Citrus Sinensis ID: 036150

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70-------
Protein Sequence
MVSYYRVLRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAALLTFSSTLATSQAFSAACCAS
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHcEEEEEEcccccccccccHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHcHHHHHHHHHcEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MVSYYRVLRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAALLTFSSTLATSQAFSAACCAS
Flexible Loop (DISEMBL)
mvsyyrvlrrkrtkkyavkrkavgiwscKYCGKVKAGALNAATLAAFTALPAAAAALLTFSSTLATSQAFSAACCAS
Low Complexity Region (SEG)
MVSYYRVLRRKRTKKYAVKRKAVGIWSCKYCGKVKagalnaatlaaftalpaaaaalltfsstlatsqafsaaCCAS
Disordered region (IsUnstruct)
***YYRVLRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAALLTFSSTLATSQAFSAAC***
Disordered Region (DISOPRED)
**SYYR*LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAALLTFSSTLATSQAFSAACCAS
Disordered Region (DISEMBL)
MVSYYRVLRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAALLTFSSTLATSQ*********
Disordered Region (DISPRO)
*VSYYRVLRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAALLTFSSTLATSQAFSAACC**
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooHHHHHHHHHHHHHHHHHHHHHHHHHi
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVSYYRVLRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAALLTFSSTLATSQAFSAACCAS
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

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	77	2.2.26 [Sep-21-2011]
Q9XHE4	92	60S ribosomal protein L37	N/A	no	0.376	0.315	0.75	3e-05
P43209	93	60S ribosomal protein L37	N/A	no	0.376	0.311	0.687	8e-05
Q8RXU5	92	60S ribosomal protein L37	yes	no	0.376	0.315	0.687	8e-05
Q5QM99	92	60S ribosomal protein L37	yes	no	0.376	0.315	0.687	0.0001
Q9ZRS8	92	60S ribosomal protein L37	N/A	no	0.311	0.260	0.833	0.0001
Q9SRK6	92	Putative 60S ribosomal pr	no	no	0.376	0.315	0.656	0.0002

>sp|Q9XHE4|RL37A_GOSHI 60S ribosomal protein L37a OS=Gossypium hirsutum GN=RPL37A PE=3 SV=1

 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/32 (75%), Positives = 25/32 (78%), Gaps = 3/32 (9%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAGA---LNAAT 43
          KYAVKRKAVGIW CK CGKVKAG    LN A+
Sbjct: 44 KYAVKRKAVGIWGCKACGKVKAGGAYTLNTAS 75

Gossypium hirsutum (taxid: 3635)

>sp|P43209|RL37A_BRARA 60S ribosomal protein L37a OS=Brassica rapa GN=RPL37A PE=3 SV=2

 Score = 45.8 bits (107), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/32 (68%), Positives = 24/32 (75%), Gaps = 3/32 (9%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAGA---LNAAT 43
          KY VKRKAVGIW CK CGKVKAG    +N A+
Sbjct: 44 KYGVKRKAVGIWGCKDCGKVKAGGAYTMNTAS 75

Brassica rapa (taxid: 51350)

>sp|Q8RXU5|R37A2_ARATH 60S ribosomal protein L37a-2 OS=Arabidopsis thaliana GN=RPL37AC PE=3 SV=1

 Score = 45.8 bits (107), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/32 (68%), Positives = 24/32 (75%), Gaps = 3/32 (9%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAGA---LNAAT 43
          KY VKRKAVGIW CK CGKVKAG    +N A+
Sbjct: 44 KYGVKRKAVGIWGCKDCGKVKAGGAYTMNTAS 75

Arabidopsis thaliana (taxid: 3702)

>sp|Q5QM99|RL37A_ORYSJ 60S ribosomal protein L37a OS=Oryza sativa subsp. japonica GN=Os01g0679700 PE=1 SV=1

 Score = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/32 (68%), Positives = 25/32 (78%), Gaps = 3/32 (9%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAGA---LNAAT 43
          K+AVKRKAVGIW CK CGKVKAG    +N A+
Sbjct: 44 KFAVKRKAVGIWGCKDCGKVKAGGAYTMNTAS 75

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9ZRS8|RL37A_PSEMZ 60S ribosomal protein L37a OS=Pseudotsuga menziesii GN=RPL37A PE=3 SV=1

 Score = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/24 (83%), Positives = 21/24 (87%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAGA 38
          K+AVKRKAVGIW CK CGKVKAG 
Sbjct: 44 KFAVKRKAVGIWGCKDCGKVKAGG 67

Pseudotsuga menziesii (taxid: 3357)

>sp|Q9SRK6|R37A1_ARATH Putative 60S ribosomal protein L37a-1 OS=Arabidopsis thaliana GN=RPL37AB PE=3 SV=1

 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/32 (65%), Positives = 24/32 (75%), Gaps = 3/32 (9%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAGA---LNAAT 43
          KY+VKRK VGIW CK CGKVKAG    +N A+
Sbjct: 44 KYSVKRKVVGIWGCKDCGKVKAGGAYTMNTAS 75

Arabidopsis thaliana (taxid: 3702)

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	77
224067552	92	predicted protein [Populus trichocarpa]	0.376	0.315	0.781	0.0003
7576200	1606	protein synthesis initiation factor-like	0.441	0.021	0.685	0.0005
297734652	141	unnamed protein product [Vitis vinifera]	0.376	0.205	0.75	0.0008
255626231	64	unknown [Glycine max]	0.376	0.453	0.75	0.0008
413968440	92	60S ribosomal protein L37a [Solanum tube	0.376	0.315	0.75	0.0009
58578274	92	60S ribosomal protein L37a [Capsicum chi	0.376	0.315	0.75	0.0009
313586497	92	60S ribosomal protein L37aA [Hevea brasi	0.376	0.315	0.75	0.0009
224126415	92	predicted protein [Populus trichocarpa]	0.376	0.315	0.75	0.0009

>gi|224067552|ref|XP_002302504.1| predicted protein [Populus trichocarpa] gi|118483173|gb|ABK93491.1| unknown [Populus trichocarpa] gi|222844230|gb|EEE81777.1| predicted protein [Populus trichocarpa]

 Score = 49.3 bits (116), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/32 (78%), Positives = 26/32 (81%), Gaps = 3/32 (9%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAGA---LNAAT 43
          KYAVKRKAVGIWSCK CGKVKAG    LN A+
Sbjct: 44 KYAVKRKAVGIWSCKDCGKVKAGGAYTLNTAS 75

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|7576200|emb|CAB87861.1| protein synthesis initiation factor-like [Arabidopsis thaliana]

 Score = 48.5 bits (114), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/35 (68%), Positives = 25/35 (71%), Gaps = 1/35 (2%)

Query: 15   KYAVKRKAVGIWSCKYCGKVKA-GALNAATLAAFT 48
            KY VKRKAVGIW CK CGKVKA GA    T +A T
Sbjct: 1558 KYGVKRKAVGIWGCKDCGKVKAGGAYTMNTASAVT 1592

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297734652|emb|CBI16703.3| unnamed protein product [Vitis vinifera]

 Score = 47.8 bits (112), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/32 (75%), Positives = 26/32 (81%), Gaps = 3/32 (9%)

Query: 15  KYAVKRKAVGIWSCKYCGKVKAGA---LNAAT 43
           KYAVKRKAVGIW+CK CGKVKAG    LN A+
Sbjct: 93  KYAVKRKAVGIWACKDCGKVKAGGAYTLNTAS 124

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255626231|gb|ACU13460.1| unknown [Glycine max]

 Score = 47.8 bits (112), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/32 (75%), Positives = 25/32 (78%), Gaps = 3/32 (9%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAGA---LNAAT 43
          KYAVKRKAVGIW CK CGKVKAG    LN A+
Sbjct: 16 KYAVKRKAVGIWGCKDCGKVKAGGAYTLNTAS 47

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413968440|gb|AFW90557.1| 60S ribosomal protein L37a [Solanum tuberosum]

 Score = 47.8 bits (112), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 24/32 (75%), Positives = 25/32 (78%), Gaps = 3/32 (9%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAGA---LNAAT 43
          KYAVKRKAVGIW CK CGKVKAG    LN A+
Sbjct: 44 KYAVKRKAVGIWGCKDCGKVKAGGAYTLNTAS 75

Source: Solanum tuberosum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|58578274|emb|CAI48073.1| 60S ribosomal protein L37a [Capsicum chinense]

 Score = 47.8 bits (112), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 24/32 (75%), Positives = 25/32 (78%), Gaps = 3/32 (9%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAGA---LNAAT 43
          KYAVKRKAVGIW CK CGKVKAG    LN A+
Sbjct: 44 KYAVKRKAVGIWGCKDCGKVKAGGAYTLNTAS 75

Source: Capsicum chinense

Species: Capsicum chinense

Genus: Capsicum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|313586497|gb|ADR71259.1| 60S ribosomal protein L37aA [Hevea brasiliensis]

 Score = 47.8 bits (112), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 24/32 (75%), Positives = 25/32 (78%), Gaps = 3/32 (9%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAGA---LNAAT 43
          KYAVKRKAVGIW CK CGKVKAG    LN A+
Sbjct: 44 KYAVKRKAVGIWGCKDCGKVKAGGAYTLNTAS 75

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224126415|ref|XP_002329548.1| predicted protein [Populus trichocarpa] gi|224136378|ref|XP_002326845.1| predicted protein [Populus trichocarpa] gi|224138784|ref|XP_002326689.1| predicted protein [Populus trichocarpa] gi|255571073|ref|XP_002526487.1| 60S ribosomal protein L37a, putative [Ricinus communis] gi|356504539|ref|XP_003521053.1| PREDICTED: 60S ribosomal protein L37a-like [Glycine max] gi|356511083|ref|XP_003524259.1| PREDICTED: 60S ribosomal protein L37a [Glycine max] gi|356520742|ref|XP_003529019.1| PREDICTED: 60S ribosomal protein L37a-like [Glycine max] gi|356563414|ref|XP_003549958.1| PREDICTED: 60S ribosomal protein L37a-like [Glycine max] gi|357477067|ref|XP_003608819.1| 60S ribosomal protein L37a [Medicago truncatula] gi|118483026|gb|ABK93424.1| unknown [Populus trichocarpa] gi|118484983|gb|ABK94356.1| unknown [Populus trichocarpa] gi|217071074|gb|ACJ83897.1| unknown [Medicago truncatula] gi|222834011|gb|EEE72488.1| predicted protein [Populus trichocarpa] gi|222835160|gb|EEE73595.1| predicted protein [Populus trichocarpa] gi|222870257|gb|EEF07388.1| predicted protein [Populus trichocarpa] gi|223534162|gb|EEF35878.1| 60S ribosomal protein L37a, putative [Ricinus communis] gi|355509874|gb|AES91016.1| 60S ribosomal protein L37a [Medicago truncatula] gi|388494042|gb|AFK35087.1| unknown [Medicago truncatula] gi|388514345|gb|AFK45234.1| unknown [Medicago truncatula] gi|388520787|gb|AFK48455.1| unknown [Medicago truncatula]

 Score = 47.8 bits (112), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 24/32 (75%), Positives = 25/32 (78%), Gaps = 3/32 (9%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAGA---LNAAT 43
          KYAVKRKAVGIW CK CGKVKAG    LN A+
Sbjct: 44 KYAVKRKAVGIWGCKDCGKVKAGGAYTLNTAS 75

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	77
TAIR|locus:505006406	92	AT3G60245 [Arabidopsis thalian	0.272	0.228	0.857	1.9e-05
TAIR|locus:2085532	92	AT3G10950 [Arabidopsis thalian	0.272	0.228	0.809	3.9e-05

TAIR|locus:505006406 AT3G60245 [Arabidopsis thaliana (taxid:3702)]

 Score = 100 (40.3 bits), Expect = 1.9e-05, P = 1.9e-05
 Identities = 18/21 (85%), Positives = 18/21 (85%)

Query:    15 KYAVKRKAVGIWSCKYCGKVK 35
             KY VKRKAVGIW CK CGKVK
Sbjct:    44 KYGVKRKAVGIWGCKDCGKVK 64

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0022625 "cytosolic large ribosomal subunit" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

TAIR|locus:2085532 AT3G10950 [Arabidopsis thaliana (taxid:3702)]

 Score = 97 (39.2 bits), Expect = 3.9e-05, P = 3.9e-05
 Identities = 17/21 (80%), Positives = 18/21 (85%)

Query:    15 KYAVKRKAVGIWSCKYCGKVK 35
             KY+VKRK VGIW CK CGKVK
Sbjct:    44 KYSVKRKVVGIWGCKDCGKVK 64


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        0.330   0.135   0.460    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       77        39   0.00091  102 3  11 22  0.42    25
                                                     29  0.46    23


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:  363 (39 KB)
  Total size of DFA:  65 KB (2062 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:  5.98u 0.22s 6.20t   Elapsed:  00:00:00
  Total cpu time:  5.98u 0.22s 6.20t   Elapsed:  00:00:00
  Start:  Sat May 11 02:10:56 2013   End:  Sat May 11 02:10:56 2013

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0022625 "cytosolic large ribosomal subunit" evidence=IDA

GO:0005829 "cytosol" 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!

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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

---

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	77
pfam01780	90	pfam01780, Ribosomal_L37ae, Ribosomal L37ae protei	2e-06
PTZ00255	90	PTZ00255, PTZ00255, 60S ribosomal protein L37a; Pr	2e-04
PRK03976	90	PRK03976, rpl37ae, 50S ribosomal protein L37Ae; Re	5e-04
COG1997	89	COG1997, RPL43A, Ribosomal protein L37AE/L43A [Tra	0.003

>gnl|CDD|216695 pfam01780, Ribosomal_L37ae, Ribosomal L37ae protein family

 Score = 41.1 bits (97), Expect = 2e-06
 Identities = 21/39 (53%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAG-ALNAATLAAFTALPA 52
          K AVKRKAVGIW C+ CGK  AG A    T A  T    
Sbjct: 43 KDAVKRKAVGIWKCRKCGKTFAGGAYTPETPAGKTVRRT 81

This ribosomal protein is found in archaebacteria and eukaryotes. It contains four conserved cysteine residues that may bind to zinc. Length = 90

>gnl|CDD|240332 PTZ00255, PTZ00255, 60S ribosomal protein L37a; Provisional

 Score = 35.8 bits (83), Expect = 2e-04
 Identities = 17/35 (48%), Positives = 21/35 (60%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTA 49
          K+AVKR+AVGIW CK C K  AG     +  A + 
Sbjct: 44 KHAVKRQAVGIWRCKGCKKTVAGGAWTLSTPAAST 78

Length = 90

>gnl|CDD|235183 PRK03976, rpl37ae, 50S ribosomal protein L37Ae; Reviewed

 Score = 34.9 bits (81), Expect = 5e-04
 Identities = 11/24 (45%), Positives = 13/24 (54%)

Query: 14 KKYAVKRKAVGIWSCKYCGKVKAG 37
           +  VKR   GIW C+ CG   AG
Sbjct: 43 GRPKVKRVGTGIWECRKCGAKFAG 66

Length = 90

>gnl|CDD|224908 COG1997, RPL43A, Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]

 Score = 32.7 bits (75), Expect = 0.003
 Identities = 12/24 (50%), Positives = 14/24 (58%)

Query: 14 KKYAVKRKAVGIWSCKYCGKVKAG 37
           +  VKR A GIW C+ CG   AG
Sbjct: 42 GRTTVKRIATGIWKCRKCGAKFAG 65

Length = 89

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	77
PF01780	90	Ribosomal_L37ae: Ribosomal L37ae protein family; I	99.8
PRK03976	90	rpl37ae 50S ribosomal protein L37Ae; Reviewed	99.8
TIGR00280	91	L37a ribosomal protein L37a. This model finds euka	99.8
PTZ00255	90	60S ribosomal protein L37a; Provisional	99.8
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	99.72
KOG0402	92	consensus 60S ribosomal protein L37 [Translation,	99.59
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	96.33
PHA00626	59	hypothetical protein	95.41
PRK00432	50	30S ribosomal protein S27ae; Validated	95.18
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	93.55
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	92.77
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	92.4
PF08646	146	Rep_fac-A_C: Replication factor-A C terminal domai	91.31
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	91.08
PRK12366	637	replication factor A; Reviewed	90.65
COG0675	364	Transposase and inactivated derivatives [DNA repli	89.22
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	89.1
cd04476	166	RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds cor	89.08
smart00661	52	RPOL9 RNA polymerase subunit 9.	87.44
PRK09710	64	lar restriction alleviation and modification prote	86.72
PRK08402	355	replication factor A; Reviewed	85.89
PHA02942	383	putative transposase; Provisional	85.46
PF09082	68	DUF1922: Domain of unknown function (DUF1922); Int	84.51
PF11781	36	RRN7: RNA polymerase I-specific transcription init	82.19
PF08273	40	Prim_Zn_Ribbon: Zinc-binding domain of primase-hel	81.72
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	81.46
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	81.42
PRK07591	421	threonine synthase; Validated	80.32

>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.80  E-value=2.1e-20  Score=124.55  Aligned_cols=49  Identities=35%  Similarity=0.480  Sum_probs=42.4

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHHHHHh
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAA   56 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~~~~~   56 (77)
                      ..||.|||++|||+++|||+|++||++||||||+|+||++...+.+-.-
T Consensus        36 y~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~~i~r   84 (90)
T PF01780_consen   36 YTCPFCGKTSVKRVATGIWKCKKCGKKFAGGAYTPSTPAAKTVKRAIRR   84 (90)
T ss_dssp             BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHHHHHH
T ss_pred             CcCCCCCCceeEEeeeEEeecCCCCCEEeCCCccccchHHHHHHHHHHH
Confidence            4699999999999999999999999999999999999999877665443

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 [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....

>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed

Probab=99.80  E-value=4.5e-20  Score=123.00  Aligned_cols=48  Identities=27%  Similarity=0.388  Sum_probs=43.2

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHHHHH
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAA   55 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~~~~   55 (77)
                      ..||.|||++|||+++|||+|++||++||||||+|+||++.....+-+
T Consensus        37 y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~~ir   84 (90)
T PRK03976         37 HVCPVCGRPKVKRVGTGIWECRKCGAKFAGGAYTPETPAGKTVTRAIR   84 (90)
T ss_pred             ccCCCCCCCceEEEEEEEEEcCCCCCEEeCCccccccchhhhHHHHHH
Confidence            469999999999999999999999999999999999999987554433

>TIGR00280 L37a ribosomal protein L37a

Probab=99.80  E-value=4.3e-20  Score=123.39  Aligned_cols=49  Identities=27%  Similarity=0.398  Sum_probs=43.5

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHHHHHh
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAA   56 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~~~~~   56 (77)
                      ..||.|||++|||+++|||+|++||++||||||+|+||++.....+-+-
T Consensus        36 y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGAy~p~T~~~~t~~~~irr   84 (91)
T TIGR00280        36 YVCPFCGKKTVKRGSTGIWTCRKCGAKFAGGAYTPVTPAGKTVRKTIRR   84 (91)
T ss_pred             ccCCCCCCCceEEEeeEEEEcCCCCCEEeCCccccccchhHHHHHHHHH
Confidence            4699999999999999999999999999999999999999875544433

This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.

>PTZ00255 60S ribosomal protein L37a; Provisional

Probab=99.80  E-value=4.9e-20  Score=122.81  Aligned_cols=50  Identities=34%  Similarity=0.428  Sum_probs=44.0

Q ss_pred             eeeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHHHHHh
Q 036150            7 VLRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAA   56 (77)
Q Consensus         7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~~~~~   56 (77)
                      -..||.|||++|||+++|||+|++||++||||||+|+||+++....+-.-
T Consensus        36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~~irr   85 (90)
T PTZ00255         36 KYFCPFCGKHAVKRQAVGIWRCKGCKKTVAGGAWTLSTPAASTVRSTIRR   85 (90)
T ss_pred             CccCCCCCCCceeeeeeEEEEcCCCCCEEeCCccccccchhHHHHHHHHH
Confidence            34699999999999999999999999999999999999999875544433

>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]

Probab=99.72  E-value=1.9e-18  Score=115.89  Aligned_cols=47  Identities=30%  Similarity=0.398  Sum_probs=42.9

Q ss_pred             eeeeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHH
Q 036150            6 RVLRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPA   52 (77)
Q Consensus         6 ~~~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~   52 (77)
                      ..-.||-||++.|||+++|||.|++||++||||||+|+||+++...-
T Consensus        34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGgay~P~t~~~k~~~~   80 (89)
T COG1997          34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGGAYTPVTPAGKAVKR   80 (89)
T ss_pred             cCCcCCCCCCcceeeeccCeEEcCCCCCeeccccccccchHHHHHHH
Confidence            34579999999999999999999999999999999999999987643

>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]

Probab=99.59  E-value=2.8e-16  Score=106.15  Aligned_cols=49  Identities=41%  Similarity=0.550  Sum_probs=43.8

Q ss_pred             eeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHHHHHhh
Q 036150            9 RRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAAL   57 (77)
Q Consensus         9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~~~~~~   57 (77)
                      .|+-|||+.|||++||||.|+.|++++|||||+.+||++.+.+.+-+-|
T Consensus        38 ~CsfCGK~~vKR~AvGiW~C~~C~kv~agga~~~~t~aa~t~rs~irrl   86 (92)
T KOG0402|consen   38 TCSFCGKKTVKRKAVGIWKCGSCKKVVAGGAYTVTTAAAATVRSTIRRL   86 (92)
T ss_pred             hhhhcchhhhhhhceeEEecCCccceeccceEEeccchhHHHHHHHHHH
Confidence            4788999999999999999999999999999999999988877655443

>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc

Probab=96.33  E-value=0.0029  Score=36.22  Aligned_cols=26  Identities=23%  Similarity=0.295  Sum_probs=22.8

Q ss_pred             eeCCCCceeeEEeEE-EEEeeCCCCcE
Q 036150            9 RRKRTKKYAVKRKAV-GIWSCKYCGKV   34 (77)
Q Consensus         9 ~~~~CGK~~VKR~AV-GIWkCkkCgkt   34 (77)
                      .||+||..++.+... +.|+|++|++.
T Consensus        20 ~CP~Cg~~~~~~~~~~~~~~C~~C~~q   46 (46)
T PF12760_consen   20 VCPHCGSTKHYRLKTRGRYRCKACRKQ   46 (46)
T ss_pred             CCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence            499999998888877 99999999873

It may be a zinc-binding beta ribbon domain that could bind DNA.

>PHA00626 hypothetical protein

Probab=95.41  E-value=0.012  Score=37.51  Aligned_cols=33  Identities=9%  Similarity=0.150  Sum_probs=27.1

Q ss_pred             eeCCCCceeeEEeE-----EEEEeeCCCCcEEeCcccc
Q 036150            9 RRKRTKKYAVKRKA-----VGIWSCKYCGKVKAGALNA   41 (77)
Q Consensus         9 ~~~~CGK~~VKR~A-----VGIWkCkkCgkt~AGGAYt   41 (77)
                      .||+||...|.|-+     ..-.+|+.||+.+.-.|+-
T Consensus         2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~~   39 (59)
T PHA00626          2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAFG   39 (59)
T ss_pred             CCCCCCCceeeeeceecccCcceEcCCCCCeechhhhh
Confidence            58999998777743     4789999999999887764

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=95.18  E-value=0.01  Score=35.40  Aligned_cols=26  Identities=19%  Similarity=0.395  Sum_probs=22.3

Q ss_pred             eeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150            9 RRKRTKKYAVKRKAVGIWSCKYCGKVK   35 (77)
Q Consensus         9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~   35 (77)
                      .||+||.. +-....+.|+|++||.+.
T Consensus        22 fCP~Cg~~-~m~~~~~r~~C~~Cgyt~   47 (50)
T PRK00432         22 FCPRCGSG-FMAEHLDRWHCGKCGYTE   47 (50)
T ss_pred             cCcCCCcc-hheccCCcEECCCcCCEE
Confidence            58999997 777777999999999875

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=93.55  E-value=0.066  Score=30.36  Aligned_cols=29  Identities=17%  Similarity=0.174  Sum_probs=22.9

Q ss_pred             eeeeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150            7 VLRRKRTKKYAVKRKAVGIWSCKYCGKVK   35 (77)
Q Consensus         7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt~   35 (77)
                      ..+|+|||..-..-...+.++|..||..+
T Consensus         3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~   31 (46)
T PRK00398          3 EYKCARCGREVELDEYGTGVRCPYCGYRI   31 (46)
T ss_pred             EEECCCCCCEEEECCCCCceECCCCCCeE
Confidence            46899999986555555689999999765

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=92.77  E-value=0.11  Score=30.43  Aligned_cols=28  Identities=18%  Similarity=0.205  Sum_probs=22.3

Q ss_pred             eeeCCCCceee-EE------eEEEEEeeCCCCcEE
Q 036150            8 LRRKRTKKYAV-KR------KAVGIWSCKYCGKVK   35 (77)
Q Consensus         8 ~~~~~CGK~~V-KR------~AVGIWkCkkCgkt~   35 (77)
                      +.||-||...+ .|      ...|+|+|..||...
T Consensus         2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~   36 (53)
T TIGR03655         2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASG   36 (53)
T ss_pred             CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCc
Confidence            57999998876 55      467899999999763

Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.

>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins

Probab=92.40  E-value=0.1  Score=30.88  Aligned_cols=29  Identities=21%  Similarity=0.356  Sum_probs=25.1

Q ss_pred             eeeeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150            7 VLRRKRTKKYAVKRKAVGIWSCKYCGKVK   35 (77)
Q Consensus         7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt~   35 (77)
                      --.||+||...-++....+|.|..||.++
T Consensus        28 Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~~   56 (69)
T PF07282_consen   28 SQTCPRCGHRNKKRRSGRVFTCPNCGFEM   56 (69)
T ss_pred             ccCccCcccccccccccceEEcCCCCCEE
Confidence            34689999998888888999999999874

More information about these proteins can be found at Protein of the Month: Transposase [].

>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing

Probab=91.31  E-value=0.11  Score=34.64  Aligned_cols=36  Identities=19%  Similarity=0.294  Sum_probs=24.2

Q ss_pred             eeeC--CCCceeeEEeEEEEEeeCCCCcEEeCccccccc
Q 036150            8 LRRK--RTKKYAVKRKAVGIWSCKYCGKVKAGALNAATL   44 (77)
Q Consensus         8 ~~~~--~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~T   44 (77)
                      .-||  .|+|. |.....|.|.|.+|++.+.---|..-+
T Consensus        19 ~aC~~~~C~kK-v~~~~~~~y~C~~C~~~~~~~~~ry~l   56 (146)
T PF08646_consen   19 PACPNEKCNKK-VTENGDGSYRCEKCNKTVENPKYRYRL   56 (146)
T ss_dssp             EE-TSTTTS-B--EEETTTEEEETTTTEEESS-EEEEEE
T ss_pred             CCCCCccCCCE-eecCCCcEEECCCCCCcCCCeeEEEEE
Confidence            3589  99985 555577999999999998665555533

It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=91.08  E-value=0.13  Score=28.80  Aligned_cols=30  Identities=20%  Similarity=0.277  Sum_probs=22.7

Q ss_pred             eeeCCCCcee-eEEeEEEEEeeCCCCcEEeC
Q 036150            8 LRRKRTKKYA-VKRKAVGIWSCKYCGKVKAG   37 (77)
Q Consensus         8 ~~~~~CGK~~-VKR~AVGIWkCkkCgkt~AG   37 (77)
                      .+||+||... +--...|-..|..||.++.-
T Consensus         1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e   31 (43)
T PF08271_consen    1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEE   31 (43)
T ss_dssp             ESBTTTSSSEEEEETTTTEEEETTT-BBEE-
T ss_pred             CCCcCCcCCceEEcCCCCeEECCCCCCEeec
Confidence            3699999987 44457899999999988754

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

>PRK12366 replication factor A; Reviewed

Probab=90.65  E-value=0.1  Score=43.46  Aligned_cols=26  Identities=23%  Similarity=0.565  Sum_probs=21.4

Q ss_pred             eeeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150            7 VLRRKRTKKYAVKRKAVGIWSCKYCGKV   34 (77)
Q Consensus         7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt   34 (77)
                      .-+||+|.|.-++  .-|.|.|.+|+++
T Consensus       532 y~aCp~CnkKv~~--~~g~~~C~~c~~~  557 (637)
T PRK12366        532 LYLCPNCRKRVEE--VDGEYICEFCGEV  557 (637)
T ss_pred             EecccccCeEeEc--CCCcEECCCCCCC
Confidence            3689999886553  5699999999998

>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=89.22  E-value=0.27  Score=34.01  Aligned_cols=27  Identities=22%  Similarity=0.436  Sum_probs=21.8

Q ss_pred             eeeeeeeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150            4 YYRVLRRKRTKKYAVKRKAVGIWSCKYCGKVK   35 (77)
Q Consensus         4 ~~~~~~~~~CGK~~VKR~AVGIWkCkkCgkt~   35 (77)
                      +|---.|+.||.     ...+.|.|..||.++
T Consensus       306 ~~tS~~C~~cg~-----~~~r~~~C~~cg~~~  332 (364)
T COG0675         306 YYTSKTCPCCGH-----LSGRLFKCPRCGFVH  332 (364)
T ss_pred             CCCcccccccCC-----ccceeEECCCCCCee
Confidence            444457999999     668999999999874

>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]

Probab=89.10  E-value=0.18  Score=31.35  Aligned_cols=27  Identities=19%  Similarity=0.337  Sum_probs=16.8

Q ss_pred             eeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150            9 RRKRTKKYAVKRKAVGIWSCKYCGKVK   35 (77)
Q Consensus         9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~   35 (77)
                      .|||||--.+-=.---=|.|.+||+|-
T Consensus        21 ~CPrCG~gvfmA~H~dR~~CGkCgyTe   47 (51)
T COG1998          21 FCPRCGPGVFMADHKDRWACGKCGYTE   47 (51)
T ss_pred             cCCCCCCcchhhhcCceeEeccccceE
Confidence            489999432211111259999999874

>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70)

Probab=89.08  E-value=0.18  Score=34.17  Aligned_cols=32  Identities=19%  Similarity=0.272  Sum_probs=23.2

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcEEeCccc
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALN   40 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAY   40 (77)
                      ..||+|+|. |.-...|.|.|.+|++.+.---|
T Consensus        35 ~aC~~C~kk-v~~~~~~~~~C~~C~~~~~~~~~   66 (166)
T cd04476          35 PACPGCNKK-VVEEGNGTYRCEKCNKSVPNPEY   66 (166)
T ss_pred             ccccccCcc-cEeCCCCcEECCCCCCcCCCccE
Confidence            469999986 44444489999999998743333

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=87.44  E-value=0.46  Score=26.56  Aligned_cols=32  Identities=9%  Similarity=0.226  Sum_probs=24.5

Q ss_pred             eeCCCCceeeEEeEEE--EEeeCCCCcEEeCccc
Q 036150            9 RRKRTKKYAVKRKAVG--IWSCKYCGKVKAGALN   40 (77)
Q Consensus         9 ~~~~CGK~~VKR~AVG--IWkCkkCgkt~AGGAY   40 (77)
                      -||+||..-..+..-+  .|.|..||+.+--.+.
T Consensus         2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~~   35 (52)
T smart00661        2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQK   35 (52)
T ss_pred             CCCCCCCccccccCCCCCEEECCcCCCeEECCCc
Confidence            3799999776665433  8999999998877665

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=86.72  E-value=1  Score=28.92  Aligned_cols=31  Identities=23%  Similarity=0.164  Sum_probs=23.0

Q ss_pred             eeeeeeeCCCCceeeEEeEEE---EEeeCCCCcE
Q 036150            4 YYRVLRRKRTKKYAVKRKAVG---IWSCKYCGKV   34 (77)
Q Consensus         4 ~~~~~~~~~CGK~~VKR~AVG---IWkCkkCgkt   34 (77)
                      |--+.-||.||...+.=++.|   +|.|++|+..
T Consensus         3 ~d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~   36 (64)
T PRK09710          3 YDNVKPCPFCGCPSVTVKAISGYYRAKCNGCESR   36 (64)
T ss_pred             cccccCCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence            445678999999986655444   5679999873

>PRK08402 replication factor A; Reviewed

Probab=85.89  E-value=0.47  Score=37.52  Aligned_cols=27  Identities=19%  Similarity=0.278  Sum_probs=21.7

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKV   34 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt   34 (77)
                      .+||+|.|.-+.-...|-|.|..|+++
T Consensus       213 ~aCp~CnKkv~~~~~~~~~~Ce~~~~v  239 (355)
T PRK08402        213 DACPECRRKVDYDPATDTWICPEHGEV  239 (355)
T ss_pred             ecCCCCCeEEEEecCCCCEeCCCCCCc
Confidence            589999885554567799999999863

>PHA02942 putative transposase; Provisional

Probab=85.46  E-value=0.44  Score=37.44  Aligned_cols=29  Identities=14%  Similarity=0.221  Sum_probs=22.4

Q ss_pred             eeeeeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150            6 RVLRRKRTKKYAVKRKAVGIWSCKYCGKVK   35 (77)
Q Consensus         6 ~~~~~~~CGK~~VKR~AVGIWkCkkCgkt~   35 (77)
                      ---.||+||... ++....+|.|..||.+.
T Consensus       324 TSq~Cs~CG~~~-~~l~~r~f~C~~CG~~~  352 (383)
T PHA02942        324 SSVSCPKCGHKM-VEIAHRYFHCPSCGYEN  352 (383)
T ss_pred             CCccCCCCCCcc-CcCCCCEEECCCCCCEe
Confidence            345799999754 45566799999999975

>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus

Probab=84.51  E-value=1.2  Score=28.88  Aligned_cols=31  Identities=23%  Similarity=0.478  Sum_probs=24.2

Q ss_pred             eeeeeeCCCCceeeEEeEEEEEeeCCCCcEEeC
Q 036150            5 YRVLRRKRTKKYAVKRKAVGIWSCKYCGKVKAG   37 (77)
Q Consensus         5 ~~~~~~~~CGK~~VKR~AVGIWkCkkCgkt~AG   37 (77)
                      |-+.|| .||+..+-+..+--=+| .||+++-=
T Consensus         1 ylifrC-~Cgr~lya~e~~kTkkC-~CG~~l~v   31 (68)
T PF09082_consen    1 YLIFRC-DCGRYLYAKEGAKTKKC-VCGKTLKV   31 (68)
T ss_dssp             EEEEEE-TTS--EEEETT-SEEEE-TTTEEEE-
T ss_pred             CEEEEe-cCCCEEEecCCcceeEe-cCCCeeee
Confidence            668899 79999999999999999 99998753

The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.

>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[]

Probab=82.19  E-value=0.96  Score=25.38  Aligned_cols=26  Identities=15%  Similarity=0.226  Sum_probs=22.6

Q ss_pred             eeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150            9 RRKRTKKYAVKRKAVGIWSCKYCGKVK   35 (77)
Q Consensus         9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~   35 (77)
                      +|+.|+.. .-+..-|-+-|..||-+.
T Consensus        10 ~C~~C~~~-~~~~~dG~~yC~~cG~~~   35 (36)
T PF11781_consen   10 PCPVCGSR-WFYSDDGFYYCDRCGHQS   35 (36)
T ss_pred             cCCCCCCe-EeEccCCEEEhhhCceEc
Confidence            48899999 888899999999999763

>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4

Probab=81.72  E-value=1.5  Score=25.32  Aligned_cols=30  Identities=23%  Similarity=0.490  Sum_probs=14.9

Q ss_pred             eeeeCCCCce-eeE----EeEEEEEeeCCCCcEEeC
Q 036150            7 VLRRKRTKKY-AVK----RKAVGIWSCKYCGKVKAG   37 (77)
Q Consensus         7 ~~~~~~CGK~-~VK----R~AVGIWkCkkCgkt~AG   37 (77)
                      -..||+||-. +.+    +...|-|.|..|+. .+|
T Consensus         3 h~pCP~CGG~DrFri~~d~~~~G~~~C~~C~~-~~G   37 (40)
T PF08273_consen    3 HGPCPICGGKDRFRIFDDKDGRGTWICRQCGG-DAG   37 (40)
T ss_dssp             EE--TTTT-TTTEEEETT----S-EEETTTTB-E--
T ss_pred             CCCCCCCcCccccccCcCcccCCCEECCCCCC-cCC
Confidence            3468999865 344    34569999999965 443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.

>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase

Probab=81.46  E-value=1.3  Score=24.40  Aligned_cols=15  Identities=33%  Similarity=1.101  Sum_probs=13.0

Q ss_pred             EEeeCCCCcEEeCcc
Q 036150           25 IWSCKYCGKVKAGAL   39 (77)
Q Consensus        25 IWkCkkCgkt~AGGA   39 (77)
                      +|.|..||+++-|..
T Consensus         2 ~~~C~~CG~i~~g~~   16 (34)
T cd00729           2 VWVCPVCGYIHEGEE   16 (34)
T ss_pred             eEECCCCCCEeECCc
Confidence            699999999998753

In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=81.42  E-value=1  Score=32.13  Aligned_cols=26  Identities=23%  Similarity=0.406  Sum_probs=19.2

Q ss_pred             eeeCCCCcee--------------eEEeEEEEEeeCCCCcEEeC
Q 036150            8 LRRKRTKKYA--------------VKRKAVGIWSCKYCGKVKAG   37 (77)
Q Consensus         8 ~~~~~CGK~~--------------VKR~AVGIWkCkkCgkt~AG   37 (77)
                      ++||-||...              |+|.    -+|..||++|.+
T Consensus         1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~----~~c~~c~~~f~~   40 (154)
T PRK00464          1 MRCPFCGHPDTRVIDSRPAEDGNAIRRR----RECLACGKRFTT   40 (154)
T ss_pred             CcCCCCCCCCCEeEeccccCCCCceeee----eeccccCCcceE
Confidence            4799999533              4444    799999999863

>PRK07591 threonine synthase; Validated

Probab=80.32  E-value=0.91  Score=35.58  Aligned_cols=28  Identities=14%  Similarity=0.060  Sum_probs=21.0

Q ss_pred             ceeeeeeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150            3 SYYRVLRRKRTKKYAVKRKAVGIWSCKYCGK   33 (77)
Q Consensus         3 ~~~~~~~~~~CGK~~VKR~AVGIWkCkkCgk   33 (77)
                      +|+..|+|.+||+.-=--   .+|.|..||-
T Consensus        14 ~~~~~l~C~~Cg~~~~~~---~~~~C~~cg~   41 (421)
T PRK07591         14 GPAVALKCRECGAEYPLG---PIHVCEECFG   41 (421)
T ss_pred             cceeEEEeCCCCCcCCCC---CCccCCCCCC
Confidence            677789999999884211   2399999973

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	77
3izr_m	92	Localization Of The Large Subunit Ribosomal Protein		5e-04
1ysh_D	73	Localization And Dynamic Behavior Of Ribosomal Prot		8e-04

>pdb|3IZR|MM Chain m, Localization Of The Large Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 92

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 18/21 (85%), Positives = 19/21 (90%)
Query: 15 KYAVKRKAVGIWSCKYCGKVK 35
          K+AVKRKAVGIW CK CGKVK
Sbjct: 44 KFAVKRKAVGIWGCKDCGKVK 64

>pdb|1YSH|D Chain D, Localization And Dynamic Behavior Of Ribosomal Protein L30e Length = 73

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 18/21 (85%), Positives = 19/21 (90%)
Query: 15 KYAVKRKAVGIWSCKYCGKVK 35
          K+AVKRKAVGIW CK CGKVK
Sbjct: 35 KFAVKRKAVGIWGCKDCGKVK 55

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	77
1ffk_W	73	Ribosomal protein L37AE; ribosome assembly, RNA-RN	6e-05
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	2e-04
3cc2_Z	116	50S ribosomal protein L37AE, 50S ribosomal protein	2e-04

>1ffk_W Ribosomal protein L37AE; ribosome assembly, RNA-RNA, protein-RNA, protein-protein; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1jj2_Y 1k73_1* 1k8a_1* 1k9m_1* 1kc8_1* 1kd1_1* 1kqs_Y* 1m1k_1* 1m90_1* 1n8r_1* 1nji_1* 1q7y_1* 1q81_1* 1q82_1* 1q86_1* 1qvf_Y 1qvg_Y 1w2b_Y 3cxc_Y* Length = 73

 Score = 36.3 bits (84), Expect = 6e-05
 Identities = 9/24 (37%), Positives = 12/24 (50%)

Query: 14 KKYAVKRKAVGIWSCKYCGKVKAG 37
              +KR +  IW C +CG   AG
Sbjct: 34 GFPKLKRASTSIWVCGHCGYKIAG 57

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ... Length = 83

 Score = 35.1 bits (81), Expect = 2e-04
 Identities = 9/24 (37%), Positives = 11/24 (45%)

Query: 14 KKYAVKRKAVGIWSCKYCGKVKAG 37
           +  V R+  GIW C YC     G
Sbjct: 34 GEDRVDRQGTGIWQCSYCDYKFTG 57

>3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic sequnece for R-proteins, ribonucleoprotein, ribosoma protein, RNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z* 3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z* 3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3i55_Z* 3i56_Z* 3cpw_Y* 4adx_Z Length = 116

 Score = 35.7 bits (82), Expect = 2e-04
 Identities = 9/23 (39%), Positives = 11/23 (47%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAG 37
          +  V R+  GIW C YC     G
Sbjct: 68 EDRVDRQGTGIWQCSYCDYKFTG 90

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	77
3iz5_m	92	60S ribosomal protein L43 (L37AE); eukaryotic ribo	99.81
3j21_i	83	50S ribosomal protein L37AE; archaea, archaeal, KI	99.81
3izc_m	92	60S ribosomal protein RPL43 (L37AE); eukaryotic ri	99.81
3jyw_9	72	60S ribosomal protein L43; eukaryotic ribosome, RA	99.8
4a17_Y	103	RPL37A, 60S ribosomal protein L32; eukaryotic ribo	99.8
1ffk_W	73	Ribosomal protein L37AE; ribosome assembly, RNA-RN	99.8
3cc2_Z	116	50S ribosomal protein L37AE, 50S ribosomal protein	99.73
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	99.7
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	97.38
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	95.35
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	94.11
1l1o_C	181	Replication protein A 70 kDa DNA-binding subunit;	93.97
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	93.6
3u50_C	172	Telomerase-associated protein 82; TEB1, processivi	93.16
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	92.26
4gop_C	444	Putative uncharacterized protein; OB fold, ssDNA b	91.14
1nui_A	255	DNA primase/helicase; zinc-biding domain, toprim f	90.18
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	88.35
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	85.66
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	85.4
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	84.89

>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=99.81  E-value=4.5e-21  Score=125.18  Aligned_cols=43  Identities=33%  Similarity=0.478  Sum_probs=40.0

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcEEeCccccccccccccc
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTAL   50 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~   50 (77)
                      ..||.|||++|||+++|||+|++||++||||||+|+||++...
T Consensus        36 y~CpfCGk~~vkR~a~GIW~C~kCg~~~AGGAy~~~T~~~~t~   78 (83)
T 3j21_i           36 HTCPVCGRKAVKRISTGIWQCQKCGATFAGGAYLPVTPAGKAV   78 (83)
T ss_dssp             BCCSSSCSSCEEEEETTEEEETTTCCEEECCSSSSSCHHHHHH
T ss_pred             cCCCCCCCceeEecCcCeEEcCCCCCEEeCCccccCccHhhhh
Confidence            4699999999999999999999999999999999999987653

>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}

Probab=99.80  E-value=1.3e-21  Score=125.02  Aligned_cols=43  Identities=35%  Similarity=0.542  Sum_probs=40.1

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcEEeCccccccccccccc
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTAL   50 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~   50 (77)
                      ..||.|||++|||+++|||+|++||++||||||+|+||+++..
T Consensus        27 y~C~fCgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~tv   69 (72)
T 3jyw_9           27 YDCSFCGKKTVKRGAAGIWTCSCCKKTVAGGAYTVSTAAAATV   69 (72)
T ss_dssp             BCCSSCCSSCBSBCSSSCBCCSSSCCCCCCSSSSSCCHHHHHH
T ss_pred             ccCCCCCCceeEecCCCeEECCCCCCEEeCCccccCCccceee
Confidence            4699999999999999999999999999999999999987654

>4a17_Y RPL37A, 60S ribosomal protein L32; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_Y 4a1c_Y 4a1e_Y

Probab=99.80  E-value=1.7e-20  Score=126.93  Aligned_cols=50  Identities=36%  Similarity=0.462  Sum_probs=45.4

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHHHHHhh
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAAL   57 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~~~~~~   57 (77)
                      ..||.|||++|||+++|||+|++||++||||||+|+||++...+.+-+-|
T Consensus        37 y~CpfCgk~~vKR~a~GIW~C~kCg~~~AGGAy~~~T~~a~tv~~~irrl   86 (103)
T 4a17_Y           37 YGCPFCGKVAVKRAAVGIWKCKPCKKIIAGGAWELTTPPAVTAKTTMNRL   86 (103)
T ss_dssp             EECTTTCCEEEEEEETTEEEETTTTEEEECCSSCSSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCceeeecCcceEEcCCCCCEEeCCcccCCCcHHHHHHHHHHHH
Confidence            46999999999999999999999999999999999999998877665544

>1ffk_W Ribosomal protein L37AE; ribosome assembly, RNA-RNA, protein-RNA, protein-protein; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1jj2_Y 1k73_1* 1k8a_1* 1k9m_1* 1kc8_1* 1kd1_1* 1kqs_Y* 1m1k_1* 1m90_1* 1n8r_1* 1nji_1* 1q7y_1* 1q81_1* 1q82_1* 1q86_1* 1qvf_Y 1qvg_Y 1w2b_Y 3cxc_Y*

Probab=99.80  E-value=1.9e-20  Score=119.50  Aligned_cols=45  Identities=24%  Similarity=0.311  Sum_probs=41.1

Q ss_pred             eeeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccH
Q 036150            7 VLRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALP   51 (77)
Q Consensus         7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~   51 (77)
                      -..||.|||++|||+++|||+|++|+++||||||+|+||++...+
T Consensus        27 ky~C~fCgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~   71 (73)
T 1ffk_W           27 KYKCPVCGFPKLKRASTSIWVCGHCGYKIAGGAYTPETVAGKAVM   71 (73)
T ss_pred             CccCCCCCCceeEEEEeEEEECCCCCcEEECCCccccccceEEEe
Confidence            346899999999999999999999999999999999999987643

>3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic sequnece for R-proteins, ribonucleoprotein, ribosoma protein, RNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z* 3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z* 3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3i55_Z* 3i56_Z* 3cpw_Y* 4adx_Z

Probab=99.73  E-value=6e-19  Score=121.10  Aligned_cols=45  Identities=20%  Similarity=0.372  Sum_probs=41.4

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHH
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPA   52 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~   52 (77)
                      ..||.|||++|||.++|||+|++|+++||||||+|+||++...+.
T Consensus        61 ytCPfCGk~~vKR~avGIW~C~~Cgk~fAGGAy~~~T~~~~t~~~  105 (116)
T 3cc2_Z           61 HACPNCGEDRVDRQGTGIWQCSYCDYKFTGGSYKPETPGGKTVRR  105 (116)
T ss_dssp             EECSSSCCEEEEEEETTEEEETTTCCEEECCSSSSSCHHHHHHHH
T ss_pred             CcCCCCCCceeEecCceeEECCCCCCEEECCCcccccchhhhHHH
Confidence            469999999999999999999999999999999999998876443

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=99.70  E-value=3.3e-18  Score=110.23  Aligned_cols=45  Identities=20%  Similarity=0.372  Sum_probs=41.4

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHH
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPA   52 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~   52 (77)
                      ..||+||++.|+|.++|||+|++||++||||||+|+||++...+.
T Consensus        28 y~Cp~CG~~~v~r~atGiW~C~~Cg~~~aggay~~~t~~~~~~~~   72 (83)
T 1vq8_Z           28 HACPNCGEDRVDRQGTGIWQCSYCDYKFTGGSYKPETPGGKTVRR   72 (83)
T ss_dssp             EECSSSCCEEEEEEETTEEEETTTCCEEECCSSSSSCHHHHHHHH
T ss_pred             CcCCCCCCcceeccCCCeEECCCCCCEecCCEecccchHHHHHHH
Confidence            479999999999999999999999999999999999998876443

>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=97.38  E-value=2.4e-05  Score=46.80  Aligned_cols=25  Identities=20%  Similarity=0.306  Sum_probs=21.6

Q ss_pred             eeeeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150            6 RVLRRKRTKKYAVKRKAVGIWSCKYCGKV   34 (77)
Q Consensus         6 ~~~~~~~CGK~~VKR~AVGIWkCkkCgkt   34 (77)
                      ....||+||..    .++|||+|++||.+
T Consensus        13 ~k~iCpkC~a~----~~~gaw~CrKCG~~   37 (51)
T 3j21_g           13 KKYVCLRCGAT----NPWGAKKCRKCGYK   37 (51)
T ss_dssp             SEEECTTTCCE----ECTTCSSCSSSSSC
T ss_pred             CCccCCCCCCc----CCCCceecCCCCCc
Confidence            34568999986    99999999999987

>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A

Probab=95.35  E-value=0.004  Score=36.82  Aligned_cols=37  Identities=14%  Similarity=0.123  Sum_probs=29.6

Q ss_pred             eeeeeeeCCCCceeeEE-eEEEEEeeCCCCcEEeCccc
Q 036150            4 YYRVLRRKRTKKYAVKR-KAVGIWSCKYCGKVKAGALN   40 (77)
Q Consensus         4 ~~~~~~~~~CGK~~VKR-~AVGIWkCkkCgkt~AGGAY   40 (77)
                      +..++.||+||...+-. ...|.+.|..||.++.....
T Consensus         8 ll~~~~Cp~C~~~~lv~D~~~ge~vC~~CGlVl~e~~i   45 (58)
T 1dl6_A            8 ALPRVTCPNHPDAILVEDYRAGDMICPECGLVVGDRVI   45 (58)
T ss_dssp             CCSCCSBTTBSSSCCEECSSSCCEECTTTCCEECCSCC
T ss_pred             ccccccCcCCCCCceeEeCCCCeEEeCCCCCEEecccc
Confidence            45678999999966544 47899999999999987643

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=94.11  E-value=0.031  Score=32.42  Aligned_cols=27  Identities=19%  Similarity=0.318  Sum_probs=22.6

Q ss_pred             eeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150            9 RRKRTKKYAVKRKAVGIWSCKYCGKVK   35 (77)
Q Consensus         9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~   35 (77)
                      -||+||...+-...-..|.|.+||.+.
T Consensus        21 ~CP~CG~~~fm~~~~~R~~C~kCG~t~   47 (50)
T 3j20_Y           21 FCPRCGPGVFMADHGDRWACGKCGYTE   47 (50)
T ss_dssp             ECSSSCSSCEEEECSSEEECSSSCCEE
T ss_pred             cCCCCCCceEEecCCCeEECCCCCCEE
Confidence            489999977766667899999999875

>1l1o_C Replication protein A 70 kDa DNA-binding subunit; eukaryotic SSB, ssDNA binding protein, OB-fold; 2.80A {Homo sapiens} SCOP: b.40.4.3

Probab=93.97  E-value=0.021  Score=39.00  Aligned_cols=34  Identities=15%  Similarity=0.201  Sum_probs=25.8

Q ss_pred             eeeCC--CCceeeEEeEEEEEeeCCCCcEEeCccccc
Q 036150            8 LRRKR--TKKYAVKRKAVGIWSCKYCGKVKAGALNAA   42 (77)
Q Consensus         8 ~~~~~--CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp   42 (77)
                      -.||+  |.|. |.-..-|.|.|.+|++.+.---|..
T Consensus        44 ~aC~~~~CnKK-v~~~~~g~~~CekC~~~~~~~~~ry   79 (181)
T 1l1o_C           44 QACPTQDCNKK-VIDQQNGLYRCEKCDTEFPNFKYRM   79 (181)
T ss_dssp             EBCCSTTCCCB-CEEETTTEEEETTTTEEESSCCEEE
T ss_pred             CCCCchhcCCc-cccCCCCeEECCCCCCcCCCceEEE
Confidence            46899  9996 4456779999999999876544444

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=93.60  E-value=0.018  Score=32.12  Aligned_cols=32  Identities=16%  Similarity=0.119  Sum_probs=24.9

Q ss_pred             eeeeCCCCceeeEE-eEEEEEeeCCCCcEEeCc
Q 036150            7 VLRRKRTKKYAVKR-KAVGIWSCKYCGKVKAGA   38 (77)
Q Consensus         7 ~~~~~~CGK~~VKR-~AVGIWkCkkCgkt~AGG   38 (77)
                      .+.||+||...+.. ...|-+.|..||.++.-.
T Consensus         5 ~~~CP~C~~~~l~~d~~~gelvC~~CG~v~~e~   37 (50)
T 1pft_A            5 QKVCPACESAELIYDPERGEIVCAKCGYVIEEN   37 (50)
T ss_dssp             CCSCTTTSCCCEEEETTTTEEEESSSCCBCCCC
T ss_pred             cEeCcCCCCcceEEcCCCCeEECcccCCccccc
Confidence            57899999855544 467999999999877543

>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1

Probab=92.26  E-value=0.095  Score=32.54  Aligned_cols=32  Identities=19%  Similarity=0.401  Sum_probs=27.2

Q ss_pred             eeeeeeCCCCceeeEEeEEEEEeeCCCCcEEeCc
Q 036150            5 YRVLRRKRTKKYAVKRKAVGIWSCKYCGKVKAGA   38 (77)
Q Consensus         5 ~~~~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGG   38 (77)
                      |-|++|| ||...+-+...-==+|. ||+++-=.
T Consensus         2 Y~vv~C~-C~~~~~~~~~~kT~~C~-CG~~~~~~   33 (71)
T 1gh9_A            2 YIIFRCD-CGRALYSREGAKTRKCV-CGRTVNVK   33 (71)
T ss_dssp             EEEEEET-TSCCEEEETTCSEEEET-TTEEEECC
T ss_pred             eEEEECC-CCCEEEEcCCCcEEECC-CCCeeeec
Confidence            8999999 99999888877777897 99987543

>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=91.14  E-value=0.077  Score=39.89  Aligned_cols=35  Identities=17%  Similarity=0.229  Sum_probs=26.8

Q ss_pred             eeeCC--CCceeeEEeEEEEEeeCCCCcEEeCcccccc
Q 036150            8 LRRKR--TKKYAVKRKAVGIWSCKYCGKVKAGALNAAT   43 (77)
Q Consensus         8 ~~~~~--CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~   43 (77)
                      ..||+  |+|. |....-|.|.|.+|++.+.-.-|...
T Consensus       309 ~aC~~~~C~kk-v~~~~~g~~~C~~C~~~~~~~~~ry~  345 (444)
T 4gop_C          309 TACASEGCNKK-VNLDHENNWRCEKCDRSYATPEYRYI  345 (444)
T ss_dssp             EECCSTTCCCB-EEECTTSCEEETTTTEEESSCEEEEC
T ss_pred             ccCCcccCCCc-cccCCCccEECCCCCCcCccccEEEE
Confidence            47888  9995 55566799999999998766655553

>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2

Probab=90.18  E-value=0.14  Score=35.42  Aligned_cols=32  Identities=13%  Similarity=0.067  Sum_probs=22.9

Q ss_pred             ceeeeeeeCCCCce-eeEEeEEEEEeeCCCCcE
Q 036150            3 SYYRVLRRKRTKKY-AVKRKAVGIWSCKYCGKV   34 (77)
Q Consensus         3 ~~~~~~~~~~CGK~-~VKR~AVGIWkCkkCgkt   34 (77)
                      .|.|-.+||.||+. .+.----|=|+|..||..
T Consensus        10 ~~~~~~~CP~Cg~~d~~~~~~dg~~~C~~Cg~~   42 (255)
T 1nui_A           10 VFLYHIPCDNCGSSDGNSLFSDGHTFCYVCEKW   42 (255)
T ss_dssp             CEEEEECCSSSCCSSCEEEETTSCEEETTTCCE
T ss_pred             ceecCCcCCCCCCCCCceEeCCCCeecccCCCc
Confidence            46788999999994 322112345999999975

>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8

Probab=88.35  E-value=0.17  Score=29.77  Aligned_cols=28  Identities=18%  Similarity=0.217  Sum_probs=21.1

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKVK   35 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~   35 (77)
                      ..||+||-.-+--.-.+.|.|.+|+++.
T Consensus        19 ~fCPkCG~~~~ma~~~dr~~C~kCgyt~   46 (55)
T 2k4x_A           19 RFCPRCGPGVFLAEHADRYSCGRCGYTE   46 (55)
T ss_dssp             CCCTTTTTTCCCEECSSEEECTTTCCCE
T ss_pred             ccCcCCCCceeEeccCCEEECCCCCCEE
Confidence            4589999865422445799999999986

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9

Probab=85.66  E-value=0.44  Score=33.87  Aligned_cols=29  Identities=10%  Similarity=-0.020  Sum_probs=22.9

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcEEe
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKA   36 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~A   36 (77)
                      -.|||||-..+=..--.=|+|.+|+.++.
T Consensus       114 ~~Cp~Cg~g~fma~h~dR~~CGkC~~t~~  142 (189)
T 2xzm_9          114 KGCPKCGPGIFMAKHYDRHYCGKCHLTLK  142 (189)
T ss_dssp             EECSTTCSSCEEEECSSCEEETTTCCCBC
T ss_pred             ccCCccCCCccccCccCCCccCCceeEEE
Confidence            34889997766666667899999999973

>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4

Probab=85.40  E-value=0.52  Score=29.47  Aligned_cols=36  Identities=22%  Similarity=0.318  Sum_probs=29.6

Q ss_pred             CcceeeeeeeCCCCceee-EEeEEEEEeeCCCCcEEe
Q 036150            1 MVSYYRVLRRKRTKKYAV-KRKAVGIWSCKYCGKVKA   36 (77)
Q Consensus         1 ~~~~~~~~~~~~CGK~~V-KR~AVGIWkCkkCgkt~A   36 (77)
                      |-|||--.+||.|++..+ ==.|.-.=.|..|+.+.+
T Consensus         1 mnS~Fm~VKCp~C~niq~VFShA~tvV~C~~Cg~~L~   37 (66)
T 1qxf_A            1 MHSRFVKVKCPDCEHEQVIFDHPSTIVKCIICGRTVA   37 (66)
T ss_dssp             CCCCEEEEECTTTCCEEEEESSCSSCEECSSSCCEEE
T ss_pred             CCceeEEEECCCCCCceEEEecCceEEEcccCCCEEe
Confidence            789999999999999974 444666678999999874

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1

Probab=84.89  E-value=1.1  Score=25.45  Aligned_cols=30  Identities=10%  Similarity=0.187  Sum_probs=21.8

Q ss_pred             eeeeCCCCceeeEEe----------EEEEEeeCCCCcEEe
Q 036150            7 VLRRKRTKKYAVKRK----------AVGIWSCKYCGKVKA   36 (77)
Q Consensus         7 ~~~~~~CGK~~VKR~----------AVGIWkCkkCgkt~A   36 (77)
                      -++||+||...+.-.          -+=++.|.+||.++-
T Consensus        15 ~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~w~   54 (57)
T 1qyp_A           15 KITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWR   54 (57)
T ss_dssp             ECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEE
T ss_pred             EeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCEec
Confidence            467999998765421          145799999999864

---

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	77
d1vqoz1	73	g.41.8.1 (Z:10-82) Ribosomal protein L37ae {Archae	3e-05
d1jj2y_	73	g.41.8.1 (Y:) Ribosomal protein L37ae {Archaeon Ha	5e-05

>d1vqoz1 g.41.8.1 (Z:10-82) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 73

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

 Score = 36.2 bits (84), Expect = 3e-05
 Identities = 9/23 (39%), Positives = 11/23 (47%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAG 37
          +  V R+  GIW C YC     G
Sbjct: 35 EDRVDRQGTGIWQCSYCDYKFTG 57

>d1jj2y_ g.41.8.1 (Y:) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 73

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

 Score = 35.4 bits (82), Expect = 5e-05
 Identities = 10/23 (43%), Positives = 12/23 (52%)

Query: 15 KYAVKRKAVGIWSCKYCGKVKAG 37
             +KR   GIW C +CG   AG
Sbjct: 35 FKKLKRAGTGIWMCGHCGYKIAG 57

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	77
d1vqoz1	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	99.82
d1jj2y_	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	99.82
d1l1oc_	178	Replication protein A 70 KDa subunit (RPA70) {Huma	91.82
d1lkoa2	44	Rubrerythrin, C-terminal domain {Desulfovibrio vul	91.11
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	87.43
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	86.02
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	85.19
d1nnqa2	37	Rubrerythrin, C-terminal domain {Archaeon Pyrococc	85.18
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	83.41

>d1vqoz1 g.41.8.1 (Z:10-82) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=99.82  E-value=1.1e-21  Score=124.63  Aligned_cols=44  Identities=20%  Similarity=0.385  Sum_probs=40.4

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccH
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALP   51 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~   51 (77)
                      ..||.||+++|||+++|||+|++|+++||||||+|+||++...+
T Consensus        28 y~Cp~Cgk~~vkR~a~GIW~C~kC~~~~AGGAy~p~T~~~~tvr   71 (73)
T d1vqoz1          28 HACPNCGEDRVDRQGTGIWQCSYCDYKFTGGSYKPETPGGKTVR   71 (73)
T ss_dssp             BCCSSSSCSCEEEEETTEEEETTTCCEEECCSSSSSCTTHHHHH
T ss_pred             ccCCCCCCceeEEEEEEEEECCCCCCEEeCCeeeeccchhheee
Confidence            46899999999999999999999999999999999999876543

>d1jj2y_ g.41.8.1 (Y:) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=99.82  E-value=1.2e-21  Score=124.36  Aligned_cols=44  Identities=27%  Similarity=0.355  Sum_probs=40.9

Q ss_pred             eeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccH
Q 036150            8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALP   51 (77)
Q Consensus         8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~   51 (77)
                      ..||.|||++|||+++|||+|++||++||||||+|+||++.+.+
T Consensus        28 y~Cp~Cgk~~vkR~a~GIW~C~kC~~~~AGgAy~p~T~a~~tv~   71 (73)
T d1jj2y_          28 HKCPVCGFKKLKRAGTGIWMCGHCGYKIAGGCYQPETVAGKAVM   71 (73)
T ss_dssp             BCCSSSCCSCEEEEETTEEEETTTCCEEECCSSSSSCHHHHHHH
T ss_pred             ccCCCCCCCceEEEEEEEEECCCCCCEEeCccceecchHHhhhc
Confidence            46999999999999999999999999999999999999887643

>d1l1oc_ b.40.4.3 (C:) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 70 KDa subunit (RPA70)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.82  E-value=0.029  Score=37.02  Aligned_cols=36  Identities=17%  Similarity=0.246  Sum_probs=27.8

Q ss_pred             eeCC--CCceeeEEeEEEEEeeCCCCcEEeCcccccccc
Q 036150            9 RRKR--TKKYAVKRKAVGIWSCKYCGKVKAGALNAATLA   45 (77)
Q Consensus         9 ~~~~--CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tp   45 (77)
                      -||+  |.|. |-...-|.|.|.+|++.+..--|...+.
T Consensus        42 aCp~~~C~KK-v~~~~~g~~~C~kC~~~~~~~~~ry~l~   79 (178)
T d1l1oc_          42 ACPTQDCNKK-VIDQQNGLYRCEKCDTEFPNFKYRMILS   79 (178)
T ss_dssp             BCCSTTCCCB-CEEETTTEEEETTTTEEESSCCEEEEEE
T ss_pred             CCCCcccCCc-cccCCCCcEECCCCCCcCCCceEEEEEE
Confidence            6887  8775 6667789999999999988777665433

>d1lkoa2 g.41.5.1 (A:148-191) Rubrerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=91.11  E-value=0.092  Score=29.13  Aligned_cols=21  Identities=33%  Similarity=0.866  Sum_probs=18.1

Q ss_pred             eEEeEEEEEeeCCCCcEEeCc
Q 036150           18 VKRKAVGIWSCKYCGKVKAGA   38 (77)
Q Consensus        18 VKR~AVGIWkCkkCgkt~AGG   38 (77)
                      .||...-+|+|..||++.-|-
T Consensus         1 Fkk~~~~~W~C~~CGyi~~g~   21 (44)
T d1lkoa2           1 FLREQATKWRCRNCGYVHEGT   21 (44)
T ss_dssp             SEEEEEEEEEETTTCCEEEEE
T ss_pred             CCCCCCeEEEcCCCCcEEECC
Confidence            378888899999999999873

>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27e
domain: Ribosomal protein S27e
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=87.43  E-value=0.17  Score=29.43  Aligned_cols=36  Identities=22%  Similarity=0.318  Sum_probs=29.4

Q ss_pred             CcceeeeeeeCCCCceee-EEeEEEEEeeCCCCcEEe
Q 036150            1 MVSYYRVLRRKRTKKYAV-KRKAVGIWSCKYCGKVKA   36 (77)
Q Consensus         1 ~~~~~~~~~~~~CGK~~V-KR~AVGIWkCkkCgkt~A   36 (77)
                      |.|||--.+||.|++..+ =-.+.-.=.|..|+.+.+
T Consensus         1 mnS~F~~VkC~~C~n~~ivFsha~t~V~C~~Cg~~L~   37 (58)
T d1qxfa_           1 MHSRFVKVKCPDCEHEQVIFDHPSTIVKCIICGRTVA   37 (58)
T ss_dssp             CCCCEEEEECTTTCCEEEEESSCSSCEECSSSCCEEE
T ss_pred             CCceeEEeECCCCCCeEEEEecCceEEEccccCCEEe
Confidence            789999999999999974 334556668999999875

>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27a
domain: Ribosomal protein S27ae
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=86.02  E-value=0.13  Score=30.00  Aligned_cols=26  Identities=19%  Similarity=0.303  Sum_probs=20.9

Q ss_pred             eCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150           10 RKRTKKYAVKRKAVGIWSCKYCGKVK   35 (77)
Q Consensus        10 ~~~CGK~~VKR~AVGIWkCkkCgkt~   35 (77)
                      |||||.-.+==.--.=|.|.+|++|.
T Consensus        21 CP~CG~GvFmA~H~dR~~CGKCgyTe   46 (55)
T d2k4xa1          21 CPRCGPGVFLAEHADRYSCGRCGYTE   46 (55)
T ss_dssp             CTTTTTTCCCEECSSEEECTTTCCCE
T ss_pred             CcCCCCcEEeeecCCCccccCCcccE
Confidence            89999876555556789999999885

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.19  E-value=0.12  Score=29.45  Aligned_cols=31  Identities=16%  Similarity=0.189  Sum_probs=25.6

Q ss_pred             eeeeCCCCceeeE-EeEEEEEeeCCCCcEEeC
Q 036150            7 VLRRKRTKKYAVK-RKAVGIWSCKYCGKVKAG   37 (77)
Q Consensus         7 ~~~~~~CGK~~VK-R~AVGIWkCkkCgkt~AG   37 (77)
                      -++||+||...+. ....|-=.|..||.++--
T Consensus        11 ~~~Cp~Cgs~~ii~D~~~Ge~vC~~CG~Vlee   42 (58)
T d1dl6a_          11 RVTCPNHPDAILVEDYRAGDMICPECGLVVGD   42 (58)
T ss_dssp             CCSBTTBSSSCCEECSSSCCEECTTTCCEECC
T ss_pred             ccCCCCCCCCCEEEECCCCcEecccCCCEecc
Confidence            3689999999854 568899999999998754

>d1nnqa2 g.41.5.1 (A:135-171) Rubrerythrin, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=85.18  E-value=0.26  Score=26.15  Aligned_cols=15  Identities=20%  Similarity=0.674  Sum_probs=13.4

Q ss_pred             EEEeeCCCCcEEeCc
Q 036150           24 GIWSCKYCGKVKAGA   38 (77)
Q Consensus        24 GIWkCkkCgkt~AGG   38 (77)
                      -||.|.-||++..|-
T Consensus         4 ~~~~C~vCG~i~~g~   18 (37)
T d1nnqa2           4 KVYICPICGYTAVDE   18 (37)
T ss_dssp             CEEECTTTCCEEESC
T ss_pred             cEEECCCCCCEecCC
Confidence            489999999999984

>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Nigerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=83.41  E-value=0.34  Score=25.58  Aligned_cols=15  Identities=27%  Similarity=0.736  Sum_probs=13.5

Q ss_pred             EEEeeCCCCcEEeCc
Q 036150           24 GIWSCKYCGKVKAGA   38 (77)
Q Consensus        24 GIWkCkkCgkt~AGG   38 (77)
                      -+|.|..||++..|-
T Consensus         4 ~~~vC~vCGyi~~g~   18 (36)
T d1yuza2           4 KFHLCPICGYIHKGE   18 (36)
T ss_dssp             CEEECSSSCCEEESS
T ss_pred             CEEECCCCCCEeeCC
Confidence            489999999999984