Citrus Sinensis ID: 030755

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170--
MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGTA
ccccccccccccccEEEEcccccEEcccccEEEccccccccccccccccccccccccEEccccccccccccccEEEEccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccccccHHHcc
ccccccccccccccEEEccccccEEcHcccEEEcccEEcccccEEEccccccccccccccccccccccccccEEEEccccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccccccHHHHc
mtdafcsdckkhtevvfdhsagdtvcsecglvleshsidetsewrtfanesgdndpvrvggptnplladgglstviakpngasgeflSSSLGrwqnrgsnpdrGLILAFKTIATMSDRLGLVATIKDRANEIYKKVedqkssrgrnQDALLAACLYIACrqedkprtvkgta
mtdafcsdcKKHTevvfdhsagdtVCSECGLVLESHSIDETSEWRTFanesgdndpvrVGGPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYkkvedqkssrgrnQDALLAACLYiacrqedkprtvkgta
MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGTA
****FCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDE***W**********************************************************RGLILAFKTIATMSDRLGLVATIKDRANEIYK**************ALLAACLYIACR************
**DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEW*************************************************************ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGTA
********CKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKK*********RNQDALLAACLYIACRQED*********
****FCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANE*******RVGGPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTV****
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGTA
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query172 2.2.26 [Sep-21-2011]
Q9SS44 312 Transcription initiation yes no 0.982 0.541 0.946 2e-94
P48513 313 Transcription initiation yes no 0.982 0.539 0.929 8e-90
Q8W0W3 312 Transcription initiation yes no 0.982 0.541 0.893 2e-89
P48512 312 Transcription initiation no no 0.982 0.541 0.852 1e-84
P29052 315 Transcription initiation yes no 0.930 0.507 0.527 6e-41
Q5R886 316 Transcription initiation yes no 0.918 0.5 0.502 6e-39
Q4R3J5 316 Transcription initiation N/A no 0.918 0.5 0.502 6e-39
Q00403 316 Transcription initiation yes no 0.918 0.5 0.502 6e-39
Q2KIN8 316 Transcription initiation yes no 0.918 0.5 0.502 6e-39
P62916 316 Transcription initiation yes no 0.918 0.5 0.502 7e-39
>sp|Q9SS44|TF2B2_ARATH Transcription initiation factor IIB-2 OS=Arabidopsis thaliana GN=TFIIB2 PE=2 SV=1 Back     alignment and function desciption
 Score =  343 bits (881), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 160/169 (94%), Positives = 169/169 (100%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M+DAFCSDCK+HTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct: 1   MSDAFCSDCKRHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLG 120
           GPTNPLLADGGL+TVI+KPNG+SG+FLSSSLGRWQNRGSNPDRGLI+AFKTIATM+DRLG
Sbjct: 61  GPTNPLLADGGLTTVISKPNGSSGDFLSSSLGRWQNRGSNPDRGLIVAFKTIATMADRLG 120

Query: 121 LVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK 169
           LVATIKDRANEIYK+VEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK
Sbjct: 121 LVATIKDRANEIYKRVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK 169
General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.
Arabidopsis thaliana (taxid: 3702)
>sp|P48513|TF2B_SOYBN Transcription initiation factor IIB OS=Glycine max GN=TFIIB1 PE=2 SV=1 Back     alignment and function description
>sp|Q8W0W3|TF2B_ORYSJ Transcription initiation factor IIB OS=Oryza sativa subsp. japonica GN=TFIIB PE=1 SV=1 Back     alignment and function description
>sp|P48512|TF2B1_ARATH Transcription initiation factor IIB-1 OS=Arabidopsis thaliana GN=TFIIB1 PE=1 SV=1 Back     alignment and function description
>sp|P29052|TF2B_DROME Transcription initiation factor IIB OS=Drosophila melanogaster GN=TfIIB PE=2 SV=1 Back     alignment and function description
>sp|Q5R886|TF2B_PONAB Transcription initiation factor IIB OS=Pongo abelii GN=GTF2B PE=2 SV=1 Back     alignment and function description
>sp|Q4R3J5|TF2B_MACFA Transcription initiation factor IIB OS=Macaca fascicularis GN=GTF2B PE=2 SV=1 Back     alignment and function description
>sp|Q00403|TF2B_HUMAN Transcription initiation factor IIB OS=Homo sapiens GN=GTF2B PE=1 SV=1 Back     alignment and function description
>sp|Q2KIN8|TF2B_BOVIN Transcription initiation factor IIB OS=Bos taurus GN=GTF2B PE=2 SV=1 Back     alignment and function description
>sp|P62916|TF2B_RAT Transcription initiation factor IIB OS=Rattus norvegicus GN=Gtf2b PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query172
317106705 312 JHL06B08.6 [Jatropha curcas] 0.982 0.541 0.982 5e-94
255588003 312 transcription initiation factor iib, put 0.982 0.541 0.976 1e-93
224138070 312 predicted protein [Populus trichocarpa] 0.982 0.541 0.976 1e-93
449465789 312 PREDICTED: transcription initiation fact 0.982 0.541 0.964 3e-93
297829558 312 transcription initiation factor IIB-2 [A 0.982 0.541 0.946 7e-93
15228267 312 transcription initiation factor IIB-2 [A 0.982 0.541 0.946 1e-92
225441886 312 PREDICTED: transcription initiation fact 0.982 0.541 0.952 4e-92
225464249 312 PREDICTED: transcription initiation fact 0.982 0.541 0.952 4e-92
224090077 312 predicted protein [Populus trichocarpa] 0.982 0.541 0.964 4e-92
357509669 313 Transcription initiation factor IIB [Med 0.982 0.539 0.928 9e-90
>gi|317106705|dbj|BAJ53205.1| JHL06B08.6 [Jatropha curcas] Back     alignment and taxonomy information
 Score =  348 bits (893), Expect = 5e-94,   Method: Compositional matrix adjust.
 Identities = 166/169 (98%), Positives = 167/169 (98%)

Query: 1   MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
           M DAFCSDCK+ TEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct: 1   MGDAFCSDCKRQTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLG 120
           GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLG
Sbjct: 61  GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLG 120

Query: 121 LVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK 169
           LVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK
Sbjct: 121 LVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK 169

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Class:

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] Back     alignment and taxonomy information
>gi|224138070|ref|XP_002322722.1| predicted protein [Populus trichocarpa] gi|222867352|gb|EEF04483.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>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] Back     alignment and taxonomy information
>gi|297829558|ref|XP_002882661.1| transcription initiation factor IIB-2 [Arabidopsis lyrata subsp. lyrata] gi|297328501|gb|EFH58920.1| transcription initiation factor IIB-2 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|15228267|ref|NP_187644.1| transcription initiation factor IIB-2 [Arabidopsis thaliana] gi|21363045|sp|Q9SS44.1|TF2B2_ARATH RecName: Full=Transcription initiation factor IIB-2; AltName: Full=General transcription factor TFIIB-2; Short=AtTFIIB2 gi|6056193|gb|AAF02810.1|AC009400_6 transcription initiation factor IIB (TFIIB) [Arabidopsis thaliana] gi|15215784|gb|AAK91437.1| AT3g10330/F14P13_7 [Arabidopsis thaliana] gi|16974427|gb|AAL31139.1| AT3g10330/F14P13_7 [Arabidopsis thaliana] gi|21593436|gb|AAM65403.1| transcription initiation factor IIB (TFIIB) [Arabidopsis thaliana] gi|39545880|gb|AAR28003.1| TFIIB2 [Arabidopsis thaliana] gi|332641371|gb|AEE74892.1| transcription initiation factor IIB-2 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|225441886|ref|XP_002284342.1| PREDICTED: transcription initiation factor IIB-2 [Vitis vinifera] gi|297739630|emb|CBI29812.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225464249|ref|XP_002269045.1| PREDICTED: transcription initiation factor IIB-2 [Vitis vinifera] gi|296088031|emb|CBI35314.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224090077|ref|XP_002308933.1| predicted protein [Populus trichocarpa] gi|222854909|gb|EEE92456.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|357509669|ref|XP_003625123.1| Transcription initiation factor IIB [Medicago truncatula] gi|355500138|gb|AES81341.1| Transcription initiation factor IIB [Medicago truncatula] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query172
TAIR|locus:2076259 312 AT3G10330 [Arabidopsis thalian 0.982 0.541 0.946 8.9e-86
TAIR|locus:2062703 312 TFIIB "transcription factor II 0.982 0.541 0.852 9e-77
FB|FBgn0004915 315 TfIIB "Transcription factor II 0.930 0.507 0.527 3.7e-39
UNIPROTKB|F1NXP2 306 GTF2B "Uncharacterized protein 0.930 0.522 0.503 1.5e-37
UNIPROTKB|F2Z4J6 316 LOC786656 "Uncharacterized pro 0.930 0.506 0.496 2.4e-37
UNIPROTKB|Q2KIN8 316 GTF2B "Transcription initiatio 0.930 0.506 0.496 2.4e-37
UNIPROTKB|E2RPG1 316 GTF2B "Uncharacterized protein 0.930 0.506 0.496 2.4e-37
UNIPROTKB|B1APE1224 GTF2B "Transcription initiatio 0.930 0.714 0.496 2.4e-37
UNIPROTKB|Q00403 316 GTF2B "Transcription initiatio 0.930 0.506 0.496 2.4e-37
UNIPROTKB|F2Z5J6 316 GTF2B "Uncharacterized protein 0.930 0.506 0.496 2.4e-37
TAIR|locus:2076259 AT3G10330 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 858 (307.1 bits), Expect = 8.9e-86, P = 8.9e-86
 Identities = 160/169 (94%), Positives = 169/169 (100%)

Query:     1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60
             M+DAFCSDCK+HTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG
Sbjct:     1 MSDAFCSDCKRHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVG 60

Query:    61 GPTNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLG 120
             GPTNPLLADGGL+TVI+KPNG+SG+FLSSSLGRWQNRGSNPDRGLI+AFKTIATM+DRLG
Sbjct:    61 GPTNPLLADGGLTTVISKPNGSSGDFLSSSLGRWQNRGSNPDRGLIVAFKTIATMADRLG 120

Query:   121 LVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK 169
             LVATIKDRANEIYK+VEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK
Sbjct:   121 LVATIKDRANEIYKRVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK 169
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)] Back     alignment and assigned GO terms
FB|FBgn0004915 TfIIB "Transcription factor IIB" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|F1NXP2 GTF2B "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F2Z4J6 LOC786656 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q2KIN8 GTF2B "Transcription initiation factor IIB" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2RPG1 GTF2B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|B1APE1 GTF2B "Transcription initiation factor IIB" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q00403 GTF2B "Transcription initiation factor IIB" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F2Z5J6 GTF2B "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms

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) ?
Q9SS44TF2B2_ARATHNo assigned EC number0.94670.98250.5416yesno
Q8W0W3TF2B_ORYSJNo assigned EC number0.89340.98250.5416yesno
P48513TF2B_SOYBNNo assigned EC number0.92940.98250.5399yesno

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:
estExt_Genewise1_v1.C_LG_XVI1817
hypothetical protein (313 aa)
(Populus trichocarpa)
Predicted Functional Partners:
GTF902
global transcription factor group (201 aa)
  • ••• 0.820
GTF901
global transcription factor group (202 aa)
  • ••• 0.816
gw1.IX.2304.1
hypothetical protein (321 aa)
  • ••• 0.602
estExt_Genewise1_v1.C_LG_I4990
hypothetical protein (176 aa)
  • ••• 0.598
gw1.IV.3113.1
hypothetical protein (690 aa)
  • ••• 0.497
gw1.II.4131.1
hypothetical protein (73 aa)
  •     0.466
estExt_Genewise1_v1.C_LG_IV3101
hypothetical protein (421 aa)
  •   • 0.461
gw1.I.2689.1
hypothetical protein (1334 aa)
  • • • 0.456
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)
  •     0.436
estExt_Genewise1_v1.C_LG_XV2760
RecName- Full=Proteasome subunit alpha type; EC=3.4.25.1; (235 aa)
  •     0.434

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query172
COG1405 285 COG1405, SUA7, Transcription initiation factor TFI 8e-42
PRK00423 310 PRK00423, tfb, transcription initiation factor IIB 6e-33
pfam0038271 pfam00382, TFIIB, Transcription factor TFIIB repea 5e-14
pfam0827140 pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding 3e-11
COG1405285 COG1405, SUA7, Transcription initiation factor TFI 1e-07
cd0004388 cd00043, CYCLIN, Cyclin box fold 4e-07
smart0038583 smart00385, CYCLIN, domain present in cyclins, TFI 9e-06
PRK00423310 PRK00423, tfb, transcription initiation factor IIB 0.002
>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information 
 Score =  140 bits (356), Expect = 8e-42
 Identities = 59/167 (35%), Positives = 88/167 (52%), Gaps = 12/167 (7%)

Query: 6   CSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNP 65
           C +C   T ++ D+  G+ VC++CGLVLE   ID   EWR F     +    RVG P  P
Sbjct: 4   CPECGS-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAF----DERHERRVGAPLTP 58

Query: 66  LLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNP---DRGLILAFKTIATMSDRLGLV 122
            + D GLST+I   +          L +WQ R       +R LI A + +  ++  LGL 
Sbjct: 59  SIHDKGLSTIIGWGDKD----KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLP 114

Query: 123 ATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK 169
            ++++ A  IY+K  D+   RGR+ +++ AAC+Y ACR    PRT+ 
Sbjct: 115 ESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLD 161

Length = 285
>gnl|CDD|234758 PRK00423, tfb, transcription initiation factor IIB; Reviewed Back     alignment and domain information
>gnl|CDD|109440 pfam00382, TFIIB, Transcription factor TFIIB repeat Back     alignment and domain information
>gnl|CDD|203895 pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding Back     alignment and domain information
>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold Back     alignment and domain information
>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>gnl|CDD|234758 PRK00423, tfb, transcription initiation factor IIB; Reviewed Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 172
PRK00423 310 tfb transcription initiation factor IIB; Reviewed 100.0
KOG1597 308 consensus Transcription initiation factor TFIIB [T 100.0
COG1405 285 SUA7 Transcription initiation factor TFIIIB, Brf1 100.0
KOG1598 521 consensus Transcription initiation factor TFIIIB, 99.92
PF0038271 TFIIB: Transcription factor TFIIB repeat; InterPro 99.81
PF0827143 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013 99.71
PRK00423310 tfb transcription initiation factor IIB; Reviewed 99.46
COG1405285 SUA7 Transcription initiation factor TFIIIB, Brf1 99.32
KOG1597308 consensus Transcription initiation factor TFIIB [T 99.17
cd0004388 CYCLIN Cyclin box fold. Protein binding domain fun 99.09
smart0038583 CYCLIN domain present in cyclins, TFIIB and Retino 98.94
TIGR00569 305 ccl1 cyclin ccl1. University). 98.26
KOG1598 521 consensus Transcription initiation factor TFIIIB, 98.24
KOG0834 323 consensus CDK9 kinase-activating protein cyclin T 98.16
PF01857135 RB_B: Retinoblastoma-associated protein B domain; 98.05
COG5333 297 CCL1 Cdk activating kinase (CAK)/RNA polymerase II 97.91
PF00134127 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR 97.88
KOG0794 264 consensus CDK8 kinase-activating protein cyclin C 97.61
KOG0835 367 consensus Cyclin L [General function prediction on 97.6
PF1178136 RRN7: RNA polymerase I-specific transcription init 97.55
PF0879233 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I 97.38
PRK00420112 hypothetical protein; Validated 97.06
KOG0835 367 consensus Cyclin L [General function prediction on 96.9
COG205167 RPS27A Ribosomal protein S27E [Translation, riboso 96.87
PF0166755 Ribosomal_S27e: Ribosomal protein S27; InterPro: I 96.84
PRK0041559 rps27e 30S ribosomal protein S27e; Reviewed 96.83
PHA0062659 hypothetical protein 96.79
PRK0039846 rpoP DNA-directed RNA polymerase subunit P; Provis 96.67
COG1645131 Uncharacterized Zn-finger containing protein [Gene 96.62
PF1480334 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C. 96.52
PF1324023 zinc_ribbon_2: zinc-ribbon domain 96.51
KOG2496 325 consensus Cdk activating kinase (CAK)/RNA polymera 96.47
PF1324826 zf-ribbon_3: zinc-ribbon domain 96.44
PLN0020986 ribosomal protein S27; Provisional 96.38
PTZ0008385 40S ribosomal protein S27; Provisional 96.34
smart0077837 Prim_Zn_Ribbon Zinc-binding domain of primase-heli 96.27
PF0215035 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I 96.23
PF0827430 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01 96.2
PF09538108 FYDLN_acid: Protein of unknown function (FYDLN_aci 96.18
PF1435461 Lar_restr_allev: Restriction alleviation protein L 96.16
PRK1182760 hypothetical protein; Provisional 95.95
COG199789 RPL43A Ribosomal protein L37AE/L43A [Translation, 95.87
TIGR0120654 lysW lysine biosynthesis protein LysW. This very s 95.83
PF0667741 Auto_anti-p27: Sjogren's syndrome/scleroderma auto 95.74
PRK0043250 30S ribosomal protein S27ae; Validated 95.65
COG283560 Uncharacterized conserved protein [Function unknow 95.64
PRK10220111 hypothetical protein; Provisional 95.61
TIGR0209838 MJ0042_CXXC MJ0042 family finger-like domain. This 95.53
TIGR02300129 FYDLN_acid conserved hypothetical protein TIGR0230 95.5
PF0396668 Trm112p: Trm112p-like protein; InterPro: IPR005651 95.48
PF1057126 UPF0547: Uncharacterised protein family UPF0547; I 95.3
smart0066152 RPOL9 RNA polymerase subunit 9. 95.07
TIGR0365553 anti_R_Lar restriction alleviation protein, Lar fa 95.0
PF0827340 Prim_Zn_Ribbon: Zinc-binding domain of primase-hel 94.89
PF0929732 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do 94.87
COG2824112 PhnA Uncharacterized Zn-ribbon-containing protein 94.65
PF02984118 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR 94.61
PRK00464154 nrdR transcriptional regulator NrdR; Validated 94.27
PF1371937 zinc_ribbon_5: zinc-ribbon domain 94.18
PRK12495226 hypothetical protein; Provisional 94.12
KOG0656 335 consensus G1/S-specific cyclin D [Cell cycle contr 94.01
PF0178090 Ribosomal_L37ae: Ribosomal L37ae protein family; I 93.9
COG199851 RPS31 Ribosomal protein S27AE [Translation, riboso 93.83
PF0728269 OrfB_Zn_ribbon: Putative transposase DNA-binding d 93.74
TIGR00244147 transcriptional regulator NrdR. Members of this al 93.58
PF09862113 DUF2089: Protein of unknown function (DUF2089); In 93.56
TIGR01384104 TFS_arch transcription factor S, archaeal. There h 93.38
PF0519136 ADK_lid: Adenylate kinase, active site lid; InterP 93.28
PF1276046 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int 93.21
smart0044040 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo 92.98
TIGR00686109 phnA alkylphosphonate utilization operon protein P 92.85
PRK0971064 lar restriction alleviation and modification prote 92.84
PTZ0025590 60S ribosomal protein L37a; Provisional 92.72
PRK1489299 putative transcription elongation factor Elf1; Pro 92.65
KOG177984 consensus 40s ribosomal protein S27 [Translation, 92.17
COG1594113 RPB9 DNA-directed RNA polymerase, subunit M/Transc 92.14
TIGR0028091 L37a ribosomal protein L37a. This model finds euka 92.04
KOG4164497 consensus Cyclin ik3-1/CABLES [Cell cycle control, 92.02
COG4888104 Uncharacterized Zn ribbon-containing protein [Gene 91.93
PF0360432 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa 91.9
smart0083441 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C 91.74
COG288861 Predicted Zn-ribbon RNA-binding protein with a fun 91.47
PRK0397690 rpl37ae 50S ribosomal protein L37Ae; Reviewed 91.28
smart0065944 RPOLCX RNA polymerase subunit CX. present in RNA p 91.13
COG347868 Predicted nucleic-acid-binding protein containing 90.84
PF1444654 Prok-RING_1: Prokaryotic RING finger family 1 90.75
COG4640 465 Predicted membrane protein [Function unknown] 90.63
cd0035033 rubredoxin_like Rubredoxin_like; nonheme iron bind 90.62
PF0512981 Elf1: Transcription elongation factor Elf1 like; I 90.61
PF1425552 Cys_rich_CPXG: Cysteine-rich CPXCG 90.49
PF0109639 TFIIS_C: Transcription factor S-II (TFIIS); InterP 90.41
PF1277350 DZR: Double zinc ribbon 90.13
PF1371736 zinc_ribbon_4: zinc-ribbon domain 90.05
PF1412287 YokU: YokU-like protein 89.52
PF15616131 TerY-C: TerY-C metal binding domain 89.48
PF0311928 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f 89.37
PF0985564 DUF2082: Nucleic-acid-binding protein containing Z 89.27
COG199649 RPC10 DNA-directed RNA polymerase, subunit RPC10 ( 89.09
TIGR0244359 conserved hypothetical metal-binding protein. Memb 89.05
COG1327156 Predicted transcriptional regulator, consists of a 89.04
PRK1228657 rpmF 50S ribosomal protein L32; Reviewed 88.86
PRK06266178 transcription initiation factor E subunit alpha; V 88.56
PF1495244 zf-tcix: Putative treble-clef, zinc-finger, Zn-bin 88.28
PRK05978148 hypothetical protein; Provisional 88.12
PHA02942383 putative transposase; Provisional 87.99
TIGR00569305 ccl1 cyclin ccl1. University). 87.74
KOG1010 920 consensus Rb (Retinoblastoma tumor suppressor)-rel 87.55
PRK12336201 translation initiation factor IF-2 subunit beta; P 86.82
PF05876 557 Terminase_GpA: Phage terminase large subunit (GpA) 86.47
cd0073050 rubredoxin Rubredoxin; nonheme iron binding domain 86.32
COG0675364 Transposase and inactivated derivatives [DNA repli 86.19
PRK0967872 DNA-binding transcriptional regulator; Provisional 86.06
PRK1313056 H/ACA RNA-protein complex component Nop10p; Review 85.9
COG5349126 Uncharacterized protein conserved in bacteria [Fun 85.82
PF0178356 Ribosomal_L32p: Ribosomal L32p protein family; Int 85.73
PF1012251 Mu-like_Com: Mu-like prophage protein Com; InterPr 85.72
KOG1088124 consensus Uncharacterized conserved protein [Funct 85.7
TIGR0103155 rpmF_bact ribosomal protein L32. This protein desc 85.69
PRK05508119 methionine sulfoxide reductase B; Provisional 85.29
PF0030147 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubred 85.27
PF11672102 DUF3268: Protein of unknown function (DUF3268); In 85.22
PF0972342 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134 84.99
KOG2906105 consensus RNA polymerase III subunit C11 [Transcri 84.53
PF0952671 DUF2387: Probable metal-binding protein (DUF2387); 84.38
PRK0835161 DNA-directed RNA polymerase subunit E''; Validated 84.35
PRK02935110 hypothetical protein; Provisional 83.99
TIGR0260552 CxxC_CxxC_SSSS putative regulatory protein, FmdB f 83.63
COG177355 Rubredoxin [Energy production and conversion] 83.58
smart0040152 ZnF_GATA zinc finger binding to DNA consensus sequ 83.26
PRK08402355 replication factor A; Reviewed 83.16
PRK00222142 methionine sulfoxide reductase B; Provisional 83.15
PF04161208 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 83.08
KOG0653 391 consensus Cyclin B and related kinase-activating p 82.6
CHL00174296 accD acetyl-CoA carboxylase beta subunit; Reviewed 82.57
TIGR03826137 YvyF flagellar operon protein TIGR03826. This gene 82.54
PRK14559 645 putative protein serine/threonine phosphatase; Pro 82.53
TIGR00515285 accD acetyl-CoA carboxylase, carboxyl transferase, 82.42
KOG0834 323 consensus CDK9 kinase-activating protein cyclin T 82.3
PRK00241256 nudC NADH pyrophosphatase; Reviewed 82.08
COG1326201 Uncharacterized archaeal Zn-finger protein [Genera 82.01
PF0639736 Desulfoferrod_N: Desulfoferrodoxin, N-terminal dom 81.64
KOG040292 consensus 60S ribosomal protein L37 [Translation, 81.45
COG406864 Uncharacterized protein containing a Zn-ribbon [Fu 81.43
KOG2593 436 consensus Transcription initiation factor IIE, alp 81.39
PF14353128 CpXC: CpXC protein 81.18
COG4530129 Uncharacterized protein conserved in bacteria [Fun 80.95
cd0020254 ZnF_GATA Zinc finger DNA binding domain; binds spe 80.85
COG3877122 Uncharacterized protein conserved in bacteria [Fun 80.43
TIGR03830127 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he 80.42
PF08006 181 DUF1700: Protein of unknown function (DUF1700); In 80.4
PF08646146 Rep_fac-A_C: Replication factor-A C terminal domai 80.37
PF1005854 DUF2296: Predicted integral membrane metal-binding 80.16
>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information 
Probab=100.00  E-value=2.6e-48  Score=317.82  Aligned_cols=167  Identities=35%  Similarity=0.691  Sum_probs=151.6

Q ss_pred             CCCCCCCCCCceeEeCCCCceEeCCCcceecccccccCcccccccCCCCCCCCcccCCCCCccccCCCceeEEecCC-CC
Q 030755            4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPN-GA   82 (172)
Q Consensus         4 ~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~~~~ewr~f~~~~~~~~~~r~g~~~~~~~~~~~~~t~i~~~~-~~   82 (172)
                      ..||+||+ +++++|+++|++||.+||+||+|++||+|||||+|++++ ..+++|||+|.++++||.|++|.|+++. +.
T Consensus        12 ~~Cp~Cg~-~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~-~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~~   89 (310)
T PRK00423         12 LVCPECGS-DKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTYTIHDKGLSTDIDWRNKDS   89 (310)
T ss_pred             CcCcCCCC-CCeeEECCCCeEeecccCCcccccccccCCCccCCCccc-cCCccccCCCCCccccCCCCceEeecCCccc
Confidence            57999998 689999999999999999999999999999999999654 4699999999999999999999999654 33


Q ss_pred             Ccccccc-------cccccccCC---CCchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHH
Q 030755           83 SGEFLSS-------SLGRWQNRG---SNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLA  152 (172)
Q Consensus        83 ~~~~l~~-------~l~~~~~~~---~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aA  152 (172)
                      .|..++.       +|++||++.   ++.|+.|..++..|+++|+.|+||+.++++|..||++++++++++||+++.++|
T Consensus        90 ~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~A  169 (310)
T PRK00423         90 YGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVA  169 (310)
T ss_pred             ccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHH
Confidence            4444442       478888764   668999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhCCCCCCccccC
Q 030755          153 ACLYIACRQEDKPRTVKGTA  172 (172)
Q Consensus       153 AclYiacR~~~~~~tl~eia  172 (172)
                      ||||+|||++++|+||+||+
T Consensus       170 AclYiACR~~~~prtl~eI~  189 (310)
T PRK00423        170 AALYAACRRCKVPRTLDEIA  189 (310)
T ss_pred             HHHHHHHHHcCCCcCHHHHH
Confidence            99999999999999999985

>KOG1597 consensus Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription] Back     alignment and domain information
>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) Back     alignment and domain information
>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 Back     alignment and domain information
>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription] Back     alignment and domain information
>cd00043 CYCLIN Cyclin box fold Back     alignment and domain information
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma Back     alignment and domain information
>TIGR00569 ccl1 cyclin ccl1 Back     alignment and domain information
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription] Back     alignment and domain information
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation Back     alignment and domain information
>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] Back     alignment and domain information
>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) Back     alignment and domain information
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription] Back     alignment and domain information
>KOG0835 consensus Cyclin L [General function prediction only] Back     alignment and domain information
>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 [],[] Back     alignment and domain information
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [] Back     alignment and domain information
>PRK00420 hypothetical protein; Validated Back     alignment and domain information
>KOG0835 consensus Cyclin L [General function prediction only] Back     alignment and domain information
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed Back     alignment and domain information
>PHA00626 hypothetical protein Back     alignment and domain information
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional Back     alignment and domain information
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only] Back     alignment and domain information
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C Back     alignment and domain information
>PF13240 zinc_ribbon_2: zinc-ribbon domain Back     alignment and domain information
>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] Back     alignment and domain information
>PF13248 zf-ribbon_3: zinc-ribbon domain Back     alignment and domain information
>PLN00209 ribosomal protein S27; Provisional Back     alignment and domain information
>PTZ00083 40S ribosomal protein S27; Provisional Back     alignment and domain information
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase Back     alignment and domain information
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues Back     alignment and domain information
>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 Back     alignment and domain information
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar Back     alignment and domain information
>PRK11827 hypothetical protein; Provisional Back     alignment and domain information
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR01206 lysW lysine biosynthesis protein LysW Back     alignment and domain information
>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) Back     alignment and domain information
>PRK00432 30S ribosomal protein S27ae; Validated Back     alignment and domain information
>COG2835 Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>PRK10220 hypothetical protein; Provisional Back     alignment and domain information
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain Back     alignment and domain information
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300 Back     alignment and domain information
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function Back     alignment and domain information
>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 Back     alignment and domain information
>smart00661 RPOL9 RNA polymerase subunit 9 Back     alignment and domain information
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family Back     alignment and domain information
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4 Back     alignment and domain information
>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 Back     alignment and domain information
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism] Back     alignment and domain information
>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) Back     alignment and domain information
>PRK00464 nrdR transcriptional regulator NrdR; Validated Back     alignment and domain information
>PF13719 zinc_ribbon_5: zinc-ribbon domain Back     alignment and domain information
>PRK12495 hypothetical protein; Provisional Back     alignment and domain information
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>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 Back     alignment and domain information
>TIGR00244 transcriptional regulator NrdR Back     alignment and domain information
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins Back     alignment and domain information
>TIGR01384 TFS_arch transcription factor S, archaeal Back     alignment and domain information
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2 Back     alignment and domain information
>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 Back     alignment and domain information
>smart00440 ZnF_C2C2 C2C2 Zinc finger Back     alignment and domain information
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA Back     alignment and domain information
>PRK09710 lar restriction alleviation and modification protein; Reviewed Back     alignment and domain information
>PTZ00255 60S ribosomal protein L37a; Provisional Back     alignment and domain information
>PRK14892 putative transcription elongation factor Elf1; Provisional Back     alignment and domain information
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription] Back     alignment and domain information
>TIGR00280 L37a ribosomal protein L37a Back     alignment and domain information
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only] Back     alignment and domain information
>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 Back     alignment and domain information
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein Back     alignment and domain information
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed Back     alignment and domain information
>smart00659 RPOLCX RNA polymerase subunit CX Back     alignment and domain information
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only] Back     alignment and domain information
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1 Back     alignment and domain information
>COG4640 Predicted membrane protein [Function unknown] Back     alignment and domain information
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center Back     alignment and domain information
>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 Back     alignment and domain information
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG Back     alignment and domain information
>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 Back     alignment and domain information
>PF12773 DZR: Double zinc ribbon Back     alignment and domain information
>PF13717 zinc_ribbon_4: zinc-ribbon domain Back     alignment and domain information
>PF14122 YokU: YokU-like protein Back     alignment and domain information
>PF15616 TerY-C: TerY-C metal binding domain Back     alignment and domain information
>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 Back     alignment and domain information
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins Back     alignment and domain information
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription] Back     alignment and domain information
>TIGR02443 conserved hypothetical metal-binding protein Back     alignment and domain information
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription] Back     alignment and domain information
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed Back     alignment and domain information
>PRK06266 transcription initiation factor E subunit alpha; Validated Back     alignment and domain information
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding Back     alignment and domain information
>PRK05978 hypothetical protein; Provisional Back     alignment and domain information
>PHA02942 putative transposase; Provisional Back     alignment and domain information
>TIGR00569 ccl1 cyclin ccl1 Back     alignment and domain information
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional Back     alignment and domain information
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA Back     alignment and domain information
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center Back     alignment and domain information
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK09678 DNA-binding transcriptional regulator; Provisional Back     alignment and domain information
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed Back     alignment and domain information
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ] Back     alignment and domain information
>KOG1088 consensus Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>TIGR01031 rpmF_bact ribosomal protein L32 Back     alignment and domain information
>PRK05508 methionine sulfoxide reductase B; Provisional Back     alignment and domain information
>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 [] Back     alignment and domain information
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150 Back     alignment and domain information
>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 Back     alignment and domain information
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription] Back     alignment and domain information
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 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 Back     alignment and domain information
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated Back     alignment and domain information
>PRK02935 hypothetical protein; Provisional Back     alignment and domain information
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family Back     alignment and domain information
>COG1773 Rubredoxin [Energy production and conversion] Back     alignment and domain information
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG] Back     alignment and domain information
>PRK08402 replication factor A; Reviewed Back     alignment and domain information
>PRK00222 methionine sulfoxide reductase B; Provisional Back     alignment and domain information
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis Back     alignment and domain information
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed Back     alignment and domain information
>TIGR03826 YvyF flagellar operon protein TIGR03826 Back     alignment and domain information
>PRK14559 putative protein serine/threonine phosphatase; Provisional Back     alignment and domain information
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit Back     alignment and domain information
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>PRK00241 nudC NADH pyrophosphatase; Reviewed Back     alignment and domain information
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only] Back     alignment and domain information
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein Back     alignment and domain information
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown] Back     alignment and domain information
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription] Back     alignment and domain information
>PF14353 CpXC: CpXC protein Back     alignment and domain information
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C Back     alignment and domain information
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family Back     alignment and domain information
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT) Back     alignment and domain information
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing Back     alignment and domain information
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query172
3k7a_M 345 Crystal Structure Of An Rna Polymerase Ii-Tfiib Com 6e-23
1c9b_A 207 Crystal Structure Of A Human Tbp Core Domain-Human 2e-16
2phg_A 206 Model For Vp16 Binding To Tfiib Length = 206 8e-16
1tfb_A 208 Nmr Studies Of Human General Transcription Factor T 8e-16
1vol_A 204 Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEME 2e-13
1rly_A60 Rdc-Derived Models Of The Zinc Ribbon Domain Of Hum 9e-07
1dl6_A58 Solution Structure Of Human Tfiib N-Terminal Domain 1e-06
3k1f_M197 Crystal Structure Of Rna Polymerase Ii In Complex W 2e-06
1pft_A50 N-Terminal Domain Of Tfiib, Nmr Length = 50 2e-04
1ais_B 200 Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA- 4e-04
1d3u_B 201 Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+T 4e-04
>pdb|3K7A|M Chain M, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex Length = 345 Back     alignment and structure 
Iteration: 1

 Score =  103 bits (256), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 63/168 (37%), Positives = 91/168 (54%), Gaps = 5/168 (2%)
Query: 6   CSDCKKHT-EVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGD-NDPVRVGGPT 63
           C +CK +  ++V   S GD VC+ CGLVL    +D  SEWRTF+N+  + +DP RVG  +
Sbjct: 24  CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEAS 83
Query: 64  NPLLADGGLSTVIAKPNGASGEFLSSSLGRWQ--NRGSNPDRGLILAFKTIATMSDRLGL 121
           NPLL    LST I K       F +  L + Q  N     D  +  AF  I  + D   L
Sbjct: 84  NPLLDGNNLSTRIGKGETTDMRF-TKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAEL 142
Query: 122 VATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK 169
              +KD A E YK   D+K+ +G++ ++++AA + I CR+ +  RT K
Sbjct: 143 PKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFK 190
>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 Back     alignment and structure
>pdb|2PHG|A Chain A, Model For Vp16 Binding To Tfiib Length = 206 Back     alignment and structure
>pdb|1TFB|A Chain A, Nmr Studies Of Human General Transcription Factor Tfiib: Dynamics And Interaction With Vp16 Activation Domain, 20 Structures Length = 208 Back     alignment and structure
>pdb|1VOL|A Chain A, Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEMENT Ternary Complex Length = 204 Back     alignment and structure
>pdb|1RLY|A Chain A, Rdc-Derived Models Of The Zinc Ribbon Domain Of Human General Transcription Tfiib (Zinc Bound Structures) Length = 60 Back     alignment and structure
>pdb|1DL6|A Chain A, Solution Structure Of Human Tfiib N-Terminal Domain Length = 58 Back     alignment and structure
>pdb|3K1F|M Chain M, Crystal Structure Of Rna Polymerase Ii In Complex With Tfiib Length = 197 Back     alignment and structure
>pdb|1PFT|A Chain A, N-Terminal Domain Of Tfiib, Nmr Length = 50 Back     alignment and structure
>pdb|1AIS|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-Box Complex From Pyrococcus Woesei Length = 200 Back     alignment and structure
>pdb|1D3U|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+TATA- Box Complex From Pyrococcus Woesei Length = 201 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query172
3k7a_M 345 Transcription initiation factor IIB; RNA polymeras 2e-41
3k7a_M345 Transcription initiation factor IIB; RNA polymeras 5e-07
3k1f_M197 Transcription initiation factor IIB; RNA polymeras 1e-27
1c9b_A 207 General transcription factor IIB; protein-DNA comp 4e-23
1c9b_A207 General transcription factor IIB; protein-DNA comp 7e-06
1ais_B 200 TFB TFIIB, protein (transcription initiation facto 2e-22
1ais_B200 TFB TFIIB, protein (transcription initiation facto 2e-07
1dl6_A58 Transcription factor II B (TFIIB); zinc ribbon, ge 3e-15
1pft_A50 TFIIB, PFTFIIBN; N-terminal domain, transcription 2e-14
>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 Back     alignment and structure
 Score =  141 bits (355), Expect = 2e-41
 Identities = 62/168 (36%), Positives = 90/168 (53%), Gaps = 5/168 (2%)

Query: 6   CSDCKKH-TEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANE-SGDNDPVRVGGPT 63
           C +CK +  ++V   S GD VC+ CGLVL    +D  SEWRTF+N+    +DP RVG  +
Sbjct: 24  CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEAS 83

Query: 64  NPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNP--DRGLILAFKTIATMSDRLGL 121
           NPLL    LST I K       F +  L + Q +      D  +  AF  I  + D   L
Sbjct: 84  NPLLDGNNLSTRIGKGETTDMRF-TKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAEL 142

Query: 122 VATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK 169
              +KD A E YK   D+K+ +G++ ++++AA + I CR+ +  RT K
Sbjct: 143 PKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFK 190
>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 Back     alignment and structure
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1 Length = 50 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query172
4bbr_M 345 Transcription initiation factor IIB; RNA polymeras 100.0
3k7a_M 345 Transcription initiation factor IIB; RNA polymeras 100.0
3k1f_M197 Transcription initiation factor IIB; RNA polymeras 99.83
1dl6_A58 Transcription factor II B (TFIIB); zinc ribbon, ge 99.78
1ais_B 200 TFB TFIIB, protein (transcription initiation facto 99.74
1pft_A50 TFIIB, PFTFIIBN; N-terminal domain, transcription 99.67
1c9b_A 207 General transcription factor IIB; protein-DNA comp 99.65
1ais_B200 TFB TFIIB, protein (transcription initiation facto 99.35
1c9b_A207 General transcription factor IIB; protein-DNA comp 99.17
4bbr_M345 Transcription initiation factor IIB; RNA polymeras 99.09
1zp2_A 235 RNA polymerase II holoenzyme cyclin-like subunit; 99.06
3k7a_M345 Transcription initiation factor IIB; RNA polymeras 98.93
2ivx_A 257 Cyclin-T2; transcription regulation, cell division 98.85
2i53_A 258 Cyclin K; cell cycle, transcription, cyclin BOX, C 98.85
1jkw_A 323 Cyclin H; cell cycle, cell division, nuclear prote 98.8
3rgf_B 285 Cyclin-C; protein kinase complex, transferase,tran 98.77
2pk2_A 358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 98.76
2b9r_A 269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 98.31
2cch_B 260 Cyclin A2, cyclin-A; complex(transferase/cell divi 98.14
2w96_A 271 G1/S-specific cyclin-D1; serine/threonine-protein 98.14
1w98_B 283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 98.01
1g3n_C 257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 98.01
2f2c_A 254 Cyclin homolog, V-cyclin; small molecule inhibitor 98.0
3h4c_A 260 Transcription factor TFIIB-like; cyclin, transcrip 97.97
1zp2_A235 RNA polymerase II holoenzyme cyclin-like subunit; 97.81
3g33_B 306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 97.72
2ivx_A257 Cyclin-T2; transcription regulation, cell division 97.62
2i53_A258 Cyclin K; cell cycle, transcription, cyclin BOX, C 97.61
3rgf_B285 Cyclin-C; protein kinase complex, transferase,tran 97.34
2b9r_A269 Human cyclin B1; cell cycle; 2.90A {Homo sapiens} 97.32
2js4_A70 UPF0434 protein BB2007; NESG, northeast structural 97.29
2jr6_A68 UPF0434 protein NMA0874; solution, structural geno 97.22
2jny_A67 Uncharacterized BCR; structure, CGR1, NESG, struct 97.21
1vq8_Z83 50S ribosomal protein L37AE; ribosome 50S, protein 97.16
2pk7_A69 Uncharacterized protein; NESG, PLR1, putative tetr 97.14
2hf1_A68 Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A 97.05
2pk2_A 358 Cyclin-T1, protein TAT; TAR, twinning, transcripti 97.03
1qxf_A66 GR2, 30S ribosomal protein S27E; structural genomi 96.96
2r7g_A347 PP110, retinoblastoma-associated protein, P105-RB, 96.9
3j20_W63 30S ribosomal protein S27E; archaea, archaeal, KIN 96.87
2cch_B260 Cyclin A2, cyclin-A; complex(transferase/cell divi 96.87
4ell_A411 Retinoblastoma-associated protein; cyclin fold, tu 96.8
1f5q_B 252 Gamma herpesvirus cyclin; herpesviral cyclin, cycl 96.69
2xzm_681 RPS27E; ribosome, translation; 3.93A {Tetrahymena 96.63
4elj_A656 Retinoblastoma-associated protein; cyclin fold, tu 96.56
3m03_A95 ORC6, origin recognition complex subunit 6; helix 96.51
3u5c_b82 RP61, YS20, 40S ribosomal protein S27-A; translati 96.49
1jkw_A323 Cyclin H; cell cycle, cell division, nuclear prote 96.34
3iz6_X86 40S ribosomal protein S27 (S27E); eukaryotic ribos 96.27
3j20_Y50 30S ribosomal protein S27AE; archaea, archaeal, KI 96.08
2w96_A271 G1/S-specific cyclin-D1; serine/threonine-protein 95.89
2qdj_A 304 Retinoblastoma-associated protein; cyclin fold, cy 95.78
2akl_A138 PHNA-like protein PA0128; two domains, Zn binding 95.77
1g3n_C257 V-cyclin; cyclin-dependent kinase, INK4 inhibitor, 95.55
2kpi_A56 Uncharacterized protein SCO3027; zinc finger, PSI- 95.45
2f2c_A254 Cyclin homolog, V-cyclin; small molecule inhibitor 95.36
2k4x_A55 30S ribosomal protein S27AE; metal-binding, ribonu 94.94
2k5r_A97 Uncharacterized protein XF2673; solution structure 94.85
6rxn_A46 Rubredoxin; electron transfer(iron-sulfur protein) 94.75
1qyp_A57 RNA polymerase II; transcription, RPB9, Zn ribbon, 94.56
1k81_A36 EIF-2-beta, probable translation initiation factor 94.37
4rxn_A54 Rubredoxin; electron transfer(iron-sulfur protein) 94.25
3g33_B306 CCND3 protein; Ser/Thr protein kinase, cell cycle, 94.19
1e8j_A52 Rubredoxin; iron-sulfur-protein, zinc-substitution 94.08
1nui_A255 DNA primase/helicase; zinc-biding domain, toprim f 93.8
3j21_i83 50S ribosomal protein L37AE; archaea, archaeal, KI 93.74
4elj_A 656 Retinoblastoma-associated protein; cyclin fold, tu 93.25
1ffk_W73 Ribosomal protein L37AE; ribosome assembly, RNA-RN 93.1
3iz5_m92 60S ribosomal protein L43 (L37AE); eukaryotic ribo 93.1
3cc2_Z116 50S ribosomal protein L37AE, 50S ribosomal protein 93.07
3h0g_I113 DNA-directed RNA polymerases I, II, and III subuni 93.04
1twf_L70 ABC10-alpha, DNA-directed RNA polymerases I, II, a 92.97
1twf_I122 B12.6, DNA-directed RNA polymerase II 14.2 kDa pol 92.88
3izc_m92 60S ribosomal protein RPL43 (L37AE); eukaryotic ri 92.8
3jyw_972 60S ribosomal protein L43; eukaryotic ribosome, RA 92.8
4a17_Y103 RPL37A, 60S ribosomal protein L32; eukaryotic ribo 92.56
1dxg_A36 Desulforedoxin; non-heme iron protein, rubredoxin 91.88
2v3b_B55 Rubredoxin 2, rubredoxin; alkane degradation, iron 91.54
1dx8_A70 Rubredoxin; electron transport, zinc-substitution; 90.77
1tfi_A50 Transcriptional elongation factor SII; transcripti 90.63
1gh9_A71 8.3 kDa protein (gene MTH1184); beta+alpha complex 90.29
1w98_B283 Cyclin E, G1/S-specific cyclin E1; cell cycle, tra 90.25
2kn9_A81 Rubredoxin; metalloprotein, ssgcid, structural gen 90.24
3qt1_I133 DNA-directed RNA polymerases I, II, and III subun; 89.71
1wii_A85 Hypothetical UPF0222 protein MGC4549; domain of un 88.49
1gnf_A46 Transcription factor GATA-1; zinc finger, transcri 87.92
3j21_g51 50S ribosomal protein L40E; archaea, archaeal, KIN 87.75
1s24_A87 Rubredoxin 2; electron transport; NMR {Pseudomonas 87.63
2apo_B60 Ribosome biogenesis protein NOP10; protein-protein 87.07
3u50_C172 Telomerase-associated protein 82; TEB1, processivi 86.13
2vut_I43 AREA, nitrogen regulatory protein AREA; transcript 85.35
2ct7_A86 Ring finger protein 31; IBR, structural genomics, 84.93
3ga8_A78 HTH-type transcriptional regulator MQSA (YGIT/B30; 84.16
3h0g_L63 DNA-directed RNA polymerases I, II, and III subuni 83.7
1twf_I122 B12.6, DNA-directed RNA polymerase II 14.2 kDa pol 83.52
3o9x_A133 Uncharacterized HTH-type transcriptional regulato; 83.52
2kv1_A124 Methionine-R-sulfoxide reductase B1; MSRB1, SELR, 83.29
1yk4_A52 Rubredoxin, RD; electron transport; 0.69A {Pyrococ 82.31
2kao_A124 Methionine-R-sulfoxide reductase B1; mouse reduced 82.14
3mao_A105 Methionine-R-sulfoxide reductase B1; oxidoreductas 81.78
4gat_A66 Nitrogen regulatory protein AREA; DNA binding prot 81.75
2kae_A71 GATA-type transcription factor; zinc finger, GATA- 80.19
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M Back     alignment and structure
Probab=100.00  E-value=4.9e-49  Score=325.04  Aligned_cols=169  Identities=36%  Similarity=0.617  Sum_probs=152.0

Q ss_pred             CCCCCCCCC-CCceeEeCCCCceEeCCCcceecccccccCcccccccCCC-CCCCCcccCCCCCccccCCCceeEEecCC
Q 030755            3 DAFCSDCKK-HTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANES-GDNDPVRVGGPTNPLLADGGLSTVIAKPN   80 (172)
Q Consensus         3 ~~~C~~Cg~-~~~i~~D~~~G~~vC~~CG~V~~e~~i~~~~ewr~f~~~~-~~~~~~r~g~~~~~~~~~~~~~t~i~~~~   80 (172)
                      ...||+||+ ++++++|+++|++||++||+||+|++||.+||||+|++++ ++.|++|+|+|.++++||+|++|.|++++
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            458999996 4689999999999999999999999999999999998654 47899999999999999999999999765


Q ss_pred             CCCcccccccccccccC--CCCchhhHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhhCcCCCCCCHHHHHHHHHHHH
Q 030755           81 GASGEFLSSSLGRWQNR--GSNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIA  158 (172)
Q Consensus        81 ~~~~~~l~~~l~~~~~~--~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~a~~~~~~~Gr~~~~~aAAclYia  158 (172)
                      ++.+ ....+|++||++  .+++|++|..++..|.++|++|+||+.++++|..||++++++++++||+.+.++|||||+|
T Consensus       101 ~~~~-~~~~~L~r~q~r~~~~~~er~L~~a~~~I~~~~~~L~Lp~~v~d~A~~lyk~a~~~~~~rGrs~e~vaAAclYiA  179 (345)
T 4bbr_M          101 TTDM-RFTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIG  179 (345)
T ss_dssp             SCCH-HHHHHHHHHHHHTCCCCSSSSTTHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTCTTTTTCCHHHHHHHHHHHH
T ss_pred             Ccch-hhHHHHHHHHHhhhcChHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHH
Confidence            4321 123457888875  3789999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhCCCCCCccccC
Q 030755          159 CRQEDKPRTVKGTA  172 (172)
Q Consensus       159 cR~~~~~~tl~eia  172 (172)
                      ||++++|+||+||+
T Consensus       180 CR~~~~prtl~eI~  193 (345)
T 4bbr_M          180 CRRAEVARTFKEIQ  193 (345)
T ss_dssp             HHHTCCBCCHHHHH
T ss_pred             HHhcCCCccHHHHH
Confidence            99999999999984
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae} Back     alignment and structure
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Back     alignment and structure
>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A Back     alignment and structure
>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* Back     alignment and structure
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1 Back     alignment and structure
>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* Back     alignment and structure
>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* Back     alignment and structure
>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* Back     alignment and structure
>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M Back     alignment and structure
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} Back     alignment and structure
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae} Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens} Back     alignment and structure
>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 Back     alignment and structure
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Back     alignment and structure
>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* ... Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>3h4c_A Transcription factor TFIIB-like; cyclin, transcription factor TFIIB repeat; 2.30A {Trypanosoma brucei brucei} Back     alignment and structure
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat domains, transcription-cell cycle complex; 3.00A {Schizosaccharomyces pombe} Back     alignment and structure
>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens} Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET: BAX; 2.20A {Homo sapiens} Back     alignment and structure
>2b9r_A Human cyclin B1; cell cycle; 2.90A {Homo sapiens} PDB: 2jgz_B* Back     alignment and structure
>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50} Back     alignment and structure
>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis} Back     alignment and structure
>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1 Back     alignment and structure
>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* ... Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4 Back     alignment and structure
>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 Back     alignment and structure
>3j20_W 30S ribosomal protein S27E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>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* ... Back     alignment and structure
>4ell_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor, cell cycle; 1.98A {Homo sapiens} Back     alignment and structure
>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 Back     alignment and structure
>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6 Back     alignment and structure
>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens} Back     alignment and structure
>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} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Back     alignment and structure
>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>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 Back     alignment and structure
>2qdj_A Retinoblastoma-associated protein; cyclin fold, cyclin wedge, antitumor protein; 2.00A {Homo sapiens} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor} Back     alignment and structure
>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 Back     alignment and structure
>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8 Back     alignment and structure
>2k5r_A Uncharacterized protein XF2673; solution structure, structural genomics, PSI-2, protein structure initiative; NMR {Xylella fastidiosa TEMECULA1} Back     alignment and structure
>6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1 Back     alignment and structure
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1 Back     alignment and structure
>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1 Back     alignment and structure
>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 ... Back     alignment and structure
>3g33_B CCND3 protein; Ser/Thr protein kinase, cell cycle, phosphorylation, ATP-BIN cell division, disease mutation, kinase; 3.00A {Homo sapiens} Back     alignment and structure
>1e8j_A Rubredoxin; iron-sulfur-protein, zinc-substitution, thermostability; NMR {Desulfovibrio gigas} SCOP: g.41.5.1 PDB: 1rdg_A 2dsx_A 1spw_A Back     alignment and structure
>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 Back     alignment and structure
>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>4elj_A Retinoblastoma-associated protein; cyclin fold, tumor suppressor protein, phosphorylation, cell; HET: TPO; 2.70A {Homo sapiens} Back     alignment and structure
>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* Back     alignment and structure
>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 Back     alignment and structure
>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>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* ... Back     alignment and structure
>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* ... Back     alignment and structure
>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2v3b_B Rubredoxin 2, rubredoxin; alkane degradation, iron-sulfur protein, oxidoreductase, ELE transfer, electron transport, FAD, NAD, iron; HET: FAD; 2.45A {Pseudomonas aeruginosa} Back     alignment and structure
>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A Back     alignment and structure
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle structural genomics center for infectious electron transport, iron; NMR {Mycobacterium tuberculosis} Back     alignment and structure
>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae} Back     alignment and structure
>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 Back     alignment and structure
>1gnf_A Transcription factor GATA-1; zinc finger, transcription regulation; NMR {Mus musculus} SCOP: g.39.1.1 PDB: 1y0j_A 2l6y_A 2l6z_A Back     alignment and structure
>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>1s24_A Rubredoxin 2; electron transport; NMR {Pseudomonas oleovorans} SCOP: g.41.5.1 Back     alignment and structure
>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 Back     alignment and structure
>2vut_I AREA, nitrogen regulatory protein AREA; transcription regulation, protein-protein interactions, metal-binding, nitrate assimilation; HET: NAD; 2.3A {Emericella nidulans} SCOP: g.39.1.1 PDB: 2vus_I* 2vuu_I* Back     alignment and structure
>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4 Back     alignment and structure
>3ga8_A HTH-type transcriptional regulator MQSA (YGIT/B30; helix-turn-helix, Zn-binding protein, DNA-binding, transcrip transcription regulation; HET: PE4; 1.70A {Escherichia coli k-12} PDB: 3hi2_A Back     alignment and structure
>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>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* ... Back     alignment and structure
>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A Back     alignment and structure
>2kv1_A Methionine-R-sulfoxide reductase B1; MSRB1, SELR, metal-binding, nucleus, oxidoreductase, seleniu; NMR {Mus musculus} Back     alignment and structure
>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 ... Back     alignment and structure
>3mao_A Methionine-R-sulfoxide reductase B1; oxidoreductase, structural genomics consortium, SGC, cytoplasm, metal-binding, nucleus, selenocysteine, zinc; HET: MLI; 1.42A {Homo sapiens} Back     alignment and structure
>4gat_A Nitrogen regulatory protein AREA; DNA binding protein, transcription factor, zinc binding domain, complex (transcription regulation/DNA); HET: DNA; NMR {Emericella nidulans} SCOP: g.39.1.1 PDB: 5gat_A* 6gat_A* 7gat_A* Back     alignment and structure
>2kae_A GATA-type transcription factor; zinc finger, GATA-type, DNA; NMR {Caenorhabditis elegans} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 172
d1aisb198 a.74.1.2 (B:1108-1205) Transcription factor IIB (T 7e-17
d1vola195 a.74.1.2 (A:113-207) Transcription factor IIB (TFI 1e-15
d1dl6a_58 g.41.3.1 (A:) Transcription initiation factor TFII 2e-15
d1vola2109 a.74.1.2 (A:208-316) Transcription factor IIB (TFI 9e-15
d1pfta_50 g.41.3.1 (A:) Transcription initiation factor TFII 4e-14
d1aisb295 a.74.1.2 (B:1206-1300) Transcription factor IIB (T 1e-13
>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 98 Back     information, alignment and structure

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 = 69.9 bits (171), Expect = 7e-17
 Identities = 19/65 (29%), Positives = 37/65 (56%)

Query: 105 LILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDK 164
           L  A   +  ++ +L L   +++ A  +Y++   +   RGR+ ++++AAC+Y ACR    
Sbjct: 2   LAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKV 61

Query: 165 PRTVK 169
           PRT+ 
Sbjct: 62  PRTLD 66
>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Length = 95 Back     information, alignment and structure
>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 58 Back     information, alignment and structure
>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Length = 109 Back     information, alignment and structure
>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 50 Back     information, alignment and structure
>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 95 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query172
d1dl6a_58 Transcription initiation factor TFIIB, N-terminal 99.84
d1pfta_50 Transcription initiation factor TFIIB, N-terminal 99.83
d1vola195 Transcription factor IIB (TFIIB), core domain {Hum 99.83
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 99.81
d1aisb295 Transcription factor IIB (TFIIB), core domain {Arc 99.75
d1vola2109 Transcription factor IIB (TFIIB), core domain {Hum 99.74
d2ivxa1143 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 98.66
d2i53a1144 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 98.66
d1jkwa1151 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 98.39
d2cchb1128 Cyclin A {Cow (Bos taurus) [TaxId: 9913]} 97.47
d2ivxa2113 Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} 97.44
d1bu2a1127 Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} 97.41
d1f5qb1141 Viral cyclin {Murine herpesvirus 68 [TaxId: 33708] 97.25
d2r7ga2142 Retinoblastoma tumor suppressor domains {Human (Ho 97.24
d1g3nc1132 Viral cyclin {Kaposi's sarcoma-associated herpesvi 97.24
d1w98b2140 G1/S-specific cyclin-E1 {Human (Homo sapiens) [Tax 97.2
d1qxfa_58 Ribosomal protein S27e {Archaeon Archaeoglobus ful 97.03
d2i53a2110 Cyclin K {Human (Homo sapiens) [TaxId: 9606]} 96.83
d2jnya159 Uncharacterized protein Cgl1405/cg1592 {Corynebact 96.81
d2pk7a159 Uncharacterized protein PFL1779 {Pseudomonas fluor 96.62
d2hf1a159 Hypothetical protein CV3345 {Chromobacterium viola 96.41
d2akla238 Hypothetical protein PA0128, N-terminal domain {Ps 96.4
d1vd4a_62 Transcription initiation factor TFIIE-alpha {Human 96.1
d1neea237 Zinc-binding domain of translation initiation fact 95.09
d1k81a_36 Zinc-binding domain of translation initiation fact 94.92
d1jj2y_73 Ribosomal protein L37ae {Archaeon Haloarcula maris 93.78
d1vqoz173 Ribosomal protein L37ae {Archaeon Haloarcula maris 93.61
d1nuia254 Zinc-binding domain of primase-helicase {Bacteriop 93.4
d1jkwa2126 Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606 92.85
d2dsxa152 Rubredoxin {Desulfovibrio gigas [TaxId: 879]} 92.84
d2ak3a237 Microbial and mitochondrial ADK, insert "zinc fing 92.8
d1u5ka2157 Recombinational repair protein RecO, C-terminal do 92.52
d1iroa_53 Rubredoxin {Clostridium pasteurianum [TaxId: 1501] 92.22
d1zina235 Microbial and mitochondrial ADK, insert "zinc fing 91.97
d1y0ja139 Erythroid transcription factor GATA-1 {Mouse (Mus 91.97
d1e4va235 Microbial and mitochondrial ADK, insert "zinc fing 91.87
d1s3ga235 Microbial and mitochondrial ADK, insert "zinc fing 91.84
d1rqga335 Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro 91.81
d1pfva335 Methionyl-tRNA synthetase (MetRS), Zn-domain {Esch 91.48
d1akya238 Microbial and mitochondrial ADK, insert "zinc fing 91.22
d6rxna_45 Rubredoxin {Desulfovibrio desulfuricans, strain 27 90.18
d2k4xa155 Ribosomal protein S27ae {Thermoplasma acidophilum 90.02
d2ct7a173 Ring finger protein 31 {Human (Homo sapiens) [TaxI 89.9
d1twfi272 RBP9 subunit of RNA polymerase II {Baker's yeast ( 89.75
d2j9ub147 Vacuolar protein-sorting-associated protein 36, VP 89.51
d2vuti142 Erythroid transcription factor GATA-1 {Emericella 89.43
d1qypa_57 RBP9 subunit of RNA polymerase II {Archaeon Thermo 88.95
d1vzia237 Desulfoferrodoxin N-terminal domain {Desulfoarculu 88.49
d3gata_66 Erythroid transcription factor GATA-1 {Chicken (Ga 88.12
d1s24a_56 Two-iron rubredoxin {Pseudomonas oleovorans [TaxId 87.65
d1dxga_36 Desulforedoxin {Desulfovibrio gigas [TaxId: 879]} 87.2
d1l1oc_178 Replication protein A 70 KDa subunit (RPA70) {Huma 85.89
d1ibia231 Cysteine-rich (intestinal) protein, CRP, CRIP {Jap 85.71
d2j015159 Ribosomal protein L32p {Thermus thermophilus [TaxI 85.39
d1dfxa236 Desulfoferrodoxin N-terminal domain {Desulfovibrio 84.78
d2zjrz158 Ribosomal protein L32p {Deinococcus radiodurans [T 83.53
d2cora235 Pinch (particularly interesting new Cys-His) prote 83.13
d1ak2a230 Microbial and mitochondrial ADK, insert "zinc fing 83.12
d2jnea171 Hypothetical protein YfgJ {Escherichia coli [TaxId 82.66
d2f9yb1263 Acetyl-coenzyme A carboxylase carboxyl transferase 82.35
d1k3xa340 Endonuclease VIII {Escherichia coli [TaxId: 562]} 81.01
d1dx8a_70 Rubredoxin {Guillardia theta [TaxId: 55529]} 81.0
>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
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=99.84  E-value=7.5e-22  Score=120.24  Aligned_cols=48  Identities=44%  Similarity=0.818  Sum_probs=45.0

Q ss_pred             CCCCCCCCCCCCCceeEeCCCCceEeCCCcceecccccccCcccccccC
Q 030755            1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFAN   49 (172)
Q Consensus         1 ~~~~~C~~Cg~~~~i~~D~~~G~~vC~~CG~V~~e~~i~~~~ewr~f~~   49 (172)
                      |+..+||+||+ +++++|..+|++||.+||+|++|++||.+||||+|++
T Consensus         9 ~~~~~Cp~Cgs-~~ii~D~~~Ge~vC~~CG~Vlee~~ID~g~EWR~f~~   56 (58)
T d1dl6a_           9 LPRVTCPNHPD-AILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSN   56 (58)
T ss_dssp             CSCCSBTTBSS-SCCEECSSSCCEECTTTCCEECCSCCCCCCSCCCSCC
T ss_pred             ccccCCCCCCC-CCEEEECCCCcEecccCCCEeccccccCCCcccccCC
Confidence            45679999998 6899999999999999999999999999999999985
>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Back     information, alignment and structure
>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Back     information, alignment and structure
>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ivxa1 a.74.1.1 (A:7-149) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2i53a1 a.74.1.1 (A:14-157) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jkwa1 a.74.1.1 (A:11-161) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cchb1 a.74.1.1 (B:181-308) Cyclin A {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d2ivxa2 a.74.1.1 (A:150-262) Cyclin-T2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1bu2a1 a.74.1.1 (A:22-148) Viral cyclin {Herpesvirus saimiri [TaxId: 10381]} Back     information, alignment and structure
>d1f5qb1 a.74.1.1 (B:6-146) Viral cyclin {Murine herpesvirus 68 [TaxId: 33708]} Back     information, alignment and structure
>d2r7ga2 a.74.1.3 (A:644-785) Retinoblastoma tumor suppressor domains {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1g3nc1 a.74.1.1 (C:16-147) Viral cyclin {Kaposi's sarcoma-associated herpesvirus [TaxId: 37296]} Back     information, alignment and structure
>d1w98b2 a.74.1.1 (B:88-227) G1/S-specific cyclin-E1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d2i53a2 a.74.1.1 (A:158-267) Cyclin K {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2jnya1 b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405/cg1592 {Corynebacterium glutamicum [TaxId: 1718]} Back     information, alignment and structure
>d2pk7a1 b.171.1.1 (A:3-61) Uncharacterized protein PFL1779 {Pseudomonas fluorescens [TaxId: 294]} Back     information, alignment and structure
>d2hf1a1 b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromobacterium violaceum [TaxId: 536]} Back     information, alignment and structure
>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1vd4a_ g.41.3.1 (A:) Transcription initiation factor TFIIE-alpha {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1neea2 g.59.1.1 (A:99-135) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1k81a_ g.59.1.1 (A:) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1jj2y_ g.41.8.1 (Y:) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure
>d1vqoz1 g.41.8.1 (Z:10-82) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure
>d1nuia2 g.41.3.2 (A:10-63) Zinc-binding domain of primase-helicase {Bacteriophage T7 [TaxId: 10760]} Back     information, alignment and structure
>d1jkwa2 a.74.1.1 (A:162-287) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2dsxa1 g.41.5.1 (A:1-52) Rubredoxin {Desulfovibrio gigas [TaxId: 879]} Back     information, alignment and structure
>d2ak3a2 g.41.2.1 (A:125-161) Microbial and mitochondrial ADK, insert "zinc finger" domain {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]} Back     information, alignment and structure
>d1u5ka2 g.45.1.2 (A:81-237) Recombinational repair protein RecO, C-terminal domain {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d1iroa_ g.41.5.1 (A:) Rubredoxin {Clostridium pasteurianum [TaxId: 1501]} Back     information, alignment and structure
>d1zina2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1y0ja1 g.39.1.1 (A:200-238) Erythroid transcription factor GATA-1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1e4va2 g.41.2.1 (A:122-156) Microbial and mitochondrial ADK, insert "zinc finger" domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1s3ga2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus globisporus [TaxId: 1459]} Back     information, alignment and structure
>d1rqga3 g.41.1.1 (A:139-173) Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyrococcus abyssi [TaxId: 29292]} Back     information, alignment and structure
>d1pfva3 g.41.1.1 (A:141-175) Methionyl-tRNA synthetase (MetRS), Zn-domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1akya2 g.41.2.1 (A:131-168) Microbial and mitochondrial ADK, insert "zinc finger" domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d6rxna_ g.41.5.1 (A:) Rubredoxin {Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]} Back     information, alignment and structure
>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]} Back     information, alignment and structure
>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2j9ub1 g.41.11.1 (B:115-161) Vacuolar protein-sorting-associated protein 36, VPS36 {Saccharomyces cerevisiae [TaxId: 4932]} Back     information, alignment and structure
>d2vuti1 g.39.1.1 (I:671-712) Erythroid transcription factor GATA-1 {Emericella nidulans [TaxId: 162425]} Back     information, alignment and structure
>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]} Back     information, alignment and structure
>d1vzia2 g.41.5.2 (A:1-37) Desulfoferrodoxin N-terminal domain {Desulfoarculus baarsii (Desulfovibrio baarsii) [TaxId: 887]} Back     information, alignment and structure
>d3gata_ g.39.1.1 (A:) Erythroid transcription factor GATA-1 {Chicken (Gallus gallus) [TaxId: 9031]} Back     information, alignment and structure
>d1s24a_ g.41.5.1 (A:) Two-iron rubredoxin {Pseudomonas oleovorans [TaxId: 301]} Back     information, alignment and structure
>d1dxga_ g.41.5.2 (A:) Desulforedoxin {Desulfovibrio gigas [TaxId: 879]} Back     information, alignment and structure
>d1l1oc_ b.40.4.3 (C:) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]} Back     information, alignment and structure
>d2j0151 g.41.8.5 (5:2-60) Ribosomal protein L32p {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1dfxa2 g.41.5.2 (A:1-36) Desulfoferrodoxin N-terminal domain {Desulfovibrio desulfuricans [TaxId: 876]} Back     information, alignment and structure
>d2zjrz1 g.41.8.5 (Z:2-59) Ribosomal protein L32p {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d2cora2 g.39.1.3 (A:8-42) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ak2a2 g.41.2.1 (A:147-176) Microbial and mitochondrial ADK, insert "zinc finger" domain {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]} Back     information, alignment and structure
>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2f9yb1 c.14.1.4 (B:23-285) Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, AccD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1k3xa3 g.39.1.8 (A:223-262) Endonuclease VIII {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1dx8a_ g.41.5.1 (A:) Rubredoxin {Guillardia theta [TaxId: 55529]} Back     information, alignment and structure