                      |+++|-.||.++ +++.|.+++.+.... +..+      -+....+||++|.+||..+..+.-..+.. .+|+++..+.+
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-LPQTQQVDLDLSRPLFTSAALLSACKILKLKVDKNKMVA-TSGVKKAIFDR   82 (95)
T ss_dssp             HHHHHHHHTCGG-GHHHHHHHHHHHHTT-SCHHHHHHCCTTSHHHHHHHHHHHHHHTTCCCCHHHHHH-TTCBCHHHHHH
T ss_pred             HHHHHHHhCCHH-HHHHHHHHHHHHHHH-hHHHhhccccccccHHHHHHHHHHHHHHccCCCHHHHHH-HHCCCHHHHHH
Confidence            788999999997 778888887776532 2211      13457889999999999999999999989 59999999998


Q ss_pred             HHHHHHHHh
Q 025357          187 AKEFIVKHL  195 (254)
Q Consensus       187 ~~k~l~~~l  195 (254)
                      ....+.+..
T Consensus        83 l~~~~e~~~   91 (95)
T 3m03_A           83 LCKQLEKIG   91 (95)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888776654

>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}

Probab=97.04  E-value=0.00057  Score=46.99  Aligned_cols=30  Identities=20%  Similarity=0.493  Sum_probs=26.5

Q ss_pred             CCCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         2 ~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      +...||.|++  .+.++..+|+++|..||.+.
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            4578999997  58899999999999999985

>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}

Probab=96.97  E-value=0.00065  Score=46.43  Aligned_cols=30  Identities=10%  Similarity=0.159  Sum_probs=26.4

Q ss_pred             CCCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         2 ~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      +...||.|++  .+.++...|+++|..||.+.
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            4578999997  58899999999999999985

>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1

Probab=96.97  E-value=0.00067  Score=46.19  Aligned_cols=30  Identities=13%  Similarity=0.066  Sum_probs=26.2

Q ss_pred             CCCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         2 ~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      +...||.|++  .+.+|..+|+++|..||.+.
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            3467999997  58899999999999999985

>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4

Probab=96.86  E-value=0.00035  Score=46.95  Aligned_cols=31  Identities=32%  Similarity=0.776  Sum_probs=28.6

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      +.+||.|+. ..+|++..+-.+.|..||.+|-
T Consensus         7 ~VKCp~C~n-iq~VFShA~tvV~C~~Cg~~L~   37 (66)
T 1qxf_A            7 KVKCPDCEH-EQVIFDHPSTIVKCIICGRTVA   37 (66)
T ss_dssp             EEECTTTCC-EEEEESSCSSCEECSSSCCEEE
T ss_pred             EEECCCCCC-ceEEEecCceEEEcccCCCEEe
Confidence            368999998 7899999999999999999995

>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=96.83  E-value=0.00068  Score=46.45  Aligned_cols=29  Identities=21%  Similarity=0.345  Sum_probs=25.7

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      ...||.|++  .+.++..+|+++|..||.+.
T Consensus         8 iL~CP~ck~--~L~~~~~~~~LiC~~cg~~Y   36 (69)
T 2pk7_A            8 ILACPICKG--PLKLSADKTELISKGAGLAY   36 (69)
T ss_dssp             TCCCTTTCC--CCEECTTSSEEEETTTTEEE
T ss_pred             heeCCCCCC--cCeEeCCCCEEEcCCCCcEe
Confidence            468999997  58889899999999999985

>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=96.78  E-value=0.00058  Score=46.66  Aligned_cols=29  Identities=34%  Similarity=0.592  Sum_probs=25.7

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      ...||.|++  .+.++..+|+++|..||.+.
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            367999997  58899999999999999985

>3j20_W 30S ribosomal protein S27E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=96.74  E-value=0.00048  Score=45.94  Aligned_cols=31  Identities=35%  Similarity=0.751  Sum_probs=28.5

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      +.+||.|+. ..+|+++.+-.+.|..||.+|-
T Consensus        15 ~VkCp~C~~-~q~VFSha~t~V~C~~Cgt~L~   45 (63)
T 3j20_W           15 RVKCIDCGN-EQIVFSHPATKVRCLICGATLV   45 (63)
T ss_dssp             EEECSSSCC-EEEEESSCSSCEECSSSCCEEE
T ss_pred             EEECCCCCC-eeEEEecCCeEEEccCcCCEEe
Confidence            367999998 7899999999999999999995

>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=96.71  E-value=0.00094  Score=60.15  Aligned_cols=90  Identities=9%  Similarity=0.089  Sum_probs=70.3

Q ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHHh-hCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHH----HHHHH-hcCCCH
Q 025357          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVK----EFCSV-ANGTTK  181 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~-~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~----eIa~~-~~~v~~  181 (254)
                      +.+.+|.+++..|+++..+...|..+..... ...+.-+..|..+||||||+|++..+.+++..    ..... ..++++
T Consensus       152 ~P~~fL~~~~~~l~~~~~l~~~A~~ll~~sl~~t~l~l~y~Ps~IAaAAI~lA~~~l~~~~p~~~~~~~W~~~~~~~vt~  231 (358)
T 2pk2_A          152 HPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTL  231 (358)
T ss_dssp             CTTHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCGGGTSCHHHHTTTTTTTHHHHTTCCCCCCSSSCCTTTTSCSSCCH
T ss_pred             CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhccCHHHHHHHHHHHHHHHhCCCCCCCccccchHHHHhccCCH
Confidence            3467889999999999999999999888776 45555678999999999999999988654432    12221 136899


Q ss_pred             HHHHHHHHHHHHHhch
Q 025357          182 KEIGRAKEFIVKHLEA  197 (254)
Q Consensus       182 ~~i~~~~k~l~~~l~~  197 (254)
                      .+|...++.|.+.+.-
T Consensus       232 ~~l~~i~~~il~~y~~  247 (358)
T 2pk2_A          232 ELLDELTHEFLQILEK  247 (358)
T ss_dssp             HHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            9999999999987753

>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens}

Probab=96.69  E-value=0.0049  Score=54.19  Aligned_cols=88  Identities=14%  Similarity=0.132  Sum_probs=64.0

Q ss_pred             HHHHHHHHhccCCCHH----HHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCC-C----HHHHHHHhcCCC
Q 025357          110 FKSISAMSDRLGLVTT----IKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPR-T----VKEFCSVANGTT  180 (254)
Q Consensus       110 ~~~I~~i~~~L~Lp~~----v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~-t----l~eIa~~~~~v~  180 (254)
                      +++|..+...++++..    +...|..+.....-...+-+.+|..+||||||+|.+..+... .    ..++..+ +|++
T Consensus       172 ~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~lsl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~w~~~w~~~L~~~-tg~~  250 (306)
T 3g33_B          172 HDFLAFILHRLSLPRDRQALVKKHAQTFLALCATDYTFAMYPPSMIATGSIGAAVQGLGACSMSGDELTELLAGI-TGTE  250 (306)
T ss_dssp             GGGHHHHHHTSSCCTTTHHHHHHHHHHHHHHHHHCGGGTTSCHHHHHHHHHHHHHHTCC---CCHHHHHHHHHHH-HTCC
T ss_pred             HHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhhhhhccCCHHHHHHHHHHHHHHHhcCCCCchhhHHHHHHHH-HCCC
Confidence            4578888888888743    445566666654443345578899999999999999777432 2    2566674 8999


Q ss_pred             HHHHHHHHHHHHHHhchh
Q 025357          181 KKEIGRAKEFIVKHLEAE  198 (254)
Q Consensus       181 ~~~i~~~~k~l~~~l~~~  198 (254)
                      ..+|..+++.|.+.+.-.
T Consensus       251 ~~~l~~c~~~I~~l~~~~  268 (306)
T 3g33_B          251 VDCLRACQEQIEAALRES  268 (306)
T ss_dssp             HHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999999999999887643

>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=96.68  E-value=0.00096  Score=47.38  Aligned_cols=32  Identities=25%  Similarity=0.447  Sum_probs=27.5

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      -.||.||+  +.++++..|.+.|..||.++....
T Consensus        28 y~Cp~CG~--~~v~r~atGiW~C~~Cg~~~agga   59 (83)
T 1vq8_Z           28 HACPNCGE--DRVDRQGTGIWQCSYCDYKFTGGS   59 (83)
T ss_dssp             EECSSSCC--EEEEEEETTEEEETTTCCEEECCS
T ss_pred             CcCCCCCC--cceeccCCCeEECCCCCCEecCCE
Confidence            46999997  578999999999999999986443

>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6

Probab=96.57  E-value=0.00068  Score=47.45  Aligned_cols=31  Identities=29%  Similarity=0.823  Sum_probs=28.4

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      +.+||.|+. ..+|+++.+-.+.|..||.||-
T Consensus        32 ~VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~   62 (81)
T 2xzm_6           32 DVKCAQCQN-IQMIFSNAQSTIICEKCSAILC   62 (81)
T ss_dssp             EEECSSSCC-EEEEETTCSSCEECSSSCCEEE
T ss_pred             EeECCCCCC-eeEEEecCccEEEccCCCCEEe
Confidence            357999998 7899999999999999999995

>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=96.38  E-value=0.00086  Score=46.98  Aligned_cols=31  Identities=29%  Similarity=0.698  Sum_probs=28.5

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      +.+||.|+. ..+|+++.+-.+.|..||.||-
T Consensus        34 ~VkCp~C~~-~q~VFSha~t~V~C~~Cg~~L~   64 (82)
T 3u5c_b           34 DVKCPGCLN-ITTVFSHAQTAVTCESCSTILC   64 (82)
T ss_dssp             EEECTTSCS-CEEEESBCSSCCCCSSSCCCCE
T ss_pred             EEECCCCCC-eeEEEecCCeEEEccccCCEEe
Confidence            367999998 7899999999999999999995

>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=96.19  E-value=0.016  Score=50.24  Aligned_cols=80  Identities=14%  Similarity=0.043  Sum_probs=57.8

Q ss_pred             HHHHHHHHHHhccCCCHH-----------HHHHHHHHHHHHh-hCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 025357          108 QAFKSISAMSDRLGLVTT-----------IKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSV  175 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~-----------v~e~A~~i~k~~~-~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~  175 (254)
                      ...++|.+++..+++++.           ....+..+..... +.. +-+.+|..+||||+|+|+.       ..++..+
T Consensus       150 tp~~fL~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~llelsl~d~~-~l~~~PS~iAaAai~la~~-------~~~l~~~  221 (283)
T 1w98_B          150 TIVSWLNVYMQVAYLNDLHEVLLPQYPQQIFIQIAELLDLCVLDVD-CLEFPYGILAASALYHFSS-------SELMQKV  221 (283)
T ss_dssp             CHHHHHHHHHHHHTCCSSCCSSSCCSCHHHHHHHHHHHHHHHHSGG-GGGSCHHHHHHHHHHHTSC-------HHHHHHH
T ss_pred             CHHHHHHHHHHHhccCchhhHHHHhhhHHHHHHHHHHHHHHHhhhh-hhcCCHHHHHHHHHHHHHC-------hHHHHHH
Confidence            356788888887776532           2233444555443 333 5678999999999999863       5678785


Q ss_pred             hcCCCHHHHHHHHHHHHHHhc
Q 025357          176 ANGTTKKEIGRAKEFIVKHLE  196 (254)
Q Consensus       176 ~~~v~~~~i~~~~k~l~~~l~  196 (254)
                       +|+++.+|..+++.|.....
T Consensus       222 -tg~~~~~i~~c~~~l~~~~~  241 (283)
T 1w98_B          222 -SGYQWCDIENCVKWMVPFAM  241 (283)
T ss_dssp             -SCCCHHHHHHHHHHHHHHHH
T ss_pred             -hCCCHHHHHHHHHHHHHHHH
Confidence             99999999999999977654

>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=96.11  E-value=0.0012  Score=46.68  Aligned_cols=30  Identities=33%  Similarity=0.654  Sum_probs=28.1

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      .+||.|+. ..+|+.+.+-.+.|..||.||-
T Consensus        37 VkCp~C~~-~~~VFShA~t~V~C~~CgtvL~   66 (86)
T 3iz6_X           37 VKCQGCFN-ITTVFSHSQTVVVCPGCQTVLC   66 (86)
T ss_dssp             EECTTTCC-EEEEETTCSSCCCCSSSCCCCS
T ss_pred             EECCCCCC-eeEEEecCCcEEEccCCCCEee
Confidence            67999998 7899999999999999999995

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=95.87  E-value=0.005  Score=39.34  Aligned_cols=28  Identities=21%  Similarity=0.614  Sum_probs=21.6

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      ..||.||+ ..+..+ .....+|..||++.
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            46999998 444444 46899999999874

>2qdj_A Retinoblastoma-associated protein; cyclin fold, cyclin wedge, antitumor protein; 2.00A {Homo sapiens}

Probab=95.78  E-value=0.041  Score=48.26  Aligned_cols=71  Identities=15%  Similarity=0.298  Sum_probs=53.1

Q ss_pred             HHHHHHhccCCCHHHHHHHHHHHHHHhhC-C---CCCCCCHHHHHHHHHHHHHHh-cCCCCCHHHHHHHhcCCCHHHH
Q 025357          112 SISAMSDRLGLVTTIKDRANEIYKKVEDQ-K---PLRGRNQEAIVAACLYIACRQ-ENKPRTVKEFCSVANGTTKKEI  184 (254)
Q Consensus       112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~-~---~~~Gr~~~~iaAAclY~AcR~-~~~p~tl~eIa~~~~~v~~~~i  184 (254)
                      ....+|..|+|++.+.++|-++|+.+... +   ...|. .+..-.||||+||.. ++..+||..|.+ +++++..++
T Consensus         5 rF~~lC~~Lnld~~~~~~Aw~~~~~~~~~~~~~~~~~~~-~~~~w~acLY~a~~~~~~n~vsLt~LLr-~~~lsi~~F   80 (304)
T 2qdj_A            5 DFTALCQKLKIPDHVRERAWLTWEKVSSVDGVLGGYIQK-KKELWGICIFIAAVDLDEMSFTFTELQK-NIEISVHKF   80 (304)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHC----------C-HHHHHHHHHHHHHHHHTCCCSCHHHHHH-HHTCCHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCCccc-hHHHHHHhHHHHhhccCCCcCcHHHHHH-HcCCCHHHH
Confidence            45678999999999999999999998774 2   23333 445555569999974 466799999999 488887765

>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=95.53  E-value=0.04  Score=49.20  Aligned_cols=72  Identities=14%  Similarity=0.259  Sum_probs=60.1

Q ss_pred             hhHHHHHHHHHHHHhccCCCH-HHHHHHHHHHHHHhh--CCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 025357          104 RNLIQAFKSISAMSDRLGLVT-TIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSV  175 (254)
Q Consensus       104 r~l~~a~~~I~~i~~~L~Lp~-~v~e~A~~i~k~~~~--~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~  175 (254)
                      |...-|..+|..+|++|+++. .+.+.+-.++..+..  ..++++|-.+.+.-.|+|..||..+..++++||-..
T Consensus       213 Kvy~La~~Rl~~LC~~L~~~~~~~~~~iWt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~tF~~Ii~~  287 (347)
T 2r7g_A          213 KVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTA  287 (347)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHhChHhhcCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence            345568889999999998875 567777777777654  457899999999999999999999999999999873

>4ell_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor, cell cycle; 1.98A {Homo sapiens}

Probab=95.30  E-value=0.049  Score=49.64  Aligned_cols=70  Identities=14%  Similarity=0.253  Sum_probs=58.4

Q ss_pred             hHHHHHHHHHHHHhccCCCH-HHHHHHHHHHHHHhh--CCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHH
Q 025357          105 NLIQAFKSISAMSDRLGLVT-TIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCS  174 (254)
Q Consensus       105 ~l~~a~~~I~~i~~~L~Lp~-~v~e~A~~i~k~~~~--~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~  174 (254)
                      ...-|..+|+.+|++|+++. .+.+..-.+|+....  ..++++|-.+.++-+|+|..|+..+..++++||..
T Consensus       278 vy~LAa~Rl~~LC~~L~~~~~~l~~~IWt~fe~~l~~~teLm~dRHLDQiiLCsiY~i~Kv~~~~~tFk~Ii~  350 (411)
T 4ell_A          278 VYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVT  350 (411)
T ss_dssp             HHHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHTTTCCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHhhhHhhccccHHHHHHHHHHHHHhhccCCCCHHHHHH
Confidence            33568899999999999875 566666666666544  45889999999999999999999999999999987

>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens}

Probab=94.85  E-value=0.086  Score=50.75  Aligned_cols=71  Identities=14%  Similarity=0.262  Sum_probs=59.9

Q ss_pred             hhHHHHHHHHHHHHhccCCCH-HHHHHHHHHHHHHhh--CCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHH
Q 025357          104 RNLIQAFKSISAMSDRLGLVT-TIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCS  174 (254)
Q Consensus       104 r~l~~a~~~I~~i~~~L~Lp~-~v~e~A~~i~k~~~~--~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~  174 (254)
                      |...-|..+|..+|++|+++. .+.+.+-.+++.+..  ..++++|-.+.++-.|+|..||..+..++.++|..
T Consensus       522 Kvy~LAa~Rl~~LC~~L~~~~~~i~~~IWt~fe~~l~~~t~L~~dRHLDQiilCsiY~icKv~~~~ltFk~Ii~  595 (656)
T 4elj_A          522 KVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVT  595 (656)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHHHHHCGGGSTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhccCCcCHHHHHH
Confidence            344568899999999998874 677777777777654  35889999999999999999999999999999977

>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}

Probab=94.79  E-value=0.026  Score=36.82  Aligned_cols=27  Identities=26%  Similarity=0.671  Sum_probs=22.3

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcC--cCceee
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICS--ECGLVL   33 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~--~CG~Vl   33 (254)
                      ...||.|++  .+..+.  |+++|.  +||...
T Consensus        10 iL~CP~c~~--~L~~~~--~~L~C~~~~c~~~Y   38 (56)
T 2kpi_A           10 ILACPACHA--PLEERD--AELICTGQDCGLAY   38 (56)
T ss_dssp             SCCCSSSCS--CEEEET--TEEEECSSSCCCEE
T ss_pred             heeCCCCCC--cceecC--CEEEcCCcCCCcEE
Confidence            457999997  476664  999999  999885

>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=94.75  E-value=0.18  Score=44.48  Aligned_cols=78  Identities=8%  Similarity=0.062  Sum_probs=54.1

Q ss_pred             cCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCC--HHHHHHH-hcCCCHHHHHHHHHHHHHHhc
Q 025357          120 LGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRT--VKEFCSV-ANGTTKKEIGRAKEFIVKHLE  196 (254)
Q Consensus       120 L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~t--l~eIa~~-~~~v~~~~i~~~~k~l~~~l~  196 (254)
                      ++.++.+...|..+...+......-+..|..+||||||+|++..+.+++  ..++-.. ..+.+...|..+.+.|...+.
T Consensus       181 ~~~~~~l~~~A~~~l~~sl~t~~~l~~~Ps~IAaAai~lA~~~~~~~~~~w~~~l~~~~~~~~~~~~l~~~~~~i~~l~~  260 (323)
T 1jkw_A          181 LENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKENRTCLSQLLDIMKSMRNLVK  260 (323)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTSTHHHHSCHHHHHHHHHHHHHHHHSCCCTTHHHHHTTSCSSSCCTHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhccHHHcCCHHHHHHHHHHHHHHHcCCChHHHHHHHhccccccccHHHHHHHHHHHHHHHH
Confidence            3455677888888888876655556789999999999999999887543  2222110 134567778777777766654


Q ss_pred             h
Q 025357          197 A  197 (254)
Q Consensus       197 ~  197 (254)
                      .
T Consensus       261 ~  261 (323)
T 1jkw_A          261 K  261 (323)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=94.67  E-value=0.078  Score=40.34  Aligned_cols=28  Identities=21%  Similarity=0.439  Sum_probs=21.0

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      +-.||.|++ ...-.|  ...+||.+||.--
T Consensus        27 lP~CP~C~s-eytYeD--g~l~vCPeC~hEW   54 (138)
T 2akl_A           27 LPPCPQCNS-EYTYED--GALLVCPECAHEW   54 (138)
T ss_dssp             SCCCTTTCC-CCCEEC--SSSEEETTTTEEE
T ss_pred             CCCCCCCCC-cceEec--CCeEECCcccccc
Confidence            367999998 444444  5679999999765

>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=94.49  E-value=0.017  Score=37.56  Aligned_cols=29  Identities=21%  Similarity=0.591  Sum_probs=21.8

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      +..||.||+ .. .+....+...|..||+..
T Consensus        18 ~~fCPkCG~-~~-~ma~~~dr~~C~kCgyt~   46 (55)
T 2k4x_A           18 HRFCPRCGP-GV-FLAEHADRYSCGRCGYTE   46 (55)
T ss_dssp             SCCCTTTTT-TC-CCEECSSEEECTTTCCCE
T ss_pred             cccCcCCCC-ce-eEeccCCEEECCCCCCEE
Confidence            467999998 33 333446799999999983

>2k5r_A Uncharacterized protein XF2673; solution structure, structural genomics, PSI-2, protein structure initiative; NMR {Xylella fastidiosa TEMECULA1}

Probab=94.04  E-value=0.029  Score=40.77  Aligned_cols=31  Identities=13%  Similarity=0.093  Sum_probs=24.5

Q ss_pred             CCCCCCCCCCCCCceEEecC---------------------------CCceEcCcCceee
Q 025357            1 MADSYCADCKRLTEVVFDHS---------------------------AGDTICSECGLVL   33 (254)
Q Consensus         1 ~~~~~Cp~Cg~~~~lv~D~~---------------------------~G~~vC~~CG~Vl   33 (254)
                      |+...||.|+.  .+..+..                           +|.+||..||...
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            34578999997  4666655                           7999999999985

>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens}

Probab=93.50  E-value=0.43  Score=45.93  Aligned_cols=71  Identities=14%  Similarity=0.193  Sum_probs=57.2

Q ss_pred             HHHHHHhccCCCHHHHHHHHHHHHHHhh-CCC----CCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHH
Q 025357          112 SISAMSDRLGLVTTIKDRANEIYKKVED-QKP----LRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (254)
Q Consensus       112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~-~~~----~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i  184 (254)
                      ....+|..|++++.+.++|-+.|+.... .+.    +.| ....+.|+++|.||+.+|..+||-.|.+ .++++..++
T Consensus         7 ~f~~lC~~Ln~d~~~~~~Aw~~~~~~~~~~~~l~~tleg-~~~~W~aC~ly~~~~~~gn~vsLt~lLr-~~~lsl~~F   82 (656)
T 4elj_A            7 DFTALCQKLKIPDHVRERAWLTWEKVSSVDGVLGGYIQK-KKELWGICIFIAAVDLDEMSFTFTELQK-NIEISVHKF   82 (656)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHCSCC-----C-CHHHHHHHHHHHHHHTTCCCSCHHHHHH-HHTCCHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHHHhccccccCCccc-chHHhhhhhheeeeeccCCeeeHHHHHH-HhcCCHHHH
Confidence            4678899999999999999999999984 222    233 4567777778888888999999999999 488887666

>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1

Probab=93.01  E-value=0.046  Score=32.29  Aligned_cols=29  Identities=21%  Similarity=0.582  Sum_probs=21.8

Q ss_pred             CCCCCCCC-CceEEecCCCceEcCcCceee
Q 025357            5 YCADCKRL-TEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         5 ~Cp~Cg~~-~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      .||.||++ +.++.+...=.+-|..||..-
T Consensus         2 lC~~C~~peT~l~~~~~~~~l~C~aCG~~~   31 (36)
T 1k81_A            2 ICRECGKPDTKIIKEGRVHLLKCMACGAIR   31 (36)
T ss_dssp             CCSSSCSCEEEEEEETTEEEEEEETTTEEE
T ss_pred             CCcCCCCCCcEEEEeCCcEEEEhhcCCCcc
Confidence            69999996 456666555667799999873

>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=91.62  E-value=0.1  Score=36.70  Aligned_cols=32  Identities=28%  Similarity=0.513  Sum_probs=26.0

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      -.||.||+ ..+ .-...|-+-|..||.++....
T Consensus        36 y~CpfCGk-~~v-kR~a~GIW~C~kCg~~~AGGA   67 (83)
T 3j21_i           36 HTCPVCGR-KAV-KRISTGIWQCQKCGATFAGGA   67 (83)
T ss_dssp             BCCSSSCS-SCE-EEEETTEEEETTTCCEEECCS
T ss_pred             cCCCCCCC-cee-EecCcCeEEcCCCCCEEeCCc
Confidence            57999998 554 556799999999999987554

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=91.20  E-value=0.17  Score=37.70  Aligned_cols=31  Identities=16%  Similarity=0.387  Sum_probs=22.1

Q ss_pred             CCCCCCCCCCCCceEEecCCC----ceEcCcCceeec
Q 025357            2 ADSYCADCKRLTEVVFDHSAG----DTICSECGLVLE   34 (254)
Q Consensus         2 ~~~~Cp~Cg~~~~lv~D~~~G----~~vC~~CG~Vl~   34 (254)
                      .+..||+||+  -+......|    ..+|..||++..
T Consensus         3 ~m~FCp~Cgn--~L~~~~~~~~~~~~~~C~~C~y~~~   37 (113)
T 3h0g_I            3 NFQYCIECNN--MLYPREDKVDRVLRLACRNCDYSEI   37 (113)
T ss_dssp             CCCCCSSSCC--CCEECCCTTTCCCCEECSSSCCEEC
T ss_pred             cceeCcCCCC--EeeEcccCCCCeeEEECCCCCCeEE
Confidence            3578999997  344443333    699999999863

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=91.12  E-value=0.23  Score=34.35  Aligned_cols=44  Identities=11%  Similarity=0.170  Sum_probs=38.8

Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357          154 ACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE  198 (254)
Q Consensus       154 AclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~  198 (254)
                      --|+-+.+..|.|....||++. +|++.++|.+++++|.+.-.+.
T Consensus        22 ekVLe~LkeaG~PlkageIae~-~GvdKKeVdKaik~LKkEgkI~   65 (80)
T 2lnb_A           22 QRILQVLTEAGSPVKLAQLVKE-CQAPKRELNQVLYRMKKELKVS   65 (80)
T ss_dssp             HHHHHHHHHHTSCEEHHHHHHH-HTSCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHH-HCCCHHHHHHHHHHHHHcCCcc
Confidence            3466788899999999999995 9999999999999999887765

>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=91.05  E-value=0.14  Score=43.42  Aligned_cols=28  Identities=25%  Similarity=0.432  Sum_probs=21.8

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V   32 (254)
                      ..||.||+.....++ ..|...|.+||.-
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            469999984456555 4688999999975

>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=91.03  E-value=0.11  Score=35.77  Aligned_cols=32  Identities=19%  Similarity=0.406  Sum_probs=25.3

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      -.||.||. ..+ .-...|-+.|..||.++....
T Consensus        28 y~C~fCgk-~~v-kR~a~GIW~C~~C~~~~AGGA   59 (73)
T 1ffk_W           28 YKCPVCGF-PKL-KRASTSIWVCGHCGYKIAGGA   59 (73)
T ss_pred             ccCCCCCC-cee-EEEEeEEEECCCCCcEEECCC
Confidence            56999998 454 445789999999999986554

>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=90.77  E-value=0.15  Score=37.22  Aligned_cols=31  Identities=19%  Similarity=0.364  Sum_probs=24.9

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeeccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~   36 (254)
                      -.||.||. .. +.-...|-+-|..||.++...
T Consensus        37 y~CpfCgk-~~-vKR~a~GIW~C~kCg~~~AGG   67 (103)
T 4a17_Y           37 YGCPFCGK-VA-VKRAAVGIWKCKPCKKIIAGG   67 (103)
T ss_dssp             EECTTTCC-EE-EEEEETTEEEETTTTEEEECC
T ss_pred             CCCCCCCC-ce-eeecCcceEEcCCCCCEEeCC
Confidence            46999998 55 455689999999999998633

>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=90.67  E-value=0.14  Score=38.25  Aligned_cols=32  Identities=25%  Similarity=0.444  Sum_probs=25.1

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      -.||.||. ..+ .-...|-+-|..||.++....
T Consensus        61 ytCPfCGk-~~v-KR~avGIW~C~~Cgk~fAGGA   92 (116)
T 3cc2_Z           61 HACPNCGE-DRV-DRQGTGIWQCSYCDYKFTGGS   92 (116)
T ss_dssp             EECSSSCC-EEE-EEEETTEEEETTTCCEEECCS
T ss_pred             CcCCCCCC-cee-EecCceeEECCCCCCEEECCC
Confidence            46999997 454 455789999999999986443

>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}

Probab=90.39  E-value=0.11  Score=35.48  Aligned_cols=32  Identities=25%  Similarity=0.371  Sum_probs=25.8

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      -.||.||. .. +.-...|-.-|..||.++....
T Consensus        27 y~C~fCgk-~~-vkR~a~GIW~C~~C~~~~AGGA   58 (72)
T 3jyw_9           27 YDCSFCGK-KT-VKRGAAGIWTCSCCKKTVAGGA   58 (72)
T ss_dssp             BCCSSCCS-SC-BSBCSSSCBCCSSSCCCCCCSS
T ss_pred             ccCCCCCC-ce-eEecCCCeEECCCCCCEEeCCc
Confidence            57999998 55 4557899999999999986544

>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=90.16  E-value=0.11  Score=36.87  Aligned_cols=31  Identities=23%  Similarity=0.485  Sum_probs=22.9

Q ss_pred             CCCCCCCCCc--eEEe--cCCCceEcCcCceeecc
Q 025357            5 YCADCKRLTE--VVFD--HSAGDTICSECGLVLEA   35 (254)
Q Consensus         5 ~Cp~Cg~~~~--lv~D--~~~G~~vC~~CG~Vl~e   35 (254)
                      .||.|+...+  +..|  ...|.+.|..||.-.+-
T Consensus        25 ~CPfCnh~~sV~vkidk~~~~g~l~C~~Cg~~~~~   59 (85)
T 1wii_A           25 TCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQT   59 (85)
T ss_dssp             CCTTTCCSSCEEEEEETTTTEEEEEESSSCCEEEE
T ss_pred             cCCCCCCCCeEEEEEEccCCEEEEEcccCCCeEEe
Confidence            5999998533  4454  35789999999987643

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1

Probab=89.81  E-value=0.3  Score=31.61  Aligned_cols=31  Identities=16%  Similarity=0.416  Sum_probs=21.2

Q ss_pred             CCCCCCCCCCceEEec------CCC---ceEcCcCceeecc
Q 025357            4 SYCADCKRLTEVVFDH------SAG---DTICSECGLVLEA   35 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~------~~G---~~vC~~CG~Vl~e   35 (254)
                      ..||.||. ..+++..      +++   ..+|.+||..-.+
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            56999998 5665442      123   4799999987543

>6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1

Probab=89.78  E-value=0.1  Score=32.58  Aligned_cols=16  Identities=19%  Similarity=0.436  Sum_probs=8.5

Q ss_pred             CCCCCCCCCCCceEEecCCC
Q 025357            3 DSYCADCKRLTEVVFDHSAG   22 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G   22 (254)
                      .-.|+.||-    |+|++.|
T Consensus         4 ~y~C~vCGy----vyd~~~G   19 (46)
T 6rxn_A            4 KYVCNVCGY----EYDPAEH   19 (46)
T ss_dssp             CEEETTTCC----EECGGGG
T ss_pred             EEECCCCCe----EEeCCcC
Confidence            345666663    4555555

>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=89.64  E-value=0.2  Score=37.79  Aligned_cols=32  Identities=25%  Similarity=0.456  Sum_probs=23.3

Q ss_pred             CCCCCCCCCCCCCceEE--e--cCCCceEcCcCceeec
Q 025357            1 MADSYCADCKRLTEVVF--D--HSAGDTICSECGLVLE   34 (254)
Q Consensus         1 ~~~~~Cp~Cg~~~~lv~--D--~~~G~~vC~~CG~Vl~   34 (254)
                      |++..||+||+  -|..  |  ...+.++|..||+...
T Consensus         2 ~~~~FCp~Cgn--lL~~~~~~~~~~~~~~C~~C~y~~~   37 (122)
T 1twf_I            2 TTFRFCRDCNN--MLYPREDKENNRLLFECRTCSYVEE   37 (122)
T ss_dssp             CCCCBCSSSCC--BCEEEEETTTTEEEEECSSSSCEEE
T ss_pred             CCCCcccccCc--cCcccccCcCCCCEEECCcCCCeee
Confidence            45688999997  3433  3  3456899999999864

>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=88.03  E-value=2.6  Score=35.52  Aligned_cols=86  Identities=13%  Similarity=0.099  Sum_probs=56.9

Q ss_pred             HHHHHHHHHHhccCCCHH----HHHHHHHHHHHHh-hCCCCCCCCHHHHHHHHHHHHHHhcCCCCC----HHHHHHHhcC
Q 025357          108 QAFKSISAMSDRLGLVTT----IKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRT----VKEFCSVANG  178 (254)
Q Consensus       108 ~a~~~I~~i~~~L~Lp~~----v~e~A~~i~k~~~-~~~~~~Gr~~~~iaAAclY~AcR~~~~p~t----l~eIa~~~~~  178 (254)
                      ..+.++..+...++++..    +...|..+...+. +.. +-.-+|..+||||+..+.  .+.+..    ...+... +|
T Consensus       148 Tp~~FL~~~l~~~~~~~~~~~~~~~~a~~~l~~~l~d~~-~l~~~PS~iAaaa~~~~l--~~~~~~~~~~~~~L~~~-t~  223 (252)
T 1f5q_B          148 LSTDLICYILHIMHAPREDYLNIYNLCRPKIFCALCDGR-SAMKRPVLITLACMHLTM--NQKYDYYENRIDGVCKS-LY  223 (252)
T ss_dssp             CHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCHH-HHTSCHHHHHHHHHHHHH--TTTCHHHHHHHHHHHHH-TT
T ss_pred             CHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHHHhchh-hhccCHHHHHHHHHHHHh--ccCCCchhhHHHHHHHH-HC
Confidence            357788888888888864    3344554444432 222 234678999999965443  443333    3456664 89


Q ss_pred             CCHHHHHHHHHHHHHHhch
Q 025357          179 TTKKEIGRAKEFIVKHLEA  197 (254)
Q Consensus       179 v~~~~i~~~~k~l~~~l~~  197 (254)
                      ++...|..+++.|.+.+..
T Consensus       224 ~~~~~l~~C~~~i~~~l~~  242 (252)
T 1f5q_B          224 ITKEELHQCCDLVDIAIVS  242 (252)
T ss_dssp             CCHHHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHHHH
Confidence            9999999999999988743

>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=87.85  E-value=0.21  Score=32.22  Aligned_cols=16  Identities=25%  Similarity=0.684  Sum_probs=7.5

Q ss_pred             CCCCCCCCCCCceEEecCCC
Q 025357            3 DSYCADCKRLTEVVFDHSAG   22 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G   22 (254)
                      .-.|+.||-    |+|++.|
T Consensus         3 ~y~C~vCGy----vYd~~~G   18 (54)
T 4rxn_A            3 KYTCTVCGY----IYDPEDG   18 (54)
T ss_dssp             CEEETTTCC----EECTTTC
T ss_pred             ceECCCCCe----EECCCcC
Confidence            334555553    3454444

>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=87.82  E-value=0.21  Score=34.01  Aligned_cols=27  Identities=26%  Similarity=0.757  Sum_probs=17.2

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCce-ee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGL-VL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~-Vl   33 (254)
                      -.|++||..  +.. .....+.|..||. ||
T Consensus        29 Y~C~~CG~~--~e~-~~~d~irCp~CG~RIL   56 (70)
T 1twf_L           29 YICAECSSK--LSL-SRTDAVRCKDCGHRIL   56 (70)
T ss_dssp             EECSSSCCE--ECC-CTTSTTCCSSSCCCCC
T ss_pred             EECCCCCCc--cee-CCCCCccCCCCCceEe
Confidence            468899872  111 2345567999998 65

>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=86.99  E-value=0.39  Score=32.74  Aligned_cols=27  Identities=26%  Similarity=0.596  Sum_probs=22.5

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      ..|| ||.  ..+.+...-..-|. ||.++.
T Consensus         5 v~C~-C~~--~~~~~~~~kT~~C~-CG~~~~   31 (71)
T 1gh9_A            5 FRCD-CGR--ALYSREGAKTRKCV-CGRTVN   31 (71)
T ss_dssp             EEET-TSC--CEEEETTCSEEEET-TTEEEE
T ss_pred             EECC-CCC--EEEEcCCCcEEECC-CCCeee
Confidence            4699 997  46778888899999 999985

>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=86.01  E-value=0.24  Score=31.71  Aligned_cols=11  Identities=27%  Similarity=0.945  Sum_probs=6.1

Q ss_pred             eEcCcCceeec
Q 025357           24 TICSECGLVLE   34 (254)
Q Consensus        24 ~vC~~CG~Vl~   34 (254)
                      .+|..||+|.+
T Consensus         4 y~C~~CGyvYd   14 (52)
T 1e8j_A            4 YVCTVCGYEYD   14 (52)
T ss_dssp             EECSSSCCCCC
T ss_pred             EEeCCCCeEEc
Confidence            45555555554

>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=85.51  E-value=2  Score=30.68  Aligned_cols=42  Identities=14%  Similarity=0.084  Sum_probs=34.1

Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHhc-CCCHHHHHHHHHHHHHHhchh
Q 025357          154 ACLYIACRQENKPRTVKEFCSVAN-GTTKKEIGRAKEFIVKHLEAE  198 (254)
Q Consensus       154 AclY~AcR~~~~p~tl~eIa~~~~-~v~~~~i~~~~k~l~~~l~~~  198 (254)
                      .+.|++-...  ..++.+|+.. + |.+..++..+++++.+.+.-+
T Consensus        36 iamyL~r~~t--~~Sl~~IG~~-fggrdHsTV~ha~~ki~~~~~~d   78 (94)
T 1j1v_A           36 MAMALAKELT--NHSLPEIGDA-FGGRDHTTVLHACRKIEQLREES   78 (94)
T ss_dssp             HHHHHHHHHS--CCCHHHHHHH-TTSCCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHH--CcCHHHHHHH-hCCCCHHHHHHHHHHHHHHHHhC
Confidence            4677765554  5889999995 7 899999999999999988643

>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=85.07  E-value=18  Score=31.23  Aligned_cols=105  Identities=9%  Similarity=0.052  Sum_probs=78.6

Q ss_pred             HHHHHHHHHhccCCCHHHHHHHHHHHHHHhhC--CC-CCCCCHHHHHHHHHHHHHH-hcCCCCCHHHHHHHhcCCCHHHH
Q 025357          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQ--KP-LRGRNQEAIVAACLYIACR-QENKPRTVKEFCSVANGTTKKEI  184 (254)
Q Consensus       109 a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~--~~-~~Gr~~~~iaAAclY~AcR-~~~~p~tl~eIa~~~~~v~~~~i  184 (254)
                      ..++|.++...-.++..+.-.|..+..++...  ++ +...+..-+..+++-+|.+ ......+-+..|.+ .|++..+|
T Consensus        77 I~~Yl~RI~k~t~ls~~~ll~ALvYLdRL~~~~p~~~l~~~nvHRLlLtALmlAsK~ldD~~ysN~~wAkV-gGisl~EL  155 (293)
T 2pmi_B           77 IFNYFIRLTKFSSLEHCVLMTSLYYIDLLQTVYPDFTLNSLTAHRFLLTATTVATKGLCDSFSTNAHYAKV-GGVRCHEL  155 (293)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHCTTCCCSTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHH-HTSCHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhCCCCccCCchHHHHHHHHHHHHHHhccccccChhHhhhc-cCcCHHHH
Confidence            45688888888899998888888777777652  22 2345666777777888887 44567888999996 89999999


Q ss_pred             HHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhc
Q 025357          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI  221 (254)
Q Consensus       185 ~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L  221 (254)
                      .+.-+++...++.+      + .+++++|..-+...+
T Consensus       156 N~LE~eFL~lLdf~------L-~V~~ee~~~cy~E~~  185 (293)
T 2pmi_B          156 NILENDFLKRVNYR------I-IPRDHNITLCSIEQK  185 (293)
T ss_dssp             HHHHHHHHHTTTTC------C-SCCTTHHHHHHHHSC
T ss_pred             HHHHHHHHHHcCCc------e-eeCHHHHHHHHHHHh
Confidence            99999999988876      3 245667765555443

>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=84.21  E-value=0.54  Score=27.48  Aligned_cols=26  Identities=27%  Similarity=0.686  Sum_probs=15.8

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V   32 (254)
                      -+|+.||. --.+.....|+++|  ||.=
T Consensus         7 Y~C~~CGn-ivev~~~g~~~l~C--CG~~   32 (36)
T 1dxg_A            7 YKCELCGQ-VVKVLEEGGGTLVC--CGED   32 (36)
T ss_dssp             EECTTTCC-EEEEEECCSSCEEE--TTEE
T ss_pred             EEcCCCCc-EEEEEeCCCcCEEe--CCcc
Confidence            46888875 22233456778887  6643

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=83.63  E-value=0.49  Score=36.31  Aligned_cols=29  Identities=21%  Similarity=0.391  Sum_probs=19.9

Q ss_pred             CCCCCCCCCCCceEEecC----CCceEcCcCceee
Q 025357            3 DSYCADCKRLTEVVFDHS----AGDTICSECGLVL   33 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~----~G~~vC~~CG~Vl   33 (254)
                      +..||+||+  -+.....    ...++|..||++.
T Consensus        24 ~~FCPeCgN--mL~pked~~~~~l~~~CrtCgY~~   56 (133)
T 3qt1_I           24 FRFCRDCNN--MLYPREDKENNRLLFECRTCSYVE   56 (133)
T ss_dssp             CCBCTTTCC--BCBCCBCTTTCCBCCBCSSSCCBC
T ss_pred             CeeCCCCCC--EeeECccCCCceeEEECCCCCCcE
Confidence            467999997  3333321    2369999999975

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=83.59  E-value=1.6  Score=29.98  Aligned_cols=33  Identities=12%  Similarity=0.082  Sum_probs=28.6

Q ss_pred             CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhch
Q 025357          164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEA  197 (254)
Q Consensus       164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~  197 (254)
                      |.|.|++||++ .+|++..++++-++.|.+.=-+
T Consensus        22 g~~psv~EIa~-~lgvS~~TVrr~L~~Le~kG~I   54 (77)
T 2jt1_A           22 GAPVKTRDIAD-AAGLSIYQVRLYLEQLHDVGVL   54 (77)
T ss_dssp             TSCEEHHHHHH-HHTCCHHHHHHHHHHHHHTTSE
T ss_pred             CCCcCHHHHHH-HHCCCHHHHHHHHHHHHHCCcE
Confidence            78999999999 5999999999999998876433

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=83.48  E-value=1.9  Score=33.87  Aligned_cols=46  Identities=9%  Similarity=0.077  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357          148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (254)
Q Consensus       148 ~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~  194 (254)
                      .+.-.-+.+|+|.+..+.|.+.++||+ ..+++...+++.+..|.+.
T Consensus        26 ~~yAlr~L~~LA~~~~~~~~s~~eIA~-~~~i~~~~l~kil~~L~~a   71 (159)
T 3lwf_A           26 GRYGLTITLELAKRIGDGPISLRSIAQ-DKNLSEHYLEQLIGPLRNA   71 (159)
T ss_dssp             HHHHHHHHHHHHHTTTSCCBCHHHHHH-HHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhcCCCCCcCHHHHHH-HHCcCHHHHHHHHHHHHHC
Confidence            345556667888765567999999999 4999999999999999874

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=83.37  E-value=1.2  Score=28.10  Aligned_cols=30  Identities=23%  Similarity=0.433  Sum_probs=18.8

Q ss_pred             CCCCCCCCCCCceEEe--------cCCCceEcCcCcee
Q 025357            3 DSYCADCKRLTEVVFD--------HSAGDTICSECGLV   32 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D--------~~~G~~vC~~CG~V   32 (254)
                      ...||.||....+.+.        +-+=..+|.+||..
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            3579999984333333        12223689999964

>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=82.80  E-value=0.49  Score=30.08  Aligned_cols=23  Identities=30%  Similarity=0.732  Sum_probs=19.3

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V   32 (254)
                      ..||.||+ .     ...|-+-|..||..
T Consensus        15 ~iCpkC~a-~-----~~~gaw~CrKCG~~   37 (51)
T 3j21_g           15 YVCLRCGA-T-----NPWGAKKCRKCGYK   37 (51)
T ss_dssp             EECTTTCC-E-----ECTTCSSCSSSSSC
T ss_pred             ccCCCCCC-c-----CCCCceecCCCCCc
Confidence            46999998 2     45899999999988

>3pvv_A Chromosomal replication initiator protein DNAA; helix-turn-helix motif, interacting with DNAA-BOX, DNAA-box; HET: DNA; 2.00A {Mycobacterium tuberculosis} PDB: 3pvp_A*

Probab=81.60  E-value=3.3  Score=29.95  Aligned_cols=42  Identities=10%  Similarity=0.181  Sum_probs=34.4

Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357          154 ACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE  198 (254)
Q Consensus       154 AclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~  198 (254)
                      .+.|++-...  ..++.+|+.. +|-+..++..+++++.+.+..+
T Consensus        40 iAmYL~r~~t--~~Sl~~IG~~-fgRDHsTV~ha~~ki~~~~~~d   81 (101)
T 3pvv_A           40 IAMYLCRELT--DLSLPKIGQA-FGRDHTTVMYAQRKILSEMAER   81 (101)
T ss_dssp             HHHHHHHHHC--CCCHHHHHHH-TTCCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHh--CCCHHHHHHH-HCCCHHHHHHHHHHHHHHHHhC
Confidence            4677765554  5889999995 8899999999999999988654

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=80.96  E-value=2.9  Score=30.97  Aligned_cols=42  Identities=10%  Similarity=0.186  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357          152 VAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (254)
Q Consensus       152 aAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~  194 (254)
                      ..+..|++-+..+.|.+..|||+. .+++...+.+.++.|.+.
T Consensus        12 l~iL~~la~~~~~~~~s~~ela~~-~~i~~~~v~~il~~L~~~   53 (129)
T 2y75_A           12 LTIMIELAKKHGEGPTSLKSIAQT-NNLSEHYLEQLVSPLRNA   53 (129)
T ss_dssp             HHHHHHHHHTTTSCCBCHHHHHHH-TTSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCCCCcCCHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence            334455554444678999999994 999999999999999874

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=80.94  E-value=1.7  Score=33.29  Aligned_cols=44  Identities=7%  Similarity=0.002  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357          150 AIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (254)
Q Consensus       150 ~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~  194 (254)
                      .-.-+.+|+|....+.|.+.+|||+ ..+++...+.+.+..|.+.
T Consensus        12 yAl~~L~~La~~~~~~~~s~~~IA~-~~~i~~~~l~kil~~L~~a   55 (143)
T 3t8r_A           12 YGLTLMISLAKKEGQGCISLKSIAE-ENNLSDLYLEQLVGPLRNA   55 (143)
T ss_dssp             HHHHHHHHHHTTTTSCCEEHHHHHH-HTTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCCCCcCHHHHHH-HHCcCHHHHHHHHHHHHHC
Confidence            3444667777655556899999999 4999999999999999874

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=80.73  E-value=2.5  Score=27.89  Aligned_cols=33  Identities=12%  Similarity=0.163  Sum_probs=28.3

Q ss_pred             HhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357          161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (254)
Q Consensus       161 R~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~  194 (254)
                      ..++.|++..|||+. ++++..++.+.++.|.+.
T Consensus        20 ~~~~~~~s~~eLA~~-lglsr~tv~~~l~~L~~~   52 (67)
T 2heo_A           20 SDDGGPVAIFQLVKK-CQVPKKTLNQVLYRLKKE   52 (67)
T ss_dssp             HHHCSCEEHHHHHHH-HCSCHHHHHHHHHHHHHT
T ss_pred             HHcCCCcCHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence            345678999999994 999999999999998764

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=80.22  E-value=5.4  Score=26.42  Aligned_cols=32  Identities=6%  Similarity=0.063  Sum_probs=28.6

Q ss_pred             CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357          166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE  198 (254)
Q Consensus       166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~  198 (254)
                      ..+.+|||+. .+++..++......+.+.|+..
T Consensus        31 g~s~~eIA~~-l~is~~tV~~~~~r~~~kl~~~   62 (79)
T 1x3u_A           31 GLPNKSIAYD-LDISPRTVEVHRANVMAKMKAK   62 (79)
T ss_dssp             TCCHHHHHHH-TTSCHHHHHHHHHHHHHHTTCC
T ss_pred             CCCHHHHHHH-HCcCHHHHHHHHHHHHHHHcCC
Confidence            4689999995 9999999999999999999865

---

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	254
d1aisb1	98	a.74.1.2 (B:1108-1205) Transcription factor IIB (T	7e-26
d1vola1	95	a.74.1.2 (A:113-207) Transcription factor IIB (TFI	7e-24
d1vola2	109	a.74.1.2 (A:208-316) Transcription factor IIB (TFI	2e-21
d1aisb2	95	a.74.1.2 (B:1206-1300) Transcription factor IIB (T	6e-20
d1dl6a_	58	g.41.3.1 (A:) Transcription initiation factor TFII	7e-13
d1pfta_	50	g.41.3.1 (A:) Transcription initiation factor TFII	2e-11
d1jkwa1	151	a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo s	0.001
d2ivxa1	143	a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens)	0.001
d2cchb1	128	a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [T	0.001
d1g3nc1	132	a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma	0.002
d2i53a1	144	a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens)	0.002
d1w98b2	140	a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human	0.003

>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 = 95.3 bits (237), Expect = 7e-26
 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

>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 = 90.0 bits (223), Expect = 7e-24
 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

>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 = 83.7 bits (207), Expect = 2e-21
 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

>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 = 79.5 bits (196), Expect = 6e-20
 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

>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 = 7e-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

>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 = 55.5 bits (134), 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

>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 = 36.5 bits (84), Expect = 0.001
 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 = 36.2 bits (83), 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

>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 = 35.7 bits (82), Expect = 0.001
 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

>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 = 35.3 bits (81), Expect = 0.002
 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

>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 = 35.3 bits (81), 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

>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 = 34.6 bits (79), Expect = 0.003
 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

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	254
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	99.9
d1vola1	95	Transcription factor IIB (TFIIB), core domain {Hum	99.89
d1aisb2	95	Transcription factor IIB (TFIIB), core domain {Arc	99.86
d1vola2	109	Transcription factor IIB (TFIIB), core domain {Hum	99.85
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	99.78
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	99.77
d2i53a1	144	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	98.49
d2ivxa1	143	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	98.34
d1jkwa1	151	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	98.23
d2cchb1	128	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	97.61
d1bu2a1	127	Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}	97.54
d1g3nc1	132	Viral cyclin {Kaposi's sarcoma-associated herpesvi	97.52
d1f5qb1	141	Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]	97.46
d1w98b2	140	G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax	97.37
d2ivxa2	113	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	96.74
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	96.7
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	96.63
d2pk7a1	59	Uncharacterized protein PFL1779 {Pseudomonas fluor	96.37
d2r7ga2	142	Retinoblastoma tumor suppressor domains {Human (Ho	96.25
d2hf1a1	59	Hypothetical protein CV3345 {Chromobacterium viola	96.19
d2i53a2	110	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	95.51
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	95.46
d1vd4a_	62	Transcription initiation factor TFIIE-alpha {Human	94.98
d1aisb2	95	Transcription factor IIB (TFIIB), core domain {Arc	94.59
d1vola2	109	Transcription factor IIB (TFIIB), core domain {Hum	94.29
d1neea2	37	Zinc-binding domain of translation initiation fact	93.96
d1k81a_	36	Zinc-binding domain of translation initiation fact	93.8
d2cchb2	124	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	93.12
d1nuia2	54	Zinc-binding domain of primase-helicase {Bacteriop	93.0
d1vqoz1	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	91.22
d1jj2y_	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	90.87
d1jkwa2	126	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	90.64
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	90.28
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	89.51
d1u5ka2	157	Recombinational repair protein RecO, C-terminal do	88.95
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	87.82
d1rqga3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro	87.76
d1y0ja1	39	Erythroid transcription factor GATA-1 {Mouse (Mus	87.45
d1pfva3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Esch	86.14
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	84.01
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	83.84
d1wiia_	85	Hypothetical UPF0222 protein MGC4549 {Mouse (Mus m	83.73
d2vuti1	42	Erythroid transcription factor GATA-1 {Emericella	83.6
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	83.54
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	82.86
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	82.83
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	82.28
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	82.01
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	80.43
d2j0151	59	Ribosomal protein L32p {Thermus thermophilus [TaxI	80.3

>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=99.90  E-value=1.2e-23  Score=155.61  Aligned_cols=93  Identities=33%  Similarity=0.629  Sum_probs=90.1

Q ss_pred             hHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHH
Q 025357          105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (254)
Q Consensus       105 ~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i  184 (254)
                      +|..|++.|+++|+.|+||+.+.++|..||+++.+.++++|+++.+++|||||+|||+++.|+|++||+++ +++++++|
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 NLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADI-ARVDKKEI   79 (98)
T ss_dssp             CHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTTTTTTCCHHHHHHHHHHHHHHHHTCCCCHHHHHHH-TTSCHHHH
T ss_pred             CHHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHH-HCCCHHHH
Confidence            47889999999999999999999999999999999999999999999999999999999999999999995 99999999


Q ss_pred             HHHHHHHHHHhchh
Q 025357          185 GRAKEFIVKHLEAE  198 (254)
Q Consensus       185 ~~~~k~l~~~l~~~  198 (254)
                      +++|+.|.+.|+++
T Consensus        80 ~k~yk~i~~~L~l~   93 (98)
T d1aisb1          80 GRSYRFIARNLNLT   93 (98)
T ss_dssp             HHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHcCCC
Confidence            99999999999986

>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=99.89  E-value=1.8e-23  Score=153.64  Aligned_cols=92  Identities=48%  Similarity=0.852  Sum_probs=89.1

Q ss_pred             HHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHH
Q 025357          106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIG  185 (254)
Q Consensus       106 l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~  185 (254)
                      |.+++..|+++|++|+||+.++++|..+|+++.+.++.+||++.+++|||||+|||+++.|+|++||++ ++++++++|+
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 MMNAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICA-VSRISKKEIG   80 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTCCCTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHT-TTCSCHHHHH
T ss_pred             hHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCChHHHHHHHHHHHHHHcCCCCCHHHHHH-HhCCCHHHHH
Confidence            568999999999999999999999999999999999999999999999999999999999999999999 4999999999


Q ss_pred             HHHHHHHHHhchh
Q 025357          186 RAKEFIVKHLEAE  198 (254)
Q Consensus       186 ~~~k~l~~~l~~~  198 (254)
                      ++|+.|.+.|+++
T Consensus        81 k~~k~i~~~L~~~   93 (95)
T d1vola1          81 RCFKLILKALETS   93 (95)
T ss_dssp             HHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHCCc
Confidence            9999999999876

>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=99.86  E-value=1e-21  Score=144.18  Aligned_cols=87  Identities=28%  Similarity=0.406  Sum_probs=84.8

Q ss_pred             HHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHH
Q 025357          111 KSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEF  190 (254)
Q Consensus       111 ~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~  190 (254)
                      ++|+++|++|+||+.+.++|.++|+++.+.++++||++.++||||||+|||++|.|+|++||+++ +|+++.+|+++|++
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 DYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEV-ARVTEVTVRNRYKE   83 (95)
T ss_dssp             GGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHH-HTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCcHHhHHHHHHHHHHHHcCCCcCHHHHHHH-HCCCHHHHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999999999999995 99999999999999


Q ss_pred             HHHHhchh
Q 025357          191 IVKHLEAE  198 (254)
Q Consensus       191 l~~~l~~~  198 (254)
                      |.+.|++.
T Consensus        84 l~~~l~~~   91 (95)
T d1aisb2          84 LVEKLKIK   91 (95)
T ss_dssp             HHHHHTCC
T ss_pred             HHHHhCCC
Confidence            99999987

>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=99.85  E-value=4.7e-22  Score=149.65  Aligned_cols=88  Identities=22%  Similarity=0.285  Sum_probs=84.2

Q ss_pred             HHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHH
Q 025357          110 FKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKE  189 (254)
Q Consensus       110 ~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k  189 (254)
                      .++|.++|++|+||+.+.+.|.++|+++.+.++.+||++.++||||||+|||++|.|+|++||+++ +||++.+|+++|+
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 GDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDI-AGVADVTIRQSYR   83 (109)
T ss_dssp             GGTHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHHHHHHHTSSSCCCHHHHHHH-HTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHH-HCCCHHHHHHHHH
Confidence            468999999999999999999999999999999999999999999999999999999999999995 8999999999999


Q ss_pred             HHHHHhchh
Q 025357          190 FIVKHLEAE  198 (254)
Q Consensus       190 ~l~~~l~~~  198 (254)
                      +|.++++.-
T Consensus        84 ~l~~~~~~l   92 (109)
T d1vola2          84 LIYPRAPDL   92 (109)
T ss_dssp             HHGGGHHHH
T ss_pred             HHHHHHHHh
Confidence            999988754

>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=99.78  E-value=3.5e-20  Score=122.52  Aligned_cols=49  Identities=41%  Similarity=0.767  Sum_probs=45.4

Q ss_pred             CCCCCCCCCCCCCceEEecCCCceEcCcCceeecccccccCcccccccCC
Q 025357            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE   50 (254)
Q Consensus         1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~   50 (254)
                      |+..+||+||+ .++++|+.+|++||.+||+|++|++||.|||||+|+++
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            45588999999 78999999999999999999999999999999999854

>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=99.77  E-value=1.1e-19  Score=116.74  Aligned_cols=44  Identities=34%  Similarity=0.940  Sum_probs=42.3

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccccccCccccccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFA   48 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~   48 (254)
                      ..||+||+ +++++|+.+|++||++||+|++|++||.|||||+|+
T Consensus         6 ~~Cp~Cgs-~~iv~D~~~Ge~vC~~CG~Viee~~iD~gpEWR~f~   49 (50)
T d1pfta_           6 KVCPACES-AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAFD   49 (50)
T ss_dssp             CSCTTTSC-CCEEEETTTTEEEESSSCCBCCCCCCCCCSSSSCCC
T ss_pred             ccCcCCCC-CcEEEECCCCeEecccCCcEeccccccCCCcccccC
Confidence            67999998 789999999999999999999999999999999996

>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=98.49  E-value=5.1e-07  Score=69.22  Aligned_cols=69  Identities=17%  Similarity=0.250  Sum_probs=64.6

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSV  175 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~  175 (254)
                      ..+.++|.+++.+|+||..+.-+|..+|.+......+...++..+++||+|+||+.+..|+.+++|..+
T Consensus        38 ~~~~~~i~~~~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~~lva~acl~LA~K~eE~~~~l~~vi~~  106 (144)
T d2i53a1          38 REGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKT  106 (144)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhhCcccchhHHHHHHHHHHHHHHhhcccccHHHHHHH
Confidence            477899999999999999999999999999999888888899999999999999999999999999764

>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=98.34  E-value=1.4e-06  Score=66.46  Aligned_cols=69  Identities=20%  Similarity=0.268  Sum_probs=64.5

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSV  175 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~  175 (254)
                      ..+.++|.+++..|+||..+.-+|..+|.+......+...++..+++||+|+||+.+..|+.+++|..+
T Consensus        32 ~~~~~~i~~~~~~l~l~~~t~~~A~~l~~Rf~~~~s~~~~~~~~va~acl~LA~K~eE~~~~~~~ii~~  100 (143)
T d2ivxa1          32 QQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKV  100 (143)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHhccccccHHHHHHH
Confidence            477899999999999999999999999999998888888899999999999999999999999999774

>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=98.23  E-value=5.7e-06  Score=63.66  Aligned_cols=91  Identities=11%  Similarity=0.196  Sum_probs=71.9

Q ss_pred             HHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCC----
Q 025357          107 IQAFKSISAMSDRL--GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT----  180 (254)
Q Consensus       107 ~~a~~~I~~i~~~L--~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~----  180 (254)
                      ......|.++|..|  +||..+.-+|..+|++....+.+.-..+..+++||+|+||+.+..|+.++++... ....    
T Consensus        48 ~~~~~~l~~~~~~~k~~l~~~~~~tA~~~~~RF~~~~s~~~~~~~li~~acl~LA~K~ee~~~~~~~~~~~-~~~~~~~~  126 (151)
T d1jkwa1          48 KYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGN-LRESPLGQ  126 (151)
T ss_dssp             HHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHGGG-SSSCHHHH
T ss_pred             HHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHhhcCccccccHHHHHHHHHHHHHHHcccCCCHHHHHHH-HHhhcccc
Confidence            35678899999966  5999999999999999999888888899999999999999999999999999764 3222    


Q ss_pred             ---HHHHHHHHHHHHHHhchh
Q 025357          181 ---KKEIGRAKEFIVKHLEAE  198 (254)
Q Consensus       181 ---~~~i~~~~k~l~~~l~~~  198 (254)
                         ..+|...=..+.+.|+.+
T Consensus       127 ~~~~~~i~~~E~~iL~~L~f~  147 (151)
T d1jkwa1         127 EKALEQILEYELLLIQQLNFH  147 (151)
T ss_dssp             HHHHHHHHHHHHHHHHHTTTC
T ss_pred             cccHHHHHHHHHHHHHHcCCe
Confidence               344444444555555543

>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=97.61  E-value=0.00035  Score=51.74  Aligned_cols=92  Identities=16%  Similarity=0.209  Sum_probs=78.7

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHh-cCCCHHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVA-NGTTKKEI  184 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~-~~v~~~~i  184 (254)
                      ....++|-+++..++++..+.-.|..++.+......+.......++++|+|+|++.+.. |.+++++.... ...+..+|
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            45789999999999999999999999999998776666667889999999999997764 78999998752 23579999


Q ss_pred             HHHHHHHHHHhchh
Q 025357          185 GRAKEFIVKHLEAE  198 (254)
Q Consensus       185 ~~~~k~l~~~l~~~  198 (254)
                      .+.-..|.+.|+.+
T Consensus       112 ~~mE~~IL~~L~~~  125 (128)
T d2cchb1         112 LRMEHLVLKVLTFD  125 (128)
T ss_dssp             HHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHCCCe
Confidence            99999999998865

>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=97.54  E-value=0.00071  Score=50.07  Aligned_cols=92  Identities=16%  Similarity=0.190  Sum_probs=79.4

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHh-cCCCHHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVA-NGTTKKEI  184 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~-~~v~~~~i  184 (254)
                      ....++|-.++..++++..+.-.|..++.+......+.......+++||+++|++.+.. |.++.++.... ...+..+|
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            45689999999999999999999999999998877777778899999999999998864 78999998852 23579999


Q ss_pred             HHHHHHHHHHhchh
Q 025357          185 GRAKEFIVKHLEAE  198 (254)
Q Consensus       185 ~~~~k~l~~~l~~~  198 (254)
                      .+.-..|.+.|+.+
T Consensus       112 ~~mE~~IL~~L~~d  125 (127)
T d1bu2a1         112 INQEKDILEALKWD  125 (127)
T ss_dssp             HHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHcCCC
Confidence            99999999888764

>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=97.52  E-value=0.00055  Score=51.01  Aligned_cols=92  Identities=13%  Similarity=0.195  Sum_probs=77.7

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcC-CCCCHHHHHHHh-cCCCHHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVA-NGTTKKEI  184 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~-~p~tl~eIa~~~-~~v~~~~i  184 (254)
                      ....+++-+++..++++..+.-.|..++.+.....-+.-.....++++|+++|++.+. .|.++.++..+. ...+..+|
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            4568899999999999999999999999999887666555677999999999999764 588999998752 25678999


Q ss_pred             HHHHHHHHHHhchh
Q 025357          185 GRAKEFIVKHLEAE  198 (254)
Q Consensus       185 ~~~~k~l~~~l~~~  198 (254)
                      .+.-..|.+.|+.+
T Consensus       117 ~~mE~~IL~~L~w~  130 (132)
T d1g3nc1         117 IDQEKELLEKLAWR  130 (132)
T ss_dssp             HHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHcCCc
Confidence            99999998888764

>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=97.46  E-value=0.00065  Score=51.20  Aligned_cols=91  Identities=12%  Similarity=0.049  Sum_probs=78.0

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcC-CCCCHHHHHHHh-cCCCHHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVA-NGTTKKEI  184 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~-~p~tl~eIa~~~-~~v~~~~i  184 (254)
                      ....++|-+++..++|+..+.-.|..++.+......+.......++++|+++|++.+. .|.++.++.... ...+..+|
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            4678999999999999999999999999999887777777889999999999999875 588999998863 23578999


Q ss_pred             HHHHHHHHHHhch
Q 025357          185 GRAKEFIVKHLEA  197 (254)
Q Consensus       185 ~~~~k~l~~~l~~  197 (254)
                      .+.-..|...|+-
T Consensus       125 ~~mE~~IL~~L~w  137 (141)
T d1f5qb1         125 LTLEVKSLDTLSW  137 (141)
T ss_dssp             HHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHCCc
Confidence            9988888888764

>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=97.37  E-value=0.0018  Score=48.55  Aligned_cols=92  Identities=17%  Similarity=0.186  Sum_probs=76.0

Q ss_pred             HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhh-CCCCCCCCHHHHHHHHHHHHHHhc-CCCCCHHHHHHHh-cCCCHHH
Q 025357          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVED-QKPLRGRNQEAIVAACLYIACRQE-NKPRTVKEFCSVA-NGTTKKE  183 (254)
Q Consensus       107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~-~~~~~Gr~~~~iaAAclY~AcR~~-~~p~tl~eIa~~~-~~v~~~~  183 (254)
                      ....++|-+++..++|+..+.-.|..++.+... ...........++++|+++|++.+ ..|.++.++.... ...+..+
T Consensus        44 ~~lidW~~~v~~~~~l~~et~~lAv~llDryl~~~~~v~~~~lqL~a~acL~IAsK~ee~~~~~~~~l~~~~~~~~t~~e  123 (140)
T d1w98b2          44 AILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDE  123 (140)
T ss_dssp             HHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHHHCCCCCGGGHHHHHHHHHHHHHHHHCSSCCCHHHHHHTTTTSSCHHH
T ss_pred             HHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhccccccHHHHhHHHHHHHHHHHHHcccCCCCHHHHHHHHcCCCCHHH
Confidence            457899999999999999999999999998765 444444567799999999999986 5689999998752 2457899


Q ss_pred             HHHHHHHHHHHhchh
Q 025357          184 IGRAKEFIVKHLEAE  198 (254)
Q Consensus       184 i~~~~k~l~~~l~~~  198 (254)
                      |.+.-..|.+.|+.+
T Consensus       124 i~~mE~~IL~~L~~~  138 (140)
T d1w98b2         124 ILTMELMIMKALKWR  138 (140)
T ss_dssp             HHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHCCCc
Confidence            999999998888765

>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=96.74  E-value=0.0044  Score=44.75  Aligned_cols=88  Identities=10%  Similarity=0.111  Sum_probs=65.3

Q ss_pred             HHHHHHHHHhccCCCHHHHHHHHHHHHHHhh-CCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHH----HHHH-hcCCCHH
Q 025357          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVED-QKPLRGRNQEAIVAACLYIACRQENKPRTVKE----FCSV-ANGTTKK  182 (254)
Q Consensus       109 a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~-~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~e----Ia~~-~~~v~~~  182 (254)
                      ..++|-.++..|+.+.++...|-.+...... -.+.---.|..+|+||||+|+|..|.+.....    --++ ..+++..
T Consensus         3 Phk~ll~~~k~l~~~~~l~q~AW~~lnDs~r~T~lcL~~~P~~IA~a~I~LA~~~~~~~~p~~~~~~~Ww~~fd~~vt~e   82 (113)
T d2ivxa2           3 PHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLE   82 (113)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCGGGTSCHHHHHHHHHHHHHHHHTCCCCCCTTCCCGGGGTCSSCCHH
T ss_pred             CcHHHHHHHHHhCCChHHHHHHHHHHHHHhccCCeeeecCcHHHHHHHHHHHHHHhCCCCCCCCCCCcHHHHHccCCCHH
Confidence            3567778888899999999999988888664 34323467999999999999999987664321    1121 1368888


Q ss_pred             HHHHHHHHHHHHhc
Q 025357          183 EIGRAKEFIVKHLE  196 (254)
Q Consensus       183 ~i~~~~k~l~~~l~  196 (254)
                      .|......|.....
T Consensus        83 ~i~~i~~~il~lYe   96 (113)
T d2ivxa2          83 LLDELTHEFLQILE   96 (113)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99988888877664

>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=96.70  E-value=0.00042  Score=43.97  Aligned_cols=30  Identities=33%  Similarity=0.797  Sum_probs=28.1

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      .+||.|+. ..+++.+.+-.+.|..||.+|.
T Consensus         8 VkC~~C~n-~~ivFsha~t~V~C~~Cg~~L~   37 (58)
T d1qxfa_           8 VKCPDCEH-EQVIFDHPSTIVKCIICGRTVA   37 (58)
T ss_dssp             EECTTTCC-EEEEESSCSSCEECSSSCCEEE
T ss_pred             eECCCCCC-eEEEEecCceEEEccccCCEEe
Confidence            57999998 7899999999999999999996

>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=96.63  E-value=0.00085  Score=42.91  Aligned_cols=29  Identities=14%  Similarity=0.068  Sum_probs=25.9

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      ...||.|++  .+.+|...+++||..||.+.
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            357999997  68999999999999999985

>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=96.37  E-value=0.001  Score=42.42  Aligned_cols=29  Identities=21%  Similarity=0.345  Sum_probs=25.9

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      ...||.|++  .+.+|.+.+++||..||+..
T Consensus         6 iL~CP~ck~--~L~~~~~~~~Lvc~~~~laY   34 (59)
T d2pk7a1           6 ILACPICKG--PLKLSADKTELISKGAGLAY   34 (59)
T ss_dssp             TCCCTTTCC--CCEECTTSSEEEETTTTEEE
T ss_pred             heECCCCCC--cceEeCCCCEEecCCcCccc
Confidence            468999997  58999999999999999885

>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=96.25  E-value=0.0089  Score=44.69  Aligned_cols=69  Identities=14%  Similarity=0.267  Sum_probs=57.0

Q ss_pred             HHHHHHHHHHHHhccCCCH-HHHHHHHHHHHHHhh--CCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHH
Q 025357          106 LIQAFKSISAMSDRLGLVT-TIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCS  174 (254)
Q Consensus       106 l~~a~~~I~~i~~~L~Lp~-~v~e~A~~i~k~~~~--~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~  174 (254)
                      ..-|..+|+.+|++|+++. .+.+..-.+|+....  -.++++|-.+.+.-+|+|..|+..+..++.+||-.
T Consensus        12 y~La~~Rl~~LC~~L~~~~~~l~~~Iw~~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~~F~~Ii~   83 (142)
T d2r7ga2          12 YRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVT   83 (142)
T ss_dssp             HHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHHHHhHHHHhccchhHHHHHHHHHHHHhccCCCCHHHHHH
Confidence            3457888999999998764 566666666666544  45789999999999999999999999999999987

>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=96.19  E-value=0.0018  Score=41.28  Aligned_cols=28  Identities=36%  Similarity=0.659  Sum_probs=25.4

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      ..||.|++  .+.+|...+++||..||+..
T Consensus         8 L~CP~ck~--~L~~~~~~~~Lvc~~~~l~Y   35 (59)
T d2hf1a1           8 LVCPLCKG--PLVFDKSKDELICKGDRLAF   35 (59)
T ss_dssp             CBCTTTCC--BCEEETTTTEEEETTTTEEE
T ss_pred             hcCCCCCC--eeeEeCCCCEEecCCcCccc
Confidence            57999997  68999999999999999885

>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=95.51  E-value=0.035  Score=39.36  Aligned_cols=88  Identities=10%  Similarity=0.004  Sum_probs=59.1

Q ss_pred             HHHHHHHHhccCCCHH----HHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHH-------HHHHH-hc
Q 025357          110 FKSISAMSDRLGLVTT----IKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVK-------EFCSV-AN  177 (254)
Q Consensus       110 ~~~I~~i~~~L~Lp~~----v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~-------eIa~~-~~  177 (254)
                      .+++-.+...|+....    +...|-.+..-...-.+.---.|..+|+||||+|++..+.++.-.       .=-.. ..
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            4667777778877753    555555555555443333345799999999999999998765321       01111 13


Q ss_pred             CCCHHHHHHHHHHHHHHhch
Q 025357          178 GTTKKEIGRAKEFIVKHLEA  197 (254)
Q Consensus       178 ~v~~~~i~~~~k~l~~~l~~  197 (254)
                      +++...|.....+|.+....
T Consensus        84 dvt~e~i~~i~~~il~lY~~  103 (110)
T d2i53a2          84 DVPVDVLEDICHQILDLYSQ  103 (110)
T ss_dssp             SCCHHHHHHHHHHHHTTTSS
T ss_pred             cCCHHHHHHHHHHHHHHHcc
Confidence            78999999988888766654

>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=95.46  E-value=0.0052  Score=35.20  Aligned_cols=27  Identities=22%  Similarity=0.505  Sum_probs=20.4

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      -.||.|++ .-.-.|  .+.+||.+||.--
T Consensus         4 P~CP~C~s-eytYed--g~l~vCPeC~hEW   30 (38)
T d2akla2           4 PPCPQCNS-EYTYED--GALLVCPECAHEW   30 (38)
T ss_dssp             CCCTTTCC-CCCEEC--SSSEEETTTTEEE
T ss_pred             CcCCCCCC-cceEcC--CCEEECCcccCcC
Confidence            47999998 343344  7889999999753

>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=94.98  E-value=0.0025  Score=40.91  Aligned_cols=31  Identities=29%  Similarity=0.598  Sum_probs=25.0

Q ss_pred             CCCCCCCC-Cc----eEEecCCCceEcCcCceeecc
Q 025357            5 YCADCKRL-TE----VVFDHSAGDTICSECGLVLEA   35 (254)
Q Consensus         5 ~Cp~Cg~~-~~----lv~D~~~G~~vC~~CG~Vl~e   35 (254)
                      .||.|++. +.    -.+|+.+|...|..|+..|.|
T Consensus        16 ~Cp~C~~~ys~Lda~~L~d~~~~~F~C~~C~~el~e   51 (62)
T d1vd4a_          16 KCPVCSSTFTDLEANQLFDPMTGTFRCTFCHTEVEE   51 (62)
T ss_dssp             ECSSSCCEEEHHHHHHHEETTTTEEBCSSSCCBCEE
T ss_pred             ECCCCCCCcchhhHHHhcCcCCCeEEecCCCCEEec
Confidence            59999973 11    147899999999999999865

>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=94.59  E-value=0.0031  Score=43.84  Aligned_cols=22  Identities=14%  Similarity=0.034  Sum_probs=19.7

Q ss_pred             CCHHHHHHHHHhhcCCCcchhh
Q 025357          208 IHASDYLVIFLLNIFKNFFFLF  229 (254)
Q Consensus       208 ~~p~~~i~r~~~~L~l~~~v~~  229 (254)
                      ++|++||+|||++|+|++++..
T Consensus         1 i~P~d~I~R~~~~L~L~~~i~~   22 (95)
T d1aisb2           1 VKPTDYVNKFADELGLSEKVRR   22 (95)
T ss_dssp             CCGGGGHHHHHHHHTCCHHHHH
T ss_pred             CCHHHHHHHHHHHcCcCHHHHH
Confidence            4689999999999999998866

>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=94.29  E-value=0.0039  Score=44.56  Aligned_cols=22  Identities=18%  Similarity=0.218  Sum_probs=19.9

Q ss_pred             CCHHHHHHHHHhhcCCCcchhh
Q 025357          208 IHASDYLVIFLLNIFKNFFFLF  229 (254)
Q Consensus       208 ~~p~~~i~r~~~~L~l~~~v~~  229 (254)
                      ++|++||+|||++|+|++++.+
T Consensus         2 i~~~d~i~Rf~s~L~L~~~i~~   23 (109)
T d1vola2           2 ITTGDFMSRFCSNLCLPKQVQM   23 (109)
T ss_dssp             CCGGGTHHHHHHHHTCCHHHHH
T ss_pred             CCHHHHHHHHHHHcCcCHHHHH
Confidence            5789999999999999998866

>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=93.96  E-value=0.015  Score=33.15  Aligned_cols=28  Identities=25%  Similarity=0.637  Sum_probs=23.9

Q ss_pred             CCCCCCCC-CceEEecCCCceEcCcCcee
Q 025357            5 YCADCKRL-TEVVFDHSAGDTICSECGLV   32 (254)
Q Consensus         5 ~Cp~Cg~~-~~lv~D~~~G~~vC~~CG~V   32 (254)
                      .|+.||++ +.++.|...-.+.|..||.-
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            59999996 56888888889999999963

>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=93.80  E-value=0.013  Score=33.18  Aligned_cols=28  Identities=21%  Similarity=0.629  Sum_probs=23.0

Q ss_pred             CCCCCCCC-CceEEecCCCceEcCcCcee
Q 025357            5 YCADCKRL-TEVVFDHSAGDTICSECGLV   32 (254)
Q Consensus         5 ~Cp~Cg~~-~~lv~D~~~G~~vC~~CG~V   32 (254)
                      .|+.||++ +.++.|...-.+.|..||.-
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            69999996 55777777778899999964

>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=93.12  E-value=0.19  Score=36.10  Aligned_cols=85  Identities=9%  Similarity=-0.028  Sum_probs=59.5

Q ss_pred             HHHHHHHH-hccCCCHHHHHHHHHHHHHHh-hCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357          110 FKSISAMS-DRLGLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (254)
Q Consensus       110 ~~~I~~i~-~~L~Lp~~v~e~A~~i~k~~~-~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~  187 (254)
                      ..++.++. ..-+.+..+...|..+..... +...+-+-+|..+|||++|+|-+..+.+-=-.++... +|.++.+|..+
T Consensus         4 ~~FL~ry~~~~~~~d~~~~~la~Yl~ElsLl~~~~~l~~~PS~lAaaai~lar~~l~~~~W~~~L~~~-t~y~~~~l~~c   82 (124)
T d2cchb2           4 NQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRK-TGYTLESLKPC   82 (124)
T ss_dssp             HHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHHHHHHHHHHHHSCCSCHHHHHH-HCCCHHHHHHH
T ss_pred             hHHHHHHHHHHccCcHHHHHHHHHHHHHHHHhHHHHHccChHHHHHHHHHHHHHHhCCCCchHHHHHH-hCCCHHHHHHH
Confidence            45666654 444566677778888888864 4332334679999999999997766543223455563 78999999999


Q ss_pred             HHHHHHHh
Q 025357          188 KEFIVKHL  195 (254)
Q Consensus       188 ~k~l~~~l  195 (254)
                      .+.|.+.+
T Consensus        83 ~~~L~~~~   90 (124)
T d2cchb2          83 LMDLHQTY   90 (124)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99998765

>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=93.00  E-value=0.032  Score=34.53  Aligned_cols=30  Identities=23%  Similarity=0.351  Sum_probs=23.2

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      ..||.||+..++ --++.|...|-.|+.-..
T Consensus         6 ~pCp~CgSSDa~-a~y~DGh~~CFsC~~~~~   35 (54)
T d1nuia2           6 IPCDNCGSSDGN-SLFSDGHTFCYVCEKWTA   35 (54)
T ss_dssp             ECCSSSCCSSCE-EEETTSCEEETTTCCEEC
T ss_pred             cCCCCCCCCCCC-eEccCCCeEeeeCCCCcC
Confidence            469999995444 345689999999998764

>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=91.22  E-value=0.058  Score=35.30  Aligned_cols=32  Identities=25%  Similarity=0.444  Sum_probs=26.0

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      -.||.||. .. |.-...|-..|..||..+....
T Consensus        28 y~Cp~Cgk-~~-vkR~a~GIW~C~kC~~~~AGGA   59 (73)
T d1vqoz1          28 HACPNCGE-DR-VDRQGTGIWQCSYCDYKFTGGS   59 (73)
T ss_dssp             BCCSSSSC-SC-EEEEETTEEEETTTCCEEECCS
T ss_pred             ccCCCCCC-ce-eEEEEEEEEECCCCCCEEeCCe
Confidence            57999998 44 4667899999999999986444

>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=90.87  E-value=0.068  Score=34.98  Aligned_cols=33  Identities=18%  Similarity=0.444  Sum_probs=26.5

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS   37 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~   37 (254)
                      ...||.||. .. +.-...|-.-|..||.++....
T Consensus        27 ky~Cp~Cgk-~~-vkR~a~GIW~C~kC~~~~AGgA   59 (73)
T d1jj2y_          27 KHKCPVCGF-KK-LKRAGTGIWMCGHCGYKIAGGC   59 (73)
T ss_dssp             CBCCSSSCC-SC-EEEEETTEEEETTTCCEEECCS
T ss_pred             CccCCCCCC-Cc-eEEEEEEEEECCCCCCEEeCcc
Confidence            357999997 44 4667899999999999986544

>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=90.64  E-value=0.83  Score=32.69  Aligned_cols=109  Identities=6%  Similarity=0.024  Sum_probs=64.6

Q ss_pred             hHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCC--CHHHHHHH-hcCCCH
Q 025357          105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPR--TVKEFCSV-ANGTTK  181 (254)
Q Consensus       105 ~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~--tl~eIa~~-~~~v~~  181 (254)
                      .|...+-.|+..+..+.-++.+...|..+.....--...---.|..+|.||||+|++..+.+.  -+.++... ....+.
T Consensus         5 pl~g~l~dl~~~~~~~~~~~~l~~~a~~~lnds~~Td~~l~y~P~qIalaal~~a~~~~~~~l~~y~~~~~~~~~~~~~~   84 (126)
T d1jkwa2           5 PFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKENRTCL   84 (126)
T ss_dssp             HHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHTTSTHHHHSCHHHHHHHHHHHHHHHHSCCCTTHHHHHTTSCSSSCCT
T ss_pred             cHHHHHHHHHHhccCcCCHHHHHHHHHHHHHHHHcCCeeeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccccchhhH
Confidence            344444444444444444567778888887776433222224799999999999999998653  35555321 124455


Q ss_pred             HHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhc
Q 025357          182 KEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI  221 (254)
Q Consensus       182 ~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L  221 (254)
                      .+|...++++...++-.       .+. ..+-|..+-.+|
T Consensus        85 ~~l~~~i~~i~~l~~~~-------~~~-~~e~vk~i~kKL  116 (126)
T d1jkwa2          85 SQLLDIMKSMRNLVKKY-------EPP-RSEEVAVLKQKL  116 (126)
T ss_dssp             HHHHHHHHHHHHHHHTC-------CCC-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcc-------CCC-CHHHHHHHHHHH
Confidence            66777777777666422       222 235566655555

>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=90.28  E-value=0.44  Score=31.04  Aligned_cols=45  Identities=13%  Similarity=0.261  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHHHhcC----------CCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357          149 EAIVAACLYIACRQEN----------KPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (254)
Q Consensus       149 ~~iaAAclY~AcR~~~----------~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~  194 (254)
                      ..-.|..++.-|+..|          .|.|..|||+ ..|++..++.+++++|.+.
T Consensus         3 ~~Rla~~L~~L~~~~g~~~~~~~~i~~~lt~~elA~-~~g~sretvsr~l~~l~~~   57 (80)
T d3e5ua1           3 TIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGE-ITGVHHVTVSRVLASLKRE   57 (80)
T ss_dssp             HHHHHHHHHHHHHHHCEEETTEEECCSCCCHHHHHH-HHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhCCCCCCCeEEeeCCCHHHHHH-HHCCCHHHHHHHHHHHHHC
Confidence            3444555555555543          5789999999 4999999999999999876

>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=89.51  E-value=0.11  Score=31.83  Aligned_cols=27  Identities=26%  Similarity=0.742  Sum_probs=21.1

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V   32 (254)
                      ..||.||. .-...++ .....|..||+.
T Consensus        19 k~CP~CG~-GvFmA~H-~dR~~CGKCgyT   45 (55)
T d2k4xa1          19 RFCPRCGP-GVFLAEH-ADRYSCGRCGYT   45 (55)
T ss_dssp             CCCTTTTT-TCCCEEC-SSEEECTTTCCC
T ss_pred             CcCcCCCC-cEEeeec-CCCccccCCccc
Confidence            46999997 5555665 468999999986

>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=88.95  E-value=0.12  Score=38.48  Aligned_cols=29  Identities=28%  Similarity=0.563  Sum_probs=24.7

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCce
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGL   31 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~   31 (254)
                      ...|..||......+|...|-++|.+|+.
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            35799999866678899999999999974

>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=87.82  E-value=0.57  Score=28.02  Aligned_cols=41  Identities=15%  Similarity=0.114  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHH
Q 025357          149 EAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI  191 (254)
Q Consensus       149 ~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l  191 (254)
                      ..+..++-||--+. ..|+++.|+|+. .|+++..+.+.|++.
T Consensus         3 ~~i~~v~~yI~~~~-~~~~tl~~lA~~-~~~s~~~l~r~Fk~~   43 (54)
T d1bl0a1           3 ITIHSILDWIEDNL-ESPLSLEKVSER-SGYSKWHLQRMFKKE   43 (54)
T ss_dssp             HHHHHHHHHHHTTT-TSCCCCHHHHHH-SSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcc-CCCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence            34566677776555 569999999995 999999998888763

>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=87.76  E-value=0.16  Score=28.33  Aligned_cols=26  Identities=31%  Similarity=0.621  Sum_probs=19.1

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeecc
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e   35 (254)
                      ...||.||.+      ...|+ -|..||..++.
T Consensus         2 ~G~CP~C~~~------~a~GD-qCe~CG~~~~p   27 (35)
T d1rqga3           2 IGTCPYCGAE------DQKGD-QCEVCGRPLTP   27 (35)
T ss_dssp             CSBCSSSCCS------CCCTT-TCSSSCCCCCT
T ss_pred             eEECCCCCCC------cccCc-chhhcCCccCH
Confidence            4689999983      23455 49999999853

>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=87.45  E-value=0.17  Score=28.84  Aligned_cols=31  Identities=23%  Similarity=0.597  Sum_probs=20.4

Q ss_pred             CCCCCCCCCCCc-eEEecCCCceEcCcCceee
Q 025357            3 DSYCADCKRLTE-VVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         3 ~~~Cp~Cg~~~~-lv~D~~~G~~vC~~CG~Vl   33 (254)
                      ...|.+||.... .-.....|...|..||+-.
T Consensus         2 ~r~C~~Cgtt~Tp~WR~gp~G~~LCNACGl~~   33 (39)
T d1y0ja1           2 ARECVNCGATATPLWRRDRTGHYLCNACGLYH   33 (39)
T ss_dssp             CCCCSSSCCCCCSCCEECTTSCEECSSHHHHH
T ss_pred             cCCCCCCCCCCCcccccCCCCCEeeHHhHHHH
Confidence            367899987422 2223456788999999753

>d1pfva3 g.41.1.1 (A:141-175) Methionyl-tRNA synthetase (MetRS), Zn-domain {Escherichia coli [TaxId: 562]}

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: Escherichia coli [TaxId: 562]

Probab=86.14  E-value=0.15  Score=28.42  Aligned_cols=25  Identities=32%  Similarity=0.761  Sum_probs=18.3

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceeecc
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e   35 (254)
                      ..||.|+..      ...|+ -|..||..++.
T Consensus         3 G~CP~C~~~------~a~GD-qCe~CG~~~~p   27 (35)
T d1pfva3           3 GTCPKCKSP------DQYGD-NCEVCGATYSP   27 (35)
T ss_dssp             EECTTTCCS------SEETT-BCTTTCCBCCG
T ss_pred             eECCCCCCc------ccccc-cHHHcCCcCCH
Confidence            579999983      23454 49999999853

>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=84.01  E-value=2.8  Score=29.88  Aligned_cols=32  Identities=13%  Similarity=0.157  Sum_probs=28.6

Q ss_pred             hcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357          162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (254)
Q Consensus       162 ~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~  194 (254)
                      .++.|.|+.||++. .|++..++.+..+.|.+.
T Consensus        37 ~~~~plt~~ela~~-l~vsk~~vs~~l~~L~~~   68 (151)
T d1ku9a_          37 LSDKPLTISDIMEE-LKISKGNVSMSLKKLEEL   68 (151)
T ss_dssp             HCSSCEEHHHHHHH-HTCCHHHHHHHHHHHHHT
T ss_pred             hCCCCcCHHHHHHH-hCCCcchHHHHHHHHHHC
Confidence            56789999999995 999999999999999873

>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=83.84  E-value=1.7  Score=27.97  Aligned_cols=43  Identities=12%  Similarity=0.045  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHhc--------CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357          151 IVAACLYIACRQE--------NKPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (254)
Q Consensus       151 iaAAclY~AcR~~--------~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~  194 (254)
                      +|...++++-+..        ..|.|..|||+ ..|++..++.+.+++|.+.
T Consensus         6 la~~Ll~l~~~~g~~~~~~~i~~~lt~~eLA~-~~G~sretvsr~L~~l~~~   56 (81)
T d2gaua1           6 LAETLLILKENFGFENDGATLSIYLSREELAT-LSNMTVSNAIRTLSTFVSE   56 (81)
T ss_dssp             HHHHHHHHHHHHCBCTTSSBBSCCCCHHHHHH-HTTSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCCCCCCEEeecCCHHHHHH-HHCCCHHHHHHHHHHHHHC
Confidence            4555566654422        25799999999 5999999999999999876

>d1wiia_ g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Putative zinc binding domain
domain: Hypothetical UPF0222 protein MGC4549
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.73  E-value=0.22  Score=33.49  Aligned_cols=31  Identities=23%  Similarity=0.485  Sum_probs=22.5

Q ss_pred             CCCCCCCCCc--eEEe--cCCCceEcCcCceeecc
Q 025357            5 YCADCKRLTE--VVFD--HSAGDTICSECGLVLEA   35 (254)
Q Consensus         5 ~Cp~Cg~~~~--lv~D--~~~G~~vC~~CG~Vl~e   35 (254)
                      .||.|+....  +..|  ...|.+.|.-||.-.+-
T Consensus        25 ~CPfCnh~~sV~vk~dkk~~~g~l~C~vCg~~~~~   59 (85)
T d1wiia_          25 TCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQT   59 (85)
T ss_dssp             CCTTTCCSSCEEEEEETTTTEEEEEESSSCCEEEE
T ss_pred             cCCCCCCCCeEEEEEEecCCEEEEEEecCCCeEEe
Confidence            5999995333  4445  46688999999987643

>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=83.60  E-value=0.17  Score=29.31  Aligned_cols=29  Identities=31%  Similarity=0.771  Sum_probs=19.5

Q ss_pred             CCCCCCCCC-ceEEecCCCceEcCcCceee
Q 025357            5 YCADCKRLT-EVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         5 ~Cp~Cg~~~-~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      .|.+||... .+-.....|..+|..||+-.
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            688898742 23233456889999999854

>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=83.54  E-value=1.3  Score=27.58  Aligned_cols=32  Identities=6%  Similarity=0.179  Sum_probs=27.9

Q ss_pred             HhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357          161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK  193 (254)
Q Consensus       161 R~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~  193 (254)
                      +.++.++|..|+|+. ++||..+|++-+..|.+
T Consensus        17 ~~~~~~vs~~~La~~-l~VS~~TI~rdi~~L~~   48 (65)
T d1j5ya1          17 ERSKEPVSGAQLAEE-LSVSRQVIVQDIAYLRS   48 (65)
T ss_dssp             HHCSSCBCHHHHHHH-HTSCHHHHHHHHHHHHH
T ss_pred             HHcCCCCcHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence            456678999999995 99999999999999864

>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=82.86  E-value=0.4  Score=30.94  Aligned_cols=28  Identities=18%  Similarity=0.695  Sum_probs=23.6

Q ss_pred             CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (254)
Q Consensus         4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl   33 (254)
                      ..||.|+.  .++.|...-.+.|..||...
T Consensus        19 k~CP~C~~--~~~~~~~~~~~~C~~C~~~f   46 (73)
T d2ct7a1          19 LWCAQCSF--GFIYEREQLEATCPQCHQTF   46 (73)
T ss_dssp             ECCSSSCC--CEECCCSCSCEECTTTCCEE
T ss_pred             CCCCCCCC--EeEECCCCCEEEcCCCCCeE
Confidence            57999997  47788777789999999986

>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=82.83  E-value=0.65  Score=29.33  Aligned_cols=29  Identities=17%  Similarity=0.289  Sum_probs=26.1

Q ss_pred             CCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357          165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (254)
Q Consensus       165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~  194 (254)
                      .|.|..|||+ ..|++..++.+.+++|.+.
T Consensus        28 l~lt~~~lA~-~~G~sRetvsr~L~~l~~~   56 (69)
T d1i5za1          28 IKITRQEIGQ-IVGCSRETVGRILKMLEDQ   56 (69)
T ss_dssp             EECCHHHHHH-HHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHH-HHCCCHHHHHHHHHHHHHC
Confidence            4799999999 5999999999999999864

>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=82.28  E-value=1.2  Score=26.45  Aligned_cols=37  Identities=11%  Similarity=0.223  Sum_probs=28.1

Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHH
Q 025357          153 AACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI  191 (254)
Q Consensus       153 AAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l  191 (254)
                      -++-|+--. -..|+++.|+|+. +++++..+.+.|++.
T Consensus         7 ~i~~yi~~~-~~~~itl~~lA~~-~~~S~~~l~r~Fk~~   43 (54)
T d1d5ya1           7 DLLIWLEGH-LDQPLSLDNVAAK-AGYSKWHLQRMFKDV   43 (54)
T ss_dssp             HHHHHHHTT-SSSSCCCHHHHTT-TSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHc-cCCCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence            345555433 3558999999995 999999999988763

>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=82.01  E-value=0.44  Score=29.61  Aligned_cols=51  Identities=6%  Similarity=-0.007  Sum_probs=36.1

Q ss_pred             CCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357          167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF  227 (254)
Q Consensus       167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v  227 (254)
                      +|++|||+. +||+..++.++++---....+         .....+-|...+.+||--+..
T Consensus         1 vTl~diA~~-agvS~sTVSrvLn~~~~~~~v---------s~~tr~rV~~~a~~lgY~pn~   51 (59)
T d1uxda_           1 MKLDEIARL-AGVSRTTASYVINGKAKQYRV---------SDKTVEKVMAVVREHNYHPNA   51 (59)
T ss_dssp             CCHHHHHHH-HTSCTTHHHHHHHTCGGGTTC---------TTTTHHHHHHHHHHHTCCCCS
T ss_pred             CCHHHHHHH-HCcCHHHHHHHHcCCCCcCcC---------CHHHHHHHHHHHHHHCCCcCH
Confidence            589999995 999999999886531111111         235678899999999876543

>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=80.43  E-value=0.58  Score=29.07  Aligned_cols=49  Identities=8%  Similarity=0.030  Sum_probs=36.4

Q ss_pred             CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357          166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF  227 (254)
Q Consensus       166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v  227 (254)
                      +.|++|||+. +|++..++.++++-       .  .   .-.....+-|...+++||--+..
T Consensus         2 ~~Ti~diA~~-agvS~sTVSr~l~~-------~--~---~vs~~tr~rI~~~a~~lgY~pn~   50 (59)
T d1efaa1           2 PVTLYDVAEY-AGVSYQTVSRVVNQ-------A--S---HVSAKTREKVEAAMAELNYIPNR   50 (59)
T ss_dssp             CCCHHHHHHT-TTSCHHHHHHHHTT-------C--S---SCCTHHHHHHHHHHHHHTCCCCH
T ss_pred             CCCHHHHHHH-HCCCHHHHHHHHCC-------C--C---cCCHHHHHHHHHHHHHHCCCcCH
Confidence            6899999995 99999999988532       1  0   11345678888899988876543

>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=80.30  E-value=0.43  Score=29.73  Aligned_cols=25  Identities=32%  Similarity=0.796  Sum_probs=17.8

Q ss_pred             CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (254)
Q Consensus         3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~   34 (254)
                      ...||+||.. .      .---||.+||+-=+
T Consensus        29 l~~C~~CG~~-~------~pHrvC~~CG~YkG   53 (59)
T d2j0151          29 LVPCPECKAM-K------PPHTVCPECGYYAG   53 (59)
T ss_dssp             CBCCSSSSSC-B------CTTCBCTTTCCSSS
T ss_pred             eeECCCCCCc-c------cceeECCCCCeECC
Confidence            4679999972 2      34469999997543