Citrus Sinensis ID: 035089

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70---
Protein Sequence
MAALPFESKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIRNKKMKKQQFKKVPKKKMKKRHGGRES
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHHcccccHHHccEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
maalpfeskpkdipirklpfpenrravvmepqeRKVHALVQHLQLIRNKKMKKQqfkkvpkkkmkkrhggres
Flexible Loop (DISEMBL)
maalpfeskpkdipirklpfpeNRRAVVMEPQERKVHALVQHLQlirnkkmkkqqfkkvpkkkmkkrhggres
Low Complexity Region (SEG)
MAALPFESKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIRNkkmkkqqfkkvpkkkmkkRHGGRES
Disordered region (IsUnstruct)
************************************HALVQHLQLI***************************
Disordered Region (DISOPRED)
*AALPFE*********************MEPQERKVHALVQHLQL****************************
Disordered Region (DISEMBL)
MAALPFESKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIRNK************************
Disordered Region (DISPRO)
*******SKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIRNKKMKKQQFK****************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAALPFESKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIRNKKMKKQQFKKVPKKKMKKRHGGRES
Positional Conservation
no confident homologs detected

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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	Length	Definition	Q cover	H cover	Identity	E-value
Query	73
359477919	1139	PREDICTED: ribosome biogenesis protein B	0.849	0.054	0.741	2e-16
298205174	1305	unnamed protein product [Vitis vinifera]	0.849	0.047	0.741	2e-16
147781739	325	hypothetical protein VITISV_005397 [Viti	0.849	0.190	0.741	6e-16
147804779	738	hypothetical protein VITISV_027071 [Viti	0.849	0.084	0.693	3e-15
356541129	1176	PREDICTED: ribosome biogenesis protein B	0.849	0.052	0.656	8e-12
356544500	1181	PREDICTED: ribosome biogenesis protein B	0.849	0.052	0.625	2e-11
224133372	1181	predicted protein [Populus trichocarpa]	0.767	0.047	0.684	2e-11
255552533	284	ribosome biogenesis protein bms1, putati	0.849	0.218	0.612	2e-10
449444194	1198	PREDICTED: ribosome biogenesis protein B	0.630	0.038	0.695	3e-09
357473083	1175	Ribosome biogenesis protein BMS1-like pr	0.863	0.053	0.569	4e-09

>gi|359477919|ref|XP_002270164.2| PREDICTED: ribosome biogenesis protein BMS1 homolog [Vitis vinifera]

 Score = 89.7 bits (221), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 46/62 (74%), Positives = 52/62 (83%)

Query: 2    AALPFESKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIRNKKMKKQQFKKVPK 61
            AALPF SKPKDI  RK P  ENRRAVVMEP ERKVHALVQHLQ+IRN+KMKK++ K+  K
Sbjct: 1039 AALPFASKPKDILKRKKPLLENRRAVVMEPHERKVHALVQHLQMIRNEKMKKRKLKETEK 1098

Query: 62   KK 63
            +K
Sbjct: 1099 RK 1100

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|298205174|emb|CBI17233.3| unnamed protein product [Vitis vinifera]

 Score = 89.7 bits (221), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 46/62 (74%), Positives = 52/62 (83%)

Query: 2    AALPFESKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIRNKKMKKQQFKKVPK 61
            AALPF SKPKDI  RK P  ENRRAVVMEP ERKVHALVQHLQ+IRN+KMKK++ K+  K
Sbjct: 1205 AALPFASKPKDILKRKKPLLENRRAVVMEPHERKVHALVQHLQMIRNEKMKKRKLKETEK 1264

Query: 62   KK 63
            +K
Sbjct: 1265 RK 1266

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147781739|emb|CAN69949.1| hypothetical protein VITISV_005397 [Vitis vinifera]

 Score = 88.2 bits (217), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 46/62 (74%), Positives = 52/62 (83%)

Query: 2   AALPFESKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIRNKKMKKQQFKKVPK 61
           AALPF SKPKDI  RK P  ENRRAVVMEP ERKVHALVQHLQ+IRN+KMKK++ K+  K
Sbjct: 225 AALPFASKPKDILKRKKPLLENRRAVVMEPHERKVHALVQHLQMIRNEKMKKRKLKETEK 284

Query: 62  KK 63
           +K
Sbjct: 285 RK 286

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147804779|emb|CAN76022.1| hypothetical protein VITISV_027071 [Vitis vinifera]

 Score = 85.9 bits (211), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 43/62 (69%), Positives = 52/62 (83%)

Query: 2   AALPFESKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIRNKKMKKQQFKKVPK 61
           AALPF SKPKDIP RK P  EN+RAVVMEP +RKVHALV+HLQ+IRN+K+KK++ K   K
Sbjct: 450 AALPFASKPKDIPKRKKPLLENQRAVVMEPHKRKVHALVRHLQMIRNEKIKKRKLKATEK 509

Query: 62  KK 63
           +K
Sbjct: 510 RK 511

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356541129|ref|XP_003539035.1| PREDICTED: ribosome biogenesis protein BMS1 homolog [Glycine max]

 Score = 74.7 bits (182), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 42/64 (65%), Positives = 49/64 (76%), Gaps = 2/64 (3%)

Query: 2    AALPFESKPKDIPIRKLPFPENRRA--VVMEPQERKVHALVQHLQLIRNKKMKKQQFKKV 59
            A+LPF SKPKDI  RK P  E RRA  VVMEP+ERKVH LVQHLQLI  +KMKK++ K+ 
Sbjct: 1073 ASLPFASKPKDISKRKKPLLEERRARGVVMEPRERKVHTLVQHLQLIDREKMKKRKLKEE 1132

Query: 60   PKKK 63
             K+K
Sbjct: 1133 NKRK 1136

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356544500|ref|XP_003540688.1| PREDICTED: ribosome biogenesis protein BMS1 homolog [Glycine max]

 Score = 73.2 bits (178), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 40/64 (62%), Positives = 49/64 (76%), Gaps = 2/64 (3%)

Query: 2    AALPFESKPKDIPIRKLPFPENRRA--VVMEPQERKVHALVQHLQLIRNKKMKKQQFKKV 59
            A+LPF SKPKDI  R  P  E RR   VVMEP+ERKVHALVQHLQLI ++K+KK++ K+ 
Sbjct: 1078 ASLPFASKPKDISKRNKPLLEERRGRGVVMEPRERKVHALVQHLQLINSEKVKKRKLKEE 1137

Query: 60   PKKK 63
             K+K
Sbjct: 1138 NKRK 1141

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133372|ref|XP_002328026.1| predicted protein [Populus trichocarpa] gi|222837435|gb|EEE75814.1| predicted protein [Populus trichocarpa]

 Score = 73.2 bits (178), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 39/57 (68%), Positives = 44/57 (77%), Gaps = 1/57 (1%)

Query: 2    AALPFESKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIRNKKMKKQQFKK 58
            A LPFESKPKDIP  +    E RRAVVMEP ERKVHALVQ L+LI N KM+K++ KK
Sbjct: 1080 ATLPFESKPKDIPKGRATL-ERRRAVVMEPDERKVHALVQQLRLITNDKMRKRKLKK 1135

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255552533|ref|XP_002517310.1| ribosome biogenesis protein bms1, putative [Ricinus communis] gi|223543573|gb|EEF45103.1| ribosome biogenesis protein bms1, putative [Ricinus communis]

 Score = 69.7 bits (169), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 38/62 (61%), Positives = 49/62 (79%)

Query: 2   AALPFESKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIRNKKMKKQQFKKVPK 61
           AALPF SKPKDIP +K    EN+RAVVMEP+ER++  L+QHLQ IR +KMKK++ K+  K
Sbjct: 183 AALPFASKPKDIPSQKRARLENKRAVVMEPRERQLSKLIQHLQRIRVEKMKKRKLKEEQK 242

Query: 62  KK 63
           +K
Sbjct: 243 RK 244

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449444194|ref|XP_004139860.1| PREDICTED: ribosome biogenesis protein BMS1 homolog [Cucumis sativus]

 Score = 65.9 bits (159), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/46 (69%), Positives = 39/46 (84%)

Query: 2    AALPFESKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIR 47
            AALPF+SKPK+ P ++ P  E RRAVVMEP++RKVHALVQ LQL+R
Sbjct: 1098 AALPFKSKPKNTPGQQRPLLEKRRAVVMEPRDRKVHALVQQLQLMR 1143

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357473083|ref|XP_003606826.1| Ribosome biogenesis protein BMS1-like protein [Medicago truncatula] gi|355507881|gb|AES89023.1| Ribosome biogenesis protein BMS1-like protein [Medicago truncatula]

 Score = 65.5 bits (158), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 37/65 (56%), Positives = 51/65 (78%), Gaps = 2/65 (3%)

Query: 2    AALPFESKPKDIPIRK-LPFPENR-RAVVMEPQERKVHALVQHLQLIRNKKMKKQQFKKV 59
            A LPFESKPK  P RK L F + R + VV+EP+ERK+HALVQHLQL++ +K+KK++ K+ 
Sbjct: 1074 ANLPFESKPKHTPKRKRLSFDDRRQKGVVVEPRERKIHALVQHLQLMKTEKIKKRKHKEG 1133

Query: 60   PKKKM 64
             K+K+
Sbjct: 1134 EKRKV 1138

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	73
TAIR|locus:2033050	1147	AT1G06720 [Arabidopsis thalian	0.616	0.039	0.577	2.4e-08
UNIPROTKB|F1NH69	1304	BMS1 "Uncharacterized protein"	0.630	0.035	0.446	0.00051

TAIR|locus:2033050 AT1G06720 [Arabidopsis thaliana (taxid:3702)]

 Score = 141 (54.7 bits), Expect = 2.4e-08, P = 2.4e-08
 Identities = 26/45 (57%), Positives = 36/45 (80%)

Query:     4 LPFESKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIRN 48
             LPF SKPK+IP RK P  E++RAV+MEP+ERK H ++Q  QL+++
Sbjct:  1048 LPFMSKPKNIPKRKRPSLEDKRAVIMEPKERKEHTIIQQFQLLQH 1092

GO:0003924 "GTPase activity" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0006406 "mRNA export from nucleus" evidence=RCA

GO:0006606 "protein import into nucleus" evidence=RCA

UNIPROTKB|F1NH69 BMS1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 101 (40.6 bits), Expect = 0.00051, P = 0.00051
 Identities = 21/47 (44%), Positives = 32/47 (68%)

Query:     3 ALPFESKPKDIPIR-KLPFPENRRAVVMEPQERKVHALVQHLQLIRN 48
             ALPF++KPK++  + K P  + R AV+MEP E+K+ AL+  L  + N
Sbjct:  1193 ALPFKNKPKNLEKKGKTPKDQWRPAVIMEPHEKKISALLNALSTVNN 1239


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        0.321   0.137   0.402    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       73        55   0.00091  102 3  11 22  0.44    27
                                                     29  0.40    27


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:  2
  No. of states in DFA:  375 (40 KB)
  Total size of DFA:  66 KB (2061 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:  7.48u 0.17s 7.65t   Elapsed:  00:00:01
  Total cpu time:  7.48u 0.17s 7.65t   Elapsed:  00:00:01
  Start:  Fri May 10 05:28:15 2013   End:  Fri May 10 05:28:16 2013

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	Length	Definition	Probability
Query	73
KOG1951	115	consensus GTP-binding protein AARP2 involved in 40	99.44
COG5192	1077	BMS1 GTP-binding protein required for 40S ribosome	94.82

>KOG1951 consensus GTP-binding protein AARP2 involved in 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]

Probab=99.44  E-value=2.3e-13  Score=90.22  Aligned_cols=67  Identities=39%  Similarity=0.554  Sum_probs=63.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCccccc--cccCchhhhHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHhh
Q 035089            2 AALPFESKPKDIPIRKLPFPENRRA--VVMEPQERKVHALVQHLQLIRNKKMKKQQFKKVPKKKMKKRH   68 (73)
Q Consensus         2 ~~LPFksKpK~~~k~k~~~~~~krA--VV~ep~EkKv~~Lmq~L~Ti~~~K~~Krk~k~~~k~~~~~k~   68 (73)
                      ++|||+|+|+...+++++.+...||  ||++|+|+|+.++|+++.|++.++..+.++.+..++++|++.
T Consensus         8 k~LPfkskpka~~~~k~~l~~~~r~~~vv~~p~e~K~~~~~~~v~t~~~~~~qk~K~~~~~krk~~~e~   76 (115)
T KOG1951|consen    8 KALPFKSKPKAAKKRKRPLQDLQRADEVVAKPRERKARAVIDAVETARSFKRQKAKKTKKKKRKEYREK   76 (115)
T ss_pred             HhCCccccchhhccccccccchhhcchhhcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999998  999999999999999999999999999999999998888764

>COG5192 BMS1 GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]

Probab=94.82  E-value=0.046  Score=45.95  Aligned_cols=59  Identities=14%  Similarity=0.178  Sum_probs=48.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCccccccccCchhhhHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHhh
Q 035089            2 AALPFESKPKDIPIRKLPFPENRRAVVMEPQERKVHALVQHLQLIRNKKMKKQQFKKVPKKKMKKRH   68 (73)
Q Consensus         2 ~~LPFksKpK~~~k~k~~~~~~krAVV~ep~EkKv~~Lmq~L~Ti~~~K~~Krk~k~~~k~~~~~k~   68 (73)
                      +.|||+        ++..+++.+|+||..|.|.+....++..-|+..-|..++++..+-.+.+..++
T Consensus       987 ~~lp~~--------kr~~~~~srr~~~~~~~e~r~k~~ik~~i~~~r~kd~~~ke~~~s~~r~k~~~ 1045 (1077)
T COG5192         987 SKLPLD--------KRSIAVVSRRIELPVPPECREKHEIKDRIVKERIKDQEEKERMESLQRAKEEE 1045 (1077)
T ss_pred             hhCCcc--------hhhhhheeeeeeccCChhhhHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHH
Confidence            357776        55668999999999999999999999999998888888888776665555544

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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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

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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

No hit with probability above 80.00