Citrus Sinensis ID: 030388

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------18
Protein Sequence
MLEPNKGPLKTYGSQQSKPGLASSPTPASFPLNFSHLSNKPPSISGRRRKPLAAVTWLPKSPVFSLFAGTCVLILFSIGTYYYELHVRSSLKTFRQRLRNSVLGHYLEKMKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQLDAENNEK
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccEEEEEccEEEEEEEEEcEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEEEcccEEEEEEHHHEEccccEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccHEEHHHHHHEEEEEEHcHEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEEcccccEEEEEEcEEcccccEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
mlepnkgplktygsqqskpglassptpasfplnfshlsnkppsisgrrrkplaavtwlpkspvfslfAGTCVLILFSIGTYYYELHVRSSLKTFRQRLRNSVLGHYLEKMkkglhpqmQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQLDAENNEK
Flexible Loop (DISEMBL)
mlepnkgplktygsqqskpglASSPTPASFPLNFSHLSNKPPSISGRRRKPLAAVTWLPKSPVFSLFAGTCVLILFSIGTYYYELHVRSSLKTFRQRLRNSVLGHYLEKmkkglhpqmQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEqqldaennek
Low Complexity Region (SEG)
MLEPNKGPLKTYGSQQSKPGLASSPTPASFPLNFSHLSNKPPSISGRRRKPLAAVTWLPKSPVFSLFAGTCVLILFSIGTYYYELHVRSSLKTFRQRLRNSVLGHYLEKMKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQLDAENNEK
Disordered region (IsUnstruct)
***************************************************LAAVTWLPKSPVFSLFAGTCVLILFSIGTYYYELHVRSSLKTFRQRLRNSVLGHYLEKMKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVA*****************
Disordered Region (DISOPRED)
****************************SFPLNFSH***************LAAVTWLPKSPVFSLFAGTCVLILFSIGTYYYELHVRSSLKTFRQRLRNSVLGHYLEKMKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARR***************************
Disordered Region (DISEMBL)
*************************TPASFPLNFSHLSNKPPSISGRRRKPLAAVTWLPKSPVFSLFAGTCVLILFSIGTYYYELHVRSSLKTFRQRLRNSVLGHYLEKMKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQ********
Disordered Region (DISPRO)
*****KGP**********************P*******N****ISGRRRKPLAAVTWLPKSPVFSLFAGTCVLILFSIGTYYYELHVRSSLKTFRQRLRNSVLGHYLEKMKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQLDA*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLEPNKGPLKTYGSQQSKPGLASSPTPASFPLNFSHLSNKPPSISGRRRKPLAAVTWLPKSPVFSLFAGTCVLILFSIGTYYYELHVRSSLKTFRQRLRNSVLGHYLEKMKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQLDAENNEK
Positional Conservation
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	Length	Definition	Q cover	H cover	Identity	E-value
Query	178
255577161	68	conserved hypothetical protein [Ricinus	0.382	1.0	0.811	6e-26
224060393	68	predicted protein [Populus trichocarpa]	0.382	1.0	0.768	2e-24
77551136	143	hypothetical protein LOC_Os11g31650 [Ory	0.387	0.482	0.728	1e-23
222616045	109	hypothetical protein OsJ_34043 [Oryza sa	0.443	0.724	0.658	2e-23
186532211	76	Ribosomal protein L31 [Arabidopsis thali	0.325	0.763	0.879	6e-23
116830209	77	unknown [Arabidopsis thaliana]	0.325	0.753	0.879	6e-23
218185821	109	hypothetical protein OsI_36268 [Oryza sa	0.438	0.715	0.654	8e-23
215694508	68	unnamed protein product [Oryza sativa Ja	0.382	1.0	0.739	1e-22
357156679	68	PREDICTED: uncharacterized protein LOC10	0.382	1.0	0.691	2e-22
195641006	68	hypothetical protein [Zea mays] gi|41392	0.382	1.0	0.691	2e-22

>gi|255577161|ref|XP_002529464.1| conserved hypothetical protein [Ricinus communis] gi|223531080|gb|EEF32930.1| conserved hypothetical protein [Ricinus communis]

 Score =  122 bits (306), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 56/69 (81%), Positives = 65/69 (94%), Gaps = 1/69 (1%)

Query: 110 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQ 169
           MKKG+HPQMQWISYVTQSGRLMH+MMTKIH+VGKVYHFRARRQ+A+S+GQVAKF+RRY Q
Sbjct: 1   MKKGIHPQMQWISYVTQSGRLMHIMMTKIHHVGKVYHFRARRQLAESLGQVAKFKRRYGQ 60

Query: 170 QLDAENNEK 178
           + DAE+  K
Sbjct: 61  E-DAEDTAK 68

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224060393|ref|XP_002300177.1| predicted protein [Populus trichocarpa] gi|222847435|gb|EEE84982.1| predicted protein [Populus trichocarpa]

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 53/69 (76%), Positives = 63/69 (91%), Gaps = 1/69 (1%)

Query: 110 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQ 169
           MKKG+HPQMQWISYVTQ GRLMH MMTKIH+VG VYHFRA+RQMA+S+GQ+AKF+RRY Q
Sbjct: 1   MKKGIHPQMQWISYVTQDGRLMHAMMTKIHHVGNVYHFRAKRQMAESLGQIAKFKRRYGQ 60

Query: 170 QLDAENNEK 178
           + +AE+ EK
Sbjct: 61  E-NAEDAEK 68

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|77551136|gb|ABA93933.1| hypothetical protein LOC_Os11g31650 [Oryza sativa Japonica Group]

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 51/70 (72%), Positives = 63/70 (90%), Gaps = 1/70 (1%)

Query: 109 KMKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYE 168
           +MKKGLHPQMQWISYVTQSGRL+++MMTK+++ GKVYH RA+RQMAQS+GQ+AKF RRY+
Sbjct: 75  RMKKGLHPQMQWISYVTQSGRLINIMMTKVNHTGKVYHMRAKRQMAQSLGQIAKFNRRYQ 134

Query: 169 QQLDAENNEK 178
           Q+   EN EK
Sbjct: 135 QE-SEENKEK 143

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222616045|gb|EEE52177.1| hypothetical protein OsJ_34043 [Oryza sativa Japonica Group]

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 54/82 (65%), Positives = 70/82 (85%), Gaps = 3/82 (3%)

Query: 99  RNSVLGHY--LEKMKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQS 156
           ++S   HY  + +MKKGLHPQMQWISYVTQSGRL+++MMTK+++ GKVYH RA+RQMAQS
Sbjct: 29  KSSRWNHYTWVVRMKKGLHPQMQWISYVTQSGRLINIMMTKVNHTGKVYHMRAKRQMAQS 88

Query: 157 IGQVAKFRRRYEQQLDAENNEK 178
           +GQ+AKF RRY+Q+ + EN EK
Sbjct: 89  LGQIAKFNRRYQQESE-ENKEK 109

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|186532211|ref|NP_001119440.1| Ribosomal protein L31 [Arabidopsis thaliana] gi|186532215|ref|NP_001119441.1| Ribosomal protein L31 [Arabidopsis thaliana] gi|297792983|ref|XP_002864376.1| hypothetical protein ARALYDRAFT_918652 [Arabidopsis lyrata subsp. lyrata] gi|98962143|gb|ABF59401.1| unknown protein [Arabidopsis thaliana] gi|297310211|gb|EFH40635.1| hypothetical protein ARALYDRAFT_918652 [Arabidopsis lyrata subsp. lyrata] gi|332009201|gb|AED96584.1| Ribosomal protein L31 [Arabidopsis thaliana] gi|332009202|gb|AED96585.1| Ribosomal protein L31 [Arabidopsis thaliana]

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 51/58 (87%), Positives = 57/58 (98%)

Query: 110 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRY 167
           MKKGLHPQMQWISYVTQSGRLMHVMMT+IH+VGKVYHF A+RQMAQSIGQ+AKF+RR+
Sbjct: 1   MKKGLHPQMQWISYVTQSGRLMHVMMTRIHHVGKVYHFGAKRQMAQSIGQIAKFKRRF 58

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116830209|gb|ABK28062.1| unknown [Arabidopsis thaliana]

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 51/58 (87%), Positives = 57/58 (98%)

Query: 110 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRY 167
           MKKGLHPQMQWISYVTQSGRLMHVMMT+IH+VGKVYHF A+RQMAQSIGQ+AKF+RR+
Sbjct: 1   MKKGLHPQMQWISYVTQSGRLMHVMMTRIHHVGKVYHFGAKRQMAQSIGQIAKFKRRF 58

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218185821|gb|EEC68248.1| hypothetical protein OsI_36268 [Oryza sativa Indica Group]

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 53/81 (65%), Positives = 69/81 (85%), Gaps = 3/81 (3%)

Query: 99  RNSVLGHY--LEKMKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQS 156
           ++S   HY  + +MKKGLHPQMQWISYVTQSGRL+++MMTK+++ GKVYH RA+RQMAQS
Sbjct: 29  KSSRWNHYTWVVRMKKGLHPQMQWISYVTQSGRLINIMMTKVNHTGKVYHMRAKRQMAQS 88

Query: 157 IGQVAKFRRRYEQQLDAENNE 177
           +GQ+AKF RRY+Q+ + EN E
Sbjct: 89  LGQIAKFNRRYQQESE-ENKE 108

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|215694508|dbj|BAG89501.1| unnamed protein product [Oryza sativa Japonica Group] gi|215701402|dbj|BAG92826.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 51/69 (73%), Positives = 63/69 (91%), Gaps = 1/69 (1%)

Query: 110 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQ 169
           MKKGLHPQMQWISYVTQSGRL+++MMTK+++ GKVYH RA+RQMAQS+GQ+AKF RRY+Q
Sbjct: 1   MKKGLHPQMQWISYVTQSGRLINIMMTKVNHTGKVYHMRAKRQMAQSLGQIAKFNRRYQQ 60

Query: 170 QLDAENNEK 178
           + + EN EK
Sbjct: 61  ESE-ENKEK 68

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357156679|ref|XP_003577539.1| PREDICTED: uncharacterized protein LOC100838519 isoform 2 [Brachypodium distachyon]

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 47/68 (69%), Positives = 62/68 (91%)

Query: 110 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQ 169
           M+KGLHPQMQWISYVTQSGRL+++MMTK+++ GKVYH RA+RQMAQS+GQ+AKF+RRYEQ
Sbjct: 1   MRKGLHPQMQWISYVTQSGRLINIMMTKVNHTGKVYHMRAKRQMAQSLGQIAKFKRRYEQ 60

Query: 170 QLDAENNE 177
           + +   ++
Sbjct: 61  EAEESKDK 68

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|195641006|gb|ACG39971.1| hypothetical protein [Zea mays] gi|413920925|gb|AFW60857.1| hypothetical protein ZEAMMB73_243654 [Zea mays]

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 47/68 (69%), Positives = 62/68 (91%)

Query: 110 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQ 169
           M+KGLHPQMQWISYVTQSGRL+++MMTK+++ GKVYH RA+RQMAQS+GQ+AKF+RRYEQ
Sbjct: 1   MRKGLHPQMQWISYVTQSGRLINIMMTKVNHTGKVYHMRAKRQMAQSLGQIAKFKRRYEQ 60

Query: 170 QLDAENNE 177
           + +   ++
Sbjct: 61  EAEKSKDK 68

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

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	178
TAIR|locus:4515103733	76	AT5G55125 [Arabidopsis thalian	0.387	0.907	0.791	3.2e-26

TAIR|locus:4515103733 AT5G55125 [Arabidopsis thaliana (taxid:3702)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 57/72 (79%), Positives = 66/72 (91%)

Query:   110 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRY-E 168
             MKKGLHPQMQWISYVTQSGRLMHVMMT+IH+VGKVYHF A+RQMAQSIGQ+AKF+RR+ E
Sbjct:     1 MKKGLHPQMQWISYVTQSGRLMHVMMTRIHHVGKVYHFGAKRQMAQSIGQIAKFKRRFNE 60

Query:   169 QQLDA--ENNEK 178
             Q+ +A  ENN +
Sbjct:    61 QEAEAAEENNNE 72


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        0.320   0.133   0.399    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      178       178   0.00086  109 3  11 22  0.39    32
                                                     31  0.39    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:  590 (63 KB)
  Total size of DFA:  156 KB (2093 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:  18.08u 0.08s 18.16t   Elapsed:  00:00:01
  Total cpu time:  18.08u 0.08s 18.16t   Elapsed:  00:00:01
  Start:  Fri May 10 23:08:16 2013   End:  Fri May 10 23:08:17 2013

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	178
pfam01197	69	pfam01197, Ribosomal_L31, Ribosomal protein L31	9e-13

>gnl|CDD|216357 pfam01197, Ribosomal_L31, Ribosomal protein L31

 Score = 59.9 bits (146), Expect = 9e-13
 Identities = 15/69 (21%), Positives = 34/69 (49%), Gaps = 10/69 (14%)

Query: 110 MKKGLHPQMQWI---------SYVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQV 160
           MKKG+HP+ + +          +VT S +   V+   + +    ++   ++ +  + G+V
Sbjct: 1   MKKGIHPEYREVVFTCSSCGNVFVTGSTKEYPVIKIDVCSACHPFYTGKQK-LVDTAGRV 59

Query: 161 AKFRRRYEQ 169
            KF +R+ +
Sbjct: 60  EKFNKRFGK 68

Length = 69

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	178
TIGR00105	68	L31 ribosomal protein L31. This family consists ex	98.7
PF01197	69	Ribosomal_L31: Ribosomal protein L31; InterPro: IP	98.5
PRK00528	71	rpmE 50S ribosomal protein L31; Reviewed	97.81
PRK01397	78	50S ribosomal protein L31; Provisional	97.38
PRK00019	72	rpmE 50S ribosomal protein L31; Reviewed	97.33
CHL00136	68	rpl31 ribosomal protein L31; Validated	97.23
PRK01678	87	rpmE2 50S ribosomal protein L31 type B; Reviewed	97.22
COG0254	75	RpmE Ribosomal protein L31 [Translation, ribosomal	96.66

>TIGR00105 L31 ribosomal protein L31

Probab=98.70  E-value=4.9e-09  Score=72.64  Aligned_cols=58  Identities=21%  Similarity=0.393  Sum_probs=45.7

Q ss_pred             HhhcCCccceeeEEeeccCeeeeeeehheec------cc--ceeehhhhhHHHHHHhHHHHHHHHHH
Q 030388          110 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHN------VG--KVYHFRARRQMAQSIGQVAKFRRRYE  168 (178)
Q Consensus       110 MkKGlHPQmQWISYVTQsGRLmhvMMtkihh------vG--kVYH~rAkRQMAqSlGQiAKFkRRy~  168 (178)
                      |||||||+.++|.++...|..+-++.|+-..      -.  -.+.-. ++++.++-|+|+||++||+
T Consensus         1 MKk~IHP~y~~v~~~~s~g~~f~~~ST~~~~~i~vdi~s~~HPfyTG-~~~~~~~~GRv~KF~kry~   66 (68)
T TIGR00105         1 MKKDIHPDYHEITVTCTCGNVFTTRSTWGKETLNLDICSKCHPFYTG-KQKIVDTGGRVDKFNKKFG   66 (68)
T ss_pred             CCCCCCCCCEEEEEEECCCCEEEEeeecCCceEEEEECCCCcccCCC-ceEEeccCCcHHHHHHHhc
Confidence            8999999999999999999999988886321      00  012222 5678899999999999996

This family consists exclusively of bacterial (and organellar) 50S ribosomal protein L31. In some species, such as Bacillus subtilis, this protein exists in two forms (RpmE and YtiA), one of which (RpmE) contains a pair of motifs, CXC and CXXC, for binding zinc.

>PF01197 Ribosomal_L31: Ribosomal protein L31; InterPro: IPR002150 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.50  E-value=6.9e-10  Score=76.70  Aligned_cols=59  Identities=22%  Similarity=0.447  Sum_probs=40.4

Q ss_pred             HhhcCCccceeeEEeec---------cCeeeeeeehheecccceeehhhhhHHHHHHhHHHHHHHHHHH
Q 030388          110 MKKGLHPQMQWISYVTQ---------SGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQ  169 (178)
Q Consensus       110 MkKGlHPQmQWISYVTQ---------sGRLmhvMMtkihhvGkVYH~rAkRQMAqSlGQiAKFkRRy~q  169 (178)
                      |||||||+++++.++..         |..-..+|.--|+.---.+.-. ++++.++-|+|+||++||+.
T Consensus         1 MKk~IHP~y~~v~v~c~s~g~~~~~~St~~~~~~~vdi~s~~HPfytG-~~~~~~~~Grv~KF~kkf~~   68 (69)
T PF01197_consen    1 MKKGIHPEYREVKVTCSSCGNTFETRSTKEYPVIKVDICSNCHPFYTG-KQKVVDTAGRVEKFNKKFGK   68 (69)
T ss_dssp             --SSTSSSHCEEEEEES-SSSCECECSSSSES-EEECSCSSSSCTTCS-CSSCSCCCCCCTSCCTCCCC
T ss_pred             CCCCCCCCCEEEEEEEcCCCCEEEEEECCcceEEEEeecCCCCEEEcC-cEEEEccccCHHHHHHHHcC
Confidence            89999999999955444         4444444544555444444445 67789999999999999975

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3D5D_4 3PYO_1 3D5B_4 3PYV_1 3PYT_1 3MRZ_1 3MS1_1 3PYR_1 3F1F_4 3F1H_4 ....

>PRK00528 rpmE 50S ribosomal protein L31; Reviewed

Probab=97.81  E-value=1e-05  Score=56.63  Aligned_cols=58  Identities=26%  Similarity=0.429  Sum_probs=41.9

Q ss_pred             HhhcCCccceeeEEeeccCeeeeeeehheecccceee----------hh-hhhHHHHHHhHHHHHHHHHH
Q 030388          110 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYH----------FR-ARRQMAQSIGQVAKFRRRYE  168 (178)
Q Consensus       110 MkKGlHPQmQWISYVTQsGRLmhvMMtkihhvGkVYH----------~r-AkRQMAqSlGQiAKFkRRy~  168 (178)
                      |||||||+..=+..+...|.-.-+.-|. -.++.+++          +- -++.+..+-|+|+||++||+
T Consensus         1 MKk~IHP~y~~v~~~~~~g~~f~~~ST~-g~~~~~i~vdv~s~~HPfyT~G~q~~~d~~GRv~kF~kky~   69 (71)
T PRK00528          1 MKKDIHPDYHPIKVVMTDGTEYETRSTW-GKTGPELRLDIDSGNHPAWTGGTQKLLDTGGRVAKFNKKFG   69 (71)
T ss_pred             CCCCCCCCCEEEEEEEeCCCEEEEEEcC-CCCCCeEEEEECCCCCccEeCCcCeEecccCcHHHHHHHHc
Confidence            8999999999998888888877666543 11122221          12 34557789999999999996

>PRK01397 50S ribosomal protein L31; Provisional

Probab=97.38  E-value=7.4e-05  Score=53.87  Aligned_cols=60  Identities=20%  Similarity=0.289  Sum_probs=40.0

Q ss_pred             HhhcCCccceeeEEeeccCeeeeeeehh----eec--ccceee-hhhhhH-HHH-HHhHHHHHHHHHHHh
Q 030388          110 MKKGLHPQMQWISYVTQSGRLMHVMMTK----IHN--VGKVYH-FRARRQ-MAQ-SIGQVAKFRRRYEQQ  170 (178)
Q Consensus       110 MkKGlHPQmQWISYVTQsGRLmhvMMtk----ihh--vGkVYH-~rAkRQ-MAq-SlGQiAKFkRRy~q~  170 (178)
                      |||||||+.+=|-... +|..+-+.-|+    |+-  -..-.= |--+++ +.. +-|+|+||++||+.-
T Consensus         1 MKk~IHP~y~~v~~~~-~G~~f~~~ST~~~~~i~vdi~s~~HPFyTG~q~~~vdt~~GRVeKF~kry~~~   69 (78)
T PRK01397          1 MKSGIHPEYKKFLIKV-GSDVFETMSTHPTGEILMDVDFRKHPAWNKDSGNVVNQSNKSVSDFNKRFSGL   69 (78)
T ss_pred             CCCCCCCCCEEEEEEE-CCCEEEEeECCCCCcEEEEeCCCCCCcCcCCeeEEecCCCccHHHHHHHHcCc
Confidence            8999999999888876 79888877775    210  000000 111232 334 479999999999876

>PRK00019 rpmE 50S ribosomal protein L31; Reviewed

Probab=97.33  E-value=9.1e-05  Score=52.54  Aligned_cols=62  Identities=23%  Similarity=0.486  Sum_probs=42.8

Q ss_pred             HhhcCCccceeeEEeeccCeeeeeeeh--h--eec--cccee-ehhhhhHHHHHHhHHHHHHHHHHHhh
Q 030388          110 MKKGLHPQMQWISYVTQSGRLMHVMMT--K--IHN--VGKVY-HFRARRQMAQSIGQVAKFRRRYEQQL  171 (178)
Q Consensus       110 MkKGlHPQmQWISYVTQsGRLmhvMMt--k--ihh--vGkVY-H~rAkRQMAqSlGQiAKFkRRy~q~~  171 (178)
                      ||||+||+.+=+.++-..|..+-+.-|  +  |+-  -.+-. -|--++++..+-|+|+||++||+...
T Consensus         1 MKk~IHP~y~~v~~~c~~g~~f~~~ST~~~~~i~vdi~s~~HPFyTG~q~~~dt~GRvekF~kry~~~~   69 (72)
T PRK00019          1 MKKDIHPKYEEVTVTCSCGNVFETRSTLGKDEINVDVCSKCHPFYTGKQKIVDTGGRVERFNKRFGKKG   69 (72)
T ss_pred             CCCCCCCCCEEEEEEECCCCEEEEeecCCCCcEEEEeCCCCCCcCcCCEeEeccCCcHHHHHHHhcccc
Confidence            899999999888877668888777766  2  110  00000 02234557889999999999998653

>CHL00136 rpl31 ribosomal protein L31; Validated

Probab=97.23  E-value=0.00015  Score=50.92  Aligned_cols=54  Identities=30%  Similarity=0.457  Sum_probs=34.6

Q ss_pred             HhhcCCccceeeEEeeccCee-eeeeehheecccceee----------hhhhhHHHHHHhHHHHHHHHHH
Q 030388          110 MKKGLHPQMQWISYVTQSGRL-MHVMMTKIHNVGKVYH----------FRARRQMAQSIGQVAKFRRRYE  168 (178)
Q Consensus       110 MkKGlHPQmQWISYVTQsGRL-mhvMMtkihhvGkVYH----------~rAkRQMAqSlGQiAKFkRRy~  168 (178)
                      |||||||+..=+..|+-+|-. +-+.-|+    +. ++          |--++.+.+.-|+|+||++||+
T Consensus         2 MKk~IHP~y~~~~~v~c~~~~~~~~~ST~----~~-i~vdv~s~~HPfyTG~~~~~~~~Grv~kF~kr~~   66 (68)
T CHL00136          2 PKKNIHPQWFPETKVYCDGQLVMTVGSTK----PE-LNVDIWSGNHPFYTGSQKIIDTEGRVERFMKKYG   66 (68)
T ss_pred             CCCCCCCCceeeEEEEEcCCCEEEEeecC----CC-EEEEeCCCCCccCcCCeeEecccccHHHHHHHhC
Confidence            899999988545444445544 3333332    11 11          2234567888999999999997

>PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed

Probab=97.22  E-value=0.00017  Score=53.02  Aligned_cols=62  Identities=26%  Similarity=0.483  Sum_probs=42.1

Q ss_pred             HhhcCCccceeeEEe-eccCeeeeeeehhee------cccc---eee----------hhhhhHHHHHHhHHHHHHHHHHH
Q 030388          110 MKKGLHPQMQWISYV-TQSGRLMHVMMTKIH------NVGK---VYH----------FRARRQMAQSIGQVAKFRRRYEQ  169 (178)
Q Consensus       110 MkKGlHPQmQWISYV-TQsGRLmhvMMtkih------hvGk---VYH----------~rAkRQMAqSlGQiAKFkRRy~q  169 (178)
                      |||||||+.+=+.++ ...|.-.-+.-|.=.      .-|+   +++          |--++++.++-|+|+||++||+.
T Consensus         1 MKk~IHP~y~~v~~~~~t~g~~f~~~ST~~~~~t~~~~dg~~yp~i~vdi~S~~HPFyTGkq~~vdt~GRVekF~kry~~   80 (87)
T PRK01678          1 MKKGIHPEYRPVVFHDTSTGFKFLTGSTITTDETIEWEDGKTYPLVKVEISSASHPFYTGKQKFVDTEGRVEKFNKRFGR   80 (87)
T ss_pred             CCCCCCCCCEEEEEEECCCCCEEEEeeeccccceeeecCCcccceEEEEeCCCCCCcCcCCeeEeccCCcHHHHHHHHhh
Confidence            899999999888887 556766555554311      0122   111          22355678889999999999987


Q ss_pred             hh
Q 030388          170 QL  171 (178)
Q Consensus       170 ~~  171 (178)
                      ..
T Consensus        81 ~~   82 (87)
T PRK01678         81 FA   82 (87)
T ss_pred             hh
Confidence            54

>COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]

Probab=96.66  E-value=0.00091  Score=48.38  Aligned_cols=62  Identities=24%  Similarity=0.435  Sum_probs=40.0

Q ss_pred             HhhcCCcc-ceeeEEeec-cCeeeeeeehheecc------cceee-hhhhhHHHHHHhHHHHHHHHHHHhh
Q 030388          110 MKKGLHPQ-MQWISYVTQ-SGRLMHVMMTKIHNV------GKVYH-FRARRQMAQSIGQVAKFRRRYEQQL  171 (178)
Q Consensus       110 MkKGlHPQ-mQWISYVTQ-sGRLmhvMMtkihhv------GkVYH-~rAkRQMAqSlGQiAKFkRRy~q~~  171 (178)
                      |||||||. .+=+-++.. .|--+-++-|+-..+      ++..= +--+......-|.++||++||+...
T Consensus         1 MKk~IHP~y~~~v~~~~~s~g~~f~~~ST~~~~~i~vdV~s~~HPFyTG~qk~~d~~Grv~kF~kRf~~~~   71 (75)
T COG0254           1 MKKDIHPEYYRPVVFVCSSCGNEFTTRSTKGTDEINLDVCSKCHPFYTGKQKIVDTEGRVEKFNKRFGGFK   71 (75)
T ss_pred             CCCCcCCCccceEEEEeCCCCCEEEEEeccCCceEEEEeCCCCCCcCcCceeEeeccccHHHHHHHhcccc
Confidence            89999999 487777776 477777777763220      11100 1123334444499999999998754

---

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	Length	Definition	E-value
Query	178
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 44.1 bits (103), Expect = 1e-05
 Identities = 22/180 (12%), Positives = 57/180 (31%), Gaps = 21/180 (11%)

Query: 8   PLKTYGSQQSKPGLASSPTPASFPLNFSHLSNKPPSISGRRRKP-----LAAVTWLPKSP 62
            L+    Q      + S   ++  L    +  +   +   +        L  V    K  
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV-QNAK-- 257

Query: 63  VFSLFAGTC-VLIL--------FSIGTYYYELHVRSSLKTFRQRLRNSVLGHYLEKMKKG 113
            ++ F  +C +L+         F        + +     T       S+L  YL+   + 
Sbjct: 258 AWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQD 317

Query: 114 LHPQMQWIS--YVTQSGRLMHVMMTKIHNVGKVYHFRARRQMAQSIGQV--AKFRRRYEQ 169
           L  ++   +   ++     +   +    N   V   +    +  S+  +  A++R+ +++
Sbjct: 318 LPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDR 377

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	178
1nkw_Y	73	50S ribosomal protein L31; ribosome, large subunit	98.35
1vs6_Z	70	50S ribosomal protein L31; ribosome, kasugamycin;	98.11
3v2d_4	71	50S ribosomal protein L31; ribosome associated inh	97.15
3f1f_4	97	50S ribosomal protein L31; RF2, ribosome, terminat	96.83
3bbo_1	144	Ribosomal protein L31; large ribosomal subunit, sp	91.78

>1nkw_Y 50S ribosomal protein L31; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB: 1nwx_Y* 1nwy_Y* 1pnu_Y 1pny_Y 1sm1_Y* 1vor_1 1vou_1 1vow_1 1voy_1 1vp0_1 1xbp_Y* 1yl3_4 2b66_4 2b9n_4 2b9p_4

Probab=98.35  E-value=8.3e-08  Score=67.33  Aligned_cols=61  Identities=23%  Similarity=0.364  Sum_probs=48.1

Q ss_pred             HhhcCCccceeeEEeeccCeeeeeeehhe------ecccceeehhhhhHHHHHHhHHHHHHHHHHHhh
Q 030388          110 MKKGLHPQMQWISYVTQSGRLMHVMMTKI------HNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQL  171 (178)
Q Consensus       110 MkKGlHPQmQWISYVTQsGRLmhvMMtki------hhvGkVYH~rAkRQMAqSlGQiAKFkRRy~q~~  171 (178)
                      |||||||+..++.++-..|..+.+..|+-      +...--+. -.++++.++-|+|+||++||+...
T Consensus         1 MKk~IHP~y~~v~~~~s~g~~f~t~ST~~~i~vdi~s~~HPFy-TGkqk~vdt~GRVekF~kry~~~~   67 (73)
T 1nkw_Y            1 MQKDLHPKAVPCKIIYQGQVVMETMSTRPEIHVDVWSGVHPFW-TGEERFLDTEGRVDKFNKRFGDSY   67 (73)
T ss_pred             CCCCCCCCCEEEEEEECCCCEEEEcccCCCEEEEECCCCCcCC-cCcEEEEeccccHHHHHHHHhccc
Confidence            89999999999999999999998888863      22222222 346678899999999999999765

>1vs6_Z 50S ribosomal protein L31; ribosome, kasugamycin; 3.46A {Escherichia coli} SCOP: d.325.1.2 PDB: 1vs8_Z 2aw4_Z 2awb_Z 2j28_Z 2rdo_Z 2vhm_Z 2vhn_Z 3bbx_Z 3e1b_S 3e1d_S 3iyx_A 3iyy_A 3izt_b* 3izu_b* 3j0t_2* 3j0w_2* 3j0y_2* 3j11_2* 3j12_2* 3j14_2*

Probab=98.11  E-value=4.6e-08  Score=67.93  Aligned_cols=60  Identities=25%  Similarity=0.470  Sum_probs=47.2

Q ss_pred             HhhcCCccceeeEEeeccCeeeeeeehhee-------cccceeehhhhhHHHHHHhHHHHHHHHHHHh
Q 030388          110 MKKGLHPQMQWISYVTQSGRLMHVMMTKIH-------NVGKVYHFRARRQMAQSIGQVAKFRRRYEQQ  170 (178)
Q Consensus       110 MkKGlHPQmQWISYVTQsGRLmhvMMtkih-------hvGkVYH~rAkRQMAqSlGQiAKFkRRy~q~  170 (178)
                      |||||||+.+++.++-..|..+.+..|+-.       ...--+ +-.++++.++-|+|+||++||+..
T Consensus         1 MKk~IHP~y~~v~~~~s~g~~f~t~ST~~~ei~vdi~s~~HPF-yTG~qk~vdt~GRV~kF~kry~~~   67 (70)
T 1vs6_Z            1 MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPF-FTGKQRDVATGGRVDRFNKRFNIP   67 (70)
T ss_dssp             CCCTTSCCCCCCBCCCCSSCCCCCBCCCCCCCCCBCCSSSCCB-CCCCCTTTTTHHHHSCSSTTTTTT
T ss_pred             CCCCCCCCCEEEEEEECCCCEEEEeecCCCcEeeeecCCCCcc-CcCcEEEEeccccHHHHHHHhhcc
Confidence            899999999999999889999888888522       111112 344677889999999999999864

>3v2d_4 50S ribosomal protein L31; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgq_3 2hgj_3 2hgu_3 2j03_4 2v47_4 2v49_4 2wdi_4 2wdj_4 2wdl_4 2wdn_4 2wh2_4 2wrj_4 2wrl_4 2wro_4 2wrr_4 2x9s_4 2x9u_4 2xg0_4 2xg2_4 2xqe_4 ...

Probab=97.15  E-value=0.00017  Score=50.39  Aligned_cols=60  Identities=23%  Similarity=0.522  Sum_probs=23.8

Q ss_pred             HhhcCCccceeeEEeeccCeeeeeeehhe------ecccceeehhhhhHHHHHHhHHHHHHHHHHHh
Q 030388          110 MKKGLHPQMQWISYVTQSGRLMHVMMTKI------HNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQ  170 (178)
Q Consensus       110 MkKGlHPQmQWISYVTQsGRLmhvMMtki------hhvGkVYH~rAkRQMAqSlGQiAKFkRRy~q~  170 (178)
                      |||||||+..-+-++-..|..+-+--|+=      +.----+ +--+..+..+-|+|+||++||+..
T Consensus         1 MKk~IHP~Y~~v~v~c~~g~~f~t~ST~~~i~vdi~S~~HPF-yTGkqk~vdt~GRVekF~kryg~~   66 (71)
T 3v2d_4            1 MKEGIHPKLVPARIICGCGNVIETYSTKPEIYVEVCSKCHPF-YTGQQRFVDTEGRVERFQRRYGDS   66 (71)
T ss_dssp             CCSSSSCCCEEEEEEETTSCEEEEEESSSEEEESCCTTTSSS-SSCC--------------------
T ss_pred             CCCCCCCCCeEEEEEECCCCEEEeeeeccCEEEEecCCCCCC-CCCCEEEEcccCcHHHHHHHHccc
Confidence            89999999988887766777666655541      1100000 123456789999999999999865

>3f1f_4 50S ribosomal protein L31; RF2, ribosome, termination, tRNA; 3.00A {Thermus thermophilus} PDB: 3d5d_4 3d5b_4 3f1h_4

Probab=96.83  E-value=0.00034  Score=51.68  Aligned_cols=64  Identities=20%  Similarity=0.495  Sum_probs=12.2

Q ss_pred             HHHHhhcCCccceeeEEeeccCeeeeeeehh------eecccceeehhhhhHHHHHHhHHHHHHHHHHHhh
Q 030388          107 LEKMKKGLHPQMQWISYVTQSGRLMHVMMTK------IHNVGKVYHFRARRQMAQSIGQVAKFRRRYEQQL  171 (178)
Q Consensus       107 ~~~MkKGlHPQmQWISYVTQsGRLmhvMMtk------ihhvGkVYH~rAkRQMAqSlGQiAKFkRRy~q~~  171 (178)
                      ...|||||||+..-+-++-..|..+-+--|+      |+.----+ +--+..+..+-|+|+||++||+...
T Consensus        24 ~~~MKk~IHP~Y~~v~v~ct~G~~f~t~ST~~~i~vDI~S~~HPF-YTGkqk~vdt~GRVeKF~kRyg~~~   93 (97)
T 3f1f_4           24 EANVKEGIHPKLVPARIICGCGNVIETYSTKPEIYVEVCSKCHPF-YTGQQRFVDTEGRVERFQRRYGDSY   93 (97)
T ss_dssp             ------------CCCEEEETTEEEEECCCSSCCEEESSCTTC-----------------------------
T ss_pred             hccccCCCCCCCeEEEEEECCCCEEEeeeeeeEEEEEECCCCCCC-CcCCEEEEcccCcHHHHHHHHcccc
Confidence            4679999999988887765566655554443      11100001 2235567899999999999998644

>3bbo_1 Ribosomal protein L31; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=91.78  E-value=0.00036  Score=54.65  Aligned_cols=60  Identities=28%  Similarity=0.398  Sum_probs=32.9

Q ss_pred             HHHHhhcCCccceeeEEeeccCeeeeeeehheecccceee----------hhh-hhHHHHHHhHHHHHHHHHHHh
Q 030388          107 LEKMKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYH----------FRA-RRQMAQSIGQVAKFRRRYEQQ  170 (178)
Q Consensus       107 ~~~MkKGlHPQmQWISYVTQsGRLmhvMMtkihhvGkVYH----------~rA-kRQMAqSlGQiAKFkRRy~q~  170 (178)
                      +..||+||||+..-+-.|.-+|--...    +..+.+.++          |-- .+++..+-|+|+||++||+..
T Consensus        46 ~~~MKk~IHPeY~~Vv~v~cs~g~~f~----t~ST~~~i~VDIcS~cHPFYTGkqkk~vDt~GRVeKF~KRyg~~  116 (144)
T 3bbo_1           46 ITCRKKELHPEFHEDAKVYCNGELVMT----TGGTKKEYVVDVWSGNHPFYLGNRSALMVDADQVEKFRKRFAGL  116 (144)
T ss_dssp             ----CTTTCCCCCHHHHHCSSSCTTTS----CSSCSCSSSCCSSCCCCCSSSSSSSCCCCCCCCCCCSSCCCCCC
T ss_pred             eeccCCCCCCCCEEeEEEEcCCCeEEE----EEecCceEEeeecCCCCccEeCceeeEecccccHHHHHHHHhcc
Confidence            468999999997765555545432221    111111111          111 223677889999999999753

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	178
d1vs6z1	70	d.325.1.2 (Z:1-70) Ribosomal protein L31p {Escheri	2e-04

>d1vs6z1 d.325.1.2 (Z:1-70) Ribosomal protein L31p {Escherichia coli [TaxId: 562]} Length = 70

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L31p
domain: Ribosomal protein L31p
species: Escherichia coli [TaxId: 562]

 Score = 36.3 bits (84), Expect = 2e-04
 Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 14/68 (20%)

Query: 110 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYH----------FRARRQMAQSIGQ 159
           MKK +HP+ + I+     G +M +  T    VG   +          F  +++   + G+
Sbjct: 1   MKKDIHPKYEEITASCSCGNVMKIRST----VGHDLNLDVCSKCHPFFTGKQRDVATGGR 56

Query: 160 VAKFRRRY 167
           V +F +R+
Sbjct: 57  VDRFNKRF 64

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	178
d1vs6z1	70	Ribosomal protein L31p {Escherichia coli [TaxId: 5	96.69

>d1vs6z1 d.325.1.2 (Z:1-70) Ribosomal protein L31p {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L31p
domain: Ribosomal protein L31p
species: Escherichia coli [TaxId: 562]

Probab=96.69  E-value=1.5e-05  Score=53.39  Aligned_cols=57  Identities=26%  Similarity=0.511  Sum_probs=40.9

Q ss_pred             HhhcCCccceeeEEeeccCeeeeeeehheecccceee----------hhhhhHHHHHHhHHHHHHHHHHHh
Q 030388          110 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVYH----------FRARRQMAQSIGQVAKFRRRYEQQ  170 (178)
Q Consensus       110 MkKGlHPQmQWISYVTQsGRLmhvMMtkihhvGkVYH----------~rAkRQMAqSlGQiAKFkRRy~q~  170 (178)
                      |||||||+.+=+..+.-.|.-+-+.-|.    ++-++          |--+++++.+-|+|+||++||+.-
T Consensus         1 MKk~IHP~y~~v~~~~s~g~~f~~~sT~----~~e~~vdi~s~~HPfyTG~q~~~dt~GRVekF~krf~~~   67 (70)
T d1vs6z1           1 MKKDIHPKYEEITASCSCGNVMKIRSTV----GHDLNLDVCSKCHPFFTGKQRDVATGGRVDRFNKRFNIP   67 (70)
T ss_dssp             CCCTTSCCCCCCBCCCCSSCCCCCBCCC----CCCCCCBCCSSSCCBCCCCCTTTTTHHHHSCSSTTTTTT
T ss_pred             CCCCCCCCCEeEEEEECCCCEEEEeeEe----CCcEEEEeCCCCCCcCcCCEEEeeccCcHHHHHHhhccc
Confidence            8999999988887777677776665442    11111          223566788899999999999754