Citrus Sinensis ID: 035641

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-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310----
MEKKLVTLFGAAKKAADAAAATNRSEPEVQRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWKQKIVLGKETNGNKRNGSKLSVDEKFQKQTSDSNAVKSGCSTAKEKKATASIRKPSHADQAKDSMRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWKC
cHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHcccccHHHHHcccccEEcccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHcccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccccHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccccEEcccccccccEEEcEEccccccccEEEEEcccccccccc
cHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccccHHHHHHccccHEHHHHcccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccccHHHccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccHHHHHHcccccHHHHHHccHHHHccHHHHHHHHHHHHHHHHHHHHcccccccccEEEccccccccEEEEEEEEccccccccEEEEEccccccccc
MEKKLVTLFGAAKKAADAAaatnrsepeVQRCADALKHLQAFPVTYDLLVSTQVGKslrhlkkhpcEKVQNAASELLHIWKQKIVlgketngnkrngsklsvdekfqkqtsdsnavksgCSTAKEKKatasirkpshadqakDSMRDKIRKDLEKALSRVAseaaddeeitdrvkardpkqVAASVERVMFEKlrpmgvaekrkhRSIMfnmsdeknpdlrrrvligevtperlatmtpeelasDERRQENEEIKAKFMfkcevpekkkgttdqfkcsgcgksncsyhqmqtrsadepmttyvtcaecnkrwkc
MEKKLVTLFGAAKKAADAAAATNRSEPEVQRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWKQKivlgketngnkrngsklsvdekfqkqtsdsnavksgcstakekkatasirkpshadqakdsmrDKIRKDLEKALsrvaseaaddeeitdrvkardpkqvaasvervmfeklrpmgvaekrkhrsimfnmsdeknpdlrrrvligevtperlatmtpeelasderRQENEEIKAkfmfkcevpekkkgttdqfkcsgcgKSNCSYHQMqtrsadepmttyVTCAecnkrwkc
MEKKLVTLFGaakkaadaaaaTNRSEPEVQRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWKQKIVLGKETNGNKRNGSKLSVDEKFQKQTSDSNAVKSGCSTAKEKKATASIRKPSHADQAKDSMRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWKC
******************************RCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWKQKIVLG**************************************************************************************************************************************************************************FMFKC**************C**C*******************TTYVTCAECN*****
**KKLVTLFG************************ALKHLQAFPVTYDLLVSTQVG************************************************************************ATASIRKPSHADQAKDSMRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEI**********************CSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWKC
MEKKLVTLFGA******************QRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWKQKIVLGKETNGNKRNGSKLSVD*****************************************MRDKIRKDLEKAL*************************AASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPE**********NEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWKC
****LVTLFGAAKKAADAAAAT**SEPEVQRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWKQKIVL***************************************************ADQAKDSMRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWKC
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SSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MEKKLVTLFGAAKKAADAAAATNRSEPEVQRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWKQKIVLGKETNGNKRNGSKLSVDEKFQKQTSDSNAVKSGCSTAKEKKATASIRKPSHADQAKDSMRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWKC
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 ?
Query314 2.2.26 [Sep-21-2011]
P23193301 Transcription elongation yes no 0.834 0.870 0.339 5e-33
Q29RL9301 Transcription elongation yes no 0.834 0.870 0.325 1e-32
Q15560299 Transcription elongation no no 0.850 0.892 0.333 1e-32
P10711301 Transcription elongation yes no 0.837 0.873 0.326 2e-32
Q148K0300 Transcription elongation no no 0.856 0.896 0.330 3e-32
Q4KLL0301 Transcription elongation yes no 0.837 0.873 0.323 3e-32
Q9QVN7299 Transcription elongation no no 0.853 0.896 0.326 6e-32
Q63799299 Transcription elongation no no 0.856 0.899 0.316 3e-31
P49373293 Transcription elongation yes no 0.792 0.849 0.322 1e-29
P20232313 Transcription elongation yes no 0.859 0.862 0.303 4e-27
>sp|P23193|TCEA1_HUMAN Transcription elongation factor A protein 1 OS=Homo sapiens GN=TCEA1 PE=1 SV=2 Back     alignment and function desciption
 Score =  141 bits (356), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 99/292 (33%), Positives = 158/292 (54%), Gaps = 30/292 (10%)

Query: 34  DALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPC-EKVQNAASELLHIWKQKIVLG----K 88
           D LK L+  P+T +LL ST++G S+  ++K    E+V + A  L+  WK K++ G    K
Sbjct: 26  DLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDEEVTSLAKSLIKSWK-KLLDGPSTEK 84

Query: 89  ETNGNKRNGSKLSVD--EKFQKQTSDSNAVKSGCST-AKEKKATASIRKPSHADQAKDSM 145
           + +  K+  +  S +  E  ++ TS  N       T A++   ++  R PS +D    S+
Sbjct: 85  DLDEKKKEPAITSQNSPEAREESTSSGNVSNRKDETNARDTYVSSFPRAPSTSD----SV 140

Query: 146 RDKIRKDLEKALSRVASE----AADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAE 201
           R K R+ L  AL R   +     AD+EE+             + +E  +++++R   +  
Sbjct: 141 RLKCREMLAAAL-RTGDDYIAIGADEEEL------------GSQIEEAIYQEIRNTDMKY 187

Query: 202 KRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFMFK 261
           K + RS + N+ D KNP+LR+ VL G + P+  A MT EE+ASDE ++  + +  + + +
Sbjct: 188 KNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDELKEMRKNLTKEAIRE 247

Query: 262 CEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313
            ++ +     TD F C  C K NC+Y Q+QTRSADEPMTT+V C EC  RWK
Sbjct: 248 HQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK 299
Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.
Homo sapiens (taxid: 9606)
>sp|Q29RL9|TCEA1_BOVIN Transcription elongation factor A protein 1 OS=Bos taurus GN=TCEA1 PE=2 SV=1 Back     alignment and function description
>sp|Q15560|TCEA2_HUMAN Transcription elongation factor A protein 2 OS=Homo sapiens GN=TCEA2 PE=1 SV=1 Back     alignment and function description
>sp|P10711|TCEA1_MOUSE Transcription elongation factor A protein 1 OS=Mus musculus GN=Tcea1 PE=1 SV=2 Back     alignment and function description
>sp|Q148K0|TCEA2_BOVIN Transcription elongation factor A protein 2 OS=Bos taurus GN=TCEA2 PE=2 SV=1 Back     alignment and function description
>sp|Q4KLL0|TCEA1_RAT Transcription elongation factor A protein 1 OS=Rattus norvegicus GN=Tcea1 PE=2 SV=1 Back     alignment and function description
>sp|Q9QVN7|TCEA2_MOUSE Transcription elongation factor A protein 2 OS=Mus musculus GN=Tcea2 PE=2 SV=2 Back     alignment and function description
>sp|Q63799|TCEA2_RAT Transcription elongation factor A protein 2 OS=Rattus norvegicus GN=Tcea2 PE=2 SV=1 Back     alignment and function description
>sp|P49373|TFS2_SCHPO Transcription elongation factor S-II OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=tfs1 PE=3 SV=1 Back     alignment and function description
>sp|P20232|TFS2_DROME Transcription elongation factor S-II OS=Drosophila melanogaster GN=TfIIS 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 ?
Query314
224139382334 predicted protein [Populus trichocarpa] 0.980 0.922 0.507 9e-82
224087871352 predicted protein [Populus trichocarpa] 0.968 0.863 0.473 6e-77
297735532322 unnamed protein product [Vitis vinifera] 0.980 0.956 0.504 3e-76
255575598342 transcription elongation factor s-II, pu 0.987 0.906 0.510 6e-76
225439709367 PREDICTED: transcription elongation fact 0.990 0.847 0.468 5e-73
224286619328 unknown [Picea sitchensis] 0.974 0.932 0.470 3e-72
388514187369 unknown [Medicago truncatula] 0.952 0.810 0.447 4e-72
449441244369 PREDICTED: transcription elongation fact 0.984 0.837 0.452 1e-71
312283193381 unnamed protein product [Thellungiella h 0.987 0.813 0.447 1e-69
116789178331 unknown [Picea sitchensis] 0.971 0.921 0.493 2e-68
>gi|224139382|ref|XP_002323085.1| predicted protein [Populus trichocarpa] gi|222867715|gb|EEF04846.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  309 bits (792), Expect = 9e-82,   Method: Compositional matrix adjust.
 Identities = 171/337 (50%), Positives = 223/337 (66%), Gaps = 29/337 (8%)

Query: 1   MEKKLVTLFGAAKKAADAAAATNRSE--PEVQRCADALKHLQAFPVTYDLLVSTQVGKSL 58
           MEK+LV LF  AKKAADA+   ++S   PEV RC D+LK L+ F VT ++LVSTQVGK L
Sbjct: 1   MEKELVELFDKAKKAADASLNDDKSSSGPEVSRCVDSLKQLRKFKVTSEILVSTQVGKKL 60

Query: 59  RHLKKHPCEKVQNAASELLHIWKQKIVLGKETNGNKRNGS------------KLSVDEKF 106
           R L KHP +K++  AS+LL  WK KIV+  +    K+N +            K+S  E  
Sbjct: 61  RPLAKHPKDKIRAVASDLLETWK-KIVI--DETMRKKNATVKVEKLQKTSMVKVSTSETV 117

Query: 107 QKQTSDSNAVKSGCSTAKEKKATASIRKPSHAD----------QAKDSMRDKIRKDLEKA 156
           + +  D +       T KE+  T+S++KPS A           +  D++RDKIR+ L +A
Sbjct: 118 KVEKMDQDKTVKVAQTCKEEIQTSSVKKPSQAPTGPPKLKTLVKCNDALRDKIRELLAEA 177

Query: 157 LSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEK 216
           LS+VASEA  DE+I D V+A DP +VA SVE  MFEKL     A+K K+RSIMFN+ D+ 
Sbjct: 178 LSKVASEA--DEDIRDEVEACDPIRVAVSVESAMFEKLGRSNGAQKMKYRSIMFNIKDQN 235

Query: 217 NPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFMFKCEVPEKKKGTTDQFK 276
           NPDLRR+VL+G+V P+RL TM PEE+AS++R++EN +IK K +F CE   K + TTDQFK
Sbjct: 236 NPDLRRKVLLGQVQPQRLVTMPPEEMASEQRKRENNQIKEKALFDCERGGKAEATTDQFK 295

Query: 277 CSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313
           C  CG+  C+Y+QMQTRSADEPMTTYVTC  CN  WK
Sbjct: 296 CGRCGQRKCTYYQMQTRSADEPMTTYVTCVNCNNHWK 332

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224087871|ref|XP_002308256.1| predicted protein [Populus trichocarpa] gi|222854232|gb|EEE91779.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|297735532|emb|CBI18026.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|255575598|ref|XP_002528699.1| transcription elongation factor s-II, putative [Ricinus communis] gi|223531871|gb|EEF33688.1| transcription elongation factor s-II, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|225439709|ref|XP_002272768.1| PREDICTED: transcription elongation factor A protein 3 [Vitis vinifera] Back     alignment and taxonomy information
>gi|224286619|gb|ACN41014.1| unknown [Picea sitchensis] Back     alignment and taxonomy information
>gi|388514187|gb|AFK45155.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|449441244|ref|XP_004138392.1| PREDICTED: transcription elongation factor A protein 3-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|312283193|dbj|BAJ34462.1| unnamed protein product [Thellungiella halophila] Back     alignment and taxonomy information
>gi|116789178|gb|ABK25146.1| unknown [Picea sitchensis] 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 ?
Query314
TAIR|locus:2064195378 TFIIS "transcript elongation f 0.863 0.716 0.455 2.7e-52
UNIPROTKB|F1NP36309 TCEA1 "Uncharacterized protein 0.850 0.864 0.347 4.9e-37
MGI|MGI:1196624301 Tcea1 "transcription elongatio 0.856 0.893 0.336 1.7e-36
UNIPROTKB|F1MIT2280 TCEA1 "Transcription elongatio 0.856 0.960 0.336 2.7e-36
UNIPROTKB|Q29RL9301 TCEA1 "Transcription elongatio 0.856 0.893 0.336 2.7e-36
RGD|1309880301 Tcea1 "transcription elongatio 0.856 0.893 0.333 3.5e-36
UNIPROTKB|F1RSG8300 TCEA1 "Uncharacterized protein 0.856 0.896 0.334 4.4e-36
UNIPROTKB|E2QVN6301 TCEA1 "Uncharacterized protein 0.856 0.893 0.329 5.7e-36
UNIPROTKB|F1NP37280 TCEA1 "Uncharacterized protein 0.853 0.957 0.342 7.2e-36
UNIPROTKB|P23193301 TCEA1 "Transcription elongatio 0.843 0.880 0.349 9.2e-36
TAIR|locus:2064195 TFIIS "transcript elongation factor IIS" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 542 (195.9 bits), Expect = 2.7e-52, P = 2.7e-52
 Identities = 132/290 (45%), Positives = 171/290 (58%)

Query:    26 EPEVQRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWKQKIV 85
             E +V +  D  K     PV    L      KS++  +K P  KV           ++K+ 
Sbjct:   104 EAKVNKM-DVEKPSNPAPVKVQKLQRGDSAKSIKVERKEPDNKVVTGVKI-----ERKVP 157

Query:    86 LGKETNGNKRNGSKLSV-DEKFQKQTSDSNAVKSGCSTAKEKKATASIRKPSHADQAKDS 144
               K TNG K +    +V DEK  K    S    +  + A  K  TA ++         D 
Sbjct:   158 DIKVTNGTKIDYRGQAVKDEKVSKDNQSSMKAPAKAANAPPK-LTAMLK-------CNDP 209

Query:   145 MRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKL-RPMGVAEKR 203
             +RDKIR+ L +AL RVA EA DD E  + V A DP +VA SVE +MFEKL R  G A+K 
Sbjct:   210 VRDKIRELLVEALCRVAGEA-DDYE-RESVNASDPLRVAVSVESLMFEKLGRSTG-AQKL 266

Query:   204 KHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFMFKCE 263
             K+RSIMFN+ D  NPDLRRRVL GE++PE+L T++ E++ASD+R+QEN +IK K +F CE
Sbjct:   267 KYRSIMFNLRDSNNPDLRRRVLTGEISPEKLITLSAEDMASDKRKQENNQIKEKALFDCE 326

Query:   264 VPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313
                  K +TDQFKC  CG+  C+Y+QMQTRSADEPMTTYVTC  C+  WK
Sbjct:   327 RGLAAKASTDQFKCGRCGQRKCTYYQMQTRSADEPMTTYVTCVNCDNHWK 376
GO:0003674 "molecular_function" evidence=ND
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0003677 "DNA binding" evidence=IEA;ISS
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0003746 "translation elongation factor activity" evidence=IEA
GO:0005634 "nucleus" evidence=ISM;IEA;ISS;IDA
GO:0006351 "transcription, DNA-dependent" evidence=IEA
GO:0006354 "DNA-dependent transcription, elongation" evidence=IEA;ISS
GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;ISS
GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA
GO:0008270 "zinc ion binding" evidence=IEA
GO:0032784 "regulation of DNA-dependent transcription, elongation" evidence=IEA
GO:0009910 "negative regulation of flower development" evidence=IMP
GO:0010162 "seed dormancy process" evidence=RCA;IMP
GO:0034243 "regulation of transcription elongation from RNA polymerase II promoter" evidence=IMP
GO:0005829 "cytosol" evidence=RCA
GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA
GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA
GO:0007062 "sister chromatid cohesion" evidence=RCA
GO:0009640 "photomorphogenesis" evidence=RCA
GO:0009793 "embryo development ending in seed dormancy" evidence=RCA
GO:0009845 "seed germination" evidence=IMP;RCA
GO:0009880 "embryonic pattern specification" evidence=RCA
GO:0009909 "regulation of flower development" evidence=RCA
GO:0009933 "meristem structural organization" evidence=RCA
GO:0010072 "primary shoot apical meristem specification" evidence=RCA
GO:0010182 "sugar mediated signaling pathway" evidence=RCA
GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA
GO:0010431 "seed maturation" evidence=RCA
GO:0010564 "regulation of cell cycle process" evidence=RCA
GO:0016567 "protein ubiquitination" evidence=RCA
GO:0019915 "lipid storage" evidence=RCA
GO:0045595 "regulation of cell differentiation" evidence=RCA
GO:0048366 "leaf development" evidence=RCA
GO:0048825 "cotyledon development" evidence=RCA
GO:0050826 "response to freezing" evidence=RCA
GO:0051301 "cell division" evidence=RCA
GO:0009739 "response to gibberellin stimulus" evidence=IMP
UNIPROTKB|F1NP36 TCEA1 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
MGI|MGI:1196624 Tcea1 "transcription elongation factor A (SII) 1" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|F1MIT2 TCEA1 "Transcription elongation factor A protein 1" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q29RL9 TCEA1 "Transcription elongation factor A protein 1" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
RGD|1309880 Tcea1 "transcription elongation factor A (SII) 1" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1RSG8 TCEA1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|E2QVN6 TCEA1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|F1NP37 TCEA1 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|P23193 TCEA1 "Transcription elongation factor A protein 1" [Homo sapiens (taxid:9606)] 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) ?
P10711TCEA1_MOUSENo assigned EC number0.32640.83750.8737yesno
P23193TCEA1_HUMANNo assigned EC number0.33900.83430.8704yesno
P52652TFS2_CAEELNo assigned EC number0.31120.88210.8993yesno
Q4KLL0TCEA1_RATNo assigned EC number0.32300.83750.8737yesno
P20232TFS2_DROMENo assigned EC number0.30370.85980.8626yesno
Q29RL9TCEA1_BOVINNo assigned EC number0.32530.83430.8704yesno

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_fgenesh4_pg.C_LG_XVI1293
hypothetical protein (335 aa)
(Populus trichocarpa)
Predicted Functional Partners:
grail3.0014029901
hypothetical protein (52 aa)
    ••• 0.400

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 ?
Query314
TIGR01385299 TIGR01385, TFSII, transcription elongation factor 4e-72
pfam07500115 pfam07500, TFIIS_M, Transcription factor S-II (TFI 6e-31
smart00510102 smart00510, TFS2M, Domain in the central regions o 2e-27
pfam0109639 pfam01096, TFIIS_C, Transcription factor S-II (TFI 2e-16
smart0050975 smart00509, TFS2N, Domain in the N-terminus of tra 8e-15
smart0044040 smart00440, ZnF_C2C2, C2C2 Zinc finger 2e-13
cd0018376 cd00183, TFIIS_I, N-terminal domain (domain I) of 2e-13
COG1594113 COG1594, RPB9, DNA-directed RNA polymerase, subuni 8e-11
pfam0871151 pfam08711, Med26, TFIIS helical bundle-like domain 3e-09
TIGR01384104 TIGR01384, TFS_arch, transcription factor S, archa 5e-05
>gnl|CDD|233390 TIGR01385, TFSII, transcription elongation factor S-II Back     alignment and domain information 
 Score =  224 bits (572), Expect = 4e-72
 Identities = 111/309 (35%), Positives = 164/309 (53%), Gaps = 17/309 (5%)

Query: 10  GAAKKAADAAAATNRSEPEVQRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKV 69
            A   +   A   N+S   V++C D L  L+ FP T +LL  T+VG  +  L+KHP E +
Sbjct: 1   SAEVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDI 60

Query: 70  QNAASELLHIWKQKIVLGKETNGNKRNGSKLSVDEKFQKQTSDSNAVKSGCSTAKEKKAT 129
              A +++  WK+ +   K  +       K +V E       ++   KS     ++ K  
Sbjct: 61  SKLAKKIIKSWKKVVDKNKSDHPGGNPEDKTTVGESVNSVKQEA---KSQSDKIEQPKYV 117

Query: 130 ASIRKPSHAD-----QAKDSMRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAA 184
           +S  + +  D        D +RDK R+ L  AL++ +             ++ DP+  A 
Sbjct: 118 SSSPRNAKNDFVPTAVTNDKVRDKCRELLYDALAKDSDHPP---------QSIDPEAKAI 168

Query: 185 SVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELAS 244
            +E + F  L     A K ++RSI  N+ D+ NPDLR  VL GE+TPE+LATMT EE+AS
Sbjct: 169 QIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMAS 228

Query: 245 DERRQENEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVT 304
            E +QE EEI  + +F+ +  + +K  TD F C  C +  C+Y+Q+QTRSADEPMTT+VT
Sbjct: 229 AELKQEREEITKENLFEAQGAKIQKAVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVT 288

Query: 305 CAECNKRWK 313
           C EC  RWK
Sbjct: 289 CEECGNRWK 297

This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end. Length = 299
>gnl|CDD|219433 pfam07500, TFIIS_M, Transcription factor S-II (TFIIS), central domain Back     alignment and domain information
>gnl|CDD|128786 smart00510, TFS2M, Domain in the central regions of transcription elongation factor S-II (and elsewhere) Back     alignment and domain information
>gnl|CDD|201594 pfam01096, TFIIS_C, Transcription factor S-II (TFIIS) Back     alignment and domain information
>gnl|CDD|197766 smart00509, TFS2N, Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) Back     alignment and domain information
>gnl|CDD|128717 smart00440, ZnF_C2C2, C2C2 Zinc finger Back     alignment and domain information
>gnl|CDD|238107 cd00183, TFIIS_I, N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme Back     alignment and domain information
>gnl|CDD|224510 COG1594, RPB9, DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription] Back     alignment and domain information
>gnl|CDD|204037 pfam08711, Med26, TFIIS helical bundle-like domain Back     alignment and domain information
>gnl|CDD|130451 TIGR01384, TFS_arch, transcription factor S, archaeal Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 314
TIGR01385299 TFSII transcription elongation factor S-II. This m 100.0
KOG1105296 consensus Transcription elongation factor TFIIS/Co 100.0
smart00510102 TFS2M Domain in the central regions of transcripti 99.95
PF07500115 TFIIS_M: Transcription factor S-II (TFIIS), centra 99.94
smart0044040 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo 99.8
PF0109639 TFIIS_C: Transcription factor S-II (TFIIS); InterP 99.79
smart0050975 TFS2N Domain in the N-terminus of transcription el 99.72
KOG2906105 consensus RNA polymerase III subunit C11 [Transcri 99.72
COG1594113 RPB9 DNA-directed RNA polymerase, subunit M/Transc 99.67
TIGR01384104 TFS_arch transcription factor S, archaeal. There h 99.65
PHA02998195 RNA polymerase subunit; Provisional 99.61
cd0018376 TFIIS_I N-terminal domain (domain I) of transcript 99.6
KOG2691113 consensus RNA polymerase II subunit 9 [Transcripti 99.54
PF0871153 Med26: TFIIS helical bundle-like domain; InterPro: 99.36
KOG1634 778 consensus Predicted transcription factor DATF1, co 99.32
KOG2907116 consensus RNA polymerase I transcription factor TF 99.26
PF11467106 LEDGF: Lens epithelium-derived growth factor (LEDG 96.64
KOG1793417 consensus Uncharacterized conserved protein [Funct 95.88
PF0827430 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01 95.79
PF0985564 DUF2082: Nucleic-acid-binding protein containing Z 95.61
KOG2821 433 consensus RNA polymerase II transcription elongati 95.33
PRK0967872 DNA-binding transcriptional regulator; Provisional 95.08
PF1371736 zinc_ribbon_4: zinc-ribbon domain 95.04
PF1371937 zinc_ribbon_5: zinc-ribbon domain 94.6
COG5139397 Uncharacterized conserved protein [Function unknow 94.57
PHA0062659 hypothetical protein 94.57
TIGR0209838 MJ0042_CXXC MJ0042 family finger-like domain. This 94.51
COG347868 Predicted nucleic-acid-binding protein containing 94.12
PF0827143 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013 94.03
PF0460647 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I 93.98
PF1276046 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int 93.96
COG4888104 Uncharacterized Zn ribbon-containing protein [Gene 92.79
TIGR00373158 conserved hypothetical protein TIGR00373. This fam 91.79
COG205167 RPS27A Ribosomal protein S27E [Translation, riboso 91.31
PF1178136 RRN7: RNA polymerase I-specific transcription init 90.48
PF05876 557 Terminase_GpA: Phage terminase large subunit (GpA) 90.25
smart0066152 RPOL9 RNA polymerase subunit 9. 89.9
smart00531147 TFIIE Transcription initiation factor IIE. 89.38
PF1435461 Lar_restr_allev: Restriction alleviation protein L 89.19
TIGR0365553 anti_R_Lar restriction alleviation protein, Lar fa 88.9
PLN0020986 ribosomal protein S27; Provisional 88.87
PTZ0008385 40S ribosomal protein S27; Provisional 88.47
PF0952671 DUF2387: Probable metal-binding protein (DUF2387); 88.36
PRK06266178 transcription initiation factor E subunit alpha; V 87.53
PF0512981 Elf1: Transcription elongation factor Elf1 like; I 87.46
PF0518066 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc 87.31
PF04216290 FdhE: Protein involved in formate dehydrogenase fo 87.24
PF1345341 zf-TFIIB: Transcription factor zinc-finger 86.94
TIGR0244359 conserved hypothetical metal-binding protein. Memb 86.5
PRK0041559 rps27e 30S ribosomal protein S27e; Reviewed 85.73
PRK06266178 transcription initiation factor E subunit alpha; V 85.45
PF0166755 Ribosomal_S27e: Ribosomal protein S27; InterPro: I 84.49
PF09538108 FYDLN_acid: Protein of unknown function (FYDLN_aci 83.77
PRK0043250 30S ribosomal protein S27ae; Validated 83.66
PRK0039846 rpoP DNA-directed RNA polymerase subunit P; Provis 82.99
PRK03988138 translation initiation factor IF-2 subunit beta; V 82.94
PF0728269 OrfB_Zn_ribbon: Putative transposase DNA-binding d 82.64
PF1057126 UPF0547: Uncharacterised protein family UPF0547; I 82.58
PLN02976 1713 amine oxidase 82.24
PRK0971064 lar restriction alleviation and modification prote 81.61
PRK1489299 putative transcription elongation factor Elf1; Pro 81.42
KOG350762 consensus DNA-directed RNA polymerase, subunit RPB 81.18
PF0381136 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0 81.12
PF01873125 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: 80.69
COG288861 Predicted Zn-ribbon RNA-binding protein with a fun 80.59
TIGR00311133 aIF-2beta translation initiation factor aIF-2, bet 80.47
>TIGR01385 TFSII transcription elongation factor S-II Back     alignment and domain information 
Probab=100.00  E-value=1.3e-70  Score=514.93  Aligned_cols=291  Identities=37%  Similarity=0.595  Sum_probs=236.1

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHhcCCCCCHHhhhcCcceeecccccCCCCHHHHHHHHHHHHHHHHhhh
Q 035641            6 VTLFGAAKKAADAAAATNRSEPEVQRCADALKHLQAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWKQKIV   85 (314)
Q Consensus         6 ~el~~~a~k~~~~~~~~~~~~~~~~~~~~~L~~L~~~~~t~~~L~~T~iG~~V~~Lrkh~~~~i~~~Ak~Li~~WK~~~v   85 (314)
                      .|+..+++++.++++    + .+++.|+++|++|+.++||+++|++|+||++||+||||++++|+.+|+.||+.||+ +|
T Consensus         2 ~ei~~~~k~L~k~~~----~-~~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~-~v   75 (299)
T TIGR01385         2 AEVASHAKALDKNKS----S-KNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKK-VV   75 (299)
T ss_pred             hHHHHHHHHhhhhcc----C-CCHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHH-HH
Confidence            467788888877773    2 47789999999999999999999999999999999999999999999999999999 98


Q ss_pred             cccccCCCCCCCCCCCc--ccccccCC--CCCccccCCCCcccccccCCCCCCCCCC--CCCCcHHHHHHHHHHHHHHHh
Q 035641           86 LGKETNGNKRNGSKLSV--DEKFQKQT--SDSNAVKSGCSTAKEKKATASIRKPSHA--DQAKDSMRDKIRKDLEKALSR  159 (314)
Q Consensus        86 ~~~~~~~~~~~~~~~~~--~~~~~~~~--~ss~s~k~~~~~~~~~~~~~~~~~~~~~--~~~~d~~R~k~~~~L~~aL~~  159 (314)
                      . .+........++...  ..++.+..  +++++.+  ...+..+++++++..++++  +.++|++|++|+++||+||..
T Consensus        76 ~-~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~t~d~~Rdk~r~~L~~aL~~  152 (299)
T TIGR01385        76 D-KNKSDHPGGNPEDKTTVGESVNSVKQEAKSQSDK--IEQPKYVSSSPRNAKNDFVPTAVTNDKVRDKCRELLYDALAK  152 (299)
T ss_pred             h-hhcccCcccccccccccCCCCCCCCccccCCccc--ccCCCCCCCcccccCCCCCCCccCCcHHHHHHHHHHHHHHhh
Confidence            7 432211100000000  00000000  0000000  0011122233444444544  589999999999999999998


Q ss_pred             hhccccchhHHHhhhhcCChHHHHHHHHHHHHHhhcCCChhhHhHHHhHHhhcCCCCChhhhhhhhcCCCChhhhhcCCh
Q 035641          160 VASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTP  239 (314)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~d~~~lA~~IE~alf~~~~~~~~~yk~k~Rsl~~NLkd~~Np~Lr~~vl~G~i~p~~lv~Ms~  239 (314)
                      +..+.++         .+++..||.+||.+||..|+.+++.|+++||||+|||||++||+||++|++|+|+|++||.|++
T Consensus       153 ~~~~~~~---------~~~~~~lA~~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~  223 (299)
T TIGR01385       153 DSDHPPQ---------SIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTA  223 (299)
T ss_pred             cCCCCcc---------ccCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCH
Confidence            7543322         2467889999999999999988889999999999999999999999999999999999999999


Q ss_pred             hhcCcHHHHHHHHHHHHhhhhhhccccccCCCccceecCCCCCCceEEEeeeccCCCCCCeEEEEcCCCCCcccC
Q 035641          240 EELASDERRQENEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWKC  314 (314)
Q Consensus       240 eEmas~e~k~~~~~~~~~~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C~~C~~~w~~  314 (314)
                      +||||++++++++++.+++|++++++....+.|+.|+||+||+++|+|||+|+|+||||||+||+|++|||+|+|
T Consensus       224 eEmas~e~k~~~e~~~ke~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~f  298 (299)
T TIGR01385       224 EEMASAELKQEREEITKENLFEAQGAKIQKAVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKF  298 (299)
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeeee
Confidence            999999999999999999999999999888999999999999999999999999999999999999999999998

This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription] Back     alignment and domain information
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere) Back     alignment and domain information
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites Back     alignment and domain information
>smart00440 ZnF_C2C2 C2C2 Zinc finger 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
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) Back     alignment and domain information
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription] Back     alignment and domain information
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription] Back     alignment and domain information
>TIGR01384 TFS_arch transcription factor S, archaeal Back     alignment and domain information
>PHA02998 RNA polymerase subunit; Provisional Back     alignment and domain information
>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme Back     alignment and domain information
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription] Back     alignment and domain information
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription Back     alignment and domain information
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription] Back     alignment and domain information
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12 Back     alignment and domain information
>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis Back     alignment and domain information
>KOG1793 consensus Uncharacterized conserved protein [Function unknown] 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
>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
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription] Back     alignment and domain information
>PRK09678 DNA-binding transcriptional regulator; Provisional Back     alignment and domain information
>PF13717 zinc_ribbon_4: zinc-ribbon domain Back     alignment and domain information
>PF13719 zinc_ribbon_5: zinc-ribbon domain Back     alignment and domain information
>COG5139 Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>PHA00626 hypothetical protein Back     alignment and domain information
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain 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
>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
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr 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
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only] Back     alignment and domain information
>TIGR00373 conserved hypothetical protein TIGR00373 Back     alignment and domain information
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis] 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
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA Back     alignment and domain information
>smart00661 RPOL9 RNA polymerase subunit 9 Back     alignment and domain information
>smart00531 TFIIE Transcription initiation factor IIE Back     alignment and domain information
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar Back     alignment and domain information
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family 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
>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
>PRK06266 transcription initiation factor E subunit alpha; Validated 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
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex [] Back     alignment and domain information
>PF13453 zf-TFIIB: Transcription factor zinc-finger Back     alignment and domain information
>TIGR02443 conserved hypothetical metal-binding protein Back     alignment and domain information
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed Back     alignment and domain information
>PRK06266 transcription initiation factor E subunit alpha; Validated 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
>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
>PRK00432 30S ribosomal protein S27ae; Validated Back     alignment and domain information
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional Back     alignment and domain information
>PRK03988 translation initiation factor IF-2 subunit beta; Validated 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
>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
>PLN02976 amine oxidase Back     alignment and domain information
>PRK09710 lar restriction alleviation and modification protein; Reviewed Back     alignment and domain information
>PRK14892 putative transcription elongation factor Elf1; Provisional Back     alignment and domain information
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7 Back     alignment and domain information
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases Back     alignment and domain information
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology [] 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
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative 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 ?
Query314
1pqv_S309 Rna Polymerase Ii-Tfiis Complex Length = 309 5e-22
1y1v_S179 Refined Rna Polymerase Ii-tfiis Complex Length = 17 1e-21
3gtm_S173 Co-Complex Of Backtracked Rna Polymerase Ii With Tf 4e-21
3po3_S178 Arrested Rna Polymerase Ii Reactivation Intermediat 3e-20
2dme_A120 Solution Structure Of The Tfiis Domain Ii Of Human 2e-11
1tfi_A50 A Novel Zn Finger Motif In The Basal Transcriptiona 4e-11
2lw4_A113 Solution Nmr Structure Of Human Transcription Elong 1e-10
3ndq_A108 Structure Of Human Tfiis Domain Ii Length = 108 1e-08
3qt1_I133 Rna Polymerase Ii Variant Containing A Chimeric Rpb 8e-05
1qyp_A57 Thermococcus Celer Rpb9, Nmr, 25 Structures Length 7e-04
>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex Length = 309 Back     alignment and structure 
Iteration: 1

 Score =  101 bits (252), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 46/114 (40%), Positives = 71/114 (62%)
Query: 200 AEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFM 259
           A K ++R I  N+  + NPDL+ ++  G++TPE LAT   ++LA    +Q+ EEI  + +
Sbjct: 194 AYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNL 253
Query: 260 FKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313
           +  +    ++  TD+F C  C +   SY+Q+QTRSADEP+TT+ TC  C  RWK
Sbjct: 254 YNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWK 307
>pdb|1Y1V|S Chain S, Refined Rna Polymerase Ii-tfiis Complex Length = 179 Back     alignment and structure
>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis Length = 173 Back     alignment and structure
>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate Length = 178 Back     alignment and structure
>pdb|2DME|A Chain A, Solution Structure Of The Tfiis Domain Ii Of Human Phd Finger Protein 3 Length = 120 Back     alignment and structure
>pdb|1TFI|A Chain A, A Novel Zn Finger Motif In The Basal Transcriptional Machinery: Three-Dimensional Nmr Studies Of The Nucleic- Acid Binding Domain Of Transcriptional Elongation Factor Tfiis Length = 50 Back     alignment and structure
>pdb|2LW4|A Chain A, Solution Nmr Structure Of Human Transcription Elongation Factor A Protein 2, Central Domain, Northeast Structural Genomics Consortium (Nesg) Target Hr8682b Length = 113 Back     alignment and structure
>pdb|3NDQ|A Chain A, Structure Of Human Tfiis Domain Ii Length = 108 Back     alignment and structure
>pdb|3QT1|I Chain I, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11 Subunit Length = 133 Back     alignment and structure
>pdb|1QYP|A Chain A, Thermococcus Celer Rpb9, Nmr, 25 Structures Length = 57 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 ?
Query314
1pqv_S309 STP-alpha, transcription elongation factor S-II, D 5e-46
3po3_S178 Transcription elongation factor S-II; RNA polymera 6e-37
2dme_A120 PHD finger protein 3; PHF3, TFS2M, glioblastoma mu 1e-22
3ndq_A108 Transcription elongation factor A protein 1; helix 6e-22
1tfi_A50 Transcriptional elongation factor SII; transcripti 9e-20
1qyp_A57 RNA polymerase II; transcription, RPB9, Zn ribbon, 1e-16
3h0g_I113 DNA-directed RNA polymerases I, II, and III subuni 6e-16
3qt1_I133 DNA-directed RNA polymerases I, II, and III subun; 5e-14
1twf_I122 B12.6, DNA-directed RNA polymerase II 14.2 kDa pol 1e-11
1wjt_A103 Transcription elongation factor S-II protein 3; fo 1e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 7e-05
2xpp_A145 IWS1, ECU08_0440; transcription, elongation, histo 4e-04
>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A Length = 309 Back     alignment and structure
 Score =  157 bits (396), Expect = 5e-46
 Identities = 72/294 (24%), Positives = 122/294 (41%), Gaps = 3/294 (1%)

Query: 23  NRSEPEVQRCADALKHLQA-FPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIWK 81
            +++       + L  L   F  T  LL  T+VG  +   KK    ++     +++  WK
Sbjct: 14  EKNKSNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWK 73

Query: 82  QKIVLGKETNGNKRNGSKLSVDEKFQKQTS--DSNAVKSGCSTAKEKKATASIRKPSHAD 139
             I   K +   +++    +      K T     N V+   S+  +             +
Sbjct: 74  DAINKNKRSRQAQQHHQDHAPGNAEDKTTVGESVNGVQQPASSQSDAMKQDKYVSTKPRN 133

Query: 140 QAKDSMRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGV 199
              D +   I     +     A      +E     ++      A   E            
Sbjct: 134 SKNDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQSILHTAKAIESEMNKVNNCDTNEA 193

Query: 200 AEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFM 259
           A K ++R I  N+  + NPDL+ ++  G++TPE LAT   ++LA    +Q+ EEI  + +
Sbjct: 194 AYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNL 253

Query: 260 FKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313
           +  +    ++  TD+F C  C +   SY+Q+QTRSADEP+TT+ TC  C  RWK
Sbjct: 254 YNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWK 307
>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A Length = 178 Back     alignment and structure
>2dme_A PHD finger protein 3; PHF3, TFS2M, glioblastoma multiforme, brain tumor, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 120 Back     alignment and structure
>3ndq_A Transcription elongation factor A protein 1; helix bundle; 1.93A {Homo sapiens} Length = 108 Back     alignment and structure
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1 Length = 50 Back     alignment and structure
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1 Length = 57 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} Length = 113 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} Length = 133 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* ... Length = 122 Back     alignment and structure
>1wjt_A Transcription elongation factor S-II protein 3; four-helix bundle, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.48.3.1 Length = 103 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>2xpp_A IWS1, ECU08_0440; transcription, elongation, histone chaperone, RNA polymerase mRNA export; 1.74A {Encephalitozoon cuniculi} PDB: 2xpo_A 2xpn_A 2xpl_A Length = 145 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query314
1pqv_S309 STP-alpha, transcription elongation factor S-II, D 100.0
3po3_S178 Transcription elongation factor S-II; RNA polymera 100.0
2lw4_A113 Transcription elongation factor A protein 2; struc 99.96
3ndq_A108 Transcription elongation factor A protein 1; helix 99.96
2dme_A120 PHD finger protein 3; PHF3, TFS2M, glioblastoma mu 99.94
1tfi_A50 Transcriptional elongation factor SII; transcripti 99.84
1wjt_A103 Transcription elongation factor S-II protein 3; fo 99.73
1qyp_A57 RNA polymerase II; transcription, RPB9, Zn ribbon, 99.72
3h0g_I113 DNA-directed RNA polymerases I, II, and III subuni 99.67
1twf_I122 B12.6, DNA-directed RNA polymerase II 14.2 kDa pol 99.66
3qt1_I133 DNA-directed RNA polymerases I, II, and III subun; 99.6
2xpp_A145 IWS1, ECU08_0440; transcription, elongation, histo 97.59
3nfq_A170 Transcription factor IWS1; SPN1, RNA polymerase II 97.39
2b4j_C98 PC4 and SFRS1 interacting protein; HIV, integratio 96.68
1z9e_A127 PC4 and SFRS1 interacting protein 2; heat repeat-l 96.19
2akl_A138 PHNA-like protein PA0128; two domains, Zn binding 93.41
1k81_A36 EIF-2-beta, probable translation initiation factor 93.29
1pft_A50 TFIIB, PFTFIIBN; N-terminal domain, transcription 87.61
1qxf_A66 GR2, 30S ribosomal protein S27E; structural genomi 87.48
2fiy_A309 Protein FDHE homolog; FDHE protein, structural gen 87.29
3j20_W63 30S ribosomal protein S27E; archaea, archaeal, KIN 85.82
1vq8_Z83 50S ribosomal protein L37AE; ribosome 50S, protein 85.61
3iz6_X86 40S ribosomal protein S27 (S27E); eukaryotic ribos 85.55
2xzm_681 RPS27E; ribosome, translation; 3.93A {Tetrahymena 85.22
1wii_A85 Hypothetical UPF0222 protein MGC4549; domain of un 85.16
2e2z_A100 TIM15; protein import, zinc finger, protein transp 82.61
3u5c_b82 RP61, YS20, 40S ribosomal protein S27-A; translati 82.21
>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A Back     alignment and structure
Probab=100.00  E-value=1.5e-66  Score=491.03  Aligned_cols=290  Identities=25%  Similarity=0.396  Sum_probs=228.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHh-cCCCCCHHhhhcCcceeecccccCCCCHHHHHHHHHHHHHH
Q 035641            2 EKKLVTLFGAAKKAADAAAATNRSEPEVQRCADALKHL-QAFPVTYDLLVSTQVGKSLRHLKKHPCEKVQNAASELLHIW   80 (314)
Q Consensus         2 ~~~~~el~~~a~k~~~~~~~~~~~~~~~~~~~~~L~~L-~~~~~t~~~L~~T~iG~~V~~Lrkh~~~~i~~~Ak~Li~~W   80 (314)
                      |+|++++++...|   ..       .+++.++++|++| +.++||+++|++|+||++||+||||++++|+.+|+.||++|
T Consensus         3 ~~el~~~~~~L~k---~~-------~~~~~~l~~L~~L~~~~~it~~~L~~T~IG~~Vn~lrkh~~~~v~~~Ak~Li~~W   72 (309)
T 1pqv_S            3 SKEVLVHVKNLEK---NK-------SNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSW   72 (309)
T ss_pred             HHHHHHHHHHHhc---cC-------CCHHHHHHHHHHHHhcCCCCHHHHHhCChhHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence            4566666666554   11       3678999999999 99999999999999999999999999999999999999999


Q ss_pred             HHhhhcccccCCCCC-----CCCCCCcccccccC-CCC--Cc---cccCCCCcccccccCCCCCCCCCCC--CCCcHHHH
Q 035641           81 KQKIVLGKETNGNKR-----NGSKLSVDEKFQKQ-TSD--SN---AVKSGCSTAKEKKATASIRKPSHAD--QAKDSMRD  147 (314)
Q Consensus        81 K~~~v~~~~~~~~~~-----~~~~~~~~~~~~~~-~~s--s~---s~k~~~~~~~~~~~~~~~~~~~~~~--~~~d~~R~  147 (314)
                      |+ +|. .+..++..     .+.+.....+..+. .++  ++   +.....+....+.+.+++...++++  .++|++|+
T Consensus        73 K~-~v~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~R~  150 (309)
T 1pqv_S           73 KD-AIN-KNKRSRQAQQHHQDHAPGNAEDKTTVGESVNGVQQPASSQSDAMKQDKYVSTKPRNSKNDGVDTAIYHHKLRD  150 (309)
T ss_pred             HH-HHH-HhccCCcccccccccccccccCCCCCCCCcCCCCCCcccccccccCCCCCCCCCCCCCCCCCCcCcCChHHHH
Confidence            99 987 43332211     00000000000000 000  00   0000000111122333444445553  78899999


Q ss_pred             HHHHHHHHHHHhhhccccchhHHHhhhhcCChHHHHHHHHHHHHHhhcCCChh--hHhHHHhHHhhcCCCCChhhhhhhh
Q 035641          148 KIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVA--EKRKHRSIMFNMSDEKNPDLRRRVL  225 (314)
Q Consensus       148 k~~~~L~~aL~~~~~~~~~~~~~~~~~~~~d~~~lA~~IE~alf~~~~~~~~~--yk~k~Rsl~~NLkd~~Np~Lr~~vl  225 (314)
                      +|+++|+++|..+..+.+.           ++..+|.+||.+||..|++.+..  |++++|||+|||||++||.||++||
T Consensus       151 k~r~~L~~aL~~~~~~~~~-----------~~~~~A~~IE~al~~~~~~~~~~~~Yk~k~Rsl~~NLKd~~N~~Lr~~vl  219 (309)
T 1pqv_S          151 QVLKALYDVLAKESEHPPQ-----------SILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIA  219 (309)
T ss_pred             HHHHHHHHHHhcCCCccch-----------hHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHcCcCCChHHHHHHH
Confidence            9999999999876433221           45689999999999999887777  9999999999999999999999999


Q ss_pred             cCCCChhhhhcCChhhcCcHHHHHHHHHHHHhhhhhhccccccCCCccceecCCCCCCceEEEeeeccCCCCCCeEEEEc
Q 035641          226 IGEVTPERLATMTPEELASDERRQENEEIKAKFMFKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTC  305 (314)
Q Consensus       226 ~G~i~p~~lv~Ms~eEmas~e~k~~~~~~~~~~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~q~rsade~mt~f~~C  305 (314)
                      +|+|+|++||.|+++||||+|++++++++.+++|++++++..+.++++.+.||+||+++++|||+|+||||||||+||+|
T Consensus       220 ~g~i~p~~lv~Ms~eElasde~k~~~~~~~~e~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~~q~Q~rsaDe~~t~f~~C  299 (309)
T 1pqv_S          220 NGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTC  299 (309)
T ss_pred             cCCCCHHHHhcCCHHHhCCHHHHHHHHHHHHHHHHHhhhccccccCcccccCCCCCCCeeEEEEeecccCCCCCcEEEEe
Confidence            99999999999999999999999999999999999999998888888899999999999999999999999999999999


Q ss_pred             CCCCCcccC
Q 035641          306 AECNKRWKC  314 (314)
Q Consensus       306 ~~C~~~w~~  314 (314)
                      ++|||+|+|
T Consensus       300 ~~Cg~~w~f  308 (309)
T 1pqv_S          300 EACGNRWKF  308 (309)
T ss_pred             CCCCCceec
Confidence            999999998
>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A Back     alignment and structure
>2lw4_A Transcription elongation factor A protein 2; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Back     alignment and structure
>3ndq_A Transcription elongation factor A protein 1; helix bundle; 1.93A {Homo sapiens} Back     alignment and structure
>2dme_A PHD finger protein 3; PHF3, TFS2M, glioblastoma multiforme, brain tumor, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1 Back     alignment and structure
>1wjt_A Transcription elongation factor S-II protein 3; four-helix bundle, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.48.3.1 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
>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_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
>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
>2xpp_A IWS1, ECU08_0440; transcription, elongation, histone chaperone, RNA polymerase mRNA export; 1.74A {Encephalitozoon cuniculi} PDB: 2xpo_A 2xpn_A 2xpl_A Back     alignment and structure
>3nfq_A Transcription factor IWS1; SPN1, RNA polymerase II; 1.85A {Saccharomyces cerevisiae} PDB: 3o8z_A 3oak_A Back     alignment and structure
>2b4j_C PC4 and SFRS1 interacting protein; HIV, integration, transcription, viral protein, recombinatio; 2.02A {Homo sapiens} SCOP: a.48.4.1 PDB: 3f9k_C 3hpg_G 3u88_C* 3hph_E Back     alignment and structure
>1z9e_A PC4 and SFRS1 interacting protein 2; heat repeat-like, ledgf, protein binding/transcription complex; NMR {Homo sapiens} SCOP: a.48.4.1 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
>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
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1 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
>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1 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
>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
>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
>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6 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
>2e2z_A TIM15; protein import, zinc finger, protein transport, chaperone regulator; NMR {Saccharomyces cerevisiae} 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

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 314
d1tfia_50 g.41.3.1 (A:) Transcriptional factor SII, C-termin 5e-19
d1enwa_114 a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Bak 1e-18
d1qypa_57 g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {A 4e-16
d1twfi272 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase 2e-11
d1eo0a_77 a.48.3.1 (A:) Transcription elongation factor TFII 9e-10
d1wjta_103 a.48.3.1 (A:) Transcription elongation factor S-II 8e-09
>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 50 Back     information, alignment and structure

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.1 bits (190), Expect = 5e-19
 Identities = 31/48 (64%), Positives = 34/48 (70%), Gaps = 1/48 (2%)

Query: 267 KKKGT-TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313
           K  GT TD F C  C K NC+Y Q+QTRSADEPMTT+V C EC  RWK
Sbjct: 1   KTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK 48
>d1enwa_ a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 114 Back     information, alignment and structure
>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]} Length = 57 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]} Length = 72 Back     information, alignment and structure
>d1eo0a_ a.48.3.1 (A:) Transcription elongation factor TFIIS N-domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 77 Back     information, alignment and structure
>d1wjta_ a.48.3.1 (A:) Transcription elongation factor S-II protein 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 103 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 ?
Query314
d1enwa_114 Elongation factor TFIIS domain 2 {Baker's yeast (S 99.89
d1tfia_50 Transcriptional factor SII, C-terminal domain {Hum 99.84
d1qypa_57 RBP9 subunit of RNA polymerase II {Archaeon Thermo 99.8
d1twfi272 RBP9 subunit of RNA polymerase II {Baker's yeast ( 99.78
d1eo0a_77 Transcription elongation factor TFIIS N-domain {Ba 99.63
d1wjta_103 Transcription elongation factor S-II protein 3 {Mo 99.58
d2b4jc181 PC4 and SFRS1-interacting protein, PSIP1 {Human (H 97.73
d2akla238 Hypothetical protein PA0128, N-terminal domain {Ps 95.6
d2fiya1290 FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId 87.48
d1qxfa_58 Ribosomal protein S27e {Archaeon Archaeoglobus ful 87.21
d1dl6a_58 Transcription initiation factor TFIIB, N-terminal 87.18
d1twfl_46 RBP12 subunit of RNA polymerase II {Baker's yeast 80.73
d1wiia_85 Hypothetical UPF0222 protein MGC4549 {Mouse (Mus m 80.32
>d1enwa_ a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: Elongation factor TFIIS domain 2
family: Elongation factor TFIIS domain 2
domain: Elongation factor TFIIS domain 2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.89  E-value=1.4e-24  Score=174.26  Aligned_cols=105  Identities=26%  Similarity=0.315  Sum_probs=91.2

Q ss_pred             CCCCCCCCCC--CCCCcHHHHHHHHHHHHHHHhhhccccchhHHHhhhhcCChHHHHHHHHHHHHHhhcCCC--hhhHhH
Q 035641          129 TASIRKPSHA--DQAKDSMRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMG--VAEKRK  204 (314)
Q Consensus       129 ~~~~~~~~~~--~~~~d~~R~k~~~~L~~aL~~~~~~~~~~~~~~~~~~~~d~~~lA~~IE~alf~~~~~~~--~~yk~k  204 (314)
                      .|++.+.+++  ..++|++|++|+++|+++|..+..+.++           +...+|.+||.+||..|+...  ..|++|
T Consensus         4 ~pr~~k~d~v~~~~~~d~~R~~~~~~L~~aL~~~~~~~~~-----------~~~~la~~IE~~lf~~~~~~~~~~~Y~~k   72 (114)
T d1enwa_           4 MPRNSKNDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQ-----------SILHTAKAIESEMNKVNNCDTNEAAYKAR   72 (114)
T ss_dssp             CSCSTTTTCCCCCSSTTTTHHHHHHHHHHHHHHHCSSSCS-----------CHHHHHHHHTTTTTSSCTTTTTHHHHHHH
T ss_pred             CCCCccCCCCCCccCCcHHHHHHHHHHHHHHhCcCccchh-----------HHHHHHHHHHHHHHHHhcccCCcHHHHHH
Confidence            4566667776  6789999999999999999877654333           345789999999999997532  579999


Q ss_pred             HHhHHhhcCCCCChhhhhhhhcCCCChhhhhcCChhhcCc
Q 035641          205 HRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELAS  244 (314)
Q Consensus       205 ~Rsl~~NLkd~~Np~Lr~~vl~G~i~p~~lv~Ms~eEmas  244 (314)
                      +|||+|||||++||+|+.+|+.|+|+|++||.|+++|||+
T Consensus        73 ~rsi~~NLkd~~N~~L~~~v~~g~i~p~~l~~M~~~ElaP  112 (114)
T d1enwa_          73 YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAP  112 (114)
T ss_dssp             HHHHHHHHTTSCCCCTTTHHHHCSSCCSSHHHHTTTTTCS
T ss_pred             HHHHHHHcCccchHHHHHHHHcCCCCHHHHhCCCHHHcCC
Confidence            9999999999999999999999999999999999999997
>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} 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
>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
>d1eo0a_ a.48.3.1 (A:) Transcription elongation factor TFIIS N-domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1wjta_ a.48.3.1 (A:) Transcription elongation factor S-II protein 3 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2b4jc1 a.48.4.1 (C:346-426) PC4 and SFRS1-interacting protein, PSIP1 {Human (Homo sapiens) [TaxId: 9606]} 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
>d2fiya1 e.59.1.1 (A:19-308) FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1twfl_ g.41.9.2 (L:) RBP12 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1wiia_ g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure