Citrus Sinensis ID: 046567

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------
MEESHNILYEALSPLRGSQASDDPTLRQSPPPDELDHYTVFRNEISLTDLHCAAEESPAQDFFSLDVNESGVDDVEEVEPKTPPAKSAEPRMENRWFKGNSRFKSPMLQLHKEIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSGVSFDIRHFMDICRVIRMVCHTWGLVGD
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHccccccEEEEEEccccccccccccEEEcccccccHHHHHHHHHHHHHHccccccEEEEccccccEEEEEEccccEEEEEEEccHHHHHHHHHHHHHccccc
ccccccHHHHcccccccccccccccccccccccccccEEEEEcccccccccccccccccccHccccccHcccccccccccccccHHccccccccccccccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHccccEEEEEEEccccccccccccEEEEEcccccccHHHHHHHHHHHHHcccccEEEEEcccEcEEEEEEcccccEEEEEEccHHHHHHHHHHHHHcccccc
MEESHNILYEalsplrgsqasddptlrqspppdeldhytvfrneisltdlhcaaeespaqdffsldvnesgvddveevepktppaksaeprmenrwfkgnsrfkspmLQLHKEIVDfcdflsptsdereVRNTAVEAVFDVIKYiwpkckpevfgsfrtglylptsdiDVVIMesgihnpaTGLQALSRALLQRGIAKKIQVIAKARVPIVKFVekksgvsfdirHFMDICRVIRMVCHTWGLVGD
MEESHNILYEALsplrgsqasddPTLRQSPPPDELDHYTVFRNEISLTDLHCAAEESPAQDFFSLDVNESgvddveevepktppaksaeprmenrWFKGNSRFKSPMLQLHKEIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIakarvpivkfvekksgvsfdirHFMDICRVIRMVCHTWGLVGD
MEESHNILYEALSPLRGSQASDDPTLRQSPPPDELDHYTVFRNEISLTDLHCAAEESPAQDFFSLDVNESGVDDVEEVEPKTPPAKSAEPRMENRWFKGNSRFKSPMLQLHKEIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSGVSFDIRHFMDICRVIRMVCHTWGLVGD
************************************HYTVFRNEISLTDLHCAA************************************************F*SPMLQLHKEIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSGVSFDIRHFMDICRVIRMVCHTWGLV**
*****NI**************************************************************************************************PMLQLHKEIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSGVSFDIRHFMDICRVIRMVCHTWGLVG*
MEESHNILYEALSPLR*************PPPDELDHYTVFRNEISLTDLHCAAEESPAQDFFSLDVNES********************RMENRWFKGNSRFKSPMLQLHKEIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSGVSFDIRHFMDICRVIRMVCHTWGLVGD
*****NIL***LSPLRG*****************LDHYTVFRNEISL**********************************************NRWFKGNSRFKSPMLQLHKEIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSGVSFDIRHFMDICRVIRMVCHTWGLVG*
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MEESHNILYEALSPLRGSQASDDPTLRQSPPPDELDHYTVFRNEISLTDLHCAAEESPAQDFFSLDVNESGVDDVEEVEPKTPPAKSAEPRMENRWFKGNSRFKSPMLQLHKEIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSGVSFDIRHFMDICRVIRMVCHTWGLVGD
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 ?
Query246 2.2.26 [Sep-21-2011]
P53632 584 Poly(A) RNA polymerase pr yes no 0.5 0.210 0.414 3e-21
Q9HFW3 626 Poly(A) RNA polymerase pr yes no 0.674 0.265 0.350 5e-21
Q68ED3 633 PAP-associated domain-con no no 0.548 0.213 0.363 2e-18
Q8NDF8 572 PAP-associated domain-con no no 0.548 0.236 0.363 3e-18
Q9UTN3 684 Poly(A) RNA polymerase ci yes no 0.467 0.168 0.401 5e-17
P48561 642 Poly(A) RNA polymerase pr no no 0.512 0.196 0.366 6e-17
Q5XG87 542 DNA polymerase sigma OS=H no no 0.430 0.195 0.396 3e-14
Q6PB75 542 DNA polymerase sigma OS=M no no 0.430 0.195 0.396 3e-14
G5EFL0 845 Poly(A) RNA polymerase gl yes no 0.5 0.145 0.365 9e-14
Q5BLK4 1491 Terminal uridylyltransfer no no 0.443 0.073 0.341 2e-07
>sp|P53632|PAP2_YEAST Poly(A) RNA polymerase protein 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PAP2 PE=1 SV=1 Back     alignment and function desciption
 Score =  102 bits (253), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 53/128 (41%), Positives = 80/128 (62%), Gaps = 5/128 (3%)

Query: 113 EIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDID-VV 171
           EI DF  ++SP+ +E E+RN  +  + + +K +WP     VFGS+ T LYLP SDID VV
Sbjct: 182 EIKDFVAYISPSREEIEIRNQTISTIREAVKQLWPDADLHVFGSYSTDLYLPGSDIDCVV 241

Query: 172 IMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSG----VSFDIRHF 227
             E G       L +L+  L ++ +A +++V+AKARVPI+KFVE  SG    VSF+  + 
Sbjct: 242 TSELGGKESRNNLYSLASHLKKKNLATEVEVVAKARVPIIKFVEPHSGIHIDVSFERTNG 301

Query: 228 MDICRVIR 235
           ++  ++IR
Sbjct: 302 IEAAKLIR 309
Catalytic subunit of the TRAMP complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates like cryptic transcripts generated by RNA polymerase II and III, or hypomethylated pre-tRNAi-Met. Polyadenylates RNA processing and degradation intermediates of snRNAs, snoRNAs and mRNAs that accumulate in strains lacking a functional exosome. TRF4 is also required for proper nuclear division in mitosis, DNA damage repair and sister chromatid cohesion. Involved in the regulation of histone mRNA levels. May mediate mitotic chromosome condensation.
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: -
>sp|Q9HFW3|TRF5_ASHGO Poly(A) RNA polymerase protein 1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=TRF5 PE=3 SV=1 Back     alignment and function description
>sp|Q68ED3|PAPD5_MOUSE PAP-associated domain-containing protein 5 OS=Mus musculus GN=Papd5 PE=2 SV=2 Back     alignment and function description
>sp|Q8NDF8|PAPD5_HUMAN PAP-associated domain-containing protein 5 OS=Homo sapiens GN=PAPD5 PE=1 SV=2 Back     alignment and function description
>sp|Q9UTN3|CID14_SCHPO Poly(A) RNA polymerase cid14 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cid14 PE=1 SV=2 Back     alignment and function description
>sp|P48561|TRF5_YEAST Poly(A) RNA polymerase protein 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TRF5 PE=1 SV=2 Back     alignment and function description
>sp|Q5XG87|PAPD7_HUMAN DNA polymerase sigma OS=Homo sapiens GN=PAPD7 PE=1 SV=2 Back     alignment and function description
>sp|Q6PB75|PAPD7_MOUSE DNA polymerase sigma OS=Mus musculus GN=Papd7 PE=2 SV=1 Back     alignment and function description
>sp|G5EFL0|GLD4_CAEEL Poly(A) RNA polymerase gld-4 OS=Caenorhabditis elegans GN=gld-4 PE=1 SV=1 Back     alignment and function description
>sp|Q5BLK4|TUT7_MOUSE Terminal uridylyltransferase 7 OS=Mus musculus GN=Zcchc6 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 ?
Query246
255566595 526 nucleic acid binding protein, putative [ 0.853 0.399 0.640 1e-71
449446931 544 PREDICTED: PAP-associated domain-contain 0.902 0.408 0.590 2e-67
84468450 518 hypothetical protein [Trifolium pratense 0.869 0.413 0.586 1e-65
224128147 543 predicted protein [Populus trichocarpa] 0.865 0.392 0.616 2e-62
449498731 384 PREDICTED: uncharacterized protein LOC10 0.739 0.473 0.627 4e-60
9759071 533 unnamed protein product [Arabidopsis tha 0.890 0.410 0.55 2e-59
297792777 530 hypothetical protein ARALYDRAFT_495454 [ 0.890 0.413 0.545 2e-59
359493669 497 PREDICTED: PAP-associated domain-contain 0.743 0.368 0.635 2e-59
18423551 530 Nucleotidyltransferase family protein [A 0.890 0.413 0.55 2e-59
343172002 501 Nucleotidyltransferase family protein, p 0.906 0.445 0.528 5e-59
>gi|255566595|ref|XP_002524282.1| nucleic acid binding protein, putative [Ricinus communis] gi|223536473|gb|EEF38121.1| nucleic acid binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  275 bits (703), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 153/239 (64%), Positives = 175/239 (73%), Gaps = 29/239 (12%)

Query: 8   LYEALSPLRGSQASDDPTLRQSP-PPDELDH-----YTVFRNEISLTDLHCAAEESPAQD 61
           LY+ LSPL        PT  QSP   D+ DH     ++VFRNEISL+  + +A ES A D
Sbjct: 18  LYQTLSPL------SLPTPDQSPRSDDDGDHRHPNPFSVFRNEISLSTANSSAIESVAPD 71

Query: 62  FFSLDVNESGVDDVEEVEPKTP-----PAKS------AEPRMENRWFKGNSRFKSPMLQL 110
           FFSLDV E+        EPKTP     P KS      +E ++E+ WF+GNSRF+SPMLQL
Sbjct: 72  FFSLDVVEAAA------EPKTPSVVAEPRKSKAAQSVSETKLESSWFRGNSRFRSPMLQL 125

Query: 111 HKEIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDV 170
           HKEIVDFCDFLSPT +E + RNTAV+ VFDVIKYIWP CK EVFGS++TGLYLPTSDIDV
Sbjct: 126 HKEIVDFCDFLSPTPEEEDARNTAVKCVFDVIKYIWPNCKVEVFGSYKTGLYLPTSDIDV 185

Query: 171 VIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSGVSFDIRHFMD 229
           VI  SGI NP  GLQALSRAL Q+GIAKKIQVIAKARVPIVKFVEK+SGVSFDI   +D
Sbjct: 186 VIFRSGIKNPQIGLQALSRALSQKGIAKKIQVIAKARVPIVKFVEKRSGVSFDISFDVD 244

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449446931|ref|XP_004141224.1| PREDICTED: PAP-associated domain-containing protein 5-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|84468450|dbj|BAE71308.1| hypothetical protein [Trifolium pratense] Back     alignment and taxonomy information
>gi|224128147|ref|XP_002329093.1| predicted protein [Populus trichocarpa] gi|222869762|gb|EEF06893.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449498731|ref|XP_004160618.1| PREDICTED: uncharacterized protein LOC101229001 [Cucumis sativus] Back     alignment and taxonomy information
>gi|9759071|dbj|BAB09549.1| unnamed protein product [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297792777|ref|XP_002864273.1| hypothetical protein ARALYDRAFT_495454 [Arabidopsis lyrata subsp. lyrata] gi|297310108|gb|EFH40532.1| hypothetical protein ARALYDRAFT_495454 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|359493669|ref|XP_002282332.2| PREDICTED: PAP-associated domain-containing protein 5-like [Vitis vinifera] gi|302143015|emb|CBI20310.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|18423551|ref|NP_568798.1| Nucleotidyltransferase family protein [Arabidopsis thaliana] gi|27754278|gb|AAO22592.1| unknown protein [Arabidopsis thaliana] gi|332009022|gb|AED96405.1| Nucleotidyltransferase family protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|343172002|gb|AEL98705.1| Nucleotidyltransferase family protein, partial [Silene latifolia] 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 ?
Query246
TAIR|locus:2164047 530 AT5G53770 "AT5G53770" [Arabido 0.898 0.416 0.563 3.2e-58
SGD|S000005475 584 PAP2 "Non-canonical poly(A) po 0.666 0.280 0.346 6.4e-21
UNIPROTKB|Q8NDF8 572 PAPD5 "PAP-associated domain-c 0.512 0.220 0.379 2.1e-20
UNIPROTKB|H3BQM0 588 PAPD5 "PAP-associated domain-c 0.512 0.214 0.379 2.3e-20
UNIPROTKB|E9PC61 619 PAPD5 "PAP-associated domain-c 0.512 0.203 0.379 2.9e-20
UNIPROTKB|B4DV38 698 PAPD5 "PAP-associated domain-c 0.512 0.180 0.379 4.5e-20
ZFIN|ZDB-GENE-041021-1 762 papd7 "PAP associated domain c 0.491 0.158 0.417 4.6e-19
UNIPROTKB|F1NCH7 501 PAPD5 "Uncharacterized protein 0.5 0.245 0.386 6.5e-19
FB|FBgn0030049 1001 Trf4-1 [Drosophila melanogaste 0.512 0.125 0.396 7.1e-19
CGD|CAL0005626 603 orf19.429 [Candida albicans (t 0.983 0.401 0.293 7.9e-19
TAIR|locus:2164047 AT5G53770 "AT5G53770" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 598 (215.6 bits), Expect = 3.2e-58, P = 3.2e-58
 Identities = 134/238 (56%), Positives = 161/238 (67%)

Query:     3 ESHNILYEALSPLRGSQASDDPTLRQSPPP--DELDHYTVFRNEISLTDLHCAAEESPAQ 60
             E+   +Y+ L PL  S ++      QSPPP  +E   Y+VFR EIS         ES   
Sbjct:     9 EAPAFVYDTLPPLSFSDSN------QSPPPTHEESHQYSVFRKEISDFPDDTTPVESATV 62

Query:    61 DFFSLDVN----ESGVDDVEEV----EPKTPPAKS-AEPRMENRWFKGNSRFKSPMLQLH 111
             DFFSLDV     E+GV+ V  V    + K+   K   EPR+E+ WF  NS  K PMLQLH
Sbjct:    63 DFFSLDVEGETTENGVEPVTPVVVASKKKSKKRKKDEEPRLESNWFSENSFSKIPMLQLH 122

Query:   112 KEIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDVV 171
             KEIVDFCDFL PT  E+  R+ AVE+V  VIKYIWP CK EVFGS++TGLYLPTSDIDVV
Sbjct:   123 KEIVDFCDFLLPTQAEKAERDAAVESVSSVIKYIWPSCKVEVFGSYKTGLYLPTSDIDVV 182

Query:   172 IMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSGVSFDIRHFMD 229
             I+ESG+ NP  GL+ALSRAL QRGIAK + VIAKARVPI+KFVEKKS ++FD+   M+
Sbjct:   183 ILESGLTNPQLGLRALSRALSQRGIAKNLLVIAKARVPIIKFVEKKSNIAFDLSFDME 240
GO:0003676 "nucleic acid binding" evidence=ISS
GO:0005634 "nucleus" evidence=ISM
GO:0016779 "nucleotidyltransferase activity" evidence=IEA
GO:0006312 "mitotic recombination" evidence=RCA
GO:0009560 "embryo sac egg cell differentiation" evidence=RCA
GO:0009688 "abscisic acid biosynthetic process" evidence=RCA
SGD|S000005475 PAP2 "Non-canonical poly(A) polymerase" [Saccharomyces cerevisiae (taxid:4932)] Back     alignment and assigned GO terms
UNIPROTKB|Q8NDF8 PAPD5 "PAP-associated domain-containing protein 5" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|H3BQM0 PAPD5 "PAP-associated domain-containing protein 5" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E9PC61 PAPD5 "PAP-associated domain-containing protein 5" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|B4DV38 PAPD5 "PAP-associated domain-containing protein 5" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-041021-1 papd7 "PAP associated domain containing 7" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|F1NCH7 PAPD5 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
FB|FBgn0030049 Trf4-1 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
CGD|CAL0005626 orf19.429 [Candida albicans (taxid:5476)] 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 ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.7LOW CONFIDENCE prediction!

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 ?
Query246
cd05402114 cd05402, NT_PAP_TUTase, Nucleotidyltransferase (NT 2e-27
COG5260 482 COG5260, TRF4, DNA polymerase sigma [DNA replicati 9e-24
pfam04928 349 pfam04928, PAP_central, Poly(A) polymerase central 5e-08
pfam0190992 pfam01909, NTP_transf_2, Nucleotidyltransferase do 6e-07
>gnl|CDD|143392 cd05402, NT_PAP_TUTase, Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases Back     alignment and domain information 
 Score =  101 bits (253), Expect = 2e-27
 Identities = 34/96 (35%), Positives = 57/96 (59%), Gaps = 1/96 (1%)

Query: 130 VRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDVVIM-ESGIHNPATGLQALS 188
            R   ++ + ++IK  +P  K   FGS+ TGL LP SDID+ ++  +   +    L+ L+
Sbjct: 1   KREEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLA 60

Query: 189 RALLQRGIAKKIQVIAKARVPIVKFVEKKSGVSFDI 224
           + L + G   +++ I  ARVPI+KFV+K +G+  DI
Sbjct: 61  KLLKKSGEVVEVEPIINARVPIIKFVDKPTGIEVDI 96

Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxylate residues are conserved. Length = 114
>gnl|CDD|227585 COG5260, TRF4, DNA polymerase sigma [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|203124 pfam04928, PAP_central, Poly(A) polymerase central domain Back     alignment and domain information
>gnl|CDD|216779 pfam01909, NTP_transf_2, Nucleotidyltransferase 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 246
cd05402114 NT_PAP_TUTase Nucleotidyltransferase (NT) domain o 99.94
KOG1906 514 consensus DNA polymerase sigma [Replication, recom 99.92
COG5260 482 TRF4 DNA polymerase sigma [DNA replication, recomb 99.91
PTZ00418 593 Poly(A) polymerase; Provisional 99.61
KOG2245 562 consensus Poly(A) polymerase and related nucleotid 99.37
COG5186 552 PAP1 Poly(A) polymerase [RNA processing and modifi 99.06
KOG2277 596 consensus S-M checkpoint control protein CID1 and 98.88
PF0190993 NTP_transf_2: Nucleotidyltransferase domain A subs 98.53
cd0539749 NT_Pol-beta-like Nucleotidyltransferase (NT) domai 98.45
TIGR03671 408 cca_archaeal CCA-adding enzyme. 98.33
cd05400143 NT_2-5OAS_ClassI-CCAase Nucleotidyltransferase (NT 98.33
PRK13300 447 tRNA CCA-pyrophosphorylase; Provisional 98.25
cd0540393 NT_KNTase_like Nucleotidyltransferase (NT) domain 98.19
COG1746 443 CCA1 tRNA nucleotidyltransferase (CCA-adding enzym 97.64
COG166997 Predicted nucleotidyltransferases [General functio 97.55
COG1708128 Predicted nucleotidyltransferases [General functio 97.55
PRK13746 262 aminoglycoside resistance protein; Provisional 97.24
PF14792112 DNA_pol_B_palm: DNA polymerase beta palm ; PDB: 1R 95.98
PRK02098221 phosphoribosyl-dephospho-CoA transferase; Provisio 95.05
TIGR03135202 malonate_mdcG holo-ACP synthase, malonate decarbox 94.95
cd00141307 NT_POLXc Nucleotidyltransferase (NT) domain of fam 92.94
PF10620213 MdcG: Phosphoribosyl-dephospho-CoA transferase Mdc 92.17
KOG3793 362 consensus Transcription factor NFAT, subunit NF45 90.48
PF14091152 DUF4269: Domain of unknown function (DUF4269) 89.48
PRK05007 884 PII uridylyl-transferase; Provisional 89.33
cd05401172 NT_GlnE_GlnD_like Nucleotidyltransferase (NT) doma 89.28
PRK01293207 phosphoribosyl-dephospho-CoA transferase; Provisio 88.56
KOG2534353 consensus DNA polymerase IV (family X) [Replicatio 87.86
PRK00227 693 glnD PII uridylyl-transferase; Provisional 85.56
PF03445138 DUF294: Putative nucleotidyltransferase DUF294; In 84.41
PF10127 247 Nuc-transf: Predicted nucleotidyltransferase; Inte 82.76
smart00483334 POLXc DNA polymerase X family. includes vertebrate 81.56
COG2413228 Predicted nucleotidyltransferase [General function 81.54
>cd05402 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases Back     alignment and domain information 
Probab=99.94  E-value=1.8e-26  Score=181.68  Aligned_cols=109  Identities=32%  Similarity=0.478  Sum_probs=97.6

Q ss_pred             HHHHHHHHHHHHHHhhCCCceEEEecccccCCCCCCCCceEEEecCCC-CChhHHHHHHHHHHHhCCCcceEEEecCCCc
Q 046567          130 VRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDVVIMESGI-HNPATGLQALSRALLQRGIAKKIQVIAKARV  208 (246)
Q Consensus       130 ~R~~ii~~l~~vv~~~~P~~~V~~FGS~~tGL~lp~SDIDl~I~~~~~-~~~~~~L~~L~~~L~~~~~~~~V~~I~~ARV  208 (246)
                      .|++++++|+++++++||++++++|||+++|+++|+||||++|..+.. ...+..+..+++.|++.+.+.+++.|.+|||
T Consensus         1 ~r~~i~~~l~~~i~~~~~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~i~~ArV   80 (114)
T cd05402           1 KREEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKKSGEVVEVEPIINARV   80 (114)
T ss_pred             CHHHHHHHHHHHHHHHCCCCEEEEecccccCCCCCCCCeeEEEEeCCCCccHHHHHHHHHHHHHhCCCceeeEEeccCCC
Confidence            488999999999999999999999999999999999999999998865 4456789999999999887789999999999


Q ss_pred             eeEEEEEcCCCeEEEEEeecc-hHHHHHHHH
Q 046567          209 PIVKFVEKKSGVSFDIRHFMD-ICRVIRMVC  238 (246)
Q Consensus       209 PIIKf~d~~tgI~~DISfnn~-g~~~~r~~~  238 (246)
                      |||||+++.+|+.|||||+|. |.+.++++.
T Consensus        81 Piik~~~~~~~i~~Dis~~~~~g~~~s~li~  111 (114)
T cd05402          81 PIIKFVDKPTGIEVDISFNNLNGIRNTKLLR  111 (114)
T ss_pred             CEEEEEEcCCCeEEEEEcccchHHHHHHHHH
Confidence            999999999999999999995 455555443

Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxyla
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair] Back     alignment and domain information
>COG5260 TRF4 DNA polymerase sigma [DNA replication, recombination, and repair] Back     alignment and domain information
>PTZ00418 Poly(A) polymerase; Provisional Back     alignment and domain information
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification] Back     alignment and domain information
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification] Back     alignment and domain information
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>PF01909 NTP_transf_2: Nucleotidyltransferase domain A subset of this Pfam family; InterPro: IPR002934 A small region that overlaps with a nuclear localization signal and binds to the RNA primer contains three aspartates that are essential for catalysis Back     alignment and domain information
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins Back     alignment and domain information
>TIGR03671 cca_archaeal CCA-adding enzyme Back     alignment and domain information
>cd05400 NT_2-5OAS_ClassI-CCAase Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme Back     alignment and domain information
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional Back     alignment and domain information
>cd05403 NT_KNTase_like Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins Back     alignment and domain information
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG1669 Predicted nucleotidyltransferases [General function prediction only] Back     alignment and domain information
>COG1708 Predicted nucleotidyltransferases [General function prediction only] Back     alignment and domain information
>PRK13746 aminoglycoside resistance protein; Provisional Back     alignment and domain information
>PF14792 DNA_pol_B_palm: DNA polymerase beta palm ; PDB: 1RZT_A 3PML_A 2PFN_A 3HX0_K 3HWT_A 2GWS_E 2BCQ_A 3UPQ_A 2BCS_A 3UQ2_A Back     alignment and domain information
>PRK02098 phosphoribosyl-dephospho-CoA transferase; Provisional Back     alignment and domain information
>TIGR03135 malonate_mdcG holo-ACP synthase, malonate decarboxylase-specific Back     alignment and domain information
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases Back     alignment and domain information
>PF10620 MdcG: Phosphoribosyl-dephospho-CoA transferase MdcG; InterPro: IPR017557 Malonate decarboxylase, like citrate lyase, has a unique acyl carrier protein subunit with a prosthetic group derived from, and distinct from, coenzyme A Back     alignment and domain information
>KOG3793 consensus Transcription factor NFAT, subunit NF45 [Transcription] Back     alignment and domain information
>PF14091 DUF4269: Domain of unknown function (DUF4269) Back     alignment and domain information
>PRK05007 PII uridylyl-transferase; Provisional Back     alignment and domain information
>cd05401 NT_GlnE_GlnD_like Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins Back     alignment and domain information
>PRK01293 phosphoribosyl-dephospho-CoA transferase; Provisional Back     alignment and domain information
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair] Back     alignment and domain information
>PRK00227 glnD PII uridylyl-transferase; Provisional Back     alignment and domain information
>PF03445 DUF294: Putative nucleotidyltransferase DUF294; InterPro: IPR005105 This domain is found associated with an N-terminal cyclic nucleotide-binding domain (IPR000595 from INTERPRO) and two CBS domains (IPR000644 from INTERPRO) Back     alignment and domain information
>PF10127 Nuc-transf: Predicted nucleotidyltransferase; InterPro: IPR018775 Proteins in this entry are predicted to catalyse the transfer of nucleotide residues from nucleoside diphosphates or triphosphates into dimer or polymer forms Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family Back     alignment and domain information
>COG2413 Predicted nucleotidyltransferase [General function prediction only] 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 ?
Query246
3nyb_A 323 Structure And Function Of The Polymerase Core Of Tr 2e-21
4e7x_A 405 Structural Basis For The Activity Of A Cytoplasmic 5e-06
4fhx_A 349 Crystal Structures Of The Cid1 Poly (U) Polymerase 1e-05
4fh3_A 349 Crystal Structures Of The Cid1 Poly (U) Polymerase 1e-05
4ep7_A 340 Functional Implications From The Cid1 Poly(U) Polym 1e-05
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A Rna Surveillance Complex Length = 323 Back     alignment and structure 
Iteration: 1

 Score = 99.4 bits (246), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 53/128 (41%), Positives = 80/128 (62%), Gaps = 5/128 (3%)
Query: 113 EIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDID-VV 171
           EI DF  ++SP+ +E E+RN  +  + + +K +WP     VFGS+ T LYLP SDID VV
Sbjct: 24  EIKDFVAYISPSREEIEIRNQTISTIREAVKQLWPDADLHVFGSYSTDLYLPGSDIDCVV 83
Query: 172 IMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSG----VSFDIRHF 227
             E G       L +L+  L ++ +A +++V+AKARVPI+KFVE  SG    VSF+  + 
Sbjct: 84  TSELGGKESRNNLYSLASHLKKKNLATEVEVVAKARVPIIKFVEPHSGIHIAVSFERTNG 143
Query: 228 MDICRVIR 235
           ++  ++IR
Sbjct: 144 IEAAKLIR 151
>pdb|4E7X|A Chain A, Structural Basis For The Activity Of A Cytoplasmic Rna Terminal U- Transferase Length = 405 Back     alignment and structure
>pdb|4FHX|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal The Mechanism For Utp Selectivity - H336n Mutant Bound To Mgatp Length = 349 Back     alignment and structure
>pdb|4FH3|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal The Mechanism For Utp Selectivity Length = 349 Back     alignment and structure
>pdb|4EP7|A Chain A, Functional Implications From The Cid1 Poly(U) Polymerase Crystal Structure Length = 340 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 ?
Query246
3nyb_A 323 Poly(A) RNA polymerase protein 2; polya RNA polyme 8e-35
3hj4_A 384 Minor editosome-associated tutase; nucleotidyltran 1e-30
3pq1_A 464 Poly(A) RNA polymerase; nucleotidyl transferase, R 6e-26
4e8f_A 405 Poly(A) RNA polymerase protein CID1; beta polymera 9e-26
2b4v_A 468 RNA editing complex protein MP57; tbret2, TBMP57, 3e-25
2b4v_A 468 RNA editing complex protein MP57; tbret2, TBMP57, 3e-04
2ikf_A 353 RNA uridylyl transferase; tutase, nucleotidyltrans 1e-23
4ep7_A 340 Poly(A) RNA polymerase protein CID1; poly(U) polym 2e-23
2hhp_A 530 Poly(A) polymerase; template-independent RNA polym 8e-18
1q79_A 514 Poly(A) polymerase alpha; mRNA processing, nucleot 1e-15
1no5_A114 Hypothetical protein HI0073; structural genomics, 5e-06
2rff_A111 Putative nucleotidyltransferase; NP_343093.1, nucl 1e-04
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-04
1r89_A 437 TRNA nucleotidyltransferase; CCA adding enzyme, in 2e-04
>3nyb_A Poly(A) RNA polymerase protein 2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Length = 323 Back     alignment and structure
 Score =  125 bits (316), Expect = 8e-35
 Identities = 50/125 (40%), Positives = 75/125 (60%), Gaps = 1/125 (0%)

Query: 101 SRFKSPMLQLHKEIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTG 160
           S+ K     L  EI DF  ++SP+ +E E+RN  +  + + +K +WP     VFGS+ T 
Sbjct: 12  SKQKEISDWLTFEIKDFVAYISPSREEIEIRNQTISTIREAVKQLWPDADLHVFGSYSTD 71

Query: 161 LYLPTSDIDVVIM-ESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSG 219
           LYLP SDID V+  E G       L +L+  L ++ +A +++V+AKARVPI+KFVE  SG
Sbjct: 72  LYLPGSDIDCVVTSELGGKESRNNLYSLASHLKKKNLATEVEVVAKARVPIIKFVEPHSG 131

Query: 220 VSFDI 224
           +   +
Sbjct: 132 IHIAV 136
>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens} Length = 464 Back     alignment and structure
>4e8f_A Poly(A) RNA polymerase protein CID1; beta polymerase-like nucleotidyl transferase, terminal uridi transferase, UTP, cytoplasmic; 2.60A {Schizosaccharomyces pombe 972h-} PDB: 4e7x_A* 4e80_A Length = 405 Back     alignment and structure
>2b4v_A RNA editing complex protein MP57; tbret2, TBMP57, terminal uridylyl transferase, editosome, transferase/RNA binding protein complex; 1.80A {Trypanosoma brucei} SCOP: a.160.1.4 d.218.1.10 PDB: 2b51_A* 2b56_A* Length = 468 Back     alignment and structure
>2b4v_A RNA editing complex protein MP57; tbret2, TBMP57, terminal uridylyl transferase, editosome, transferase/RNA binding protein complex; 1.80A {Trypanosoma brucei} SCOP: a.160.1.4 d.218.1.10 PDB: 2b51_A* 2b56_A* Length = 468 Back     alignment and structure
>2ikf_A RNA uridylyl transferase; tutase, nucleotidyltransferase, UTP-binding, RNA editing; HET: UTP; 2.00A {Trypanosoma brucei} PDB: 2nom_A* 2q0c_A* 2q0d_A* 2q0e_A* 2q0f_A* 2q0g_A* Length = 353 Back     alignment and structure
>4ep7_A Poly(A) RNA polymerase protein CID1; poly(U) polymerase, UTP binding, transferase; HET: UTP; 2.28A {Schizosaccharomyces pombe} Length = 340 Back     alignment and structure
>2hhp_A Poly(A) polymerase; template-independent RNA polymerase, transferase; HET: FLC; 1.80A {Saccharomyces cerevisiae} SCOP: a.160.1.1 d.218.1.3 d.58.16.1 PDB: 1fa0_A* 3c66_A* 2o1p_A 2q66_A* Length = 530 Back     alignment and structure
>1no5_A Hypothetical protein HI0073; structural genomics, nucleotidyl transferase structure 2 function project, S2F, unknown function; 1.80A {Haemophilus influenzae} SCOP: d.218.1.5 Length = 114 Back     alignment and structure
>2rff_A Putative nucleotidyltransferase; NP_343093.1, nucleotidyltransferase domain, structural genomics; HET: MSE; 1.40A {Sulfolobus solfataricus P2} Length = 111 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
>1r89_A TRNA nucleotidyltransferase; CCA adding enzyme, incoming nucleotide, nucleotidyltransfera superfamily; HET: CTP; 1.80A {Archaeoglobus fulgidus} SCOP: a.160.1.3 d.218.1.7 d.58.16.2 PDB: 1r8a_A 1r8b_A* 1r8c_A* 1sz1_A* 1tfw_A* 1tfy_A* 1uet_A 1ueu_A* 1uev_A* 2dr5_A 2dr7_A 2dr8_A* 2dr9_A 2dra_A* 2drb_A 2dvi_A* 2zh1_A 2zh2_A 2zh3_A 2zh4_A ... Length = 437 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query246
3nyb_A 323 Poly(A) RNA polymerase protein 2; polya RNA polyme 99.97
3pq1_A 464 Poly(A) RNA polymerase; nucleotidyl transferase, R 99.95
3hj4_A 384 Minor editosome-associated tutase; nucleotidyltran 99.94
4e8f_A 405 Poly(A) RNA polymerase protein CID1; beta polymera 99.94
4fh3_A 349 Poly(A) RNA polymerase protein CID1; nucleotidyltr 99.92
2ikf_A 353 RNA uridylyl transferase; tutase, nucleotidyltrans 99.91
2hhp_A 530 Poly(A) polymerase; template-independent RNA polym 99.86
1q79_A 514 Poly(A) polymerase alpha; mRNA processing, nucleot 99.86
2b4v_A 468 RNA editing complex protein MP57; tbret2, TBMP57, 99.85
1no5_A114 Hypothetical protein HI0073; structural genomics, 98.5
1ylq_A96 Putative nucleotidyltransferase, hypothetical Pro 98.35
1wot_A98 Putative minimal nucleotidyltransferase; alpha and 97.96
1px5_A 349 2'-5'-oligoadenylate synthetase 1; 5-stranded anti 97.89
2rff_A111 Putative nucleotidyltransferase; NP_343093.1, nucl 97.84
1r89_A 437 TRNA nucleotidyltransferase; CCA adding enzyme, in 97.75
4ebj_A 272 Aminoglycoside nucleotidyltransferase; structural 97.13
1kny_A 253 Kntase, kanamycin nucleotidyltransferase; antibiot 96.98
4at7_A 364 Interleukin enhancer-binding factor 2; transcripti 96.58
2fmp_A335 DNA polymerase beta; nucleotidyl transferase, tran 94.38
2bcq_A335 DNA polymerase lambda; misalignment, extrahelical, 93.91
3jz0_A 287 Lincosamide nucleotidyltransferase; alpha-beta str 93.08
2ihm_A360 POL MU, DNA polymerase MU; helix-turn-helix, trans 88.61
2pbe_A 294 AAD6, aminoglycoside 6-adenylyltransferase; NYSGXR 84.78
1jms_A381 Terminal deoxynucleotidyltransferase; polymerase; 84.22
>3nyb_A Poly(A) RNA polymerase protein 2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Back     alignment and structure
Probab=99.97  E-value=5.1e-31  Score=242.00  Aligned_cols=143  Identities=34%  Similarity=0.574  Sum_probs=128.2

Q ss_pred             CCCCCCCCC--CCCchHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhhCCCceEEEecccccCCCCCCCCceE
Q 046567           93 ENRWFKGNS--RFKSPMLQLHKEIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDV  170 (246)
Q Consensus        93 ~~pW~~~~~--~~~~~~~~L~~EI~~f~~~l~Pt~eE~~~R~~ii~~l~~vv~~~~P~~~V~~FGS~~tGL~lp~SDIDl  170 (246)
                      ++||+..+.  ..++...+||+||.+|+++++|+++|.+.|+.+++.|++++++.||+++|++|||+++|+++|+||||+
T Consensus         2 ~~pw~~~~~~~~~~~~~~~L~~Ei~~f~~~i~Pt~eE~~~R~~~~~~l~~~~~~~~p~~~v~~fGS~~~g~~~~~SDiDl   81 (323)
T 3nyb_A            2 SYPWILNHDHSKQKEISDWLTFEIKDFVAYISPSREEIEIRNQTISTIREAVKQLWPDADLHVFGSYSTDLYLPGSDIDC   81 (323)
T ss_dssp             CCGGGTTCCCTTCSSHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHTTCTTCCEEEESTTTTTCCCTTSCEEE
T ss_pred             CCCCccCCCccccchHHHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEeCccccCCCCCCCCceE
Confidence            579998654  456789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCC-ChhHHHHHHHHHHHhCCCcceEEEecCCCceeEEEEEcCCCeEEEEEeecc-hHHHHH
Q 046567          171 VIMESGIH-NPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSGVSFDIRHFMD-ICRVIR  235 (246)
Q Consensus       171 ~I~~~~~~-~~~~~L~~L~~~L~~~~~~~~V~~I~~ARVPIIKf~d~~tgI~~DISfnn~-g~~~~r  235 (246)
                      +|..+... .....|+.+++.|++.+++.+|++|.+||||||||+|+.+|++|||||+|. |.+.++
T Consensus        82 ~v~~~~~~~~~~~~l~~l~~~L~~~~~~~~v~~I~~ArVPIIk~~~~~~gi~vDIs~~~~~g~~~t~  148 (323)
T 3nyb_A           82 VVTSELGGKESRNNLYSLASHLKKKNLATEVEVVAKARVPIIKFVEPHSGIHIAVSFERTNGIEAAK  148 (323)
T ss_dssp             EECSSCCGGGHHHHHHHHHHHHHHTTSCSSCEEEESSSCEEEEEEETTTTEEEEEESSCSSTTHHHH
T ss_pred             EEecCCCChhHHHHHHHHHHHHhhCCCceEEEEEeccCCCEEEEEEcCCCceEEEEecCcHHHHHHH
Confidence            99987532 235678999999999999899999999999999999999999999999984 433333
>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens} Back     alignment and structure
>4e8f_A Poly(A) RNA polymerase protein CID1; beta polymerase-like nucleotidyl transferase, terminal uridi transferase, UTP, cytoplasmic; 2.60A {Schizosaccharomyces pombe 972h-} PDB: 4e7x_A* 4e80_A Back     alignment and structure
>4fh3_A Poly(A) RNA polymerase protein CID1; nucleotidyltransferase, poly(U) polymerase, transferase; 2.00A {Schizosaccharomyces pombe} PDB: 4fh5_A* 4fhp_A* 4fhv_A* 4fhw_A* 4fhy_A* 4fhx_A* 4ep7_A* Back     alignment and structure
>2ikf_A RNA uridylyl transferase; tutase, nucleotidyltransferase, UTP-binding, RNA editing; HET: UTP; 2.00A {Trypanosoma brucei} PDB: 2nom_A* 2q0c_A* 2q0d_A* 2q0e_A* 2q0f_A* 2q0g_A* Back     alignment and structure
>2hhp_A Poly(A) polymerase; template-independent RNA polymerase, transferase; HET: FLC; 1.80A {Saccharomyces cerevisiae} SCOP: a.160.1.1 d.218.1.3 d.58.16.1 PDB: 1fa0_A* 3c66_A* 2o1p_A 2q66_A* Back     alignment and structure
>2b4v_A RNA editing complex protein MP57; tbret2, TBMP57, terminal uridylyl transferase, editosome, transferase/RNA binding protein complex; 1.80A {Trypanosoma brucei} SCOP: a.160.1.4 d.218.1.10 PDB: 2b51_A* 2b56_A* Back     alignment and structure
>1no5_A Hypothetical protein HI0073; structural genomics, nucleotidyl transferase structure 2 function project, S2F, unknown function; 1.80A {Haemophilus influenzae} SCOP: d.218.1.5 Back     alignment and structure
>1ylq_A Putative nucleotidyltransferase, hypothetical Pro AF0614; structural genomics, PSI, protein ST initiative; 2.02A {Archaeoglobus fulgidus} SCOP: d.218.1.5 Back     alignment and structure
>1wot_A Putative minimal nucleotidyltransferase; alpha and beta, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Thermus thermophilus} SCOP: d.218.1.5 Back     alignment and structure
>1px5_A 2'-5'-oligoadenylate synthetase 1; 5-stranded antiparalel beta sheet, four helix bundle, transferase; HET: YCM; 1.74A {Sus scrofa} SCOP: a.160.1.2 d.218.1.6 Back     alignment and structure
>2rff_A Putative nucleotidyltransferase; NP_343093.1, nucleotidyltransferase domain, structural genomics; HET: MSE; 1.40A {Sulfolobus solfataricus P2} Back     alignment and structure
>1r89_A TRNA nucleotidyltransferase; CCA adding enzyme, incoming nucleotide, nucleotidyltransfera superfamily; HET: CTP; 1.80A {Archaeoglobus fulgidus} SCOP: a.160.1.3 d.218.1.7 d.58.16.2 PDB: 1r8a_A 1r8b_A* 1r8c_A* 1sz1_A* 1tfw_A* 1tfy_A* 1uet_A 1ueu_A* 1uev_A* 2dr5_A 2dr7_A 2dr8_A* 2dr9_A 2dra_A* 2drb_A 2dvi_A* 2zh1_A 2zh2_A 2zh3_A 2zh4_A ... Back     alignment and structure
>4ebj_A Aminoglycoside nucleotidyltransferase; structural genomics, center for structural genomics of infec diseases, csgid, niaid; HET: MSE; 1.60A {Pseudomonas aeruginosa} PDB: 4ebk_A* Back     alignment and structure
>1kny_A Kntase, kanamycin nucleotidyltransferase; antibiotic resistance, plasmid; HET: APC KAN; 2.50A {Staphylococcus aureus} SCOP: a.24.16.1 d.218.1.1 PDB: 1kan_A Back     alignment and structure
>4at7_A Interleukin enhancer-binding factor 2; transcription, DRPB76, NFAR, ILF3, ILF2, template-free nucleotidyltransferase fold; HET: 1PE; 1.902A {Mus musculus} PDB: 4at8_A* 4at9_A* 4atb_A* Back     alignment and structure
>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ... Back     alignment and structure
>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ... Back     alignment and structure
>3jz0_A Lincosamide nucleotidyltransferase; alpha-beta structure, transferase-antibiotic CO; HET: APC CLY; 2.00A {Enterococcus faecium} PDB: 3jyy_A* Back     alignment and structure
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Back     alignment and structure
>2pbe_A AAD6, aminoglycoside 6-adenylyltransferase; NYSGXRC, aminoglycoside 6-adenyltransferase, PSI-2, structural genomics; 2.65A {Bacillus subtilis} SCOP: a.160.1.5 d.218.1.13 Back     alignment and structure
>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_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 246
d2q66a2197 d.218.1.3 (A:5-201) Poly(A) polymerase, PAP, N-ter 2e-20
d1q79a2196 d.218.1.3 (A:19-214) Poly(A) polymerase, PAP, N-te 4e-20
d1no5a_100 d.218.1.5 (A:) Hypothetical protein HI0073 {Haemop 4e-09
>d2q66a2 d.218.1.3 (A:5-201) Poly(A) polymerase, PAP, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 197 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Nucleotidyltransferase
superfamily: Nucleotidyltransferase
family: Poly(A) polymerase, PAP, N-terminal domain
domain: Poly(A) polymerase, PAP, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 83.8 bits (207), Expect = 2e-20
 Identities = 26/131 (19%), Positives = 48/131 (36%), Gaps = 20/131 (15%)

Query: 110 LHKEIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPK----------------CKPEV 153
           L +E+         T  E   R   ++ + ++ +    +                 K   
Sbjct: 25  LIQELKKEG--SFETEQETANRVQVLKILQELAQRFVYEVSKKKNMSDGMARDAGGKIFT 82

Query: 154 FGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKF 213
           +GS+R G++ P SDID +++                 L +R    +I  +  A VPI+K 
Sbjct: 83  YGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVPIIKI 142

Query: 214 VEKKSGVSFDI 224
               SG+S  +
Sbjct: 143 KF--SGISIAL 151
>d1q79a2 d.218.1.3 (A:19-214) Poly(A) polymerase, PAP, N-terminal domain {Cow (Bos taurus) [TaxId: 9913]} Length = 196 Back     information, alignment and structure
>d1no5a_ d.218.1.5 (A:) Hypothetical protein HI0073 {Haemophilus influenzae [TaxId: 727]} Length = 100 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 ?
Query246
d2q66a2197 Poly(A) polymerase, PAP, N-terminal domain {Baker' 99.92
d1q79a2196 Poly(A) polymerase, PAP, N-terminal domain {Cow (B 99.9
d1no5a_100 Hypothetical protein HI0073 {Haemophilus influenza 99.1
d2b4va2 259 RNA editing terminal uridyl transferase 2, TUTase 98.78
d1r89a2142 tRNA nucleotidyltransferase, N-terminal domain {Ar 98.74
d1ylqa190 Putative nucleotidyltransferase AF0614 {Archaeon A 98.61
d1wota_98 Unnamed putative nucleotidyltransferase {Thermus t 97.99
d1knya2125 Kanamycin nucleotidyltransferase (KNTase), N-termi 97.69
d1px5a2200 2'-5'-oligoadenylate synthetase 1, OAS1, N-termina 97.46
d2bcqa3190 DNA polymerase lambda {Human (Homo sapiens) [TaxId 96.41
d1jmsa4208 Terminal deoxynucleotidyl transferase {Mouse (Mus 96.08
d2fmpa3187 DNA polymerase beta, catalytic (31 kD) fragment {H 95.13
d2pbea2135 Aminoglycoside 6-adenylyltransferase AadK {Bacillu 90.78
>d2q66a2 d.218.1.3 (A:5-201) Poly(A) polymerase, PAP, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Nucleotidyltransferase
superfamily: Nucleotidyltransferase
family: Poly(A) polymerase, PAP, N-terminal domain
domain: Poly(A) polymerase, PAP, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.92  E-value=2e-24  Score=184.43  Aligned_cols=134  Identities=19%  Similarity=0.183  Sum_probs=113.8

Q ss_pred             CCCCCCCCCCCCCCchHHHHHHHHHHHHHH--hCCCHHHHHHHHHHHHHHHHHHHhh----------------CCCceEE
Q 046567           91 RMENRWFKGNSRFKSPMLQLHKEIVDFCDF--LSPTSDEREVRNTAVEAVFDVIKYI----------------WPKCKPE  152 (246)
Q Consensus        91 ~~~~pW~~~~~~~~~~~~~L~~EI~~f~~~--l~Pt~eE~~~R~~ii~~l~~vv~~~----------------~P~~~V~  152 (246)
                      |..+||--..+.  ..-..++.+|..++..  +-|+++|.+.|+.++++|+++++++                +++++|+
T Consensus         4 Gvt~Pis~~~Pt--~~d~~~s~~L~~~L~~~~~~~s~ee~~~R~~vl~~l~~iv~~~v~~~~~~~~~~~~~~~~~~~~v~   81 (197)
T d2q66a2           4 GITGPVSTVGAT--AAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMSDGMARDAGGKIF   81 (197)
T ss_dssp             SSSCCSCCCCCC--HHHHHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHTBCEEE
T ss_pred             cCCCCcccCCCC--hHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCccccccCCcEEE
Confidence            445555444432  3345777888887765  5599999999999999999999874                4679999


Q ss_pred             EecccccCCCCCCCCceEEEecCCCCChhHHHHHHHHHHHhCCCcceEEEecCCCceeEEEEEcCCCeEEEEEeec
Q 046567          153 VFGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSGVSFDIRHFM  228 (246)
Q Consensus       153 ~FGS~~tGL~lp~SDIDl~I~~~~~~~~~~~L~~L~~~L~~~~~~~~V~~I~~ARVPIIKf~d~~tgI~~DISfnn  228 (246)
                      +|||+.+|+++|+||||+|++.+...++..++..++..|++...+++++.|.+|+||||||+.  +||+|||||+.
T Consensus        82 ~fGS~~lg~~~p~SDID~~~~~p~~~~~~~ff~~l~~~L~~~~~v~~i~~I~~A~VPIIK~~~--~gi~iDlsfa~  155 (197)
T d2q66a2          82 TYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVPIIKIKF--SGISIALICAR  155 (197)
T ss_dssp             EEHHHHHTCCCTTCCEEEEEEECTTCCHHHHHHHHHHHHHTCTTEEEEEEECSSSSCEEEEEE--TTEEEEEEEEE
T ss_pred             ecccccccccCCCCCcceEEecCCcCCHHHHHHHHHHHHHhCCCCceeEEeecccccEEEEEE--cCEEEEeeccc
Confidence            999999999999999999999987777788899999999998888999999999999999974  89999999984
>d1q79a2 d.218.1.3 (A:19-214) Poly(A) polymerase, PAP, N-terminal domain {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d1no5a_ d.218.1.5 (A:) Hypothetical protein HI0073 {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d2b4va2 d.218.1.10 (A:30-288) RNA editing terminal uridyl transferase 2, TUTase 2, RET2 {Trypanosoma brucei [TaxId: 5691]} Back     information, alignment and structure
>d1r89a2 d.218.1.7 (A:1-142) tRNA nucleotidyltransferase, N-terminal domain {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1ylqa1 d.218.1.5 (A:1-90) Putative nucleotidyltransferase AF0614 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1wota_ d.218.1.5 (A:) Unnamed putative nucleotidyltransferase {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1knya2 d.218.1.1 (A:1-125) Kanamycin nucleotidyltransferase (KNTase), N-terminal domain {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d1px5a2 d.218.1.6 (A:1-200) 2'-5'-oligoadenylate synthetase 1, OAS1, N-terminal domain {Pig (Sus scrofa) [TaxId: 9823]} Back     information, alignment and structure
>d2bcqa3 d.218.1.2 (A:386-575) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jmsa4 d.218.1.2 (A:303-510) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2fmpa3 d.218.1.2 (A:149-335) DNA polymerase beta, catalytic (31 kD) fragment {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2pbea2 d.218.1.13 (A:1-135) Aminoglycoside 6-adenylyltransferase AadK {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure