Citrus Sinensis ID: 023713

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------28
Protein Sequence
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRLILVFFSLFLVETHIQLIVWAFMRCIYTFRCYGY
Secondary Structure (PSIPRED)
ccccccccccccccEEEEcccccEEcccccEEEccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHcccccEEEEccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccEEEEcccccEEcHHccEEEcccEccccccHEEccccccccccccccccccccccccccEEEEcccccccccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHccccHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MADSYCADCKRLTEVvfdhsagdticseCGLVLEaysvdetsewrifanessdhdpvrvggplnpllsggglstviakptaggstellsgslgklqarsshpdrNLIQAFKSISAMSDRLGLVTTIKDRANEIYKkvedqkplrgrnQEAIVAACLYIACrqenkprtvKEFCSVANGTTKKEIGRAKEFIVKHLEAemgqsvemgtiHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRLILVFFSLFLVETHIQLIVWAFMRCIYTFRCYGY
Flexible Loop (DISEMBL)
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFAnessdhdpvrVGGPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKsisamsdrlGLVTTIKDRANEIykkvedqkplrgrnQEAIVAACLYIACrqenkprtvKEFCSvangttkkeigRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRLILVFFSLFLVETHIQLIVWAFMRCIYTFRCYGY
Low Complexity Region (SEG)
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVggplnpllsggglsTVIAKPTAggstellsgslgklQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNqavkaaqeavqkSEDLDIRLILVFFSLFLVETHIQLIVWAFMRCIYTFRCYGY
Disordered region (IsUnstruct)
****YCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFAN**********************L*TV*******************************IQAFKSISAMSDRLGLVTTIKDRANEIYKKV*******GRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRLILVFFSLFLVETHIQLIVWAFMRCIYTFRCYG*
Disordered Region (DISOPRED)
**DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEW********************PLLSGGGL********************************NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRLILVFFSLFLVETHIQLIVWAFMRCIYTFRCYGY
Disordered Region (DISEMBL)
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGGSTELLSGSL*********PDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ*********QKSEDLDIRLILVFFSLFLVETHIQLIVWAFMRCIYTFRCYGY
Disordered Region (DISPRO)
****YCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFAN***********GPLNPLLSGGGLSTVIAKPTA***TELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRLILVFFSLFLVETHIQLIVWAFMRCIYTFRCYGY
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRLILVFFSLFLVETHIQLIVWAFMRCIYTFRCYGY
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	278	2.2.26 [Sep-21-2011]
Q8W0W3	312	Transcription initiation	yes	no	0.935	0.833	0.743	1e-112
P48513	313	Transcription initiation	yes	no	0.938	0.833	0.731	1e-111
Q9SS44	312	Transcription initiation	yes	no	0.874	0.778	0.762	1e-110
P48512	312	Transcription initiation	no	no	0.935	0.833	0.674	1e-102
P29052	315	Transcription initiation	yes	no	0.805	0.711	0.476	8e-53
P29054	316	Transcription initiation	N/A	no	0.798	0.702	0.467	2e-51
Q5R886	316	Transcription initiation	yes	no	0.798	0.702	0.458	8e-49
Q4R3J5	316	Transcription initiation	N/A	no	0.798	0.702	0.458	8e-49
Q00403	316	Transcription initiation	yes	no	0.798	0.702	0.458	8e-49
P62916	316	Transcription initiation	yes	no	0.798	0.702	0.458	8e-49

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

 Score =  405 bits (1041), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 194/261 (74%), Positives = 222/261 (85%), Gaps = 1/261 (0%)

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

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

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

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

Query: 241 LDIRLILVFFSLFLVETHIQL 261
           LDIR   +  +  ++    QL
Sbjct: 240 LDIRRSPISIAAAVIYMITQL 260

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

 Score =  402 bits (1033), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 191/261 (73%), Positives = 219/261 (83%)

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

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

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

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

Query: 241 LDIRLILVFFSLFLVETHIQL 261
            DIR   +  +  ++    QL
Sbjct: 241 FDIRRSPISIAAAVIYIITQL 261

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

Glycine max (taxid: 3847)

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

 Score =  396 bits (1017), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 186/244 (76%), Positives = 214/244 (87%), Gaps = 1/244 (0%)

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

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

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

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

Query: 241 LDIR 244
            DIR
Sbjct: 240 FDIR 243

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 =  373 bits (957), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 176/261 (67%), Positives = 214/261 (81%), Gaps = 1/261 (0%)

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

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

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

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

Query: 241 LDIRLILVFFSLFLVETHIQL 261
            DIR   +  +  ++    QL
Sbjct: 240 FDIRRSPISIAAVVIYIITQL 260

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 =  207 bits (526), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 110/231 (47%), Positives = 149/231 (64%), Gaps = 7/231 (3%)

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

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

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

Query: 193 KHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI 243
           K LE     SV++  I  +D++ RFC+NL + N   +AA    +K+ ++DI
Sbjct: 199 KALET----SVDL--ITTADFMCRFCANLDLPNMVQRAATHIAKKAVEMDI 243

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 =  202 bits (515), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 107/229 (46%), Positives = 144/229 (62%), Gaps = 7/229 (3%)

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

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

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

Query: 195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI 243
           LE        +  I   D++ RFCSNLG+T Q   AA    +K+ +LD+
Sbjct: 202 LE------TNVDLITTGDFMSRFCSNLGLTKQVQMAATHIARKAVELDL 244

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 =  194 bits (492), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 105/229 (45%), Positives = 142/229 (62%), Gaps = 7/229 (3%)

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

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

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

Query: 195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI 243
           LE     SV++  I   D++ RFCSNL +  Q   AA    +K+ +LD+
Sbjct: 202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDL 244

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 =  194 bits (492), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 105/229 (45%), Positives = 142/229 (62%), Gaps = 7/229 (3%)

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

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

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

Query: 195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI 243
           LE     SV++  I   D++ RFCSNL +  Q   AA    +K+ +LD+
Sbjct: 202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDL 244

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 =  194 bits (492), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 105/229 (45%), Positives = 142/229 (62%), Gaps = 7/229 (3%)

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

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

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

Query: 195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI 243
           LE     SV++  I   D++ RFCSNL +  Q   AA    +K+ +LD+
Sbjct: 202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDL 244

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

Homo sapiens (taxid: 9606)

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

 Score =  194 bits (492), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 105/229 (45%), Positives = 142/229 (62%), Gaps = 7/229 (3%)

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

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

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

Query: 195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI 243
           LE     SV++  I   D++ RFCSNL +  Q   AA    +K+ +LD+
Sbjct: 202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDL 244

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

Rattus norvegicus (taxid: 10116)

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	278
224135681	311	predicted protein [Populus trichocarpa]	0.874	0.781	0.852	1e-120
255544920	312	transcription initiation factor iib, put	0.935	0.833	0.758	1e-115
225436547	314	PREDICTED: transcription initiation fact	0.877	0.777	0.791	1e-113
225464249	312	PREDICTED: transcription initiation fact	0.935	0.833	0.754	1e-111
225441886	312	PREDICTED: transcription initiation fact	0.935	0.833	0.754	1e-111
255588003	312	transcription initiation factor iib, put	0.874	0.778	0.790	1e-111
115480363	312	Os09g0534800 [Oryza sativa Japonica Grou	0.935	0.833	0.743	1e-111
242045402	312	hypothetical protein SORBIDRAFT_02g03102	0.935	0.833	0.739	1e-110
317106705	312	JHL06B08.6 [Jatropha curcas]	0.874	0.778	0.786	1e-110
449465789	312	PREDICTED: transcription initiation fact	0.935	0.833	0.739	1e-110

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

 Score =  436 bits (1120), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 208/244 (85%), Positives = 225/244 (92%), Gaps = 1/244 (0%)

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

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

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

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

Query: 241 LDIR 244
           LDIR
Sbjct: 240 LDIR 243

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 =  419 bits (1077), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 198/261 (75%), Positives = 229/261 (87%), Gaps = 1/261 (0%)

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

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

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

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

Query: 241 LDIRLILVFFSLFLVETHIQL 261
           LDIR   +  +  ++    QL
Sbjct: 240 LDIRRSPISIAAAIIYMITQL 260

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 =  412 bits (1059), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 194/245 (79%), Positives = 220/245 (89%), Gaps = 1/245 (0%)

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

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

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

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

Query: 240 DLDIR 244
           +LDIR
Sbjct: 241 ELDIR 245

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  407 bits (1047), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 197/261 (75%), Positives = 222/261 (85%), Gaps = 1/261 (0%)

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

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

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

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

Query: 241 LDIRLILVFFSLFLVETHIQL 261
            DIR   V  +  ++    QL
Sbjct: 240 FDIRRSPVSIAAAVIYIITQL 260

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 =  407 bits (1047), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 197/261 (75%), Positives = 222/261 (85%), Gaps = 1/261 (0%)

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

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

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

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

Query: 241 LDIRLILVFFSLFLVETHIQL 261
            DIR   V  +  ++    QL
Sbjct: 240 FDIRRSPVSIAAAVIYIITQL 260

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 =  405 bits (1042), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 193/244 (79%), Positives = 214/244 (87%), Gaps = 1/244 (0%)

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

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

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

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

Query: 241 LDIR 244
            DIR
Sbjct: 240 FDIR 243

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

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 =  405 bits (1041), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 194/261 (74%), Positives = 222/261 (85%), Gaps = 1/261 (0%)

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

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

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

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

Query: 241 LDIRLILVFFSLFLVETHIQL 261
           LDIR   +  +  ++    QL
Sbjct: 240 LDIRRSPISIAAAVIYMITQL 260

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242045402|ref|XP_002460572.1| hypothetical protein SORBIDRAFT_02g031020 [Sorghum bicolor] gi|241923949|gb|EER97093.1| hypothetical protein SORBIDRAFT_02g031020 [Sorghum bicolor]

 Score =  405 bits (1040), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 193/261 (73%), Positives = 222/261 (85%), Gaps = 1/261 (0%)

Query: 1   MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVG 60
           M+DS+C DCK+ TEV FDHSAGDT+C+ECGLVLEA+SVDETSEWR FANES+D+DPVRVG
Sbjct: 1   MSDSFCPDCKKQTEVAFDHSAGDTVCTECGLVLEAHSVDETSEWRTFANESNDNDPVRVG 60

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

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

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

Query: 241 LDIRLILVFFSLFLVETHIQL 261
           LDIR   +  +  ++    QL
Sbjct: 240 LDIRRSPISIAAAVIYMITQL 260

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  404 bits (1038), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 192/244 (78%), Positives = 214/244 (87%), Gaps = 1/244 (0%)

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

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

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

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

Query: 241 LDIR 244
            DIR
Sbjct: 240 FDIR 243

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  403 bits (1035), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 193/261 (73%), Positives = 221/261 (84%), Gaps = 1/261 (0%)

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

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

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

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

Query: 241 LDIRLILVFFSLFLVETHIQL 261
            DIR   +  +  ++    QL
Sbjct: 240 FDIRRSPISIAAAVIYIITQL 260

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	278
TAIR|locus:2076259	312	AT3G10330 [Arabidopsis thalian	0.874	0.778	0.651	2.5e-81
TAIR|locus:2062703	312	TFIIB "transcription factor II	0.874	0.778	0.606	3.1e-76
ZFIN|ZDB-GENE-030131-3544	316	gtf2b "general transcription f	0.798	0.702	0.401	2.3e-39
FB|FBgn0004915	315	TfIIB "Transcription factor II	0.798	0.704	0.410	2.9e-39
UNIPROTKB|F1NXP2	306	GTF2B "Uncharacterized protein	0.798	0.725	0.401	3.7e-39
UNIPROTKB|F2Z4J6	316	LOC786656 "Uncharacterized pro	0.798	0.702	0.393	1.5e-37
UNIPROTKB|Q2KIN8	316	GTF2B "Transcription initiatio	0.798	0.702	0.393	1.5e-37
UNIPROTKB|E2RPG1	316	GTF2B "Uncharacterized protein	0.798	0.702	0.393	1.5e-37
UNIPROTKB|Q00403	316	GTF2B "Transcription initiatio	0.798	0.702	0.393	1.5e-37
UNIPROTKB|F2Z5J6	316	GTF2B "Uncharacterized protein	0.798	0.702	0.393	1.5e-37

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

 Score = 816 (292.3 bits), Expect = 2.5e-81, P = 2.5e-81
 Identities = 159/244 (65%), Positives = 182/244 (74%)

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

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

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

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

Query:   241 LDIR 244
              DIR
Sbjct:   240 FDIR 243

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 = 768 (275.4 bits), Expect = 3.1e-76, P = 3.1e-76
 Identities = 148/244 (60%), Positives = 178/244 (72%)

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

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

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

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

Query:   241 LDIR 244
              DIR
Sbjct:   240 FDIR 243

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

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

 Score = 420 (152.9 bits), Expect = 2.3e-39, P = 2.3e-39
 Identities = 92/229 (40%), Positives = 127/229 (55%)

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

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

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

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI 243
             LE     SV++  I   D++ RFCSNLG+              + +LD+
Sbjct:   202 LET----SVDL--ITTGDFMSRFCSNLGLPKQVQMAATYIARKAVELDL 244

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

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

 Score = 419 (152.6 bits), Expect = 2.9e-39, P = 2.9e-39
 Identities = 94/229 (41%), Positives = 128/229 (55%)

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

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

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

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI 243
             LE     SV++  I  +D++ RFC+NL + N            + ++DI
Sbjct:   201 LET----SVDL--ITTADFMCRFCANLDLPNMVQRAATHIAKKAVEMDI 243

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

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

 Score = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 92/229 (40%), Positives = 127/229 (55%)

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

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

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

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI 243
             LE     SV++  I   D++ RFCSNLG+              + +LD+
Sbjct:   192 LET----SVDL--ITTGDFMSRFCSNLGLPKQVQMAATHIARKAVELDL 234

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 = 403 (146.9 bits), Expect = 1.5e-37, P = 1.5e-37
 Identities = 90/229 (39%), Positives = 124/229 (54%)

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

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

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

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI 243
             LE     SV++  I   D++ RFCSNL +              + +LD+
Sbjct:   202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDL 244

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 = 403 (146.9 bits), Expect = 1.5e-37, P = 1.5e-37
 Identities = 90/229 (39%), Positives = 124/229 (54%)

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

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

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

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI 243
             LE     SV++  I   D++ RFCSNL +              + +LD+
Sbjct:   202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDL 244

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 = 403 (146.9 bits), Expect = 1.5e-37, P = 1.5e-37
 Identities = 90/229 (39%), Positives = 124/229 (54%)

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

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

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

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI 243
             LE     SV++  I   D++ RFCSNL +              + +LD+
Sbjct:   202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDL 244

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

 Score = 403 (146.9 bits), Expect = 1.5e-37, P = 1.5e-37
 Identities = 90/229 (39%), Positives = 124/229 (54%)

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

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

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

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI 243
             LE     SV++  I   D++ RFCSNL +              + +LD+
Sbjct:   202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDL 244

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

UNIPROTKB|F2Z5J6 GTF2B "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 403 (146.9 bits), Expect = 1.5e-37, P = 1.5e-37
 Identities = 90/229 (39%), Positives = 124/229 (54%)

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

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

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

Query:   195 LEAEMGQSVEMGTIHASDYLRRFCSNLGMTNXXXXXXXXXXXXSEDLDI 243
             LE     SV++  I   D++ RFCSNL +              + +LD+
Sbjct:   202 LET----SVDL--ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDL 244

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

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8W0W3	TF2B_ORYSJ	No assigned EC number	0.7432	0.9352	0.8333	yes	no
Q9SS44	TF2B2_ARATH	No assigned EC number	0.7622	0.8741	0.7788	yes	no
P48513	TF2B_SOYBN	No assigned EC number	0.7318	0.9388	0.8338	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	278
COG1405	285	COG1405, SUA7, Transcription initiation factor TFI	4e-55
PRK00423	310	PRK00423, tfb, transcription initiation factor IIB	1e-47
pfam00382	71	pfam00382, TFIIB, Transcription factor TFIIB repea	6e-20
cd00043	88	cd00043, CYCLIN, Cyclin box fold	6e-13
smart00385	83	smart00385, CYCLIN, domain present in cyclins, TFI	6e-10
pfam08271	40	pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding	7e-09
COG1405	285	COG1405, SUA7, Transcription initiation factor TFI	9e-08
COG5333	297	COG5333, CCL1, Cdk activating kinase (CAK)/RNA pol	7e-06
PRK00423	310	PRK00423, tfb, transcription initiation factor IIB	7e-05
pfam00134	127	pfam00134, Cyclin_N, Cyclin, N-terminal domain	0.003

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

 Score =  179 bits (456), Expect = 4e-55
 Identities = 85/238 (35%), Positives = 129/238 (54%), Gaps = 20/238 (8%)

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

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

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

Query: 183 EIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240
           EIGR    +V+ L       +++  +  SDY+ RF S LG++++  + A E V+K++ 
Sbjct: 173 EIGRTYRLLVREL------KLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKR 224

Length = 285

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

 Score =  160 bits (407), Expect = 1e-47
 Identities = 78/241 (32%), Positives = 133/241 (55%), Gaps = 18/241 (7%)

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

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

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

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

Query: 243 I 243
           +
Sbjct: 252 L 252

Length = 310

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

 Score = 81.2 bits (201), Expect = 6e-20
 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 = 63.0 bits (154), Expect = 6e-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 = 54.5 bits (132), Expect = 6e-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 = 50.4 bits (121), 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 = 51.9 bits (125), Expect = 9e-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 = 46.3 bits (110), Expect = 7e-06
 Identities = 22/98 (22%), Positives = 46/98 (46%), Gaps = 1/98 (1%)

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

Query: 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVE 204
           R +      A     +E   ++E I++  E E+ ++++
Sbjct: 106 RDISIESFEARDLWSEEPKSSRERILE-YEFELLEALD 142

Length = 297

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

 Score = 43.1 bits (102), Expect = 7e-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 = 36.4 bits (85), Expect = 0.003
 Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 2/52 (3%)

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

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	278
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,	100.0
PF00382	71	TFIIB: Transcription factor TFIIB repeat; InterPro	99.79
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	99.63
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	99.58
KOG0834	323	consensus CDK9 kinase-activating protein cyclin T	99.44
KOG0835	367	consensus Cyclin L [General function prediction on	99.43
TIGR00569	305	ccl1 cyclin ccl1. University).	99.42
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	99.41
KOG1597	308	consensus Transcription initiation factor TFIIB [T	99.34
cd00043	88	CYCLIN Cyclin box fold. Protein binding domain fun	99.16
COG5333	297	CCL1 Cdk activating kinase (CAK)/RNA polymerase II	99.12
smart00385	83	CYCLIN domain present in cyclins, TFIIB and Retino	99.06
KOG0794	264	consensus CDK8 kinase-activating protein cyclin C	98.85
PF00382	71	TFIIB: Transcription factor TFIIB repeat; InterPro	98.81
KOG0656	335	consensus G1/S-specific cyclin D [Cell cycle contr	98.77
KOG1598	521	consensus Transcription initiation factor TFIIIB,	98.64
PF00134	127	Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR	98.09
cd00043	88	CYCLIN Cyclin box fold. Protein binding domain fun	97.91
KOG0653	391	consensus Cyclin B and related kinase-activating p	97.8
smart00385	83	CYCLIN domain present in cyclins, TFIIB and Retino	97.73
COG5024	440	Cyclin [Cell division and chromosome partitioning]	97.69
PF01857	135	RB_B: Retinoblastoma-associated protein B domain;	97.68
KOG2496	325	consensus Cdk activating kinase (CAK)/RNA polymera	97.67
PF11781	36	RRN7: RNA polymerase I-specific transcription init	97.11
KOG0835	367	consensus Cyclin L [General function prediction on	96.93
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	96.83
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	96.58
PRK00420	112	hypothetical protein; Validated	96.56
PHA00626	59	hypothetical protein	96.49
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	96.44
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	96.42
PF02984	118	Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR	96.39
PF13248	26	zf-ribbon_3: zinc-ribbon domain	96.27
PF02984	118	Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR	96.24
KOG0655	408	consensus G1/S-specific cyclin E [Cell cycle contr	96.22
KOG4164	497	consensus Cyclin ik3-1/CABLES [Cell cycle control,	96.21
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	96.2
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	96.09
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	95.96
PLN00209	86	ribosomal protein S27; Provisional	95.92
PTZ00083	85	40S ribosomal protein S27; Provisional	95.86
smart00778	37	Prim_Zn_Ribbon Zinc-binding domain of primase-heli	95.74
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	95.63
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	95.46
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	95.2
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	95.05
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	95.02
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	95.01
PRK00432	50	30S ribosomal protein S27ae; Validated	94.92
PRK11827	60	hypothetical protein; Provisional	94.9
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	94.74
smart00661	52	RPOL9 RNA polymerase subunit 9.	94.35
PRK10220	111	hypothetical protein; Provisional	94.34
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	94.28
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	94.23
TIGR02300	129	FYDLN_acid conserved hypothetical protein TIGR0230	94.07
PF08273	40	Prim_Zn_Ribbon: Zinc-binding domain of primase-hel	94.06
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	94.04
PF03966	68	Trm112p: Trm112p-like protein; InterPro: IPR005651	94.03
PF08613	149	Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eu	93.99
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	93.83
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	93.65
COG2835	60	Uncharacterized conserved protein [Function unknow	93.65
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	93.22
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	93.17
KOG4557	262	consensus Origin recognition complex, subunit 6 [R	93.12
COG2824	112	PhnA Uncharacterized Zn-ribbon-containing protein	92.63
TIGR00244	147	transcriptional regulator NrdR. Members of this al	92.47
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	92.12
TIGR00686	109	phnA alkylphosphonate utilization operon protein P	91.99
PRK12495	226	hypothetical protein; Provisional	91.89
KOG1779	84	consensus 40s ribosomal protein S27 [Translation,	91.59
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	90.98
PRK14892	99	putative transcription elongation factor Elf1; Pro	90.96
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	90.52
PF01780	90	Ribosomal_L37ae: Ribosomal L37ae protein family; I	90.35
PF00134	127	Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR	90.33
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	90.24
COG4888	104	Uncharacterized Zn ribbon-containing protein [Gene	90.16
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	89.95
PF05129	81	Elf1: Transcription elongation factor Elf1 like; I	89.9
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	89.67
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	89.52
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	89.41
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	89.41
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	89.22
PF05191	36	ADK_lid: Adenylate kinase, active site lid; InterP	89.08
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	88.94
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	88.93
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	88.85
PTZ00255	90	60S ribosomal protein L37a; Provisional	88.63
KOG4557	262	consensus Origin recognition complex, subunit 6 [R	88.49
COG4640	465	Predicted membrane protein [Function unknown]	87.91
PF12773	50	DZR: Double zinc ribbon	87.48
PF14255	52	Cys_rich_CPXG: Cysteine-rich CPXCG	87.38
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	87.35
COG4068	64	Uncharacterized protein containing a Zn-ribbon [Fu	87.32
TIGR00280	91	L37a ribosomal protein L37a. This model finds euka	87.05
PRK06266	178	transcription initiation factor E subunit alpha; V	87.04
TIGR00569	305	ccl1 cyclin ccl1. University).	86.9
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	86.81
PRK05978	148	hypothetical protein; Provisional	86.57
PRK09710	64	lar restriction alleviation and modification prote	86.44
COG1656	165	Uncharacterized conserved protein [Function unknow	86.34
PF05460	353	ORC6: Origin recognition complex subunit 6 (ORC6);	86.18
PF00301	47	Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubred	85.89
PRK03976	90	rpl37ae 50S ribosomal protein L37Ae; Reviewed	85.67
PRK12286	57	rpmF 50S ribosomal protein L32; Reviewed	85.65
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	85.53
PRK09678	72	DNA-binding transcriptional regulator; Provisional	85.51
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	85.24
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	84.91
PRK13130	56	H/ACA RNA-protein complex component Nop10p; Review	84.86
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	84.49
cd00730	50	rubredoxin Rubredoxin; nonheme iron binding domain	84.36
KOG1010	920	consensus Rb (Retinoblastoma tumor suppressor)-rel	84.01
COG3877	122	Uncharacterized protein conserved in bacteria [Fun	83.94
COG5349	126	Uncharacterized protein conserved in bacteria [Fun	83.82
COG1327	156	Predicted transcriptional regulator, consists of a	83.6
PF01783	56	Ribosomal_L32p: Ribosomal L32p protein family; Int	83.57
TIGR02443	59	conserved hypothetical metal-binding protein. Memb	82.88
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	82.64
PF12773	50	DZR: Double zinc ribbon	82.59
KOG0794	264	consensus CDK8 kinase-activating protein cyclin C	82.46
PF14122	87	YokU: YokU-like protein	81.41
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	81.38
PRK02935	110	hypothetical protein; Provisional	81.19
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	81.06
PF11672	102	DUF3268: Protein of unknown function (DUF3268); In	81.05
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	80.88
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	80.78
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	80.78
TIGR01031	55	rpmF_bact ribosomal protein L32. This protein desc	80.63
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	80.46
TIGR03826	137	YvyF flagellar operon protein TIGR03826. This gene	80.3
KOG1088	124	consensus Uncharacterized conserved protein [Funct	80.26
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	80.04

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=100.00  E-value=3.8e-63  Score=449.46  Aligned_cols=252  Identities=31%  Similarity=0.554  Sum_probs=233.6

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhccCCCCCCCCCcccCCCCCcccCCCcceEEecCCCC
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG   82 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~   82 (278)
                      ...||+||+ +++|+|+.+|++||.+||+|++|++||+|||||+|++++ .+|++|+|+|.++++||.|++|.|+++..+
T Consensus        11 ~~~Cp~Cg~-~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~-~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~   88 (310)
T PRK00423         11 KLVCPECGS-DKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTYTIHDKGLSTDIDWRNKD   88 (310)
T ss_pred             CCcCcCCCC-CCeeEECCCCeEeecccCCcccccccccCCCccCCCccc-cCCccccCCCCCccccCCCCceEeecCCcc
Confidence            367999998 689999999999999999999999999999999999754 468999999999999999999999977655


Q ss_pred             CCccccc-------cccccccccC---CCchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHH
Q 023713           83 GSTELLS-------GSLGKLQARS---SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIV  152 (278)
Q Consensus        83 ~~~~~l~-------~~l~~~~~~~---~~~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~a  152 (278)
                      ++|..++       .+|++||++.   +++||+|..+++.|+++|+.|+||+.++|+|..||+++++.++++||+.++++
T Consensus        89 ~~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~  168 (310)
T PRK00423         89 SYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVV  168 (310)
T ss_pred             cccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHH
Confidence            5555443       2477888875   56899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHH
Q 023713          153 AACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQ  232 (278)
Q Consensus       153 AAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~  232 (278)
                      |||||+|||++++|+|++||+.+ +++++++|+++|+.|.+.|+++      +++.+|++||+|||+.|+|++++.+.|.
T Consensus       169 AAclYiACR~~~~prtl~eI~~~-~~v~~k~i~~~~~~l~k~L~~~------~~~~~p~~~i~r~~~~L~L~~~v~~~A~  241 (310)
T PRK00423        169 AAALYAACRRCKVPRTLDEIAEV-SRVSRKEIGRCYRFLLRELNLK------LPPTDPIDYVPRFASELGLSGEVQKKAI  241 (310)
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC------CCCCCHHHHHHHHHHHcCCCHHHHHHHH
Confidence            99999999999999999999995 8999999999999999999987      7889999999999999999999999999


Q ss_pred             HHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHH
Q 023713          233 EAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWA  265 (278)
Q Consensus       233 ~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~  265 (278)
                      +|++++.+.|  .||+|.+||||+|  ||++.+..
T Consensus       242 ~i~~~a~~~~l~~Gr~P~sIAAAaI--YlA~~~~g  274 (310)
T PRK00423        242 EILQKAKEKGLTSGKGPTGLAAAAI--YIASLLLG  274 (310)
T ss_pred             HHHHHHHhcCcccCCCHHHHHHHHH--HHHHHHhC
Confidence            9999999888  6999999999999  99998764

>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]

Probab=100.00  E-value=3.1e-60  Score=410.80  Aligned_cols=253  Identities=53%  Similarity=0.812  Sum_probs=230.7

Q ss_pred             CCCCCCCCCCc-eeEeCCCCceEcCCCcccccccccccccchhhccCCCCCCCCCcccCCCCCcccCCCcceEEecCCCC
Q 023713            4 SYCADCKRLTE-VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG   82 (278)
Q Consensus         4 ~~Cp~Cg~~~~-vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~   82 (278)
                      +.||+|+..+. +|+|+.+|++||..||+|+++++||+++|||+|+++.++.||+|||+|.||+|.+++++|+|+++. +
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            47999998766 999999999999999999999999999999999998888999999999999999999999999987 5


Q ss_pred             CCccccccccccccccC--CCchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHH
Q 023713           83 GSTELLSGSLGKLQARS--SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIAC  160 (278)
Q Consensus        83 ~~~~~l~~~l~~~~~~~--~~~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~ac  160 (278)
                      .++..++ .+.++|++.  +++|+.+..+|..|..||+.++||..+.++|.++||++.+.+.++||+.++++|||||+||
T Consensus        80 ~~s~~~s-~l~~~Q~~~sm~~~d~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiAC  158 (308)
T KOG1597|consen   80 TSSSFAS-SLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIAC  158 (308)
T ss_pred             CCHHHHH-HHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHH
Confidence            5544343 488899854  6789999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh
Q 023713          161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED  240 (278)
Q Consensus       161 R~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~  240 (278)
                      |+++.|||++||+.+ .+|++++|+|.+|.|.+.|+...    ++..++..+||+|||+.|+|+++++.+|.++++++..
T Consensus       159 Rq~~~pRT~kEI~~~-anv~kKEIgr~~K~i~~~l~~s~----~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~  233 (308)
T KOG1597|consen  159 RQEDVPRTFKEISAV-ANVSKKEIGRCVKLIGEALETSV----DLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEE  233 (308)
T ss_pred             HhcCCCchHHHHHHH-HcCCHHHHHHHHHHHHHHHhccc----hhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence            999999999999996 78999999999999999998651    2334568999999999999999999999999999999


Q ss_pred             cC--CCCChhHHHHHHHHHHHHHHHHH
Q 023713          241 LD--IRLILVFFSLFLVETHIQLIVWA  265 (278)
Q Consensus       241 ~~--~Gr~P~~iaaA~v~~~~~~~~~~  265 (278)
                      ++  .||+|.+||||+|  |++..+-.
T Consensus       234 ~~~~~gRsPiSIAAa~I--Ymisqls~  258 (308)
T KOG1597|consen  234 MDIRAGRSPISIAAAAI--YMISQLSD  258 (308)
T ss_pred             hccccCCCchhHHHHHH--HHHHHhcc
Confidence            88  5899999999999  87766543

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

Probab=100.00  E-value=3.8e-58  Score=407.79  Aligned_cols=245  Identities=34%  Similarity=0.612  Sum_probs=226.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhccCCCCCCCCCcccCCCCCcccCCCcceEEecCCCC
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG   82 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~   82 (278)
                      ++.||+||+ ++++.|+++|++||.+||+|++|..||.|||||.|+  + ...+ |+|.|.++.+||.|++|.|+++...
T Consensus         1 ~~~CpeCg~-~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f~--e-~~~~-r~g~P~t~~~~d~~l~t~i~~~~~~   75 (285)
T COG1405           1 VMSCPECGS-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFD--E-RHER-RVGAPLTPSIHDKGLSTIIGWGDKD   75 (285)
T ss_pred             CCCCCCCCC-ccceeeccCCeEEeccCCEEeccccccCCCCccccc--c-cccc-cccCCCccccCccchhhhcccchhH
Confidence            368999999 699999999999999999999999999999999993  2 2234 9999999999999999999987532


Q ss_pred             CCccccccccccccccC---CCchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHH
Q 023713           83 GSTELLSGSLGKLQARS---SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIA  159 (278)
Q Consensus        83 ~~~~~l~~~l~~~~~~~---~~~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~a  159 (278)
                           ...+|++||.+.   +..||++..++.+|.++++.|+||.++.|+|..||++++++++++||+.++++|||+|+|
T Consensus        76 -----~~~rlr~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~a  150 (285)
T COG1405          76 -----KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAA  150 (285)
T ss_pred             -----HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHH
Confidence                 234588898654   468999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhh
Q 023713          160 CRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSE  239 (278)
Q Consensus       160 cR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~  239 (278)
                      ||+++.|+|+.||+.. +++++++|+++|+.+.+.|++.      +++.+|.+||+|||+.|+|++++.+.|.+|+++++
T Consensus       151 cR~~~~prtl~eIa~a-~~V~~kei~rtyr~~~~~L~l~------~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~  223 (285)
T COG1405         151 CRINGVPRTLDEIAKA-LGVSKKEIGRTYRLLVRELKLK------IPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAK  223 (285)
T ss_pred             HHHcCCCccHHHHHHH-HCCCHHHHHHHHHHHHHhcCCC------CCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence            9999999999999995 8999999999999999999997      78899999999999999999999999999999999


Q ss_pred             hcC--CCCChhHHHHHHHHHHHHHHHHHH
Q 023713          240 DLD--IRLILVFFSLFLVETHIQLIVWAF  266 (278)
Q Consensus       240 ~~~--~Gr~P~~iaaA~v~~~~~~~~~~~  266 (278)
                      +.+  .||+|.++|||+|  ||+.++.+.
T Consensus       224 ~~g~~~Gk~P~glAaaai--y~as~l~~~  250 (285)
T COG1405         224 RAGLTAGKSPAGLAAAAI--YLASLLLGE  250 (285)
T ss_pred             HhCcccCCCchhHHHHHH--HHHHHHhCC
Confidence            988  6999999999999  999998763

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

Probab=100.00  E-value=1.1e-36  Score=283.18  Aligned_cols=226  Identities=21%  Similarity=0.314  Sum_probs=196.1

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhccCCCCCCCCCcccCCCCCcccCCCcceEEecCCCCC
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGG   83 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~~   83 (278)
                      ++|++||+ +++..|+.+|..+|+.||+|++++.|..  | .+|.+..                    -|+.|+....+.
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-VTFVEGA--------------------QGQFVRVGQSGA   56 (521)
T ss_pred             CcCCCCCC-CCcccccccCCceeccccceeeccceeE--E-eeeeccc--------------------ceeEEeccccCC
Confidence            47999999 7899999999999999999999999984  4 4787421                    123443222111


Q ss_pred             CccccccccccccccCCCchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhc
Q 023713           84 STELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE  163 (278)
Q Consensus        84 ~~~~l~~~l~~~~~~~~~~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~  163 (278)
                      ..            ...++++++.++...|.+++..|+|++ +++.|..+|+.+.+.++++||+...++|+|+|++||++
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            124678999999999999999999999 99999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCC---HHHHHHHHHHHHHhhh
Q 023713          164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMT---NQAVKAAQEAVQKSED  240 (278)
Q Consensus       164 ~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~---~~v~~~A~~i~~~~~~  240 (278)
                      +.++.+.|++++ ++|++++||+.|++|.+.|.+...   -.|.+||..||+||...|.+.   ++|+..|.+|++.|++
T Consensus       124 ~t~hlliDfS~~-Lqv~Vy~LG~~~l~l~~~L~i~en---~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkr  199 (521)
T KOG1598|consen  124 KTDHLLIDFSSY-LQVSVYDLGSNFLEVTDSLSIGEN---VSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKR  199 (521)
T ss_pred             CCceEEEEeccc-eEEehhhhhHHHHHHHHHhccccc---cccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHH
Confidence            999999999995 999999999999999999988521   168899999999999999775   4689999999999999


Q ss_pred             cC--CCCChhHHHHHHHHHHHHHHHHHHHhcccc
Q 023713          241 LD--IRLILVFFSLFLVETHIQLIVWAFMRCIYT  272 (278)
Q Consensus       241 ~~--~Gr~P~~iaaA~v~~~~~~~~~~~~~~~~~  272 (278)
                      .|  +||+|.+|++|||  +|++++.+|++.++-
T Consensus       200 dwm~tGRRPsglcGAaL--liAar~h~~~rsi~d  231 (521)
T KOG1598|consen  200 DWMQTGRRPSGLCGAAL--LIAARMHGFRRTIGD  231 (521)
T ss_pred             HHHHhCCCccchhHHHH--HHHHHHcCccccHHH
Confidence            99  7999999999999  999999999987754

>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=99.79  E-value=8.2e-19  Score=125.43  Aligned_cols=71  Identities=44%  Similarity=0.836  Sum_probs=65.9

Q ss_pred             HHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHH
Q 023713          113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (278)
Q Consensus       113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i  184 (278)
                      |+++|+.|+||+.+.++|.++|+++.+.++.+||++.+++|||||+|||+++.|+|++||+++ ++|++++|
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.

>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=99.63  E-value=1.7e-16  Score=102.03  Aligned_cols=43  Identities=47%  Similarity=1.025  Sum_probs=38.9

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIF   47 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f   47 (278)
                      ++||+||+ +.+++|+.+|++||++||.|++|+.++.++|||+|
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 67999999999999999999999999999999998

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.

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=99.58  E-value=1.5e-14  Score=131.51  Aligned_cols=89  Identities=22%  Similarity=0.382  Sum_probs=85.5

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHH
Q 023713          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK  188 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~  188 (278)
                      ..++|.++|+.|+||..+.+.|.+|++++.+.+++.||+|.++||||||+||+.++.|+|++||+.+ .+|++.+|++.|
T Consensus       219 p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v-~~Vs~~tI~~~y  297 (310)
T PRK00423        219 PIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEV-AGVTEVTVRNRY  297 (310)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHH-cCCCHHHHHHHH
Confidence            5689999999999999999999999999999999999999999999999999999999999999996 999999999999


Q ss_pred             HHHHHHhhhh
Q 023713          189 EFIVKHLEAE  198 (278)
Q Consensus       189 ~~l~~~L~~~  198 (278)
                      ++|.+.|++.
T Consensus       298 kel~~~l~~~  307 (310)
T PRK00423        298 KELAEKLDIK  307 (310)
T ss_pred             HHHHHHhCcc
Confidence            9999999864

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

Probab=99.44  E-value=2.7e-13  Score=122.43  Aligned_cols=158  Identities=16%  Similarity=0.225  Sum_probs=130.7

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcC-CCH--HH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG-TTK--KE  183 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~-v~~--~~  183 (278)
                      ..+..+|.+++.+|++|...+.+|..+|.+++-...++.-.+..+|++|+|+|++.++.|+.++||..+... ..+  .+
T Consensus        40 ~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~  119 (323)
T KOG0834|consen   40 QEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLE  119 (323)
T ss_pred             HHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCccccc
Confidence            678999999999999999999999999999999888888889999999999999999999999999765221 122  12


Q ss_pred             HHHH-----------HHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHH----HHHHHHHHHHHhhhcC--CCCC
Q 023713          184 IGRA-----------KEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ----AVKAAQEAVQKSEDLD--IRLI  246 (278)
Q Consensus       184 i~~~-----------~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~----v~~~A~~i~~~~~~~~--~Gr~  246 (278)
                      ....           .+.|.+.|+++      +...+|..|+.+|+..|+....    +...|+.+++......  .--.
T Consensus       120 ~~~~~~~~~~~Iv~~E~~lL~tl~Fd------l~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~  193 (323)
T KOG0834|consen  120 LEEVYWELKERIVQLELLLLETLGFD------LNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYS  193 (323)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHccCc------eeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeec
Confidence            3333           34445566665      7778999999999999998875    8899999999988754  5779


Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhcccc
Q 023713          247 LVFFSLFLVETHIQLIVWAFMRCIYT  272 (278)
Q Consensus       247 P~~iaaA~v~~~~~~~~~~~~~~~~~  272 (278)
                      |..||.|+|  |||+.+.+..-+..+
T Consensus       194 p~~IAva~i--~lA~~~~~~~~~~~~  217 (323)
T KOG0834|consen  194 PHSIAVACI--HLAAKLLGVELPSDT  217 (323)
T ss_pred             CcEEEeehh--hHHHHHcCCCCCCCc
Confidence            999999999  999999877554443

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=99.43  E-value=2e-12  Score=114.61  Aligned_cols=152  Identities=17%  Similarity=0.211  Sum_probs=133.1

Q ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC------
Q 023713          106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT------  179 (278)
Q Consensus       106 l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v------  179 (278)
                      ..=+..+|++.|-.|+||+...-++..+|++....+.+.+.+.+.++.|||.+|.+.+..|++++||..|+..+      
T Consensus        23 ~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~~~  102 (367)
T KOG0835|consen   23 RILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRRES  102 (367)
T ss_pred             HHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHHhc
Confidence            34578999999999999999999999999999998888899999999999999999999999999998763221      


Q ss_pred             --------------CHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHH--HHHHHHHHHHhhhcC-
Q 023713          180 --------------TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQA--VKAAQEAVQKSEDLD-  242 (278)
Q Consensus       180 --------------~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v--~~~A~~i~~~~~~~~-  242 (278)
                                    -+..+.++..+|.+.||+.      +...+|+.+|--|.+-|++++..  .+.+|.+.+.+.+.+ 
T Consensus       103 ~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~------~Hv~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v  176 (367)
T KOG0835|consen  103 EAAEHLILARLYINLKMQVIRAERRILRELGFD------VHVEHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDV  176 (367)
T ss_pred             cCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCe------eeeeccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccce
Confidence                          1334557778899999987      77889999999999999998764  899999999998876 


Q ss_pred             -CCCChhHHHHHHHHHHHHHHHHH
Q 023713          243 -IRLILVFFSLFLVETHIQLIVWA  265 (278)
Q Consensus       243 -~Gr~P~~iaaA~v~~~~~~~~~~  265 (278)
                       ..-.|.+||+|+|  |+++...+
T Consensus       177 ~vry~pe~iACaci--yLaAR~~e  198 (367)
T KOG0835|consen  177 FVRYSPESIACACI--YLAARNLE  198 (367)
T ss_pred             eeecCHHHHHHHHH--HHHHhhhc
Confidence             5889999999999  99888766

>TIGR00569 ccl1 cyclin ccl1

Probab=99.42  E-value=8.1e-12  Score=112.89  Aligned_cols=154  Identities=12%  Similarity=0.139  Sum_probs=129.5

Q ss_pred             hhHH-HHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC
Q 023713          103 DRNL-IQAFKSISAMSDRLG--LVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT  179 (278)
Q Consensus       103 er~l-~~~~~~I~~i~~~L~--Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v  179 (278)
                      |+.+ ......|.++|..|+  ||+.++-+|..+|++.+-.+.+.-..+..++++|||+||+.+..|+++.+++.. ..-
T Consensus        52 E~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~-~~~  130 (305)
T TIGR00569        52 ELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGN-LKE  130 (305)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhh-ccC
Confidence            3444 466889999999999  999999999999999999888877899999999999999999999999999874 333


Q ss_pred             C----HHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcC-------CCHHHHHHHHHHHHHhhhcC--CCCC
Q 023713          180 T----KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG-------MTNQAVKAAQEAVQKSEDLD--IRLI  246 (278)
Q Consensus       180 ~----~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~-------l~~~v~~~A~~i~~~~~~~~--~Gr~  246 (278)
                      +    ...|......|.+.|++.      +...+|..++..|...|+       -.+.+.+.|+.+++.+...+  .=-.
T Consensus       131 ~~~~~~~~Il~~E~~lL~~L~F~------L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~  204 (305)
T TIGR00569       131 TPLKALEQVLEYELLLIQQLNFH------LIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYT  204 (305)
T ss_pred             CchhhHHHHHHHHHHHHHHCCCc------EEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCC
Confidence            2    478999999999999987      667789998888886543       22457788999999888766  5689


Q ss_pred             hhHHHHHHHHHHHHHHHHH
Q 023713          247 LVFFSLFLVETHIQLIVWA  265 (278)
Q Consensus       247 P~~iaaA~v~~~~~~~~~~  265 (278)
                      |.-||+|||  |+++....
T Consensus       205 Ps~IAlAAI--~lA~~~~~  221 (305)
T TIGR00569       205 PSQIALAAI--LHTASRAG  221 (305)
T ss_pred             HHHHHHHHH--HHHHHHhC
Confidence            999999999  99886543

University).

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

Probab=99.41  E-value=8.7e-13  Score=117.80  Aligned_cols=91  Identities=26%  Similarity=0.379  Sum_probs=87.2

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGR  186 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~  186 (278)
                      .+..++|.+||+.|+||+.+...|.+|.+++.+.+.+.||+|..+||||||+|+++++.++|.+||+.+ +++++.+|++
T Consensus       192 ~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v-~~vtevTIrn  270 (285)
T COG1405         192 VDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKV-AGVTEVTIRN  270 (285)
T ss_pred             CCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHH-hCCeeeHHHH
Confidence            366789999999999999999999999999999999999999999999999999999999999999996 9999999999


Q ss_pred             HHHHHHHHhhhh
Q 023713          187 AKEFIVKHLEAE  198 (278)
Q Consensus       187 ~~~~l~~~L~~~  198 (278)
                      .|++|.+.+++.
T Consensus       271 rykel~~~~~i~  282 (285)
T COG1405         271 RYKELADALDIE  282 (285)
T ss_pred             HHHHHHHhhccc
Confidence            999999999874

>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]

Probab=99.34  E-value=5.6e-12  Score=110.48  Aligned_cols=88  Identities=24%  Similarity=0.348  Sum_probs=83.8

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHH
Q 023713          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (278)
Q Consensus       108 ~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~  187 (278)
                      +.-++|.+||+.|+||.++++.|.++.+++.+.+...||+|.++|||.||+++++...++|++||..+ +||.+.+|+..
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            36789999999999999999999999999999999999999999999999999999999999999996 99999999999


Q ss_pred             HHHHHHHhh
Q 023713          188 KEFIVKHLE  196 (278)
Q Consensus       188 ~~~l~~~L~  196 (278)
                      ||.|..++.
T Consensus       281 YK~Lyp~~~  289 (308)
T KOG1597|consen  281 YKDLYPHAD  289 (308)
T ss_pred             HHHHhhchh
Confidence            999987764

>cd00043 CYCLIN Cyclin box fold

Probab=99.16  E-value=5.3e-10  Score=81.33  Aligned_cols=83  Identities=24%  Similarity=0.378  Sum_probs=77.7

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC-CHHHHHH
Q 023713          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGR  186 (278)
Q Consensus       108 ~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v-~~~~i~~  186 (278)
                      .+.++|.+++..+++|..+...|..+++++...+.+.++++..+++||+|+||+.++.|.+++|+... .+. +..+|.+
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 888 9999999


Q ss_pred             HHHHH
Q 023713          187 AKEFI  191 (278)
Q Consensus       187 ~~~~l  191 (278)
                      .++.|
T Consensus        83 ~e~~i   87 (88)
T cd00043          83 MEKLL   87 (88)
T ss_pred             HHHHh
Confidence            88875

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.

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

Probab=99.12  E-value=9.1e-10  Score=97.63  Aligned_cols=149  Identities=19%  Similarity=0.280  Sum_probs=125.9

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHH-------cCC
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVA-------NGT  179 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~-------~~v  179 (278)
                      ...+..|..+|.+|+||..+..+|..+|++.+-+....+.+...++++|||+|||.++.|+-+.-.+-.+       ..-
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            4568999999999999999999999999999998889999999999999999999999765544332221       123


Q ss_pred             CHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCH--HHHHHHHHHHHHhhhcC--CCCChhHHHHHHH
Q 023713          180 TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN--QAVKAAQEAVQKSEDLD--IRLILVFFSLFLV  255 (278)
Q Consensus       180 ~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~--~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v  255 (278)
                      +.+.|-....++.+.|+..      .-..+|..++.-|...+.+..  +..+.|+.+++.+.+..  .=-.|-.||.|++
T Consensus       126 sr~~Il~~E~~lLEaL~fd------~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~l  199 (297)
T COG5333         126 SRERILEYEFELLEALDFD------LHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAAL  199 (297)
T ss_pred             cHHHHHHHHHHHHHHcccc------eEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHHH
Confidence            5788888888999999987      677889999999999987764  48999999999998866  4567999999999


Q ss_pred             HHHHHHHH
Q 023713          256 ETHIQLIV  263 (278)
Q Consensus       256 ~~~~~~~~  263 (278)
                        +|++-+
T Consensus       200 --~ia~~~  205 (297)
T COG5333         200 --LIACEV  205 (297)
T ss_pred             --HHHHHh
Confidence              888765

>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma

Probab=99.06  E-value=1.1e-09  Score=78.88  Aligned_cols=80  Identities=23%  Similarity=0.303  Sum_probs=71.9

Q ss_pred             HHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC-CHHHHHHHHHH
Q 023713          112 SISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGRAKEF  190 (278)
Q Consensus       112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v-~~~~i~~~~~~  190 (278)
                      +|.++++.+++|+.+...|..+++++.....+.++++..+++||+|+|||.++.+++..++... ++. +..+|.+.++.
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            6889999999999999999999999988433445999999999999999999999999999885 888 99999999988


Q ss_pred             HH
Q 023713          191 IV  192 (278)
Q Consensus       191 l~  192 (278)
                      |.
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.

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

Probab=98.85  E-value=1e-08  Score=87.22  Aligned_cols=148  Identities=18%  Similarity=0.275  Sum_probs=116.7

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCH-HHHHHHH----------
Q 023713          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTV-KEFCSVA----------  176 (278)
Q Consensus       108 ~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl-~eia~~~----------  176 (278)
                      .....|..+++.|+|-+.++-+|.-++++.+-++.+++-.+..+|.-|||+||+.+..|++. +-+...+          
T Consensus        43 ~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~  122 (264)
T KOG0794|consen   43 FMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYW  122 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccc
Confidence            45678999999999999999999999999999888999999999999999999999998222 2222110          


Q ss_pred             ---cCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCC-CHHHHHHHHHHHHHhhhcC--CCCChhHH
Q 023713          177 ---NGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGM-TNQAVKAAQEAVQKSEDLD--IRLILVFF  250 (278)
Q Consensus       177 ---~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l-~~~v~~~A~~i~~~~~~~~--~Gr~P~~i  250 (278)
                         ...+.+.|-...-.|.+.|+--      +-..+|..=+..+++.+|+ +......++.|++..-+.+  .=-.|--|
T Consensus       123 ~e~~~~~~~~I~e~Ef~llE~Ld~~------LIVhHPYrsL~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~I  196 (264)
T KOG0794|consen  123 PEKFPYERKDILEMEFYLLEALDCY------LIVHHPYRSLLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQI  196 (264)
T ss_pred             hhhcCCCcCcchhhhhhHHhhhcee------EEEecCCccHHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHH
Confidence               1123344555555666666643      3445677779999999999 5558999999999999877  57899999


Q ss_pred             HHHHHHHHHHHHH
Q 023713          251 SLFLVETHIQLIV  263 (278)
Q Consensus       251 aaA~v~~~~~~~~  263 (278)
                      |-|+|  ||+.-+
T Consensus       197 alAcl--~Ia~~~  207 (264)
T KOG0794|consen  197 ALACL--YIACVI  207 (264)
T ss_pred             HHHHH--HHHHhh
Confidence            99999  998753

>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=98.81  E-value=1.4e-08  Score=72.25  Aligned_cols=51  Identities=16%  Similarity=0.206  Sum_probs=43.8

Q ss_pred             HHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHHH
Q 023713          214 LRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWAF  266 (278)
Q Consensus       214 i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~~  266 (278)
                      |+|||+.|+|++++.+.|.+|++.+.+.+  .||+|.++|||+|  |+++...+.
T Consensus         1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~i--Y~acr~~~~   53 (71)
T PF00382_consen    1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACI--YLACRLNGV   53 (71)
T ss_dssp             HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHH--HHHHHHTTS
T ss_pred             ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHH--HHHHHHcCC
Confidence            68999999999999999999999999887  5999999999999  999876543

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.

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

Probab=98.77  E-value=4.4e-07  Score=82.49  Aligned_cols=151  Identities=15%  Similarity=0.169  Sum_probs=116.9

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCC-CCCCC--cHHHHHHHHHHHHHHhcCC--CCCHHHHHHH-HcCCC
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQK-PLRGR--NQEAIVAACLYIACRQENK--PRTVKEFCSV-ANGTT  180 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~-~~~gr--~~~~~aAAclY~acR~~~~--p~tl~eia~~-~~~v~  180 (278)
                      .+|+++|-+.|...+..+.+.=.|.+++.+..... +.+++  -...+|+||+.+|.+.+..  |.++.-.... ..-..
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            57999999999999999999999999999977644 33443  3789999999999999886  5444322221 13467


Q ss_pred             HHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCC----HHHHHHHHH-HHHHhhhcC-CCCChhHHHHHH
Q 023713          181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMT----NQAVKAAQE-AVQKSEDLD-IRLILVFFSLFL  254 (278)
Q Consensus       181 ~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~----~~v~~~A~~-i~~~~~~~~-~Gr~P~~iaaA~  254 (278)
                      .++|.|....+...|+=+      +..+.|.+|+.-|++++++.    ..+...+.. ++..+++.. .+-.|..||+|+
T Consensus       159 aktI~rmELLVLstL~Wr------l~aVTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~  232 (335)
T KOG0656|consen  159 AKTIQRMELLVLSTLKWR------LRAVTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAA  232 (335)
T ss_pred             HHHHHHHHHHHHhhcccc------ccCCCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHH
Confidence            999999999999999877      77889999999999999985    334555554 444445444 689999999998


Q ss_pred             HHHHHHHHHHHHHh
Q 023713          255 VETHIQLIVWAFMR  268 (278)
Q Consensus       255 v~~~~~~~~~~~~~  268 (278)
                      +     +++++.+.
T Consensus       233 ~-----~~v~~~~~  241 (335)
T KOG0656|consen  233 I-----LSVSASVD  241 (335)
T ss_pred             H-----HHHHHhhc
Confidence            8     56665554

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

Probab=98.64  E-value=2.3e-08  Score=94.54  Aligned_cols=91  Identities=19%  Similarity=0.212  Sum_probs=75.0

Q ss_pred             HHHHHHHHHHHHHhcC-CCH--HHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHH
Q 023713          106 LIQAFKSISAMSDRLG-LVT--TIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKK  182 (278)
Q Consensus       106 l~~~~~~I~~i~~~L~-Lp~--~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~  182 (278)
                      |.+..-+|.+++..|- .|.  .++.+|..+..++.......||+|..+++||||+|||.+|+++|..||+.+ ..|+..
T Consensus       163 lvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~v-vhV~e~  241 (521)
T KOG1598|consen  163 LVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKV-VHVCES  241 (521)
T ss_pred             ccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHH-HHHhHH
Confidence            3445557777777763 343  477777777777766667789999999999999999999999999999996 899999


Q ss_pred             HHHHHHHHHHHHhhh
Q 023713          183 EIGRAKEFIVKHLEA  197 (278)
Q Consensus       183 ~i~~~~~~l~~~L~~  197 (278)
                      +|.+.|+++.+.+..
T Consensus       242 Tl~kRl~Ef~~T~s~  256 (521)
T KOG1598|consen  242 TLSKRLKEFSDTLSG  256 (521)
T ss_pred             HHHHHHHHHhccccc
Confidence            999999999876654

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

Probab=98.09  E-value=5.3e-05  Score=59.34  Aligned_cols=92  Identities=21%  Similarity=0.342  Sum_probs=77.1

Q ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCC-CCCHHHHHHHHc--CCCHH
Q 023713          106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN--GTTKK  182 (278)
Q Consensus       106 l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~-p~tl~eia~~~~--~v~~~  182 (278)
                      -....++|..++..++++..+.-.|..++.+..........+...++++|+++||+.+.. +.++.++... .  ..+.+
T Consensus        31 r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~-~~~~~~~~  109 (127)
T PF00134_consen   31 RQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRI-SDNTFTKK  109 (127)
T ss_dssp             HHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHH-TTTSSHHH
T ss_pred             HHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHH-HcCCCCHH
Confidence            356789999999999999999999999999998887777788999999999999999887 7888998774 3  35789


Q ss_pred             HHHHHHHHHHHHhhhh
Q 023713          183 EIGRAKEFIVKHLEAE  198 (278)
Q Consensus       183 ~i~~~~~~l~~~L~~~  198 (278)
                      +|....+.+.+.|+.+
T Consensus       110 ~i~~~E~~iL~~L~f~  125 (127)
T PF00134_consen  110 DILEMEREILSALNFD  125 (127)
T ss_dssp             HHHHHHHHHHHHTTT-
T ss_pred             HHHHHHHHHHHHCCCC
Confidence            9999999999988864

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 ....

>cd00043 CYCLIN Cyclin box fold

Probab=97.91  E-value=2.6e-05  Score=56.19  Aligned_cols=58  Identities=14%  Similarity=0.089  Sum_probs=53.1

Q ss_pred             CCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHHHH
Q 023713          208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWAFM  267 (278)
Q Consensus       208 ~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~~~  267 (278)
                      ..|.+||.++++.+++++++...|..++++.....  .+++|..+|+|+|  |||..+....
T Consensus         3 ~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l--~lA~k~~~~~   62 (88)
T cd00043           3 PTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAAL--YLAAKVEEIP   62 (88)
T ss_pred             chHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHH--HHHHHHcCCC
Confidence            46889999999999999999999999999998765  6999999999999  9999988773

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.

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

Probab=97.80  E-value=0.00046  Score=65.00  Aligned_cols=145  Identities=14%  Similarity=0.163  Sum_probs=115.1

Q ss_pred             HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHH-HHHHhcCCC-CCHHHHHHHH-cCCCH
Q 023713          105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLY-IACRQENKP-RTVKEFCSVA-NGTTK  181 (278)
Q Consensus       105 ~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY-~acR~~~~p-~tl~eia~~~-~~v~~  181 (278)
                      ....-.+++-++-.+++|..++.-.|..|+.+.........+....+..+|++ +||+.+... -++.|+.-+. -..+.
T Consensus       157 mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~  236 (391)
T KOG0653|consen  157 MRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSR  236 (391)
T ss_pred             HHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccch
Confidence            33456789999999999999999999999999988766777777777777756 999965544 3356654321 23689


Q ss_pred             HHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHH
Q 023713          182 KEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLV  255 (278)
Q Consensus       182 ~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v  255 (278)
                      .+|.++.+.+...|+..      +....|..|+.||........+....+..+++...-.-  +...|..+|||+.
T Consensus       237 ~~il~mE~~il~~L~f~------l~~p~~~~FLrr~~ka~~~d~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~  306 (391)
T KOG0653|consen  237 EEILRMEKYILNVLEFD------LSVPTPLSFLRRFLKAADYDIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASF  306 (391)
T ss_pred             HHHHHHHHHHHhccCee------ecCCchHHHHHHHHHhhhcchhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHH
Confidence            99999999999999886      67778999999999999977777888888888776432  6788888888888

>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma

Probab=97.73  E-value=6.8e-05  Score=53.40  Aligned_cols=54  Identities=13%  Similarity=0.218  Sum_probs=48.6

Q ss_pred             HHHHHHHhhcCCCHHHHHHHHHHHHHhhhc-C-CCCChhHHHHHHHHHHHHHHHHHHH
Q 023713          212 DYLRRFCSNLGMTNQAVKAAQEAVQKSEDL-D-IRLILVFFSLFLVETHIQLIVWAFM  267 (278)
Q Consensus       212 ~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~-~-~Gr~P~~iaaA~v~~~~~~~~~~~~  267 (278)
                      +||.++++.+++++++...|..++++.... . .+++|..+|+|+|  |||..+.+.-
T Consensus         1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l--~lA~k~~~~~   56 (83)
T smart00385        1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAAL--YLAAKTEEIP   56 (83)
T ss_pred             CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHH--HHHHHHhcCC
Confidence            489999999999999999999999999873 3 6899999999999  9999988754

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

>COG5024 Cyclin [Cell division and chromosome partitioning]

Probab=97.69  E-value=0.00038  Score=65.78  Aligned_cols=150  Identities=13%  Similarity=0.156  Sum_probs=120.3

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCC-CCHHHHHHHH-cCCCHHHHHH
Q 023713          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP-RTVKEFCSVA-NGTTKKEIGR  186 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p-~tl~eia~~~-~~v~~~~i~~  186 (278)
                      ..++|.++=.+|+|-+.+...|..|..+.+..+...=.+...+++.|+|+||+-+.+. .++++++-+. ...+.++|.+
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            4678888888999988999999999999999887776678899999999999988754 5567775532 3568999999


Q ss_pred             HHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHH
Q 023713          187 AKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVW  264 (278)
Q Consensus       187 ~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~  264 (278)
                      +.+.+...|+..      +....|..|+.|+-....-+......+..+.+...-.-  .+-.|..+|||+-  |++..+.
T Consensus       296 aE~~ml~~l~f~------is~P~P~sFLRriSka~dyd~~srt~~k~~~e~s~~~~~f~~~~~S~~~aaa~--~~s~~~~  367 (440)
T COG5024         296 AERYMLEVLDFN------ISWPSPMSFLRRISKASDYDIFSRTPAKFSSEISPVDYKFIQISPSWCAAAAM--YLSRKIL  367 (440)
T ss_pred             HHHHHhhhcccc------cCCCChHHHHHHHHhhcccchhhhhhHhhhCCchHhhhhhccCCchHHHHHHH--HHHHhhh
Confidence            999999999987      77778999988888877777777777777766655432  3344888999988  9888776


Q ss_pred             HH
Q 023713          265 AF  266 (278)
Q Consensus       265 ~~  266 (278)
                      +-
T Consensus       368 ~~  369 (440)
T COG5024         368 SQ  369 (440)
T ss_pred             cc
Confidence            53

>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=97.68  E-value=0.00024  Score=56.91  Aligned_cols=84  Identities=11%  Similarity=0.245  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh--CCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHH
Q 023713          106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKE  183 (278)
Q Consensus       106 l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~--~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~  183 (278)
                      +.-|..+|+.+|++|+|++.+.+....+|+.+..  -.++++|..+.+..+|+|..||..+.++|++||-.. ..-.+..
T Consensus        11 y~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~-Yr~qpq~   89 (135)
T PF01857_consen   11 YKLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKA-YRKQPQA   89 (135)
T ss_dssp             HHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHH-HTTSTT-
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHH-HHhcccc
Confidence            3457889999999999999999999999988764  457899999999999999999999999999999774 4444444


Q ss_pred             HHHHHHH
Q 023713          184 IGRAKEF  190 (278)
Q Consensus       184 i~~~~~~  190 (278)
                      -..+|+.
T Consensus        90 ~~~Vyr~   96 (135)
T PF01857_consen   90 SSHVYRS   96 (135)
T ss_dssp             -THHHHS
T ss_pred             cccceEE
Confidence            4444543

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.

>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=97.67  E-value=0.0009  Score=59.65  Aligned_cols=142  Identities=14%  Similarity=0.229  Sum_probs=95.6

Q ss_pred             HHHHHHHHhc--CCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcC----CCHHHH
Q 023713          111 KSISAMSDRL--GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG----TTKKEI  184 (278)
Q Consensus       111 ~~I~~i~~~L--~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~----v~~~~i  184 (278)
                      ..+-++++++  .||.+|+-+|..+|++++=.+...--+++.+.++|+|+||+.+..-+|..+|+.- ..    -+...|
T Consensus        61 ~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn-~~~~~~k~~e~v  139 (325)
T KOG2496|consen   61 LSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKN-MNGRKWKTHEIV  139 (325)
T ss_pred             HHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhh-ccCcccccHHHH
Confidence            3445555555  7899999999999999987777777889999999999999999999999999874 43    334555


Q ss_pred             HHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCC--CHHHH---HHHHHHHHHhhhcC--CCCChhHHHHHHH
Q 023713          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGM--TNQAV---KAAQEAVQKSEDLD--IRLILVFFSLFLV  255 (278)
Q Consensus       185 ~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l--~~~v~---~~A~~i~~~~~~~~--~Gr~P~~iaaA~v  255 (278)
                      -+.-..+.+.|+...  .+..|.-..+-|+..+-..|..  +++..   ....+.++.+.-.+  .=-.|.=||-|+|
T Consensus       140 Lk~E~~llqsL~f~L--~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAi  215 (325)
T KOG2496|consen  140 LKYEFLLLQSLKFSL--TVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAI  215 (325)
T ss_pred             HhchHHHHHhhhhhh--eecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHH
Confidence            555557777777652  1112322334455444444321  22221   22235556555544  4578999999999

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

Probab=97.11  E-value=0.00034  Score=42.80  Aligned_cols=28  Identities=29%  Similarity=0.545  Sum_probs=23.9

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      ..|+.||+ .  .+...+|..+|..||.|.+
T Consensus         9 ~~C~~C~~-~--~~~~~dG~~yC~~cG~~~E   36 (36)
T PF11781_consen    9 EPCPVCGS-R--WFYSDDGFYYCDRCGHQSE   36 (36)
T ss_pred             CcCCCCCC-e--EeEccCCEEEhhhCceEcC
Confidence            34999998 3  7778999999999999974

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=96.93  E-value=0.005  Score=55.52  Aligned_cols=107  Identities=20%  Similarity=0.207  Sum_probs=77.4

Q ss_pred             HHHHHHHHHHHHhcCCCHHH--HHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTI--KDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v--~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i  184 (278)
                      .+....|-.+.+.|+||++.  ...+.++......-.+..--+++.+|+||+|+|.|..++|.+..-..-.+++.++.+|
T Consensus       139 ~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~ei  218 (367)
T KOG0835|consen  139 EHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREI  218 (367)
T ss_pred             eccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHH
Confidence            44567788889999999754  6777777776665566666789999999999999999988665533222578899988


Q ss_pred             HHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcC
Q 023713          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG  222 (278)
Q Consensus       185 ~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~  222 (278)
                      -..-..+.......      .|   -..+|.-|+..+.
T Consensus       219 d~ic~~l~~lY~~~------~p---~~~li~~~vd~~k  247 (367)
T KOG0835|consen  219 DEICYRLIPLYKRA------KP---DETLIEAFVDRLK  247 (367)
T ss_pred             HHHHHHHHHHHHhc------cc---CHHHHHHHHHHhh
Confidence            87776666655542      11   2467777777664

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

Probab=96.83  E-value=0.0011  Score=39.71  Aligned_cols=31  Identities=16%  Similarity=0.442  Sum_probs=25.4

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      |....|+.||+ + .++....+..+|.+||.+.
T Consensus         1 ~~~~~C~~C~~-~-~i~~~~~~~~~C~~Cg~~~   31 (33)
T PF08792_consen    1 SNLKKCSKCGG-N-GIVNKEDDYEVCIFCGSSF   31 (33)
T ss_pred             CCceEcCCCCC-C-eEEEecCCeEEcccCCcEe
Confidence            45678999998 3 4555789999999999885

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=96.58  E-value=0.0015  Score=44.14  Aligned_cols=31  Identities=35%  Similarity=0.745  Sum_probs=28.2

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      .+||.|+. ..+||++.+-.+.|..||.+|.+
T Consensus        12 VkCp~C~n-~q~vFsha~t~V~C~~Cg~~L~~   42 (59)
T PRK00415         12 VKCPDCGN-EQVVFSHASTVVRCLVCGKTLAE   42 (59)
T ss_pred             EECCCCCC-eEEEEecCCcEEECcccCCCccc
Confidence            47999998 58999999999999999999963

>PRK00420 hypothetical protein; Validated

Probab=96.56  E-value=0.0017  Score=50.08  Aligned_cols=31  Identities=26%  Similarity=0.560  Sum_probs=24.4

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      |-...||.||.+   .+-..+|+.+|..||.++.
T Consensus        21 ml~~~CP~Cg~p---Lf~lk~g~~~Cp~Cg~~~~   51 (112)
T PRK00420         21 MLSKHCPVCGLP---LFELKDGEVVCPVHGKVYI   51 (112)
T ss_pred             HccCCCCCCCCc---ceecCCCceECCCCCCeee
Confidence            344789999983   3434899999999999874

>PHA00626 hypothetical protein

Probab=96.49  E-value=0.0025  Score=42.33  Aligned_cols=31  Identities=19%  Similarity=0.538  Sum_probs=23.7

Q ss_pred             CCCCCCCCCCceeEe----CCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFD----HSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D----~~~G~~vC~~CG~Vl~e   35 (278)
                      +.||.||+ .+++..    -.+..++|.+||.-...
T Consensus         1 m~CP~CGS-~~Ivrcg~cr~~snrYkCkdCGY~ft~   35 (59)
T PHA00626          1 MSCPKCGS-GNIAKEKTMRGWSDDYVCCDCGYNDSK   35 (59)
T ss_pred             CCCCCCCC-ceeeeeceecccCcceEcCCCCCeech
Confidence            47999999 466643    23789999999998753

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

Probab=96.44  E-value=0.0018  Score=44.61  Aligned_cols=31  Identities=35%  Similarity=0.764  Sum_probs=28.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      ..||.||. ..++|++.+-.+.|..||.+|-+
T Consensus        20 VkCpdC~N-~q~vFshast~V~C~~CG~~l~~   50 (67)
T COG2051          20 VKCPDCGN-EQVVFSHASTVVTCLICGTTLAE   50 (67)
T ss_pred             EECCCCCC-EEEEeccCceEEEecccccEEEe
Confidence            46999998 57999999999999999999963

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

Probab=96.42  E-value=0.0015  Score=43.65  Aligned_cols=31  Identities=32%  Similarity=0.687  Sum_probs=23.3

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      .+||.|+. ..+||++.+-.+.|..||.+|.+
T Consensus         8 VkCp~C~~-~q~vFSha~t~V~C~~Cg~~L~~   38 (55)
T PF01667_consen    8 VKCPGCYN-IQTVFSHAQTVVKCVVCGTVLAQ   38 (55)
T ss_dssp             EE-TTT-S-EEEEETT-SS-EE-SSSTSEEEE
T ss_pred             EECCCCCC-eeEEEecCCeEEEcccCCCEecC
Confidence            57999998 68999999999999999999963

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.

>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=96.39  E-value=0.008  Score=45.97  Aligned_cols=55  Identities=13%  Similarity=0.064  Sum_probs=45.0

Q ss_pred             CHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHH
Q 023713          209 HASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWA  265 (278)
Q Consensus       209 ~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~  265 (278)
                      .|.+|+.+|....+.+.++...|+.+++.+.-..  .+-+|..||||+|  +++..+..
T Consensus         2 Tp~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai--~lA~~~~~   58 (118)
T PF02984_consen    2 TPYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAI--LLARKILG   58 (118)
T ss_dssp             -HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHH--HHHHHHHH
T ss_pred             cHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHH--HHHHHHhC
Confidence            5899999997766677889999999999876543  7999999999999  88887754

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 ....

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=96.27  E-value=0.0023  Score=36.16  Aligned_cols=23  Identities=22%  Similarity=0.897  Sum_probs=18.4

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGL   31 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~   31 (278)
                      +..||+||..  +    ..+..+|.+||.
T Consensus         2 ~~~Cp~Cg~~--~----~~~~~fC~~CG~   24 (26)
T PF13248_consen    2 EMFCPNCGAE--I----DPDAKFCPNCGA   24 (26)
T ss_pred             cCCCcccCCc--C----CcccccChhhCC
Confidence            3899999983  2    356999999996

>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=96.24  E-value=0.025  Score=43.22  Aligned_cols=87  Identities=14%  Similarity=0.129  Sum_probs=62.0

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCC-CCCHHHHHHHHcCCCHHHHHHH
Q 023713          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVANGTTKKEIGRA  187 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~-p~tl~eia~~~~~v~~~~i~~~  187 (278)
                      .+.+|+.+....+....+...|..+.....-...+-.-++..+||||+|+|.+..+. +.--..+.. .++++..+|..+
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            456777775544555677788888877755443355678999999999999998765 333344555 478999999999


Q ss_pred             HHHHHHHhh
Q 023713          188 KEFIVKHLE  196 (278)
Q Consensus       188 ~~~l~~~L~  196 (278)
                      ++.|.+.+.
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 ....

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

Probab=96.22  E-value=0.1  Score=47.42  Aligned_cols=142  Identities=15%  Similarity=0.226  Sum_probs=104.1

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCC-CCCCCcHHHHHHHHHHHHHHhcC-CCCCHHHHHHHH-cCCCHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQK-PLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVA-NGTTKKE  183 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~-~~~gr~~~~~aAAclY~acR~~~-~p~tl~eia~~~-~~v~~~~  183 (278)
                      .-.++++-++|+-.+|...+.-.|..+|.+...-. -...-....+--+|+|+|.+.+. .|--+.|||.+. .-.+..+
T Consensus       146 aILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~dd  225 (408)
T KOG0655|consen  146 AILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDD  225 (408)
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHH
Confidence            34589999999999999999999999999975422 12223456777899999999876 578889998762 3468999


Q ss_pred             HHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCH-----------H-HHHHHHHHHHHh-hhcC-CCCChhH
Q 023713          184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN-----------Q-AVKAAQEAVQKS-EDLD-IRLILVF  249 (278)
Q Consensus       184 i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~-----------~-v~~~A~~i~~~~-~~~~-~Gr~P~~  249 (278)
                      |.+....|.+.|+-+      +.++.....+.-|.+-+.+++           + ..+.| +|++.. .+.+ .-.+...
T Consensus       226 IltmE~iilkal~W~------l~PiTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqia-qlLDlc~ldids~~fsYri  298 (408)
T KOG0655|consen  226 ILTMELIILKALKWE------LSPITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIA-QLLDLCILDIDSLEFSYRI  298 (408)
T ss_pred             HHHHHHHHHHHhccc------ccceehHHHHHHHHHHHhcCCCCceeccccchHHHHHHH-HHHHHHHhccccccchHHH
Confidence            999999999999987      677788888888887765541           1 22222 233322 2223 4677788


Q ss_pred             HHHHHH
Q 023713          250 FSLFLV  255 (278)
Q Consensus       250 iaaA~v  255 (278)
                      +|||||
T Consensus       299 laAAal  304 (408)
T KOG0655|consen  299 LAAAAL  304 (408)
T ss_pred             HHHHHH
Confidence            888888

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

Probab=96.21  E-value=0.02  Score=52.82  Aligned_cols=92  Identities=12%  Similarity=0.147  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCC----CCHHHHHHHHcCCCHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP----RTVKEFCSVANGTTKK  182 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p----~tl~eia~~~~~v~~~  182 (278)
                      .-..+++.+++..-+|...++.+|-.+|.++.=++++...++..+|+|||.+|.+.++..    .++.|=.+..+..+..
T Consensus       383 rSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrr  462 (497)
T KOG4164|consen  383 RSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRR  462 (497)
T ss_pred             HHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHH
Confidence            334567777777788888899999999999887788877788999999999999988765    2333333323455555


Q ss_pred             HHHHHHHHHHHHhhhh
Q 023713          183 EIGRAKEFIVKHLEAE  198 (278)
Q Consensus       183 ~i~~~~~~l~~~L~~~  198 (278)
                      +|-...--+.-.|.+.
T Consensus       463 dLia~Ef~VlvaLefa  478 (497)
T KOG4164|consen  463 DLIAFEFPVLVALEFA  478 (497)
T ss_pred             hhhhhhhhHHHhhhhh
Confidence            5555444444444443

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

Probab=96.20  E-value=0.0036  Score=40.39  Aligned_cols=31  Identities=39%  Similarity=0.748  Sum_probs=25.3

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      |....||+||.  .+.+|+..+...|..||.-+
T Consensus         1 ~~~y~C~~CG~--~~~~~~~~~~~~Cp~CG~~~   31 (46)
T PRK00398          1 MAEYKCARCGR--EVELDEYGTGVRCPYCGYRI   31 (46)
T ss_pred             CCEEECCCCCC--EEEECCCCCceECCCCCCeE
Confidence            56689999997  47778777799999999643

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=96.09  E-value=0.0031  Score=34.57  Aligned_cols=22  Identities=27%  Similarity=0.916  Sum_probs=17.1

Q ss_pred             CCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713            5 YCADCKRLTEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V   32 (278)
                      .||+||.+   +   ..+..+|++||.-
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            59999984   2   2468889999974

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

Probab=95.96  E-value=0.0023  Score=38.60  Aligned_cols=28  Identities=18%  Similarity=0.662  Sum_probs=15.9

Q ss_pred             CCCCCCCCCCceeEe----CCCCceEcCCCcccc
Q 023713            4 SYCADCKRLTEVVFD----HSAGDTICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D----~~~G~~vC~~CG~Vl   33 (278)
                      ..||.||++  +...    ...-..||+.||.|-
T Consensus         1 kfC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~Ih   32 (34)
T PF14803_consen    1 KFCPQCGGP--LERRIPEGDDRERLVCPACGFIH   32 (34)
T ss_dssp             -B-TTT--B---EEE--TT-SS-EEEETTTTEEE
T ss_pred             CccccccCh--hhhhcCCCCCccceECCCCCCEE
Confidence            369999984  4333    355568999999983

>PLN00209 ribosomal protein S27; Provisional

Probab=95.92  E-value=0.0051  Score=44.68  Aligned_cols=31  Identities=32%  Similarity=0.641  Sum_probs=28.2

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      ..||.|+. ..+||++++-.+.|..||.+|.+
T Consensus        37 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~   67 (86)
T PLN00209         37 VKCQGCFN-ITTVFSHSQTVVVCGSCQTVLCQ   67 (86)
T ss_pred             EECCCCCC-eeEEEecCceEEEccccCCEeec
Confidence            47999998 58999999999999999999963

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=95.86  E-value=0.0058  Score=44.27  Aligned_cols=31  Identities=26%  Similarity=0.624  Sum_probs=28.2

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      ..||.|+. ..+||++++-.+.|..||.+|.+
T Consensus        36 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~   66 (85)
T PTZ00083         36 VKCPGCSQ-ITTVFSHAQTVVLCGGCSSQLCQ   66 (85)
T ss_pred             EECCCCCC-eeEEEecCceEEEccccCCEeec
Confidence            57999998 68999999999999999999953

>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase

Probab=95.74  E-value=0.008  Score=36.90  Aligned_cols=28  Identities=32%  Similarity=0.736  Sum_probs=22.0

Q ss_pred             CCCCCCCCCCceeEeC--CCCceEcCCCcc
Q 023713            4 SYCADCKRLTEVVFDH--SAGDTICSECGL   31 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~--~~G~~vC~~CG~   31 (278)
                      ..||.||+....-+|.  .+|..+|..||.
T Consensus         4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~   33 (37)
T smart00778        4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA   33 (37)
T ss_pred             cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence            5799999865555665  559999999984

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.

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

Probab=95.63  E-value=0.01  Score=36.07  Aligned_cols=31  Identities=16%  Similarity=0.452  Sum_probs=19.5

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      |..||+||. --+......+...|..||.+.+
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            468999997 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 ....

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

Probab=95.46  E-value=0.0068  Score=47.83  Aligned_cols=24  Identities=29%  Similarity=0.895  Sum_probs=20.0

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECG   30 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG   30 (278)
                      ...||.||.+  + |- .+|+++|+.||
T Consensus        28 ~~hCp~Cg~P--L-F~-KdG~v~CPvC~   51 (131)
T COG1645          28 AKHCPKCGTP--L-FR-KDGEVFCPVCG   51 (131)
T ss_pred             HhhCcccCCc--c-ee-eCCeEECCCCC
Confidence            3679999984  3 43 89999999999

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

Probab=95.20  E-value=0.017  Score=42.05  Aligned_cols=30  Identities=30%  Similarity=0.560  Sum_probs=25.9

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      ...||.||+ + .|.-..+|-+.|..||.++.
T Consensus        35 ~~~Cp~C~~-~-~VkR~a~GIW~C~kCg~~fA   64 (89)
T COG1997          35 KHVCPFCGR-T-TVKRIATGIWKCRKCGAKFA   64 (89)
T ss_pred             CCcCCCCCC-c-ceeeeccCeEEcCCCCCeec
Confidence            467999998 4 57778999999999999875

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

Probab=95.05  E-value=0.018  Score=33.67  Aligned_cols=27  Identities=22%  Similarity=0.367  Sum_probs=14.6

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V   32 (278)
                      .-.||.|+++ ..-.  +...+||.+||.-
T Consensus         2 ~p~Cp~C~se-~~y~--D~~~~vCp~C~~e   28 (30)
T PF08274_consen    2 LPKCPLCGSE-YTYE--DGELLVCPECGHE   28 (30)
T ss_dssp             S---TTT------EE---SSSEEETTTTEE
T ss_pred             CCCCCCCCCc-ceec--cCCEEeCCccccc
Confidence            3579999995 3333  4789999999964

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.

>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=95.02  E-value=0.014  Score=44.87  Aligned_cols=31  Identities=19%  Similarity=0.602  Sum_probs=26.4

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      .+.||.||..   .||-..--+||..||.++...
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            4789999984   788888889999999998644

The function of members of this family is unknown.

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=95.01  E-value=0.013  Score=39.24  Aligned_cols=31  Identities=39%  Similarity=0.768  Sum_probs=21.2

Q ss_pred             CCCCCCCCCCCceeEeCCCCc-eEcCCCccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGD-TICSECGLVLE   34 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~-~vC~~CG~Vl~   34 (278)
                      +..||.||..-+ +.|...|+ +.|.+||.-++
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            368999998422 23333355 56999999885

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

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=94.92  E-value=0.019  Score=37.76  Aligned_cols=27  Identities=19%  Similarity=0.605  Sum_probs=21.1

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      ..||.||+ + +..+ ..+...|..||...
T Consensus        21 ~fCP~Cg~-~-~m~~-~~~r~~C~~Cgyt~   47 (50)
T PRK00432         21 KFCPRCGS-G-FMAE-HLDRWHCGKCGYTE   47 (50)
T ss_pred             CcCcCCCc-c-hhec-cCCcEECCCcCCEE
Confidence            57999998 4 4444 45899999999864

>PRK11827 hypothetical protein; Provisional

Probab=94.90  E-value=0.021  Score=38.98  Aligned_cols=28  Identities=18%  Similarity=0.494  Sum_probs=24.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      ..||.|++  .+.+|....+++|..||.+.
T Consensus         9 LaCP~ckg--~L~~~~~~~~Lic~~~~laY   36 (60)
T PRK11827          9 IACPVCNG--KLWYNQEKQELICKLDNLAF   36 (60)
T ss_pred             eECCCCCC--cCeEcCCCCeEECCccCeec
Confidence            57999997  48888888899999999986

>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=94.74  E-value=0.019  Score=32.42  Aligned_cols=25  Identities=28%  Similarity=0.771  Sum_probs=19.3

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      ..||+|+..  |    ......|..||.++.
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    356889999999864

Several members are annotated as putative helicases.

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=94.35  E-value=0.031  Score=36.72  Aligned_cols=29  Identities=17%  Similarity=0.612  Sum_probs=19.9

Q ss_pred             CCCCCCCCCCceeEeCCC--CceEcCCCccccc
Q 023713            4 SYCADCKRLTEVVFDHSA--GDTICSECGLVLE   34 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~--G~~vC~~CG~Vl~   34 (278)
                      ..||.||.  .+......  ...+|+.||.+..
T Consensus         1 ~FCp~Cg~--~l~~~~~~~~~~~vC~~Cg~~~~   31 (52)
T smart00661        1 KFCPKCGN--MLIPKEGKEKRRFVCRKCGYEEP   31 (52)
T ss_pred             CCCCCCCC--ccccccCCCCCEEECCcCCCeEE
Confidence            36999997  23333222  3899999998764

>PRK10220 hypothetical protein; Provisional

Probab=94.34  E-value=0.12  Score=39.27  Aligned_cols=31  Identities=26%  Similarity=0.467  Sum_probs=23.1

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      |..-.||.|+++ -.-.  ....+||.+||.--.
T Consensus         1 m~lP~CP~C~se-ytY~--d~~~~vCpeC~hEW~   31 (111)
T PRK10220          1 MSLPHCPKCNSE-YTYE--DNGMYICPECAHEWN   31 (111)
T ss_pred             CCCCcCCCCCCc-ceEc--CCCeEECCcccCcCC
Confidence            677889999984 3333  356799999997553

>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=94.28  E-value=0.041  Score=34.61  Aligned_cols=25  Identities=32%  Similarity=0.828  Sum_probs=19.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECG   30 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG   30 (278)
                      ...||.||.+  +.. ..+|+++|..|+
T Consensus        17 ~~~Cp~C~~P--L~~-~k~g~~~Cv~C~   41 (41)
T PF06677_consen   17 DEHCPDCGTP--LMR-DKDGKIYCVSCG   41 (41)
T ss_pred             cCccCCCCCe--eEE-ecCCCEECCCCC
Confidence            4689999863  444 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 [].

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=94.23  E-value=0.054  Score=36.89  Aligned_cols=29  Identities=24%  Similarity=0.634  Sum_probs=21.2

Q ss_pred             CCCCCCCCCCCCceeEeCCCC-------ceEcCCCcc
Q 023713            2 ADSYCADCKRLTEVVFDHSAG-------DTICSECGL   31 (278)
Q Consensus         2 ~~~~Cp~Cg~~~~vv~D~~~G-------~~vC~~CG~   31 (278)
                      +...||-||+ ..+.++...+       .+.|.+||.
T Consensus         2 ~LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga   37 (61)
T PF14354_consen    2 ELKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA   37 (61)
T ss_pred             CCcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence            3568999998 5666665544       366999999

>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300

Probab=94.07  E-value=0.032  Score=43.69  Aligned_cols=31  Identities=10%  Similarity=0.203  Sum_probs=26.6

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      .+.||.||..   .||-..--+||..||.++...
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            4789999984   788888999999999998644

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.

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

Probab=94.06  E-value=0.042  Score=34.34  Aligned_cols=29  Identities=31%  Similarity=0.620  Sum_probs=16.4

Q ss_pred             CCCCCCCCCCcee-EeC--CCCceEcCCCccc
Q 023713            4 SYCADCKRLTEVV-FDH--SAGDTICSECGLV   32 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv-~D~--~~G~~vC~~CG~V   32 (278)
                      ..||.||+....- +|.  .+|..+|..|+-+
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            4699999855544 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.

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=94.04  E-value=0.043  Score=44.92  Aligned_cols=30  Identities=27%  Similarity=0.569  Sum_probs=20.6

Q ss_pred             CCCCCCCCCCceeEeCC---CCce-----EcCCCcccc
Q 023713            4 SYCADCKRLTEVVFDHS---AGDT-----ICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~---~G~~-----vC~~CG~Vl   33 (278)
                      +.||+||++.+-+.|..   .|..     -|++||.-.
T Consensus         1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f   38 (154)
T PRK00464          1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF   38 (154)
T ss_pred             CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence            57999998533566643   4543     499999765

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

Probab=94.03  E-value=0.053  Score=37.99  Aligned_cols=18  Identities=33%  Similarity=0.752  Sum_probs=16.0

Q ss_pred             EeCCCCceEcCCCccccc
Q 023713           17 FDHSAGDTICSECGLVLE   34 (278)
Q Consensus        17 ~D~~~G~~vC~~CG~Vl~   34 (278)
                      ++..+|.++|.+||.+..
T Consensus        47 ~~i~eg~L~Cp~c~r~YP   64 (68)
T PF03966_consen   47 VEIVEGELICPECGREYP   64 (68)
T ss_dssp             EETTTTEEEETTTTEEEE
T ss_pred             ccccCCEEEcCCCCCEEe
Confidence            688999999999999863

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.

>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=93.99  E-value=1.4  Score=35.63  Aligned_cols=89  Identities=15%  Similarity=0.154  Sum_probs=65.9

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh---CCC--CCCCcHHHHHHHHHHHHHH-hcCCCCCHHHHHHHHcCCCHH
Q 023713          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVED---QKP--LRGRNQEAIVAACLYIACR-QENKPRTVKEFCSVANGTTKK  182 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~---~~~--~~gr~~~~~aAAclY~acR-~~~~p~tl~eia~~~~~v~~~  182 (278)
                      ..+++.++....+++..+.-.|..+..++..   ...  +...+..-+..+|+-+|.+ ..+...+.+..+.+ .|++.+
T Consensus        54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v-~gis~~  132 (149)
T PF08613_consen   54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKV-GGISLK  132 (149)
T ss_dssp             HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHH-HTS-HH
T ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhh-cCCCHH
Confidence            5778999999999999999999999999877   222  3345666677777777877 56788999999996 899999


Q ss_pred             HHHHHHHHHHHHhhhh
Q 023713          183 EIGRAKEFIVKHLEAE  198 (278)
Q Consensus       183 ~i~~~~~~l~~~L~~~  198 (278)
                      +|++..+.+...++.+
T Consensus       133 eln~lE~~fL~~l~~~  148 (149)
T PF08613_consen  133 ELNELEREFLKLLDYN  148 (149)
T ss_dssp             HHHHHHHHHHHHTTT-
T ss_pred             HHHHHHHHHHHHCCCc
Confidence            9999999999888753

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.

>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=93.83  E-value=0.07  Score=31.53  Aligned_cols=27  Identities=19%  Similarity=0.465  Sum_probs=16.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V   32 (278)
                      ..|+.||++  .+.....-..+|++||..
T Consensus         4 rfC~~CG~~--t~~~~~g~~r~C~~Cg~~   30 (32)
T PF09297_consen    4 RFCGRCGAP--TKPAPGGWARRCPSCGHE   30 (32)
T ss_dssp             SB-TTT--B--EEE-SSSS-EEESSSS-E
T ss_pred             cccCcCCcc--ccCCCCcCEeECCCCcCE
Confidence            689999984  455566788999999975

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

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=93.65  E-value=0.026  Score=34.70  Aligned_cols=29  Identities=28%  Similarity=0.607  Sum_probs=20.7

Q ss_pred             CCCCCCCCCCceeEe-----CCCCceEcCCCccccc
Q 023713            4 SYCADCKRLTEVVFD-----HSAGDTICSECGLVLE   34 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D-----~~~G~~vC~~CG~Vl~   34 (278)
                      ..||+||..  ..++     ...+.+.|++||.++.
T Consensus         3 ~~CP~C~~~--~~v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         3 IQCPNCKTS--FRVVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             EECCCCCCE--EEeCHHHcCCCCCEEECCCCCCEEE
Confidence            579999983  2222     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.

>COG2835 Uncharacterized conserved protein [Function unknown]

Probab=93.65  E-value=0.049  Score=36.96  Aligned_cols=30  Identities=30%  Similarity=0.651  Sum_probs=26.5

Q ss_pred             CCCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         2 ~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      +...||.|.+.  +.+|.+.++++|..||...
T Consensus         7 eiLaCP~~kg~--L~~~~~~~~L~c~~~~~aY   36 (60)
T COG2835           7 EILACPVCKGP--LVYDEEKQELICPRCKLAY   36 (60)
T ss_pred             eeeeccCcCCc--ceEeccCCEEEecccCcee
Confidence            45679999983  9999999999999999986

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

Probab=93.22  E-value=0.06  Score=41.59  Aligned_cols=25  Identities=32%  Similarity=0.634  Sum_probs=20.4

Q ss_pred             CCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            6 CADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         6 Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ||.||+ .-+|.     .+-|.+||+.++.+
T Consensus         1 CPvCg~-~l~vt-----~l~C~~C~t~i~G~   25 (113)
T PF09862_consen    1 CPVCGG-ELVVT-----RLKCPSCGTEIEGE   25 (113)
T ss_pred             CCCCCC-ceEEE-----EEEcCCCCCEEEee
Confidence            999998 44454     89999999999643

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

Probab=93.17  E-value=0.052  Score=35.21  Aligned_cols=27  Identities=26%  Similarity=0.733  Sum_probs=22.1

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V   32 (278)
                      ..||.||. ..+..|+.. .+.|..||..
T Consensus        20 ~~CPrCG~-gvfmA~H~d-R~~CGkCgyT   46 (51)
T COG1998          20 RFCPRCGP-GVFMADHKD-RWACGKCGYT   46 (51)
T ss_pred             ccCCCCCC-cchhhhcCc-eeEeccccce
Confidence            57999996 566777766 8999999986

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

Probab=93.12  E-value=5.2  Score=34.43  Aligned_cols=138  Identities=17%  Similarity=0.219  Sum_probs=95.8

Q ss_pred             HHHHHHHhcCCC--HHHHHHHHHHHHHHhh--CCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHH
Q 023713          112 SISAMSDRLGLV--TTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (278)
Q Consensus       112 ~I~~i~~~L~Lp--~~v~e~A~~i~k~~~~--~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~  187 (278)
                      .|.+++.+|||.  +.+.+.|.+|.+...-  .+..-|-.-..-|.-|+=+|.-.-++|..-.-... ..|.++++-.+.
T Consensus         2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avK-LSGl~k~~Y~~~   80 (262)
T KOG4557|consen    2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVK-LSGLSKKAYSRS   80 (262)
T ss_pred             cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHH-hccccHHHHHHH
Confidence            478899999993  5789999999887643  23334445566777888888888888877666667 489999999999


Q ss_pred             HHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh-------cCC-CCChhHHHHHHHHHHH
Q 023713          188 KEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED-------LDI-RLILVFFSLFLVETHI  259 (278)
Q Consensus       188 ~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~-------~~~-Gr~P~~iaaA~v~~~~  259 (278)
                      ++.+...||+.      . ..+    |..+|=+||. .++++.|.+++..-+.       .+. =.+|. .++||+  |.
T Consensus        81 ~~sfe~llgln------~-~~~----VrdlaVQfgc-~evi~~a~~vl~syk~~lpaT~~~~~D~SrP~-ft~aA~--~~  145 (262)
T KOG4557|consen   81 FNSFENLLGLN------I-KLN----VRDLAVQFGC-VEVIKSAQNVLSSYKERLPATRRANADFSRPV-FTAAAF--YL  145 (262)
T ss_pred             HHHHHHHhcch------h-hcC----HHHHHHHHhH-HHHHHHHHHHHHHHHhcCchhhhcCCcccchH-HHHHHH--HH
Confidence            99999999986      1 122    3445555554 3566677777765544       122 22454 556667  78


Q ss_pred             HHHHHH
Q 023713          260 QLIVWA  265 (278)
Q Consensus       260 ~~~~~~  265 (278)
                      ++.+..
T Consensus       146 ack~lK  151 (262)
T KOG4557|consen  146 ACKKLK  151 (262)
T ss_pred             HHHHHH
Confidence            877653

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

Probab=92.63  E-value=0.29  Score=37.04  Aligned_cols=33  Identities=24%  Similarity=0.614  Sum_probs=24.5

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      |.+-.||.|.++  -+++ ..+.++|++|+.--.+.
T Consensus         1 ~~lp~cp~c~sE--ytYe-d~~~~~cpec~~ew~~~   33 (112)
T COG2824           1 MSLPPCPKCNSE--YTYE-DGGQLICPECAHEWNEN   33 (112)
T ss_pred             CCCCCCCccCCc--eEEe-cCceEeCchhccccccc
Confidence            566789999983  4554 45599999999876544

>TIGR00244 transcriptional regulator NrdR

Probab=92.47  E-value=0.13  Score=41.53  Aligned_cols=30  Identities=30%  Similarity=0.633  Sum_probs=23.5

Q ss_pred             CCCCCCCCCCceeEeC---CCCceE-----cCCCcccc
Q 023713            4 SYCADCKRLTEVVFDH---SAGDTI-----CSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~---~~G~~v-----C~~CG~Vl   33 (278)
                      |.||.||...+-|.|.   ..|..|     |.+||.=.
T Consensus         1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF   38 (147)
T TIGR00244         1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF   38 (147)
T ss_pred             CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence            5799999866668886   667666     99999754

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.

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=92.12  E-value=0.14  Score=34.04  Aligned_cols=31  Identities=26%  Similarity=0.382  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCce-eE---eC--CCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEV-VF---DH--SAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~v-v~---D~--~~G~~vC~~CG~Vl~e   35 (278)
                      ..||.||+. +. +.   |.  ..|-..|.+||.....
T Consensus         2 kPCPfCGg~-~~~~~~~~~~~~~~~~~~C~~Cga~~~~   38 (53)
T TIGR03655         2 KPCPFCGGA-DVYLRRGFDPLDLSHYFECSTCGASGPV   38 (53)
T ss_pred             CCCCCCCCc-ceeeEeccCCCCCEEEEECCCCCCCccc
Confidence            579999994 44 32   32  3444579999998653

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.

>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA

Probab=91.99  E-value=0.4  Score=36.47  Aligned_cols=30  Identities=20%  Similarity=0.432  Sum_probs=21.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      -.||.|+++ -.-.|  ...+||++||.--.+.
T Consensus         3 p~CP~C~se-ytY~d--g~~~iCpeC~~EW~~~   32 (109)
T TIGR00686         3 PPCPKCNSE-YTYHD--GTQLICPSCLYEWNEN   32 (109)
T ss_pred             CcCCcCCCc-ceEec--CCeeECcccccccccc
Confidence            479999984 33433  5579999999876544

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).

>PRK12495 hypothetical protein; Provisional

Probab=91.89  E-value=0.1  Score=44.75  Aligned_cols=32  Identities=22%  Similarity=0.668  Sum_probs=25.8

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      |....|+.||.+   |+ ...|..+|..|+.++.+.
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            456789999984   44 458999999999998753

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

Probab=91.59  E-value=0.1  Score=37.15  Aligned_cols=30  Identities=27%  Similarity=0.683  Sum_probs=27.1

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      .+||.|-. .+.+|.+++..++|.+|++|+=
T Consensus        35 VkC~gc~~-iT~vfSHaqtvVvc~~c~~il~   64 (84)
T KOG1779|consen   35 VKCPGCFK-ITTVFSHAQTVVVCEGCSTILC   64 (84)
T ss_pred             EEcCCceE-EEEEeecCceEEEcCCCceEEE
Confidence            57999997 6889999999999999999973

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=90.98  E-value=0.14  Score=38.78  Aligned_cols=28  Identities=29%  Similarity=0.789  Sum_probs=21.8

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      ..||.||+.    +.+..+.++|..||.+...
T Consensus         1 ~fC~~Cg~~----l~~~~~~~~C~~C~~~~~~   28 (104)
T TIGR01384         1 KFCPKCGSL----MTPKNGVYVCPSCGYEKEK   28 (104)
T ss_pred             CCCcccCcc----cccCCCeEECcCCCCcccc
Confidence            379999972    3456789999999998653

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.

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=90.96  E-value=0.15  Score=38.49  Aligned_cols=41  Identities=22%  Similarity=0.467  Sum_probs=28.1

Q ss_pred             CCCCCCCCCCce--eEeCCCCceEcCCCccccccc------ccccccchh
Q 023713            4 SYCADCKRLTEV--VFDHSAGDTICSECGLVLEAY------SVDETSEWR   45 (278)
Q Consensus         4 ~~Cp~Cg~~~~v--v~D~~~G~~vC~~CG~Vl~e~------~id~~~ewr   45 (278)
                      ..||+||. ..+  -.|...+..+|..||..-+-.      .||-..+|.
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            46999996 333  355677899999999986432      245455564

>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=90.52  E-value=0.16  Score=30.11  Aligned_cols=24  Identities=29%  Similarity=0.641  Sum_probs=17.4

Q ss_pred             CCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713            5 YCADCKRLTEVVFDHSAGDTICSECGL   31 (278)
Q Consensus         5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~   31 (278)
                      .|.+||.+   +.+.....+-|.+||.
T Consensus         2 ~C~~Cg~~---~~~~~~~~irC~~CG~   25 (32)
T PF03604_consen    2 ICGECGAE---VELKPGDPIRCPECGH   25 (32)
T ss_dssp             BESSSSSS---E-BSTSSTSSBSSSS-
T ss_pred             CCCcCCCe---eEcCCCCcEECCcCCC
Confidence            58999984   3356677889999996

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 ....

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

Probab=90.35  E-value=0.16  Score=37.58  Aligned_cols=32  Identities=25%  Similarity=0.440  Sum_probs=25.3

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ...||.||. .. +.-...|-+-|..||.++...
T Consensus        35 ky~Cp~Cgk-~~-vkR~a~GIW~C~~C~~~~AGG   66 (90)
T PF01780_consen   35 KYTCPFCGK-TS-VKRVATGIWKCKKCGKKFAGG   66 (90)
T ss_dssp             -BEESSSSS-SE-EEEEETTEEEETTTTEEEE-B
T ss_pred             CCcCCCCCC-ce-eEEeeeEEeecCCCCCEEeCC
Confidence            357999998 44 666799999999999998643

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 ....

>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=90.33  E-value=1.3  Score=33.99  Aligned_cols=55  Identities=13%  Similarity=0.129  Sum_probs=46.8

Q ss_pred             HHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHHH
Q 023713          210 ASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWAF  266 (278)
Q Consensus       210 p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~~  266 (278)
                      ..+||.+.+..+++++++...|..+.++.....  ...++.-+++|++  +||..++..
T Consensus        34 ~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl--~lA~K~~e~   90 (127)
T PF00134_consen   34 IIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACL--FLASKMEED   90 (127)
T ss_dssp             HHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHH--HHHHHHHTS
T ss_pred             HHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHH--HHhhhhhcc
Confidence            457899999999999999999999999887654  4678889999999  999999865

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 ....

>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=90.24  E-value=0.32  Score=31.21  Aligned_cols=27  Identities=22%  Similarity=0.438  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGL   31 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~   31 (278)
                      ..||.||+ ..+..-...+..-|.+|+.
T Consensus        19 ~~CP~Cg~-~~~~~~~~~~~~~C~~C~~   45 (46)
T PF12760_consen   19 FVCPHCGS-TKHYRLKTRGRYRCKACRK   45 (46)
T ss_pred             CCCCCCCC-eeeEEeCCCCeEECCCCCC
Confidence            56999998 4555555579999999974

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

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

Probab=90.16  E-value=0.2  Score=37.55  Aligned_cols=30  Identities=30%  Similarity=0.746  Sum_probs=23.2

Q ss_pred             CCCCCCCCCCcee---Ee--CCCCceEcCCCccccc
Q 023713            4 SYCADCKRLTEVV---FD--HSAGDTICSECGLVLE   34 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv---~D--~~~G~~vC~~CG~Vl~   34 (278)
                      ..||.||+. .++   +|  ..-|..+|.+||.-.+
T Consensus        23 FtCp~Cghe-~vs~ctvkk~~~~g~~~Cg~CGls~e   57 (104)
T COG4888          23 FTCPRCGHE-KVSSCTVKKTVNIGTAVCGNCGLSFE   57 (104)
T ss_pred             EecCccCCe-eeeEEEEEecCceeEEEcccCcceEE
Confidence            469999984 555   55  3678999999998764

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=89.95  E-value=0.16  Score=31.47  Aligned_cols=31  Identities=32%  Similarity=0.555  Sum_probs=20.4

Q ss_pred             CCCCCCCCCCCceeEeCC-CCceEcCCCcccc
Q 023713            3 DSYCADCKRLTEVVFDHS-AGDTICSECGLVL   33 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~-~G~~vC~~CG~Vl   33 (278)
                      ...|++||..-++..... .....|.+||.-+
T Consensus         5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~   36 (41)
T smart00834        5 EYRCEDCGHTFEVLQKISDDPLATCPECGGDV   36 (41)
T ss_pred             EEEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence            357999997323333322 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.

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

Probab=89.90  E-value=0.14  Score=37.25  Aligned_cols=33  Identities=24%  Similarity=0.466  Sum_probs=18.1

Q ss_pred             CCCCCCCCCCcee--EeC--CCCceEcCCCccccccc
Q 023713            4 SYCADCKRLTEVV--FDH--SAGDTICSECGLVLEAY   36 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv--~D~--~~G~~vC~~CG~Vl~e~   36 (278)
                      ..||.|+...+|.  .|.  ..|.+.|..||...+-.
T Consensus        23 F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~   59 (81)
T PF05129_consen   23 FDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK   59 (81)
T ss_dssp             ---TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred             EcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence            4699999545553  343  57899999999987543

; PDB: 1WII_A.

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

Probab=89.67  E-value=0.25  Score=29.41  Aligned_cols=24  Identities=25%  Similarity=0.729  Sum_probs=18.8

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGL   31 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~   31 (278)
                      ..|+.||-    ++|.......|..||.
T Consensus         2 ~~C~~CGy----~y~~~~~~~~CP~Cg~   25 (33)
T cd00350           2 YVCPVCGY----IYDGEEAPWVCPVCGA   25 (33)
T ss_pred             EECCCCCC----EECCCcCCCcCcCCCC
Confidence            46888885    5677777888999886

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.

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=89.52  E-value=1.7  Score=30.21  Aligned_cols=71  Identities=17%  Similarity=0.216  Sum_probs=44.0

Q ss_pred             HHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC-CHHHHHHHHHHH
Q 023713          113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGRAKEFI  191 (278)
Q Consensus       113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v-~~~~i~~~~~~l  191 (278)
                      |.+++..++++.....+   +|+.........-.....+.-|.-|+.-    .+.++.|||.. .|. +...+.+.+++.
T Consensus         4 ~~~la~~~~~s~~~l~~---~f~~~~~~s~~~~~~~~r~~~a~~~l~~----~~~~~~~ia~~-~g~~s~~~f~r~Fk~~   75 (84)
T smart00342        4 LEDLAEALGMSPRHLQR---LFKKETGTTPKQYLRDRRLERARRLLRD----TDLSVTEIALR-VGFSSQSYFSRAFKKL   75 (84)
T ss_pred             HHHHHHHhCCCHHHHHH---HHHHHhCcCHHHHHHHHHHHHHHHHHHc----CCCCHHHHHHH-hCCCChHHHHHHHHHH
Confidence            67888999998655444   4444432211110112233444444431    28999999995 999 999999998764

>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=89.41  E-value=0.25  Score=34.39  Aligned_cols=29  Identities=21%  Similarity=0.540  Sum_probs=21.8

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      ..||.||...  ..+......+|..||...+
T Consensus        29 q~C~~CG~~~--~~~~~~r~~~C~~Cg~~~~   57 (69)
T PF07282_consen   29 QTCPRCGHRN--KKRRSGRVFTCPNCGFEMD   57 (69)
T ss_pred             cCccCccccc--ccccccceEEcCCCCCEEC
Confidence            6799999731  2246777899999999864

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

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=89.41  E-value=0.29  Score=31.22  Aligned_cols=27  Identities=30%  Similarity=0.645  Sum_probs=20.1

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      ..|.+||.+  +..+ ..+.+-|++||.=+
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            679999984  3333 57889999999643

present in RNA polymerase I, II and III

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

Probab=89.22  E-value=0.25  Score=33.39  Aligned_cols=27  Identities=30%  Similarity=0.641  Sum_probs=15.5

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V   32 (278)
                      ..|..||..  |-.+..--...|.+||.|
T Consensus        10 ~~CtSCg~~--i~p~e~~v~F~CPnCGe~   36 (61)
T COG2888          10 PVCTSCGRE--IAPGETAVKFPCPNCGEV   36 (61)
T ss_pred             ceeccCCCE--eccCCceeEeeCCCCCce
Confidence            367777752  324444445667777743

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

Probab=89.08  E-value=0.052  Score=33.12  Aligned_cols=29  Identities=28%  Similarity=0.775  Sum_probs=21.0

Q ss_pred             CCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            5 YCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      .||.||+.=++.+++..-+.+|..||.-|
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            68999974466777778888999998754

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 ....

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=88.94  E-value=0.17  Score=31.02  Aligned_cols=29  Identities=28%  Similarity=0.636  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCceeEe----CCCCceEcCCCcccc
Q 023713            4 SYCADCKRLTEVVFD----HSAGDTICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D----~~~G~~vC~~CG~Vl   33 (278)
                      ..||+|+..-. |.|    ...+.+-|+.||.+.
T Consensus         3 i~CP~C~~~f~-v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    3 ITCPNCQTRFR-VPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             EECCCCCceEE-cCHHHcccCCcEEECCCCCcEe
Confidence            57999997322 222    357789999999886

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=88.93  E-value=0.35  Score=30.14  Aligned_cols=27  Identities=26%  Similarity=0.541  Sum_probs=18.9

Q ss_pred             CCCCCCCCCceeEe---------CCCCceEcCCCccc
Q 023713            5 YCADCKRLTEVVFD---------HSAGDTICSECGLV   32 (278)
Q Consensus         5 ~Cp~Cg~~~~vv~D---------~~~G~~vC~~CG~V   32 (278)
                      .||.||.. +.++=         +.+-..+|.+||..
T Consensus         2 ~Cp~C~~~-~a~~~q~Q~RsaDE~mT~fy~C~~C~~~   37 (40)
T smart00440        2 PCPKCGNR-EATFFQLQTRSADEPMTVFYVCTKCGHR   37 (40)
T ss_pred             cCCCCCCC-eEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence            69999984 44431         23447899999964

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

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

Probab=88.85  E-value=0.34  Score=37.54  Aligned_cols=32  Identities=31%  Similarity=0.729  Sum_probs=24.3

Q ss_pred             CCCCCCCCCCCceeE--eCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVF--DHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~--D~~~G~~vC~~CG~Vl~e~   36 (278)
                      |..||.||+-  ++.  |...+.++|..||...+-.
T Consensus         2 m~FCp~Cgsl--l~p~~~~~~~~l~C~kCgye~~~~   35 (113)
T COG1594           2 MRFCPKCGSL--LYPKKDDEGGKLVCRKCGYEEEAS   35 (113)
T ss_pred             ccccCCccCe--eEEeEcCCCcEEECCCCCcchhcc
Confidence            6799999982  333  3367799999999987644

>PTZ00255 60S ribosomal protein L37a; Provisional

Probab=88.63  E-value=0.32  Score=35.94  Aligned_cols=32  Identities=19%  Similarity=0.421  Sum_probs=25.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ...||.||. .. +.-...|-+.|..||.++...
T Consensus        36 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGG   67 (90)
T PTZ00255         36 KYFCPFCGK-HA-VKRQAVGIWRCKGCKKTVAGG   67 (90)
T ss_pred             CccCCCCCC-Cc-eeeeeeEEEEcCCCCCEEeCC
Confidence            468999997 44 455688999999999998644

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

Probab=88.49  E-value=1.9  Score=37.01  Aligned_cols=83  Identities=14%  Similarity=0.312  Sum_probs=58.2

Q ss_pred             HHHHHHHhcCCCHHHHHHHHHHHHHHhhC-CCC----CCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHH
Q 023713          112 SISAMSDRLGLVTTIKDRANEIYKKVEDQ-KPL----RGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGR  186 (278)
Q Consensus       112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~-~~~----~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~  186 (278)
                      -|+++|=.||+-+ ++..|.++.+...+. ..+    .-.+.-..++|++|.|||..+..+.-..+..+ .|+++.++..
T Consensus        95 ~VrdlaVQfgc~e-vi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~~-sg~~~s~F~~  172 (262)
T KOG4557|consen   95 NVRDLAVQFGCVE-VIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIEV-SGTSESEFSC  172 (262)
T ss_pred             CHHHHHHHHhHHH-HHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhcccc-cCCCHHHHHH
Confidence            4566666666654 667777777766542 111    12345679999999999999988877766664 8999988887


Q ss_pred             HHHHHHHHhh
Q 023713          187 AKEFIVKHLE  196 (278)
Q Consensus       187 ~~~~l~~~L~  196 (278)
                      .-+.+.+...
T Consensus       173 l~kqler~~~  182 (262)
T KOG4557|consen  173 LSKQLERNYK  182 (262)
T ss_pred             HHHHHHHHHH
Confidence            7777766553

>COG4640 Predicted membrane protein [Function unknown]

Probab=87.91  E-value=0.28  Score=45.59  Aligned_cols=28  Identities=21%  Similarity=0.692  Sum_probs=21.5

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      |..||.||+.      -.+++.-|+.||.=+...
T Consensus         1 M~fC~kcG~q------k~Ed~~qC~qCG~~~t~~   28 (465)
T COG4640           1 MKFCPKCGSQ------KAEDDVQCTQCGHKFTSR   28 (465)
T ss_pred             CCcccccccc------cccccccccccCCcCCch
Confidence            6789999973      235677799999887644

>PF12773 DZR: Double zinc ribbon

Probab=87.48  E-value=0.31  Score=31.62  Aligned_cols=27  Identities=22%  Similarity=0.662  Sum_probs=12.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      ..||.||..  +. .......+|..||..+
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            445555542  11 2223345555555544

>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG

Probab=87.38  E-value=0.42  Score=31.66  Aligned_cols=29  Identities=34%  Similarity=0.673  Sum_probs=20.9

Q ss_pred             CCCCCCCCCceeEeCCCCce----EcCCCcccc
Q 023713            5 YCADCKRLTEVVFDHSAGDT----ICSECGLVL   33 (278)
Q Consensus         5 ~Cp~Cg~~~~vv~D~~~G~~----vC~~CG~Vl   33 (278)
                      .||+||....+..|.+.|.-    =|.-|-.=+
T Consensus         2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI   34 (52)
T PF14255_consen    2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPI   34 (52)
T ss_pred             CCCCCCCeeEEEEecCCCCeeEEeehhhcCCcc
Confidence            69999987788999888842    255555443

>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=87.35  E-value=0.56  Score=26.86  Aligned_cols=22  Identities=23%  Similarity=0.533  Sum_probs=12.1

Q ss_pred             CCCCCCCCCceeEeCCCCceEcCC
Q 023713            5 YCADCKRLTEVVFDHSAGDTICSE   28 (278)
Q Consensus         5 ~Cp~Cg~~~~vv~D~~~G~~vC~~   28 (278)
                      .||.||+  .++.+..+-.+.|.+
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            4999998  477776777788875

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.

>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]

Probab=87.32  E-value=0.15  Score=34.32  Aligned_cols=25  Identities=32%  Similarity=0.883  Sum_probs=19.7

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCC-Cccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSE-CGLVLE   34 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~-CG~Vl~   34 (278)
                      ..|+.||.+  +-    .++.+|++ ||.+++
T Consensus         9 ~HC~VCg~a--Ip----~de~~CSe~C~eil~   34 (64)
T COG4068           9 RHCVVCGKA--IP----PDEQVCSEECGEILN   34 (64)
T ss_pred             ccccccCCc--CC----CccchHHHHHHHHHH
Confidence            579999984  33    56999996 999885

>TIGR00280 L37a ribosomal protein L37a

Probab=87.05  E-value=0.42  Score=35.40  Aligned_cols=32  Identities=25%  Similarity=0.459  Sum_probs=25.9

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ...||.||. .. +.-...|-+.|..||.++...
T Consensus        35 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGG   66 (91)
T TIGR00280        35 KYVCPFCGK-KT-VKRGSTGIWTCRKCGAKFAGG   66 (91)
T ss_pred             CccCCCCCC-Cc-eEEEeeEEEEcCCCCCEEeCC
Confidence            468999997 44 556789999999999998643

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

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=87.04  E-value=0.16  Score=42.64  Aligned_cols=31  Identities=23%  Similarity=0.491  Sum_probs=23.3

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      ..||.|+.. =...|.-+....|+.||.+|.+
T Consensus       118 Y~Cp~C~~r-ytf~eA~~~~F~Cp~Cg~~L~~  148 (178)
T PRK06266        118 FFCPNCHIR-FTFDEAMEYGFRCPQCGEMLEE  148 (178)
T ss_pred             EECCCCCcE-EeHHHHhhcCCcCCCCCCCCee
Confidence            569999973 2234456678999999999974

>TIGR00569 ccl1 cyclin ccl1

Probab=86.90  E-value=14  Score=33.74  Aligned_cols=72  Identities=6%  Similarity=-0.009  Sum_probs=47.3

Q ss_pred             CHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC--CHHHHHHHHHHHHHHhh
Q 023713          123 VTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT--TKKEIGRAKEFIVKHLE  196 (278)
Q Consensus       123 p~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v--~~~~i~~~~~~l~~~L~  196 (278)
                      ++.+...|..+...+.--...--..|..+|+||||+|+|..++...-.+- ++ .++  +..+++..+..+++...
T Consensus       180 ~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA~~~~~~~l~~~~~-e~-~~~~~~~~~~~~l~~~~~~~~~  253 (305)
T TIGR00569       180 PEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNMESYLT-EQ-LSVPGNREELPQLIDIMRELRI  253 (305)
T ss_pred             hHHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHHHHHHhCCCCcccch-hh-hcccccHHHHHHHHHHHHHHHH
Confidence            34567777777776554333223678999999999999999876544332 32 344  66777777666655443

University).

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

Probab=86.81  E-value=1  Score=26.66  Aligned_cols=28  Identities=18%  Similarity=0.297  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713          165 KPRTVKEFCSVANGTTKKEIGRAKEFIVK  193 (278)
Q Consensus       165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~  193 (278)
                      .|.|-.|||+. +|.+..++.|.++++.+
T Consensus         1 l~mtr~diA~~-lG~t~ETVSR~l~~l~~   28 (32)
T PF00325_consen    1 LPMTRQDIADY-LGLTRETVSRILKKLER   28 (32)
T ss_dssp             EE--HHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred             CCcCHHHHHHH-hCCcHHHHHHHHHHHHH
Confidence            36788999994 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 ....

>PRK05978 hypothetical protein; Provisional

Probab=86.57  E-value=0.49  Score=38.39  Aligned_cols=35  Identities=17%  Similarity=0.369  Sum_probs=23.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVD   39 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id   39 (278)
                      .+||+||. ..+..-+-.=..-|..||.-++-..-|
T Consensus        34 grCP~CG~-G~LF~g~Lkv~~~C~~CG~~~~~~~a~   68 (148)
T PRK05978         34 GRCPACGE-GKLFRAFLKPVDHCAACGEDFTHHRAD   68 (148)
T ss_pred             CcCCCCCC-CcccccccccCCCccccCCccccCCcc
Confidence            68999997 555333333456799999988644333

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=86.44  E-value=0.82  Score=31.49  Aligned_cols=30  Identities=20%  Similarity=0.353  Sum_probs=20.4

Q ss_pred             CCCCCCCCCCCceeEeCCCC--ceEcCCCcccc
Q 023713            3 DSYCADCKRLTEVVFDHSAG--DTICSECGLVL   33 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G--~~vC~~CG~Vl   33 (278)
                      ...||.||.. ++..-...|  ..+|..||...
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 443333344  36899999964

>COG1656 Uncharacterized conserved protein [Function unknown]

Probab=86.34  E-value=0.38  Score=39.56  Aligned_cols=39  Identities=23%  Similarity=0.438  Sum_probs=26.0

Q ss_pred             CCCCCCCCCCCceeEe---------------CCCCceEcCCCcccccccccccccchhhcc
Q 023713            3 DSYCADCKRLTEVVFD---------------HSAGDTICSECGLVLEAYSVDETSEWRIFA   48 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D---------------~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~   48 (278)
                      ...||+|+++  ++.-               ..+-..+|++||.+.-     -|+.|+...
T Consensus        97 ~~RCp~CN~~--L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW-----~GsHw~~m~  150 (165)
T COG1656          97 FSRCPECNGE--LEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYW-----KGSHWRRMV  150 (165)
T ss_pred             cccCcccCCE--eccCcHHHHhhccchhhhhcccceeECCCCccccc-----CchHHHHHH
Confidence            5789999973  3222               2233677999999986     456776543

>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=86.18  E-value=0.22  Score=46.31  Aligned_cols=78  Identities=15%  Similarity=0.210  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHHHHh-hCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhc
Q 023713          121 GLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM  199 (278)
Q Consensus       121 ~Lp~~v~e~A~~i~k~~~-~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~  199 (278)
                      ++|+.++..|.++|+... ....+++..-.+-+.+|+|+||...+.+..+..... ..+++++...+.|..|.+.|+...
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 GLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIK-RSPLPPKVYKKLLNTFENLLGNSS   89 (353)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcC-CCCCCHHHHHHHHHHHHHHHhCCC
Confidence            456889999999999887 455667766678889999999999999998888666 489999999999999999888763

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.

>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []

Probab=85.89  E-value=0.39  Score=31.09  Aligned_cols=14  Identities=29%  Similarity=0.669  Sum_probs=7.3

Q ss_pred             eEcCCCcccccccc
Q 023713           24 TICSECGLVLEAYS   37 (278)
Q Consensus        24 ~vC~~CG~Vl~e~~   37 (278)
                      ..|..||.|.++..
T Consensus         2 y~C~~CgyvYd~~~   15 (47)
T PF00301_consen    2 YQCPVCGYVYDPEK   15 (47)
T ss_dssp             EEETTTSBEEETTT
T ss_pred             cCCCCCCEEEcCCc
Confidence            34555555555443

The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....

>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed

Probab=85.67  E-value=0.53  Score=34.80  Aligned_cols=32  Identities=25%  Similarity=0.481  Sum_probs=25.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ...||.||. .. +.-...|-+-|..||.++...
T Consensus        36 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGG   67 (90)
T PRK03976         36 KHVCPVCGR-PK-VKRVGTGIWECRKCGAKFAGG   67 (90)
T ss_pred             CccCCCCCC-Cc-eEEEEEEEEEcCCCCCEEeCC
Confidence            468999997 34 555789999999999998644

>PRK12286 rpmF 50S ribosomal protein L32; Reviewed

Probab=85.65  E-value=0.6  Score=31.53  Aligned_cols=28  Identities=21%  Similarity=0.533  Sum_probs=19.9

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSV   38 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~i   38 (278)
                      ..||+||..       ..-..||.+||+--+..++
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            469999973       2348899999987654443

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=85.53  E-value=0.71  Score=31.27  Aligned_cols=28  Identities=25%  Similarity=0.557  Sum_probs=16.6

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V   32 (278)
                      ...|..||..  |..-...-...|.+||.+
T Consensus         7 ~~~CtSCg~~--i~~~~~~~~F~CPnCG~~   34 (59)
T PRK14890          7 PPKCTSCGIE--IAPREKAVKFLCPNCGEV   34 (59)
T ss_pred             CccccCCCCc--ccCCCccCEeeCCCCCCe
Confidence            3568888862  221112345678888876

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=85.51  E-value=0.85  Score=32.35  Aligned_cols=31  Identities=13%  Similarity=0.275  Sum_probs=22.3

Q ss_pred             CCCCCCCCCCCceeEeC-------CCCceEcC--CCccccc
Q 023713            3 DSYCADCKRLTEVVFDH-------SAGDTICS--ECGLVLE   34 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~-------~~G~~vC~--~CG~Vl~   34 (278)
                      |+.||.||+ .+.|.+.       .+--..|+  +||....
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            579999998 4666664       23345788  8998874

>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=85.24  E-value=0.66  Score=28.71  Aligned_cols=28  Identities=25%  Similarity=0.555  Sum_probs=15.5

Q ss_pred             CCCCCCCCCceeEe--------CCCCceEcCCCccc
Q 023713            5 YCADCKRLTEVVFD--------HSAGDTICSECGLV   32 (278)
Q Consensus         5 ~Cp~Cg~~~~vv~D--------~~~G~~vC~~CG~V   32 (278)
                      .||.||+...+.+.        +.+-..+|.+||..
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            69999985333332        12335789999964

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 ....

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=84.91  E-value=0.71  Score=30.75  Aligned_cols=28  Identities=21%  Similarity=0.545  Sum_probs=20.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      ..+|+.||..   +. ...--+||.+||++.-
T Consensus         5 ~~~C~~Cg~~---~~-~~dDiVvCp~CgapyH   32 (54)
T PF14446_consen    5 GCKCPVCGKK---FK-DGDDIVVCPECGAPYH   32 (54)
T ss_pred             CccChhhCCc---cc-CCCCEEECCCCCCccc
Confidence            3689999973   22 3445789999999973

>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed

Probab=84.86  E-value=0.48  Score=31.87  Aligned_cols=25  Identities=24%  Similarity=0.538  Sum_probs=19.2

Q ss_pred             CCCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         2 ~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      -+..|+.||. -++       ..+|..||....
T Consensus         4 ~mr~C~~Cgv-YTL-------k~~CP~CG~~t~   28 (56)
T PRK13130          4 KIRKCPKCGV-YTL-------KEICPVCGGKTK   28 (56)
T ss_pred             cceECCCCCC-EEc-------cccCcCCCCCCC
Confidence            4678999997 333       678999998753

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

Probab=84.49  E-value=0.34  Score=31.63  Aligned_cols=27  Identities=33%  Similarity=0.635  Sum_probs=21.3

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V   32 (278)
                      ..|-.||..  +..|.....+.|+.||.=
T Consensus         7 Y~C~~Cg~~--~~~~~~~~~irCp~Cg~r   33 (49)
T COG1996           7 YKCARCGRE--VELDQETRGIRCPYCGSR   33 (49)
T ss_pred             EEhhhcCCe--eehhhccCceeCCCCCcE
Confidence            579999983  445678889999999963

>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center

Probab=84.36  E-value=0.81  Score=30.03  Aligned_cols=11  Identities=27%  Similarity=0.911  Sum_probs=5.9

Q ss_pred             EcCCCcccccc
Q 023713           25 ICSECGLVLEA   35 (278)
Q Consensus        25 vC~~CG~Vl~e   35 (278)
                      +|+.||.|.++
T Consensus         3 ~C~~CgyiYd~   13 (50)
T cd00730           3 ECRICGYIYDP   13 (50)
T ss_pred             CCCCCCeEECC
Confidence            45555555543

Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.

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

Probab=84.01  E-value=2.4  Score=43.31  Aligned_cols=84  Identities=12%  Similarity=0.229  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh--CCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~--~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i  184 (278)
                      .-|..+|+.+|++|.|.+.+.+...-+|.-...  -.+++.|..+.+.-+|+|+.+|..+...|+.||-.. ..-.....
T Consensus       678 ~LAavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~-YR~QPqa~  756 (920)
T KOG1010|consen  678 HLAAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRA-YRRQPQAV  756 (920)
T ss_pred             HHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHH-HhcCchhh
Confidence            346788999999999999999998888876543  346788999999999999999999999999999763 55556666


Q ss_pred             HHHHHHH
Q 023713          185 GRAKEFI  191 (278)
Q Consensus       185 ~~~~~~l  191 (278)
                      ..+|+.+
T Consensus       757 ~~vyRsV  763 (920)
T KOG1010|consen  757 SLVYRSV  763 (920)
T ss_pred             hhhhhhe
Confidence            6666654

>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=83.94  E-value=0.78  Score=34.76  Aligned_cols=27  Identities=26%  Similarity=0.609  Sum_probs=22.2

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ..||.||. ..+|+     ++-|.+||+-++.+
T Consensus         7 ~~cPvcg~-~~iVT-----eL~c~~~etTVrg~   33 (122)
T COG3877           7 NRCPVCGR-KLIVT-----ELKCSNCETTVRGN   33 (122)
T ss_pred             CCCCcccc-cceeE-----EEecCCCCceEecc
Confidence            68999998 46776     89999999998633

>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=83.82  E-value=0.52  Score=36.62  Aligned_cols=39  Identities=18%  Similarity=0.364  Sum_probs=25.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSE   43 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~e   43 (278)
                      ..||+||. ..+..-.-.=.-.|..||.=+..+--|++|-
T Consensus        22 grCP~CGe-GrLF~gFLK~~p~C~aCG~dyg~~~a~DgPa   60 (126)
T COG5349          22 GRCPRCGE-GRLFRGFLKVVPACEACGLDYGFADADDGPA   60 (126)
T ss_pred             CCCCCCCC-chhhhhhcccCchhhhccccccCCcccCCCc
Confidence            57999997 5543223333558999998876665555543

>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]

Probab=83.60  E-value=0.89  Score=36.79  Aligned_cols=30  Identities=30%  Similarity=0.604  Sum_probs=21.6

Q ss_pred             CCCCCCCCCCceeEeC---CCCce-----EcCCCcccc
Q 023713            4 SYCADCKRLTEVVFDH---SAGDT-----ICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~---~~G~~-----vC~~CG~Vl   33 (278)
                      |.||.|+++.+=|.|+   ..|..     .|.+||.=.
T Consensus         1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RF   38 (156)
T COG1327           1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERF   38 (156)
T ss_pred             CCCCCCCCCCCeeeecccccccchhhhhhccccccccc
Confidence            5799999865667785   44543     599998654

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

Probab=83.57  E-value=0.67  Score=31.14  Aligned_cols=24  Identities=21%  Similarity=0.642  Sum_probs=17.4

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      ..||+||..       .....+|.+||+.=.
T Consensus        27 ~~c~~cg~~-------~~~H~vc~~cG~y~~   50 (56)
T PF01783_consen   27 VKCPNCGEP-------KLPHRVCPSCGYYKG   50 (56)
T ss_dssp             EESSSSSSE-------ESTTSBCTTTBBSSS
T ss_pred             eeeccCCCE-------ecccEeeCCCCeECC
Confidence            469999962       245789999996644

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 ....

>TIGR02443 conserved hypothetical metal-binding protein

Probab=82.88  E-value=1.3  Score=30.07  Aligned_cols=30  Identities=20%  Similarity=0.459  Sum_probs=20.2

Q ss_pred             CCCCCCCCCCceeEeCCCC--ceEcCCCcccc
Q 023713            4 SYCADCKRLTEVVFDHSAG--DTICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G--~~vC~~CG~Vl   33 (278)
                      -.||.|+.-..++.=.++|  ..-|.+||.--
T Consensus        10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~   41 (59)
T TIGR02443        10 AVCPACSAQDTLAMWKENNIELVECVECGYQE   41 (59)
T ss_pred             ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence            4799999854554323333  37799999863

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.

>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=82.64  E-value=3.8  Score=26.73  Aligned_cols=34  Identities=21%  Similarity=0.265  Sum_probs=28.3

Q ss_pred             HhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHh
Q 023713          161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL  195 (278)
Q Consensus       161 R~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L  195 (278)
                      ..++-|+|..|+|+. ++|+..+|.+.++.|.+.+
T Consensus        10 ~~~~~~it~~eLa~~-l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen   10 LESKEPITAKELAEE-LGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHTTTSBEHHHHHHH-CTS-HHHHHHHHHHHHHTT
T ss_pred             HHcCCCcCHHHHHHH-hCCCHHHHHHHHHHHHHCC
Confidence            345667999999995 9999999999999997665

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 ....

>PF12773 DZR: Double zinc ribbon

Probab=82.59  E-value=0.99  Score=29.20  Aligned_cols=22  Identities=23%  Similarity=0.832  Sum_probs=16.5

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECG   30 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG   30 (278)
                      ...||.||..      ...+..+|..||
T Consensus        29 ~~~C~~Cg~~------~~~~~~fC~~CG   50 (50)
T PF12773_consen   29 KKICPNCGAE------NPPNAKFCPNCG   50 (50)
T ss_pred             CCCCcCCcCC------CcCCcCccCccc
Confidence            3579999973      235688999998

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

Probab=82.46  E-value=8.3  Score=33.64  Aligned_cols=100  Identities=18%  Similarity=0.195  Sum_probs=63.3

Q ss_pred             HHHHHHhcCC-CHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHH
Q 023713          113 ISAMSDRLGL-VTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI  191 (278)
Q Consensus       113 I~~i~~~L~L-p~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l  191 (278)
                      +.++-+.+|+ +....+-+..|...-+...+.-=-.|..+|-||+|+||-..+.+.+-.=+++  +.+|...+....++|
T Consensus       157 L~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~~~~w~~e--l~vD~ekV~~~v~~I  234 (264)
T KOG0794|consen  157 LLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDIPKAWFAE--LSVDMEKVKDIVQEI  234 (264)
T ss_pred             HHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCChHHHHHHH--HhccHHHHHHHHHHH
Confidence            3444444555 3446666666655544444333356889999999999998887775444444  468888888888888


Q ss_pred             HHHhhhhcccccccCCCCHHHHHHHHHhhcC
Q 023713          192 VKHLEAEMGQSVEMGTIHASDYLRRFCSNLG  222 (278)
Q Consensus       192 ~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~  222 (278)
                      .+....-       ...+-.. |....++|-
T Consensus       235 ~~lYe~w-------k~~~E~~-v~~ll~kl~  257 (264)
T KOG0794|consen  235 LKLYELW-------KIFDEKK-VKKLLSKLP  257 (264)
T ss_pred             HHHHHHH-------hhhhHHH-HHHHHHhcc
Confidence            8777653       1223333 555555554

>PF14122 YokU: YokU-like protein

Probab=81.41  E-value=1.1  Score=32.74  Aligned_cols=24  Identities=33%  Similarity=0.595  Sum_probs=18.0

Q ss_pred             CCCceEcCCCcccccccccccccc
Q 023713           20 SAGDTICSECGLVLEAYSVDETSE   43 (278)
Q Consensus        20 ~~G~~vC~~CG~Vl~e~~id~~~e   43 (278)
                      .+=.++|.+||.|..+..+...-|
T Consensus        32 ~tP~i~C~~CgmvYq~d~vi~EIE   55 (87)
T PF14122_consen   32 DTPAIICSNCGMVYQDDEVIKEIE   55 (87)
T ss_pred             CCceeeecCCCcEEehhHHHHHHh
Confidence            344589999999998877665554

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=81.38  E-value=6.7  Score=28.74  Aligned_cols=42  Identities=19%  Similarity=0.186  Sum_probs=34.1

Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHcC-CCHHHHHHHHHHHHHHhhh
Q 023713          153 AACLYIACRQENKPRTVKEFCSVANG-TTKKEIGRAKEFIVKHLEA  197 (278)
Q Consensus       153 AAclY~acR~~~~p~tl~eia~~~~~-v~~~~i~~~~~~l~~~L~~  197 (278)
                      ..++|++-+..  ..|+.+|+.. +| .+..++..+++++.+.+..
T Consensus        33 ~ia~yl~~~~~--~~s~~~Ig~~-fg~r~hStV~~a~~ri~~~~~~   75 (90)
T cd06571          33 QIAMYLARELT--GLSLPEIGRA-FGGRDHSTVLHAVRKIEELLEE   75 (90)
T ss_pred             HHHHHHHHHHh--CCCHHHHHHH-hCCCCHhHHHHHHHHHHHHHHh
Confidence            35677775544  5689999995 77 9999999999999998864

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.

>PRK02935 hypothetical protein; Provisional

Probab=81.19  E-value=1.1  Score=34.03  Aligned_cols=27  Identities=22%  Similarity=0.541  Sum_probs=19.5

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      ..||+|+.++...=    -...|..|+.-+.
T Consensus        71 V~CP~C~K~TKmLG----rvD~CM~C~~PLT   97 (110)
T PRK02935         71 VICPSCEKPTKMLG----RVDACMHCNQPLT   97 (110)
T ss_pred             eECCCCCchhhhcc----ceeecCcCCCcCC
Confidence            46999998654332    2458999998875

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=81.06  E-value=0.76  Score=30.04  Aligned_cols=29  Identities=28%  Similarity=0.549  Sum_probs=17.9

Q ss_pred             CCCCCCCCCCCceeEe-CCCCceEcCCCcc
Q 023713            3 DSYCADCKRLTEVVFD-HSAGDTICSECGL   31 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D-~~~G~~vC~~CG~   31 (278)
                      ..+|++||..-++... .+.....|..||.
T Consensus         5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~   34 (52)
T TIGR02605         5 EYRCTACGHRFEVLQKMSDDPLATCPECGG   34 (52)
T ss_pred             EEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence            3579999973222221 2245678999997

This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.

>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150

Probab=81.05  E-value=1.4  Score=33.46  Aligned_cols=32  Identities=19%  Similarity=0.451  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCCceeEe------CC--C-Cc-eEcCCCcccccc
Q 023713            3 DSYCADCKRLTEVVFD------HS--A-GD-TICSECGLVLEA   35 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D------~~--~-G~-~vC~~CG~Vl~e   35 (278)
                      ...||+||.. ....+      ..  . .. ++|+.|+.-|.=
T Consensus         2 p~~CpYCg~~-~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG~   43 (102)
T PF11672_consen    2 PIICPYCGGP-AELVDGSEIYGHRYDDGPYLYVCTPCDAYVGC   43 (102)
T ss_pred             CcccCCCCCe-eEEcccchhcCccCCCCceeEECCCCCceeee
Confidence            3689999984 34333      11  2 32 799999888763

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>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=80.88  E-value=5.1  Score=27.86  Aligned_cols=43  Identities=19%  Similarity=0.238  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHhcC----------CCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713          151 IVAACLYIACRQEN----------KPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (278)
Q Consensus       151 ~aAAclY~acR~~~----------~p~tl~eia~~~~~v~~~~i~~~~~~l~~~  194 (278)
                      +|...++++-+...          .|.|..|||+. +|++..++.+.+++|.+.
T Consensus         3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~-~g~sr~tv~r~l~~l~~~   55 (76)
T PF13545_consen    3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADM-LGVSRETVSRILKRLKDE   55 (76)
T ss_dssp             HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHH-HTSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence            45556666665442          57899999994 999999999999999874

...

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=80.78  E-value=4.8  Score=31.86  Aligned_cols=46  Identities=20%  Similarity=0.186  Sum_probs=39.3

Q ss_pred             cHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713          147 NQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK  193 (278)
Q Consensus       147 ~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~  193 (278)
                      +.+.-..+++|+|-...+.|.+..|||+. .+++...+.+....|.+
T Consensus         6 ~~~YAl~~l~~La~~~~~~~~s~~~ia~~-~~ip~~~l~kil~~L~~   51 (135)
T TIGR02010         6 KGRYAVTAMLDLALNAETGPVTLADISER-QGISLSYLEQLFAKLRK   51 (135)
T ss_pred             HHHHHHHHHHHHHhCCCCCcCcHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence            45666778899997766778999999995 99999999999999976

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

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=80.78  E-value=0.9  Score=44.92  Aligned_cols=43  Identities=19%  Similarity=0.515  Sum_probs=29.7

Q ss_pred             CCCCCCCCCCcee-----Ee----CCCCceEcCCCcccccccc---cccccchhh
Q 023713            4 SYCADCKRLTEVV-----FD----HSAGDTICSECGLVLEAYS---VDETSEWRI   46 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv-----~D----~~~G~~vC~~CG~Vl~e~~---id~~~ewr~   46 (278)
                      ..||+||....+.     +|    +.+-.++|..||..++|+.   ....-+|+.
T Consensus       201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~~~G~Wv~  255 (557)
T PF05876_consen  201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMVRRGRWVA  255 (557)
T ss_pred             ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhccCCeEEEe
Confidence            4799999754433     22    4567899999999998863   223456755

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>TIGR01031 rpmF_bact ribosomal protein L32

Probab=80.63  E-value=1.2  Score=29.85  Aligned_cols=25  Identities=20%  Similarity=0.679  Sum_probs=17.7

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      ..||+||..       ..-.-||..||.--+.
T Consensus        27 ~~C~~cG~~-------~~~H~vc~~cG~Y~gr   51 (55)
T TIGR01031        27 VVCPNCGEF-------KLPHRVCPSCGYYKGR   51 (55)
T ss_pred             eECCCCCCc-------ccCeeECCccCeECCE
Confidence            469999972       2347899999976543

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.

>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=80.46  E-value=3.1  Score=29.97  Aligned_cols=46  Identities=20%  Similarity=0.273  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713          148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (278)
Q Consensus       148 ~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~  194 (278)
                      .+.-.-+.+|++-...+.|.|..|||+. .+++...+.+....|.+.
T Consensus         7 ~~~Al~~l~~la~~~~~~~~s~~eiA~~-~~i~~~~l~kil~~L~~~   52 (83)
T PF02082_consen    7 TDYALRILLYLARHPDGKPVSSKEIAER-LGISPSYLRKILQKLKKA   52 (83)
T ss_dssp             HHHHHHHHHHHHCTTTSC-BEHHHHHHH-HTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCCCCCCCCHHHHHHH-HCcCHHHHHHHHHHHhhC
Confidence            3455567788887777778999999995 999999999999999873

(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.

>TIGR03826 YvyF flagellar operon protein TIGR03826

Probab=80.30  E-value=0.42  Score=38.29  Aligned_cols=29  Identities=31%  Similarity=0.685  Sum_probs=23.6

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      |+...||.||+    +|-. +|..+|.+|....+
T Consensus         1 m~l~nC~~Cgk----lF~~-~~~~iCp~C~~~~e   29 (137)
T TIGR03826         1 MELANCPKCGR----LFVK-TGRDVCPSCYEEEE   29 (137)
T ss_pred             CCCccccccch----hhhh-cCCccCHHHhHHHH
Confidence            77899999998    2444 48999999998864

This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.

>KOG1088 consensus Uncharacterized conserved protein [Function unknown]

Probab=80.26  E-value=0.67  Score=35.75  Aligned_cols=18  Identities=33%  Similarity=0.691  Sum_probs=15.3

Q ss_pred             EeCCCCceEcCCCccccc
Q 023713           17 FDHSAGDTICSECGLVLE   34 (278)
Q Consensus        17 ~D~~~G~~vC~~CG~Vl~   34 (278)
                      .|-.+|+++|.+||.|..
T Consensus        92 ~~v~EG~l~CpetG~vfp  109 (124)
T KOG1088|consen   92 IDVIEGELVCPETGRVFP  109 (124)
T ss_pred             hhhccceEecCCCCcEee
Confidence            455789999999999974

>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria

Probab=80.04  E-value=0.88  Score=28.59  Aligned_cols=29  Identities=28%  Similarity=0.566  Sum_probs=18.4

Q ss_pred             CCCCCCCCCCceeEeC-CCCceEcCCCccc
Q 023713            4 SYCADCKRLTEVVFDH-SAGDTICSECGLV   32 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~-~~G~~vC~~CG~V   32 (278)
                      ..|+.||..-++..-. +.....|..||..
T Consensus         6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~   35 (42)
T PF09723_consen    6 YRCEECGHEFEVLQSISEDDPVPCPECGST   35 (42)
T ss_pred             EEeCCCCCEEEEEEEcCCCCCCcCCCCCCC
Confidence            5789998632333222 2467889999873

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	278
1c9b_A	207	Crystal Structure Of A Human Tbp Core Domain-Human		2e-26
2phg_A	206	Model For Vp16 Binding To Tfiib Length = 206		9e-26
1tfb_A	208	Nmr Studies Of Human General Transcription Factor T		1e-25
1vol_A	204	Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEME		1e-23
3k7a_M	345	Crystal Structure Of An Rna Polymerase Ii-Tfiib Com		6e-20
1d3u_B	201	Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+T		4e-12
1ais_B	200	Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-		4e-12
1rly_A	60	Rdc-Derived Models Of The Zinc Ribbon Domain Of Hum		5e-05
1dl6_A	58	Solution Structure Of Human Tfiib N-Terminal Domain		7e-05
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 =  115 bits (289), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 62/141 (43%), Positives = 87/141 (61%), Gaps = 7/141 (4%)
Query: 103 DRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQ 162
           DR ++ AFK I+ M+DR+ L   I DR N ++K+V +QK L+GR  +AI +ACLYIACRQ
Sbjct: 2   DRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQ 61
Query: 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG 222
           E  PRT KE C+V+   +KKEIGR  + I+K LE     SV++  I   D++ RFCSNL 
Sbjct: 62  EGVPRTFKEICAVSR-ISKKEIGRCFKLILKALET----SVDL--ITTGDFMSRFCSNLC 114
Query: 223 MTNXXXXXXXXXXXXSEDLDI 243
           +              + +LD+
Sbjct: 115 LPKQVQMAATHIARKAVELDL 135

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

Iteration: 1
 Score =  113 bits (283), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 61/140 (43%), Positives = 86/140 (61%), Gaps = 7/140 (5%)
Query: 104 RNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE 163
           R ++ AFK I+ M+DR+ L   I DR N ++K+V +QK L+GR  +AI +ACLYIACRQE
Sbjct: 2   RAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQE 61
Query: 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGM 223
             PRT KE C+V+   +KKEIGR  + I+K LE     SV++  I   D++ RFCSNL +
Sbjct: 62  GVPRTFKEICAVSR-ISKKEIGRCFKLILKALET----SVDL--ITTGDFMSRFCSNLCL 114
Query: 224 TNXXXXXXXXXXXXSEDLDI 243
                         + +LD+
Sbjct: 115 PKQVQMAATHIARKAVELDL 134

>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 =  113 bits (283), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 61/140 (43%), Positives = 86/140 (61%), Gaps = 7/140 (5%)
Query: 104 RNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE 163
           R ++ AFK I+ M+DR+ L   I DR N ++K+V +QK L+GR  +AI +ACLYIACRQE
Sbjct: 4   RAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQE 63
Query: 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGM 223
             PRT KE C+V+   +KKEIGR  + I+K LE     SV++  I   D++ RFCSNL +
Sbjct: 64  GVPRTFKEICAVSR-ISKKEIGRCFKLILKALET----SVDL--ITTGDFMSRFCSNLCL 116
Query: 224 TNXXXXXXXXXXXXSEDLDI 243
                         + +LD+
Sbjct: 117 PKQVQMAATHIARKAVELDL 136

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

Iteration: 1
 Score =  106 bits (264), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/138 (41%), Positives = 83/138 (60%), Gaps = 7/138 (5%)
Query: 106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK 165
           ++ AFK I+ M+DR+ L     DR N ++++  +QK L+GR  +AI +ACLYIACRQE  
Sbjct: 2   MMNAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGV 61
Query: 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN 225
           PRT KE C+V+   +KKEIGR  + I+K LE     SV++  I   D++ RFCSNL +  
Sbjct: 62  PRTFKEICAVSR-ISKKEIGRCFKLILKALET----SVDL--ITTGDFMSRFCSNLCLPK 114
Query: 226 XXXXXXXXXXXXSEDLDI 243
                       + +LD+
Sbjct: 115 QVQMAATHIARKAVELDL 132

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

Iteration: 1
 Score = 94.4 bits (233), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 73/228 (32%), Positives = 103/228 (45%), Gaps = 13/228 (5%)
Query: 6   CADCKRLT-EVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDH---DPVRVXX 61
           C +CK    ++V   S GD +C+ CGLVL    VD  SEWR F+N+  DH   DP RV  
Sbjct: 24  CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSND--DHNGDDPSRVGE 81
Query: 62  XXXXXXXXXXXXTVIAKPTAXXXXXXXXXXXXXXQARSSHPDRNLIQAFKSISAMSDRLG 121
                       T I K                 +      D  +  AF  I+ + D   
Sbjct: 82  ASNPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAE 141
Query: 122 LVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTK 181
           L   +KD A E YK   D+K L+G++ E+I+AA + I CR+    RT KE  S+ +  T 
Sbjct: 142 LPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLIHVKT- 200
Query: 182 KEIGRAKEFIVKHL--EAEMG----QSVEMGTIHASDYLRRFCSNLGM 223
           KE G+    +   L  ++E G     +  M       Y+ RFCS+LG+
Sbjct: 201 KEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGL 248

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

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 39/126 (30%), Positives = 70/126 (55%), Gaps = 5/126 (3%)
Query: 99  SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI 158
           S   +RNL  A   +  ++ +L L   +++ A  +Y++   +  +RGR+ E+++AAC+Y 
Sbjct: 3   SDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYA 62
Query: 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFC 218
           ACR    PRT+ E   +A    KKEIGR+  FI ++L      + +   +  +DY+ +F 
Sbjct: 63  ACRLLKVPRTLDEIADIAR-VDKKEIGRSYRFIARNL----NLTPKKLFVKPTDYVNKFA 117
Query: 219 SNLGMT 224
             LG++
Sbjct: 118 DELGLS 123

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

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 39/126 (30%), Positives = 70/126 (55%), Gaps = 5/126 (3%)
Query: 99  SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI 158
           S   +RNL  A   +  ++ +L L   +++ A  +Y++   +  +RGR+ E+++AAC+Y 
Sbjct: 2   SDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYA 61
Query: 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFC 218
           ACR    PRT+ E   +A    KKEIGR+  FI ++L      + +   +  +DY+ +F 
Sbjct: 62  ACRLLKVPRTLDEIADIAR-VDKKEIGRSYRFIARNL----NLTPKKLFVKPTDYVNKFA 116
Query: 219 SNLGMT 224
             LG++
Sbjct: 117 DELGLS 122

>pdb|1RLY|A Chain A, Rdc-Derived Models Of The Zinc Ribbon Domain Of Human General Transcription Tfiib (Zinc Bound Structures) Length = 60

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 19/38 (50%), Positives = 26/38 (68%)
Query: 15 VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESS 52
          +V D+ AGD IC ECGLV+    +D  SEWR F+N+ +
Sbjct: 23 LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKA 60

>pdb|1DL6|A Chain A, Solution Structure Of Human Tfiib N-Terminal Domain Length = 58

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   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	278
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	2e-50
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	6e-10
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	3e-36
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	3e-11
1c9b_A	207	General transcription factor IIB; protein-DNA comp	2e-34
1c9b_A	207	General transcription factor IIB; protein-DNA comp	6e-10
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	5e-23
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	1e-12
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	1e-11
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	1e-04
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	2e-04
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	9e-04

>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae} Length = 345

 Score =  168 bits (425), Expect = 2e-50
 Identities = 79/246 (32%), Positives = 116/246 (47%), Gaps = 9/246 (3%)

Query: 6   CADCKRL-TEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE-SSDHDPVRVGGPL 63
           C +CK    ++V   S GD +C+ CGLVL    VD  SEWR F+N+  +  DP RVG   
Sbjct: 24  CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEAS 83

Query: 64  NPLLSGGGLSTVIAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLV 123
           NPLL G  LST I K            +  + +      D  +  AF  I+ + D   L 
Sbjct: 84  NPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAELP 143

Query: 124 TTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKE 183
             +KD A E YK   D+K L+G++ E+I+AA + I CR+    RT KE  S+ +    KE
Sbjct: 144 KIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLIH-VKTKE 202

Query: 184 IGRAKEFIVKHLE------AEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQK 237
            G+    +   L            +  M       Y+ RFCS+LG+  Q   +A+   +K
Sbjct: 203 FGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSAEYTAKK 262

Query: 238 SEDLDI 243
            +++  
Sbjct: 263 CKEIKE 268

>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 = 58.0 bits (139), Expect = 6e-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 =  127 bits (319), Expect = 3e-36
 Identities = 38/145 (26%), Positives = 76/145 (52%), Gaps = 5/145 (3%)

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

Query: 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFC 218
           ACR    PRT+ E   +A    KKEIGR+     + +   +  + +   +  +DY+ +F 
Sbjct: 62  ACRLLKVPRTLDEIADIAR-VDKKEIGRS----YRFIARNLNLTPKKLFVKPTDYVNKFA 116

Query: 219 SNLGMTNQAVKAAQEAVQKSEDLDI 243
             LG++ +  + A E + ++    +
Sbjct: 117 DELGLSEKVRRRAIEILDEAYKRGL 141

>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 = 60.4 bits (146), Expect = 3e-11
 Identities = 29/124 (23%), Positives = 55/124 (44%), Gaps = 1/124 (0%)

Query: 76  IAKPTAGGSTELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYK 135
           IA        E+        +  +  P +  ++    ++  +D LGL   ++ RA EI  
Sbjct: 75  IADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLSEKVRRRAIEILD 134

Query: 136 KVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195
           +   +    G++   +VAA LYIA   E + RT +E   VA   T+  +    + +V+ L
Sbjct: 135 EAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVA-RVTEVTVRNRYKELVEKL 193

Query: 196 EAEM 199
           + ++
Sbjct: 194 KIKV 197

>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 =  122 bits (308), Expect = 2e-34
 Identities = 62/141 (43%), Positives = 87/141 (61%), Gaps = 7/141 (4%)

Query: 103 DRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQ 162
           DR ++ AFK I+ M+DR+ L   I DR N ++K+V +QK L+GR  +AI +ACLYIACRQ
Sbjct: 2   DRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQ 61

Query: 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG 222
           E  PRT KE C+V+   +KKEIGR  + I+K           +  I   D++ RFCSNL 
Sbjct: 62  EGVPRTFKEICAVSR-ISKKEIGRCFKLILKA------LETSVDLITTGDFMSRFCSNLC 114

Query: 223 MTNQAVKAAQEAVQKSEDLDI 243
           +  Q   AA    +K+ +LD+
Sbjct: 115 LPKQVQMAATHIARKAVELDL 135

>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 = 57.0 bits (137), Expect = 6e-10
 Identities = 22/110 (20%), Positives = 40/110 (36%), Gaps = 3/110 (2%)

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

Query: 168 TVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRF 217
           T KE   +A G     I ++   I            +       D L + 
Sbjct: 161 TQKEIGDIA-GVADVTIRQSYRLIYPRAPDLFPT--DFKFDTPVDKLPQL 207

>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 = 5e-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 = 60.3 bits (146), Expect = 1e-12
 Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 6  CADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE 50
          C +      +V D+ AGD IC ECGLV+    +D  SEWR F+N+
Sbjct: 14 CPNHPD-AILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND 57

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1 Length = 50

 Score = 57.5 bits (139), Expect = 1e-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

>2cch_B Cyclin A2, cyclin-A; complex(transferase/cell division), ATP-binding, CDK2, cell cycle, cyclin, mitosis, nuclear protein; HET: TPO ATP; 1.7A {Homo sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1fvv_B* 1jsu_B* 1okv_B 1okw_B* 1ol1_B* 1ol2_B* 1urc_B 1fin_B* 2c5p_B* 2c5o_B* 2i40_B* 2wev_B* 2wfy_B 2whb_B* 3eid_B* 3ej1_B* 3eoc_B* 2wha_B* 2x1n_B* 1vyw_B* ... Length = 260

 Score = 41.9 bits (99), Expect = 1e-04
 Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 8/69 (11%)

Query: 153 AACLYIACR-QENKPRTVKEFCSVANGT-TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHA 210
            A + +A + +E  P  V EF  + + T TKK++ R +  ++K L        ++     
Sbjct: 86  TAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLKVLT------FDLAAPTV 139

Query: 211 SDYLRRFCS 219
           + +L ++  
Sbjct: 140 NQFLTQYFL 148

>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Length = 269

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 8/68 (11%)

Query: 153 AACLYIACR-QENKPRTVKEFCSVANGT-TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHA 210
              ++IA + +E  P  + +F  V + T TK +I + +  I++ L         +G    
Sbjct: 85  VTAMFIASKYEEMYPPEIGDFAFVTDNTYTKHQIRQMEMKILRALN------FGLGRPLP 138

Query: 211 SDYLRRFC 218
             +LRR  
Sbjct: 139 LHFLRRAS 146

>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens} Length = 306

 Score = 39.0 bits (91), Expect = 9e-04
 Identities = 12/76 (15%), Positives = 32/76 (42%), Gaps = 8/76 (10%)

Query: 153 AACLYIACRQ-ENKPRTVKEFCSVANGT-TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHA 210
           A C+ +A +  E  P T+++ C   +   + +++   +  ++  L+       ++  + A
Sbjct: 118 AVCMLLASKLRETTPLTIEKLCIYTDHAVSPRQLRDWEVLVLGKLK------WDLAAVIA 171

Query: 211 SDYLRRFCSNLGMTNQ 226
            D+L      L +   
Sbjct: 172 HDFLAFILHRLSLPRD 187

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	278
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	100.0
1c9b_A	207	General transcription factor IIB; protein-DNA comp	99.97
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	99.89
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	99.82
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	99.81
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	99.8
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	99.77
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	99.76
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	99.76
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	99.74
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	99.71
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	99.71
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	99.69
1g3n_C	257	V-cyclin; cyclin-dependent kinase, INK4 inhibitor,	99.63
2f2c_A	254	Cyclin homolog, V-cyclin; small molecule inhibitor	99.6
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	99.58
1ais_B	200	TFB TFIIB, protein (transcription initiation facto	99.57
1w98_B	283	Cyclin E, G1/S-specific cyclin E1; cell cycle, tra	99.55
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	99.52
1c9b_A	207	General transcription factor IIB; protein-DNA comp	99.39
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	99.17
1f5q_B	252	Gamma herpesvirus cyclin; herpesviral cyclin, cycl	99.16
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	98.99
3h4c_A	260	Transcription factor TFIIB-like; cyclin, transcrip	97.82
1zp2_A	235	RNA polymerase II holoenzyme cyclin-like subunit;	97.66
2cch_B	260	Cyclin A2, cyclin-A; complex(transferase/cell divi	97.64
2b9r_A	269	Human cyclin B1; cell cycle; 2.90A {Homo sapiens}	97.58
3rgf_B	285	Cyclin-C; protein kinase complex, transferase,tran	97.45
2w96_A	271	G1/S-specific cyclin-D1; serine/threonine-protein	97.37
2i53_A	258	Cyclin K; cell cycle, transcription, cyclin BOX, C	97.35
2ivx_A	257	Cyclin-T2; transcription regulation, cell division	97.27
2f2c_A	254	Cyclin homolog, V-cyclin; small molecule inhibitor	97.16
3m03_A	95	ORC6, origin recognition complex subunit 6; helix	97.1
1g3n_C	257	V-cyclin; cyclin-dependent kinase, INK4 inhibitor,	97.06
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	96.73
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	96.64
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	96.64
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	96.6
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	96.52
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	96.49
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	96.47
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	96.42
2pk2_A	358	Cyclin-T1, protein TAT; TAR, twinning, transcripti	96.38
3g33_B	306	CCND3 protein; Ser/Thr protein kinase, cell cycle,	96.24
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	96.18
2r7g_A	347	PP110, retinoblastoma-associated protein, P105-RB,	96.1
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	96.1
4ell_A	411	Retinoblastoma-associated protein; cyclin fold, tu	96.07
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	95.87
4elj_A	656	Retinoblastoma-associated protein; cyclin fold, tu	95.57
2qdj_A	304	Retinoblastoma-associated protein; cyclin fold, cy	95.39
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	95.3
1w98_B	283	Cyclin E, G1/S-specific cyclin E1; cell cycle, tra	95.16
2akl_A	138	PHNA-like protein PA0128; two domains, Zn binding	94.76
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	94.28
1jkw_A	323	Cyclin H; cell cycle, cell division, nuclear prote	94.24
6rxn_A	46	Rubredoxin; electron transfer(iron-sulfur protein)	93.85
2kpi_A	56	Uncharacterized protein SCO3027; zinc finger, PSI-	93.64
4rxn_A	54	Rubredoxin; electron transfer(iron-sulfur protein)	93.11
1e8j_A	52	Rubredoxin; iron-sulfur-protein, zinc-substitution	92.6
4elj_A	656	Retinoblastoma-associated protein; cyclin fold, tu	92.52
2k5r_A	97	Uncharacterized protein XF2673; solution structure	92.01
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	91.51
2pmi_B	293	PHO85 cyclin PHO80, aminoglycoside anti; cyclin-de	91.26
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	91.17
1k81_A	36	EIF-2-beta, probable translation initiation factor	91.16
1nui_A	255	DNA primase/helicase; zinc-biding domain, toprim f	91.09
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	90.99
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	90.78
3j21_i	83	50S ribosomal protein L37AE; archaea, archaeal, KI	90.1
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	89.54
3jyw_9	72	60S ribosomal protein L43; eukaryotic ribosome, RA	89.45
3iz5_m	92	60S ribosomal protein L43 (L37AE); eukaryotic ribo	89.08
2v3b_B	55	Rubredoxin 2, rubredoxin; alkane degradation, iron	89.08
1ffk_W	73	Ribosomal protein L37AE; ribosome assembly, RNA-RN	88.72
3cc2_Z	116	50S ribosomal protein L37AE, 50S ribosomal protein	88.37
3izc_m	92	60S ribosomal protein RPL43 (L37AE); eukaryotic ri	88.33
4a17_Y	103	RPL37A, 60S ribosomal protein L32; eukaryotic ribo	88.24
2kn9_A	81	Rubredoxin; metalloprotein, ssgcid, structural gen	88.16
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	87.77
1dx8_A	70	Rubredoxin; electron transport, zinc-substitution;	87.75
1dxg_A	36	Desulforedoxin; non-heme iron protein, rubredoxin	86.76
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	86.56
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	85.7
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	85.64
2apo_B	60	Ribosome biogenesis protein NOP10; protein-protein	85.47
1s24_A	87	Rubredoxin 2; electron transport; NMR {Pseudomonas	84.38
1tfi_A	50	Transcriptional elongation factor SII; transcripti	83.56
1f5q_B	252	Gamma herpesvirus cyclin; herpesviral cyclin, cycl	83.5
1yk4_A	52	Rubredoxin, RD; electron transport; 0.69A {Pyrococ	80.7
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	80.2

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

Probab=100.00  E-value=8e-64  Score=458.71  Aligned_cols=261  Identities=31%  Similarity=0.535  Sum_probs=173.4

Q ss_pred             CCCCCCCCC-CCceeEeCCCCceEcCCCcccccccccccccchhhccCCC-CCCCCCcccCCCCCcccCCCcceEEecCC
Q 023713            3 DSYCADCKR-LTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANES-SDHDPVRVGGPLNPLLSGGGLSTVIAKPT   80 (278)
Q Consensus         3 ~~~Cp~Cg~-~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~-~~~~~~r~G~~~~~~~~~~~~~t~i~~~~   80 (278)
                      ...||+||+ ++++++|+.+|++||.+||+|++|++||+|||||+|++++ ++.|++|+|+|.++++||.|++|.|++++
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 4689999999999999999999999999999999999765 47889999999999999999999999764


Q ss_pred             CCCCccccccccccccccC--CCchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHH
Q 023713           81 AGGSTELLSGSLGKLQARS--SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI  158 (278)
Q Consensus        81 ~~~~~~~l~~~l~~~~~~~--~~~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~  158 (278)
                       +.++ ...++|++||++.  +++||+|.+++..|.++|+.|+||+.++++|..||+++++.++++||+.+.++|||||+
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             2321 1234588898875  68999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccc------cccCCCCHHHHHHHHHhhcCCCHHHHHHHH
Q 023713          159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQS------VEMGTIHASDYLRRFCSNLGMTNQAVKAAQ  232 (278)
Q Consensus       159 acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~------~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~  232 (278)
                      |||++++|+|++||+++ +++++++|+++|+.|.+.|+++..+.      .++++++|++||+|||++|+|++++.+.|+
T Consensus       179 ACR~~~~prtl~eI~~~-~~v~~keigr~~k~l~~~L~l~~~~~~~~~~~~~~~~~~p~~~i~Rf~s~L~l~~~v~~~A~  257 (345)
T 4bbr_M          179 GCRRAEVARTFKEIQSL-IHVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSAE  257 (345)
T ss_dssp             HHHHTCCBCCHHHHHHH-HTCCTTHHHHHHHHHHHCC-------------------------------------------
T ss_pred             HHHhcCCCccHHHHHHH-hCCCHHHHHHHHHHHHHHhCccccccccccccccCCCCCHHHHHHHHHHHcCCcHHHHHHHH
Confidence            99999999999999996 89999999999999999999752111      136788999999999999999999999999


Q ss_pred             HHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHHHHh
Q 023713          233 EAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWAFMR  268 (278)
Q Consensus       233 ~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~~~~  268 (278)
                      +|++.+.+.|  .||+|.+||||+|  |+++.++.+-+
T Consensus       258 ~i~~~~~~~~i~~GR~P~~IAAAaI--ylAa~l~g~~~  293 (345)
T 4bbr_M          258 YTAKKCKEIKEIAGKSPITIAVVSI--YLNILLFQIPI  293 (345)
T ss_dssp             --------------------------------------
T ss_pred             HHHHHHHhcccccCCChHHHHHHHH--HHHHHHhCCCC
Confidence            9999999988  6999999999999  99999887644

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

Probab=100.00  E-value=1.5e-60  Score=437.86  Aligned_cols=262  Identities=31%  Similarity=0.533  Sum_probs=163.3

Q ss_pred             CCCCCCCCCCC-ceeEeCCCCceEcCCCcccccccccccccchhhccCCC-CCCCCCcccCCCCCcccCCCcceEEecCC
Q 023713            3 DSYCADCKRLT-EVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANES-SDHDPVRVGGPLNPLLSGGGLSTVIAKPT   80 (278)
Q Consensus         3 ~~~Cp~Cg~~~-~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~-~~~~~~r~G~~~~~~~~~~~~~t~i~~~~   80 (278)
                      ...||+||+.+ ++++|+.+|++||++||+|++|++||++||||+|++++ ++.|++|+|+|.++++||.|++|.|++++
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 69999999999999999999999999999999999753 46789999999999999999999998753


Q ss_pred             -CCCCccccccccccccccC--CCchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHH
Q 023713           81 -AGGSTELLSGSLGKLQARS--SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLY  157 (278)
Q Consensus        81 -~~~~~~~l~~~l~~~~~~~--~~~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY  157 (278)
                       .++++   .++|++||++.  +++||+|.+++.+|+++|+.|+||+.++++|..||+++++.++++||+.+.++|||||
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   23578888763  7899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcc------cccccCCCCHHHHHHHHHhhcCCCHHHHHHH
Q 023713          158 IACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMG------QSVEMGTIHASDYLRRFCSNLGMTNQAVKAA  231 (278)
Q Consensus       158 ~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~------~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A  231 (278)
                      +|||++++|+|++||+.+ +++++++|+++|+.|.+.|+....      ..+.+++.+|.+||+|||+.|+|++++.+.|
T Consensus       178 iAcR~e~~prtl~ei~~~-~~v~~keIgr~~~~l~~~L~~~~~~~~~~~~~~~~~~~~p~~~i~Rf~~~L~l~~~v~~~A  256 (345)
T 3k7a_M          178 IGCRRAEVARTFKEIQSL-IHVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSA  256 (345)
T ss_dssp             TTSBTTBSSCCHHHHHHS-SSCCSHHHHHHHHHHHHHHTCC---------------------------------------
T ss_pred             HHHHHcCCCccHHHHHHH-HCCCHHHHHHHHHHHHHHHhhhhccccccccccccCCCCHHHHHHHHHHHcCCCHHHHHHH
Confidence            999999999999999996 899999999999999999982100      0012788999999999999999999999999


Q ss_pred             HHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHHHHhcc
Q 023713          232 QEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWAFMRCI  270 (278)
Q Consensus       232 ~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~~~~~~  270 (278)
                      ++|++.+.+.|  .||+|.+||||+|  |||..+.++-+..
T Consensus       257 ~~i~~~~~~~~l~~Gr~P~~IAaAaI--ylAa~~~~~~~t~  295 (345)
T 3k7a_M          257 EYTAKKCKEIKEIAGKSPITIAVVSI--YLNILLFQIPITA  295 (345)
T ss_dssp             -----------------------------------------
T ss_pred             HHHHHHHHHhchhcCCCHHHHHHHHH--HHHHHHHCCCCCH
Confidence            99999999988  6999999999999  9999998765443

>1ais_B TFB TFIIB, protein (transcription initiation factor IIB); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B*

Probab=100.00  E-value=3.4e-34  Score=243.74  Aligned_cols=158  Identities=25%  Similarity=0.450  Sum_probs=147.6

Q ss_pred             CCchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC
Q 023713          100 SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT  179 (278)
Q Consensus       100 ~~~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v  179 (278)
                      +++||+|.+++++|.++|+.|+||+.+.++|..+|+++++++.++|++++.++|||||+|||+++.|++++||+.+ +++
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            4679999999999999999999999999999999999999999999999999999999999999999999999996 899


Q ss_pred             CHHHHHHHHHHHHHHhhhhcccccccCC--CCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHH
Q 023713          180 TKKEIGRAKEFIVKHLEAEMGQSVEMGT--IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLV  255 (278)
Q Consensus       180 ~~~~i~~~~~~l~~~L~~~~~~~~~~~~--~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v  255 (278)
                      ++++|+++|+.|.+.|++.      +++  .+|.+||+||++.|++++++.+.|++|++.+.+.|  .||+|.+||||+|
T Consensus        82 ~~~~i~~~~~~l~~~L~~~------~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~~~~gr~P~~iAaAal  155 (200)
T 1ais_B           82 DKKEIGRSYRFIARNLNLT------PKKLFVKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAAL  155 (200)
T ss_dssp             CHHHHHHHHHHHHHHTTCC------TTTTCCCGGGGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhccc------CCcCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHH
Confidence            9999999999999999987      777  89999999999999999999999999999999987  6999999999999


Q ss_pred             HHHHHHHHHHH
Q 023713          256 ETHIQLIVWAF  266 (278)
Q Consensus       256 ~~~~~~~~~~~  266 (278)
                        |+++.+.+.
T Consensus       156 --y~A~~~~~~  164 (200)
T 1ais_B          156 --YIASLLEGE  164 (200)
T ss_dssp             --HHHHHHTTC
T ss_pred             --HHHHHHhCC
Confidence              999987654

>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=99.97  E-value=5.5e-31  Score=225.10  Aligned_cols=155  Identities=42%  Similarity=0.678  Sum_probs=148.8

Q ss_pred             chhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCH
Q 023713          102 PDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTK  181 (278)
Q Consensus       102 ~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~  181 (278)
                      +||+|.+++++|+++|.+|+||+.++++|..+|+++++.+.++|++++.++|||+|+|||.++.|++++||+.+ ++++.
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            47999999999999999999999999999999999999999999999999999999999999999999999996 89999


Q ss_pred             HHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHH
Q 023713          182 KEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHI  259 (278)
Q Consensus       182 ~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~  259 (278)
                      ++|+++|+.|.+.|+++      ++..+|..||.||++.|++++++.+.|+.+++.+.+.+  .||+|.+||||+|  |+
T Consensus        80 ~~i~~~~~~ll~~L~~~------l~~~~p~~~l~r~~~~l~l~~~~~~~A~~i~~~~~~~~l~~g~~P~~IAaAai--yl  151 (207)
T 1c9b_A           80 KEIGRCFKLILKALETS------VDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAI--YM  151 (207)
T ss_dssp             HHHHHHHHHHHHHTTCC------CCCCCTHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHH--HH
T ss_pred             HHHHHHHHHHHHHHCCC------cCcCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHH--HH
Confidence            99999999999999987      78899999999999999999999999999999999877  6999999999999  99


Q ss_pred             HHHHHH
Q 023713          260 QLIVWA  265 (278)
Q Consensus       260 ~~~~~~  265 (278)
                      |+.+.+
T Consensus       152 A~~~~~  157 (207)
T 1c9b_A          152 ASQASA  157 (207)
T ss_dssp             HHHTSS
T ss_pred             HHHHHC
Confidence            988754

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

Probab=99.89  E-value=7.3e-22  Score=171.68  Aligned_cols=152  Identities=20%  Similarity=0.228  Sum_probs=141.0

Q ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCC-CcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHc-------
Q 023713          106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRG-RNQEAIVAACLYIACRQENKPRTVKEFCSVAN-------  177 (278)
Q Consensus       106 l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~g-r~~~~~aAAclY~acR~~~~p~tl~eia~~~~-------  177 (278)
                      ...+.++|.+++..|+||+.+..+|..+|++++..+.+++ +++..+++||+|+|||.++.|++++||+.+..       
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            4678999999999999999999999999999999988888 99999999999999999999999999988532       


Q ss_pred             CCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHH
Q 023713          178 GTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLV  255 (278)
Q Consensus       178 ~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v  255 (278)
                      ..+.++|.++++.|.+.|+++      +...+|..||.+|++.+++++++.+.|+.+++.+...+  .|++|..||+|||
T Consensus       108 ~~~~~~I~~~E~~iL~~L~f~------l~~~~P~~~l~~~~~~~~~~~~~~~~A~~~l~~s~~~~~~l~~~Ps~IAaAai  181 (235)
T 1zp2_A          108 KLSRSNISEIEFEIISVLDAF------LIVHHPYTSLEQAFHDGIINQKQLEFAWSIVNDSYASSLCLMAHPHQLAYAAL  181 (235)
T ss_dssp             CCCHHHHHHHHHHHHHHTTTC------CCCCCTHHHHHHHHHTTSSCHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHH
T ss_pred             hccHHHHHHHHHHHHHHCCCc------EEecChHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCCchhccCHHHHHHHHH
Confidence            578999999999999999987      77889999999999999999999999999999998766  7999999999999


Q ss_pred             HHHHHHHHHH
Q 023713          256 ETHIQLIVWA  265 (278)
Q Consensus       256 ~~~~~~~~~~  265 (278)
                        |+|..+.+
T Consensus       182 --~lA~~~~~  189 (235)
T 1zp2_A          182 --LISCCNDE  189 (235)
T ss_dssp             --HHHHTSCT
T ss_pred             --HHHHHhcC
Confidence              99987654

>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=99.82  E-value=1.6e-18  Score=152.34  Aligned_cols=152  Identities=14%  Similarity=0.165  Sum_probs=137.5

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHc---------
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVAN---------  177 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~---------  177 (278)
                      ..+.++|.+++..|+||+.+..+|..+|++++..+.++++++..+++||+|+|||.++.|++++||..+..         
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            46799999999999999999999999999999999999999999999999999999999999999986521         


Q ss_pred             -CCC-------HHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhh-hcC--CCCC
Q 023713          178 -GTT-------KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSE-DLD--IRLI  246 (278)
Q Consensus       178 -~v~-------~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~-~~~--~Gr~  246 (278)
                       .++       .++|.++.+.|.+.|+++      +...+|..|+.+|++.++.++++.+.|+.+++.+. ..+  .+..
T Consensus       112 ~~~~~~~y~~~~~~I~~~E~~iL~~L~f~------l~~~~P~~fl~~~~~~l~~~~~~~~~A~~~~~~sl~~~~~~l~~~  185 (257)
T 2ivx_A          112 LDTKCDAYLQQTRELVILETIMLQTLGFE------ITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYK  185 (257)
T ss_dssp             CCTTSHHHHHHHHHHHHHHHHHHHHTTTC------CCCCCHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCGGGTSC
T ss_pred             CCcchHHHHHHHHHHHHHHHHHHHHcccc------eEeeCcHHHHHHHHHHhCCCcHHHHHHHHHHHhhhhcccHHHcCC
Confidence             122       788999999999999987      77889999999999999999999999999998876 344  7999


Q ss_pred             hhHHHHHHHHHHHHHHHHHH
Q 023713          247 LVFFSLFLVETHIQLIVWAF  266 (278)
Q Consensus       247 P~~iaaA~v~~~~~~~~~~~  266 (278)
                      |..||+|||  |+|..+.+.
T Consensus       186 Ps~IAaAai--~lA~~~~~~  203 (257)
T 2ivx_A          186 PTVIACVCI--HLACKWSNW  203 (257)
T ss_dssp             HHHHHHHHH--HHHHHHHTC
T ss_pred             HHHHHHHHH--HHHHHHhCC
Confidence            999999999  999998764

>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=99.81  E-value=1e-18  Score=153.62  Aligned_cols=152  Identities=15%  Similarity=0.213  Sum_probs=137.1

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcC-C------
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG-T------  179 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~-v------  179 (278)
                      ..+.++|.+++..|+||+.+..+|..+|++++..+.+++++...+++||+|+|||.++.|++++||..+... +      
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            467899999999999999999999999999999999999999999999999999999999999999864110 1      


Q ss_pred             -----CHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCH----HHHHHHHHHHHHhhhcC--CCCChh
Q 023713          180 -----TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN----QAVKAAQEAVQKSEDLD--IRLILV  248 (278)
Q Consensus       180 -----~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~----~v~~~A~~i~~~~~~~~--~Gr~P~  248 (278)
                           +.++|.+..+.|.+.|+.+      +...+|..|+.+|++.|+.++    ++.+.|+.+++.+....  .+.+|.
T Consensus       122 ~~~~~~~~~i~~~E~~iL~~L~f~------l~~~~P~~fl~~~~~~l~~~~~~~~~~~~~A~~l~~~s~~~~~~l~~~Ps  195 (258)
T 2i53_A          122 QFGDDPKEEVMVLERILLQTIKFD------LQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPE  195 (258)
T ss_dssp             GGCSCHHHHHHHHHHHHHHHTTTC------CCCCCHHHHHHHHHHTBCSCHHHHHHHHHHHHHHHHHHTTTTGGGTSCHH
T ss_pred             hhhhhHHHHHHHHHHHHHHHCCCc------eeccChHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHHHcCCchhccChH
Confidence                 3679999999999999987      778899999999999999987    68899999999998765  799999


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 023713          249 FFSLFLVETHIQLIVWAF  266 (278)
Q Consensus       249 ~iaaA~v~~~~~~~~~~~  266 (278)
                      .||+|+|  |+|..+.+.
T Consensus       196 ~IAaAai--~lA~~~~~~  211 (258)
T 2i53_A          196 IIAVAVM--YLAGRLCKF  211 (258)
T ss_dssp             HHHHHHH--HHHHHHHTC
T ss_pred             HHHHHHH--HHHHHHhCC
Confidence            9999999  999988764

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

Probab=99.80  E-value=1.6e-18  Score=154.74  Aligned_cols=150  Identities=15%  Similarity=0.224  Sum_probs=136.3

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCC-CHHHHHHHHc--------
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPR-TVKEFCSVAN--------  177 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~-tl~eia~~~~--------  177 (278)
                      ..+.++|.+++..|+||+.+..+|..+|++++..+.++++++..+++||+|+|||.++.|+ ++.||..+..        
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            4679999999999999999999999999999999999999999999999999999999998 7888866421        


Q ss_pred             -------CCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChh
Q 023713          178 -------GTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILV  248 (278)
Q Consensus       178 -------~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~  248 (278)
                             ....++|.++.+.|.+.|+++      +...+|..|+.+|+..|++++++.+.|+.+++.+....  .+..|.
T Consensus       124 ~~~~~~~~~~~~~Il~~E~~iL~~L~f~------l~v~~P~~fL~~~~~~l~~~~~~~~~A~~~l~~sl~t~~~l~~~Ps  197 (285)
T 3rgf_B          124 YAFPKEFPYRMNHILECEFYLLELMDCC------LIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPF  197 (285)
T ss_dssp             TTCCSCCCCCHHHHHHHHHHHHHHTTTC------CCCCCSHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSHHHHSCHH
T ss_pred             ccCchhhHHHHHHHHHHHHHHHHHcCCC------eEeCChHHHHHHHHHHhCCCHHHHHHHHHHHHHHHccChhhccCHH
Confidence                   146799999999999999987      77789999999999999999999999999999988765  699999


Q ss_pred             HHHHHHHHHHHHHHHH
Q 023713          249 FFSLFLVETHIQLIVW  264 (278)
Q Consensus       249 ~iaaA~v~~~~~~~~~  264 (278)
                      .||+|+|  |+|..+.
T Consensus       198 ~IAaAai--ylA~~~~  211 (285)
T 3rgf_B          198 MIALACL--HVACVVQ  211 (285)
T ss_dssp             HHHHHHH--HHHHHHT
T ss_pred             HHHHHHH--HHHHHHc
Confidence            9999999  9988754

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

Probab=99.77  E-value=1e-19  Score=146.52  Aligned_cols=66  Identities=32%  Similarity=0.617  Sum_probs=58.2

Q ss_pred             CCCCCCCCCC-CceeEeCCCCceEcCCCcccccccccccccchhhccCCC-CCCCCCcccCCCCCccc
Q 023713            3 DSYCADCKRL-TEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANES-SDHDPVRVGGPLNPLLS   68 (278)
Q Consensus         3 ~~~Cp~Cg~~-~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~-~~~~~~r~G~~~~~~~~   68 (278)
                      ...||+||+. +++++|+.+|++||.+||+|++|++||.|||||+|++++ ++.+++|+|+|.++...
T Consensus        21 ~~~CPECGs~~t~IV~D~erGE~VCsdCGLVLEEriID~GPEWRAFsnDD~~~dDpSRVGAPs~~~~~   88 (197)
T 3k1f_M           21 VLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNXXXXXXXXXXXXXXXXXXXX   88 (197)
T ss_dssp             CCCCTTTCCSSCCEEEEGGGTEEEETTTCBBCCCCCBCHHHHHHHHHCCCTTTTCSCCCBCCBCCHHH
T ss_pred             CeECcCCCCcCCeEEEeCCCCEEEEcCCCCCcCCceeECCCCCcCcCCcccccccccccccccccccc
Confidence            4689999982 479999999999999999999999999999999999754 46789999999887653

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

Probab=99.76  E-value=4.9e-17  Score=143.93  Aligned_cols=150  Identities=13%  Similarity=0.122  Sum_probs=137.1

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCC-CCCHHHHHHHHc--CCCHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN--GTTKKE  183 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~-p~tl~eia~~~~--~v~~~~  183 (278)
                      ....++|.+++..++|++.+...|..+++++.....+++++...+++||+|+|||.++. |++++|+..+ .  ..+.++
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 8999999885 4  378999


Q ss_pred             HHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHH
Q 023713          184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQL  261 (278)
Q Consensus       184 i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~  261 (278)
                      |.++.+.|.+.|+.+      +...+|.+|+.||++.++++.++...|+.+++.+....  .+.+|..||||+|  |++.
T Consensus       118 I~~mE~~IL~~L~f~------l~~~tp~~fl~~~~~~~~~~~~~~~~a~~l~e~sl~~~~~~~~~Ps~iAaAai--~lA~  189 (269)
T 2b9r_A          118 IRQMEMKILRALNFG------LGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFPPSQIAAGAF--SLAL  189 (269)
T ss_dssp             HHHHHHHHHHHTTSC------CCCCCHHHHHHHHHHSSCCCHHHHHHHHHHHHHGGGCGGGSSSCTTHHHHHHH--HHHH
T ss_pred             HHHHHHHHHHHcCCc------cCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhhhcCCHHHHHHHHH--HHHH
Confidence            999999999999987      77889999999999999999999999999999887644  7999999999999  8887


Q ss_pred             HHHH
Q 023713          262 IVWA  265 (278)
Q Consensus       262 ~~~~  265 (278)
                      .+.+
T Consensus       190 ~~l~  193 (269)
T 2b9r_A          190 KILD  193 (269)
T ss_dssp             HHHT
T ss_pred             HHhC
Confidence            7653

>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=99.76  E-value=2.4e-17  Score=149.61  Aligned_cols=153  Identities=11%  Similarity=0.114  Sum_probs=134.9

Q ss_pred             hhHH-HHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC
Q 023713          103 DRNL-IQAFKSISAMSDRLG--LVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT  179 (278)
Q Consensus       103 er~l-~~~~~~I~~i~~~L~--Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v  179 (278)
                      |+.+ ..+.++|.++|..|+  ||+.+..+|..+|++++..+.+++.++..+++||+|+|||.++.|+++.||+.+ ...
T Consensus        53 E~~lr~~~~~~I~ev~~~l~~~Lp~~t~~tA~~~~~RF~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~d~v~~-~~~  131 (323)
T 1jkw_A           53 EMTLCKYYEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGN-LRE  131 (323)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHGGG-SSS
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhhCChhhcCHHHHHHHHHHHHHhhhcCCCCHHHHHHH-hcc
Confidence            4444 456799999999999  999999999999999999999999999999999999999999999999999774 444


Q ss_pred             C-------HHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhc-------CCCHHHHHHHHHHHHHhhhcC--C
Q 023713          180 T-------KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNL-------GMTNQAVKAAQEAVQKSEDLD--I  243 (278)
Q Consensus       180 ~-------~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L-------~l~~~v~~~A~~i~~~~~~~~--~  243 (278)
                      +       .++|.++.+.|.+.|+++      +...+|..||.+|+..|       +.++++.+.|+.+++.+....  .
T Consensus       132 ~p~~~~~~~~~Il~~E~~iL~~L~f~------l~v~~P~~~L~~~l~~l~~~~~~~~~~~~l~~~A~~~l~~sl~t~~~l  205 (323)
T 1jkw_A          132 SPLGQEKALEQILEYELLLIQQLNFH------LIVHNPYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYL  205 (323)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHTTTC------CCCCCSHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHTTSTHHH
T ss_pred             ChhhhHHHHHHHHHHHHHHHHHCCCc------EEcCChHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHhccHHH
Confidence            4       588999999999999987      77889999999999776       334678899999999987765  6


Q ss_pred             CCChhHHHHHHHHHHHHHHHH
Q 023713          244 RLILVFFSLFLVETHIQLIVW  264 (278)
Q Consensus       244 Gr~P~~iaaA~v~~~~~~~~~  264 (278)
                      +..|..||+|||  |+|..+.
T Consensus       206 ~~~Ps~IAaAai--~lA~~~~  224 (323)
T 1jkw_A          206 LYTPSQIALTAI--LSSASRA  224 (323)
T ss_dssp             HSCHHHHHHHHH--HHHHHHH
T ss_pred             cCCHHHHHHHHH--HHHHHHc
Confidence            999999999999  9998763

>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=99.74  E-value=7.1e-18  Score=154.99  Aligned_cols=152  Identities=13%  Similarity=0.162  Sum_probs=135.9

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHc---------
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVAN---------  177 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~---------  177 (278)
                      ..+.++|.+++..|+||+.+..+|..||++++....++++++..+++||||+|||.++.|++++||..++.         
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            46799999999999999999999999999999999999999999999999999999999999999976421         


Q ss_pred             -CC-------CHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh-cC--CCCC
Q 023713          178 -GT-------TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED-LD--IRLI  246 (278)
Q Consensus       178 -~v-------~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~-~~--~Gr~  246 (278)
                       .+       ..++|.++.+.|.+.|+++      +...+|..||.+|+..|++++++.+.|+.+++.+.. ..  .+..
T Consensus       119 ~~~~~~~y~~~~~~Il~~E~~IL~~L~f~------L~v~~P~~fL~~~~~~l~~~~~l~~~A~~ll~~sl~~t~l~l~y~  192 (358)
T 2pk2_A          119 PDTRSEAYLQQVQDLVILESIILQTLGFE------LTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYT  192 (358)
T ss_dssp             CCTTSHHHHGGGTGGGTHHHHHHHHTTTC------CCCCCTTHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCGGGTSC
T ss_pred             ccccchhhhHHHHHHHHHHHHHHHHcCCc------eeCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhccC
Confidence             11       2567889999999999987      778899999999999999999999999999988763 33  7999


Q ss_pred             hhHHHHHHHHHHHHHHHHHH
Q 023713          247 LVFFSLFLVETHIQLIVWAF  266 (278)
Q Consensus       247 P~~iaaA~v~~~~~~~~~~~  266 (278)
                      |..||+|||  |+|+.+.+.
T Consensus       193 Ps~IAaAAI--~lA~~~l~~  210 (358)
T 2pk2_A          193 PPVVACVCI--HLACKWSNW  210 (358)
T ss_dssp             HHHHTTTTT--TTHHHHTTC
T ss_pred             HHHHHHHHH--HHHHHHhCC
Confidence            999999999  999988664

>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=99.71  E-value=3.4e-18  Score=115.76  Aligned_cols=47  Identities=43%  Similarity=0.777  Sum_probs=43.5

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhccCC
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE   50 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~   50 (278)
                      ...||+||+ ..+++|+.+|++||.+||+|++|++||.|||||+|+++
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            358999998 57999999999999999999999999999999999854

>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=99.71  E-value=4.3e-16  Score=137.18  Aligned_cols=150  Identities=15%  Similarity=0.178  Sum_probs=134.8

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCC-CCCHHHHHHHHc--CCCHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN--GTTKKE  183 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~-p~tl~eia~~~~--~v~~~~  183 (278)
                      ..+.++|.+++..++|+..+.-.|..+++++.....+..++...+++||+|+|||.++. |++++|+..+ .  ..+.++
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            45789999999999999999999999999999887777788999999999999999998 9999999875 4  378999


Q ss_pred             HHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCH-HHHHHHHHHHHHhh-hcC--CCCChhHHHHHHHHHHH
Q 023713          184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN-QAVKAAQEAVQKSE-DLD--IRLILVFFSLFLVETHI  259 (278)
Q Consensus       184 i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~-~v~~~A~~i~~~~~-~~~--~Gr~P~~iaaA~v~~~~  259 (278)
                      |.++.+.|.+.|+.+      +...+|.+|+.+|++.+++++ ++...|+.+++.+. +..  .+.+|..||||+|  |+
T Consensus       119 i~~mE~~iL~~L~~~------l~~~tp~~fl~~~~~~l~~~~~~~~~~a~~l~e~sl~~~~~~~~~~Ps~iAaAai--~l  190 (260)
T 2cch_B          119 VLRMEHLVLKVLTFD------LAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAF--HL  190 (260)
T ss_dssp             HHHHHHHHHHHTTTC------CCCCCHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHHHH--HH
T ss_pred             HHHHHHHHHHHcCCc------cCCCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHhHHHHhCCCHHHHHHHHH--HH
Confidence            999999999999987      778899999999999999876 88999999999865 322  6999999999999  99


Q ss_pred             HHHHHH
Q 023713          260 QLIVWA  265 (278)
Q Consensus       260 ~~~~~~  265 (278)
                      +..+.+
T Consensus       191 A~~~~~  196 (260)
T 2cch_B          191 ALYTVT  196 (260)
T ss_dssp             HHHHHH
T ss_pred             HHHHhC
Confidence            887654

>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=99.69  E-value=1.4e-15  Score=134.58  Aligned_cols=151  Identities=13%  Similarity=0.176  Sum_probs=133.4

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCC-CCCHHHHHHHHc--CCCHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN--GTTKKE  183 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~-p~tl~eia~~~~--~v~~~~  183 (278)
                      ....++|.+++..+++++.+.-.|..+++++.....+..++...+++||+|+|||.++. |+++.|++.+ .  ..+.++
T Consensus        58 ~~lv~wl~~v~~~~~l~~~tl~lAv~~lDRfls~~~v~~~~lqlv~~acL~iAsK~EE~~p~~~~~~~~~-~~~~~~~~e  136 (271)
T 2w96_A           58 KIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIY-TDNSIRPEE  136 (271)
T ss_dssp             HHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHTTSCCCTTTHHHHHHHHHHHHHHHHCSSCCCHHHHHHH-TTTSSCHHH
T ss_pred             HHHHHHHHHHHHHHCCchhHHHHHHHHHHHhCCcCCcCHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHH-hcCCCCHHH
Confidence            45788999999999999999999999999999988888889999999999999999998 9999999874 4  378999


Q ss_pred             HHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHH----HHHHHHHHHHhhhcC--CCCChhHHHHHHHHH
Q 023713          184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQA----VKAAQEAVQKSEDLD--IRLILVFFSLFLVET  257 (278)
Q Consensus       184 i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v----~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~  257 (278)
                      |.++.+.|.+.|+.+      +...+|.+|+.+|++.++++++.    .+.|+.+++.+....  .+.+|..||||+|  
T Consensus       137 I~~mE~~IL~~L~~~------l~~~tp~~fl~~~~~~l~~~~~~~~~~~~~a~~~l~~~~~d~~~~~~~PS~iAaAai--  208 (271)
T 2w96_A          137 LLQMELLLVNKLKWN------LAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISNPPSMVAAGSV--  208 (271)
T ss_dssp             HHHHHHHHHHHTTTC------CCCCCHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHTSTHHHHSCHHHHHHHHH--
T ss_pred             HHHHHHHHHHHCCCc------cCCCCHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHHHhhhhhhccCHHHHHHHHH--
Confidence            999999999999987      77889999999999999999775    356778888765332  5999999999999  


Q ss_pred             HHHHHHHHH
Q 023713          258 HIQLIVWAF  266 (278)
Q Consensus       258 ~~~~~~~~~  266 (278)
                      |++....+.
T Consensus       209 ~lA~~~l~~  217 (271)
T 2w96_A          209 VAAVQGLNL  217 (271)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhCc
Confidence            999877654

>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=99.63  E-value=8e-15  Score=128.81  Aligned_cols=149  Identities=12%  Similarity=0.068  Sum_probs=130.4

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCC-CCCHHHHHHHHc--CCCHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN--GTTKKE  183 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~-p~tl~eia~~~~--~v~~~~  183 (278)
                      ....++|.+++..++++..+.-.|..+++++.....+++++...+++||+|+|||.++. |.++.|+..+ .  ..+.++
T Consensus        52 ~~lvdwl~ev~~~~~l~~etl~lAv~~~DRfls~~~v~~~~lqLv~~acl~iA~K~eE~~~p~~~d~~~~-~~~~~~~~~  130 (257)
T 1g3n_C           52 KLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYA-AADSFSRQE  130 (257)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHH-TTTCSCHHH
T ss_pred             HHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHccccCCCHHHHHHH-HCCCCCHHH
Confidence            45789999999999999999999999999999988888889999999999999998765 9999999875 4  378999


Q ss_pred             HHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHH----HHHHHHHHHHhhhcC--CCCChhHHHHHHHHH
Q 023713          184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQA----VKAAQEAVQKSEDLD--IRLILVFFSLFLVET  257 (278)
Q Consensus       184 i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v----~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~  257 (278)
                      |.+..+.|.+.|+.+      +...+|.+|+.+|++.++++.+.    ...|+.+++.+....  .+.+|..||||+|  
T Consensus       131 i~~mE~~iL~~L~~~------l~~~tp~~fl~~~~~~~~~~~~~~~~~~~~a~~~le~~l~d~~~~~~~PS~iAaAai--  202 (257)
T 1g3n_C          131 LIDQEKELLEKLAWR------TEAVLATDVTSFLLLKLVGGSQHLDFWHHEVNTLITKALVDPLTGSLPASIISAAGC--  202 (257)
T ss_dssp             HHHHHHHHHHHTTTC------CCCCCHHHHHHHHHHHHSCSSTTHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHH--
T ss_pred             HHHHHHHHHHHCCCc------CCCCCHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhCcchhCcCHHHHHHHHH--
Confidence            999999999999987      77889999999999999987653    566888888766433  6999999999999  


Q ss_pred             HHHHHHH
Q 023713          258 HIQLIVW  264 (278)
Q Consensus       258 ~~~~~~~  264 (278)
                      |++..+.
T Consensus       203 ~lA~~~l  209 (257)
T 1g3n_C          203 ALLVPAN  209 (257)
T ss_dssp             HHHCCGG
T ss_pred             HHHHHHh
Confidence            8876544

>2f2c_A Cyclin homolog, V-cyclin; small molecule inhibitor bound between N-terminal and C-TERM domain of kinase, cell cycle-transferase complex; HET: AP9; 2.80A {Herpesvirus saimiri} SCOP: a.74.1.1 a.74.1.1 PDB: 1jow_A* 2euf_A* 1xo2_A* 1bu2_A

Probab=99.60  E-value=1.9e-14  Score=126.25  Aligned_cols=149  Identities=17%  Similarity=0.178  Sum_probs=129.2

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcC-CCCCHHHHHHHH-cCCCHHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVA-NGTTKKEI  184 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~-~p~tl~eia~~~-~~v~~~~i  184 (278)
                      ....++|.+++..++++..+.-.|..++.++.....+++++...+++||+|+|||.+. .|.++.|+..+. ...+.++|
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            4578899999999999999999999999999998888899999999999999999976 699999997641 23689999


Q ss_pred             HHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHH----HHHHHHHHHHhhhcC--CCCChhHHHHHHHHHH
Q 023713          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQA----VKAAQEAVQKSEDLD--IRLILVFFSLFLVETH  258 (278)
Q Consensus       185 ~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v----~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~  258 (278)
                      .+..+.|.+.|+.+      +...+|.+|+.+|++.++++.+.    ...|+.+++.+....  .+.+|..||||+|  |
T Consensus       133 ~~mE~~IL~~L~~~------l~~~tp~~fl~~~~~~~~~~~~~~~~~~~~a~~ll~~~l~d~~~~~~~PS~iAaAai--~  204 (254)
T 2f2c_A          133 INQEKDILEALKWD------TEAVLATDFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPNIALLSPGLICAGGL--L  204 (254)
T ss_dssp             HHHHHHHHHHTTTC------CCCCCGGGSHHHHHHHTTCCGGGHHHHHHHHHHHHHHHTTSGGGTTSCHHHHHHHHH--H
T ss_pred             HHHHHHHHHHCCCc------CCCCCHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHHHcCcchhccCHHHHHHHHH--H
Confidence            99999999999987      77889999999999999998653    456788887665422  7999999999999  8


Q ss_pred             HHHHH
Q 023713          259 IQLIV  263 (278)
Q Consensus       259 ~~~~~  263 (278)
                      ++...
T Consensus       205 la~~~  209 (254)
T 2f2c_A          205 TTIET  209 (254)
T ss_dssp             HHHHT
T ss_pred             HHHHh
Confidence            88765

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

Probab=99.58  E-value=8.7e-16  Score=101.15  Aligned_cols=44  Identities=34%  Similarity=0.940  Sum_probs=42.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhcc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFA   48 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~   48 (278)
                      ..||+||+ ..+++|+.+|++||..||+|++++.||.+||||+|+
T Consensus         6 ~~CP~C~~-~~l~~d~~~gelvC~~CG~v~~e~~id~~~ewr~f~   49 (50)
T 1pft_A            6 KVCPACES-AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAFD   49 (50)
T ss_dssp             CSCTTTSC-CCEEEETTTTEEEESSSCCBCCCCCCCCCSSSSCCC
T ss_pred             EeCcCCCC-cceEEcCCCCeEECcccCCcccccccccCCcccccC
Confidence            57999998 589999999999999999999999999999999997

>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=99.57  E-value=1.7e-14  Score=121.90  Aligned_cols=90  Identities=27%  Similarity=0.391  Sum_probs=86.2

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHH
Q 023713          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (278)
Q Consensus       108 ~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~  187 (278)
                      +...+|.++|+.|+||+.+.+.|..|++.+.+.+...||+|..+||||||+|||..+.|+|++||+.+ .++++.+|++.
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            35679999999999999999999999999999999999999999999999999999999999999996 89999999999


Q ss_pred             HHHHHHHhhhh
Q 023713          188 KEFIVKHLEAE  198 (278)
Q Consensus       188 ~~~l~~~L~~~  198 (278)
                      |++|.+.|+++
T Consensus       186 ~~~l~~~l~~~  196 (200)
T 1ais_B          186 YKELVEKLKIK  196 (200)
T ss_dssp             HHHHHHHHTCC
T ss_pred             HHHHHHHcCCC
Confidence            99999999986

>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=99.55  E-value=1.2e-13  Score=123.08  Aligned_cols=146  Identities=12%  Similarity=0.125  Sum_probs=124.4

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhC-CCCCCCcHHHHHHHHHHHHHHhcCC-CCCHHHHHHHHc--CCCHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQ-KPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN--GTTKK  182 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~-~~~~gr~~~~~aAAclY~acR~~~~-p~tl~eia~~~~--~v~~~  182 (278)
                      ....++|.+++..++++..+.-.|..++.++... +.+++++...+++||+|+|||.++. |.+++|+..+ .  ..+.+
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 5778899999999999999999976 8999999875 4  36899


Q ss_pred             HHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHH-----------HHHHHHHHHHHhhh-cC-CCCChhH
Q 023713          183 EIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ-----------AVKAAQEAVQKSED-LD-IRLILVF  249 (278)
Q Consensus       183 ~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~-----------v~~~A~~i~~~~~~-~~-~Gr~P~~  249 (278)
                      +|.++.+.|.+.|+.+      +.+.+|.+|+.+|++.++++++           ....+.++++.+.. .. .+.+|..
T Consensus       130 ei~~mE~~IL~~L~~~------l~~~tp~~fL~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~llelsl~d~~~l~~~PS~  203 (283)
T 1w98_B          130 EILTMELMIMKALKWR------LSPLTIVSWLNVYMQVAYLNDLHEVLLPQYPQQIFIQIAELLDLCVLDVDCLEFPYGI  203 (283)
T ss_dssp             HHHHHHHHHHHHTTTC------CCCCCHHHHHHHHHHHHTCCSSCCSSSCCSCHHHHHHHHHHHHHHHHSGGGGGSCHHH
T ss_pred             HHHHHHHHHHHHcCCc------CCCCCHHHHHHHHHHHhccCchhhHHHHhhhHHHHHHHHHHHHHHHhhhhhhcCCHHH
Confidence            9999999999999987      7788999999999998877532           22345567776653 22 6999999


Q ss_pred             HHHHHHHHHHHH
Q 023713          250 FSLFLVETHIQL  261 (278)
Q Consensus       250 iaaA~v~~~~~~  261 (278)
                      ||||+|  |++.
T Consensus       204 iAaAai--~la~  213 (283)
T 1w98_B          204 LAASAL--YHFS  213 (283)
T ss_dssp             HHHHHH--HHTS
T ss_pred             HHHHHH--HHHH
Confidence            999999  8764

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

Probab=99.52  E-value=3e-13  Score=121.73  Aligned_cols=150  Identities=11%  Similarity=0.126  Sum_probs=130.0

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhc-CCCCCHHHHHHHHcC--CCHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE-NKPRTVKEFCSVANG--TTKKE  183 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~-~~p~tl~eia~~~~~--v~~~~  183 (278)
                      ....++|.+++..++|+..+.-.|..+++++.....++......++++|+|+|||.+ ..|.++.|+..+ .+  .+..+
T Consensus        72 ~~lvdwl~ev~~~~~l~~~t~~lAv~~lDRfls~~~v~~~~lqLv~~tcL~lAsK~eE~~p~~~~~l~~~-~~~~~~~~~  150 (306)
T 3g33_B           72 KMLAYWMLEVCEEQRCEEEVFPLAMNYLDRYLSCVPTRKAQLQLLGAVCMLLASKLRETTPLTIEKLCIY-TDHAVSPRQ  150 (306)
T ss_dssp             HHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHHCCCCGGGHHHHHHHHHHHHHHHHCSSCCCTTHHHHH-TTTSSCHHH
T ss_pred             HHHHHHHHHHHHHhCCcHhHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHH-hccCccHHH
Confidence            467899999999999999999999999999999888888899999999999999985 467899999874 43  68999


Q ss_pred             HHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHH----HHHHHHHHHHHhhhcC--CCCChhHHHHHHHHH
Q 023713          184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ----AVKAAQEAVQKSEDLD--IRLILVFFSLFLVET  257 (278)
Q Consensus       184 i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~----v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~  257 (278)
                      |.+..+.|.+.|+.+      +...+|.+|+.+|+..++++.+    +.+.|+.+++.+....  .+..|..||||+|  
T Consensus       151 i~~mE~~IL~~L~f~------l~~~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~lsl~d~~~l~~~PS~IAaAai--  222 (306)
T 3g33_B          151 LRDWEVLVLGKLKWD------LAAVIAHDFLAFILHRLSLPRDRQALVKKHAQTFLALCATDYTFAMYPPSMIATGSI--  222 (306)
T ss_dssp             HHHHHHHHHHHTTTC------CCCCCGGGGHHHHHHTSSCCTTTHHHHHHHHHHHHHHHHHCGGGTTSCHHHHHHHHH--
T ss_pred             HHHHHHHHHHHcCCc------cCCCCHHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhhhhhccCCHHHHHHHHH--
Confidence            999999999999987      7788999999999999998744    4567778888665433  7999999999999  


Q ss_pred             HHHHHHHH
Q 023713          258 HIQLIVWA  265 (278)
Q Consensus       258 ~~~~~~~~  265 (278)
                      |+|....+
T Consensus       223 ~lA~~~l~  230 (306)
T 3g33_B          223 GAAVQGLG  230 (306)
T ss_dssp             HHHHHTCC
T ss_pred             HHHHHHhc
Confidence            88876543

>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=99.39  E-value=2.7e-12  Score=108.99  Aligned_cols=90  Identities=21%  Similarity=0.281  Sum_probs=85.7

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHH
Q 023713          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (278)
Q Consensus       108 ~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~  187 (278)
                      +...+|.++++.|++|+.+.+.|..+++.+.+.++..|++|..+||||||+||+..+.|++++||+++ +++++.+|+++
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            45789999999999999999999999999999999999999999999999999999999999999996 89999999999


Q ss_pred             HHHHHHHhhhh
Q 023713          188 KEFIVKHLEAE  198 (278)
Q Consensus       188 ~~~l~~~L~~~  198 (278)
                      |+.|.+.++..
T Consensus       180 ~~~l~~~l~~~  190 (207)
T 1c9b_A          180 YRLIYPRAPDL  190 (207)
T ss_dssp             HHHHGGGHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99999999875

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

Probab=99.17  E-value=2.6e-12  Score=117.31  Aligned_cols=89  Identities=19%  Similarity=0.258  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHH
Q 023713          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (278)
Q Consensus       108 ~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~  187 (278)
                      +...+|.++|+.|+|+..+...|.+|.+++.+.+++.||+|.++||||||+|++.++.++|++||+++ ++|++.+|++.
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            56679999999999999999999999999999999999999999999999999999999999999996 99999999999


Q ss_pred             HHHHHHHhhh
Q 023713          188 KEFIVKHLEA  197 (278)
Q Consensus       188 ~~~l~~~L~~  197 (278)
                      |++|.+.++.
T Consensus       313 ykel~~~~~~  322 (345)
T 4bbr_M          313 YKILYEHRDK  322 (345)
T ss_dssp             ----------
T ss_pred             HHHHHHHHHh
Confidence            9999998874

>1f5q_B Gamma herpesvirus cyclin; herpesviral cyclin, cyclin dependent kinase. protein/protein complex, transferase; 2.50A {Murid herpesvirus 4} SCOP: a.74.1.1 a.74.1.1

Probab=99.16  E-value=1.7e-09  Score=94.51  Aligned_cols=147  Identities=10%  Similarity=0.030  Sum_probs=122.7

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcC-CCCCHHHHHHHH-cCCCHHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVA-NGTTKKEI  184 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~-~p~tl~eia~~~-~~v~~~~i  184 (278)
                      ....++|-+++..++|+..+.-.|..++.+......++......++++|+|+|++.+. .|.++.++.... ...+..+|
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            3568899999999999999999999999999887777777889999999999999766 488999987642 24689999


Q ss_pred             HHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHH----HHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHH
Q 023713          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ----AVKAAQEAVQKSEDLD--IRLILVFFSLFLVETH  258 (278)
Q Consensus       185 ~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~----v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~  258 (278)
                      .+..+.|.+.|+.+      +..+.|.+|+.+|...++.+.+    +...|..+++.+.-.-  ..-+|+.||||++  +
T Consensus       130 ~~mE~~IL~~L~w~------l~~pTp~~FL~~~l~~~~~~~~~~~~~~~~a~~~l~~~l~d~~~l~~~PS~iAaaa~--~  201 (252)
T 1f5q_B          130 LTLEVKSLDTLSWV------ADRCLSTDLICYILHIMHAPREDYLNIYNLCRPKIFCALCDGRSAMKRPVLITLACM--H  201 (252)
T ss_dssp             HHHHHHHHHHTTTC------CCCCCHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHH--H
T ss_pred             HHHHHHHHHHCCCc------cCCCCHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHHHhchhhhccCHHHHHHHHH--H
Confidence            99999999999987      7788999999999999999865    3456677766654322  5889999999997  4


Q ss_pred             HHH
Q 023713          259 IQL  261 (278)
Q Consensus       259 ~~~  261 (278)
                      .++
T Consensus       202 ~~l  204 (252)
T 1f5q_B          202 LTM  204 (252)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            443

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

Probab=98.99  E-value=4.3e-11  Score=109.32  Aligned_cols=88  Identities=19%  Similarity=0.262  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHH
Q 023713          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA  187 (278)
Q Consensus       108 ~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~  187 (278)
                      +...+|.++|+.|+|+..+...|..|.+.+.+.++..||+|..+||||||+|++..+.++|.+||+.+ ++|++.+|+..
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            34677889999999999999999999999999999999999999999999999999999999999996 99999999999


Q ss_pred             HHHHHHHhh
Q 023713          188 KEFIVKHLE  196 (278)
Q Consensus       188 ~~~l~~~L~  196 (278)
                      |++|.+.+.
T Consensus       313 ykel~~~~~  321 (345)
T 3k7a_M          313 YKILYEHRD  321 (345)
T ss_dssp             ---------
T ss_pred             HHHHHHHHH
Confidence            999998775

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

Probab=97.82  E-value=3.6e-05  Score=63.68  Aligned_cols=114  Identities=20%  Similarity=0.335  Sum_probs=82.0

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCC---CcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHH
Q 023713          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRG---RNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIG  185 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~g---r~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~  185 (278)
                      ....|.++..+-++|+.+.+.|.++.+.++...--+|   .++..+||||+.+|..+.+.|+++.|+-.  ++-+..+|.
T Consensus        15 M~nclr~L~kKs~~~eaVL~~AieLar~fvg~rR~rgqRvE~q~dVAAAc~miAae~~~~PiplaE~r~--lD~sL~Dve   92 (260)
T 3h4c_A           15 MLNCMRGLHKKAVLPEPVLDRGIELARAFVGGRRARGQRVERQPDVAAACLMIAAEEAQQPLPLAEVRC--LDSSLGDVE   92 (260)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHHHTTCCCCHHHHHH--HCTTCCCHH
T ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHHHhhhhhhhcccccccHHHHHHHHHHHHHHcCCCccHHHHHH--HhhhhhHHH
Confidence            3566788888999999999999999999876443333   36779999999999999999999999955  344444555


Q ss_pred             HHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCH
Q 023713          186 RAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN  225 (278)
Q Consensus       186 ~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~  225 (278)
                      -.-.+|.+.+++.+.... +...=...+|..|+.+|+|.-
T Consensus        93 lrr~Eiv~~l~l~e~e~r-l~~~~~~NLl~~Yv~kL~Lq~  131 (260)
T 3h4c_A           93 LRRADIVRELHLEDSERR-LRDTFADNLLVKYILKLGLQV  131 (260)
T ss_dssp             HHHHHHHHHTTCHHHHHH-HHHHHHHHHHHHHHHHTTCCH
T ss_pred             HHHHHHHHHccCCHHHHH-HHHHhhhhHHHHHHHHhccch
Confidence            555578888876531000 111113467778888888873

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

Probab=97.66  E-value=8.4e-05  Score=63.72  Aligned_cols=87  Identities=11%  Similarity=0.022  Sum_probs=73.5

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHH
Q 023713          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK  188 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~  188 (278)
                      ...+|.+++..+++++.+...|..+..........-+++|..+||||||+|++..+.+.+ .+.... .+++..+|..++
T Consensus       134 P~~~l~~~~~~~~~~~~~~~~A~~~l~~s~~~~~~l~~~Ps~IAaAai~lA~~~~~~~~~-~~~~~~-~~~~~~~i~~~~  211 (235)
T 1zp2_A          134 PYTSLEQAFHDGIINQKQLEFAWSIVNDSYASSLCLMAHPHQLAYAALLISCCNDENTIP-KLLDLI-KSTDAFKVILCV  211 (235)
T ss_dssp             THHHHHHHHHTTSSCHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHHHHHHTSCTTHHH-HHHHHC-CHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCCchhccCHHHHHHHHHHHHHHhcCCCCC-CCcchh-hcCCHHHHHHHH
Confidence            467889999999999999999999999998777778999999999999999999887543 344443 478899999999


Q ss_pred             HHHHHHhhh
Q 023713          189 EFIVKHLEA  197 (278)
Q Consensus       189 ~~l~~~L~~  197 (278)
                      +.|.+.+..
T Consensus       212 ~~i~~ly~~  220 (235)
T 1zp2_A          212 QRIISIYYF  220 (235)
T ss_dssp             HHHHHHHTS
T ss_pred             HHHHHHHhh
Confidence            999887654

>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=97.64  E-value=0.00014  Score=63.31  Aligned_cols=89  Identities=9%  Similarity=-0.047  Sum_probs=74.9

Q ss_pred             HHHHHHHHHHHhcCCCH-HHHHHHHHHHHHHh-hCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHH
Q 023713          108 QAFKSISAMSDRLGLVT-TIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIG  185 (278)
Q Consensus       108 ~~~~~I~~i~~~L~Lp~-~v~e~A~~i~k~~~-~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~  185 (278)
                      ...++|.+++..+++++ .+...|..+..... +...+-+.+|..+||||+|+|++..+.|....+++.+ +|++..+|.
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            35789999999999986 78888888887754 3332567899999999999999988888888889885 899999999


Q ss_pred             HHHHHHHHHhhh
Q 023713          186 RAKEFIVKHLEA  197 (278)
Q Consensus       186 ~~~~~l~~~L~~  197 (278)
                      .+++.|.+.+..
T Consensus       217 ~~~~~l~~~~~~  228 (260)
T 2cch_B          217 PCLMDLHQTYLK  228 (260)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999999987753

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

Probab=97.58  E-value=8.6e-05  Score=65.04  Aligned_cols=87  Identities=8%  Similarity=-0.028  Sum_probs=76.2

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHH
Q 023713          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK  188 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~  188 (278)
                      ..++|.+++..++++..+...|..+.........+-+.+|..+||||||+|++..+.+....++... +|++..+|..++
T Consensus       138 p~~fl~~~~~~~~~~~~~~~~a~~l~e~sl~~~~~~~~~Ps~iAaAai~lA~~~l~~~~w~~~l~~~-tg~~~~~l~~~~  216 (269)
T 2b9r_A          138 PLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFPPSQIAAGAFSLALKILDNGEWTPTLQHY-LSYTEESLLPVM  216 (269)
T ss_dssp             HHHHHHHHHHSSCCCHHHHHHHHHHHHHGGGCGGGSSSCTTHHHHHHHHHHHHHHTCCCSCTTHHHH-SCCCSSTTTTHH
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhhhhhhcCCHHHHHHHHHHHHHHHhCCCCCCHHHHHH-HCCCHHHHHHHH
Confidence            5678999999999999999999999888776666678999999999999999999888777888885 899999999999


Q ss_pred             HHHHHHhh
Q 023713          189 EFIVKHLE  196 (278)
Q Consensus       189 ~~l~~~L~  196 (278)
                      +.|.+.+.
T Consensus       217 ~~l~~~~~  224 (269)
T 2b9r_A          217 QHLAKNVV  224 (269)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99987664

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

Probab=97.45  E-value=0.00059  Score=60.22  Aligned_cols=86  Identities=16%  Similarity=0.172  Sum_probs=73.5

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHH
Q 023713          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK  188 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~  188 (278)
                      ..++|.+++..|+++..+...|..+..........-+..|..+||||||+|++..+.+.  ...... ++++..+|..++
T Consensus       157 P~~fL~~~~~~l~~~~~~~~~A~~~l~~sl~t~~~l~~~Ps~IAaAaiylA~~~~~~~~--~~W~~~-~~~~~~~l~~~~  233 (285)
T 3rgf_B          157 PYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDA--RQWFAE-LSVDMEKILEII  233 (285)
T ss_dssp             SHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSHHHHSCHHHHHHHHHHHHHHHTTCCC--HHHHHT-SCSCHHHHHHHH
T ss_pred             hHHHHHHHHHHhCCCHHHHHHHHHHHHHHHccChhhccCHHHHHHHHHHHHHHHcCCCh--hhHHHH-HCCCHHHHHHHH
Confidence            46788999999999999999999999988766666678999999999999999988754  455564 899999999999


Q ss_pred             HHHHHHhhh
Q 023713          189 EFIVKHLEA  197 (278)
Q Consensus       189 ~~l~~~L~~  197 (278)
                      +.|.+....
T Consensus       234 ~~il~ly~~  242 (285)
T 3rgf_B          234 RVILKLYEQ  242 (285)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999887764

>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=97.37  E-value=0.00051  Score=60.09  Aligned_cols=89  Identities=13%  Similarity=0.074  Sum_probs=69.1

Q ss_pred             HHHHHHHHHHhcCCCHHHH----HHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCC---------CCCHHHHHHH
Q 023713          109 AFKSISAMSDRLGLVTTIK----DRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK---------PRTVKEFCSV  175 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~v~----e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~---------p~tl~eia~~  175 (278)
                      .+++|..+...++++....    ..|..+...+.....+-+.+|..+||||||+|++..+.         +.+..+++.+
T Consensus       157 p~~fl~~~~~~l~~~~~~~~~~~~~a~~~l~~~~~d~~~~~~~PS~iAaAai~lA~~~l~~~~~~~~~w~~~~~~~l~~~  236 (271)
T 2w96_A          157 PHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISNPPSMVAAGSVVAAVQGLNLRSPNNFLSYYRLTRFLSRV  236 (271)
T ss_dssp             HHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHTSTHHHHSCHHHHHHHHHHHHHHHHHHHSTTSCGGGTTHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHHHhhhhhhccCHHHHHHHHHHHHHHHhCcCCCCCCCcHHHHHHHHHHH
Confidence            5678899999999987653    45666666654333345789999999999999986543         1246788885


Q ss_pred             HcCCCHHHHHHHHHHHHHHhhhh
Q 023713          176 ANGTTKKEIGRAKEFIVKHLEAE  198 (278)
Q Consensus       176 ~~~v~~~~i~~~~~~l~~~L~~~  198 (278)
                       +|++..+|..+++.|.+.++..
T Consensus       237 -~~v~~~~l~~c~~~i~~l~~~~  258 (271)
T 2w96_A          237 -IKCDPDCLRACQEQIEALLESS  258 (271)
T ss_dssp             -HTSCHHHHHHHHHHHHHHHTTT
T ss_pred             -HCcCHHHHHHHHHHHHHHHHHH
Confidence             8999999999999999998765

>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=97.35  E-value=0.00051  Score=59.47  Aligned_cols=90  Identities=10%  Similarity=-0.024  Sum_probs=72.4

Q ss_pred             HHHHHHHHHHHhcCCCH----HHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHH-------HH-
Q 023713          108 QAFKSISAMSDRLGLVT----TIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFC-------SV-  175 (278)
Q Consensus       108 ~~~~~I~~i~~~L~Lp~----~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia-------~~-  175 (278)
                      ....+|.+++..|+.+.    .+...|..+..........-+.+|..+||||||+|++..+.+++..+..       .. 
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            35678999999999987    5788888888888777777789999999999999999998876543221       21 


Q ss_pred             HcCCCHHHHHHHHHHHHHHhhh
Q 023713          176 ANGTTKKEIGRAKEFIVKHLEA  197 (278)
Q Consensus       176 ~~~v~~~~i~~~~~~l~~~L~~  197 (278)
                      ..+++..+|...++.|.+.+..
T Consensus       230 ~~~~~~~~l~~~~~~il~ly~~  251 (258)
T 2i53_A          230 VQDVPVDVLEDICHQILDLYSQ  251 (258)
T ss_dssp             SSSCCHHHHHHHHHHHHTTTSS
T ss_pred             ccCCCHHHHHHHHHHHHHHHhc
Confidence            1489999999999999887754

>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=97.27  E-value=0.0012  Score=57.02  Aligned_cols=89  Identities=10%  Similarity=0.100  Sum_probs=70.9

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHh-hCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHH----HHHHH-HcCCCH
Q 023713          108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVK----EFCSV-ANGTTK  181 (278)
Q Consensus       108 ~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~-~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~----eia~~-~~~v~~  181 (278)
                      ..+.+|.+++..++.+..+...|..+..... .....-+..|..+||||||+|++..+.+++..    ...+. ..+++.
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            4577899999999999999999999987765 45556678999999999999999988665432    12221 137899


Q ss_pred             HHHHHHHHHHHHHhh
Q 023713          182 KEIGRAKEFIVKHLE  196 (278)
Q Consensus       182 ~~i~~~~~~l~~~L~  196 (278)
                      .+|...++.|.+.+.
T Consensus       225 ~~l~~~~~~i~~~~~  239 (257)
T 2ivx_A          225 ELLDELTHEFLQILE  239 (257)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999988775

>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=97.16  E-value=0.0016  Score=56.31  Aligned_cols=86  Identities=12%  Similarity=0.133  Sum_probs=66.7

Q ss_pred             HHHHHHHHHhcCCCHHH----HHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhc-CCCCC----HHHHHHHHcCCC
Q 023713          110 FKSISAMSDRLGLVTTI----KDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE-NKPRT----VKEFCSVANGTT  180 (278)
Q Consensus       110 ~~~I~~i~~~L~Lp~~v----~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~-~~p~t----l~eia~~~~~v~  180 (278)
                      .+++..+...++++...    ...|..+.....-...+-+.+|..+||||+|+|.+.. +.|.+    ..+++.+ +|++
T Consensus       153 ~~fl~~~~~~~~~~~~~~~~~~~~a~~ll~~~l~d~~~~~~~PS~iAaAai~la~~~~~~~~~~w~~~~~~l~~~-tg~~  231 (254)
T 2f2c_A          153 TDFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPNIALLSPGLICAGGLLTTIETDNTNCRPWTCYLEDLSSI-LNFS  231 (254)
T ss_dssp             GGSHHHHHHHTTCCGGGHHHHHHHHHHHHHHHTTSGGGTTSCHHHHHHHHHHHHHHTTCCSSCCTHHHHHHHHHH-HTCC
T ss_pred             HHHHHHHHHHcCCChhhHHHHHHHHHHHHHHHHcCcchhccCHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHH-HCcC
Confidence            46788889999988643    3456666665544334567899999999999999986 44555    7788885 8999


Q ss_pred             HHHHHHHHHHHHHHhh
Q 023713          181 KKEIGRAKEFIVKHLE  196 (278)
Q Consensus       181 ~~~i~~~~~~l~~~L~  196 (278)
                      ..+|..+++.|.+.+.
T Consensus       232 ~~~l~~c~~~i~~~~~  247 (254)
T 2f2c_A          232 TNTVRTVKDQVSEAFS  247 (254)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999988764

>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=97.10  E-value=0.0026  Score=46.51  Aligned_cols=80  Identities=16%  Similarity=0.175  Sum_probs=64.5

Q ss_pred             HHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCC------CcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHH
Q 023713          113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRG------RNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGR  186 (278)
Q Consensus       113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~g------r~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~  186 (278)
                      |+++|-.|++++ +++.|.+++.+.... +..+      .+.-..+||++|.+||..+..+.-..+.+ +.++.+.++.+
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            788999999998 888888888877533 2111      23457899999999999999999999988 59999999998


Q ss_pred             HHHHHHHHh
Q 023713          187 AKEFIVKHL  195 (278)
Q Consensus       187 ~~~~l~~~L  195 (278)
                      ....+.+..
T Consensus        83 l~~~~e~~~   91 (95)
T 3m03_A           83 LCKQLEKIG   91 (95)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888876654

>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=97.06  E-value=0.0018  Score=56.07  Aligned_cols=88  Identities=16%  Similarity=0.028  Sum_probs=69.1

Q ss_pred             HHHHHHHHHHhcCCCHHH----HHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCC------CCCHHHHHHHHcC
Q 023713          109 AFKSISAMSDRLGLVTTI----KDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK------PRTVKEFCSVANG  178 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~v----~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~------p~tl~eia~~~~~  178 (278)
                      ..++|..++..++++...    ...|..+.....-...+-+.+|..+||||+|+|.+..+.      +....+++.. +|
T Consensus       151 p~~fl~~~~~~~~~~~~~~~~~~~~a~~~le~~l~d~~~~~~~PS~iAaAai~lA~~~l~~~~~~~~~~w~~~l~~~-t~  229 (257)
T 1g3n_C          151 ATDVTSFLLLKLVGGSQHLDFWHHEVNTLITKALVDPLTGSLPASIISAAGCALLVPANVIPQDTHSGGVVPQLASI-LG  229 (257)
T ss_dssp             HHHHHHHHHHHHSCSSTTHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHCCGGGSCC-----CHHHHHHHH-HT
T ss_pred             HHHHHHHHHHHcCCChhHHHHHHHHHHHHHHHHHhCcchhCcCHHHHHHHHHHHHHHHhCCCcccchhhHHHHHHHH-HC
Confidence            577899999999987543    455776766655444456789999999999999988875      3456788875 89


Q ss_pred             CCHHHHHHHHHHHHHHhhh
Q 023713          179 TTKKEIGRAKEFIVKHLEA  197 (278)
Q Consensus       179 v~~~~i~~~~~~l~~~L~~  197 (278)
                      ++..+|..+++.|.+.+.-
T Consensus       230 ~~~~~l~~c~~~i~~l~~~  248 (257)
T 1g3n_C          230 CDVSVLQAAVEQILTSVSD  248 (257)
T ss_dssp             CCHHHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHHHH
Confidence            9999999999999988753

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

Probab=96.73  E-value=0.0012  Score=45.74  Aligned_cols=30  Identities=20%  Similarity=0.493  Sum_probs=26.5

Q ss_pred             CCCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         2 ~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      +...||.|++  .+.+|..+|+++|..||.+.
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            4468999997  58999999999999999986

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

Probab=96.64  E-value=0.0014  Score=44.92  Aligned_cols=29  Identities=14%  Similarity=0.068  Sum_probs=25.9

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      ...||.|++  .+.+|..+|+++|..||.+.
T Consensus        10 iL~CP~ck~--~L~~~~~~g~LvC~~c~~~Y   38 (67)
T 2jny_A           10 VLACPKDKG--PLRYLESEQLLVNERLNLAY   38 (67)
T ss_dssp             CCBCTTTCC--BCEEETTTTEEEETTTTEEE
T ss_pred             HhCCCCCCC--cCeEeCCCCEEEcCCCCccc
Confidence            467999997  58999999999999999886

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

Probab=96.64  E-value=0.0013  Score=45.15  Aligned_cols=30  Identities=10%  Similarity=0.159  Sum_probs=26.4

Q ss_pred             CCCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         2 ~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      +...||.|++  .+.++...|+++|..||.+.
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            4468999997  58899999999999999986

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

Probab=96.60  E-value=0.00098  Score=45.01  Aligned_cols=30  Identities=33%  Similarity=0.797  Sum_probs=27.9

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      .+||.|+. ..+||+.++-.+.|..||.||-
T Consensus         8 VKCp~C~n-iq~VFShA~tvV~C~~Cg~~L~   37 (66)
T 1qxf_A            8 VKCPDCEH-EQVIFDHPSTIVKCIICGRTVA   37 (66)
T ss_dssp             EECTTTCC-EEEEESSCSSCEECSSSCCEEE
T ss_pred             EECCCCCC-ceEEEecCceEEEcccCCCEEe
Confidence            47999998 6899999999999999999996

>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=96.52  E-value=0.001  Score=47.63  Aligned_cols=31  Identities=23%  Similarity=0.438  Sum_probs=27.2

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ..||.||.  +.++++..|.+.|..||.++...
T Consensus        28 y~Cp~CG~--~~v~r~atGiW~C~~Cg~~~agg   58 (83)
T 1vq8_Z           28 HACPNCGE--DRVDRQGTGIWQCSYCDYKFTGG   58 (83)
T ss_dssp             EECSSSCC--EEEEEEETTEEEETTTCCEEECC
T ss_pred             CcCCCCCC--cceeccCCCeEECCCCCCEecCC
Confidence            57999997  57999999999999999997644

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

Probab=96.49  E-value=0.0013  Score=44.15  Aligned_cols=31  Identities=35%  Similarity=0.754  Sum_probs=28.2

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      .+||.|+. ..+||++.+-.+.|..||.+|-+
T Consensus        16 VkCp~C~~-~q~VFSha~t~V~C~~Cgt~L~~   46 (63)
T 3j20_W           16 VKCIDCGN-EQIVFSHPATKVRCLICGATLVE   46 (63)
T ss_dssp             EECSSSCC-EEEEESSCSSCEECSSSCCEEEE
T ss_pred             EECCCCCC-eeEEEecCCeEEEccCcCCEEec
Confidence            47999998 68999999999999999999963

>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=96.47  E-value=0.0014  Score=45.26  Aligned_cols=29  Identities=21%  Similarity=0.345  Sum_probs=25.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      ...||.|++  .+.++..+|+++|..||.+.
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  48889899999999999986

>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=96.42  E-value=0.0018  Score=44.54  Aligned_cols=28  Identities=36%  Similarity=0.659  Sum_probs=25.3

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      ..||.|++  .+.++..+|.++|..||.+.
T Consensus         9 L~CP~ck~--~L~~~~~~~~LiC~~cg~~Y   36 (68)
T 2hf1_A            9 LVCPLCKG--PLVFDKSKDELICKGDRLAF   36 (68)
T ss_dssp             CBCTTTCC--BCEEETTTTEEEETTTTEEE
T ss_pred             eECCCCCC--cCeEeCCCCEEEcCCCCcEe
Confidence            57999997  58899999999999999986

>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=96.38  E-value=0.0027  Score=57.82  Aligned_cols=89  Identities=9%  Similarity=0.085  Sum_probs=69.7

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHh-hCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHH----HHHHH-HcCCCHH
Q 023713          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVK----EFCSV-ANGTTKK  182 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~-~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~----eia~~-~~~v~~~  182 (278)
                      .+.+|.+++..++++..+...|..+..... ...+.-+..|..+||||||+|++..+.+++..    ..... ..+++..
T Consensus       153 P~~fL~~~~~~l~~~~~l~~~A~~ll~~sl~~t~l~l~y~Ps~IAaAAI~lA~~~l~~~~p~~~~~~~W~~~~~~~vt~~  232 (358)
T 2pk2_A          153 PHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLE  232 (358)
T ss_dssp             TTHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCGGGTSCHHHHTTTTTTTHHHHTTCCCCCCSSSCCTTTTSCSSCCHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhccCHHHHHHHHHHHHHHHhCCCCCCCccccchHHHHhccCCHH
Confidence            456888999999999999999999988776 44555678999999999999999988655432    12221 1368999


Q ss_pred             HHHHHHHHHHHHhhh
Q 023713          183 EIGRAKEFIVKHLEA  197 (278)
Q Consensus       183 ~i~~~~~~l~~~L~~  197 (278)
                      +|...++.|.+.+.-
T Consensus       233 ~l~~i~~~il~~y~~  247 (358)
T 2pk2_A          233 LLDELTHEFLQILEK  247 (358)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHh
Confidence            999999999987753

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

Probab=96.24  E-value=0.015  Score=51.72  Aligned_cols=87  Identities=14%  Similarity=0.125  Sum_probs=64.2

Q ss_pred             HHHHHHHHHhcCCCHH----HHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCC-----HHHHHHHHcCCC
Q 023713          110 FKSISAMSDRLGLVTT----IKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRT-----VKEFCSVANGTT  180 (278)
Q Consensus       110 ~~~I~~i~~~L~Lp~~----v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~t-----l~eia~~~~~v~  180 (278)
                      +++|..+...++++..    +...|..+.....-...+-+.+|..+||||||+|.+..+....     ..++..+ +|++
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    4456666666654444455788999999999999997774322     2566674 8999


Q ss_pred             HHHHHHHHHHHHHHhhh
Q 023713          181 KKEIGRAKEFIVKHLEA  197 (278)
Q Consensus       181 ~~~i~~~~~~l~~~L~~  197 (278)
                      ..+|..+++.|.+.+.-
T Consensus       251 ~~~l~~c~~~I~~l~~~  267 (306)
T 3g33_B          251 VDCLRACQEQIEAALRE  267 (306)
T ss_dssp             HHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999988864

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

Probab=96.18  E-value=0.0021  Score=45.22  Aligned_cols=31  Identities=26%  Similarity=0.769  Sum_probs=28.1

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      ..||.|+. ..+||++++-.+.|..||.||-+
T Consensus        33 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~   63 (81)
T 2xzm_6           33 VKCAQCQN-IQMIFSNAQSTIICEKCSAILCK   63 (81)
T ss_dssp             EECSSSCC-EEEEETTCSSCEECSSSCCEEEE
T ss_pred             eECCCCCC-eeEEEecCccEEEccCCCCEEee
Confidence            47999998 68999999999999999999963

>2r7g_A PP110, retinoblastoma-associated protein, P105-RB, RB; retinoblastoma protein, E2F displacement, transcription repressor; 1.67A {Homo sapiens} SCOP: a.74.1.3 a.74.1.3 PDB: 1n4m_A 3pom_A 1gh6_B 1gux_A 1o9k_A 1ad6_A 1gux_B 1o9k_B

Probab=96.10  E-value=0.016  Score=52.29  Aligned_cols=71  Identities=14%  Similarity=0.250  Sum_probs=60.4

Q ss_pred             HHHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHHhh--CCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 023713          105 NLIQAFKSISAMSDRLGLVT-TIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSV  175 (278)
Q Consensus       105 ~l~~~~~~I~~i~~~L~Lp~-~v~e~A~~i~k~~~~--~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~  175 (278)
                      .+.-|..+|..+|+.|+++. .+.+.+..+|..+..  -.++++|..+.+.-+|+|..||..+...|++||-..
T Consensus       214 vy~La~~Rl~~LC~~L~~~~~~~~~~iWt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~tF~~Ii~~  287 (347)
T 2r7g_A          214 VYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTA  287 (347)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHhChHhhcCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence            34557889999999998875 577888888877654  357899999999999999999999999999999764

>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=96.10  E-value=0.0023  Score=45.04  Aligned_cols=31  Identities=26%  Similarity=0.654  Sum_probs=28.2

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      ..||.|+. ..+||++.+-.+.|..||.||-+
T Consensus        35 VkCp~C~~-~q~VFSha~t~V~C~~Cg~~L~~   65 (82)
T 3u5c_b           35 VKCPGCLN-ITTVFSHAQTAVTCESCSTILCT   65 (82)
T ss_dssp             EECTTSCS-CEEEESBCSSCCCCSSSCCCCEE
T ss_pred             EECCCCCC-eeEEEecCCeEEEccccCCEEec
Confidence            46999998 68999999999999999999963

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

Probab=96.07  E-value=0.016  Score=53.35  Aligned_cols=70  Identities=14%  Similarity=0.275  Sum_probs=60.0

Q ss_pred             HHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHHhhC--CCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 023713          106 LIQAFKSISAMSDRLGLVT-TIKDRANEIYKKVEDQ--KPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSV  175 (278)
Q Consensus       106 l~~~~~~I~~i~~~L~Lp~-~v~e~A~~i~k~~~~~--~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~  175 (278)
                      ..-|..+|+.+|++|++++ .+.+....+|+.....  .++++|..+.++-+|+|..||..+..++++||-..
T Consensus       279 y~LAa~Rl~~LC~~L~~~~~~l~~~IWt~fe~~l~~~teLm~dRHLDQiiLCsiY~i~Kv~~~~~tFk~Ii~~  351 (411)
T 4ell_A          279 YRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTA  351 (411)
T ss_dssp             HHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHTTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHhhhHhhccccHHHHHHHHHHHHHhhccCCCCHHHHHHH
Confidence            3558889999999999875 6778888888776543  57899999999999999999999999999999763

>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=95.87  E-value=0.0031  Score=44.85  Aligned_cols=31  Identities=32%  Similarity=0.630  Sum_probs=28.3

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      ..||.|+. ..+||++.+-.+.|..||.||-+
T Consensus        37 VkCp~C~~-~~~VFShA~t~V~C~~CgtvL~~   67 (86)
T 3iz6_X           37 VKCQGCFN-ITTVFSHSQTVVVCPGCQTVLCQ   67 (86)
T ss_dssp             EECTTTCC-EEEEETTCSSCCCCSSSCCCCSC
T ss_pred             EECCCCCC-eeEEEecCCcEEEccCCCCEeec
Confidence            47999998 68999999999999999999963

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

Probab=95.57  E-value=0.041  Score=53.53  Aligned_cols=70  Identities=14%  Similarity=0.266  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHHHHHhcCCC-HHHHHHHHHHHHHHhhC--CCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHH
Q 023713          105 NLIQAFKSISAMSDRLGLV-TTIKDRANEIYKKVEDQ--KPLRGRNQEAIVAACLYIACRQENKPRTVKEFCS  174 (278)
Q Consensus       105 ~l~~~~~~I~~i~~~L~Lp-~~v~e~A~~i~k~~~~~--~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~  174 (278)
                      ...-|..+|+.+|+.|+++ +.+.+.+..+|+.....  .++++|..+.++-+|+|..||..+..++++||-.
T Consensus       523 vy~LAa~Rl~~LC~~L~~~~~~i~~~IWt~fe~~l~~~t~L~~dRHLDQiilCsiY~icKv~~~~ltFk~Ii~  595 (656)
T 4elj_A          523 VYRLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVT  595 (656)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHHHHHCGGGSTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhccCCcCHHHHHH
Confidence            3455889999999999887 46888888888876553  5789999999999999999999999999999976

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

Probab=95.39  E-value=0.075  Score=47.07  Aligned_cols=71  Identities=15%  Similarity=0.277  Sum_probs=52.5

Q ss_pred             HHHHHHHhcCCCHHHHHHHHHHHHHHhhC-C---CCCCCcHHHHHHHHHHHHHH-hcCCCCCHHHHHHHHcCCCHHHH
Q 023713          112 SISAMSDRLGLVTTIKDRANEIYKKVEDQ-K---PLRGRNQEAIVAACLYIACR-QENKPRTVKEFCSVANGTTKKEI  184 (278)
Q Consensus       112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~-~---~~~gr~~~~~aAAclY~acR-~~~~p~tl~eia~~~~~v~~~~i  184 (278)
                      .-..+|..|+|++.+.++|..+|+.+... +   .+.+. .+..-.||||+||. .++..+||-.|... .+++..+.
T Consensus         5 rF~~lC~~Lnld~~~~~~Aw~~~~~~~~~~~~~~~~~~~-~~~~w~acLY~a~~~~~~n~vsLt~LLr~-~~lsi~~F   80 (304)
T 2qdj_A            5 DFTALCQKLKIPDHVRERAWLTWEKVSSVDGVLGGYIQK-KKELWGICIFIAAVDLDEMSFTFTELQKN-IEISVHKF   80 (304)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHC----------C-HHHHHHHHHHHHHHHHTCCCSCHHHHHHH-HTCCHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCCccc-hHHHHHHhHHHHhhccCCCcCcHHHHHHH-cCCCHHHH
Confidence            45678999999999999999999998774 2   23333 44555556999996 45677999999884 78887665

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

Probab=95.30  E-value=0.0096  Score=38.26  Aligned_cols=28  Identities=18%  Similarity=0.563  Sum_probs=21.4

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      ..||.||+ ..+.. +.....+|..||.+.
T Consensus        20 k~CP~CG~-~~fm~-~~~~R~~C~kCG~t~   47 (50)
T 3j20_Y           20 KFCPRCGP-GVFMA-DHGDRWACGKCGYTE   47 (50)
T ss_dssp             EECSSSCS-SCEEE-ECSSEEECSSSCCEE
T ss_pred             ccCCCCCC-ceEEe-cCCCeEECCCCCCEE
Confidence            56999998 44444 446899999999874

>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=95.16  E-value=0.077  Score=46.40  Aligned_cols=80  Identities=13%  Similarity=0.005  Sum_probs=57.2

Q ss_pred             HHHHHHHHHHhcCCCHH-----------HHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHc
Q 023713          109 AFKSISAMSDRLGLVTT-----------IKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVAN  177 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~-----------v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~  177 (278)
                      ..++|..++..+++++.           ....+..+.....-...+-+.+|..+||||||+|+.       ..++..+ +
T Consensus       151 p~~fL~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~llelsl~d~~~l~~~PS~iAaAai~la~~-------~~~l~~~-t  222 (283)
T 1w98_B          151 IVSWLNVYMQVAYLNDLHEVLLPQYPQQIFIQIAELLDLCVLDVDCLEFPYGILAASALYHFSS-------SELMQKV-S  222 (283)
T ss_dssp             HHHHHHHHHHHHTCCSSCCSSSCCSCHHHHHHHHHHHHHHHHSGGGGGSCHHHHHHHHHHHTSC-------HHHHHHH-S
T ss_pred             HHHHHHHHHHHhccCchhhHHHHhhhHHHHHHHHHHHHHHHhhhhhhcCCHHHHHHHHHHHHHC-------hHHHHHH-h
Confidence            46788888888776532           223344555554422225678999999999999863       5677775 8


Q ss_pred             CCCHHHHHHHHHHHHHHhh
Q 023713          178 GTTKKEIGRAKEFIVKHLE  196 (278)
Q Consensus       178 ~v~~~~i~~~~~~l~~~L~  196 (278)
                      |++..+|..+++.|.....
T Consensus       223 g~~~~~i~~c~~~l~~~~~  241 (283)
T 1w98_B          223 GYQWCDIENCVKWMVPFAM  241 (283)
T ss_dssp             CCCHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHH
Confidence            9999999999999876554

>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=94.76  E-value=0.058  Score=41.28  Aligned_cols=28  Identities=21%  Similarity=0.407  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      .-.||.|+++ -.-.|  ...+||++||.--
T Consensus        27 lP~CP~C~se-ytYeD--g~l~vCPeC~hEW   54 (138)
T 2akl_A           27 LPPCPQCNSE-YTYED--GALLVCPECAHEW   54 (138)
T ss_dssp             SCCCTTTCCC-CCEEC--SSSEEETTTTEEE
T ss_pred             CCCCCCCCCc-ceEec--CCeEECCcccccc
Confidence            4679999994 33333  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=94.28  E-value=0.021  Score=37.37  Aligned_cols=28  Identities=25%  Similarity=0.708  Sum_probs=21.5

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V   32 (278)
                      +..||.||+ . +......+...|..||..
T Consensus        18 ~~fCPkCG~-~-~~ma~~~dr~~C~kCgyt   45 (55)
T 2k4x_A           18 HRFCPRCGP-G-VFLAEHADRYSCGRCGYT   45 (55)
T ss_dssp             SCCCTTTTT-T-CCCEECSSEEECTTTCCC
T ss_pred             cccCcCCCC-c-eeEeccCCEEECCCCCCE
Confidence            578999997 3 333344579999999997

>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=94.24  E-value=0.22  Score=44.41  Aligned_cols=78  Identities=8%  Similarity=0.050  Sum_probs=54.7

Q ss_pred             cCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCH--HHHHHH-HcCCCHHHHHHHHHHHHHHhh
Q 023713          120 LGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTV--KEFCSV-ANGTTKKEIGRAKEFIVKHLE  196 (278)
Q Consensus       120 L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl--~eia~~-~~~v~~~~i~~~~~~l~~~L~  196 (278)
                      ++.|+.+...|..+..........-+..|..+||||||+|++..+.+.+.  .++-.. ..+.+...|..+.+.|...+.
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            34556788889888888766555557889999999999999998876442  222110 024467788888888877665


Q ss_pred             h
Q 023713          197 A  197 (278)
Q Consensus       197 ~  197 (278)
                      .
T Consensus       261 ~  261 (323)
T 1jkw_A          261 K  261 (323)
T ss_dssp             T
T ss_pred             c
Confidence            3

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

Probab=93.85  E-value=0.016  Score=36.53  Aligned_cols=27  Identities=30%  Similarity=0.679  Sum_probs=18.0

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCc----------eEcCCCcc
Q 023713            1 MADSYCADCKRLTEVVFDHSAGD----------TICSECGL   31 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~D~~~G~----------~vC~~CG~   31 (278)
                      |....|+.||-    |+|++.|+          .+|..||.
T Consensus         2 m~~y~C~vCGy----vyd~~~Gd~t~f~~lP~dw~CP~Cg~   38 (46)
T 6rxn_A            2 MQKYVCNVCGY----EYDPAEHDNVPFDQLPDDWCCPVCGV   38 (46)
T ss_dssp             CCCEEETTTCC----EECGGGGTTCCGGGSCTTCBCTTTCC
T ss_pred             CCEEECCCCCe----EEeCCcCCCcchhhCCCCCcCcCCCC
Confidence            45567888885    57766663          47777775

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

Probab=93.64  E-value=0.054  Score=35.53  Aligned_cols=27  Identities=26%  Similarity=0.671  Sum_probs=22.4

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcC--CCcccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICS--ECGLVL   33 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~--~CG~Vl   33 (278)
                      ...||.|++  .+.+|.  |+++|.  +||...
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            357999998  477764  999999  999876

>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=93.11  E-value=0.036  Score=36.12  Aligned_cols=18  Identities=28%  Similarity=0.680  Sum_probs=12.0

Q ss_pred             CCCCCCCCCCCCCceeEeCCCC
Q 023713            1 MADSYCADCKRLTEVVFDHSAG   22 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~D~~~G   22 (278)
                      |....|+.||-    |+|++.|
T Consensus         1 m~~y~C~vCGy----vYd~~~G   18 (54)
T 4rxn_A            1 MKKYTCTVCGY----IYDPEDG   18 (54)
T ss_dssp             CCCEEETTTCC----EECTTTC
T ss_pred             CCceECCCCCe----EECCCcC
Confidence            55566777774    5776666

>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=92.60  E-value=0.039  Score=35.64  Aligned_cols=19  Identities=32%  Similarity=0.593  Sum_probs=9.7

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCc
Q 023713            1 MADSYCADCKRLTEVVFDHSAGD   23 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~D~~~G~   23 (278)
                      |....|+.||-    |+|++.|+
T Consensus         1 m~~y~C~~CGy----vYd~~~Gd   19 (52)
T 1e8j_A            1 MDIYVCTVCGY----EYDPAKGD   19 (52)
T ss_dssp             CCCEECSSSCC----CCCTTTCC
T ss_pred             CCcEEeCCCCe----EEcCCcCC
Confidence            44455666664    35555443

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

Probab=92.52  E-value=0.79  Score=44.62  Aligned_cols=71  Identities=14%  Similarity=0.184  Sum_probs=56.6

Q ss_pred             HHHHHHHhcCCCHHHHHHHHHHHHHHhh-CCC----CCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHH
Q 023713          112 SISAMSDRLGLVTTIKDRANEIYKKVED-QKP----LRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (278)
Q Consensus       112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~-~~~----~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i  184 (278)
                      .-..+|..|++++.+.++|.+.|+.... .+.    +.| ....+.|+.+|.||+.+|..+||-.|-.. .+++..+.
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-KKELWGICIFIAAVDLDEMSFTFTELQKN-IEISVHKF   82 (656)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHCSCC-----C-CHHHHHHHHHHHHHHTTCCCSCHHHHHHH-HTCCHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHHHhccccccCCccc-chHHhhhhhheeeeeccCCeeeHHHHHHH-hcCCHHHH
Confidence            4678899999999999999999999874 222    223 56677777888888899999999999884 78876554

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

Probab=92.01  E-value=0.066  Score=39.19  Aligned_cols=30  Identities=13%  Similarity=0.065  Sum_probs=23.9

Q ss_pred             CCCCCCCCCCCCceeEeCC---------------------------CCceEcCCCcccc
Q 023713            2 ADSYCADCKRLTEVVFDHS---------------------------AGDTICSECGLVL   33 (278)
Q Consensus         2 ~~~~Cp~Cg~~~~vv~D~~---------------------------~G~~vC~~CG~Vl   33 (278)
                      +...||.|+.  .+.++..                           +|.++|.+||...
T Consensus         7 dILaCP~cK~--pL~l~~~~~~~~~~ca~~~~~~~~~~~~~~~e~~~~~LvC~~c~~~Y   63 (97)
T 2k5r_A            7 HLLCSPDTRQ--PLSLLESKGLEALNKAIVSGTVQRADGSIQNQSLHEALITRDRKQVF   63 (97)
T ss_dssp             SSCCCCTTSS--CCEECCHHHHHHHHHHHHHTCCBCTTSCBCCCCCSEEEECTTSCEEE
T ss_pred             hheECCCCCC--cccccccchhhhhhhhhhccccccccccccccccCCeEEcCCCCCCc
Confidence            4568999997  3566554                           7899999999986

>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=91.51  E-value=0.054  Score=37.23  Aligned_cols=27  Identities=26%  Similarity=0.757  Sum_probs=18.0

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcc-cc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGL-VL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~-Vl   33 (278)
                      ..|++||..  +.. .....+.|.+||. ||
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            579999973  222 2345567999998 65

>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=91.26  E-value=6.3  Score=34.44  Aligned_cols=104  Identities=9%  Similarity=0.040  Sum_probs=78.8

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhC--CC-CCCCcHHHHHHHHHHHHHH-hcCCCCCHHHHHHHHcCCCHHHH
Q 023713          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQ--KP-LRGRNQEAIVAACLYIACR-QENKPRTVKEFCSVANGTTKKEI  184 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~--~~-~~gr~~~~~aAAclY~acR-~~~~p~tl~eia~~~~~v~~~~i  184 (278)
                      ..++|.++...-.++..+.-.|..++.++...  ++ +...+..-+..+++-+|.+ ..+...+-+..|.+ .|++..+|
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            45688888888899998888888888887663  22 2344666677777777777 66777888999996 89999999


Q ss_pred             HHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhh
Q 023713          185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSN  220 (278)
Q Consensus       185 ~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~  220 (278)
                      ++..+++...++.+      + .+++++|..-+...
T Consensus       156 N~LE~eFL~lLdf~------L-~V~~ee~~~cy~E~  184 (293)
T 2pmi_B          156 NILENDFLKRVNYR------I-IPRDHNITLCSIEQ  184 (293)
T ss_dssp             HHHHHHHHHTTTTC------C-SCCTTHHHHHHHHS
T ss_pred             HHHHHHHHHHcCCc------e-eeCHHHHHHHHHHH
Confidence            99999999999876      2 24556666544444

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

Probab=91.17  E-value=0.15  Score=38.40  Aligned_cols=31  Identities=16%  Similarity=0.439  Sum_probs=22.1

Q ss_pred             CCCCCCCCCCCCceeEeCCCC----ceEcCCCccccc
Q 023713            2 ADSYCADCKRLTEVVFDHSAG----DTICSECGLVLE   34 (278)
Q Consensus         2 ~~~~Cp~Cg~~~~vv~D~~~G----~~vC~~CG~Vl~   34 (278)
                      .|..||+||+-  +......|    .++|..||.+..
T Consensus         3 ~m~FCp~Cgn~--L~~~~~~~~~~~~~~C~~C~y~~~   37 (113)
T 3h0g_I            3 NFQYCIECNNM--LYPREDKVDRVLRLACRNCDYSEI   37 (113)
T ss_dssp             CCCCCSSSCCC--CEECCCTTTCCCCEECSSSCCEEC
T ss_pred             cceeCcCCCCE--eeEcccCCCCeeEEECCCCCCeEE
Confidence            46899999972  44433322    699999999763

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

Probab=91.16  E-value=0.079  Score=31.43  Aligned_cols=29  Identities=21%  Similarity=0.582  Sum_probs=20.4

Q ss_pred             CCCCCCCC-CceeEeCCCCceEcCCCcccc
Q 023713            5 YCADCKRL-TEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         5 ~Cp~Cg~~-~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      .||.||++ +.++.+...=.+-|..||..-
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            59999995 344554455556799999763

>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=91.09  E-value=0.13  Score=44.10  Aligned_cols=28  Identities=25%  Similarity=0.432  Sum_probs=21.9

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V   32 (278)
                      ..||.||+.....++ ..|...|-+||.-
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            479999984456655 4688999999975

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

Probab=90.99  E-value=0.31  Score=33.90  Aligned_cols=45  Identities=11%  Similarity=0.166  Sum_probs=38.7

Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713          153 AACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE  198 (278)
Q Consensus       153 AAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~  198 (278)
                      ---|+-+.+..+.|....||+.. +|++.+++.++++.|.+.-.+.
T Consensus        21 eekVLe~LkeaG~PlkageIae~-~GvdKKeVdKaik~LKkEgkI~   65 (80)
T 2lnb_A           21 EQRILQVLTEAGSPVKLAQLVKE-CQAPKRELNQVLYRMKKELKVS   65 (80)
T ss_dssp             HHHHHHHHHHHTSCEEHHHHHHH-HTSCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHH-HCCCHHHHHHHHHHHHHcCCcc
Confidence            33466788999999999999995 9999999999999999877653

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

Probab=90.78  E-value=0.17  Score=33.07  Aligned_cols=31  Identities=16%  Similarity=0.416  Sum_probs=21.5

Q ss_pred             CCCCCCCCCCceeEeC------CCC---ceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDH------SAG---DTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~------~~G---~~vC~~CG~Vl~e   35 (278)
                      ..||.||. ..+++..      +++   .++|.+||..-.+
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            57999998 5665442      223   4799999987654

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

Probab=90.10  E-value=0.16  Score=35.93  Aligned_cols=32  Identities=28%  Similarity=0.507  Sum_probs=25.9

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ...||.||+ .. +.-...|-+-|..||.++...
T Consensus        35 ky~CpfCGk-~~-vkR~a~GIW~C~kCg~~~AGG   66 (83)
T 3j21_i           35 KHTCPVCGR-KA-VKRISTGIWQCQKCGATFAGG   66 (83)
T ss_dssp             CBCCSSSCS-SC-EEEEETTEEEETTTCCEEECC
T ss_pred             ccCCCCCCC-ce-eEecCcCeEEcCCCCCEEeCC
Confidence            467999998 45 445679999999999998654

>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=89.54  E-value=0.19  Score=38.32  Aligned_cols=32  Identities=25%  Similarity=0.456  Sum_probs=23.4

Q ss_pred             CCCCCCCCCCCCCceeE--e--CCCCceEcCCCccccc
Q 023713            1 MADSYCADCKRLTEVVF--D--HSAGDTICSECGLVLE   34 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~--D--~~~G~~vC~~CG~Vl~   34 (278)
                      |.+..||+||+  -+..  |  ...+.++|..||....
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            46789999997  2332  3  3456899999999764

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

Probab=89.45  E-value=0.19  Score=34.54  Aligned_cols=32  Identities=25%  Similarity=0.357  Sum_probs=25.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ...||.||. .. +.-...|-+-|..||.++...
T Consensus        26 ky~C~fCgk-~~-vkR~a~GIW~C~~C~~~~AGG   57 (72)
T 3jyw_9           26 RYDCSFCGK-KT-VKRGAAGIWTCSCCKKTVAGG   57 (72)
T ss_dssp             CBCCSSCCS-SC-BSBCSSSCBCCSSSCCCCCCS
T ss_pred             CccCCCCCC-ce-eEecCCCeEECCCCCCEEeCC
Confidence            367999998 44 445789999999999998644

>2v3b_B Rubredoxin 2, rubredoxin; alkane degradation, iron-sulfur protein, oxidoreductase, ELE transfer, electron transport, FAD, NAD, iron; HET: FAD; 2.45A {Pseudomonas aeruginosa}

Probab=89.08  E-value=0.12  Score=33.71  Aligned_cols=18  Identities=28%  Similarity=0.646  Sum_probs=9.5

Q ss_pred             CCCCCCCCCCCCCceeEeCCCC
Q 023713            1 MADSYCADCKRLTEVVFDHSAG   22 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~D~~~G   22 (278)
                      |....|+.||-    |+|++.|
T Consensus         1 m~~y~C~~CGy----vYd~~~G   18 (55)
T 2v3b_B            1 MRKWQCVVCGF----IYDEALG   18 (55)
T ss_dssp             CCEEEETTTCC----EEETTTC
T ss_pred             CCcEEeCCCCe----EECCCcC
Confidence            34455666664    4555544

>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=88.72  E-value=0.2  Score=34.60  Aligned_cols=32  Identities=19%  Similarity=0.400  Sum_probs=25.1

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ...||.||. ..+ .-...|-+.|..||.++...
T Consensus        27 ky~C~fCgk-~~v-kR~a~GIW~C~~C~~~~AGG   58 (73)
T 1ffk_W           27 KYKCPVCGF-PKL-KRASTSIWVCGHCGYKIAGG   58 (73)
T ss_pred             CccCCCCCC-cee-EEEEeEEEECCCCCcEEECC
Confidence            367999998 444 44578999999999998644

>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=88.37  E-value=0.22  Score=37.44  Aligned_cols=31  Identities=23%  Similarity=0.434  Sum_probs=24.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ..||.||. .++ .-...|-+-|..||.++...
T Consensus        61 ytCPfCGk-~~v-KR~avGIW~C~~Cgk~fAGG   91 (116)
T 3cc2_Z           61 HACPNCGE-DRV-DRQGTGIWQCSYCDYKFTGG   91 (116)
T ss_dssp             EECSSSCC-EEE-EEEETTEEEETTTCCEEECC
T ss_pred             CcCCCCCC-cee-EecCceeEECCCCCCEEECC
Confidence            57999998 444 44568999999999998644

>4a17_Y RPL37A, 60S ribosomal protein L32; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_Y 4a1c_Y 4a1e_Y

Probab=88.24  E-value=0.23  Score=36.45  Aligned_cols=30  Identities=20%  Similarity=0.420  Sum_probs=24.5

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      ..||.||. +. +.-...|-+-|..||.++..
T Consensus        37 y~CpfCgk-~~-vKR~a~GIW~C~kCg~~~AG   66 (103)
T 4a17_Y           37 YGCPFCGK-VA-VKRAAVGIWKCKPCKKIIAG   66 (103)
T ss_dssp             EECTTTCC-EE-EEEEETTEEEETTTTEEEEC
T ss_pred             CCCCCCCC-ce-eeecCcceEEcCCCCCEEeC
Confidence            57999998 44 55567999999999999863

>2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle structural genomics center for infectious electron transport, iron; NMR {Mycobacterium tuberculosis}

Probab=88.16  E-value=0.16  Score=35.83  Aligned_cols=16  Identities=19%  Similarity=0.380  Sum_probs=11.8

Q ss_pred             CCceEcCCCccccccc
Q 023713           21 AGDTICSECGLVLEAY   36 (278)
Q Consensus        21 ~G~~vC~~CG~Vl~e~   36 (278)
                      ...++|..||.|.++.
T Consensus        25 m~~y~C~vCGyvYD~~   40 (81)
T 2kn9_A           25 YKLFRCIQCGFEYDEA   40 (81)
T ss_dssp             CCEEEETTTCCEEETT
T ss_pred             cceEEeCCCCEEEcCC
Confidence            3468888888888754

>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4

Probab=87.77  E-value=0.18  Score=35.98  Aligned_cols=43  Identities=23%  Similarity=0.414  Sum_probs=28.4

Q ss_pred             CCCCCCCCCCce--eEeC--CCCceEcCCCccccccc------ccccccchhh
Q 023713            4 SYCADCKRLTEV--VFDH--SAGDTICSECGLVLEAY------SVDETSEWRI   46 (278)
Q Consensus         4 ~~Cp~Cg~~~~v--v~D~--~~G~~vC~~CG~Vl~e~------~id~~~ewr~   46 (278)
                      ..||.|+.+..+  ..|.  ..|.+.|..||.-.+-.      .||-.++|..
T Consensus        24 F~CPfCnh~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epiDVYs~WiD   76 (85)
T 1wii_A           24 FTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWID   76 (85)
T ss_dssp             CCCTTTCCSSCEEEEEETTTTEEEEEESSSCCEEEEECCSSCCTTHHHHHHHH
T ss_pred             EcCCCCCCCCeEEEEEEccCCEEEEEcccCCCeEEeccCccCcchhhHHHHHH
Confidence            569999985334  4443  57899999999876433      2444455643

>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A

Probab=87.75  E-value=0.18  Score=34.55  Aligned_cols=8  Identities=25%  Similarity=0.634  Sum_probs=4.1

Q ss_pred             CCCCCCCC
Q 023713            4 SYCADCKR   11 (278)
Q Consensus         4 ~~Cp~Cg~   11 (278)
                      ..|+.||-
T Consensus         8 y~C~vCGy   15 (70)
T 1dx8_A            8 YECEACGY   15 (70)
T ss_dssp             EEETTTCC
T ss_pred             EEeCCCCE
Confidence            44555553

>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=86.76  E-value=0.33  Score=28.60  Aligned_cols=27  Identities=26%  Similarity=0.679  Sum_probs=15.9

Q ss_pred             CCCCCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713            2 ADSYCADCKRLTEVVFDHSAGDTICSECGL   31 (278)
Q Consensus         2 ~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~   31 (278)
                      +...|+.||.. -.+.....|+++|  ||.
T Consensus         5 ~fY~C~~CGni-vev~~~g~~~l~C--CG~   31 (36)
T 1dxg_A            5 DVYKCELCGQV-VKVLEEGGGTLVC--CGE   31 (36)
T ss_dssp             CEEECTTTCCE-EEEEECCSSCEEE--TTE
T ss_pred             cEEEcCCCCcE-EEEEeCCCcCEEe--CCc
Confidence            34568888752 2233456677777  554

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

Probab=86.56  E-value=0.33  Score=37.57  Aligned_cols=29  Identities=21%  Similarity=0.391  Sum_probs=20.1

Q ss_pred             CCCCCCCCCCCceeEeCC----CCceEcCCCcccc
Q 023713            3 DSYCADCKRLTEVVFDHS----AGDTICSECGLVL   33 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~----~G~~vC~~CG~Vl   33 (278)
                      +..||+||+  -+.....    ...++|+.||.+.
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            578999997  2332221    2269999999975

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

Probab=85.70  E-value=0.2  Score=32.11  Aligned_cols=23  Identities=26%  Similarity=0.677  Sum_probs=19.7

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V   32 (278)
                      ..||.||+.      ...|-+-|..||..
T Consensus        15 ~iCpkC~a~------~~~gaw~CrKCG~~   37 (51)
T 3j21_g           15 YVCLRCGAT------NPWGAKKCRKCGYK   37 (51)
T ss_dssp             EECTTTCCE------ECTTCSSCSSSSSC
T ss_pred             ccCCCCCCc------CCCCceecCCCCCc
Confidence            679999982      46899999999998

>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=85.64  E-value=0.39  Score=32.99  Aligned_cols=27  Identities=26%  Similarity=0.581  Sum_probs=22.3

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      ..|| ||..  .+.|...-..-|. ||.++.
T Consensus         5 v~C~-C~~~--~~~~~~~kT~~C~-CG~~~~   31 (71)
T 1gh9_A            5 FRCD-CGRA--LYSREGAKTRKCV-CGRTVN   31 (71)
T ss_dssp             EEET-TSCC--EEEETTCSEEEET-TTEEEE
T ss_pred             EECC-CCCE--EEEcCCCcEEECC-CCCeee
Confidence            3699 9983  6777788889999 999985

>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A

Probab=85.47  E-value=0.29  Score=32.47  Aligned_cols=25  Identities=24%  Similarity=0.569  Sum_probs=19.1

Q ss_pred             CCCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         2 ~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      -+..||.||. -++       ..+|..||....
T Consensus         5 ~mr~C~~Cgv-YTL-------k~~CP~CG~~T~   29 (60)
T 2apo_B            5 RMKKCPKCGL-YTL-------KEICPKCGEKTV   29 (60)
T ss_dssp             CCEECTTTCC-EES-------SSBCSSSCSBCB
T ss_pred             hceeCCCCCC-Eec-------cccCcCCCCcCC
Confidence            4678999997 333       667999998864

>1s24_A Rubredoxin 2; electron transport; NMR {Pseudomonas oleovorans} SCOP: g.41.5.1

Probab=84.38  E-value=0.25  Score=35.32  Aligned_cols=16  Identities=25%  Similarity=0.497  Sum_probs=12.1

Q ss_pred             CCceEcCCCccccccc
Q 023713           21 AGDTICSECGLVLEAY   36 (278)
Q Consensus        21 ~G~~vC~~CG~Vl~e~   36 (278)
                      ...++|..||.|.++.
T Consensus        33 m~~y~C~vCGyvYD~~   48 (87)
T 1s24_A           33 YLKWICITCGHIYDEA   48 (87)
T ss_dssp             CCEEEETTTTEEEETT
T ss_pred             CceEECCCCCeEecCC
Confidence            4568888888888753

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

Probab=83.56  E-value=0.87  Score=28.93  Aligned_cols=30  Identities=23%  Similarity=0.433  Sum_probs=19.2

Q ss_pred             CCCCCCCCCCCceeEe--------CCCCceEcCCCccc
Q 023713            3 DSYCADCKRLTEVVFD--------HSAGDTICSECGLV   32 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D--------~~~G~~vC~~CG~V   32 (278)
                      ...||.||....+.+.        +.+=.++|.+||..
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            3589999985443332        12234799999963

>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=83.50  E-value=6.1  Score=33.63  Aligned_cols=86  Identities=12%  Similarity=0.063  Sum_probs=56.8

Q ss_pred             HHHHHHHHHHhcCCCHH----HHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCC----HHHHHHHHcCCC
Q 023713          109 AFKSISAMSDRLGLVTT----IKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRT----VKEFCSVANGTT  180 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~----v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~t----l~eia~~~~~v~  180 (278)
                      .+.++..+...++.+..    +.+.|..+.....-.-.+-..+|..+||||+..+.  .+.+..    ...++.. ++++
T Consensus       149 p~~FL~~~l~~~~~~~~~~~~~~~~a~~~l~~~l~d~~~l~~~PS~iAaaa~~~~l--~~~~~~~~~~~~~L~~~-t~~~  225 (252)
T 1f5q_B          149 STDLICYILHIMHAPREDYLNIYNLCRPKIFCALCDGRSAMKRPVLITLACMHLTM--NQKYDYYENRIDGVCKS-LYIT  225 (252)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHH--TTTCHHHHHHHHHHHHH-TTCC
T ss_pred             HHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHHHhchhhhccCHHHHHHHHHHHHh--ccCCCchhhHHHHHHHH-HCcC
Confidence            56788888888888864    33455554444332211234678889999965554  343333    3346664 8999


Q ss_pred             HHHHHHHHHHHHHHhhh
Q 023713          181 KKEIGRAKEFIVKHLEA  197 (278)
Q Consensus       181 ~~~i~~~~~~l~~~L~~  197 (278)
                      ..+|..+++.|.+.+..
T Consensus       226 ~~~l~~C~~~i~~~l~~  242 (252)
T 1f5q_B          226 KEELHQCCDLVDIAIVS  242 (252)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999988753

>1yk4_A Rubredoxin, RD; electron transport; 0.69A {Pyrococcus abyssi} PDB: 2pya_A 1yk5_A 1bq8_A 1bq9_A* 3kyu_A 3kyv_A 3kyw_A 3kyx_A 3kyy_A 3ryg_A 3rz6_A 3rzt_A 3ss2_A 1brf_A 1caa_A 1cad_A 1vcx_A 1zrp_A 1iu5_A 1iu6_A ...

Probab=80.70  E-value=0.65  Score=29.79  Aligned_cols=12  Identities=25%  Similarity=0.825  Sum_probs=6.2

Q ss_pred             eEcCCCcccccc
Q 023713           24 TICSECGLVLEA   35 (278)
Q Consensus        24 ~vC~~CG~Vl~e   35 (278)
                      .+|+.||.|.++
T Consensus         3 ~~C~~CGyvYd~   14 (52)
T 1yk4_A            3 LSCKICGYIYDE   14 (52)
T ss_dssp             EEESSSSCEEET
T ss_pred             EEeCCCCeEECC
Confidence            355555555543

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

Probab=80.20  E-value=3.6  Score=32.53  Aligned_cols=48  Identities=8%  Similarity=0.060  Sum_probs=40.0

Q ss_pred             CcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713          146 RNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (278)
Q Consensus       146 r~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~  194 (278)
                      ++.+.-.-+.+|+|.+..+.|.|..|||+. .+++...+.+.+..|.+.
T Consensus        24 ~~~~yAlr~L~~LA~~~~~~~~s~~eIA~~-~~i~~~~l~kil~~L~~a   71 (159)
T 3lwf_A           24 TKGRYGLTITLELAKRIGDGPISLRSIAQD-KNLSEHYLEQLIGPLRNA   71 (159)
T ss_dssp             HHHHHHHHHHHHHHHTTTSCCBCHHHHHHH-HTCCHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHhcCCCCCcCHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence            345667778888887766779999999994 999999999999999863

---

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	278
d1aisb1	98	a.74.1.2 (B:1108-1205) Transcription factor IIB (T	6e-25
d1vola1	95	a.74.1.2 (A:113-207) Transcription factor IIB (TFI	7e-23
d1vola2	109	a.74.1.2 (A:208-316) Transcription factor IIB (TFI	8e-21
d1vola2	109	a.74.1.2 (A:208-316) Transcription factor IIB (TFI	1e-06
d1aisb2	95	a.74.1.2 (B:1206-1300) Transcription factor IIB (T	3e-19
d1aisb2	95	a.74.1.2 (B:1206-1300) Transcription factor IIB (T	3e-04
d1dl6a_	58	g.41.3.1 (A:) Transcription initiation factor TFII	1e-12
d1pfta_	50	g.41.3.1 (A:) Transcription initiation factor TFII	4e-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)	0.002
d2cchb1	128	a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [T	0.002
d1g3nc1	132	a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma	0.003
d2i53a1	144	a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens)	0.003
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 = 93.4 bits (232), Expect = 6e-25
 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 = 87.7 bits (217), Expect = 7e-23
 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 = 82.9 bits (205), Expect = 8e-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

>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 = 44.0 bits (104), Expect = 1e-06
 Identities = 14/36 (38%), Positives = 21/36 (58%)

Query: 208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI 243
           I   D++ RFCSNL +  Q   AA    +K+ +LD+
Sbjct: 2   ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDL 37

>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 = 78.3 bits (193), Expect = 3e-19
 Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 1/87 (1%)

Query: 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEF 172
           ++  +D LGL   ++ RA EI  +   +    G++   +VAA LYIA   E + RT +E 
Sbjct: 7   VNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREV 66

Query: 173 CSVANGTTKKEIGRAKEFIVKHLEAEM 199
             VA   T+  +    + +V+ L+ ++
Sbjct: 67  AEVAR-VTEVTVRNRYKELVEKLKIKV 92

>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 95

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

 Score = 37.1 bits (86), Expect = 3e-04
 Identities = 7/36 (19%), Positives = 19/36 (52%)

Query: 208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDI 243
           +  +DY+ +F   LG++ +  + A E + ++    +
Sbjct: 1   VKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGL 36

>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 = 59.5 bits (144), Expect = 1e-12
 Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 6  CADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE 50
          C +      +V D+ AGD IC ECGLV+    +D  SEWR F+N+
Sbjct: 14 CPNHPD-AILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND 57

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 50

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 55.2 bits (133), Expect = 4e-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 = 36.1 bits (83), 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 = 35.8 bits (82), Expect = 0.002
 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 = 35.3 bits (81), Expect = 0.002
 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 = 34.9 bits (80), Expect = 0.003
 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 = 35.0 bits (80), Expect = 0.003
 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 = 35.0 bits (80), 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	278
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	99.89
d1vola1	95	Transcription factor IIB (TFIIB), core domain {Hum	99.89
d1aisb2	95	Transcription factor IIB (TFIIB), core domain {Arc	99.84
d1vola2	109	Transcription factor IIB (TFIIB), core domain {Hum	99.82
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	99.78
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	99.77
d1aisb2	95	Transcription factor IIB (TFIIB), core domain {Arc	99.12
d1vola2	109	Transcription factor IIB (TFIIB), core domain {Hum	99.07
d2i53a1	144	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	98.7
d2ivxa1	143	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	98.62
d1vola1	95	Transcription factor IIB (TFIIB), core domain {Hum	98.53
d1jkwa1	151	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	98.49
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	98.41
d2cchb1	128	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	97.83
d1bu2a1	127	Viral cyclin {Herpesvirus saimiri [TaxId: 10381]}	97.78
d1g3nc1	132	Viral cyclin {Kaposi's sarcoma-associated herpesvi	97.78
d1f5qb1	141	Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]	97.68
d1w98b2	140	G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax	97.63
d2ivxa2	113	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	97.38
d2i53a2	110	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	96.96
d2ivxa2	113	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	96.78
d2r7ga2	142	Retinoblastoma tumor suppressor domains {Human (Ho	96.75
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	96.67
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	96.01
d2pk7a1	59	Uncharacterized protein PFL1779 {Pseudomonas fluor	95.66
d2hf1a1	59	Hypothetical protein CV3345 {Chromobacterium viola	95.65
d2i53a2	110	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	95.57
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	95.53
d1vd4a_	62	Transcription initiation factor TFIIE-alpha {Human	95.42
d2cchb2	124	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	94.25
d1nuia2	54	Zinc-binding domain of primase-helicase {Bacteriop	93.09
d1neea2	37	Zinc-binding domain of translation initiation fact	92.72
d1k81a_	36	Zinc-binding domain of translation initiation fact	92.2
d1jkwa2	126	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	90.81
d2i53a1	144	Cyclin K {Human (Homo sapiens) [TaxId: 9606]}	90.57
d2ivxa1	143	Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}	90.45
d2dsxa1	52	Rubredoxin {Desulfovibrio gigas [TaxId: 879]}	90.39
d1jj2y_	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	89.87
d1rqga3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro	89.62
d1vqoz1	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	89.41
d1u5ka2	157	Recombinational repair protein RecO, C-terminal do	89.35
d1iroa_	53	Rubredoxin {Clostridium pasteurianum [TaxId: 1501]	88.75
d2cchb2	124	Cyclin A {Cow (Bos taurus) [TaxId: 9913]}	88.36
d6rxna_	45	Rubredoxin {Desulfovibrio desulfuricans, strain 27	88.14
d1y0ja1	39	Erythroid transcription factor GATA-1 {Mouse (Mus	87.57
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	87.14
d2ak3a2	37	Microbial and mitochondrial ADK, insert "zinc fing	87.06
d1pfva3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Esch	86.41
d1zina2	35	Microbial and mitochondrial ADK, insert "zinc fing	86.02
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	85.65
d1e4va2	35	Microbial and mitochondrial ADK, insert "zinc fing	85.49
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	85.44
d1s3ga2	35	Microbial and mitochondrial ADK, insert "zinc fing	84.44
d1jkwa1	151	Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606	84.32
d1akya2	38	Microbial and mitochondrial ADK, insert "zinc fing	84.24
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	83.71
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	83.5
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	81.48
d2j0151	59	Ribosomal protein L32p {Thermus thermophilus [TaxI	81.07
d1s24a_	56	Two-iron rubredoxin {Pseudomonas oleovorans [TaxId	80.96

>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=99.89  E-value=3.8e-23  Score=154.27  Aligned_cols=93  Identities=33%  Similarity=0.629  Sum_probs=90.1

Q ss_pred             HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHH
Q 023713          105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI  184 (278)
Q Consensus       105 ~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i  184 (278)
                      +|..+++.|+++|+.|+||+.+.++|..||+++.+.+.++|+++.+++|||||+|||+++.|+|++||+++ +++++++|
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             HHHHHHHHHHhhhh
Q 023713          185 GRAKEFIVKHLEAE  198 (278)
Q Consensus       185 ~~~~~~l~~~L~~~  198 (278)
                      +++|+.|.+.|+++
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=6.8e-23  Score=152.01  Aligned_cols=92  Identities=49%  Similarity=0.864  Sum_probs=89.0

Q ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHH
Q 023713          106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIG  185 (278)
Q Consensus       106 l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~  185 (278)
                      |.++++.|+++|+.|+||+.+.++|..+|+++.+.++.+|+++.+++|||||+|||+++.|+|++||+++ +++++++|+
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 MMNAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAV-SRISKKEIG   80 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTCCCTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHTT-TCSCHHHHH
T ss_pred             hHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCChHHHHHHHHHHHHHHcCCCCCHHHHHHH-hCCCHHHHH
Confidence            5689999999999999999999999999999999999999999999999999999999999999999995 999999999


Q ss_pred             HHHHHHHHHhhhh
Q 023713          186 RAKEFIVKHLEAE  198 (278)
Q Consensus       186 ~~~~~l~~~L~~~  198 (278)
                      ++|+.|.+.|+++
T Consensus        81 k~~k~i~~~L~~~   93 (95)
T d1vola1          81 RCFKLILKALETS   93 (95)
T ss_dssp             HHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHCCc
Confidence            9999999999875

>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=99.84  E-value=7.9e-21  Score=140.72  Aligned_cols=87  Identities=28%  Similarity=0.406  Sum_probs=84.7

Q ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHH
Q 023713          111 KSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEF  190 (278)
Q Consensus       111 ~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~  190 (278)
                      ++|+++|++|+||+.+.++|..+|+++.+.++++||++.+++|||||+|||+++.|+|++||+++ +++++.+|+++|++
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             HHHHhhhh
Q 023713          191 IVKHLEAE  198 (278)
Q Consensus       191 l~~~L~~~  198 (278)
                      |.+.|++.
T Consensus        84 l~~~l~~~   91 (95)
T d1aisb2          84 LVEKLKIK   91 (95)
T ss_dssp             HHHHHTCC
T ss_pred             HHHHhCCC
Confidence            99999986

>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=99.82  E-value=9.2e-21  Score=143.86  Aligned_cols=88  Identities=22%  Similarity=0.298  Sum_probs=83.9

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHH
Q 023713          109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK  188 (278)
Q Consensus       109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~  188 (278)
                      +.++|.++|++|+||+.+.++|..+|+++.+.++.+||++.++||||||+|||+++.|+|++||+++ +++++.+|+++|
T Consensus         4 ~~d~i~Rf~s~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~iaAa~iY~a~r~~~~~~t~~eIa~~-~~vs~~tI~k~y   82 (109)
T d1vola2           4 TGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDI-AGVADVTIRQSY   82 (109)
T ss_dssp             GGGTHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHHHHHHHTSSSCCCHHHHHHH-HTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCCHHHHHHHHHHHHHHHcCCCCCHHHHHHH-HCCCHHHHHHHH
Confidence            3468999999999999999999999999999999999999999999999999999999999999995 899999999999


Q ss_pred             HHHHHHhhh
Q 023713          189 EFIVKHLEA  197 (278)
Q Consensus       189 ~~l~~~L~~  197 (278)
                      ++|.++++.
T Consensus        83 k~l~~~~~~   91 (109)
T d1vola2          83 RLIYPRAPD   91 (109)
T ss_dssp             HHHGGGHHH
T ss_pred             HHHHHHHHH
Confidence            999988874

>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=4.3e-20  Score=122.77  Aligned_cols=49  Identities=41%  Similarity=0.767  Sum_probs=45.6

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhccCC
Q 023713            1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE   50 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~   50 (278)
                      |+..+||+||+ +++++|+.+|++||.+||+|++|++||.|||||+|+++
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            45689999999 68999999999999999999999999999999999854

>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=8.1e-20  Score=117.95  Aligned_cols=45  Identities=33%  Similarity=0.926  Sum_probs=42.9

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhcc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFA   48 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~   48 (278)
                      ...||+||+ +++++|+.+|++||++||+|++|++||.|||||+|+
T Consensus         5 ~~~Cp~Cgs-~~iv~D~~~Ge~vC~~CG~Viee~~iD~gpEWR~f~   49 (50)
T d1pfta_           5 QKVCPACES-AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAFD   49 (50)
T ss_dssp             CCSCTTTSC-CCEEEETTTTEEEESSSCCBCCCCCCCCCSSSSCCC
T ss_pred             cccCcCCCC-CcEEEECCCCeEecccCCcEeccccccCCCcccccC
Confidence            478999998 689999999999999999999999999999999996

>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=99.12  E-value=3.5e-11  Score=87.85  Aligned_cols=57  Identities=14%  Similarity=0.198  Sum_probs=52.4

Q ss_pred             CCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHHH
Q 023713          208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWAF  266 (278)
Q Consensus       208 ~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~~  266 (278)
                      ++|++||+|||++|+|++++.+.|.++.+.+.+.+  .||+|.++|||+|  |+++.+.+.
T Consensus         1 i~P~d~I~R~~~~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~vaAA~i--Y~a~r~~~~   59 (95)
T d1aisb2           1 VKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAAL--YIASLLEGE   59 (95)
T ss_dssp             CCGGGGHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCCTTSCHHHHHHHHH--HHHHHHTTC
T ss_pred             CCHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCcHHhHHHHHH--HHHHHHcCC
Confidence            47999999999999999999999999999999876  6999999999999  999887643

>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=99.07  E-value=8.4e-11  Score=88.00  Aligned_cols=56  Identities=27%  Similarity=0.341  Sum_probs=51.9

Q ss_pred             CCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHH
Q 023713          208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWA  265 (278)
Q Consensus       208 ~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~  265 (278)
                      ++|.+||+|||++|+|++++.+.|.++++++.+.+  .||+|.++|||+|  |+++.+.+
T Consensus         2 i~~~d~i~Rf~s~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~p~~iaAa~i--Y~a~r~~~   59 (109)
T d1vola2           2 ITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAI--YMASQASA   59 (109)
T ss_dssp             CCGGGTHHHHHHHHTCCHHHHHHHHHHHHHHHHTTCSTTCCHHHHHHHHH--HHHHHTSS
T ss_pred             CCHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHcCCcCCCCHHHHHHHHH--HHHHHHcC
Confidence            57999999999999999999999999999999877  6999999999999  99887654

>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=98.70  E-value=5.7e-08  Score=75.56  Aligned_cols=92  Identities=16%  Similarity=0.257  Sum_probs=76.9

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC-------
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-------  179 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v-------  179 (278)
                      ..+.++|.+++..|+||..+.-+|..+|++.+....+...++..+++||+|+||+.+..|+.+++|..+...+       
T Consensus        38 ~~~~~~i~~~~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~~lva~acl~LA~K~eE~~~~l~~vi~~~~~~~~~~~~~  117 (144)
T d2i53a1          38 REGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFG  117 (144)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHSCHHHHG
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhhCcccchhHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHhhhhhhh
Confidence            4678999999999999999999999999999998888888999999999999999999999999986542111       


Q ss_pred             -----CHHHHHHHHHHHHHHhhhh
Q 023713          180 -----TKKEIGRAKEFIVKHLEAE  198 (278)
Q Consensus       180 -----~~~~i~~~~~~l~~~L~~~  198 (278)
                           ...+|-.+...|.+.|+++
T Consensus       118 ~~~~~~~~~i~~~E~~iL~~L~Fd  141 (144)
T d2i53a1         118 QFGDDPKEEVMVLERILLQTIKFD  141 (144)
T ss_dssp             GGCSCHHHHHHHHHHHHHHHTTTC
T ss_pred             hhchhhHHHHHHHHHHHHHHCCCe
Confidence                 2345666677777777654

>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=98.62  E-value=1.4e-07  Score=73.05  Aligned_cols=92  Identities=20%  Similarity=0.266  Sum_probs=75.5

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcC--------
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG--------  178 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~--------  178 (278)
                      ..+.++|.+++..|+||..+.-+|..+|++.+....+...++..+++||+|+||+.++.|+.+.++..++..        
T Consensus        32 ~~~~~~i~~~~~~l~l~~~t~~~A~~l~~Rf~~~~s~~~~~~~~va~acl~LA~K~eE~~~~~~~ii~~~~~~~~~~~~~  111 (143)
T d2ivxa1          32 QQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHACLHPLEPL  111 (143)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHCTTSCC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHhccccccHHHHHHHHHHHhcccchh
Confidence            467899999999999999999999999999999888888899999999999999999999999998754210        


Q ss_pred             ----C-----CHHHHHHHHHHHHHHhhhh
Q 023713          179 ----T-----TKKEIGRAKEFIVKHLEAE  198 (278)
Q Consensus       179 ----v-----~~~~i~~~~~~l~~~L~~~  198 (278)
                          .     ..++|-.+...|.+.|+++
T Consensus       112 ~~~~~~~~~~~~~~i~~~E~~iL~~L~Fd  140 (143)
T d2ivxa1         112 LDTKCDAYLQQTRELVILETIMLQTLGFE  140 (143)
T ss_dssp             CCTTSHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             hhhchhhhHHHHHHHHHHHHHHHHHcCCe
Confidence                0     1245556666666666654

>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=98.53  E-value=7.1e-08  Score=69.72  Aligned_cols=55  Identities=5%  Similarity=-0.033  Sum_probs=50.7

Q ss_pred             CHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHH
Q 023713          209 HASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWA  265 (278)
Q Consensus       209 ~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~  265 (278)
                      ++...|++||+.|+|++.+.+.|.++.+.+.+.+  .||+|.+++||+|  |+++...+
T Consensus         4 ~a~~~I~~~~~~L~L~~~i~~~A~~i~~~~~~~~~~~Gr~~~~i~AA~i--Y~acr~~~   60 (95)
T d1vola1           4 NAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACL--YIACRQEG   60 (95)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTCCCTTSCHHHHHHHHH--HHHHHHTT
T ss_pred             HHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCChHHHHHHHH--HHHHHHcC
Confidence            3568999999999999999999999999999987  6999999999999  99998765

>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=98.49  E-value=6.2e-07  Score=70.11  Aligned_cols=91  Identities=11%  Similarity=0.186  Sum_probs=76.8

Q ss_pred             HHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC-----
Q 023713          107 IQAFKSISAMSDRLG--LVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-----  179 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~--Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v-----  179 (278)
                      ....+.|.++|..|+  ||..+.-+|..+|++.+......-.++..+++||+|+||+.++.|+++.++... ..-     
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            356788999999765  999999999999999999888888899999999999999999999999998664 322     


Q ss_pred             --CHHHHHHHHHHHHHHhhhh
Q 023713          180 --TKKEIGRAKEFIVKHLEAE  198 (278)
Q Consensus       180 --~~~~i~~~~~~l~~~L~~~  198 (278)
                        +..+|......|.+.|+.+
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              3566777777777887765

>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=98.41  E-value=3e-07  Score=66.69  Aligned_cols=54  Identities=11%  Similarity=-0.017  Sum_probs=49.3

Q ss_pred             HHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHH
Q 023713          210 ASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWA  265 (278)
Q Consensus       210 p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~  265 (278)
                      ....|.|||+.|+||+++.+.|.+|.+.+.+.+  .||+|.++|||+|  |+++...+
T Consensus         5 a~~~I~~~~~~L~L~~~i~~~A~~i~k~~~~~~~~~g~~~~~iaaA~i--Y~Acr~~~   60 (98)
T d1aisb1           5 ALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACV--YAACRLLK   60 (98)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTTTTTTCCHHHHHHHHH--HHHHHHHT
T ss_pred             HHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHHH--HHHHHHcC
Confidence            456799999999999999999999999999887  5999999999999  99997754

>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=97.83  E-value=8.2e-05  Score=55.93  Aligned_cols=92  Identities=16%  Similarity=0.209  Sum_probs=78.6

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCC-CCCHHHHHHHH-cCCCHHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVA-NGTTKKEI  184 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~-p~tl~eia~~~-~~v~~~~i  184 (278)
                      ....++|-+++..++++..+.-.|..++.+..............++++|+|+|++.+.. |.++.++.... ...+..+|
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            45789999999999999999999999999998876666667889999999999997765 67899987741 23579999


Q ss_pred             HHHHHHHHHHhhhh
Q 023713          185 GRAKEFIVKHLEAE  198 (278)
Q Consensus       185 ~~~~~~l~~~L~~~  198 (278)
                      .+..+.|.+.|+.+
T Consensus       112 ~~mE~~IL~~L~~~  125 (128)
T d2cchb1         112 LRMEHLVLKVLTFD  125 (128)
T ss_dssp             HHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHCCCe
Confidence            99999999999875

>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=97.78  E-value=0.00022  Score=53.53  Aligned_cols=91  Identities=18%  Similarity=0.201  Sum_probs=79.5

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcC-CCCCHHHHHHHHc--CCCHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVAN--GTTKKE  183 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~-~p~tl~eia~~~~--~v~~~~  183 (278)
                      ....+++-+++..++++..+.-.|..++.+......+.......+++||+++|++.+. .|.++.++... .  ..+..+
T Consensus        32 ~~lidWl~~v~~~~~l~~eTl~lAv~llDryl~~~~i~~~~lqLi~~tcL~IAsK~ee~~~~~l~~l~~~-~~~~~t~~e  110 (127)
T d1bu2a1          32 TILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYL-SCDCFTNLE  110 (127)
T ss_dssp             HHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHTTTSCCCTTTHHHHHHHHHHHHHHHSSSSCCCHHHHHHT-TTTSSCHHH
T ss_pred             HHHHHHHHHHHHHHCCChHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHH-HcCCCCHHH
Confidence            3468999999999999999999999999999888777777889999999999999776 47899999774 3  347999


Q ss_pred             HHHHHHHHHHHhhhh
Q 023713          184 IGRAKEFIVKHLEAE  198 (278)
Q Consensus       184 i~~~~~~l~~~L~~~  198 (278)
                      |.+....|.+.|+.+
T Consensus       111 i~~mE~~IL~~L~~d  125 (127)
T d1bu2a1         111 LINQEKDILEALKWD  125 (127)
T ss_dssp             HHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHcCCC
Confidence            999999999999864

>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=97.78  E-value=0.00014  Score=54.97  Aligned_cols=92  Identities=13%  Similarity=0.195  Sum_probs=78.4

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcC-CCCCHHHHHHHH-cCCCHHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVA-NGTTKKEI  184 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~-~p~tl~eia~~~-~~v~~~~i  184 (278)
                      ....+++-+++..++++..+.-.|..++.+......+.......++++|+++|++.+. .|.++.++.... ...+..+|
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            4578899999999999999999999999999887766655678999999999999764 578899987641 25679999


Q ss_pred             HHHHHHHHHHhhhh
Q 023713          185 GRAKEFIVKHLEAE  198 (278)
Q Consensus       185 ~~~~~~l~~~L~~~  198 (278)
                      .+....|.+.|+.+
T Consensus       117 ~~mE~~IL~~L~w~  130 (132)
T d1g3nc1         117 IDQEKELLEKLAWR  130 (132)
T ss_dssp             HHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHcCCc
Confidence            99999999999865

>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=97.68  E-value=0.00024  Score=54.22  Aligned_cols=91  Identities=12%  Similarity=0.049  Sum_probs=78.6

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcC-CCCCHHHHHHHHc-CCCHHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVAN-GTTKKEI  184 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~-~p~tl~eia~~~~-~v~~~~i  184 (278)
                      ....+++-+++..++|+..+.-.|..++.+......+.......++++|+++|++.+. .|.++.++..... ..+..+|
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            4578999999999999999999999999999887777777889999999999999775 5788999987522 3589999


Q ss_pred             HHHHHHHHHHhhh
Q 023713          185 GRAKEFIVKHLEA  197 (278)
Q Consensus       185 ~~~~~~l~~~L~~  197 (278)
                      .+....|.+.|+-
T Consensus       125 ~~mE~~IL~~L~w  137 (141)
T d1f5qb1         125 LTLEVKSLDTLSW  137 (141)
T ss_dssp             HHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHCCc
Confidence            9999999998874

>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=97.63  E-value=0.0005  Score=52.24  Aligned_cols=92  Identities=17%  Similarity=0.186  Sum_probs=76.8

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh-CCCCCCCcHHHHHHHHHHHHHHhc-CCCCCHHHHHHHH-cCCCHHH
Q 023713          107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVED-QKPLRGRNQEAIVAACLYIACRQE-NKPRTVKEFCSVA-NGTTKKE  183 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~-~~~~~gr~~~~~aAAclY~acR~~-~~p~tl~eia~~~-~~v~~~~  183 (278)
                      ....+++-+++..++|+..+.-.|..++.+... ...........+++||+|+|++.+ ..|.++.++.... ...+..+
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            457899999999999999999999999998865 443444567899999999999986 5789999997641 2457899


Q ss_pred             HHHHHHHHHHHhhhh
Q 023713          184 IGRAKEFIVKHLEAE  198 (278)
Q Consensus       184 i~~~~~~l~~~L~~~  198 (278)
                      |.+....|.+.|+.+
T Consensus       124 i~~mE~~IL~~L~~~  138 (140)
T d1w98b2         124 ILTMELMIMKALKWR  138 (140)
T ss_dssp             HHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHCCCc
Confidence            999999999999865

>d2ivxa2 a.74.1.1 (A:150-262) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin-T2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.38  E-value=0.00026  Score=52.01  Aligned_cols=56  Identities=5%  Similarity=0.032  Sum_probs=51.2

Q ss_pred             CHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh-cC--CCCChhHHHHHHHHHHHHHHHHHH
Q 023713          209 HASDYLRRFCSNLGMTNQAVKAAQEAVQKSED-LD--IRLILVFFSLFLVETHIQLIVWAF  266 (278)
Q Consensus       209 ~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~-~~--~Gr~P~~iaaA~v~~~~~~~~~~~  266 (278)
                      +|..||-.++..|+.++++.+.|+.+++.+.+ ..  .--.|..||+|+|  |+|+.+.+.
T Consensus         2 HPhk~ll~~~k~l~~~~~l~q~AW~~lnDs~r~T~lcL~~~P~~IA~a~I--~LA~~~~~~   60 (113)
T d2ivxa2           2 HPHTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCI--HLACKWSNW   60 (113)
T ss_dssp             CHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCGGGTSCHHHHHHHHH--HHHHHHHTC
T ss_pred             CCcHHHHHHHHHhCCChHHHHHHHHHHHHHhccCCeeeecCcHHHHHHHH--HHHHHHhCC
Confidence            69999999999999999999999999999877 43  6899999999999  999988764

>d2i53a2 a.74.1.1 (A:158-267) Cyclin K {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Cyclin
domain: Cyclin K
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.96  E-value=0.0011  Score=48.26  Aligned_cols=56  Identities=14%  Similarity=0.160  Sum_probs=50.1

Q ss_pred             CHHHHHHHHHhhcCCCH----HHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHHH
Q 023713          209 HASDYLRRFCSNLGMTN----QAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWAF  266 (278)
Q Consensus       209 ~p~~~i~r~~~~L~l~~----~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~~  266 (278)
                      +|..|+-.|+..|+...    ++.+.|+.+++.+.+..  .--.|..||+|+|  |+|+.+.++
T Consensus         2 HP~~~L~~~~~~l~~~~~~~~~l~q~AW~~lNDs~rT~lcL~~~P~~IA~a~I--~lA~~~~~~   63 (110)
T d2i53a2           2 HPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVM--YLAGRLCKF   63 (110)
T ss_dssp             CHHHHHHHHHHTBCSCHHHHHHHHHHHHHHHHHHTTTTGGGTSCHHHHHHHHH--HHHHHHHTC
T ss_pred             CCcHHHHHHHHHhcCccccchHHHHHHHHHHHHHhcCCchhccCcHHHHHHHH--HHHHHHhCC
Confidence            69999999999999885    57899999999999865  6899999999999  999998764

>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=96.78  E-value=0.0052  Score=44.73  Aligned_cols=87  Identities=10%  Similarity=0.113  Sum_probs=65.8

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHHhh-CCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHH----HHHHH-cCCCHHH
Q 023713          110 FKSISAMSDRLGLVTTIKDRANEIYKKVED-QKPLRGRNQEAIVAACLYIACRQENKPRTVKE----FCSVA-NGTTKKE  183 (278)
Q Consensus       110 ~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~-~~~~~gr~~~~~aAAclY~acR~~~~p~tl~e----ia~~~-~~v~~~~  183 (278)
                      .++|-.++..|+.+..+.+.|-.+...... -.+.--..+..+|+||||+|+|..+++.....    --+++ .+++..+
T Consensus         4 hk~ll~~~k~l~~~~~l~q~AW~~lnDs~r~T~lcL~~~P~~IA~a~I~LA~~~~~~~~p~~~~~~~Ww~~fd~~vt~e~   83 (113)
T d2ivxa2           4 HTDVVKCTQLVRASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDPTVTLEL   83 (113)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCCGGGTSCHHHHHHHHHHHHHHHHTCCCCCCTTCCCGGGGTCSSCCHHH
T ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHHHhccCCeeeecCcHHHHHHHHHHHHHHhCCCCCCCCCCCcHHHHHccCCCHHH
Confidence            467778888899999999999999998764 34323467999999999999999987765321    11221 2688889


Q ss_pred             HHHHHHHHHHHhh
Q 023713          184 IGRAKEFIVKHLE  196 (278)
Q Consensus       184 i~~~~~~l~~~L~  196 (278)
                      |......|.+...
T Consensus        84 i~~i~~~il~lYe   96 (113)
T d2ivxa2          84 LDELTHEFLQILE   96 (113)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9988888877765

>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=96.75  E-value=0.0027  Score=48.01  Aligned_cols=69  Identities=14%  Similarity=0.267  Sum_probs=58.0

Q ss_pred             HHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHHhh--CCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 023713          107 IQAFKSISAMSDRLGLVT-TIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSV  175 (278)
Q Consensus       107 ~~~~~~I~~i~~~L~Lp~-~v~e~A~~i~k~~~~--~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~  175 (278)
                      .-|..+|+.+|++|++++ .+.+....+|+-...  -.++++|..+.+.-+|+|..||..+..++++||-..
T Consensus        13 ~La~~Rl~~LC~~L~~~~~~l~~~Iw~~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~~F~~Ii~~   84 (142)
T d2r7ga2          13 RLAYLRLNTLCERLLSEHPELEHIIWTLFQHTLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTA   84 (142)
T ss_dssp             HHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCGGGGTTSCHHHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHHHHhHHHHhccchhHHHHHHHHHHHHhccCCCCHHHHHHH
Confidence            347788999999998764 677778888877654  347899999999999999999999999999999763

>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=96.67  E-value=0.00038  Score=44.41  Aligned_cols=31  Identities=32%  Similarity=0.771  Sum_probs=28.3

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      .+||.|+. ..+||++++-.+.|..||.+|.+
T Consensus         8 VkC~~C~n-~~ivFsha~t~V~C~~Cg~~L~~   38 (58)
T d1qxfa_           8 VKCPDCEH-EQVIFDHPSTIVKCIICGRTVAE   38 (58)
T ss_dssp             EECTTTCC-EEEEESSCSSCEECSSSCCEEEE
T ss_pred             eECCCCCC-eEEEEecCceEEEccccCCEEec
Confidence            47999998 68999999999999999999963

>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=96.01  E-value=0.0024  Score=40.93  Aligned_cols=29  Identities=14%  Similarity=0.068  Sum_probs=25.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      ...||.|++  .+.+|...++++|..||.+.
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  58999999999999999886

>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=95.66  E-value=0.0028  Score=40.63  Aligned_cols=29  Identities=21%  Similarity=0.345  Sum_probs=25.7

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      ...||.|++  .+.+|..++++||..||...
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            467999997  58999999999999999876

>d2hf1a1 b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromobacterium violaceum [TaxId: 536]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Hypothetical protein CV3345
species: Chromobacterium violaceum [TaxId: 536]

Probab=95.65  E-value=0.0033  Score=40.24  Aligned_cols=28  Identities=36%  Similarity=0.659  Sum_probs=25.2

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      ..||.|++  .+.+|...+++||..||...
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  58999999999999999876

>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=95.57  E-value=0.037  Score=39.63  Aligned_cols=88  Identities=10%  Similarity=-0.006  Sum_probs=61.5

Q ss_pred             HHHHHHHHHhcCCCH----HHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHH-------HHHHHH-c
Q 023713          110 FKSISAMSDRLGLVT----TIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVK-------EFCSVA-N  177 (278)
Q Consensus       110 ~~~I~~i~~~L~Lp~----~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~-------eia~~~-~  177 (278)
                      .+++-.+...|+...    .+.+.|-.+....+.-.+.--..+..+|+||||+|+|..++++.-.       .=-..+ .
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            456677777777764    4677777777777654444456799999999999999998765321       111111 2


Q ss_pred             CCCHHHHHHHHHHHHHHhhh
Q 023713          178 GTTKKEIGRAKEFIVKHLEA  197 (278)
Q Consensus       178 ~v~~~~i~~~~~~l~~~L~~  197 (278)
                      +++..+|.....+|.+....
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            78999999988888766653

>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=95.53  E-value=0.0042  Score=35.75  Aligned_cols=28  Identities=18%  Similarity=0.408  Sum_probs=20.8

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      .-.||.|+++ -.-  ...+.+||.+||.--
T Consensus         3 lP~CP~C~se-ytY--edg~l~vCPeC~hEW   30 (38)
T d2akla2           3 LPPCPQCNSE-YTY--EDGALLVCPECAHEW   30 (38)
T ss_dssp             SCCCTTTCCC-CCE--ECSSSEEETTTTEEE
T ss_pred             CCcCCCCCCc-ceE--cCCCEEECCcccCcC
Confidence            3479999984 333  347899999999754

>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=95.42  E-value=0.0017  Score=41.97  Aligned_cols=32  Identities=28%  Similarity=0.551  Sum_probs=25.9

Q ss_pred             CCCCCCCCC-Cc----eeEeCCCCceEcCCCcccccc
Q 023713            4 SYCADCKRL-TE----VVFDHSAGDTICSECGLVLEA   35 (278)
Q Consensus         4 ~~Cp~Cg~~-~~----vv~D~~~G~~vC~~CG~Vl~e   35 (278)
                      .+||.|++. ++    -.+|+.+|...|..|+..|.|
T Consensus        15 y~Cp~C~~~ys~Lda~~L~d~~~~~F~C~~C~~el~e   51 (62)
T d1vd4a_          15 FKCPVCSSTFTDLEANQLFDPMTGTFRCTFCHTEVEE   51 (62)
T ss_dssp             EECSSSCCEEEHHHHHHHEETTTTEEBCSSSCCBCEE
T ss_pred             eECCCCCCCcchhhHHHhcCcCCCeEEecCCCCEEec
Confidence            579999973 11    258899999999999999875

>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=94.25  E-value=0.059  Score=39.40  Aligned_cols=55  Identities=11%  Similarity=0.070  Sum_probs=44.1

Q ss_pred             CHHHHHHHHH-hhcCCCHHHHHHHHHHHHHhhh-cC--CCCChhHHHHHHHHHHHHHHHHH
Q 023713          209 HASDYLRRFC-SNLGMTNQAVKAAQEAVQKSED-LD--IRLILVFFSLFLVETHIQLIVWA  265 (278)
Q Consensus       209 ~p~~~i~r~~-~~L~l~~~v~~~A~~i~~~~~~-~~--~Gr~P~~iaaA~v~~~~~~~~~~  265 (278)
                      .|..|+.||. ..-+.+.++...|..|++.+.- ..  .+-.|+-+|||+|  |++-.+.+
T Consensus         2 T~~~FL~ry~~~~~~~d~~~~~la~Yl~ElsLl~~~~~l~~~PS~lAaaai--~lar~~l~   60 (124)
T d2cchb2           2 TVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAF--HLALYTVT   60 (124)
T ss_dssp             CHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHHHH--HHHHHHHH
T ss_pred             chhHHHHHHHHHHccCcHHHHHHHHHHHHHHHHhHHHHHccChHHHHHHHH--HHHHHHhC
Confidence            4789999975 4556778899999999999764 33  6889999999999  88766544

>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=93.09  E-value=0.029  Score=34.93  Aligned_cols=30  Identities=23%  Similarity=0.351  Sum_probs=23.2

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      ..||.||+..++ --++.|...|-.|+.-..
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 345799999999998764

>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=92.72  E-value=0.031  Score=31.93  Aligned_cols=28  Identities=25%  Similarity=0.637  Sum_probs=23.3

Q ss_pred             CCCCCCCC-CceeEeCCCCceEcCCCccc
Q 023713            5 YCADCKRL-TEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         5 ~Cp~Cg~~-~~vv~D~~~G~~vC~~CG~V   32 (278)
                      .|+.||++ +.++-|...-.+.|..||.-
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 56788888888999999963

>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=92.20  E-value=0.027  Score=32.00  Aligned_cols=28  Identities=21%  Similarity=0.629  Sum_probs=21.8

Q ss_pred             CCCCCCCC-CceeEeCCCCceEcCCCccc
Q 023713            5 YCADCKRL-TEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         5 ~Cp~Cg~~-~~vv~D~~~G~~vC~~CG~V   32 (278)
                      .|+.||++ +.++-|...-.+.|..||.-
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 45566666677889999963

>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=90.81  E-value=0.63  Score=33.69  Aligned_cols=93  Identities=8%  Similarity=0.037  Sum_probs=58.6

Q ss_pred             hHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCC--CHHHHHHH-HcCCC
Q 023713          104 RNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPR--TVKEFCSV-ANGTT  180 (278)
Q Consensus       104 r~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~--tl~eia~~-~~~v~  180 (278)
                      |.|...+-.|+..+..+.=++.+...|..+.....--...-=..|..+|.||||+|++..+.+.  -+.++... ....+
T Consensus         4 Rpl~g~l~dl~~~~~~~~~~~~l~~~a~~~lnds~~Td~~l~y~P~qIalaal~~a~~~~~~~l~~y~~~~~~~~~~~~~   83 (126)
T d1jkwa2           4 RPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKENRTC   83 (126)
T ss_dssp             HHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHTTSTHHHHSCHHHHHHHHHHHHHHHHSCCCTTHHHHHTTSCSSSCC
T ss_pred             ccHHHHHHHHHHhccCcCCHHHHHHHHHHHHHHHHcCCeeeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccccchhh
Confidence            4444444445444444444578888899988877543322224689999999999999998654  34555221 12345


Q ss_pred             HHHHHHHHHHHHHHhh
Q 023713          181 KKEIGRAKEFIVKHLE  196 (278)
Q Consensus       181 ~~~i~~~~~~l~~~L~  196 (278)
                      ..+|....+++...+.
T Consensus        84 ~~~l~~~i~~i~~l~~   99 (126)
T d1jkwa2          84 LSQLLDIMKSMRNLVK   99 (126)
T ss_dssp             THHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            5667777777766654

>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=90.57  E-value=0.38  Score=35.43  Aligned_cols=55  Identities=5%  Similarity=-0.031  Sum_probs=46.4

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHHHH
Q 023713          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWAFM  267 (278)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~~~  267 (278)
                      .+||...+.+|+++.++...|..+..+-....  ...+|.-+|+|+|  |||.++.-..
T Consensus        41 ~~~i~~~~~~l~l~~~t~~~A~~~~dRf~~~~~~~~~~~~lva~acl--~LA~K~eE~~   97 (144)
T d2i53a1          41 ARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCL--FLAGKVEETP   97 (144)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHH--HHHHHHTTCC
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHHHhhCcccchhHHHHHHHHH--HHHHHhhccc
Confidence            57899999999999999999999988776543  4678999999999  9999986543

>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=90.45  E-value=0.4  Score=35.17  Aligned_cols=55  Identities=7%  Similarity=0.028  Sum_probs=46.4

Q ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHHHH
Q 023713          211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWAFM  267 (278)
Q Consensus       211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~~~  267 (278)
                      .++|...+..|+++.++...|..+.++--...  ...+|.-||+|+|  |||.++.-+.
T Consensus        35 ~~~i~~~~~~l~l~~~t~~~A~~l~~Rf~~~~s~~~~~~~~va~acl--~LA~K~eE~~   91 (143)
T d2ivxa1          35 ANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTAL--FLAAKVEEQA   91 (143)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHTTTSCTTTSCHHHHHHHHH--HHHHHHTTCC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCccccCHHHHHHHHH--HHHHHhcccc
Confidence            57999999999999999999999988765433  4668999999999  9999986543

>d2dsxa1 g.41.5.1 (A:1-52) Rubredoxin {Desulfovibrio gigas [TaxId: 879]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio gigas [TaxId: 879]

Probab=90.39  E-value=0.05  Score=33.55  Aligned_cols=18  Identities=28%  Similarity=0.540  Sum_probs=8.6

Q ss_pred             CCCCCCCCCCCCCceeEeCCCC
Q 023713            1 MADSYCADCKRLTEVVFDHSAG   22 (278)
Q Consensus         1 ~~~~~Cp~Cg~~~~vv~D~~~G   22 (278)
                      |....|+.||-    ++|+..|
T Consensus         1 M~~y~C~~Cgy----iYdp~~G   18 (52)
T d2dsxa1           1 MDIYVCTVCGY----EYDPAKG   18 (52)
T ss_dssp             CCCEEETTTCC----EECTTTC
T ss_pred             CCeEEeCCCCe----EECcccC
Confidence            44445555553    4444443

>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=89.87  E-value=0.082  Score=34.78  Aligned_cols=32  Identities=19%  Similarity=0.457  Sum_probs=25.9

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ...||.||. .. +.-...|-+-|..||.++...
T Consensus        27 ky~Cp~Cgk-~~-vkR~a~GIW~C~kC~~~~AGg   58 (73)
T d1jj2y_          27 KHKCPVCGF-KK-LKRAGTGIWMCGHCGYKIAGG   58 (73)
T ss_dssp             CBCCSSSCC-SC-EEEEETTEEEETTTCCEEECC
T ss_pred             CccCCCCCC-Cc-eEEEEEEEEECCCCCCEEeCc
Confidence            468999998 34 555789999999999998644

>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=89.62  E-value=0.12  Score=28.95  Aligned_cols=27  Identities=30%  Similarity=0.565  Sum_probs=19.8

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ...||.||.+      .+.|+ -|..||..++..
T Consensus         2 ~G~CP~C~~~------~a~GD-qCe~CG~~~~p~   28 (35)
T d1rqga3           2 IGTCPYCGAE------DQKGD-QCEVCGRPLTPE   28 (35)
T ss_dssp             CSBCSSSCCS------CCCTT-TCSSSCCCCCTT
T ss_pred             eEECCCCCCC------cccCc-chhhcCCccCHH
Confidence            4789999983      23455 499999998644

>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=89.41  E-value=0.091  Score=34.55  Aligned_cols=32  Identities=25%  Similarity=0.470  Sum_probs=25.9

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ...||.||. .. +--...|-+.|..||..+...
T Consensus        27 ky~Cp~Cgk-~~-vkR~a~GIW~C~kC~~~~AGG   58 (73)
T d1vqoz1          27 DHACPNCGE-DR-VDRQGTGIWQCSYCDYKFTGG   58 (73)
T ss_dssp             CBCCSSSSC-SC-EEEEETTEEEETTTCCEEECC
T ss_pred             CccCCCCCC-ce-eEEEEEEEEECCCCCCEEeCC
Confidence            367999998 44 555789999999999998644

>d1u5ka2 g.45.1.2 (A:81-237) Recombinational repair protein RecO, C-terminal domain {Deinococcus radiodurans [TaxId: 1299]}

class: Small proteins
fold: ArfGap/RecO-like zinc finger
superfamily: ArfGap/RecO-like zinc finger
family: RecO C-terminal domain-like
domain: Recombinational repair protein RecO, C-terminal domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=89.35  E-value=0.11  Score=39.28  Aligned_cols=29  Identities=28%  Similarity=0.563  Sum_probs=25.0

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGL   31 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~   31 (278)
                      ...|..||.+....+|...|-.+|.+|+.
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            36799999877778899999999999974

>d1iroa_ g.41.5.1 (A:) Rubredoxin {Clostridium pasteurianum [TaxId: 1501]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Clostridium pasteurianum [TaxId: 1501]

Probab=88.75  E-value=0.078  Score=32.75  Aligned_cols=11  Identities=27%  Similarity=0.930  Sum_probs=5.1

Q ss_pred             eEcCCCccccc
Q 023713           24 TICSECGLVLE   34 (278)
Q Consensus        24 ~vC~~CG~Vl~   34 (278)
                      .+|..||.|.+
T Consensus         4 y~C~~CgyiYd   14 (53)
T d1iroa_           4 YTCTVCGYIYN   14 (53)
T ss_dssp             EEETTTCCEEC
T ss_pred             eEcCCCCcEEC
Confidence            34444444443

>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=88.36  E-value=1.4  Score=31.49  Aligned_cols=84  Identities=10%  Similarity=-0.011  Sum_probs=55.5

Q ss_pred             HHHHHHH-HhcCCCHHHHHHHHHHHHHHh-hCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHH
Q 023713          111 KSISAMS-DRLGLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK  188 (278)
Q Consensus       111 ~~I~~i~-~~L~Lp~~v~e~A~~i~k~~~-~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~  188 (278)
                      .++.++. ..-+.+..+...|..+..... +...+-+-.+-.+|||+||+|-+..+.+-=-.++.. .+|.+..+|..+.
T Consensus         5 ~FL~ry~~~~~~~d~~~~~la~Yl~ElsLl~~~~~l~~~PS~lAaaai~lar~~l~~~~W~~~L~~-~t~y~~~~l~~c~   83 (124)
T d2cchb2           5 QFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIR-KTGYTLESLKPCL   83 (124)
T ss_dssp             HHHHHHHTTCSSCCHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHHHHHHHHHHHHSCCSCHHHHH-HHCCCHHHHHHHH
T ss_pred             HHHHHHHHHHccCcHHHHHHHHHHHHHHHHhHHHHHccChHHHHHHHHHHHHHHhCCCCchHHHHH-HhCCCHHHHHHHH
Confidence            4555543 233445566667777777754 323233467889999999999765554322344545 3788999999999


Q ss_pred             HHHHHHh
Q 023713          189 EFIVKHL  195 (278)
Q Consensus       189 ~~l~~~L  195 (278)
                      +.|.+.+
T Consensus        84 ~~L~~~~   90 (124)
T d2cchb2          84 MDLHQTY   90 (124)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9997765

>d6rxna_ g.41.5.1 (A:) Rubredoxin {Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]

Probab=88.14  E-value=0.059  Score=32.16  Aligned_cols=12  Identities=25%  Similarity=0.858  Sum_probs=6.3

Q ss_pred             eEcCCCcccccc
Q 023713           24 TICSECGLVLEA   35 (278)
Q Consensus        24 ~vC~~CG~Vl~e   35 (278)
                      .+|+.||.|.++
T Consensus         4 y~C~~CgyiYd~   15 (45)
T d6rxna_           4 YVCNVCGYEYDP   15 (45)
T ss_dssp             EEETTTCCEECG
T ss_pred             eEeCCCCeEECc
Confidence            455555555543

>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=87.57  E-value=0.2  Score=28.67  Aligned_cols=32  Identities=22%  Similarity=0.575  Sum_probs=22.1

Q ss_pred             CCCCCCCCCCCC-ceeEeCCCCceEcCCCcccc
Q 023713            2 ADSYCADCKRLT-EVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         2 ~~~~Cp~Cg~~~-~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      +...|.+||... ..-.....|...|.-||+-.
T Consensus         1 e~r~C~~Cgtt~Tp~WR~gp~G~~LCNACGl~~   33 (39)
T d1y0ja1           1 EARECVNCGATATPLWRRDRTGHYLCNACGLYH   33 (39)
T ss_dssp             CCCCCSSSCCCCCSCCEECTTSCEECSSHHHHH
T ss_pred             CcCCCCCCCCCCCcccccCCCCCEeeHHhHHHH
Confidence            356899999742 22333467889999999854

>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=87.14  E-value=0.21  Score=30.74  Aligned_cols=27  Identities=22%  Similarity=0.726  Sum_probs=20.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V   32 (278)
                      ..||.||. .-...++. ....|..||+-
T Consensus        19 k~CP~CG~-GvFmA~H~-dR~~CGKCgyT   45 (55)
T d2k4xa1          19 RFCPRCGP-GVFLAEHA-DRYSCGRCGYT   45 (55)
T ss_dssp             CCCTTTTT-TCCCEECS-SEEECTTTCCC
T ss_pred             CcCcCCCC-cEEeeecC-CCccccCCccc
Confidence            46999996 54555554 58999999975

>d2ak3a2 g.41.2.1 (A:125-161) Microbial and mitochondrial ADK, insert "zinc finger" domain {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=87.06  E-value=0.028  Score=32.15  Aligned_cols=30  Identities=17%  Similarity=0.088  Sum_probs=21.4

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      ..||.||..=++.+.+..=+.+|-.||.-|
T Consensus         3 ~vc~~cG~~Yh~~~~pPk~~g~CD~cg~~L   32 (37)
T d2ak3a2           3 WIHPGSGRVYNIEFNPPKTMGIDDLTGEPL   32 (37)
T ss_dssp             EEETTTTEEEETTTBCCSSTTBCTTTCCBC
T ss_pred             eeeCCcCChhhhccCCccccCCccCCCCcC
Confidence            358888874456677777788888888543

>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=86.41  E-value=0.16  Score=28.37  Aligned_cols=26  Identities=31%  Similarity=0.708  Sum_probs=18.9

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY   36 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~   36 (278)
                      ..||.|+.+      .+.|+ -|..||..++..
T Consensus         3 G~CP~C~~~------~a~GD-qCe~CG~~~~p~   28 (35)
T d1pfva3           3 GTCPKCKSP------DQYGD-NCEVCGATYSPT   28 (35)
T ss_dssp             EECTTTCCS------SEETT-BCTTTCCBCCGG
T ss_pred             eECCCCCCc------ccccc-cHHHcCCcCCHH
Confidence            579999983      23454 499999998644

>d1zina2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=86.02  E-value=0.045  Score=30.85  Aligned_cols=27  Identities=26%  Similarity=0.747  Sum_probs=14.5

Q ss_pred             CCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713            5 YCADCKRLTEVVFDHSAGDTICSECGL   31 (278)
Q Consensus         5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~   31 (278)
                      .||.||..=++.+.+..=+-+|..||.
T Consensus         4 ~C~~CG~~Yh~~~~pPk~~g~CD~cG~   30 (35)
T d1zina2           4 ICRNCGATYHLIFHPPAKPGVCDKCGG   30 (35)
T ss_dssp             EETTTCCEEETTTBCCSSTTBCTTTCC
T ss_pred             CCcCcCchhccccCCCCCCCcCCCCCC
Confidence            466666533444555555556666654

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.65  E-value=0.44  Score=31.11  Aligned_cols=34  Identities=21%  Similarity=0.485  Sum_probs=22.7

Q ss_pred             CCCCCCCCCCCceeEe--------CCCCceEcCCCccccccc
Q 023713            3 DSYCADCKRLTEVVFD--------HSAGDTICSECGLVLEAY   36 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D--------~~~G~~vC~~CG~Vl~e~   36 (278)
                      ...||.||+...+.+-        +.+=.++|.+||.--.++
T Consensus        23 ~~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~C~h~Wr~~   64 (72)
T d1twfi2          23 DRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSD   64 (72)
T ss_dssp             CCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECC
T ss_pred             CCCCCCCCCCeEEEEEeecCccCCCceEEEEcCCCCCCcccc
Confidence            3689999985333333        233368999999876554

>d1e4va2 g.41.2.1 (A:122-156) Microbial and mitochondrial ADK, insert "zinc finger" domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Escherichia coli [TaxId: 562]

Probab=85.49  E-value=0.038  Score=31.19  Aligned_cols=27  Identities=19%  Similarity=0.101  Sum_probs=14.9

Q ss_pred             CCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713            5 YCADCKRLTEVVFDHSAGDTICSECGL   31 (278)
Q Consensus         5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~   31 (278)
                      .||.||..=++.+++..=+-+|..||.
T Consensus         4 ~c~~cG~~Yh~~~~PPk~~g~CD~cg~   30 (35)
T d1e4va2           4 VHAPSGRVYHVKFNPPKVEGKDDVTGE   30 (35)
T ss_dssp             EETTTTEEEETTTBCCSSTTBCTTTCC
T ss_pred             CCcCcCChhhhccCccccCCcccCCCC
Confidence            466666533445555555556666664

>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=85.44  E-value=1.3  Score=28.81  Aligned_cols=29  Identities=14%  Similarity=0.220  Sum_probs=26.4

Q ss_pred             CCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713          165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH  194 (278)
Q Consensus       165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~  194 (278)
                      +|.|..|||+ .+|++..++.+++++|.+.
T Consensus        29 ~~lt~~elA~-~~g~sretvsr~l~~l~~~   57 (80)
T d3e5ua1          29 MPLSQKSIGE-ITGVHHVTVSRVLASLKRE   57 (80)
T ss_dssp             SCCCHHHHHH-HHTCCHHHHHHHHHHHHHT
T ss_pred             eCCCHHHHHH-HHCCCHHHHHHHHHHHHHC
Confidence            6789999999 5999999999999999875

>d1s3ga2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus globisporus [TaxId: 1459]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus globisporus [TaxId: 1459]

Probab=84.44  E-value=0.061  Score=30.29  Aligned_cols=27  Identities=19%  Similarity=0.426  Sum_probs=14.1

Q ss_pred             CCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713            5 YCADCKRLTEVVFDHSAGDTICSECGL   31 (278)
Q Consensus         5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~   31 (278)
                      .||.||..=++.+.+..=+-+|..||.
T Consensus         4 ~C~~CG~~Yh~~~~pPk~~g~CD~cg~   30 (35)
T d1s3ga2           4 ICKVCGTSYHLLFNPPQVEGKCDKDGG   30 (35)
T ss_dssp             EETTTCCEEETTTBCCSBTTBCTTTCC
T ss_pred             CCcCcCchhccccCCCCCCCccCCCCC
Confidence            455666532344555555555666554

>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=84.32  E-value=1.7  Score=31.90  Aligned_cols=53  Identities=19%  Similarity=0.125  Sum_probs=41.6

Q ss_pred             HHHHHHHhhcC--CCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHHH
Q 023713          212 DYLRRFCSNLG--MTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWAF  266 (278)
Q Consensus       212 ~~i~r~~~~L~--l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~~  266 (278)
                      +.|.++++.|+  |++++...|..+.++--...  .-.+|.-+|+|+|  |||.++-.+
T Consensus        52 ~~l~~~~~~~k~~l~~~~~~tA~~~~~RF~~~~s~~~~~~~li~~acl--~LA~K~ee~  108 (151)
T d1jkwa1          52 KRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCA--FLACKVDEF  108 (151)
T ss_dssp             HHHHHHHHHCTTTCCHHHHHHHHHHHHHHGGGSCTTTSCHHHHHHHHH--HHHHHHTTC
T ss_pred             HHHHHHHHHHccCCCHHHHHHHHHHHHHHhhcCccccccHHHHHHHHH--HHHHHHccc
Confidence            45778888654  88999999988887665544  4678999999999  999987543

>d1akya2 g.41.2.1 (A:131-168) Microbial and mitochondrial ADK, insert "zinc finger" domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=84.24  E-value=0.082  Score=30.31  Aligned_cols=28  Identities=14%  Similarity=0.093  Sum_probs=16.9

Q ss_pred             CCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713            5 YCADCKRLTEVVFDHSAGDTICSECGLV   32 (278)
Q Consensus         5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V   32 (278)
                      .||.||..=++.+.+..=+-+|..||.-
T Consensus         4 ~C~~cG~~Yh~~~~ppk~~g~CD~cg~~   31 (38)
T d1akya2           4 IHPASGRSYHKIFNPPKEDMKDDVTGEA   31 (38)
T ss_dssp             ECTTTCCEEETTTBCCSSTTBCTTTCCB
T ss_pred             CCcCccchhhhhccCcCcCCccCCCCCE
Confidence            4777776334555565666677777643

>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=83.71  E-value=0.31  Score=31.80  Aligned_cols=28  Identities=18%  Similarity=0.695  Sum_probs=23.5

Q ss_pred             CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713            4 SYCADCKRLTEVVFDHSAGDTICSECGLVL   33 (278)
Q Consensus         4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl   33 (278)
                      ..||.|+.  .++.|...-.+.|..||...
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            67999997  47778777788999999886

>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=83.50  E-value=1.4  Score=26.32  Aligned_cols=41  Identities=15%  Similarity=0.114  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHH
Q 023713          149 EAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI  191 (278)
Q Consensus       149 ~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l  191 (278)
                      ..+-.++-|+--.. ..|+++.|+|.. ++++...+.+.|++.
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            34556666766554 578999999995 999999999988874

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=81.48  E-value=4.3  Score=29.12  Aligned_cols=31  Identities=13%  Similarity=0.183  Sum_probs=28.2

Q ss_pred             hcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713          162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVK  193 (278)
Q Consensus       162 ~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~  193 (278)
                      .++-|.|+.||++. ++++...+.+..+.|.+
T Consensus        37 ~~~~plt~~ela~~-l~vsk~~vs~~l~~L~~   67 (151)
T d1ku9a_          37 LSDKPLTISDIMEE-LKISKGNVSMSLKKLEE   67 (151)
T ss_dssp             HCSSCEEHHHHHHH-HTCCHHHHHHHHHHHHH
T ss_pred             hCCCCcCHHHHHHH-hCCCcchHHHHHHHHHH
Confidence            46789999999995 99999999999999986

>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=81.07  E-value=0.43  Score=29.93  Aligned_cols=25  Identities=32%  Similarity=0.781  Sum_probs=17.8

Q ss_pred             CCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713            3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE   34 (278)
Q Consensus         3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~   34 (278)
                      ...||+||..       ..-.-||.+||+-=+
T Consensus        29 l~~C~~CG~~-------~~pHrvC~~CG~YkG   53 (59)
T d2j0151          29 LVPCPECKAM-------KPPHTVCPECGYYAG   53 (59)
T ss_dssp             CBCCSSSSSC-------BCTTCBCTTTCCSSS
T ss_pred             eeECCCCCCc-------ccceeECCCCCeECC
Confidence            3679999973       234679999997543

>d1s24a_ g.41.5.1 (A:) Two-iron rubredoxin {Pseudomonas oleovorans [TaxId: 301]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Two-iron rubredoxin
species: Pseudomonas oleovorans [TaxId: 301]

Probab=80.96  E-value=0.19  Score=31.22  Aligned_cols=13  Identities=31%  Similarity=0.767  Sum_probs=7.2

Q ss_pred             eEcCCCccccccc
Q 023713           24 TICSECGLVLEAY   36 (278)
Q Consensus        24 ~vC~~CG~Vl~e~   36 (278)
                      .+|..||.|.++.
T Consensus         5 y~C~~CgyiYdp~   17 (56)
T d1s24a_           5 WICITCGHIYDEA   17 (56)
T ss_dssp             EEETTTTEEEETT
T ss_pred             EECCCCCcEECcc
Confidence            4566666665443