Citrus Sinensis ID: 042443

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-----
Protein Sequence
MALQILKLPINLRCYNNPTSTANSGLFLLSNSNSHALLGRLLKGQRQYPIRSFAVASNAKSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ
Secondary Structure (PSIPRED)
ccccccccccHHccccccccccccHHEEEcccccccccccccccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
cccEcccccHHEEccccccccccHHHHHHccccccccccEEEEcccccccHHHHHHccccccccccHHHHHcHHHHHHHHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
malqilklpinlrcynnptstansgLFLLSNSNSHALLGRLLkgqrqypirsfavasnaksekiqlpkkkrRLDEICLERFQQYSRTYIQSWILQ
Flexible Loop (DISEMBL)
MALQILKLPINLRCYNNPTSTANSGLFLLSNSNSHALLGRLLKGQRQYPIRSfavasnaksekiqlpkkkrrldEICLERFQQYSRTYIQSWILQ
Low Complexity Region (SEG)
MALQILKLPINLRCYNNPTSTAnsglfllsnsnsHALLGRLLKGQRQYPIRSFAVASNAKSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ
Disordered region (IsUnstruct)
***QILKLPINLRCYNNPTSTANSGLFLLSNSNSHALLGRLLKGQRQYPIRSFAVA***************RLDEICLERFQQYSRTYIQSWIL*
Disordered Region (DISOPRED)
******KLPINLRCYNNPTSTANSGLFLLSNSNSHALLGRLLKGQRQYPIRSF*********************EICLERFQQYSRTYIQSWILQ
Disordered Region (DISEMBL)
MALQILKLPINLRCYNNPTSTANSGLFLLSNSNSHALLGRLLKGQRQYPIRSFAVASNAKSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ
Disordered Region (DISPRO)
*ALQILKLPINLRCYNNPTSTANSGLFLLSNSNSHALLGRLLKGQRQYPIRSFAVASNAKSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MALQILKLPINLRCYNNPTSTANSGLFLLSNSNSHALLGRLLKGQRQYPIRSFAVASNAKSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	95
255572704	312	Hemolysin A, putative [Ricinus communis]	0.968	0.294	0.568	2e-17
359494815	300	PREDICTED: uncharacterized protein yqxC-	0.884	0.28	0.526	2e-14
357156985	299	PREDICTED: uncharacterized protein yqxC-	0.463	0.147	0.808	4e-14
226507814	297	hemolysin A [Zea mays] gi|195655423|gb|A	0.463	0.148	0.765	6e-14
223948145	293	unknown [Zea mays] gi|413920637|gb|AFW60	0.463	0.150	0.765	1e-13
242089543	299	hypothetical protein SORBIDRAFT_09g00389	0.463	0.147	0.744	4e-13
413920638	102	hypothetical protein ZEAMMB73_014233 [Ze	0.463	0.431	0.765	2e-12
115484941	295	Os11g0247400 [Oryza sativa Japonica Grou	0.463	0.149	0.723	3e-12
356503149	308	PREDICTED: uncharacterized protein yqxC-	0.947	0.292	0.468	5e-11
356520707	315	PREDICTED: uncharacterized protein yqxC-	0.947	0.285	0.437	1e-10

>gi|255572704|ref|XP_002527285.1| Hemolysin A, putative [Ricinus communis] gi|223533378|gb|EEF35129.1| Hemolysin A, putative [Ricinus communis]

 Score = 93.2 bits (230), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 54/95 (56%), Positives = 67/95 (70%), Gaps = 3/95 (3%)

Query: 1  MALQILKLPINLRCYNNPTSTANSGLFLLSNSNSHALLGRLLKGQRQYPIRSFAVASNAK 60
          MA++ LKLP+  R  NN  S+++S    LS      L  + +K + Q+  RSFAVA   K
Sbjct: 1  MAMRFLKLPLISRYCNNYNSSSSSSFVSLSKFYPTRLTVKWVKPEMQFSFRSFAVA---K 57

Query: 61 SEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ 95
          + KIQ+PKKKRRLDEICLERFQQYSRT+IQSWILQ
Sbjct: 58 TGKIQIPKKKRRLDEICLERFQQYSRTFIQSWILQ 92

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359494815|ref|XP_002271057.2| PREDICTED: uncharacterized protein yqxC-like [Vitis vinifera] gi|302144209|emb|CBI23336.3| unnamed protein product [Vitis vinifera]

 Score = 83.2 bits (204), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 50/95 (52%), Positives = 57/95 (60%), Gaps = 11/95 (11%)

Query: 1  MALQILKLPINLRCYNNPTSTANSGLFLLSNSNSHALLGRLLKGQRQYPIRSFAVASNAK 60
          MALQI KLP   RC        +S LF  S S S  +    ++   +   RSFA     K
Sbjct: 1  MALQIPKLPTISRC-------CSSTLFFFSKSTS-PVNASWVRTHLRSSFRSFATT---K 49

Query: 61 SEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ 95
            KIQ  KKKRRLDE+CLERFQQYSRT+IQSWILQ
Sbjct: 50 PGKIQPLKKKRRLDEVCLERFQQYSRTFIQSWILQ 84

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357156985|ref|XP_003577643.1| PREDICTED: uncharacterized protein yqxC-like [Brachypodium distachyon]

 Score = 82.0 bits (201), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 38/47 (80%), Positives = 40/47 (85%), Gaps = 3/47 (6%)

Query: 49 PIRSFAVASNAKSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ 95
          P R FA     KS+KIQLPKKKRRLDE+CLERFQQYSRTYIQSWILQ
Sbjct: 23 PSREFAAV---KSKKIQLPKKKRRLDEVCLERFQQYSRTYIQSWILQ 66

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226507814|ref|NP_001152354.1| hemolysin A [Zea mays] gi|195655423|gb|ACG47179.1| hemolysin A [Zea mays]

 Score = 81.3 bits (199), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 36/47 (76%), Positives = 41/47 (87%), Gaps = 3/47 (6%)

Query: 49 PIRSFAVASNAKSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ 95
          P R+FA     +++KIQLPKKKRRLDE+CLERFQQYSRTYIQSWILQ
Sbjct: 24 PSRAFAAV---RAQKIQLPKKKRRLDEVCLERFQQYSRTYIQSWILQ 67

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|223948145|gb|ACN28156.1| unknown [Zea mays] gi|413920637|gb|AFW60569.1| hemolysin A [Zea mays]

 Score = 80.1 bits (196), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 36/47 (76%), Positives = 41/47 (87%), Gaps = 3/47 (6%)

Query: 49 PIRSFAVASNAKSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ 95
          P R+FA     +++KIQLPKKKRRLDE+CLERFQQYSRTYIQSWILQ
Sbjct: 24 PSRAFAAV---RAQKIQLPKKKRRLDEVCLERFQQYSRTYIQSWILQ 67

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242089543|ref|XP_002440604.1| hypothetical protein SORBIDRAFT_09g003890 [Sorghum bicolor] gi|241945889|gb|EES19034.1| hypothetical protein SORBIDRAFT_09g003890 [Sorghum bicolor]

 Score = 78.6 bits (192), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/47 (74%), Positives = 40/47 (85%), Gaps = 3/47 (6%)

Query: 49 PIRSFAVASNAKSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ 95
          P R+FA     +++KIQLPKKKRRLDE+CL RFQQYSRTYIQSWILQ
Sbjct: 24 PSRAFAAV---RAQKIQLPKKKRRLDEVCLGRFQQYSRTYIQSWILQ 67

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413920638|gb|AFW60570.1| hypothetical protein ZEAMMB73_014233 [Zea mays]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 36/47 (76%), Positives = 41/47 (87%), Gaps = 3/47 (6%)

Query: 49 PIRSFAVASNAKSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ 95
          P R+FA     +++KIQLPKKKRRLDE+CLERFQQYSRTYIQSWILQ
Sbjct: 24 PSRAFAAV---RAQKIQLPKKKRRLDEVCLERFQQYSRTYIQSWILQ 67

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115484941|ref|NP_001067614.1| Os11g0247400 [Oryza sativa Japonica Group] gi|62734664|gb|AAX96773.1| hemolysin A, putative [Oryza sativa Japonica Group] gi|77549558|gb|ABA92355.1| hemolysin A family protein, expressed [Oryza sativa Japonica Group] gi|113644836|dbj|BAF27977.1| Os11g0247400 [Oryza sativa Japonica Group]

 Score = 75.9 bits (185), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 34/47 (72%), Positives = 39/47 (82%), Gaps = 3/47 (6%)

Query: 49 PIRSFAVASNAKSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ 95
          P R FA     +++K+QL KKKRRLDE+CLERFQQYSRTYIQSWILQ
Sbjct: 25 PSRDFAAV---RTQKLQLAKKKRRLDEVCLERFQQYSRTYIQSWILQ 68

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356503149|ref|XP_003520374.1| PREDICTED: uncharacterized protein yqxC-like [Glycine max]

 Score = 72.0 bits (175), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 45/96 (46%), Positives = 56/96 (58%), Gaps = 6/96 (6%)

Query: 1  MALQILKLPINL-RCYNNPTSTANSGLFLLSNSNSHALLGRLLKGQRQYPIRSFAVASNA 59
          MALQ LK P+ + R   N T+      FL    N    L    +   Q P  SF   + A
Sbjct: 1  MALQFLKHPLTISRGLQNETTLT----FLSRLRNPKLPLSVRCEDNVQIPT-SFRSYATA 55

Query: 60 KSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ 95
          KSEK+   KKK+RLDEIC+E++QQYSR+ IQSWILQ
Sbjct: 56 KSEKVLQVKKKKRLDEICVEKYQQYSRSIIQSWILQ 91

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356520707|ref|XP_003529002.1| PREDICTED: uncharacterized protein yqxC-like [Glycine max]

 Score = 70.5 bits (171), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 42/96 (43%), Positives = 57/96 (59%), Gaps = 6/96 (6%)

Query: 1  MALQILKLPINL-RCYNNPTSTANSGLFLLSNSNSHALLGRLLKGQRQYPIRSFAVASNA 59
          MALQ LK P+ + R  +N T+     L  +S   +  LL  +          SF   + A
Sbjct: 1  MALQFLKHPVTISRGLHNETT-----LTFISRLRNPKLLFSVRCEDNAQIATSFRSYATA 55

Query: 60 KSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ 95
          KSEK+   +KK+RLDEIC+E++QQYSR+ IQSWILQ
Sbjct: 56 KSEKVLQVRKKKRLDEICVEKYQQYSRSVIQSWILQ 91

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	95
TAIR|locus:2094478	301	AT3G25470 [Arabidopsis thalian	0.547	0.172	0.474	5.9e-07

TAIR|locus:2094478 AT3G25470 [Arabidopsis thaliana (taxid:3702)]

 Score = 120 (47.3 bits), Expect = 5.9e-07, P = 5.9e-07
 Identities = 28/59 (47%), Positives = 37/59 (62%)

Query:    37 LLGRLLKGQRQYPIRSFAVASNAKSEKIQLPKKKRRLDEICLERFQQYSRTYIQSWILQ 95
             L GR ++      +R FA A+  K+       KK+RLDE C+ERF +YSRT IQSWI+Q
Sbjct:    28 LPGRWVQAGECSTMRCFASATRGKN-------KKQRLDEACVERFNEYSRTLIQSWIMQ 79


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.323   0.135   0.396    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       95        83   0.00091  102 3  11 22  0.37    29
                                                     29  0.44    30


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:  540 (57 KB)
  Total size of DFA:  104 KB (2071 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:  8.75u 0.09s 8.84t   Elapsed:  00:00:03
  Total cpu time:  8.75u 0.09s 8.84t   Elapsed:  00:00:03
  Start:  Fri May 10 08:34:57 2013   End:  Fri May 10 08:35:00 2013

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0019836 "hemolysis by symbiont of host erythrocytes" evidence=IEA

GO:0032259 "methylation" evidence=IEA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	BRADI4G20930.1	annotation not avaliable (299 aa)
		(Brachypodium distachyon)
Predicted Functional Partners:
	BRADI1G23510.1	annotation not avaliable (356 aa)	•						•		0.828
	BRADI2G25550.1	annotation not avaliable (706 aa)	•								0.783
	BRADI1G54890.1	annotation not avaliable (713 aa)	•								0.783
	BRADI2G08730.1	annotation not avaliable (383 aa)	•						•		0.761
	BRADI4G25740.1	annotation not avaliable (226 aa)	•			•					0.746
	BRADI3G27090.1	annotation not avaliable (278 aa)	•			•			•		0.695
	BRADI1G04210.2	annotation not avaliable (911 aa)							•		0.683
	BRADI4G19460.1	annotation not avaliable (466 aa)	•								0.675
	BRADI3G20590.1	annotation not avaliable (542 aa)	•								0.641
	BRADI1G67790.1	annotation not avaliable (440 aa)	•								0.636

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	95
TIGR02988	59	YaaA_near_RecF S4 domain protein YaaA. This small	97.21
PF01479	48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	96.79
PLN00051	267	RNA-binding S4 domain-containing protein; Provisio	96.43
COG0564	289	RluA Pseudouridylate synthases, 23S RNA-specific [	95.74
cd00165	70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	95.26
PRK11180	325	rluD 23S rRNA pseudouridine synthase D; Provisiona	94.73
PRK11025	317	23S rRNA pseudouridylate synthase C; Provisional	94.57
smart00363	60	S4 S4 RNA-binding domain.	94.02
TIGR03069	257	PS_II_S4 photosystem II S4 domain protein. Members	93.73
PF06353	142	DUF1062: Protein of unknown function (DUF1062); In	91.76

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA

Probab=97.21  E-value=0.00026  Score=42.99  Aligned_cols=27  Identities=11%  Similarity=-0.079  Sum_probs=22.7

Q ss_pred             ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443           69 KKRRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      .+.|||++|++....+||+++|.||++
T Consensus         7 ~~~rLd~~L~~~~~~~SR~~~k~li~~   33 (59)
T TIGR02988         7 EYITLGQLLKELGIIDSGGQAKWFLQE   33 (59)
T ss_pred             hHHHHHHHHHHcCCccCHHHHHHHHHc
Confidence            579999999999333499999999974

This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.

>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.79  E-value=0.0014  Score=37.82  Aligned_cols=25  Identities=28%  Similarity=0.131  Sum_probs=23.4

Q ss_pred             ChhHHHHHHhchhchHHHHHHHHhC
Q 042443           71 RRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        71 ~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      .|||.+|+++.+.-||+.+++||++
T Consensus         1 ~RLd~~L~~~~~~~sr~~a~~~I~~   25 (48)
T PF01479_consen    1 MRLDKFLSRLGLASSRSEARRLIKQ   25 (48)
T ss_dssp             EBHHHHHHHTTSSSSHHHHHHHHHT
T ss_pred             CCHHHHHHHcCCcCCHHHHHHhcCC
Confidence            4999999999999999999999975

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 [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....

>PLN00051 RNA-binding S4 domain-containing protein; Provisional

Probab=96.43  E-value=0.0024  Score=50.21  Aligned_cols=25  Identities=28%  Similarity=0.392  Sum_probs=23.7

Q ss_pred             cChhHHHHHHhchhchHHHHHHHHhC
Q 042443           70 KRRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        70 G~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      +.|||.++|..+ .+|||++|+||++
T Consensus       191 s~RLD~vla~~~-~~SRsk~~~lI~~  215 (267)
T PLN00051        191 SLRLDALASAGF-RMSRSKLVDLISS  215 (267)
T ss_pred             cccHHHHHHHHh-ccCHHHHHHHHHc
Confidence            799999999999 9999999999974

>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]

Probab=95.74  E-value=0.0081  Score=47.13  Aligned_cols=26  Identities=31%  Similarity=0.373  Sum_probs=24.0

Q ss_pred             ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443           69 KKRRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      .|+|||++|+++++ +||++++.||++
T Consensus        11 ~g~rld~~L~~l~~-~sr~~~~~~i~~   36 (289)
T COG0564          11 AGQRLDKFLAKLLP-ISRSRIQKLIRK   36 (289)
T ss_pred             cCCCHHHHHHHccC-cCHHHHHHHHHC
Confidence            48999999999888 999999999974

>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes

Probab=95.26  E-value=0.022  Score=32.10  Aligned_cols=25  Identities=28%  Similarity=0.153  Sum_probs=22.7

Q ss_pred             ChhHHHHHHhchhchHHHHHHHHhC
Q 042443           71 RRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        71 ~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      .|||.+|.+.++..||+.+++||.+
T Consensus         1 ~rl~~~l~~~~~~~sr~~~~~~i~~   25 (70)
T cd00165           1 MRLDKILARLGLAPSRSEARQLIKH   25 (70)
T ss_pred             CcHHHHHHHhccccCHHHHHHHHHc
Confidence            4899999999889999999999974

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional

Probab=94.73  E-value=0.027  Score=43.94  Aligned_cols=27  Identities=44%  Similarity=0.768  Sum_probs=24.8

Q ss_pred             ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443           69 KKRRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      -|.|||++|++.++.+||+.++++|.+
T Consensus        16 ~g~RLd~~L~~~~~~~Sr~~~~~lI~~   42 (325)
T PRK11180         16 LGQRLDQALAELFPDYSRSRIKEWILD   42 (325)
T ss_pred             CCccHHHHHHhhccccCHHHHHHHHHC
Confidence            378999999999999999999999974

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional

Probab=94.57  E-value=0.043  Score=42.77  Aligned_cols=27  Identities=11%  Similarity=0.249  Sum_probs=24.8

Q ss_pred             ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443           69 KKRRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      .|.|||++|+..++.+||+.++.+|++
T Consensus        18 ~g~RLd~~L~~~~~~~sr~~i~~li~~   44 (317)
T PRK11025         18 AGQRIDNFLRTQLKGVPKSMIYRILRK   44 (317)
T ss_pred             CCchHHHHHHHhcccCCHHHHHHHHHc
Confidence            378999999999999999999999974

>smart00363 S4 S4 RNA-binding domain

Probab=94.02  E-value=0.066  Score=29.34  Aligned_cols=25  Identities=32%  Similarity=0.220  Sum_probs=22.0

Q ss_pred             ChhHHHHHHhchhchHHHHHHHHhC
Q 042443           71 RRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        71 ~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      .|||+++.+.+..+||+.++.+|.+
T Consensus         1 ~rl~~~l~~~~~~~s~~~~~~~i~~   25 (60)
T smart00363        1 RRLDKFLARLGLAPSRSQARKLIEQ   25 (60)
T ss_pred             CcHHHHHHHcCcccCHHHHHHHHHc
Confidence            4899999998788999999999863

>TIGR03069 PS_II_S4 photosystem II S4 domain protein

Probab=93.73  E-value=0.056  Score=41.98  Aligned_cols=26  Identities=31%  Similarity=0.327  Sum_probs=23.5

Q ss_pred             ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443           69 KKRRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      .+.|||.+++..+ .+||+.+++||++
T Consensus       182 ~s~RLD~lls~~~-~~SRs~a~~lI~~  207 (257)
T TIGR03069       182 ASLRIDAIASAGF-GLSRSKIVDQIKA  207 (257)
T ss_pred             ccccHHHHHHhhh-hhhHHHHHHHHHC
Confidence            4789999999999 8999999999974

Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.

>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=91.76  E-value=0.16  Score=37.15  Aligned_cols=25  Identities=28%  Similarity=0.373  Sum_probs=23.4

Q ss_pred             cChhHHHHHHhchhchHHHHHHHHhC
Q 042443           70 KRRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        70 G~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      ..|||.+||+.+ ..|||+|+++|++
T Consensus       102 ~~Rld~lLa~~L-~lSrs~l~~l~~~  126 (142)
T PF06353_consen  102 PLRLDRLLARQL-GLSRSRLKRLIEQ  126 (142)
T ss_pred             CccHHHHHHHHh-CcCHHHHHHHHHC
Confidence            789999999999 8999999999974

---

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	95
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	1e-04

>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Length = 325

 Score = 37.9 bits (89), Expect = 1e-04
 Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 6/41 (14%)

Query: 61 SEKIQL------PKKKRRLDEICLERFQQYSRTYIQSWILQ 95
          ++++QL       +  +RLD+   E F  YSR+ I+ WIL 
Sbjct: 1  AQRVQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILD 41

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	95
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	94.56
1dm9_A	133	Hypothetical 15.5 KD protein in MRCA-PCKA intergen	93.84
3r8n_D	205	30S ribosomal protein S4; protein biosynthesis, RN	93.26
1c05_A	159	Ribosomal protein S4 delta 41; two subdomains, uni	92.94
1p9k_A	79	ORF, hypothetical protein; alfal motif, RNA-bindin	92.85
2vqe_D	209	30S ribosomal protein S4; tRNA-binding, rRNA-bindi	91.38
2cqj_A	71	BRMS2, U3 small nucleolar ribonucleoprotein protei	86.21

>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A

Probab=94.56  E-value=0.0062  Score=46.01  Aligned_cols=27  Identities=44%  Similarity=0.774  Sum_probs=0.0

Q ss_pred             ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443           69 KKRRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      .|.|||++|++.++.+||+.+|+||++
T Consensus        15 ~g~RLd~~L~~~~~~~SR~~~~~lI~~   41 (325)
T 1v9f_A           15 LGQRLDQALAEMFPDYSRSRIKEWILD   41 (325)
T ss_dssp             ---------------------------
T ss_pred             CCchHHHHHHhhccccCHHHHHHHHHC
Confidence            478999999999999999999999974

>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A

Probab=93.84  E-value=0.04  Score=37.75  Aligned_cols=27  Identities=19%  Similarity=0.062  Sum_probs=23.3

Q ss_pred             ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443           69 KKRRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      .+.|||++|+......||+.++.||.+
T Consensus         7 ~~~RLDk~L~~~~~~~SRs~a~~li~~   33 (133)
T 1dm9_A            7 VEVRLDKWLWAARFYKTRALAREMIEG   33 (133)
T ss_dssp             TCCBHHHHHHHTTSSSSHHHHHHHHHT
T ss_pred             cchhHHHHHHHCCCCCCHHHHHHHHHC
Confidence            378999999997666799999999964

>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C

Probab=92.94  E-value=0.046  Score=38.44  Aligned_cols=26  Identities=15%  Similarity=0.194  Sum_probs=23.9

Q ss_pred             cChhHHHHHHhchhchHHHHHHHHhC
Q 042443           70 KRRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        70 G~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      +.|||.+|++.....||+.+++||.+
T Consensus        50 e~RLD~~L~~~g~~~SR~~ar~lI~~   75 (159)
T 1c05_A           50 ESRLDNLVYRLGLARTRRQARQLVTH   75 (159)
T ss_dssp             HHBHHHHHHHTTSCSSHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCcCCHHHHHHHHHC
Confidence            57999999999889999999999974

>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6

Probab=92.85  E-value=0.015  Score=36.00  Aligned_cols=27  Identities=11%  Similarity=-0.143  Sum_probs=21.7

Q ss_pred             ccChhHHHHHHhchhchHHHHHHHHhC
Q 042443           69 KKRRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        69 ~G~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      .+.|||++|++.--..||+.+++||++
T Consensus        19 ~~~RLdk~L~~~g~~~SR~~a~~lI~~   45 (79)
T 1p9k_A           19 PHVELCDLLKLEGWSESGAQAKIAIAE   45 (79)
T ss_dssp             SCCCHHHHHHHHTSCSSSSTTSHHHHH
T ss_pred             CCchHHHHHHHCCCCCCHHHHHHHHHC
Confidence            357999999998323499999999963

>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ...

Probab=91.38  E-value=0.11  Score=38.23  Aligned_cols=26  Identities=19%  Similarity=0.192  Sum_probs=23.8

Q ss_pred             cChhHHHHHHhchhchHHHHHHHHhC
Q 042443           70 KRRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        70 G~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      +.|||.+|++.....||+.+++||.+
T Consensus        98 e~RLD~~L~~~g~~~SR~~arqLI~~  123 (209)
T 2vqe_D           98 ESRLDNVVYRLGFAVSRRQARQLVRH  123 (209)
T ss_dssp             HTBHHHHHHHTTSSSSHHHHHHHHHT
T ss_pred             HHHHHHHHHHhcCcCCHHHHHHHHHC
Confidence            68999999999888999999999964

>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=86.21  E-value=0.44  Score=29.55  Aligned_cols=26  Identities=19%  Similarity=0.140  Sum_probs=23.4

Q ss_pred             cChhHHHHHHhchhchHHHHHHHHhC
Q 042443           70 KRRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        70 G~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      ..|||.+|.++----||+..+++|.+
T Consensus         7 ~~RLD~~l~~~gla~SR~~A~~lI~~   32 (71)
T 2cqj_A            7 GRRLPTVLLKLRMAQHLQAAVAFVEQ   32 (71)
T ss_dssp             EEEHHHHHHHTTCSSSHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCcCCHHHHHHHHHC
Confidence            36999999999988899999999974

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	95
d1kska3	59	Pseudouridine synthase RsuA N-terminal domain {Esc	96.88
d1vioa2	58	Pseudouridine synthase RsuA N-terminal domain {Hae	96.8

>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.88  E-value=0.00028  Score=41.08  Aligned_cols=23  Identities=26%  Similarity=0.258  Sum_probs=21.5

Q ss_pred             hhHHHHHHhchhchHHHHHHHHhC
Q 042443           72 RLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        72 RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      |||++|++.. .+||+.+++||++
T Consensus         2 RLdk~l~~~~-~~SR~~a~~lI~~   24 (59)
T d1kska3           2 RLDKFIAQQL-GVSRAIAGREIRG   24 (59)
T ss_dssp             EHHHHHHHHH-TCCHHHHHHHHHT
T ss_pred             cHHHHHHHcC-CCCHHHHHHHHHc
Confidence            9999999997 8999999999974

>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=96.80  E-value=0.00035  Score=40.61  Aligned_cols=24  Identities=29%  Similarity=0.284  Sum_probs=21.7

Q ss_pred             ChhHHHHHHhchhchHHHHHHHHhC
Q 042443           71 RRLDEICLERFQQYSRTYIQSWILQ   95 (95)
Q Consensus        71 ~RLDqvLAeLfPeySRSrIQ~WI~~   95 (95)
                      .|||++|++.. .+||+++++||++
T Consensus         2 mRLD~~Ls~~~-~~SR~~a~~lI~~   25 (58)
T d1vioa2           2 LRLDKFIAENV-GLTRSQATKAIRQ   25 (58)
T ss_dssp             EEHHHHHHHHH-TCCHHHHHHHHHT
T ss_pred             cHHHHHHHHcC-CCCHHHHHHHHHc
Confidence            49999999887 7899999999975