Citrus Sinensis ID: 017145

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-------320-------330-------340-------350-------360-------370------
MEQELVELFDAAKKAADSAAIDGVSSGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPREKIQIVASNLLDIWKKIVIEETTRNKKNGSTGDKSSVTTGVVKPDSGKIDKVQKTSAVKVEKVSTAETVKVEKTGSVSRSETVQVEKKETNGDSVMDRGEAVKVEKIIEEEKQAPSVRKPSQGTIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC
cHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHccccccHHHHHcccccEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccHHHHHHHHccccccccHHcHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHcHHcccccccHHccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccEEcccccccEEEEEEEEEcccccccccEEEccccccccccc
cHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHcccccHHHHHHccccHEHHHHccccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccHHHHHHcccccHHHHHHccHHHHccHHHHHHHHHHHHHHHHHHHHcccccccccEEEccccccccEEEEEEEEcccccccEEEEEEccccccEEEc
MEQELVELFDAAKKAADSaaidgvssggpevSRCVDALKrlksfpvtyDVLVstqvgkrlrpltkhpreKIQIVASNLLDIWKKIVIEETtrnkkngstgdkssvttgvvkpdsgkidkvqKTSAVKVEKVSTAETVkvektgsvsrsetvqvekketngdsvmdrgeAVKVEKIIEEekqapsvrkpsqgtiatpkltqlikcndsSRDKIRELLANALSKVTSEADEEIIdevnacdpirVAVSVESVMFEKlgrstgaekLKYRSIMFNirdeknpdlrkrvllgevtperlvtmspeemasDERQRQIENIKEKALFEcqrggeatattdqfkcsrcgqrkctyyqmqtrsadepmttyvtcvncskrwkfc
MEQELVELFDAAKKAADsaaidgvssggpeVSRCVDALKrlksfpvtydvlvstqvgkrlrpltkhprekiqivasNLLDIWKKIVIEettrnkkngstgdkssvttgvvkpdsgkidkvqktsavkvekvstaetvkvektgsvsrsetvqvekketngdsvmdrgeAVKVEKIIeeekqapsvrkpsqgtiatpkltqlikcndsSRDKIRELLANALSKVTSEADEEIidevnacdpiRVAVSVESVMfeklgrstgaeklkyrsimfnirdeknpdlrkrvllgevtperlvtmspeemasdeRQRQIENIKEKALFECQRggeatattdqfkcsrcgqRKCTYYQMqtrsadepmttyvtcvncskrwkfc
MEQELVELFdaakkaadsaaIDGVSSGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPREKIQIVASNLLDIWKKIVIEETTRNKKNGSTGDKSSVTTGVVKPDSGKIDKVQKTSAVKVEKVSTAETVKVEKTGSVSRSETVQVEKKETNGDSVMDRGEAvkvekiieeekQAPSVRKPSQGTIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC
******************************VSRCVDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPREKIQIVASNLLDIWKKIVIE****************************************************************************************************************LIK**********ELLANALSKVT**ADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRD********RVLL********************************LFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF*
*EQELVELFDAAK********************CVDALKRLKSFPVTYDVLVSTQVGKRLRPLTK***********NLLDIW*****************************************************************************************************SVRKPSQGTIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEK***********TATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC
MEQELVELFDAAKKAADSAAIDGVSSGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPREKIQIVASNLLDIWKKIVIEETTR************VTTGVVKPDSGKIDKVQKTSAVKVEKVSTAETVKV********************GDSVMDRGEAVKVEKIIEEEK*********QGTIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC
****LVELFDAAKKAADSAAID**SSGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPREKIQIVASNLLDIWKKIVIE************************************************************************************************************KLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC
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MEQELVELFDAAKKAADSAAIDGVSSGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPREKIQIVASNLLDIWKKIVIEETTRNKKNGSTGDKSSVTTGVVKPDSGKIDKVQKTSAVKVEKVSTAETVKVEKTGSVSRSETVQVEKKETNGDSVMDRGEAVKVEKIIEEEKQAPSVRKPSQGTIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC
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 ?
Query376 2.2.26 [Sep-21-2011]
P23193301 Transcription elongation yes no 0.723 0.903 0.302 3e-32
Q15560299 Transcription elongation no no 0.494 0.622 0.376 3e-31
P23881347 Transcription elongation yes no 0.837 0.907 0.304 3e-31
Q148K0300 Transcription elongation yes no 0.505 0.633 0.379 5e-31
Q63799299 Transcription elongation no no 0.492 0.618 0.383 1e-30
Q9QVN7299 Transcription elongation no no 0.492 0.618 0.383 2e-30
Q2KI09349 Transcription elongation no no 0.827 0.891 0.302 5e-30
Q4KLL0301 Transcription elongation no no 0.425 0.531 0.405 8e-30
P10711301 Transcription elongation no no 0.425 0.531 0.405 8e-30
Q29RL9301 Transcription elongation no no 0.425 0.531 0.4 1e-29
>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 =  139 bits (350), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 105/347 (30%), Positives = 164/347 (47%), Gaps = 75/347 (21%)

Query: 35  VDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPR-EKIQIVASNLLDIWKKIVIEETTRN 93
           +D LK LK+ P+T ++L ST++G  +  + K    E++  +A +L+  WKK++       
Sbjct: 25  LDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDEEVTSLAKSLIKSWKKLL------- 77

Query: 94  KKNGSTGDKSSVTTGVVKPDSGKIDKVQKTSAVKVEKVSTAETVKVEKTGSVSRSETVQV 153
             +G + +K              +D+ +K  A+  +    A   + E T S +    V  
Sbjct: 78  --DGPSTEKD-------------LDEKKKEPAITSQNSPEA---REESTSSGN----VSN 115

Query: 154 EKKETNGDSVMDRGEAVKVEKIIEEEKQAPSVRKPSQGTIATPKLTQLIKCNDSSRDKIR 213
            K ETN             +  +    +APS                    +DS R K R
Sbjct: 116 RKDETNAR-----------DTYVSSFPRAPST-------------------SDSVRLKCR 145

Query: 214 ELLANAL----SKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLKYRSI 269
           E+LA AL      +   ADEE            +   +E  +++++  +    K + RS 
Sbjct: 146 EMLAAALRTGDDYIAIGADEE-----------ELGSQIEEAIYQEIRNTDMKYKNRVRSR 194

Query: 270 MFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQRGGEA 329
           + N++D KNP+LRK VL G + P+    M+ EEMASDE +   +N+ ++A+ E Q     
Sbjct: 195 ISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDELKEMRKNLTKEAIREHQMAKTG 254

Query: 330 TATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC 376
              TD F C +C ++ CTY Q+QTRSADEPMTT+V C  C  RWKFC
Sbjct: 255 GTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWKFC 301
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|Q15560|TCEA2_HUMAN Transcription elongation factor A protein 2 OS=Homo sapiens GN=TCEA2 PE=1 SV=1 Back     alignment and function description
>sp|P23881|TCEA3_MOUSE Transcription elongation factor A protein 3 OS=Mus musculus GN=Tcea3 PE=1 SV=3 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|Q63799|TCEA2_RAT Transcription elongation factor A protein 2 OS=Rattus norvegicus GN=Tcea2 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|Q2KI09|TCEA3_BOVIN Transcription elongation factor A protein 3 OS=Bos taurus GN=TCEA3 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|P10711|TCEA1_MOUSE Transcription elongation factor A protein 1 OS=Mus musculus GN=Tcea1 PE=1 SV=2 Back     alignment and function description
>sp|Q29RL9|TCEA1_BOVIN Transcription elongation factor A protein 1 OS=Bos taurus GN=TCEA1 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 ?
Query376
224087871352 predicted protein [Populus trichocarpa] 0.936 1.0 0.659 1e-139
225439709367 PREDICTED: transcription elongation fact 0.954 0.978 0.653 1e-135
255575598342 transcription elongation factor s-II, pu 0.909 1.0 0.672 1e-135
224139382334 predicted protein [Populus trichocarpa] 0.888 1.0 0.643 1e-132
297735532322 unnamed protein product [Vitis vinifera] 0.856 1.0 0.619 1e-121
449441244369 PREDICTED: transcription elongation fact 0.954 0.972 0.601 1e-120
312283193381 unnamed protein product [Thellungiella h 0.992 0.979 0.588 1e-119
18377737378 putative elongation factor [Arabidopsis 0.978 0.973 0.585 1e-113
15224901378 transcript elongation factor IIS [Arabid 0.978 0.973 0.585 1e-113
388514187369 unknown [Medicago truncatula] 0.944 0.962 0.550 1e-111
>gi|224087871|ref|XP_002308256.1| predicted protein [Populus trichocarpa] gi|222854232|gb|EEE91779.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  499 bits (1286), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 248/376 (65%), Positives = 296/376 (78%), Gaps = 24/376 (6%)

Query: 1   MEQELVELFDAAKKAADSAAIDGVSSGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRL 60
           ME E VELFD AKKAAD++  D VSS GPEV+RCVD+LK+L+ F VT ++LVSTQVGK+L
Sbjct: 1   MEMEFVELFDEAKKAADASLNDDVSSSGPEVTRCVDSLKQLRKFKVTSELLVSTQVGKKL 60

Query: 61  RPLTKHPREKIQIVASNLLDIWKKIVIEETTRNKKNGSTGDKSSVTTGVVKPDSGKIDKV 120
           RPL KHP+EKI+ VAS+LL++WKK+VI+ET   KKNGS   KSSV   V K ++ K++K+
Sbjct: 61  RPLAKHPKEKIRAVASDLLEMWKKMVIDET--RKKNGSIDSKSSVKAEVSKSETVKVEKL 118

Query: 121 QKTSAVKVEKVSTAETVKVEKTGSVSRSETVQVEKKETNGDSVMDRGEAVKVEKIIEEEK 180
           +KTS VKVE+ ST+ETVKVEK                      MD+ + VKVEK+ ++E 
Sbjct: 119 RKTSVVKVERASTSETVKVEK----------------------MDQDKTVKVEKMSKQEI 156

Query: 181 QAPSVRKPSQGTIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEVNACDP 240
           Q  SV++PSQ  I  PKL  L+KCND+ RDKIRELLA ALSKV SEADE+I DEV ACDP
Sbjct: 157 QTSSVKQPSQSPIGPPKLKTLVKCNDALRDKIRELLAEALSKVASEADEDIRDEVEACDP 216

Query: 241 IRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSP 300
           IRVAVSVES+MFEKLGRS GA+KLKYRSIMFNI+D+ NPD R++VLLGEV PERLVTM P
Sbjct: 217 IRVAVSVESMMFEKLGRSNGAQKLKYRSIMFNIKDQNNPDFRRKVLLGEVQPERLVTMGP 276

Query: 301 EEMASDERQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPM 360
           EEMAS++R+R+   IKEK LF+C+R G+A ATTDQFKC RC QRKCTYYQMQTRSADEPM
Sbjct: 277 EEMASEQRKRENNQIKEKVLFDCERSGQAQATTDQFKCGRCRQRKCTYYQMQTRSADEPM 336

Query: 361 TTYVTCVNCSKRWKFC 376
           TTYVTCVNC+  WKFC
Sbjct: 337 TTYVTCVNCNNHWKFC 352

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225439709|ref|XP_002272768.1| PREDICTED: transcription elongation factor A protein 3 [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|224139382|ref|XP_002323085.1| predicted protein [Populus trichocarpa] gi|222867715|gb|EEF04846.1| 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|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|18377737|gb|AAL67018.1| putative elongation factor [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|15224901|ref|NP_181390.1| transcript elongation factor IIS [Arabidopsis thaliana] gi|3786016|gb|AAC67362.1| putative elongation factor [Arabidopsis thaliana] gi|23297820|gb|AAN13033.1| putative elongation factor [Arabidopsis thaliana] gi|26450199|dbj|BAC42218.1| putative elongation factor [Arabidopsis thaliana] gi|330254456|gb|AEC09550.1| transcript elongation factor IIS [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|388514187|gb|AFK45155.1| unknown [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 ?
Query376
TAIR|locus:2064195378 TFIIS "transcript elongation f 0.978 0.973 0.559 2.1e-107
ZFIN|ZDB-GENE-030131-8049309 tcea1 "transcription elongatio 0.438 0.533 0.412 1.2e-41
UNIPROTKB|Q15560299 TCEA2 "Transcription elongatio 0.494 0.622 0.376 4.6e-40
FB|FBgn0010422313 TfIIS "RNA polymerase II elong 0.430 0.517 0.412 4.6e-40
MGI|MGI:107368299 Tcea2 "transcription elongatio 0.492 0.618 0.393 5.8e-40
RGD|61825299 Tcea2 "transcription elongatio 0.492 0.618 0.383 9.4e-40
UNIPROTKB|Q63799299 Tcea2 "Transcription elongatio 0.492 0.618 0.383 9.4e-40
UNIPROTKB|Q148K0300 TCEA2 "Transcription elongatio 0.5 0.626 0.378 1.2e-39
UNIPROTKB|F1MIT2280 TCEA1 "Transcription elongatio 0.438 0.589 0.406 2.5e-39
UNIPROTKB|Q29RL9301 TCEA1 "Transcription elongatio 0.438 0.548 0.406 2.5e-39
TAIR|locus:2064195 TFIIS "transcript elongation factor IIS" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1062 (378.9 bits), Expect = 2.1e-107, P = 2.1e-107
 Identities = 216/386 (55%), Positives = 278/386 (72%)

Query:     1 MEQELVELFXXXXXXXXXXXIDGVSSGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRL 60
             ME +L++LF           +DGV+S GPEVS+C+DALK+LK FPVTYD LV+TQVGK+L
Sbjct:     1 MESDLIDLFEGAKKAADAAALDGVTSSGPEVSQCIDALKQLKKFPVTYDTLVATQVGKKL 60

Query:    61 RPLTKHPREKIQIVASNLLDIWKKIVIEETTRNKKN-GSTGDKSSVTTGVVKPDSGKIDK 119
             R L KHP E I+ VA++LL+IWKK+VIEET + KK  G+ G K +    V K D   ++K
Sbjct:    61 RSLAKHPVEDIKSVATDLLEIWKKVVIEETAKAKKTEGTNGCKEAK---VNKMD---VEK 114

Query:   120 VQKTSAVKVEKVS---TAETVKVEKTGSVSRSET-VQVEKKE-----TNGDSVMDRGEAX 170
                 + VKV+K+    +A+++KVE+    ++  T V++E+K      TNG  +  RG+A 
Sbjct:   115 PSNPAPVKVQKLQRGDSAKSIKVERKEPDNKVVTGVKIERKVPDIKVTNGTKIDYRGQAV 174

Query:   171 XXXXXXXXXXQAPSVRKPSQGTIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEE 230
                          S++ P++   A PKLT ++KCND  RDKIRELL  AL +V  EAD+ 
Sbjct:   175 KDEKVSKDNQS--SMKAPAKAANAPPKLTAMLKCNDPVRDKIRELLVEALCRVAGEADDY 232

Query:   231 IIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEV 290
               + VNA DP+RVAVSVES+MFEKLGRSTGA+KLKYRSIMFN+RD  NPDLR+RVL GE+
Sbjct:   233 ERESVNASDPLRVAVSVESLMFEKLGRSTGAQKLKYRSIMFNLRDSNNPDLRRRVLTGEI 292

Query:   291 TPERLVTMSPEEMASDERQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQ 350
             +PE+L+T+S E+MASD+R+++   IKEKALF+C+RG  A A+TDQFKC RCGQRKCTYYQ
Sbjct:   293 SPEKLITLSAEDMASDKRKQENNQIKEKALFDCERGLAAKASTDQFKCGRCGQRKCTYYQ 352

Query:   351 MQTRSADEPMTTYVTCVNCSKRWKFC 376
             MQTRSADEPMTTYVTCVNC   WKFC
Sbjct:   353 MQTRSADEPMTTYVTCVNCDNHWKFC 378
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
ZFIN|ZDB-GENE-030131-8049 tcea1 "transcription elongation factor A (SII), 1" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|Q15560 TCEA2 "Transcription elongation factor A protein 2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
FB|FBgn0010422 TfIIS "RNA polymerase II elongation factor" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
MGI|MGI:107368 Tcea2 "transcription elongation factor A (SII), 2" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|61825 Tcea2 "transcription elongation factor A (SII), 2" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q63799 Tcea2 "Transcription elongation factor A protein 2" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q148K0 TCEA2 "Transcription elongation factor A protein 2" [Bos taurus (taxid:9913)] 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

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) ?
P23881TCEA3_MOUSENo assigned EC number0.30450.83770.9077yesno

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

Fail to connect to STRING server

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 ?
Query376
TIGR01385299 TIGR01385, TFSII, transcription elongation factor 1e-90
pfam07500115 pfam07500, TFIIS_M, Transcription factor S-II (TFI 2e-41
smart00510102 smart00510, TFS2M, Domain in the central regions o 2e-31
pfam0109639 pfam01096, TFIIS_C, Transcription factor S-II (TFI 6e-19
smart0044040 smart00440, ZnF_C2C2, C2C2 Zinc finger 5e-18
smart0050975 smart00509, TFS2N, Domain in the N-terminus of tra 4e-17
cd0018376 cd00183, TFIIS_I, N-terminal domain (domain I) of 7e-16
COG1594113 COG1594, RPB9, DNA-directed RNA polymerase, subuni 9e-15
pfam0871151 pfam08711, Med26, TFIIS helical bundle-like domain 6e-09
TIGR01384104 TIGR01384, TFS_arch, transcription factor S, archa 3e-07
>gnl|CDD|233390 TIGR01385, TFSII, transcription elongation factor S-II Back     alignment and domain information 
 Score =  274 bits (702), Expect = 1e-90
 Identities = 129/365 (35%), Positives = 179/365 (49%), Gaps = 67/365 (18%)

Query: 12  AKKAADSAAIDGVSSGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPREKI 71
           A+ A+ + A+D   S    V +C+D L +LK FP T ++L  T+VG ++  L KHP E I
Sbjct: 2   AEVASHAKALDKNKSS-KNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDI 60

Query: 72  QIVASNLLDIWKKIVIEETTRNKKNGSTGDKSSVTTGVVKPDSGKIDKVQKTSAVKVEKV 131
             +A  ++  WKK+V +                              K         +K 
Sbjct: 61  SKLAKKIIKSWKKVVDKN-----------------------------KSDHPGGNPEDKT 91

Query: 132 STAETVKVEKTGSVSRSETVQVEKKETNGDSVMDRGEAVKVEKIIEEEKQAPSVRKPSQG 191
           +  E+V            +V+ E K              + +KI + +  + S R     
Sbjct: 92  TVGESVN-----------SVKQEAKS-------------QSDKIEQPKYVSSSPRN---- 123

Query: 192 TIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVM 251
             A          ND  RDK RELL +AL+K +            + DP   A+ +E + 
Sbjct: 124 --AKNDFVPTAVTNDKVRDKCRELLYDALAKDSDHP-------PQSIDPEAKAIQIEELK 174

Query: 252 FEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQ 311
           F  LG +  A K +YRSI  N+RD+ NPDLR  VL GE+TPE+L TM+ EEMAS E +++
Sbjct: 175 FNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQE 234

Query: 312 IENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSK 371
            E I ++ LFE Q      A TD F C +C Q+KCTYYQ+QTRSADEPMTT+VTC  C  
Sbjct: 235 REEITKENLFEAQGAKIQKAVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGN 294

Query: 372 RWKFC 376
           RWKFC
Sbjct: 295 RWKFC 299

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|128717 smart00440, ZnF_C2C2, C2C2 Zinc finger 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|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 376
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 99.93
smart0044040 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo 99.76
PF0109639 TFIIS_C: Transcription factor S-II (TFIIS); InterP 99.75
smart0050975 TFS2N Domain in the N-terminus of transcription el 99.73
KOG2906105 consensus RNA polymerase III subunit C11 [Transcri 99.68
COG1594113 RPB9 DNA-directed RNA polymerase, subunit M/Transc 99.67
TIGR01384104 TFS_arch transcription factor S, archaeal. There h 99.62
PHA02998195 RNA polymerase subunit; Provisional 99.62
cd0018376 TFIIS_I N-terminal domain (domain I) of transcript 99.59
KOG2691113 consensus RNA polymerase II subunit 9 [Transcripti 99.48
PF0871153 Med26: TFIIS helical bundle-like domain; InterPro: 99.37
KOG1634 778 consensus Predicted transcription factor DATF1, co 99.31
KOG2907116 consensus RNA polymerase I transcription factor TF 99.19
PF11467106 LEDGF: Lens epithelium-derived growth factor (LEDG 96.78
KOG2821433 consensus RNA polymerase II transcription elongati 96.31
KOG1793417 consensus Uncharacterized conserved protein [Funct 95.89
COG5139397 Uncharacterized conserved protein [Function unknow 94.88
PF0827430 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01 94.67
PF0985564 DUF2082: Nucleic-acid-binding protein containing Z 94.44
PF1371736 zinc_ribbon_4: zinc-ribbon domain 93.72
PRK0967872 DNA-binding transcriptional regulator; Provisional 93.54
TIGR0209838 MJ0042_CXXC MJ0042 family finger-like domain. This 93.16
PF1371937 zinc_ribbon_5: zinc-ribbon domain 93.05
PF1276046 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int 92.76
PF0460647 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I 92.43
COG347868 Predicted nucleic-acid-binding protein containing 91.09
PF0827143 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013 90.78
PHA0062659 hypothetical protein 90.35
COG4888104 Uncharacterized Zn ribbon-containing protein [Gene 89.58
PF1435461 Lar_restr_allev: Restriction alleviation protein L 89.45
PLN029761713 amine oxidase 89.04
PF1178136 RRN7: RNA polymerase I-specific transcription init 87.11
TIGR0365553 anti_R_Lar restriction alleviation protein, Lar fa 87.1
COG205167 RPS27A Ribosomal protein S27E [Translation, riboso 86.26
PF05876 557 Terminase_GpA: Phage terminase large subunit (GpA) 85.9
TIGR00373158 conserved hypothetical protein TIGR00373. This fam 85.75
TIGR0244359 conserved hypothetical metal-binding protein. Memb 85.41
PRK0971064 lar restriction alleviation and modification prote 85.36
PF04216290 FdhE: Protein involved in formate dehydrogenase fo 85.24
PF0512981 Elf1: Transcription elongation factor Elf1 like; I 84.93
smart00531147 TFIIE Transcription initiation factor IIE. 84.82
PF0952671 DUF2387: Probable metal-binding protein (DUF2387); 84.41
PRK06266178 transcription initiation factor E subunit alpha; V 83.73
smart0066152 RPOL9 RNA polymerase subunit 9. 83.11
PF1057126 UPF0547: Uncharacterised protein family UPF0547; I 82.36
PRK06266178 transcription initiation factor E subunit alpha; V 81.09
TIGR01562305 FdhE formate dehydrogenase accessory protein FdhE. 80.93
PF01873125 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: 80.73
>TIGR01385 TFSII transcription elongation factor S-II Back     alignment and domain information 
Probab=100.00  E-value=3.5e-70  Score=527.60  Aligned_cols=298  Identities=42%  Similarity=0.678  Sum_probs=233.7

Q ss_pred             HHHHHHHHHHHhHhhhcCCCCCCCCHHHHHHHHHHhcCCCCCHHhhhcCccceecccccCCCCHHHHHHHHHHHHHHHHH
Q 017145            6 VELFDAAKKAADSAAIDGVSSGGPEVSRCVDALKRLKSFPVTYDVLVSTQVGKRLRPLTKHPREKIQIVASNLLDIWKKI   85 (376)
Q Consensus         6 ~el~~~a~k~a~~~~~~~~~~~~~~~~~~l~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~I~~~Ak~Lv~~WK~~   85 (376)
                      .|+..+++.+.+++.       +.+++.||++|++|+.++||.++|++|+||++||+||||++++|+.+|+.||++||++
T Consensus         2 ~ei~~~~k~L~k~~~-------~~~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~   74 (299)
T TIGR01385         2 AEVASHAKALDKNKS-------SKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKV   74 (299)
T ss_pred             hHHHHHHHHhhhhcc-------CCCHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHH
Confidence            477888888777663       2467899999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhccCCCCCCCCCCCcccCccCCCCCCccccccccchhhcccccchhhhhhccCCCCCchhhhhhhcccCCCcccC
Q 017145           86 VIEETTRNKKNGSTGDKSSVTTGVVKPDSGKIDKVQKTSAVKVEKVSTAETVKVEKTGSVSRSETVQVEKKETNGDSVMD  165 (376)
Q Consensus        86 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (376)
                      |..++.++....+. ..+ .     .+.+.+   ..+.                +.+.                      
T Consensus        75 v~~~k~~~~~~~~~-~~~-~-----~~~~~~---~~~~----------------~~~~----------------------  106 (299)
T TIGR01385        75 VDKNKSDHPGGNPE-DKT-T-----VGESVN---SVKQ----------------EAKS----------------------  106 (299)
T ss_pred             HhhhcccCcccccc-ccc-c-----cCCCCC---CCCc----------------cccC----------------------
Confidence            98762221100000 000 0     000000   0000                0000                      


Q ss_pred             CCcchhhhHHHhhhhcCCCCCCCCCCCCCCCcccccccCCchhHHHHHHHHHHHHhhhhccChhhhhhhhcccChHHHHH
Q 017145          166 RGEAVKVEKIIEEEKQAPSVRKPSQGTIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAV  245 (376)
Q Consensus       166 ~~~~~~~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~~~~~~lA~  245 (376)
                        ++.+.++      +  .. .++......++..+++.++|++|++||++||+||.....+..       ..+++..+|.
T Consensus       107 --~~~~~~~------~--~~-~~~~~~~~~~~~~~~~~t~d~~Rdk~r~~L~~aL~~~~~~~~-------~~~~~~~lA~  168 (299)
T TIGR01385       107 --QSDKIEQ------P--KY-VSSSPRNAKNDFVPTAVTNDKVRDKCRELLYDALAKDSDHPP-------QSIDPEAKAI  168 (299)
T ss_pred             --CcccccC------C--CC-CCCcccccCCCCCCCccCCcHHHHHHHHHHHHHHhhcCCCCc-------cccCHHHHHH
Confidence              0000000      0  00 000011122334445679999999999999999996443221       2346678999


Q ss_pred             HHHHHHHHHhCCCchhhhHHHHHHHhhccCCCChhhhhchhcCCCChhhhccCChhhcCcHHHHHHHHHHHHHHHHHhhh
Q 017145          246 SVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQR  325 (376)
Q Consensus       246 ~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kN~~Lr~~vl~G~i~p~~l~~Ms~eEmas~e~k~~~~~~~ee~l~~~~~  325 (376)
                      +||.+||..|+.+++.|+++||+|+|||||++||+||++||+|+|+|++||.|+++||||++++++++++.+++|+++++
T Consensus       169 ~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e~~~ke~l~~~~~  248 (299)
T TIGR01385       169 QIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFEAQG  248 (299)
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999888999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCccccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccccC
Q 017145          326 GGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC  376 (376)
Q Consensus       326 ~~~~~~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkfc  376 (376)
                      +.....+++.|+|++||+++|+|||+|||+||||||+||+|.+|||+|+||
T Consensus       249 ~~~~~~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~fc  299 (299)
T TIGR01385       249 AKIQKAVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKFC  299 (299)
T ss_pred             hhhhcCCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeeeeC
Confidence            988888999999999999999999999999999999999999999999999

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
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription] Back     alignment and domain information
>KOG1793 consensus Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>COG5139 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
>PF13717 zinc_ribbon_4: zinc-ribbon domain Back     alignment and domain information
>PRK09678 DNA-binding transcriptional regulator; Provisional Back     alignment and domain information
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain Back     alignment and domain information
>PF13719 zinc_ribbon_5: zinc-ribbon domain 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
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr 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
>PHA00626 hypothetical protein Back     alignment and domain information
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only] Back     alignment and domain information
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar Back     alignment and domain information
>PLN02976 amine oxidase 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
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family Back     alignment and domain information
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis] 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
>TIGR00373 conserved hypothetical protein TIGR00373 Back     alignment and domain information
>TIGR02443 conserved hypothetical metal-binding protein Back     alignment and domain information
>PRK09710 lar restriction alleviation and modification protein; Reviewed 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
>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
>smart00531 TFIIE Transcription initiation factor IIE 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
>smart00661 RPOL9 RNA polymerase subunit 9 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
>PRK06266 transcription initiation factor E subunit alpha; Validated Back     alignment and domain information
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE 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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query376
1pqv_S309 Rna Polymerase Ii-Tfiis Complex Length = 309 4e-26
1y1v_S179 Refined Rna Polymerase Ii-tfiis Complex Length = 17 8e-26
3gtm_S173 Co-Complex Of Backtracked Rna Polymerase Ii With Tf 3e-25
3po3_S178 Arrested Rna Polymerase Ii Reactivation Intermediat 3e-24
2dme_A120 Solution Structure Of The Tfiis Domain Ii Of Human 8e-13
2lw4_A113 Solution Nmr Structure Of Human Transcription Elong 3e-12
1tfi_A50 A Novel Zn Finger Motif In The Basal Transcriptiona 2e-11
3qt1_I133 Rna Polymerase Ii Variant Containing A Chimeric Rpb 2e-09
3ndq_A108 Structure Of Human Tfiis Domain Ii Length = 108 8e-09
1qyp_A57 Thermococcus Celer Rpb9, Nmr, 25 Structures Length 6e-05
1enw_A114 Elongation Factor Tfiis Domain Ii Length = 114 7e-04
>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex Length = 309 Back     alignment and structure 
Iteration: 1

 Score =  115 bits (288), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 58/169 (34%), Positives = 95/169 (56%), Gaps = 11/169 (6%)
Query: 209 RDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVM--FEKLGRSTGAEKLKY 266
           RD++ + L + L+K +    + I+           A ++ES M        +  A K +Y
Sbjct: 149 RDQVLKALYDVLAKESEHPPQSIL---------HTAKAIESEMNKVNNCDTNEAAYKARY 199
Query: 267 RSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQRG 326
           R I  N+  + NPDL+ ++  G++TPE L T   +++A    +++IE I ++ L+  Q  
Sbjct: 200 RIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNAQGA 259
Query: 327 GEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375
               + TD+F C +C ++K +YYQ+QTRSADEP+TT+ TC  C  RWKF
Sbjct: 260 TIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWKF 308
>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|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|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|3QT1|I Chain I, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11 Subunit Length = 133 Back     alignment and structure
>pdb|3NDQ|A Chain A, Structure Of Human Tfiis Domain Ii Length = 108 Back     alignment and structure
>pdb|1QYP|A Chain A, Thermococcus Celer Rpb9, Nmr, 25 Structures Length = 57 Back     alignment and structure
>pdb|1ENW|A Chain A, Elongation Factor Tfiis Domain Ii Length = 114 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 ?
Query376
1pqv_S309 STP-alpha, transcription elongation factor S-II, D 4e-50
3po3_S178 Transcription elongation factor S-II; RNA polymera 3e-48
2dme_A120 PHD finger protein 3; PHF3, TFS2M, glioblastoma mu 2e-29
3ndq_A108 Transcription elongation factor A protein 1; helix 3e-29
1tfi_A50 Transcriptional elongation factor SII; transcripti 2e-25
1qyp_A57 RNA polymerase II; transcription, RPB9, Zn ribbon, 2e-20
3h0g_I113 DNA-directed RNA polymerases I, II, and III subuni 6e-19
3qt1_I133 DNA-directed RNA polymerases I, II, and III subun; 6e-18
1twf_I122 B12.6, DNA-directed RNA polymerase II 14.2 kDa pol 4e-15
1wjt_A103 Transcription elongation factor S-II protein 3; fo 1e-08
2xpp_A145 IWS1, ECU08_0440; transcription, elongation, histo 6e-05
>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 =  169 bits (428), Expect = 4e-50
 Identities = 75/376 (19%), Positives = 141/376 (37%), Gaps = 69/376 (18%)

Query: 1   MEQELVELFDAAKKAADSAAIDGVSSGGPEVSRCVDALKRL-KSFPVTYDVLVSTQVGKR 59
           M+ +  E+    K    + +           +  ++ L  L K F  T  +L  T+VG  
Sbjct: 1   MDSK--EVLVHVKNLEKNKS---------NDAAVLEILHVLDKEFVPTEKLLRETKVGVE 49

Query: 60  LRPLTKHPREKIQIVASNLLDIWKKIVIEETTRNKKNGSTGDKSSVTTGVVKPDSGKIDK 119
           +    K    +I  +   ++  WK  + +     +      D +             ++ 
Sbjct: 50  VNKFKKSTNVEISKLVKKMISSWKDAINKNKRSRQAQQHHQDHAPGNAEDKTTVGESVNG 109

Query: 120 VQKTSAVKVEKVSTAETVKVEKTGSVSRSETVQVEKKETNGDSVMDRGEAVKVEKIIEEE 179
           VQ+ ++ +                                                   +
Sbjct: 110 VQQPASSQ--------------------------------------------------SD 119

Query: 180 KQAPSVRKPSQGTIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEVNACD 239
                    ++   +          +   RD++ + L + L+K +    + I+       
Sbjct: 120 AMKQDKYVSTKPRNSKNDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQSILHTA---- 175

Query: 240 PIRVAVSVESVMFEKLGRSTGAEKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMS 299
               A+  E         +  A K +YR I  N+  + NPDL+ ++  G++TPE L T  
Sbjct: 176 ---KAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCD 232

Query: 300 PEEMASDERQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEP 359
            +++A    +++IE I ++ L+  Q      + TD+F C +C ++K +YYQ+QTRSADEP
Sbjct: 233 AKDLAPAPLKQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEP 292

Query: 360 MTTYVTCVNCSKRWKF 375
           +TT+ TC  C  RWKF
Sbjct: 293 LTTFCTCEACGNRWKF 308
>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
>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 ?
Query376
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 99.95
2dme_A120 PHD finger protein 3; PHF3, TFS2M, glioblastoma mu 99.94
1tfi_A50 Transcriptional elongation factor SII; transcripti 99.85
1wjt_A103 Transcription elongation factor S-II protein 3; fo 99.73
1qyp_A57 RNA polymerase II; transcription, RPB9, Zn ribbon, 99.69
3h0g_I113 DNA-directed RNA polymerases I, II, and III subuni 99.66
1twf_I122 B12.6, DNA-directed RNA polymerase II 14.2 kDa pol 99.63
3qt1_I133 DNA-directed RNA polymerases I, II, and III subun; 99.62
2xpp_A145 IWS1, ECU08_0440; transcription, elongation, histo 97.61
3nfq_A170 Transcription factor IWS1; SPN1, RNA polymerase II 97.42
2b4j_C98 PC4 and SFRS1 interacting protein; HIV, integratio 96.91
1z9e_A127 PC4 and SFRS1 interacting protein 2; heat repeat-l 96.79
1k81_A36 EIF-2-beta, probable translation initiation factor 92.65
2akl_A138 PHNA-like protein PA0128; two domains, Zn binding 88.53
2fiy_A309 Protein FDHE homolog; FDHE protein, structural gen 87.55
1wii_A85 Hypothetical UPF0222 protein MGC4549; domain of un 80.99
1vq8_Z83 50S ribosomal protein L37AE; ribosome 50S, protein 80.61
>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=5.7e-66  Score=502.14  Aligned_cols=302  Identities=25%  Similarity=0.427  Sum_probs=225.8

Q ss_pred             hhHHHHHHHHHHHHHhHhhhcCCCCCCCCHHHHHHHHHHh-cCCCCCHHhhhcCccceecccccCCCCHHHHHHHHHHHH
Q 017145            2 EQELVELFDAAKKAADSAAIDGVSSGGPEVSRCVDALKRL-KSFPVTYDVLVSTQVGKRLRPLTKHPREKIQIVASNLLD   80 (376)
Q Consensus         2 e~e~~el~~~a~k~a~~~~~~~~~~~~~~~~~~l~~L~~L-~~~~it~~~L~~T~iG~~V~~Lrkh~~~~I~~~Ak~Lv~   80 (376)
                      |+|++++++...+   ..         .+.+.++++|++| +.++||.++|++|+||++||+||||++++|+.+|+.||+
T Consensus         3 ~~el~~~~~~L~k---~~---------~~~~~~l~~L~~L~~~~~it~~~L~~T~IG~~Vn~lrkh~~~~v~~~Ak~Li~   70 (309)
T 1pqv_S            3 SKEVLVHVKNLEK---NK---------SNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMIS   70 (309)
T ss_pred             HHHHHHHHHHHhc---cC---------CCHHHHHHHHHHHHhcCCCCHHHHHhCChhHHHHHHHcCCCHHHHHHHHHHHH
Confidence            4556665555544   11         2578999999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhhccCCCCCCCCCCCcccCccCCCCCCccccccccchhhcccccchhhhhhccCCCCCchhhhhhhcccCC
Q 017145           81 IWKKIVIEETTRNKKNGSTGDKSSVTTGVVKPDSGKIDKVQKTSAVKVEKVSTAETVKVEKTGSVSRSETVQVEKKETNG  160 (376)
Q Consensus        81 ~WK~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (376)
                      +||++|..+..++.+.+.. +.  ..+. ...+.++   +...+...    +.         +   . .+    .     
T Consensus        71 ~WK~~v~~~~~~~~~~~~~-~~--~~~~-~~~~~~~---~~~~~~~~----~~---------~---~-~~----~-----  117 (309)
T 1pqv_S           71 SWKDAINKNKRSRQAQQHH-QD--HAPG-NAEDKTT---VGESVNGV----QQ---------P---A-SS----Q-----  117 (309)
T ss_pred             HHHHHHHHhccCCcccccc-cc--cccc-cccCCCC---CCCCcCCC----CC---------C---c-cc----c-----
Confidence            9999998775433211100 00  0000 0000000   00000000    00         0   0 00    0     


Q ss_pred             CcccCCCcchhhhHHHhhhhcCCCCCCCCCCCCCCCcccc--cccCCchhHHHHHHHHHHHHhhhhccChhhhhhhhccc
Q 017145          161 DSVMDRGEAVKVEKIIEEEKQAPSVRKPSQGTIATPKLTQ--LIKCNDSSRDKIRELLANALSKVTSEADEEIIDEVNAC  238 (376)
Q Consensus       161 ~~~~~~~~~~~~e~~~~~~~~~~~~~~~s~~~~~~~~~~~--~~~~~d~vR~k~r~~L~~aL~~~~~~~~~~~~~~~~~~  238 (376)
                           .+             +..+...+++. ..++....  .+.++|.+|++||++|+++|.....+.+.         
T Consensus       118 -----~~-------------~~~~~~~~~~~-~~~~~~~~~~~~~~~d~~R~k~r~~L~~aL~~~~~~~~~---------  169 (309)
T 1pqv_S          118 -----SD-------------AMKQDKYVSTK-PRNSKNDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQ---------  169 (309)
T ss_pred             -----cc-------------cccCCCCCCCC-CCCCCCCCCCcCcCChHHHHHHHHHHHHHHhcCCCccch---------
Confidence                 00             00000000000 01111122  33678999999999999999864322211         


Q ss_pred             ChHHHHHHHHHHHHHHhCCCchh--hhHHHHHHHhhccCCCChhhhhchhcCCCChhhhccCChhhcCcHHHHHHHHHHH
Q 017145          239 DPIRVAVSVESVMFEKLGRSTGA--EKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIK  316 (376)
Q Consensus       239 ~~~~lA~~IE~alf~~~~~~~~~--Yk~k~Rsl~~NLkd~kN~~Lr~~vl~G~i~p~~l~~Ms~eEmas~e~k~~~~~~~  316 (376)
                      ++..+|.+||.+||+.|++++..  |+++||+|+|||||++||+||++||.|+|+|.+||.|+++||||+|++++++++.
T Consensus       170 ~~~~~A~~IE~al~~~~~~~~~~~~Yk~k~Rsl~~NLKd~~N~~Lr~~vl~g~i~p~~lv~Ms~eElasde~k~~~~~~~  249 (309)
T 1pqv_S          170 SILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIA  249 (309)
T ss_pred             hHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHcCcCCChHHHHHHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHH
Confidence            45689999999999999887777  9999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhcCCCccccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccccC
Q 017145          317 EKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC  376 (376)
Q Consensus       317 ee~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkfc  376 (376)
                      +++|++++++..+..+++.+.||+||+++|+|||+|+||||||||+||+|++|||+|+||
T Consensus       250 ~e~l~~~~~~~~~~~~~~~~~C~~C~~~~~~~~q~Q~rsaDe~~t~f~~C~~Cg~~w~fc  309 (309)
T 1pqv_S          250 KQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWKFS  309 (309)
T ss_pred             HHHHHHhhhccccccCcccccCCCCCCCeeEEEEeecccCCCCCcEEEEeCCCCCceecC
Confidence            999999999888888888999999999999999999999999999999999999999999
>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
>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
>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
>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
>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
>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

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 376
d1enwa_114 a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Bak 2e-25
d1tfia_50 g.41.3.1 (A:) Transcriptional factor SII, C-termin 4e-24
d1qypa_57 g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {A 2e-19
d1twfi272 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase 4e-17
d1wjta_103 a.48.3.1 (A:) Transcription elongation factor S-II 4e-11
d1eo0a_77 a.48.3.1 (A:) Transcription elongation factor TFII 7e-11
>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

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]

 Score = 97.2 bits (242), Expect = 2e-25
 Identities = 27/102 (26%), Positives = 50/102 (49%), Gaps = 11/102 (10%)

Query: 205 NDSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAE-- 262
           +   RD++ + L + L+K +    + I+           A ++ES M +     T     
Sbjct: 19  HHKLRDQVLKALYDVLAKESEHPPQSILH---------TAKAIESEMNKVNNCDTNEAAY 69

Query: 263 KLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMA 304
           K +YR I  N+  + NPDL+ ++  G++TPE L T   +++A
Sbjct: 70  KARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 111
>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 50 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
>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
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query376
d1tfia_50 Transcriptional factor SII, C-terminal domain {Hum 99.88
d1enwa_114 Elongation factor TFIIS domain 2 {Baker's yeast (S 99.86
d1twfi272 RBP9 subunit of RNA polymerase II {Baker's yeast ( 99.79
d1qypa_57 RBP9 subunit of RNA polymerase II {Archaeon Thermo 99.79
d1eo0a_77 Transcription elongation factor TFIIS N-domain {Ba 99.64
d1wjta_103 Transcription elongation factor S-II protein 3 {Mo 99.59
d2b4jc181 PC4 and SFRS1-interacting protein, PSIP1 {Human (H 97.82
d2akla238 Hypothetical protein PA0128, N-terminal domain {Ps 93.89
d2fiya1290 FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId 88.32
d1k81a_36 Zinc-binding domain of translation initiation fact 84.12
>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-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: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=8.3e-24  Score=148.49  Aligned_cols=48  Identities=58%  Similarity=1.239  Sum_probs=45.8

Q ss_pred             CccccccccccccCCcceEEEEEeccCCCCCCeEEEEcCCCCCccccC
Q 017145          329 ATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC  376 (376)
Q Consensus       329 ~~~~t~~~~C~~C~~~~~~~~q~qtrsaDEpmt~f~~C~~C~~~Wkfc  376 (376)
                      .+++|+.|+||+||++++.|+|+|+||||||||+||.|.+|||+||||
T Consensus         3 ~g~~T~~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~Cg~~Wr~c   50 (50)
T d1tfia_           3 GGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWKFC   50 (50)
T ss_dssp             SCEECCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEECC
T ss_pred             CCcccCCEECCCCCCCccEEEEEEccCCCCCceEEEEccccCCeeecC
Confidence            346789999999999999999999999999999999999999999999
>d1enwa_ a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]} 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
>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