Citrus Sinensis ID: 020974

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-------32
MEKKVMDLCEAAKRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCWDVEDVEYVAVTKKAKLVENVKVEEVTNGEERRHDSGNVPKKSISCMIKCNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTNLSFGVLPI
cHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHcccccHHHHcccccEEEcccccccccHHHHHHHHHHHHHcccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccHHHHHHHHcccccHHHHHHHHHHHHHHHHcccccccHHHHHHHccccccccHHHHHHHHccccccHHHHcccHHHcccHHHHHHHHHHccccHHcccccccccccccccccccccccccccccEEEEEEEEccccccEEEEEEccccccccccccccccccc
cHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccHHHHHHccccHEHHHHcccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccccHHHHHHHccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccHHHHHHcccccHHHHHHccHHHHccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccEEEccccccccEEEEEEEccccccccEEEEEccccccccccEccccEccc
MEKKVMDLCEAAKRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLlpmlkhpsqKIQKLAYDLISSWRDMCWDVEDVEYVAVTKKAKLVENVkveevtngeerrhdsgnvpkksisCMIKCNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWcrsngmykfkYRCLLfnisdpenqdFRRKVLlghvkpetIINMSAKEMASDKIQLWNHhldkdgalvtghifpvglsrKIIVSDiyecgrcghnkisyqhssilddynltrhvtclncnqywvstnlsfgvlpi
MEKKVMDLCEAAKRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLLpmlkhpsqKIQKLAYDLISSWRDMCWDVEDVEYVAvtkkaklvenvkveevtngeerrhdsgnvpkksiscMIKCNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYwvstnlsfgvlpi
MEKKVMDLCEaakraavaavWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCWDVEDVEYVAVTKKAKLVENVKVEEVTNGEERRHDSGNVPKKSISCMIKCNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTNLSFGVLPI
******DLCEAAKRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCWDVEDVEYVAVTKKAKLVENVKV********************ISCMIKCNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTNLSFGVL**
******D**************************ALDQIKNSSITYQLLVSTQV*************************************************************RRHDSGNVPKKSISCMIKCNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDK**************************GRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTNLSFGVLPI
MEKKVMDLCEAAKRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCWDVEDVEYVAVTKKAKLVENVKVEEVTNGEERRHDSGNVPKKSISCMIKCNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTNLSFGVLPI
**KKVMDLCEAAKRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCWD*******************************************CMIKCNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTGHIFPVG****IIVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTNLSFGVLPI
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MEKKVMDLCEAAKRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCWDVEDVEYVAVTKKAKLVENVKVEEVTNGEERRHDSGNVPKKSISCMIKCNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISYQHSSILDDYNLTRHVTCLNCNQYWVSTNLSFGVLPI
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 ?
Query319 2.2.26 [Sep-21-2011]
P23193301 Transcription elongation yes no 0.833 0.883 0.255 5e-16
P10711301 Transcription elongation yes no 0.833 0.883 0.255 2e-15
Q4KLL0301 Transcription elongation yes no 0.833 0.883 0.255 3e-15
Q29RL9301 Transcription elongation yes no 0.833 0.883 0.251 3e-15
Q148K0300 Transcription elongation no no 0.805 0.856 0.259 9e-14
Q15560299 Transcription elongation no no 0.805 0.859 0.246 9e-14
Q9QVN7299 Transcription elongation no no 0.805 0.859 0.249 4e-12
P52652308 Putative transcription el yes no 0.420 0.435 0.307 4e-12
Q63799299 Transcription elongation no no 0.805 0.859 0.249 6e-12
Q92576 2039 PHD finger protein 3 OS=H no no 0.291 0.045 0.339 5e-10
>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 = 85.5 bits (210), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 74/290 (25%), Positives = 136/290 (46%), Gaps = 24/290 (8%)

Query: 29  ARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPS-QKIQKLAYDLISSWRDMCWDVE 87
           A  +D L ++KN  +T +LL ST++   +  + K  + +++  LA  LI SW+ +     
Sbjct: 22  AGALDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDEEVTSLAKSLIKSWKKLLDGPS 81

Query: 88  DVEYVAVTKKAKLVEN-----VKVEEVTNGE-ERRHDSGNVPKKSISCMIKC---NDSFR 138
             + +   KK   + +      + E  ++G    R D  N     +S   +    +DS R
Sbjct: 82  TEKDLDEKKKEPAITSQNSPEAREESTSSGNVSNRKDETNARDTYVSSFPRAPSTSDSVR 141

Query: 139 EIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRC 198
              RE L  AL +  D   D + I      D  ++   +E A+Y++   ++  YK + R 
Sbjct: 142 LKCREMLAAAL-RTGD---DYIAI----GADEEELGSQIEEAIYQEIRNTDMKYKNRVRS 193

Query: 199 LLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTGHIFP 258
            + N+ D +N + R+ VL G++ P+    M+A+EMASD+++    +L K+ A+    +  
Sbjct: 194 RISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDELKEMRKNLTKE-AIREHQMAK 252

Query: 259 VGLSRKIIVSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYW 307
            G ++    +D++ CG+C     +Y Q  +   D  +T  V C  C   W
Sbjct: 253 TGGTQ----TDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRW 298
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|P10711|TCEA1_MOUSE Transcription elongation factor A protein 1 OS=Mus musculus GN=Tcea1 PE=1 SV=2 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|Q29RL9|TCEA1_BOVIN Transcription elongation factor A protein 1 OS=Bos taurus GN=TCEA1 PE=2 SV=1 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|Q15560|TCEA2_HUMAN Transcription elongation factor A protein 2 OS=Homo sapiens GN=TCEA2 PE=1 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|P52652|TFS2_CAEEL Putative transcription elongation factor S-II OS=Caenorhabditis elegans GN=T24H10.1 PE=3 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|Q92576|PHF3_HUMAN PHD finger protein 3 OS=Homo sapiens GN=PHF3 PE=1 SV=3 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 ?
Query319
297735532322 unnamed protein product [Vitis vinifera] 0.855 0.847 0.432 7e-56
225439709367 PREDICTED: transcription elongation fact 0.858 0.746 0.388 4e-53
224139382334 predicted protein [Populus trichocarpa] 0.937 0.895 0.383 5e-53
255559741330 transcription elongation factor s-II, pu 0.924 0.893 0.404 7e-53
116789178331 unknown [Picea sitchensis] 0.862 0.830 0.405 1e-51
224286619328 unknown [Picea sitchensis] 0.927 0.902 0.384 2e-51
388514187369 unknown [Medicago truncatula] 0.927 0.802 0.364 4e-51
224087871352 predicted protein [Populus trichocarpa] 0.937 0.849 0.375 7e-51
255575598342 transcription elongation factor s-II, pu 0.862 0.804 0.382 1e-50
255637690368 unknown [Glycine max] 0.940 0.815 0.362 1e-48
>gi|297735532|emb|CBI18026.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  223 bits (569), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 129/298 (43%), Positives = 174/298 (58%), Gaps = 25/298 (8%)

Query: 27  EEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCWDV 86
           E  RC+DAL Q+K+  +TY+ L STQV + L  + KHP  KIQ LA DL+  W+ +  D 
Sbjct: 30  EVGRCVDALKQLKSFPVTYEALASTQVGKRLRHLTKHPKGKIQSLASDLLEMWKKVVIDE 89

Query: 87  E--------DVEYVAVTKKAKLVENVKVEEVTNGEERRH--------DSGNVPKKSISCM 130
                    D    A  +KA  VE V+ + V N +ER+          + N P K ++ M
Sbjct: 90  TRNKKNGGLDNNGSAKAEKASKVETVE-KRVENVDERKQFSSVKKPPQASNGPPK-LTAM 147

Query: 131 IKCNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNG 190
           IKCND+ R+ VRE L +AL KV+ EA + +  D V ACDPI+VA+ VES M+EK  RSNG
Sbjct: 148 IKCNDALRDKVRELLAEALFKVASEADEDIK-DEVNACDPIRVAVSVESVMFEKMGRSNG 206

Query: 191 MYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGA 250
             KFKYR ++FNI DP N D RRKVLLG VKP+ +INMS +EMAS++ Q  N  + +   
Sbjct: 207 TQKFKYRSIMFNIKDPNNPDLRRKVLLGEVKPDRLINMSPEEMASNQRQRENSQIKEKAL 266

Query: 251 LVTGHIFPVGLSRKIIVSDIYECGRCGHNKIS-YQHSSILDDYNLTRHVTCLNCNQYW 307
                  P   +     +D ++CGRCG  K + YQ  +   D  +T  VTC+NCN +W
Sbjct: 267 FDCERGGPPKAT-----TDQFKCGRCGQRKTTYYQLQTRSADEPMTTFVTCVNCNNHW 319

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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|224139382|ref|XP_002323085.1| predicted protein [Populus trichocarpa] gi|222867715|gb|EEF04846.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|255559741|ref|XP_002520890.1| transcription elongation factor s-II, putative [Ricinus communis] gi|223540021|gb|EEF41599.1| transcription elongation factor s-II, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|116789178|gb|ABK25146.1| unknown [Picea sitchensis] 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|224087871|ref|XP_002308256.1| predicted protein [Populus trichocarpa] gi|222854232|gb|EEE91779.1| predicted protein [Populus trichocarpa] 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|255637690|gb|ACU19168.1| unknown [Glycine max] 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 ?
Query319
TAIR|locus:2064195378 TFIIS "transcript elongation f 0.673 0.568 0.387 1.3e-34
TAIR|locus:2124097266 AT4G18720 [Arabidopsis thalian 0.391 0.469 0.417 1.4e-22
TAIR|locus:2052351737 AT2G42730 [Arabidopsis thalian 0.404 0.175 0.453 1.5e-22
ZFIN|ZDB-GENE-030131-8049309 tcea1 "transcription elongatio 0.833 0.860 0.274 7.2e-20
UNIPROTKB|P23193301 TCEA1 "Transcription elongatio 0.833 0.883 0.258 1.1e-18
UNIPROTKB|F1RSG8300 TCEA1 "Uncharacterized protein 0.840 0.893 0.257 1.4e-18
UNIPROTKB|F1MIT2280 TCEA1 "Transcription elongatio 0.830 0.946 0.264 1.7e-18
UNIPROTKB|Q29RL9301 TCEA1 "Transcription elongatio 0.830 0.880 0.264 1.7e-18
UNIPROTKB|E2QVN6301 TCEA1 "Uncharacterized protein 0.830 0.880 0.268 2.8e-18
MGI|MGI:1196624301 Tcea1 "transcription elongatio 0.833 0.883 0.255 1.1e-17
TAIR|locus:2064195 TFIIS "transcript elongation factor IIS" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 375 (137.1 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 88/227 (38%), Positives = 134/227 (59%)

Query:    86 VEDVEYVAVTK---KAKLVENVKVEEVTNGEERRH-DSGNVPKKSISCMIKCNDSFREIV 141
             V D++    TK   + + V++ KV +      +    + N P K ++ M+KCND  R+ +
Sbjct:   156 VPDIKVTNGTKIDYRGQAVKDEKVSKDNQSSMKAPAKAANAPPK-LTAMLKCNDPVRDKI 214

Query:   142 REKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLF 201
             RE L +AL +V+ EA D    + V A DP++VA+ VES M+EK  RS G  K KYR ++F
Sbjct:   215 RELLVEALCRVAGEA-DDYERESVNASDPLRVAVSVESLMFEKLGRSTGAQKLKYRSIMF 273

Query:   202 NISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTGHIFPVGL 261
             N+ D  N D RR+VL G + PE +I +SA++MASDK +  N+ + K+ AL        GL
Sbjct:   274 NLRDSNNPDLRRRVLTGEISPEKLITLSAEDMASDKRKQENNQI-KEKALFDCER---GL 329

Query:   262 SRKIIVSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYW 307
             + K   +D ++CGRCG  K +Y Q  +   D  +T +VTC+NC+ +W
Sbjct:   330 AAKAS-TDQFKCGRCGQRKCTYYQMQTRSADEPMTTYVTCVNCDNHW 375
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
TAIR|locus:2124097 AT4G18720 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2052351 AT2G42730 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-8049 tcea1 "transcription elongation factor A (SII), 1" [Danio rerio (taxid:7955)] 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
UNIPROTKB|F1RSG8 TCEA1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] 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
UNIPROTKB|E2QVN6 TCEA1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] 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

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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:
GSVIVG00029469001
SubName- Full=Chromosome chr13 scaffold_48, whole genome shotgun sequence; (309 aa)
(Vitis vinifera)
Predicted Functional Partners:
GSVIVG00033123001
SubName- Full=Putative uncharacterized protein (Chromosome chr5 scaffold_64, whole genome shotg [...] (114 aa)
   •••• 0.725
GSVIVG00002607001
SubName- Full=Chromosome undetermined scaffold_133, whole genome shotgun sequence; (114 aa)
   •••• 0.560
GSVIVG00036639001
SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (318 aa)
   •••  0.548
GSVIVG00032808001
SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (116 aa)
    ••  0.547
GSVIVG00002744001
SubName- Full=Chromosome chr1 scaffold_135, whole genome shotgun sequence; (78 aa)
    ••• 0.546
GSVIVG00015507001
RecName- Full=DNA-directed RNA polymerase; EC=2.7.7.6; (1010 aa)
    ••• 0.493
GSVIVG00016705001
SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (206 aa)
    ••  0.459
GSVIVG00024229001
SubName- Full=Putative uncharacterized protein (Chromosome chr6 scaffold_3, whole genome shotgu [...] (176 aa)
    ••• 0.436
GSVIVG00018575001
RecName- Full=DNA-directed RNA polymerase; EC=2.7.7.6; (1220 aa)
    ••  0.428
GSVIVG00018833001
SubName- Full=Chromosome chr12 scaffold_18, whole genome shotgun sequence; (141 aa)
    ••• 0.412

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 ?
Query319
TIGR01385299 TIGR01385, TFSII, transcription elongation factor 2e-43
smart00510102 smart00510, TFS2M, Domain in the central regions o 7e-27
pfam07500115 pfam07500, TFIIS_M, Transcription factor S-II (TFI 5e-26
cd0018376 cd00183, TFIIS_I, N-terminal domain (domain I) of 2e-09
smart0050975 smart00509, TFS2N, Domain in the N-terminus of tra 2e-07
pfam0871151 pfam08711, Med26, TFIIS helical bundle-like domain 2e-04
>gnl|CDD|233390 TIGR01385, TFSII, transcription elongation factor S-II Back     alignment and domain information 
 Score =  150 bits (381), Expect = 2e-43
 Identities = 85/317 (26%), Positives = 134/317 (42%), Gaps = 42/317 (13%)

Query: 11  AAKRAAVAAVWKEGVV---EEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQK 67
           A   +   A+  +         +C+D L Q+K    T +LL  T+V   +  + KHP++ 
Sbjct: 2   AEVASHAKAL--DKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNED 59

Query: 68  IQKLAYDLISSWRDMCWDVEDVEYVAVTKKAKL-----VENVKVEEVTNGEERRHDSGNV 122
           I KLA  +I SW+ +  D    ++     + K      V +VK E  +  ++        
Sbjct: 60  ISKLAKKIIKSWKKVV-DKNKSDHPGGNPEDKTTVGESVNSVKQEAKSQSDKIEQPKYVS 118

Query: 123 P-----KKSISCMIKCNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILV 177
                 K         ND  R+  RE LYDAL+K SD           ++ DP   AI +
Sbjct: 119 SSPRNAKNDFVPTAVTNDKVRDKCRELLYDALAKDSDHPP--------QSIDPEAKAIQI 170

Query: 178 ESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDK 237
           E   +     +   YK +YR +  N+ D  N D R  VL G + PE +  M+A+EMAS +
Sbjct: 171 EELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAE 230

Query: 238 IQLWNHHLDKD------GALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISY-QHSSILD 290
           ++     + K+      GA +              V+D++ CG+C   K +Y Q  +   
Sbjct: 231 LKQEREEITKENLFEAQGAKIQK-----------AVTDLFTCGKCKQKKCTYYQLQTRSA 279

Query: 291 DYNLTRHVTCLNCNQYW 307
           D  +T  VTC  C   W
Sbjct: 280 DEPMTTFVTCEECGNRW 296

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|128786 smart00510, TFS2M, Domain in the central regions of transcription elongation factor S-II (and elsewhere) Back     alignment and domain information
>gnl|CDD|219433 pfam07500, TFIIS_M, Transcription factor S-II (TFIIS), central domain 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|197766 smart00509, TFS2N, Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) Back     alignment and domain information
>gnl|CDD|204037 pfam08711, Med26, TFIIS helical bundle-like domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 319
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 99.75
PF0109639 TFIIS_C: Transcription factor S-II (TFIIS); InterP 99.73
smart0050975 TFS2N Domain in the N-terminus of transcription el 99.69
KOG2906105 consensus RNA polymerase III subunit C11 [Transcri 99.67
COG1594113 RPB9 DNA-directed RNA polymerase, subunit M/Transc 99.6
cd0018376 TFIIS_I N-terminal domain (domain I) of transcript 99.59
PHA02998195 RNA polymerase subunit; Provisional 99.55
TIGR01384104 TFS_arch transcription factor S, archaeal. There h 99.55
PF0871153 Med26: TFIIS helical bundle-like domain; InterPro: 99.38
KOG1634 778 consensus Predicted transcription factor DATF1, co 99.34
KOG2691113 consensus RNA polymerase II subunit 9 [Transcripti 99.31
KOG2907116 consensus RNA polymerase I transcription factor TF 99.2
KOG2821 433 consensus RNA polymerase II transcription elongati 96.89
PF11467106 LEDGF: Lens epithelium-derived growth factor (LEDG 96.78
KOG1793417 consensus Uncharacterized conserved protein [Funct 95.92
PF0985564 DUF2082: Nucleic-acid-binding protein containing Z 95.45
PRK0967872 DNA-binding transcriptional regulator; Provisional 95.09
PF0460647 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I 94.8
COG5139397 Uncharacterized conserved protein [Function unknow 94.2
PF1371736 zinc_ribbon_4: zinc-ribbon domain 94.03
PF0827430 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01 93.1
TIGR0209838 MJ0042_CXXC MJ0042 family finger-like domain. This 92.89
COG347868 Predicted nucleic-acid-binding protein containing 92.85
TIGR00686109 phnA alkylphosphonate utilization operon protein P 92.45
PF1276046 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int 92.34
PF1371937 zinc_ribbon_5: zinc-ribbon domain 91.97
PHA0062659 hypothetical protein 91.62
PRK10220111 hypothetical protein; Provisional 91.29
COG4888104 Uncharacterized Zn ribbon-containing protein [Gene 91.09
PF0827143 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013 90.4
COG205167 RPS27A Ribosomal protein S27E [Translation, riboso 89.86
TIGR00244147 transcriptional regulator NrdR. Members of this al 89.19
PF0512981 Elf1: Transcription elongation factor Elf1 like; I 88.65
PF1435461 Lar_restr_allev: Restriction alleviation protein L 88.16
TIGR0244359 conserved hypothetical metal-binding protein. Memb 88.01
PF1179243 Baculo_LEF5_C: Baculoviridae late expression facto 87.88
TIGR0365553 anti_R_Lar restriction alleviation protein, Lar fa 87.37
COG4332 203 Uncharacterized protein conserved in bacteria [Fun 87.09
KOG350762 consensus DNA-directed RNA polymerase, subunit RPB 86.99
PF05876 557 Terminase_GpA: Phage terminase large subunit (GpA) 86.8
PF0952671 DUF2387: Probable metal-binding protein (DUF2387); 85.84
PRK03988138 translation initiation factor IF-2 subunit beta; V 85.81
PF04216290 FdhE: Protein involved in formate dehydrogenase fo 85.18
COG288861 Predicted Zn-ribbon RNA-binding protein with a fun 85.05
PF0360432 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa 83.92
PF0518066 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc 83.38
COG1779 201 C4-type Zn-finger protein [General function predic 82.54
smart0065944 RPOLCX RNA polymerase subunit CX. present in RNA p 82.3
KOG1886464 consensus BAH domain proteins [Transcription] 82.26
PF0972342 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134 82.25
PRK1489299 putative transcription elongation factor Elf1; Pro 81.72
COG199789 RPL43A Ribosomal protein L37AE/L43A [Translation, 81.38
TIGR01562305 FdhE formate dehydrogenase accessory protein FdhE. 81.11
smart00653110 eIF2B_5 domain present in translation initiation f 80.94
PF01873125 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: 80.85
PF14353128 CpXC: CpXC protein 80.49
PLN0020986 ribosomal protein S27; Provisional 80.33
>TIGR01385 TFSII transcription elongation factor S-II Back     alignment and domain information 
Probab=100.00  E-value=1.3e-67  Score=496.51  Aligned_cols=286  Identities=30%  Similarity=0.435  Sum_probs=224.0

Q ss_pred             HHHHHHHHHHHHHHhhcCCccHHHHHHHHHHhhcCCCCHHhhhcccceeecccccCCCCHHHHHHHHHHHHHHHhhcccc
Q 020974            7 DLCEAAKRAAVAAVWKEGVVEEARCIDALDQIKNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCWDV   86 (319)
Q Consensus         7 el~~~~~k~~~~a~~~~~~~~~~~~l~~L~~L~~~~it~~~L~~T~IG~~V~~Lrkh~~~~I~~~Ak~lv~~WK~~v~~~   86 (319)
                      |+...++ +++.+..  + .+++.|+++|++|+.++||.++|++|+||++||+||||++++|+.+|+.||+.||++|..+
T Consensus         3 ei~~~~k-~L~k~~~--~-~~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~v~~~   78 (299)
T TIGR01385         3 EVASHAK-ALDKNKS--S-KNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDKN   78 (299)
T ss_pred             HHHHHHH-Hhhhhcc--C-CCHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhhh
Confidence            4444444 4455422  2 5788999999999999999999999999999999999999999999999999999999875


Q ss_pred             cchhhhhhccccc-----cccccccccc--c-CCccccCCCCCCCCC--CcccccCCChHHHHHHHHHHHHHHhhhhhhc
Q 020974           87 EDVEYVAVTKKAK-----LVENVKVEEV--T-NGEERRHDSGNVPKK--SISCMIKCNDSFREIVREKLYDALSKVSDEA  156 (319)
Q Consensus        87 ~~~~~~~~~~~~~-----~s~~~~~~~~--~-~~~~s~~~~~~~ps~--~~~~~~~~~d~vR~k~r~~L~~aL~~~~~e~  156 (319)
                      ...... ..++..     ++.+.+.+..  + ........++..+..  ....++.++|++|++||++|++||....++.
T Consensus        79 k~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~d~~Rdk~r~~L~~aL~~~~~~~  157 (299)
T TIGR01385        79 KSDHPG-GNPEDKTTVGESVNSVKQEAKSQSDKIEQPKYVSSSPRNAKNDFVPTAVTNDKVRDKCRELLYDALAKDSDHP  157 (299)
T ss_pred             cccCcc-cccccccccCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCccCCcHHHHHHHHHHHHHHhhcCCCC
Confidence            332111 100000     0000000000  0 000000000111111  1223458999999999999999999754322


Q ss_pred             hhhhhhhhhccCChHHHHHHHHHHHHHHhccCchhHHHHHHHHHHhcCCCCCHHHHHHHhcCCCChhhhhcCChhhcCch
Q 020974          157 ADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASD  236 (319)
Q Consensus       157 ~~~~~~~~~~~~d~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~~NLkd~kN~~Lr~~vl~G~i~p~~lv~Ms~eElas~  236 (319)
                      +        ..+++..+|.+||.+||..|+.....|++++|+|+|||||++||+||++|++|+|+|++||.|+++||||+
T Consensus       158 ~--------~~~~~~~lA~~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmas~  229 (299)
T TIGR01385       158 P--------QSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASA  229 (299)
T ss_pred             c--------cccCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCH
Confidence            1        23467889999999999999988889999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhhhhchhhhhcCCCCccccccccccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceec
Q 020974          237 KIQLWNHHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVST  310 (319)
Q Consensus       237 e~k~~~~~~~~~e~l~~~q~~~~~~~~~~~~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~  310 (319)
                      +++++++++ .+++|+++|++   .... +.|++|+|++||+++|+| |+|||+||||||+||+|.+|||+|+||
T Consensus       230 e~k~~~e~~-~ke~l~~~~~~---~~~~-~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~fc  299 (299)
T TIGR01385       230 ELKQEREEI-TKENLFEAQGA---KIQK-AVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKFC  299 (299)
T ss_pred             HHHHHHHHH-HHHHHHHHHhh---hhhc-CCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeeeeC
Confidence            999999999 99999999944   3344 899999999999999999 999999999999999999999999998

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
>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
>PHA02998 RNA polymerase subunit; Provisional Back     alignment and domain information
>TIGR01384 TFS_arch transcription factor S, archaeal 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
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription] Back     alignment and domain information
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12 Back     alignment and domain information
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription] 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
>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
>PRK09678 DNA-binding transcriptional regulator; Provisional 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
>COG5139 Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>PF13717 zinc_ribbon_4: zinc-ribbon domain 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
>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
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA 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
>PF13719 zinc_ribbon_5: zinc-ribbon domain Back     alignment and domain information
>PHA00626 hypothetical protein Back     alignment and domain information
>PRK10220 hypothetical protein; Provisional Back     alignment and domain information
>COG4888 Uncharacterized Zn ribbon-containing protein [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
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00244 transcriptional regulator NrdR 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
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar Back     alignment and domain information
>TIGR02443 conserved hypothetical metal-binding protein Back     alignment and domain information
>PF11792 Baculo_LEF5_C: Baculoviridae late expression factor 5 C-terminal domain; InterPro: IPR021758 This C-terminal domain is likely to be a zinc-binding domain Back     alignment and domain information
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family Back     alignment and domain information
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7 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
>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
>PRK03988 translation initiation factor IF-2 subunit beta; Validated 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
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates Back     alignment and domain information
>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
>COG1779 C4-type Zn-finger protein [General function prediction only] Back     alignment and domain information
>smart00659 RPOLCX RNA polymerase subunit CX Back     alignment and domain information
>KOG1886 consensus BAH domain proteins [Transcription] Back     alignment and domain information
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria Back     alignment and domain information
>PRK14892 putative transcription elongation factor Elf1; Provisional Back     alignment and domain information
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE Back     alignment and domain information
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5 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
>PF14353 CpXC: CpXC protein Back     alignment and domain information
>PLN00209 ribosomal protein S27; Provisional 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 ?
Query319
2dme_A120 Solution Structure Of The Tfiis Domain Ii Of Human 8e-11
3gtm_S173 Co-Complex Of Backtracked Rna Polymerase Ii With Tf 3e-09
1y1v_S179 Refined Rna Polymerase Ii-tfiis Complex Length = 17 8e-09
1pqv_S309 Rna Polymerase Ii-Tfiis Complex Length = 309 1e-08
3po3_S178 Arrested Rna Polymerase Ii Reactivation Intermediat 6e-08
2lw4_A113 Solution Nmr Structure Of Human Transcription Elong 2e-06
3ndq_A108 Structure Of Human Tfiis Domain Ii Length = 108 2e-06
1enw_A114 Elongation Factor Tfiis Domain Ii Length = 114 6e-04
>pdb|2DME|A Chain A, Solution Structure Of The Tfiis Domain Ii Of Human Phd Finger Protein 3 Length = 120 Back     alignment and structure 
Iteration: 1

 Score = 64.3 bits (155), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 36/109 (33%), Positives = 59/109 (54%), Gaps = 13/109 (11%)
Query: 136 SFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFK 195
           S ++I+ ++L D+  KV +E A KV             A  +E  ++  +  ++  YK K
Sbjct: 19  SLKDILMKRLTDSNLKVPEEKAAKV-------------ATKIEKELFSFFRDTDAKYKNK 65
Query: 196 YRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHH 244
           YR L+FN+ DP+N    +KVL G V P+ +I MS +E+AS ++  W   
Sbjct: 66  YRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKELAAWRRR 114
>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis Length = 173 Back     alignment and structure
>pdb|1Y1V|S Chain S, Refined Rna Polymerase Ii-tfiis Complex Length = 179 Back     alignment and structure
>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex Length = 309 Back     alignment and structure
>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate Length = 178 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|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 ?
Query319
1pqv_S309 STP-alpha, transcription elongation factor S-II, D 4e-25
3ndq_A108 Transcription elongation factor A protein 1; helix 8e-25
2dme_A120 PHD finger protein 3; PHF3, TFS2M, glioblastoma mu 1e-24
3po3_S178 Transcription elongation factor S-II; RNA polymera 2e-21
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-08
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-08
1tfi_A50 Transcriptional elongation factor SII; transcripti 9e-05
1wjt_A103 Transcription elongation factor S-II protein 3; fo 3e-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 =  101 bits (252), Expect = 4e-25
 Identities = 64/305 (20%), Positives = 107/305 (35%), Gaps = 41/305 (13%)

Query: 27  EEARCIDALDQI-KNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWRDMCWD 85
            +A  ++ L  + K    T +LL  T+V   +    K  + +I KL   +ISSW+D    
Sbjct: 19  NDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKDAINK 78

Query: 86  VEDVEYVAVTKKAKLVENVKVEEVTNGEERRHDSGNVPKKSISCMIK------------- 132
            +         +     N + +                +       K             
Sbjct: 79  NKRSRQAQQHHQDHAPGNAEDKTTVGESVNGVQQPASSQSDAMKQDKYVSTKPRNSKNDG 138

Query: 133 -----CNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCR 187
                 +   R+ V + LYD L+K S+     +          +  A  +ES M +    
Sbjct: 139 VDTAIYHHKLRDQVLKALYDVLAKESEHPPQSI----------LHTAKAIESEMNKVNNC 188

Query: 188 SN--GMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHL 245
                 YK +YR +  N+    N D + K+  G + PE +    AK++A   ++     +
Sbjct: 189 DTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEI 248

Query: 246 DKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISY---QHSSILDDYNLTRHVTCLN 302
            K            G + +  V+D + CG+C   K+SY   Q  S   D  LT   TC  
Sbjct: 249 AKQ-----NLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSA--DEPLTTFCTCEA 301

Query: 303 CNQYW 307
           C   W
Sbjct: 302 CGNRW 306
>3ndq_A Transcription elongation factor A protein 1; helix bundle; 1.93A {Homo sapiens} Length = 108 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
>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
>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
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1 Length = 50 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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query319
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 99.8
1wjt_A103 Transcription elongation factor S-II protein 3; fo 99.74
1qyp_A57 RNA polymerase II; transcription, RPB9, Zn ribbon, 99.65
3h0g_I113 DNA-directed RNA polymerases I, II, and III subuni 99.56
1twf_I122 B12.6, DNA-directed RNA polymerase II 14.2 kDa pol 99.56
3qt1_I133 DNA-directed RNA polymerases I, II, and III subun; 99.48
2xpp_A145 IWS1, ECU08_0440; transcription, elongation, histo 97.64
3nfq_A170 Transcription factor IWS1; SPN1, RNA polymerase II 97.35
2b4j_C98 PC4 and SFRS1 interacting protein; HIV, integratio 96.97
1z9e_A127 PC4 and SFRS1 interacting protein 2; heat repeat-l 96.73
1k81_A36 EIF-2-beta, probable translation initiation factor 92.56
2akl_A138 PHNA-like protein PA0128; two domains, Zn binding 91.33
2fiy_A309 Protein FDHE homolog; FDHE protein, structural gen 88.4
1wii_A85 Hypothetical UPF0222 protein MGC4549; domain of un 85.42
1pft_A50 TFIIB, PFTFIIBN; N-terminal domain, transcription 84.8
>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=7.7e-65  Score=481.04  Aligned_cols=285  Identities=23%  Similarity=0.332  Sum_probs=223.4

Q ss_pred             hhhHHHHHHHHHHHHHHHHhhcCCccHHHHHHHHHHh-hcCCCCHHhhhcccceeecccccCCCCHHHHHHHHHHHHHHH
Q 020974            2 EKKVMDLCEAAKRAAVAAVWKEGVVEEARCIDALDQI-KNSSITYQLLVSTQVIRHLLPMLKHPSQKIQKLAYDLISSWR   80 (319)
Q Consensus         2 ~~~~~el~~~~~k~~~~a~~~~~~~~~~~~l~~L~~L-~~~~it~~~L~~T~IG~~V~~Lrkh~~~~I~~~Ak~lv~~WK   80 (319)
                      |.||++++..+.+   ..      .+++.++++|++| +.++||+++|++|+||++||+||||++++|+.+|+.||++||
T Consensus         3 ~~el~~~~~~L~k---~~------~~~~~~l~~L~~L~~~~~it~~~L~~T~IG~~Vn~lrkh~~~~v~~~Ak~Li~~WK   73 (309)
T 1pqv_S            3 SKEVLVHVKNLEK---NK------SNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWK   73 (309)
T ss_pred             HHHHHHHHHHHhc---cC------CCHHHHHHHHHHHHhcCCCCHHHHHhCChhHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence            6788888866666   11      4689999999999 999999999999999999999999999999999999999999


Q ss_pred             hhcccccchhhh-------h-hccccccccccccccccCC---ccccCCC-----CCCCCCCcccc--cCCChHHHHHHH
Q 020974           81 DMCWDVEDVEYV-------A-VTKKAKLVENVKVEEVTNG---EERRHDS-----GNVPKKSISCM--IKCNDSFREIVR  142 (319)
Q Consensus        81 ~~v~~~~~~~~~-------~-~~~~~~~s~~~~~~~~~~~---~~s~~~~-----~~~ps~~~~~~--~~~~d~vR~k~r  142 (319)
                      ++|.........       . .+.....++.......+.+   ..++.++     ...++++...+  +.++|++|++|+
T Consensus        74 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~R~k~r  153 (309)
T 1pqv_S           74 DAINKNKRSRQAQQHHQDHAPGNAEDKTTVGESVNGVQQPASSQSDAMKQDKYVSTKPRNSKNDGVDTAIYHHKLRDQVL  153 (309)
T ss_pred             HHHHHhccCCcccccccccccccccCCCCCCCCcCCCCCCcccccccccCCCCCCCCCCCCCCCCCCcCcCChHHHHHHH
Confidence            999876543111       0 0000000000000000000   0000011     00111122223  368899999999


Q ss_pred             HHHHHHHhhhhhhchhhhhhhhhccCChHHHHHHHHHHHHHHhccCchh--HHHHHHHHHHhcCCCCCHHHHHHHhcCCC
Q 020974          143 EKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGM--YKFKYRCLLFNISDPENQDFRRKVLLGHV  220 (319)
Q Consensus       143 ~~L~~aL~~~~~e~~~~~~~~~~~~~d~~~lA~~IE~~lf~~~~~~~~~--Yk~k~Rsl~~NLkd~kN~~Lr~~vl~G~i  220 (319)
                      ++|+++|..+..+.+          .++..+|.+||.+||..|+++...  |++++|+|+|||||++||.||++|++|+|
T Consensus       154 ~~L~~aL~~~~~~~~----------~~~~~~A~~IE~al~~~~~~~~~~~~Yk~k~Rsl~~NLKd~~N~~Lr~~vl~g~i  223 (309)
T 1pqv_S          154 KALYDVLAKESEHPP----------QSILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDI  223 (309)
T ss_pred             HHHHHHHhcCCCccc----------hhHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHcCcCCChHHHHHHHcCCC
Confidence            999999986432211          156799999999999999876666  99999999999999999999999999999


Q ss_pred             ChhhhhcCChhhcCchHHHHHhhhhhhchhhhhcCCCCccccccccccccccccCCCCcceEE-EEeccCCCCCceeEEE
Q 020974          221 KPETIINMSAKEMASDKIQLWNHHLDKDGALVTGHIFPVGLSRKIIVSDIYECGRCGHNKISY-QHSSILDDYNLTRHVT  299 (319)
Q Consensus       221 ~p~~lv~Ms~eElas~e~k~~~~~~~~~e~l~~~q~~~~~~~~~~~~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~  299 (319)
                      +|++||.|+++||||++++++++++ .+++|++++++...   . +.++.+.||+||+++++| |+|+||||||||+||+
T Consensus       224 ~p~~lv~Ms~eElasde~k~~~~~~-~~e~l~~~~~~~~~---~-~~~~~~~C~~C~~~~~~~~q~Q~rsaDe~~t~f~~  298 (309)
T 1pqv_S          224 TPEFLATCDAKDLAPAPLKQKIEEI-AKQNLYNAQGATIE---R-SVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCT  298 (309)
T ss_pred             CHHHHhcCCHHHhCCHHHHHHHHHH-HHHHHHHhhhcccc---c-cCcccccCCCCCCCeeEEEEeecccCCCCCcEEEE
Confidence            9999999999999999999999999 99999999954332   3 677889999999999999 9999999999999999


Q ss_pred             ccCCCCcceec
Q 020974          300 CLNCNQYWVST  310 (319)
Q Consensus       300 C~~C~~~w~~~  310 (319)
                      |.+|||+|+||
T Consensus       299 C~~Cg~~w~fc  309 (309)
T 1pqv_S          299 CEACGNRWKFS  309 (309)
T ss_pred             eCCCCCceecC
Confidence            99999999998
>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
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1 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 319
d1enwa_114 a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Bak 3e-22
d1eo0a_77 a.48.3.1 (A:) Transcription elongation factor TFII 5e-07
d1wjta_103 a.48.3.1 (A:) Transcription elongation factor S-II 2e-06
d1twfi272 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase 2e-04
d1tfia_50 g.41.3.1 (A:) Transcriptional factor SII, C-termin 5e-04
d1qypa_57 g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {A 0.004
>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 = 87.6 bits (217), Expect = 3e-22
 Identities = 26/103 (25%), Positives = 44/103 (42%), Gaps = 12/103 (11%)

Query: 134 NDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNG--M 191
           +   R+ V + LYD L+K S+     +          +  A  +ES M +          
Sbjct: 19  HHKLRDQVLKALYDVLAKESEHPPQSI----------LHTAKAIESEMNKVNNCDTNEAA 68

Query: 192 YKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMA 234
           YK +YR +  N+    N D + K+  G + PE +    AK++A
Sbjct: 69  YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 111
>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
>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
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query319
d1tfia_50 Transcriptional factor SII, C-terminal domain {Hum 99.85
d1enwa_114 Elongation factor TFIIS domain 2 {Baker's yeast (S 99.85
d1qypa_57 RBP9 subunit of RNA polymerase II {Archaeon Thermo 99.76
d1twfi272 RBP9 subunit of RNA polymerase II {Baker's yeast ( 99.7
d1eo0a_77 Transcription elongation factor TFIIS N-domain {Ba 99.65
d1wjta_103 Transcription elongation factor S-II protein 3 {Mo 99.62
d2b4jc181 PC4 and SFRS1-interacting protein, PSIP1 {Human (H 97.93
d2akla238 Hypothetical protein PA0128, N-terminal domain {Ps 95.13
d2fiya1290 FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId 86.2
d1twfl_46 RBP12 subunit of RNA polymerase II {Baker's yeast 84.25
d1dl6a_58 Transcription initiation factor TFIIB, N-terminal 83.13
d1k81a_36 Zinc-binding domain of translation initiation fact 81.46
>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=99.85  E-value=1.5e-22  Score=138.57  Aligned_cols=45  Identities=27%  Similarity=0.667  Sum_probs=43.8

Q ss_pred             cccccccccCCCCcceEE-EEeccCCCCCceeEEEccCCCCcceec
Q 020974          266 IVSDIYECGRCGHNKISY-QHSSILDDYNLTRHVTCLNCNQYWVST  310 (319)
Q Consensus       266 ~~t~~~~C~~C~~~~~~~-q~q~rsade~mt~f~~C~~C~~~w~~~  310 (319)
                      +.|+.|+||+||++++.| |+|+||||||||+||+|.+|||+|++|
T Consensus         5 ~~T~~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~Cg~~Wr~c   50 (50)
T d1tfia_           5 TQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWKFC   50 (50)
T ss_dssp             EECCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEECC
T ss_pred             cccCCEECCCCCCCccEEEEEEccCCCCCceEEEEccccCCeeecC
Confidence            688999999999999999 999999999999999999999999997
>d1enwa_ a.5.4.1 (A:) Elongation factor TFIIS domain 2 {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
>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
>d1twfl_ g.41.9.2 (L:) RBP12 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>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