Citrus Sinensis ID: 028893

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--
MDFRDTMQKVYSWACQIGNLGLWIIWLLIHFAVDLWYFALHIACAIESYLISSGILKRYKALDIDKLRYLAIVIESEEAYHIPAVIQLLQWLVDIGVKHVCLYDAEGILKKSKESILGKLNNATLFEEAGESNLLLDHKHITLEFASFPDGKEAVAKAANLLFMKYVKLGGSGKIQEEKIFTEAHMSEALRAVAKARNLTCY
ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEEEccccccHHHHHHHHHHHHHHcccEEEEEcccHHHHHHHHHHHHHcccccHHHHHccccccccccEEEEEEEEccccHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHccccccccc
cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHccHHHcEEEEEEEEcHHHHHHHHHHHHHHHHHHcccEEEEEEccccHHHccHHHHHHHccccccEEEEcccccccccccEEEEEEEccccHHHHHHHHHHHHHHHHccccccccccccEcccHHHHHHHHHHHHHHHcccc
MDFRDTMQKVYSWACQIGNLGLWIIWLLIHFAVDLWYFALHIACAIESYLISSGILKrykaldidKLRYLAIVIESEEAYHIPAVIQLLQWLVDIGVKHVCLYDAEGILKKSKESILGKlnnatlfeeagesnllldhkhitlefasfpdgKEAVAKAANLLFMKYVKlggsgkiqeekIFTEAHMSEALRAVAKARNLTCY
MDFRDTMQKVYSWACQIGNLGLWIIWLLIHFAVDLWYFALHIACAIESYLISSGILKRYKALDIDKLRYLAIVIESEEAYHIPAVIQLLQWLVDIGVKHVCLYDAEGILKKSKESILGKLNNATLFEEAGESNLLLDHKHITLEFASFPDGKEAVAKAANLLFMKYVKLGGSGKIQEEKIFTEAHMSEALRAVAKARNLTCY
MDFRDTMQKVYSWACQignlglwiiwlliHFAVDLWYFALHIACAIESYLISSGILKRYKALDIDKLRYLAIVIESEEAYHIPAVIQLLQWLVDIGVKHVCLYDAEGILKKSKESILGKLNNATLFEEAGESNLLLDHKHITLEFASFPDGKEAVAKAANLLFMKYVKLGGSGKIQEEKIFTEAHMSEALRAVAKARNLTCY
*******QKVYSWACQIGNLGLWIIWLLIHFAVDLWYFALHIACAIESYLISSGILKRYKALDIDKLRYLAIVIESEEAYHIPAVIQLLQWLVDIGVKHVCLYDAEGILKKSKESILGKLNNATLFEEAGESNLLLDHKHITLEFASFPDGKEAVAKAANLLFMKYVKLGGSGKIQEEKIFTEA******************
********KVYSWACQIGNLGLWIIWLLIHFAVDLWYFALHIACAIESYLISSGILKRYKALDIDKLRYLAIVIESEEAYHIPAVIQLLQWLVDIGVKHVCLYDAEGILKKSKES****************SNLLLDHKHITLEFASFPDGKEAVAKAANLLFMKYV************IFTEAHMSEALRAVAKARNLTCY
********KVYSWACQIGNLGLWIIWLLIHFAVDLWYFALHIACAIESYLISSGILKRYKALDIDKLRYLAIVIESEEAYHIPAVIQLLQWLVDIGVKHVCLYDAEGILKKSKESILGKLNNATLFEEAGESNLLLDHKHITLEFASFPDGKEAVAKAANLLFMKYVKLGGSGKIQEEKIFTEAHMSEALRAVAKARNLTCY
*DFRDTMQKVYSWACQIGNLGLWIIWLLIHFAVDLWYFALHIACAIESYLISSGILKRYKALDIDKLRYLAIVIESEEAYHIPAVIQLLQWLVDIGVKHVCLYDAEGILKKSKESILGKLNNATLFEEAGESNLLLDHKHITLEFASFPDGKEAVAKAANLLFMKYVKLGGSGKIQEEKIFTEAHMSEALRAVAKARNLTCY
iiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MDFRDTMQKVYSWACQIGNLGLWIIWLLIHFAVDLWYFALHIACAIESYLISSGILKRYKALDIDKLRYLAIVIESEEAYHIPAVIQLLQWLVDIGVKHVCLYDAEGILKKSKESILGKLNNATLFEEAGESNLLLDHKHITLEFASFPDGKEAVAKAANLLFMKYVKLGGSGKIQEEKIFTEAHMSEALRAVAKARNLTCY
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

No hits with e-value below 0.001 by BLAST

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 ?
Query202
224077818254 predicted protein [Populus trichocarpa] 0.960 0.763 0.649 1e-65
359475282255 PREDICTED: nogo-B receptor-like isoform 0.960 0.760 0.639 2e-63
255556087243 conserved hypothetical protein [Ricinus 0.891 0.740 0.613 7e-56
147800089199 hypothetical protein VITISV_032483 [Viti 0.915 0.929 0.596 3e-52
363814545254 uncharacterized protein LOC100796301 [Gl 0.940 0.748 0.517 1e-44
297849548 414 predicted protein [Arabidopsis lyrata su 0.960 0.468 0.466 9e-41
357481047287 Nogo-B receptor [Medicago truncatula] gi 0.900 0.634 0.486 7e-40
4835781 417 F25C20.9 [Arabidopsis thaliana] 0.960 0.465 0.456 8e-40
449460714262 PREDICTED: nogo-B receptor-like [Cucumis 0.871 0.671 0.516 8e-40
145323858254 cis-prenyltransferase, dehydrodolichyl d 0.960 0.763 0.456 2e-39
>gi|224077818|ref|XP_002305421.1| predicted protein [Populus trichocarpa] gi|222848385|gb|EEE85932.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  254 bits (650), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 126/194 (64%), Positives = 151/194 (77%)

Query: 1   MDFRDTMQKVYSWACQIGNLGLWIIWLLIHFAVDLWYFALHIACAIESYLISSGILKRYK 60
           MDF+D +Q+V     QIGN GL ++W  +H  V  WY  + +A  IESYLISSG+LKRY+
Sbjct: 1   MDFKDEVQRVKFGINQIGNFGLRLVWHSVHLLVRFWYLGVGVANVIESYLISSGLLKRYR 60

Query: 61  ALDIDKLRYLAIVIESEEAYHIPAVIQLLQWLVDIGVKHVCLYDAEGILKKSKESILGKL 120
           ++D+ KLRYLAIVIES++A  I  VIQLLQWL  IGVKH+CLYD EG+LKKSKESIL KL
Sbjct: 61  SIDVGKLRYLAIVIESDDACRISKVIQLLQWLQAIGVKHLCLYDTEGVLKKSKESILAKL 120

Query: 121 NNATLFEEAGESNLLLDHKHITLEFASFPDGKEAVAKAANLLFMKYVKLGGSGKIQEEKI 180
            NATLFEEA E + LLD KH+TLEFAS  DGKEAVAK  N+LFMKY K+  SG  Q+E+I
Sbjct: 121 KNATLFEEADERDSLLDQKHMTLEFASISDGKEAVAKGGNVLFMKYSKVANSGAEQKEQI 180

Query: 181 FTEAHMSEALRAVA 194
           FTEA+M+EALRAV 
Sbjct: 181 FTEANMTEALRAVG 194

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|359475282|ref|XP_003631634.1| PREDICTED: nogo-B receptor-like isoform 1 [Vitis vinifera] gi|359475284|ref|XP_003631635.1| PREDICTED: nogo-B receptor-like isoform 2 [Vitis vinifera] gi|297741434|emb|CBI32565.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|255556087|ref|XP_002519078.1| conserved hypothetical protein [Ricinus communis] gi|223541741|gb|EEF43289.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|147800089|emb|CAN70934.1| hypothetical protein VITISV_032483 [Vitis vinifera] Back     alignment and taxonomy information
>gi|363814545|ref|NP_001242452.1| uncharacterized protein LOC100796301 [Glycine max] gi|255645054|gb|ACU23026.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|297849548|ref|XP_002892655.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297338497|gb|EFH68914.1| predicted protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|357481047|ref|XP_003610809.1| Nogo-B receptor [Medicago truncatula] gi|355512144|gb|AES93767.1| Nogo-B receptor [Medicago truncatula] Back     alignment and taxonomy information
>gi|4835781|gb|AAD30247.1|AC007296_8 F25C20.9 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|449460714|ref|XP_004148090.1| PREDICTED: nogo-B receptor-like [Cucumis sativus] gi|449483980|ref|XP_004156749.1| PREDICTED: nogo-B receptor-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|145323858|ref|NP_001077518.1| cis-prenyltransferase, dehydrodolichyl diphosphate synthase [Arabidopsis thaliana] gi|25083010|gb|AAN72032.1| Unknown protein [Arabidopsis thaliana] gi|332190659|gb|AEE28780.1| cis-prenyltransferase, dehydrodolichyl diphosphate synthase [Arabidopsis thaliana] 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 ?
Query202
TAIR|locus:4010713435254 LEW1 "LEAF WILTING 1" [Arabido 0.960 0.763 0.420 8.3e-35
TAIR|locus:4010713435 LEW1 "LEAF WILTING 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 377 (137.8 bits), Expect = 8.3e-35, P = 8.3e-35
 Identities = 82/195 (42%), Positives = 117/195 (60%)

Query:     1 MDFRDTMQKVYSWACQXXXXXXXXXXXXXHFAVDLWYFALHIACAIESYLISSGILKRYK 60
             MD   +M+ + +W  Q             H  V LWY    I  AIESY I+ G+ K+Y 
Sbjct:     1 MDSNQSMRLLSAWIGQIGDLGLNLLWRFIHIVVSLWYIVSGIFEAIESYAITLGLNKKYG 60

Query:    61 ALDIDKLRYLAIVIESEEAYHIPAVIQLLQWLVDIGVKHVCLYDAEGILKKSKESILGKL 120
             ++D++KLR LA+V++ E A  +  V++LLQWL  IGVK V L+D++G+LKKSK+ IL  +
Sbjct:    61 SIDLEKLRCLAVVVDIEAAQDVANVVELLQWLTTIGVKQVGLFDSQGLLKKSKDLILETV 120

Query:   121 NNATLFEEAGESNLLLDHKHITLEFASFPDGKEAVAKAANLLFMKYVKLGGSGKIQEEKI 180
               + L EE  E ++  D K I LEF S  D KEAV KAAN+L  +Y+K       + E  
Sbjct:   121 PGSMLLEEI-EKDVAPDGKRIALEFISSSDNKEAVMKAANILLQRYLKSSHPEDDKGEDF 179

Query:   181 FTEAHMSEALRAVAK 195
             FTE+H+++ALR V +
Sbjct:   180 FTESHLNDALRVVGE 194


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.323   0.136   0.401    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      202       189   0.00089  110 3  11 22  0.40    32
                                                     31  0.42    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  600 (64 KB)
  Total size of DFA:  162 KB (2096 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  16.68u 0.14s 16.82t   Elapsed:  00:00:01
  Total cpu time:  16.68u 0.14s 16.82t   Elapsed:  00:00:01
  Start:  Thu May  9 20:33:30 2013   End:  Thu May  9 20:33:31 2013
GO:0016765 "transferase activity, transferring alkyl or aryl (other than methyl) groups" evidence=IEA
GO:0006487 "protein N-linked glycosylation" evidence=IMP
GO:0009414 "response to water deprivation" evidence=IMP
GO:0009645 "response to low light intensity stimulus" evidence=IMP
GO:0019408 "dolichol biosynthetic process" evidence=IMP
GO:0030968 "endoplasmic reticulum unfolded protein response" evidence=IMP
GO:0045547 "dehydrodolichyl diphosphate synthase activity" evidence=IDA

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
estExt_Genewise1_v1.C_LG_IV0453
hypothetical protein (254 aa)
(Populus trichocarpa)
Predicted Functional Partners:
gw1.XV.832.1
hypothetical protein (236 aa)
     •  0.899
gw1.VII.3333.1
annotation not avaliable (311 aa)
     •  0.899
gw1.IV.3487.1
hypothetical protein (293 aa)
     •  0.899
gw1.II.860.1
hypothetical protein (306 aa)
     •  0.899
grail3.0137000601
hypothetical protein (134 aa)
     •  0.899
grail3.0045022601
hypothetical protein (259 aa)
     •  0.899
grail3.0001025501
hypothetical protein (314 aa)
     •  0.899
fgenesh4_pm.C_LG_II001087
hypothetical protein (287 aa)
     •  0.899
eugene3.00060040
SubName- Full=Putative uncharacterized protein; (342 aa)
     •  0.899
estExt_Genewise1_v1.C_570227
hypothetical protein (366 aa)
     •  0.899

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 202
KOG2818263 consensus Predicted undecaprenyl diphosphate synth 99.25
PRK14829243 undecaprenyl pyrophosphate synthase; Provisional 98.67
PRK14831249 undecaprenyl pyrophosphate synthase; Provisional 98.62
PRK14830251 undecaprenyl pyrophosphate synthase; Provisional 98.49
PRK14827296 undecaprenyl pyrophosphate synthase; Provisional 98.43
PRK14836253 undecaprenyl pyrophosphate synthase; Provisional 98.42
PRK14828256 undecaprenyl pyrophosphate synthase; Provisional 98.42
cd00475221 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases ( 98.29
PRK14834249 undecaprenyl pyrophosphate synthase; Provisional 98.27
PRK14840250 undecaprenyl pyrophosphate synthase; Provisional 98.16
PRK14842241 undecaprenyl pyrophosphate synthase; Provisional 97.92
PF01255223 Prenyltransf: Putative undecaprenyl diphosphate sy 97.85
PRK14832253 undecaprenyl pyrophosphate synthase; Provisional 97.73
PRK10240229 undecaprenyl pyrophosphate synthase; Provisional 97.65
PRK14835275 undecaprenyl pyrophosphate synthase; Provisional 97.64
PRK14841233 undecaprenyl pyrophosphate synthase; Provisional 97.61
PRK14838242 undecaprenyl pyrophosphate synthase; Provisional 97.54
COG0020245 UppS Undecaprenyl pyrophosphate synthase [Lipid me 97.53
PRK14833233 undecaprenyl pyrophosphate synthase; Provisional 97.42
TIGR00055226 uppS undecaprenyl diphosphate synthase. Alternate 97.39
PRK14837230 undecaprenyl pyrophosphate synthase; Provisional 97.26
PRK14839239 undecaprenyl pyrophosphate synthase; Provisional 96.93
PTZ00349 322 dehydrodolichyl diphosphate synthetase; Provisiona 96.07
KOG1602271 consensus Cis-prenyltransferase [Lipid transport a 92.5
>KOG2818 consensus Predicted undecaprenyl diphosphate synthase [Lipid transport and metabolism] Back     alignment and domain information 
Probab=99.25  E-value=1.8e-10  Score=102.59  Aligned_cols=126  Identities=19%  Similarity=0.251  Sum_probs=103.2

Q ss_pred             ccCcceEEEEEecccc--cChHHHHHHHHHHHHhccceeEEecccchhhhchhHHHhhcc--cCC-----------cccc
Q 028893           64 IDKLRYLAIVIESEEA--YHIPAVIQLLQWLVDIGVKHVCLYDAEGILKKSKESILGKLN--NAT-----------LFEE  128 (202)
Q Consensus        64 ~~kl~~LaiVvdseea--~~~~kv~~Ll~Wl~~iGVk~v~lYD~~GvLKks~e~l~~~~~--n~~-----------~~~~  128 (202)
                      .++|+||++||..-+.  -++++.++++.|+.++||||++|||..|.+|++-.....++.  +++           .++.
T Consensus        62 ~k~p~hl~lvI~~v~~~~~~~~da~~~v~w~v~~gik~~~lyd~~g~~~r~~~~~~~~I~s~la~~~g~~~~~~~~~~~~  141 (263)
T KOG2818|consen   62 KKGPKHLALVIHPVEDGEGSFSDASSIVFWAVTVGIKYLSLYDRVGIKKRNMPVVRDEIISHLANYFGLDEPTLAVTIKL  141 (263)
T ss_pred             hhcchhheEEEEecccCCceehhhHHHHHHHHHhccceeeHHHHHHHhccCcHHHHHHHHHhhhhhcCCCCCcccccCCC
Confidence            7888999999888555  589999999999999999999999999999999999999985  443           3444


Q ss_pred             cccccccccCCceEEEeecCCCCH---HHHHHHHHHHHHHHhhcCCCCccccchhcchHhHHHHHHHhcc
Q 028893          129 AGESNLLLDHKHITLEFASFPDGK---EAVAKAANLLFMKYVKLGGSGKIQEEKIFTEAHMSEALRAVAK  195 (202)
Q Consensus       129 aN~k~~~~~~~~MtlE~LS~sDGK---EaIaKAAnlLc~~~~k~~~~~~~~~~~~fTEadm~eALkaVG~  195 (202)
                      +|+.+.+.+.+++.+-.+|.+||+   -++.++++.+|..+.++-...      -.|=..|+.-|+.-++
T Consensus       142 snD~~nQ~~~~~L~~~~~s~~DGr~~i~Dl~r~i~~~~~~~~~~~~~~------~itve~vds~l~e~~~  205 (263)
T KOG2818|consen  142 SNDEPNQEDKCKLGTHAISLEDGRMIIIDLTRLIQELCYLYELYRSET------DITVETVDSELKEFVE  205 (263)
T ss_pred             CCCCcccccccchhheecccccccHHHHHHHHHHHHHHHHHHHhCCCc------cccHHHHHHHHHhcCC
Confidence            888888899999999999999999   555678888888777333322      2677888888887443

>PRK14829 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PRK14831 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PRK14830 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PRK14827 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PRK14836 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates Back     alignment and domain information
>PRK14834 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PRK14840 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PRK14842 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PF01255 Prenyltransf: Putative undecaprenyl diphosphate synthase; InterPro: IPR001441 Synonym(s): Di-trans-poly-cis-undecaprenyl-diphosphate synthase, Undecaprenyl pyrophosphate synthetase, Undecaprenyl pyrophosphate synthase, UPP synthetase Di-trans-poly-cis-decaprenylcistransferase (2 Back     alignment and domain information
>PRK14832 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PRK10240 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PRK14835 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PRK14841 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PRK14838 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>COG0020 UppS Undecaprenyl pyrophosphate synthase [Lipid metabolism] Back     alignment and domain information
>PRK14833 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>TIGR00055 uppS undecaprenyl diphosphate synthase Back     alignment and domain information
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PRK14839 undecaprenyl pyrophosphate synthase; Provisional Back     alignment and domain information
>PTZ00349 dehydrodolichyl diphosphate synthetase; Provisional Back     alignment and domain information
>KOG1602 consensus Cis-prenyltransferase [Lipid transport and metabolism] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query202
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-07
>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
 Score = 49.9 bits (118), Expect = 2e-07
 Identities = 26/145 (17%), Positives = 52/145 (35%), Gaps = 24/145 (16%)

Query: 14  ACQIGNLGLWIIWLLIHFAVDLWYFALHIACAIESYLISSGILKRYKALDIDKLR--YLA 71
                   L II   I   +  W    H+ C   + +I S +      L+  + R  +  
Sbjct: 322 VLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL----NVLEPAEYRKMFDR 377

Query: 72  IVIESEEAYHIPA-VIQLLQWLVDIGVKHVCLYDAEGILKKSKESILGKLNNATLFEEAG 130
           + +    A HIP  ++ L+ W                ++K     ++ KL+  +L E+  
Sbjct: 378 LSVFPPSA-HIPTILLSLI-W--------------FDVIKSDVMVVVNKLHKYSLVEKQP 421

Query: 131 ESNLLLDHKHITLEFASFPDGKEAV 155
           + + +     I LE     + + A+
Sbjct: 422 KESTISIP-SIYLELKVKLENEYAL 445

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query202
2vg0_A227 Short-chain Z-isoprenyl diphosphate synthetase; pe 99.05
2vg3_A284 Undecaprenyl pyrophosphate synthetase; transferase 99.02
3qas_B253 Undecaprenyl pyrophosphate synthase; alpha-helix, 99.0
1f75_A249 Undecaprenyl pyrophosphate synthetase; parallel be 98.97
2d2r_A245 Undecaprenyl pyrophosphate synthase; prenyltransfe 98.85
3sgv_B253 Undecaprenyl pyrophosphate synthase; alpha/beta, t 98.21
4h8e_A256 Undecaprenyl pyrophosphate synthase; alpha-helix, 98.12
3ugs_B225 Undecaprenyl pyrophosphate synthase; niaid, csgid, 97.64
>2vg0_A Short-chain Z-isoprenyl diphosphate synthetase; peptidoglycan synthesis, cell WALL biogenesis/degradation, secreted, cell shape; HET: GPP; 1.7A {Mycobacterium tuberculosis} PDB: 2vfw_A* 2vg1_A* Back     alignment and structure
Probab=99.05  E-value=4.7e-10  Score=95.93  Aligned_cols=128  Identities=16%  Similarity=0.253  Sum_probs=92.1

Q ss_pred             CcceEEEEEeccc--------c-------cChHHHHHHHHHHHHhccceeEEec-ccchhhhchhH---HHhh-------
Q 028893           66 KLRYLAIVIESEE--------A-------YHIPAVIQLLQWLVDIGVKHVCLYD-AEGILKKSKES---ILGK-------  119 (202)
Q Consensus        66 kl~~LaiVvdsee--------a-------~~~~kv~~Ll~Wl~~iGVk~v~lYD-~~GvLKks~e~---l~~~-------  119 (202)
                      -|+|+||+.|...        -       .-+.++.+++.||..+||++|+||+ ..+.+|+.++.   +|+-       
T Consensus         2 iP~HvAiImDGN~RwA~~~g~l~~~~GH~~G~~~l~~i~~~c~~~GI~~lTlYaFSteN~kRp~~Ev~~Lm~l~~~~l~~   81 (227)
T 2vg0_A            2 LPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIITDVVEE   81 (227)
T ss_dssp             CCSEEEEECCCHHHHHHHTTCSCTHHHHHHHHHHHHHHHHHHHHHTCSEEEEEEEETGGGGSCHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEecCChHHHHHcCCCchhHHHHHHHHHHHHHHHHHHHcCCCEEEEEeecccccCCCHHHHHHHHHHHHHHHHH
Confidence            3789999999732        1       2468999999999999999999999 59999999852   2222       


Q ss_pred             -cccCC-----------ccccc------ccccccccCCceEEEeecCCCCHHHHHHHHHHHHHHHhhcCCCCccccchhc
Q 028893          120 -LNNAT-----------LFEEA------GESNLLLDHKHITLEFASFPDGKEAVAKAANLLFMKYVKLGGSGKIQEEKIF  181 (202)
Q Consensus       120 -~~n~~-----------~~~~a------N~k~~~~~~~~MtlE~LS~sDGKEaIaKAAnlLc~~~~k~~~~~~~~~~~~f  181 (202)
                       +..++           .+|..      .-...+..+.+|+|++++.-+||+.|+.|++.+++++.++.-+.++. ...+
T Consensus        82 ~~~~~~~vrv~~iG~~~~lp~~~~~~i~~~~~~T~~n~~l~lnia~~YggR~eI~~A~r~l~~~v~~g~l~~~~~-~~~I  160 (227)
T 2vg0_A           82 ICAPANHWSVRTVGDLGLIGEEPARRLRGAVESTPEVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEEL-VDAV  160 (227)
T ss_dssp             HTCTTTCCEEEEESCGGGSCHHHHHHHHHHHHTSCSSCSCEEEEEEEECHHHHHHHHHHHHHHHHHHTTCCHHHH-HHHC
T ss_pred             HhccccCeEEEecCChhhCCHHHHHHHHHHHHHhcCCCceEEEEEecCCCHHHHHHHHHHHHHHHHcCCCChhHh-hccC
Confidence             21111           11110      01133567889999999999999999999999999987654322111 2248


Q ss_pred             chHhHHHHHHHhc
Q 028893          182 TEAHMSEALRAVA  194 (202)
Q Consensus       182 TEadm~eALkaVG  194 (202)
                      ||..+++-|...+
T Consensus       161 ~e~~i~~~L~t~~  173 (227)
T 2vg0_A          161 TVEGISENLYTSG  173 (227)
T ss_dssp             CHHHHHHHSTTTT
T ss_pred             CHHHHHHhhccCC
Confidence            9999999886544
>2vg3_A Undecaprenyl pyrophosphate synthetase; transferase, cell WALL biogenesis/degradation, cell cycle, P transferase; HET: GPP; 1.8A {Mycobacterium tuberculosis} PDB: 2vg2_A* 2vg4_A Back     alignment and structure
>3qas_B Undecaprenyl pyrophosphate synthase; alpha-helix, isoprenoid biosynthesis, transferase; 1.70A {Escherichia coli} PDB: 1jp3_A* 1v7u_A* 1x06_A* 1x07_A* 2e98_A* 2e99_A* 2e9a_A* 2e9c_A* 2e9d_A* 1ueh_A 1x09_A* 1x08_A* Back     alignment and structure
>1f75_A Undecaprenyl pyrophosphate synthetase; parallel beta sheet, NEW fold for isoprenoid synthase, peptidoglycan synthesis, transferase; 2.20A {Micrococcus luteus} SCOP: c.101.1.1 Back     alignment and structure
>2d2r_A Undecaprenyl pyrophosphate synthase; prenyltransferase, transferase; 1.88A {Helicobacter pylori} PDB: 2dtn_A Back     alignment and structure
>3sgv_B Undecaprenyl pyrophosphate synthase; alpha/beta, transferase; HET: 2BJ; 1.61A {Escherichia coli} PDB: 1jp3_A* 1v7u_A* 1x06_A* 1x07_A* 2e98_A* 2e99_A* 2e9a_A* 2e9c_A* 2e9d_A* 1ueh_A 3sgt_B* 3qas_B* 3sgx_A* 3sh0_B* 3th8_A* 4h2j_A* 4h2m_A* 4h2o_B* 4h38_A* 4h3a_A* ... Back     alignment and structure
>4h8e_A Undecaprenyl pyrophosphate synthase; alpha-helix, prenyl transferase, cell WALL biosynthesis, FAR diphosphate binding; HET: FPP; 1.30A {Staphylococcus aureus subsp} Back     alignment and structure
>3ugs_B Undecaprenyl pyrophosphate synthase; niaid, csgid, structural genomics, center for structural GEN infectious diseases; HET: FFT; 2.46A {Campylobacter jejuni} SCOP: c.101.1.0 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query202
d1ueha_228 Undecaprenyl diphosphate synthase {Escherichia col 98.33
d1f75a_229 Undecaprenyl diphosphate synthase {Micrococcus lut 97.94
>d1ueha_ c.101.1.1 (A:) Undecaprenyl diphosphate synthase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Undecaprenyl diphosphate synthase
superfamily: Undecaprenyl diphosphate synthase
family: Undecaprenyl diphosphate synthase
domain: Undecaprenyl diphosphate synthase
species: Escherichia coli [TaxId: 562]

Probab=98.33  E-value=5.9e-07  Score=74.69  Aligned_cols=123  Identities=13%  Similarity=0.184  Sum_probs=83.0

Q ss_pred             ccCcceEEEEEec-------c-----cc--cChHHHHHHHHHHHHhccceeEEe------------cccchhhhchhHHH
Q 028893           64 IDKLRYLAIVIES-------E-----EA--YHIPAVIQLLQWLVDIGVKHVCLY------------DAEGILKKSKESIL  117 (202)
Q Consensus        64 ~~kl~~LaiVvds-------e-----ea--~~~~kv~~Ll~Wl~~iGVk~v~lY------------D~~GvLKks~e~l~  117 (202)
                      ...|+|+||+.|.       .     +.  +-..++.+++.||...||++|++|            ..+.+++-..+.+.
T Consensus         3 ~~~P~HiaiImDGNrRwAk~~gl~~~~GH~~G~~~l~~ii~~~~~~gI~~lTvYaFStEN~~R~~~Ev~~Lm~l~~~~l~   82 (228)
T d1ueha_           3 AHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALD   82 (228)
T ss_dssp             TTCCCEEEEECCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTCSEEEEEEEC--------------CHHHHHHHH
T ss_pred             CCCCCEEEEeccCCHHHHHHCCCChhHHHHHHHHHHHHHHHHHHHcCCcEEEeehhhhhhcccccchhHHHHHHHHHHHH
Confidence            4579999999995       0     11  236789999999999999999999            45555555555544


Q ss_pred             hhcc----c---------CCcccc------cccccccccCCceEEEeecCCCCHHHHHHHHHHHHHHHhhcCCCCccccc
Q 028893          118 GKLN----N---------ATLFEE------AGESNLLLDHKHITLEFASFPDGKEAVAKAANLLFMKYVKLGGSGKIQEE  178 (202)
Q Consensus       118 ~~~~----n---------~~~~~~------aN~k~~~~~~~~MtlE~LS~sDGKEaIaKAAnlLc~~~~k~~~~~~~~~~  178 (202)
                      +...    +         ...+|.      ......+-.+.+|+|++.-.=+|++.|++|++.++.+..+..-..++   
T Consensus        83 ~~~~~~~~~~i~i~~iG~~~~lp~~~~~~i~~~e~~T~~n~~~~Lnia~~Yggr~EI~~A~~~~~~~~~~~~~~~~~---  159 (228)
T d1ueha_          83 SEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQ---  159 (228)
T ss_dssp             HTHHHHHHTTCEEEEESCCTTSCHHHHHHHHHHHHHHTTCCSCEEEEEESCCHHHHHHHHHHHHHHHHHTTSCCGGG---
T ss_pred             HhHHHHHhccEEEEEECCcchhhhhhhhhhhhHHHhccCCCCceEEEEeccccchHHHHHHHHHHHHHHhCCCCHhH---
Confidence            3321    1         112222      11122356788999999999999999999999999998766554433   


Q ss_pred             hhcchHhHHHHHH
Q 028893          179 KIFTEAHMSEALR  191 (202)
Q Consensus       179 ~~fTEadm~eALk  191 (202)
                        +||..+.+-|-
T Consensus       160 --i~~~~~~~~l~  170 (228)
T d1ueha_         160 --IDEEMLNQHVC  170 (228)
T ss_dssp             --CCHHHHHTTST
T ss_pred             --hhhhheecccc
Confidence              67766655443
>d1f75a_ c.101.1.1 (A:) Undecaprenyl diphosphate synthase {Micrococcus luteus [TaxId: 1270]} Back     information, alignment and structure