Citrus Sinensis ID: 036389

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-------20
YIHVIFSTNVPKASKVVKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLVSPKNIVYGICKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNPEIRVLPI
cccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHcccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccccHHHHHHHHHcccccHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccEEEEccccccccccccccccccc
cEEEEEEcccccccccccccHHHHHHHHHHHHHHHHcccccccccHHHHHccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccHHHHHHcccccHHHHHHccHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEccccccccccEcccEEEEEEcccccccccccccEEEccc
YIHVIFstnvpkaskvvkcnDCIREIVRKNLYGALSKVSIeaahdknvidqvkacnpIQVAISMESAMYEKWGRSSETYKFKYRRLLfnfndpknhefrkkvllgdvkpetIVNMTAKEMASDKMQLWYENSrkgraetngrifsglvspknivygickcsrcghkrmsfiplrrhitclncyqywastnpeirvlpi
yihvifstnvpkaskvvkcNDCIREIVRKNLYGALSKVSIEaahdknvidqVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFnfndpknhefrkkvllgdvkpETIVNMTAKEMASDKMQLWYENSRKgraetngrifsglvspknivYGICKCSRCGHKRMSFIPLRRHITCLNCYQYwastnpeirvlpi
YIHVIFSTNVPKASKVVKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLVSPKNIVYGICKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNPEIRVLPI
*IHVIFSTNVPKASKVVKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAK*****KMQLWYEN******ETNGRIFSGLVSPKNIVYGICKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNP*******
***V***********************RKNLYGALSKVSIE*A******DQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMA**KMQ*****SRK******************IVYGICKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNPEIRVLPI
YIHVIFSTNVPKASKVVKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLVSPKNIVYGICKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNPEIRVLPI
YIHVIFSTNVPKASKVVKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLVSPKNIVYGICKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNPEIRVLPI
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YIHVIFSTNVPKASKVVKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLVSPKNIVYGICKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNPEIRVLPI
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 ?
Query198 2.2.26 [Sep-21-2011]
Q92576 2039 PHD finger protein 3 OS=H yes no 0.565 0.054 0.347 4e-10
Q148K0300 Transcription elongation no no 0.792 0.523 0.270 2e-08
P10711301 Transcription elongation no no 0.646 0.425 0.272 2e-08
Q4KLL0301 Transcription elongation no no 0.646 0.425 0.272 2e-08
P23193301 Transcription elongation no no 0.646 0.425 0.272 3e-08
Q8C9B9 2256 Death-inducer obliterator no no 0.590 0.051 0.25 3e-08
Q29RL9301 Transcription elongation no no 0.646 0.425 0.272 3e-08
Q6ZMY3 1216 SPOC domain-containing pr no no 0.378 0.061 0.346 3e-08
P52652308 Putative transcription el yes no 0.631 0.405 0.269 6e-08
Q6C0K9 822 Transcription factor BYE1 yes no 0.560 0.135 0.305 1e-07
>sp|Q92576|PHF3_HUMAN PHD finger protein 3 OS=Homo sapiens GN=PHF3 PE=1 SV=3 Back     alignment and function desciption
 Score = 64.7 bits (156), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 41/118 (34%), Positives = 62/118 (52%), Gaps = 6/118 (5%)

Query: 11   PKASKVVKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYE 70
            P AS      D IR+ VR +L   L K       D N+  +V      +VA  +E  ++ 
Sbjct: 915  PAASASKPSADQIRQSVRHSLKDILMK----RLTDSNL--KVPEEKAAKVATKIEKELFS 968

Query: 71   KWGRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQLW 128
             +  +   YK KYR L+FN  DPKN+   KKVL G+V P+ ++ M+ +E+AS ++  W
Sbjct: 969  FFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKELAAW 1026

Homo sapiens (taxid: 9606)
>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|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|P23193|TCEA1_HUMAN Transcription elongation factor A protein 1 OS=Homo sapiens GN=TCEA1 PE=1 SV=2 Back     alignment and function description
>sp|Q8C9B9|DIDO1_MOUSE Death-inducer obliterator 1 OS=Mus musculus GN=Dido1 PE=1 SV=4 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|Q6ZMY3|SPOC1_HUMAN SPOC domain-containing protein 1 OS=Homo sapiens GN=SPOCD1 PE=2 SV=1 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|Q6C0K9|BYE1_YARLI Transcription factor BYE1 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=BYE1 PE=3 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 ?
Query198
225439709 367 PREDICTED: transcription elongation fact 0.848 0.457 0.417 2e-33
297735532 322 unnamed protein product [Vitis vinifera] 0.848 0.521 0.417 2e-33
255575598 342 transcription elongation factor s-II, pu 0.853 0.494 0.414 4e-33
224139382 334 predicted protein [Populus trichocarpa] 0.823 0.488 0.385 7e-32
224087871 352 predicted protein [Populus trichocarpa] 0.808 0.454 0.381 4e-31
449441244 369 PREDICTED: transcription elongation fact 0.828 0.444 0.384 1e-28
449499153290 PREDICTED: transcription elongation fact 0.828 0.565 0.384 1e-28
224286619 328 unknown [Picea sitchensis] 0.858 0.518 0.364 5e-28
255637690 368 unknown [Glycine max] 0.848 0.456 0.365 5e-28
116789178 331 unknown [Picea sitchensis] 0.853 0.510 0.388 9e-28
>gi|225439709|ref|XP_002272768.1| PREDICTED: transcription elongation factor A protein 3 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 81/194 (41%), Positives = 120/194 (61%), Gaps = 26/194 (13%)

Query: 7   STNVPKASKVVKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMES 66
           S   PK + ++KCND +R+ VR+ L  AL KV+ EA  D+++ D+V AC+PI+VA+S+ES
Sbjct: 183 SNGPPKLTAMIKCNDALRDKVRELLAEALFKVASEA--DEDIKDEVNACDPIRVAVSVES 240

Query: 67  AMYEKWGRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQ 126
            M+EK GRS+ T KFKYR ++FN  DP N + R+KVLLG+VKP+ ++NM+ +EMAS++ Q
Sbjct: 241 VMFEKMGRSNGTQKFKYRSIMFNIKDPNNPDLRRKVLLGEVKPDRLINMSPEEMASNQRQ 300

Query: 127 LWYENSR-KGRA----ETNGRIFSGLVSPKNIVYGICKCSRCGHKRMSFI---------P 172
              ENS+ K +A    E  G        P        KC RCG ++ ++          P
Sbjct: 301 --RENSQIKEKALFDCERGG--------PPKATTDQFKCGRCGQRKTTYYQLQTRSADEP 350

Query: 173 LRRHITCLNCYQYW 186
           +   +TC+NC  +W
Sbjct: 351 MTTFVTCVNCNNHW 364

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|297735532|emb|CBI18026.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|255575598|ref|XP_002528699.1| transcription elongation factor s-II, putative [Ricinus communis] gi|223531871|gb|EEF33688.1| transcription elongation factor s-II, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224139382|ref|XP_002323085.1| predicted protein [Populus trichocarpa] gi|222867715|gb|EEF04846.1| predicted protein [Populus trichocarpa] 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|449441244|ref|XP_004138392.1| PREDICTED: transcription elongation factor A protein 3-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449499153|ref|XP_004160740.1| PREDICTED: transcription elongation factor A protein 2-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|224286619|gb|ACN41014.1| unknown [Picea sitchensis] Back     alignment and taxonomy information
>gi|255637690|gb|ACU19168.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|116789178|gb|ABK25146.1| unknown [Picea sitchensis] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query198
TAIR|locus:2064195378 TFIIS "transcript elongation f 0.848 0.444 0.354 4e-26
TAIR|locus:2124097266 AT4G18720 [Arabidopsis thalian 0.621 0.462 0.390 5.8e-18
TAIR|locus:2052351737 AT2G42730 [Arabidopsis thalian 0.585 0.157 0.418 4.7e-17
UNIPROTKB|E7ER40 861 PHF3 "PHD finger protein 3" [H 0.621 0.142 0.340 7.6e-11
UNIPROTKB|E7EVH3 1072 PHF3 "PHD finger protein 3" [H 0.621 0.114 0.340 1e-10
FB|FBgn0030663162 CG8117 [Drosophila melanogaste 0.646 0.790 0.3 1.5e-10
RGD|1304925 2020 Phf3 "PHD finger protein 3" [R 0.621 0.060 0.338 2.1e-10
UNIPROTKB|Q92576 2039 PHF3 "PHD finger protein 3" [H 0.621 0.060 0.340 2.1e-10
UNIPROTKB|F1MIT2280 TCEA1 "Transcription elongatio 0.646 0.457 0.272 3.6e-10
UNIPROTKB|F1RSG8300 TCEA1 "Uncharacterized protein 0.646 0.426 0.272 4.5e-10
TAIR|locus:2064195 TFIIS "transcript elongation factor IIS" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 66/186 (35%), Positives = 112/186 (60%)

Query:    11 PKASKVVKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYE 70
             PK + ++KCND +R+ +R+ L  AL +V+ EA  D    + V A +P++VA+S+ES M+E
Sbjct:   198 PKLTAMLKCNDPVRDKIRELLVEALCRVAGEA--DDYERESVNASDPLRVAVSVESLMFE 255

Query:    71 KWGRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYE 130
             K GRS+   K KYR ++FN  D  N + R++VL G++ PE ++ ++A++MASDK +   E
Sbjct:   256 KLGRSTGAQKLKYRSIMFNLRDSNNPDLRRRVLTGEISPEKLITLSAEDMASDKRK--QE 313

Query:   131 NSR-KGRAETNGRIFSGLVSPKNIVYGICKCSRCGHKRMSFI---------PLRRHITCL 180
             N++ K +A  +     GL +  +      KC RCG ++ ++          P+  ++TC+
Sbjct:   314 NNQIKEKALFDCE--RGLAAKASTDQ--FKCGRCGQRKCTYYQMQTRSADEPMTTYVTCV 369

Query:   181 NCYQYW 186
             NC  +W
Sbjct:   370 NCDNHW 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
UNIPROTKB|E7ER40 PHF3 "PHD finger protein 3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E7EVH3 PHF3 "PHD finger protein 3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
FB|FBgn0030663 CG8117 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
RGD|1304925 Phf3 "PHD finger protein 3" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q92576 PHF3 "PHD finger protein 3" [Homo sapiens (taxid:9606)] 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|F1RSG8 TCEA1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

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 ?
Query198
pfam07500115 pfam07500, TFIIS_M, Transcription factor S-II (TFI 2e-26
smart00510102 smart00510, TFS2M, Domain in the central regions o 3e-25
TIGR01385299 TIGR01385, TFSII, transcription elongation factor 2e-21
>gnl|CDD|219433 pfam07500, TFIIS_M, Transcription factor S-II (TFIIS), central domain Back     alignment and domain information 
 Score = 97.3 bits (243), Expect = 2e-26
 Identities = 41/116 (35%), Positives = 67/116 (57%), Gaps = 9/116 (7%)

Query: 19  CNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSET 78
            ND +R+  R+ LY AL+K            D +      ++A  +E  +++ +G + + 
Sbjct: 1   TNDKVRDKCRELLYDALAKG---------SEDSMSEEEVERLAAEIEEELFKLYGNTGKK 51

Query: 79  YKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENSRK 134
           YK KYR L+FN  DPKN + R+KVL G++ PE +VNM+ +E+ASD+++   E   K
Sbjct: 52  YKNKYRSLMFNLKDPKNPDLRRKVLNGEISPERLVNMSPEELASDELKKEREEIEK 107

Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity. Length = 115
>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|233390 TIGR01385, TFSII, transcription elongation factor S-II Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 198
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 99.97
PF07500115 TFIIS_M: Transcription factor S-II (TFIIS), centra 99.96
KOG1634 778 consensus Predicted transcription factor DATF1, co 99.55
smart0044040 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo 99.12
PF0109639 TFIIS_C: Transcription factor S-II (TFIIS); InterP 99.07
COG1594113 RPB9 DNA-directed RNA polymerase, subunit M/Transc 98.89
KOG2906105 consensus RNA polymerase III subunit C11 [Transcri 98.83
PHA02998195 RNA polymerase subunit; Provisional 98.69
TIGR01384104 TFS_arch transcription factor S, archaeal. There h 98.68
KOG2691113 consensus RNA polymerase II subunit 9 [Transcripti 98.01
KOG2907116 consensus RNA polymerase I transcription factor TF 97.53
PF1371736 zinc_ribbon_4: zinc-ribbon domain 95.71
PF0827143 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013 95.24
PF1276046 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int 94.94
PF1371937 zinc_ribbon_5: zinc-ribbon domain 94.9
TIGR0209838 MJ0042_CXXC MJ0042 family finger-like domain. This 94.34
COG4888104 Uncharacterized Zn ribbon-containing protein [Gene 94.34
COG347868 Predicted nucleic-acid-binding protein containing 93.99
COG205167 RPS27A Ribosomal protein S27E [Translation, riboso 93.98
PF0985564 DUF2082: Nucleic-acid-binding protein containing Z 93.92
PF0827430 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01 93.73
PRK0967872 DNA-binding transcriptional regulator; Provisional 92.89
PF0460647 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I 91.85
PF0518066 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc 91.27
KOG1886464 consensus BAH domain proteins [Transcription] 91.23
PRK0039846 rpoP DNA-directed RNA polymerase subunit P; Provis 90.89
PRK0041559 rps27e 30S ribosomal protein S27e; Reviewed 90.5
PLN0020986 ribosomal protein S27; Provisional 90.15
TIGR00311133 aIF-2beta translation initiation factor aIF-2, bet 90.0
PRK03988138 translation initiation factor IF-2 subunit beta; V 89.82
TIGR00686109 phnA alkylphosphonate utilization operon protein P 89.42
PF0512981 Elf1: Transcription elongation factor Elf1 like; I 89.16
PTZ0008385 40S ribosomal protein S27; Provisional 89.14
smart00653110 eIF2B_5 domain present in translation initiation f 89.07
PF1178136 RRN7: RNA polymerase I-specific transcription init 88.54
PF01873125 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: 88.13
TIGR0244359 conserved hypothetical metal-binding protein. Memb 87.9
PRK10220111 hypothetical protein; Provisional 87.59
PF0360432 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa 87.42
smart0065944 RPOLCX RNA polymerase subunit CX. present in RNA p 87.38
PF0952671 DUF2387: Probable metal-binding protein (DUF2387); 87.22
PF0166755 Ribosomal_S27e: Ribosomal protein S27; InterPro: I 87.15
PF04216290 FdhE: Protein involved in formate dehydrogenase fo 87.03
PRK1489299 putative transcription elongation factor Elf1; Pro 86.84
PHA0062659 hypothetical protein 86.73
PRK12336201 translation initiation factor IF-2 subunit beta; P 86.68
PF1345341 zf-TFIIB: Transcription factor zinc-finger 85.7
PF1435461 Lar_restr_allev: Restriction alleviation protein L 85.7
smart00531147 TFIIE Transcription initiation factor IIE. 85.02
PRK05978148 hypothetical protein; Provisional 84.93
PRK0971064 lar restriction alleviation and modification prote 84.67
PRK03564309 formate dehydrogenase accessory protein FdhE; Prov 82.51
PRK0043250 30S ribosomal protein S27ae; Validated 81.99
TIGR0365553 anti_R_Lar restriction alleviation protein, Lar fa 81.9
PRK06266178 transcription initiation factor E subunit alpha; V 81.74
PF09332344 Mcm10: Mcm10 replication factor; InterPro: IPR0154 81.03
>TIGR01385 TFSII transcription elongation factor S-II Back     alignment and domain information 
Probab=100.00  E-value=1.6e-47  Score=335.58  Aligned_cols=158  Identities=30%  Similarity=0.550  Sum_probs=145.2

Q ss_pred             ccCCcHHHHHHHHHHHHHHhhhhhhccccchhhhhhcccChHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcCCCCCH
Q 036389           17 VKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNH   96 (198)
Q Consensus        17 ~~~~d~iR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~~~~A~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kNp   96 (198)
                      +.++|++|+++|++|++||.....+.+.         .+++..+|.+||.+||..++.++.+|++++|||+|||||++||
T Consensus       132 ~~t~d~~Rdk~r~~L~~aL~~~~~~~~~---------~~~~~~lA~~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp  202 (299)
T TIGR01385       132 AVTNDKVRDKCRELLYDALAKDSDHPPQ---------SIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNP  202 (299)
T ss_pred             ccCCcHHHHHHHHHHHHHHhhcCCCCcc---------ccCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCH
Confidence            5799999999999999999975432222         2467789999999999999988889999999999999999999


Q ss_pred             HHHHHhhcCCCCchhcccCCHHhhccHHHHHHHHHHhccccccccccccccc-CCCcccccceEcCCCCCCCceEe----
Q 036389           97 EFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLV-SPKNIVYGICKCSRCGHKRMSFI----  171 (198)
Q Consensus        97 ~Lr~~vl~G~isp~~lv~Ms~eELas~e~k~~~e~~~~~e~~~~~~l~~~~~-~~~~~~t~~~~C~~C~~~~~~~~----  171 (198)
                      +||.+|++|+|+|++||.|+++||||+++|++++++.+ ++     |+++|+ ...++.|++|+|++||+++|+|+    
T Consensus       203 ~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e~~~k-e~-----l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~Qt  276 (299)
T TIGR01385       203 DLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITK-EN-----LFEAQGAKIQKAVTDLFTCGKCKQKKCTYYQLQT  276 (299)
T ss_pred             HHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHHH-HH-----HHHHHhhhhhcCCcccccCCCCCCccceEEEecc
Confidence            99999999999999999999999999999999999999 99     999988 44555899999999999999999    


Q ss_pred             -----ccceEEEeccCCCccccc
Q 036389          172 -----PLRRHITCLNCYQYWAST  189 (198)
Q Consensus       172 -----pmt~fv~C~~Cg~~W~~~  189 (198)
                           |||+||+|.+|||+|+||
T Consensus       277 rsaDEpmT~f~~C~~Cg~~w~fc  299 (299)
T TIGR01385       277 RSADEPMTTFVTCEECGNRWKFC  299 (299)
T ss_pred             cCCCCCCeEEEEcCCCCCeeeeC
Confidence                 999999999999999998

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
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription] 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
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription] Back     alignment and domain information
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription] 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
>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
>PF13717 zinc_ribbon_4: zinc-ribbon domain 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
>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
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain Back     alignment and domain information
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only] 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
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis] 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
>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
>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
>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
>KOG1886 consensus BAH domain proteins [Transcription] Back     alignment and domain information
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional Back     alignment and domain information
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed Back     alignment and domain information
>PLN00209 ribosomal protein S27; Provisional Back     alignment and domain information
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative Back     alignment and domain information
>PRK03988 translation initiation factor IF-2 subunit beta; Validated Back     alignment and domain information
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA 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
>PTZ00083 40S ribosomal protein S27; Provisional Back     alignment and domain information
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5 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
>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
>TIGR02443 conserved hypothetical metal-binding protein Back     alignment and domain information
>PRK10220 hypothetical protein; Provisional 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
>smart00659 RPOLCX RNA polymerase subunit CX 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
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>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
>PRK14892 putative transcription elongation factor Elf1; Provisional Back     alignment and domain information
>PHA00626 hypothetical protein Back     alignment and domain information
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional Back     alignment and domain information
>PF13453 zf-TFIIB: Transcription factor zinc-finger Back     alignment and domain information
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar Back     alignment and domain information
>smart00531 TFIIE Transcription initiation factor IIE Back     alignment and domain information
>PRK05978 hypothetical protein; Provisional Back     alignment and domain information
>PRK09710 lar restriction alleviation and modification protein; Reviewed Back     alignment and domain information
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional Back     alignment and domain information
>PRK00432 30S ribosomal protein S27ae; Validated Back     alignment and domain information
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family Back     alignment and domain information
>PRK06266 transcription initiation factor E subunit alpha; Validated Back     alignment and domain information
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha [] 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 ?
Query198
2dme_A120 Solution Structure Of The Tfiis Domain Ii Of Human 1e-10
2lw4_A113 Solution Nmr Structure Of Human Transcription Elong 2e-07
3ndq_A108 Structure Of Human Tfiis Domain Ii Length = 108 6e-07
3po3_S178 Arrested Rna Polymerase Ii Reactivation Intermediat 4e-04
1y1v_S179 Refined Rna Polymerase Ii-tfiis Complex Length = 17 5e-04
3gtm_S173 Co-Complex Of Backtracked Rna Polymerase Ii With Tf 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 = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 39/112 (34%), Positives = 60/112 (53%), Gaps = 6/112 (5%)
Query: 21  DCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYK 80
           D IR+ VR +L   L K       D N+  +V      +VA  +E  ++  +  +   YK
Sbjct: 10  DQIRQSVRHSLKDILMK----RLTDSNL--KVPEEKAAKVATKIEKELFSFFRDTDAKYK 63
Query: 81  FKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENS 132
            KYR L+FN  DPKN+   KKVL G+V P+ ++ M+ +E+AS ++  W   S
Sbjct: 64  NKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKELAAWRRRS 115
>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|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate Length = 178 Back     alignment and structure
>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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query198
2dme_A120 PHD finger protein 3; PHF3, TFS2M, glioblastoma mu 6e-27
3ndq_A108 Transcription elongation factor A protein 1; helix 3e-25
3po3_S178 Transcription elongation factor S-II; RNA polymera 2e-18
1pqv_S309 STP-alpha, transcription elongation factor S-II, D 4e-14
>2dme_A PHD finger protein 3; PHF3, TFS2M, glioblastoma multiforme, brain tumor, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 120 Back     alignment and structure
 Score = 98.5 bits (245), Expect = 6e-27
 Identities = 38/122 (31%), Positives = 60/122 (49%), Gaps = 6/122 (4%)

Query: 13  ASKVVKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKW 72
           +S      D IR+ VR +L   L K   ++         V      +VA  +E  ++  +
Sbjct: 2   SSGSSGSADQIRQSVRHSLKDILMKRLTDSNLK------VPEEKAAKVATKIEKELFSFF 55

Query: 73  GRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENS 132
             +   YK KYR L+FN  DPKN+   KKVL G+V P+ ++ M+ +E+AS ++  W   S
Sbjct: 56  RDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKELAAWRRRS 115

Query: 133 RK 134
             
Sbjct: 116 GP 117
>3ndq_A Transcription elongation factor A protein 1; helix bundle; 1.93A {Homo sapiens} Length = 108 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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query198
3po3_S178 Transcription elongation factor S-II; RNA polymera 100.0
1pqv_S309 STP-alpha, transcription elongation factor S-II, D 100.0
2lw4_A113 Transcription elongation factor A protein 2; struc 99.98
3ndq_A108 Transcription elongation factor A protein 1; helix 99.97
2dme_A120 PHD finger protein 3; PHF3, TFS2M, glioblastoma mu 99.97
1tfi_A50 Transcriptional elongation factor SII; transcripti 99.42
1qyp_A57 RNA polymerase II; transcription, RPB9, Zn ribbon, 98.94
3h0g_I113 DNA-directed RNA polymerases I, II, and III subuni 98.82
1twf_I122 B12.6, DNA-directed RNA polymerase II 14.2 kDa pol 98.76
3qt1_I133 DNA-directed RNA polymerases I, II, and III subun; 98.6
1k81_A36 EIF-2-beta, probable translation initiation factor 94.79
1pft_A50 TFIIB, PFTFIIBN; N-terminal domain, transcription 93.26
1vq8_Z83 50S ribosomal protein L37AE; ribosome 50S, protein 89.95
1qxf_A66 GR2, 30S ribosomal protein S27E; structural genomi 89.5
1wii_A85 Hypothetical UPF0222 protein MGC4549; domain of un 89.01
2e2z_A100 TIM15; protein import, zinc finger, protein transp 88.32
2akl_A138 PHNA-like protein PA0128; two domains, Zn binding 87.62
3j20_W63 30S ribosomal protein S27E; archaea, archaeal, KIN 87.15
2xzm_681 RPS27E; ribosome, translation; 3.93A {Tetrahymena 86.99
3iz6_X86 40S ribosomal protein S27 (S27E); eukaryotic ribos 85.21
2d74_B148 Translation initiation factor 2 beta subunit; prot 85.03
2fiy_A309 Protein FDHE homolog; FDHE protein, structural gen 84.56
3u5c_b82 RP61, YS20, 40S ribosomal protein S27-A; translati 83.5
1nee_A138 EIF-2-beta, probable translation initiation factor 83.31
1dl6_A58 Transcription factor II B (TFIIB); zinc ribbon, ge 80.04
>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
Probab=100.00  E-value=9.5e-48  Score=314.22  Aligned_cols=162  Identities=26%  Similarity=0.429  Sum_probs=138.3

Q ss_pred             CCCCcc--ccCCcHHHHHHHHHHHHHHhhhhhhccccchhhhhhcccChHHHHHHHHHHHHHHhCC-CcH-HHHHHHHHH
Q 036389           11 PKASKV--VKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGR-SSE-TYKFKYRRL   86 (198)
Q Consensus        11 ~~~~~~--~~~~d~iR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~~~~A~~IE~alf~~~~~-~~~-~Yk~k~Rsl   86 (198)
                      ++..++  +.++|++|++++++|++||.....+.+           .++..+|.+||++||+.|++ ++. +|++++|||
T Consensus         3 ~~~d~v~~~~~~d~vRdk~~~lL~~aL~~~~~~~~-----------~~~~~~A~~IE~~if~~~~~~~~~k~Yk~k~Rsl   71 (178)
T 3po3_S            3 SKNDGVDTAIYHHKLRDQVLKALYDVLAKESEHPP-----------QSILHTAKAIESEMNKVNNCDTNEAAYKARYRII   71 (178)
T ss_dssp             ------------CHHHHHHHHHHHHHTTSSSSCST-----------THHHHHHHHHHHHHHHHTSCSSSSTHHHHHHHHH
T ss_pred             ccCCCcCcCcCCChHHHHHHHHHHHHHhcCCCCch-----------hhHHHHHHHHHHHHHHHhcCCCchhhhhhhhhHH
Confidence            344445  679999999999999999998653322           23578999999999999986 555 899999999


Q ss_pred             HHhcCCCCCHHHHHHhhcCCCCchhcccCCHHhhccHHHHHHHHHHhccccccccccccccc-CCCcccccceEcCCCCC
Q 036389           87 LFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLV-SPKNIVYGICKCSRCGH  165 (198)
Q Consensus        87 ~~NLkd~kNp~Lr~~vl~G~isp~~lv~Ms~eELas~e~k~~~e~~~~~e~~~~~~l~~~~~-~~~~~~t~~~~C~~C~~  165 (198)
                      +|||||++||+|+.+|++|+|+|+.||.|+++||||+|++++++++++ ++     |++++. ....+.|+.++||+||+
T Consensus        72 ~~NLKd~~N~~Lr~~vl~g~isp~~lv~Ms~eElas~elk~~~e~~~~-e~-----l~~~~~~~~~~~~t~~~~Cp~C~~  145 (178)
T 3po3_S           72 YSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAK-QN-----LYNAQGATIERSVTDRFTCGKCKE  145 (178)
T ss_dssp             HHHHHSSSCSHHHHHHHHCCCTTHHHHCCTTTTSSCSHHHHHHHHHHH-HH-----HHHTBCCCCCCCCBSSSCCSSSCC
T ss_pred             HHHcCCCCCHHHHHHHhcCCCCHHHHHhcCchhhCCHHHHHHHHHHHH-HH-----HHHhhhccccCCCcCCcCCCCCCC
Confidence            999999999999999999999999999999999999999999999999 88     999988 33344788999999999


Q ss_pred             CCceEe---------ccceEEEeccCCCccccc
Q 036389          166 KRMSFI---------PLRRHITCLNCYQYWAST  189 (198)
Q Consensus       166 ~~~~~~---------pmt~fv~C~~Cg~~W~~~  189 (198)
                      ++|+|+         |||+||+|.+|||+|+||
T Consensus       146 ~~a~~~q~Q~rsaDE~mt~f~~C~~C~~~w~f~  178 (178)
T 3po3_S          146 KKVSYYQLQTRSAAAPLTTFCTCEACGNRWKFS  178 (178)
T ss_dssp             SCEECCCCCCSCTTSCCCCCEEETTTCCEECCC
T ss_pred             CceEEEEeecccCCCCCcEEEEcCCCCCeeccC
Confidence            999999         999999999999999997
>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
>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
>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
>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1 Back     alignment and structure
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1 Back     alignment and structure
>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
>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4 Back     alignment and structure
>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4 Back     alignment and structure
>2e2z_A TIM15; protein import, zinc finger, protein transport, chaperone regulator; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>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
>3j20_W 30S ribosomal protein S27E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6 Back     alignment and structure
>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Back     alignment and structure
>2d74_B Translation initiation factor 2 beta subunit; protein complex; 2.80A {Pyrococcus furiosus} PDB: 2dcu_B* 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
>3u5c_b RP61, YS20, 40S ribosomal protein S27-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_X 3u5g_b Back     alignment and structure
>1nee_A EIF-2-beta, probable translation initiation factor 2 beta subunit; two domain protein, mixed alpha-beta structure; NMR {Methanothermobacterthermautotrophicus} SCOP: d.241.1.1 g.59.1.1 Back     alignment and structure
>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A Back     alignment and structure

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 198
d1enwa_114 a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Bak 1e-21
>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 = 83.4 bits (206), Expect = 1e-21
 Identities = 29/121 (23%), Positives = 52/121 (42%), Gaps = 18/121 (14%)

Query: 8   TNVPKASKVVK-----CNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAI 62
           +++P+ SK         +  +R+ V K LY  L+K S                + +  A 
Sbjct: 2   SHMPRNSKNDGVDTAIYHHKLRDQVLKALYDVLAKESEH-----------PPQSILHTAK 50

Query: 63  SMESAMYEKWGRSS--ETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEM 120
           ++ES M +     +    YK +YR +  N     N + + K+  GD+ PE +    AK++
Sbjct: 51  AIESEMNKVNNCDTNEAAYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDL 110

Query: 121 A 121
           A
Sbjct: 111 A 111

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query198
d1enwa_114 Elongation factor TFIIS domain 2 {Baker's yeast (S 99.91
d1tfia_50 Transcriptional factor SII, C-terminal domain {Hum 99.59
d1qypa_57 RBP9 subunit of RNA polymerase II {Archaeon Thermo 99.17
d1twfi272 RBP9 subunit of RNA polymerase II {Baker's yeast ( 99.04
d2akla238 Hypothetical protein PA0128, N-terminal domain {Ps 93.54
d1k81a_36 Zinc-binding domain of translation initiation fact 92.88
d1neea237 Zinc-binding domain of translation initiation fact 92.0
d1qxfa_58 Ribosomal protein S27e {Archaeon Archaeoglobus ful 90.42
d1vd4a_62 Transcription initiation factor TFIIE-alpha {Human 89.35
d1dl6a_58 Transcription initiation factor TFIIB, N-terminal 85.72
d2fiya1290 FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId 85.48
d1wiia_85 Hypothetical UPF0222 protein MGC4549 {Mouse (Mus m 84.55
d1pfta_50 Transcription initiation factor TFIIB, N-terminal 80.95
>d1enwa_ a.5.4.1 (A:) Elongation factor TFIIS domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: Elongation factor TFIIS domain 2
family: Elongation factor TFIIS domain 2
domain: Elongation factor TFIIS domain 2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.91  E-value=1.3e-25  Score=169.38  Aligned_cols=102  Identities=27%  Similarity=0.386  Sum_probs=88.0

Q ss_pred             CCCCcc--ccCCcHHHHHHHHHHHHHHhhhhhhccccchhhhhhcccChHHHHHHHHHHHHHHhCC--CcHHHHHHHHHH
Q 036389           11 PKASKV--VKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGR--SSETYKFKYRRL   86 (198)
Q Consensus        11 ~~~~~~--~~~~d~iR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~~~~A~~IE~alf~~~~~--~~~~Yk~k~Rsl   86 (198)
                      |+...+  ..++|++|++|+++|+++|.....+.+           .....+|.+||++||..|+.  ++..|++|+|||
T Consensus         8 ~k~d~v~~~~~~d~~R~~~~~~L~~aL~~~~~~~~-----------~~~~~la~~IE~~lf~~~~~~~~~~~Y~~k~rsi   76 (114)
T d1enwa_           8 SKNDGVDTAIYHHKLRDQVLKALYDVLAKESEHPP-----------QSILHTAKAIESEMNKVNNCDTNEAAYKARYRII   76 (114)
T ss_dssp             TTTTCCCCCSSTTTTHHHHHHHHHHHHHHHCSSSC-----------SCHHHHHHHHTTTTTSSCTTTTTHHHHHHHHHHH
T ss_pred             ccCCCCCCccCCcHHHHHHHHHHHHHHhCcCccch-----------hHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHH
Confidence            555555  468899999999999999986543322           23578999999999998863  457899999999


Q ss_pred             HHhcCCCCCHHHHHHhhcCCCCchhcccCCHHhhccH
Q 036389           87 LFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASD  123 (198)
Q Consensus        87 ~~NLkd~kNp~Lr~~vl~G~isp~~lv~Ms~eELas~  123 (198)
                      +|||||++||+|+.+|++|+|+|++||.|+++|||+.
T Consensus        77 ~~NLkd~~N~~L~~~v~~g~i~p~~l~~M~~~ElaP~  113 (114)
T d1enwa_          77 YSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPA  113 (114)
T ss_dssp             HHHHTTSCCCCTTTHHHHCSSCCSSHHHHTTTTTCSC
T ss_pred             HHHcCccchHHHHHHHHcCCCCHHHHhCCCHHHcCCC
Confidence            9999999999999999999999999999999999973
>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]} Back     information, alignment and structure
>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {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
>d1neea2 g.59.1.1 (A:99-135) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1vd4a_ g.41.3.1 (A:) Transcription initiation factor TFIIE-alpha {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} 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
>d1wiia_ g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure