Psyllid ID: psy4327

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------
Protein Sequence
MAQAIFDLQTYRVSVMAAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHKRLRLRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI
Secondary Structure (PSIPRED)
cccccccccEEEEEEEEEHHHcccHHHcccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccEEEEEEEEEEccccccccccEEEEEEcccccHHHHHHHHcccEEEEEEccccccccccccccEEEEEEEEEEcccccccEEEEEEcccccccccccEEEEEEEcccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHcHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccEEEEEEEEEEcccccccccccEEEEEEEccccccccEEEEccEEEEEEEEcccccccccccccEEEEEEEEEEcccccccEEEEEEcccccHHHcccEEEEEEccccc
Coil and Loop (DISEMBL)
MAQAIFDLQTYRVSVMAAATEVkkdekkkvakpktpktgeekKVAKKatattpskdakatdtkkvkktkkhkrlrlrHGRLYARAIFTgfkrgqrnqhpntsLLAIEKCNTKEDARFYVGKRCVFLYKAKtkelkphskrKSRLRAIWgkvtrphgssgsvrakfhrnlpaiymgRKVRIMLYPSNI
Flexible Loop (DISEMBL)
maqaifdlqtyrvSVMAAatevkkdekkkvakpktpktgeekkvakkatattpskdakatdtkkvkktkkhkrlrlrhgrlyARAIftgfkrgqrnqhpntsllaiEKCNTKEDARFYVGKRCVFLYkaktkelkphskrksrlraiwgkvtrphgssgsvrakfhrnlpaiymgrkvrimlypsni
Low Complexity Region (SEG)
MAQAIFDLQTYRVSVMaaatevkkdekkkvakpktpktgeekkvakkatattpskdakatdtkkvkktkkhkRLRLRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI
Disordered region (IsUnstruct)
****IFDLQTYRVSVM**********************************************************RLRHGRLYARAIFTGFKRGQR***PNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKT*************RAIWGKVT********VRAKFHRNLPAIYMGRKVRIMLY****
Disordered Region (DISOPRED)
***AIFDLQTYRVSVMA***************************************************************LYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKA**************LRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI
Disordered Region (DISEMBL)
MAQAIFDLQTYRVSVMAAA*******************************************************RLRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKE*********RLRAIWGKVT********VRAKFHRNLPAIYMGRKVRIMLYPSNI
Disordered Region (DISPRO)
*AQAIFDLQTYRVSVMAAAT********************************************************RHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSN*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAQAIFDLQTYRVSVMAAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHKRLRLRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI
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

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	187	2.2.26 [Sep-21-2011]
P49180	124	60S ribosomal protein L35	yes	N/A	0.582	0.879	0.605	3e-34
Q5R8K6	110	60S ribosomal protein L35	yes	N/A	0.577	0.981	0.541	6e-29
P61272	110	60S ribosomal protein L35	N/A	N/A	0.577	0.981	0.541	6e-29
P18077	110	60S ribosomal protein L35	yes	N/A	0.577	0.981	0.541	6e-29
Q9C912	112	60S ribosomal protein L35	yes	N/A	0.545	0.910	0.564	8e-29
Q56JY1	110	60S ribosomal protein L35	yes	N/A	0.577	0.981	0.532	9e-29
P04646	110	60S ribosomal protein L35	yes	N/A	0.577	0.981	0.541	1e-28
O55142	110	60S ribosomal protein L35	yes	N/A	0.577	0.981	0.541	1e-28
Q9FZH0	111	60S ribosomal protein L35	no	N/A	0.545	0.918	0.555	3e-28
Q9LMK0	112	60S ribosomal protein L35	yes	N/A	0.545	0.910	0.555	3e-28

>sp|P49180|RL35A_CAEEL 60S ribosomal protein L35a OS=Caenorhabditis elegans GN=rpl-33 PE=1 SV=3

 Score =  144 bits (363), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 66/109 (60%), Positives = 82/109 (75%)

Query: 79  GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
           GRLY +AIFTGFKRG R Q  +TSLL +E    KEDA FY GKR V+LYKA  K LK   
Sbjct: 16  GRLYVKAIFTGFKRGLRTQSEHTSLLKLEGVFNKEDAGFYAGKRVVYLYKAHNKTLKTGH 75

Query: 139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
              +R RAIWGK+TRPHG++G+VRAKFH N+P   +G+++R++LYPSNI
Sbjct: 76  TVATRTRAIWGKITRPHGNAGAVRAKFHHNIPPSALGKRIRVLLYPSNI 124

Caenorhabditis elegans (taxid: 6239)

>sp|Q5R8K6|RL35A_PONAB 60S ribosomal protein L35a OS=Pongo abelii GN=RPL35A PE=3 SV=1

 Score =  126 bits (317), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 59/109 (54%), Positives = 79/109 (72%), Gaps = 1/109 (0%)

Query: 79  GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
           GRL+++AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P  
Sbjct: 3   GRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGG 62

Query: 139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
           K  ++ R IWGKVTR HG+SG VRAKF  NLPA  +G ++R+MLYPS I
Sbjct: 63  K-PNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

Required for the proliferation and viability of hematopoietic cells (By similarity). Plays a role in 60S ribosomal subunit formation (By similarity). The protein was found to bind to both initiator and elongator tRNAs and consequently was assigned to the P site or P and A site.

Pongo abelii (taxid: 9601)

>sp|P61272|RL35A_MACFA 60S ribosomal protein L35a OS=Macaca fascicularis GN=RPL35A PE=3 SV=1

 Score =  126 bits (317), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 59/109 (54%), Positives = 79/109 (72%), Gaps = 1/109 (0%)

Query: 79  GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
           GRL+++AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P  
Sbjct: 3   GRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGG 62

Query: 139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
           K  ++ R IWGKVTR HG+SG VRAKF  NLPA  +G ++R+MLYPS I
Sbjct: 63  K-PNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

Required for the proliferation and viability of hematopoietic cells (By similarity). Plays a role in 60S ribosomal subunit formation (By similarity). The protein was found to bind to both initiator and elongator tRNAs and consequently was assigned to the P site or P and A site.

Macaca fascicularis (taxid: 9541)

>sp|P18077|RL35A_HUMAN 60S ribosomal protein L35a OS=Homo sapiens GN=RPL35A PE=1 SV=2

 Score =  126 bits (317), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 59/109 (54%), Positives = 79/109 (72%), Gaps = 1/109 (0%)

Query: 79  GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
           GRL+++AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P  
Sbjct: 3   GRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGG 62

Query: 139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
           K  ++ R IWGKVTR HG+SG VRAKF  NLPA  +G ++R+MLYPS I
Sbjct: 63  K-PNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

Required for the proliferation and viability of hematopoietic cells. Plays a role in 60S ribosomal subunit formation. The protein was found to bind to both initiator and elongator tRNAs and consequently was assigned to the P site or P and A site.

Homo sapiens (taxid: 9606)

>sp|Q9C912|R35A3_ARATH 60S ribosomal protein L35a-3 OS=Arabidopsis thaliana GN=RPL35AC PE=3 SV=1

 Score =  126 bits (317), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 61/108 (56%), Positives = 74/108 (68%), Gaps = 6/108 (5%)

Query: 80  RLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSK 139
           RLY R    G+KR + NQ+PNTSL+ IE  NT+E+  +Y GKR  ++YKAKTK      K
Sbjct: 11  RLYVRGTILGYKRSKSNQYPNTSLVQIEGVNTQEEVNWYKGKRMAYIYKAKTK------K 64

Query: 140 RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             S  R IWGKVTRPHG+SG VRAKF  NLP   MG +VR+ +YPSNI
Sbjct: 65  NGSHYRCIWGKVTRPHGNSGVVRAKFTSNLPPKSMGSRVRVFMYPSNI 112

Arabidopsis thaliana (taxid: 3702)

>sp|Q56JY1|RL35A_BOVIN 60S ribosomal protein L35a OS=Bos taurus GN=RPL35A PE=2 SV=1

 Score =  126 bits (316), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 58/109 (53%), Positives = 79/109 (72%), Gaps = 1/109 (0%)

Query: 79  GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
           GRL+++AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P  
Sbjct: 3   GRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGG 62

Query: 139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
           K  ++ R IWGK+TR HG+SG VRAKF  NLPA  +G ++R+MLYPS I
Sbjct: 63  K-PNKTRVIWGKITRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

Required for the proliferation and viability of hematopoietic cells. Plays a role in 60S ribosomal subunit formation (By similarity). The protein was found to bind to both initiator and elongator tRNAs and consequently was assigned to the P site or P and A site.

Bos taurus (taxid: 9913)

>sp|P04646|RL35A_RAT 60S ribosomal protein L35a OS=Rattus norvegicus GN=Rpl35a PE=3 SV=1

 Score =  126 bits (316), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 59/109 (54%), Positives = 78/109 (71%), Gaps = 1/109 (0%)

Query: 79  GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
           GRL+ +AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P  
Sbjct: 3   GRLWCKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGG 62

Query: 139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
           K  ++ R IWGKVTR HG+SG VRAKF  NLPA  +G ++R+MLYPS I
Sbjct: 63  K-PNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

Required for the proliferation and viability of hematopoietic cells (By similarity). Plays a role in 60S ribosomal subunit formation (By similarity). The protein was found to bind to both initiator and elongator tRNAs and consequently was assigned to the P site or P and A site.

Rattus norvegicus (taxid: 10116)

>sp|O55142|RL35A_MOUSE 60S ribosomal protein L35a OS=Mus musculus GN=Rpl35a PE=2 SV=2

 Score =  126 bits (316), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 59/109 (54%), Positives = 78/109 (71%), Gaps = 1/109 (0%)

Query: 79  GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
           GRL+ +AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P  
Sbjct: 3   GRLWCKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGG 62

Query: 139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
           K  ++ R IWGKVTR HG+SG VRAKF  NLPA  +G ++R+MLYPS I
Sbjct: 63  K-PNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

Required for the proliferation and viability of hematopoietic cells (By similarity). Plays a role in 60S ribosomal subunit formation (By similarity). The protein was found to bind to both initiator and elongator tRNAs and consequently was assigned to the P site or P and A site.

Mus musculus (taxid: 10090)

>sp|Q9FZH0|R35A2_ARATH 60S ribosomal protein L35a-2 OS=Arabidopsis thaliana GN=RPL35AB PE=3 SV=1

 Score =  124 bits (312), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 60/108 (55%), Positives = 74/108 (68%), Gaps = 6/108 (5%)

Query: 80  RLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSK 139
           RLY R    G+KR + NQ+PNTSL+ IE  NT+E+  +Y GKR  ++YKAKTK      K
Sbjct: 10  RLYVRGTVLGYKRSKSNQYPNTSLIQIEGVNTQEEVNWYKGKRLAYIYKAKTK------K 63

Query: 140 RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             S  R IWGKVTRPHG+SG VR+KF  NLP   MG +VR+ +YPSNI
Sbjct: 64  NGSHYRCIWGKVTRPHGNSGVVRSKFTSNLPPKSMGARVRVFMYPSNI 111

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LMK0|R35A1_ARATH 60S ribosomal protein L35a-1 OS=Arabidopsis thaliana GN=RPL35AA PE=3 SV=1

 Score =  124 bits (312), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 60/108 (55%), Positives = 73/108 (67%), Gaps = 6/108 (5%)

Query: 80  RLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSK 139
           RLY R    G+KR + NQ+PNTSL+ +E  NT E+  +Y GKR  ++YKAKTK      K
Sbjct: 11  RLYVRGTILGYKRSKSNQYPNTSLVQVEGVNTTEEVSWYKGKRMAYIYKAKTK------K 64

Query: 140 RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             S  R IWGKVTRPHG+SG VRAKF  NLP   MG +VR+ +YPSNI
Sbjct: 65  NGSHYRCIWGKVTRPHGNSGVVRAKFTSNLPPKSMGSRVRVFMYPSNI 112

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	187
110671426	172	putative ribosomal protein L35Ae [Diapho	0.919	1.0	0.994	1e-92
389032461	132	ribosomal protein L35Ae, partial [Ctenoc	0.593	0.840	0.716	7e-40
289742173	156	ribosomal protein L35A [Glossina morsita	0.791	0.948	0.557	1e-39
307204228	138	60S ribosomal protein L35a [Harpegnathos	0.593	0.804	0.696	5e-39
70909869	146	ribosomal protein L35Ae [Cicindela campe	0.652	0.835	0.645	1e-38
91094995	143	PREDICTED: similar to ribosomal protein	0.620	0.811	0.669	1e-37
350399080	146	PREDICTED: 60S ribosomal protein L35a-li	0.593	0.760	0.687	1e-37
340719155	169	PREDICTED: 60S ribosomal protein L35a-li	0.593	0.656	0.687	1e-37
383847897	145	PREDICTED: 60S ribosomal protein L35a-li	0.593	0.765	0.687	1e-37
66515955	146	PREDICTED: 60S ribosomal protein L35a is	0.593	0.760	0.678	2e-37

>gi|110671426|gb|ABG81964.1| putative ribosomal protein L35Ae [Diaphorina citri]

 Score =  344 bits (882), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 171/172 (99%), Positives = 171/172 (99%)

Query: 16  MAAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHKRLR 75
           MAAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKK KRLR
Sbjct: 1   MAAATEVKKDEKKKVAKPKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKLKRLR 60

Query: 76  LRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELK 135
           LRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELK
Sbjct: 61  LRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELK 120

Query: 136 PHSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
           PHSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI
Sbjct: 121 PHSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 172

Source: Diaphorina citri

Species: Diaphorina citri

Genus: Diaphorina

Family: Psyllidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|389032461|gb|AFK82367.1| ribosomal protein L35Ae, partial [Ctenocephalides felis]

 Score =  168 bits (426), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 81/113 (71%), Positives = 91/113 (80%), Gaps = 2/113 (1%)

Query: 77  RHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKP 136
           RHGRLYA+AIFTG+KRG RNQH NT+LL +E C TK D+ FYVGKRCVF+YKAK K   P
Sbjct: 20  RHGRLYAKAIFTGYKRGLRNQHENTALLKVEGCGTKADSWFYVGKRCVFVYKAKNKTCVP 79

Query: 137 H--SKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
               K KS++RAIWGKVTRPHG SG VRAKFHRNLPA  MG +VRIML+PS I
Sbjct: 80  GKPKKVKSKVRAIWGKVTRPHGCSGCVRAKFHRNLPAKAMGHRVRIMLFPSRI 132

Source: Ctenocephalides felis

Species: Ctenocephalides felis

Genus: Ctenocephalides

Family: Pulicidae

Order: Siphonaptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|289742173|gb|ADD19834.1| ribosomal protein L35A [Glossina morsitans morsitans]

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 87/156 (55%), Positives = 111/156 (71%), Gaps = 8/156 (5%)

Query: 33  PKTPKTGEEKKVAKKATATTPSKDAKATDTKKVKKTKKHKRLRLRHGRLYARAIFTGFKR 92
           P    T +  KV+K   A  P+K  KATD   VK T K+K    RHGRL+A+A+FTG+KR
Sbjct: 8   PAAIPTAKATKVSKTPKAAKPAKIEKATD---VKSTAKYK----RHGRLFAKAVFTGYKR 60

Query: 93  GQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKP-HSKRKSRLRAIWGKV 151
           G RNQH   ++L +E C  KE   FYVGKRCV++YKA+TK+  P H +RK+R+RA+WGKV
Sbjct: 61  GLRNQHETQAILKVEGCRRKEHGTFYVGKRCVYVYKAETKKCVPQHPERKTRIRAVWGKV 120

Query: 152 TRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
           TR HG+SG+VRA+F RNLP   MG +VRIMLYPS +
Sbjct: 121 TRLHGNSGAVRARFRRNLPGHAMGHRVRIMLYPSRL 156

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307204228|gb|EFN83035.1| 60S ribosomal protein L35a [Harpegnathos saltator]

 Score =  166 bits (419), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 78/112 (69%), Positives = 95/112 (84%), Gaps = 1/112 (0%)

Query: 77  RHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKP 136
           RHGRLYA+AIFTG+KRG RNQH +T+LL IE  +TK+D+ FYVGKRCV++YKAK K   P
Sbjct: 27  RHGRLYAKAIFTGYKRGLRNQHEHTALLKIEGADTKQDSNFYVGKRCVYVYKAKNKTPVP 86

Query: 137 -HSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
            ++ RK+++RAIWGKVTRPHG+SGSVRAKF RNLPA  MG ++RIMLYPS I
Sbjct: 87  ENTTRKTKVRAIWGKVTRPHGASGSVRAKFKRNLPAKAMGHRIRIMLYPSRI 138

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|70909869|emb|CAJ17421.1| ribosomal protein L35Ae [Cicindela campestris]

 Score =  165 bits (417), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 80/124 (64%), Positives = 96/124 (77%), Gaps = 2/124 (1%)

Query: 66  KKTKKHKRLRLRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVF 125
           KK K  +R   RHGRLYA+AIFTG+KRG RNQH NT+LL IE C  K D+ FYVGK+CVF
Sbjct: 23  KKPKTQRRPFQRHGRLYAKAIFTGYKRGLRNQHENTALLKIEGCGKKVDSWFYVGKKCVF 82

Query: 126 LYKAKTKELKP--HSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLY 183
           +YKA  K   P  H  +KS++RAIWGKVTRPHG++G+VRAKF RNLPA  MG ++RIMLY
Sbjct: 83  VYKAAKKTSVPGAHKTKKSKVRAIWGKVTRPHGTTGAVRAKFKRNLPAKAMGHRIRIMLY 142

Query: 184 PSNI 187
           PS +
Sbjct: 143 PSTV 146

Source: Cicindela campestris

Species: Cicindela campestris

Genus: Cicindela

Family: Carabidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91094995|ref|XP_969089.1| PREDICTED: similar to ribosomal protein L35Ae [Tribolium castaneum] gi|270015389|gb|EFA11837.1| hypothetical protein TcasGA2_TC002098 [Tribolium castaneum]

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 79/118 (66%), Positives = 93/118 (78%), Gaps = 2/118 (1%)

Query: 72  KRLRLRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKT 131
           KR   RHGRLYA+AIFTG+KRG RNQH NT+LL IE  N K D+ FYVGK+CV++YKAK 
Sbjct: 26  KRPHKRHGRLYAKAIFTGYKRGLRNQHENTALLKIEGTNAKPDSWFYVGKKCVYVYKAKN 85

Query: 132 KELKPHSKR--KSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
           K   P   +  KS++RAIWGKVTRPHG+SG+VRAKF RNLPA  MG ++RIMLYPS I
Sbjct: 86  KTCVPGKPKSVKSKVRAIWGKVTRPHGTSGAVRAKFKRNLPAKAMGHRIRIMLYPSRI 143

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350399080|ref|XP_003485411.1| PREDICTED: 60S ribosomal protein L35a-like [Bombus impatiens]

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 77/112 (68%), Positives = 92/112 (82%), Gaps = 1/112 (0%)

Query: 77  RHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKP 136
           RHGRLYA+AIFTG+KRG RNQH +T+LL +E   TK D+ FYVGKRCV++YKAK K   P
Sbjct: 35  RHGRLYAKAIFTGYKRGLRNQHEHTALLKVEGARTKGDSDFYVGKRCVYVYKAKNKTPVP 94

Query: 137 HSK-RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             K RK+++RAIWGKVTRPHG+SGSVRAKF +NLPA  MG ++RIMLYPS I
Sbjct: 95  GKKSRKTKVRAIWGKVTRPHGTSGSVRAKFKKNLPAKAMGHRIRIMLYPSRI 146

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340719155|ref|XP_003398022.1| PREDICTED: 60S ribosomal protein L35a-like [Bombus terrestris]

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 77/112 (68%), Positives = 92/112 (82%), Gaps = 1/112 (0%)

Query: 77  RHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKP 136
           RHGRLYA+AIFTG+KRG RNQH +T+LL +E   TK D+ FYVGKRCV++YKAK K   P
Sbjct: 58  RHGRLYAKAIFTGYKRGLRNQHEHTALLKVEGARTKGDSDFYVGKRCVYVYKAKNKTPVP 117

Query: 137 HSK-RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             K RK+++RAIWGKVTRPHG+SGSVRAKF +NLPA  MG ++RIMLYPS I
Sbjct: 118 GKKSRKTKVRAIWGKVTRPHGTSGSVRAKFKKNLPAKAMGHRIRIMLYPSRI 169

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383847897|ref|XP_003699589.1| PREDICTED: 60S ribosomal protein L35a-like [Megachile rotundata]

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 77/112 (68%), Positives = 92/112 (82%), Gaps = 1/112 (0%)

Query: 77  RHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKP 136
           RHGRLYA+AIFTG+KRG RNQH +T+LL +E   TK D+ FYVGKRCV++YKAK K   P
Sbjct: 34  RHGRLYAKAIFTGYKRGLRNQHEHTTLLKVEGARTKSDSDFYVGKRCVYVYKAKNKTPVP 93

Query: 137 HSK-RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             K +K+++RAIWGKVTRPHG+SGSVRAKF RNLPA  MG ++RIMLYPS I
Sbjct: 94  GKKGKKTKIRAIWGKVTRPHGTSGSVRAKFKRNLPAKAMGHRIRIMLYPSRI 145

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66515955|ref|XP_623272.1| PREDICTED: 60S ribosomal protein L35a isoform 2 [Apis mellifera] gi|380012612|ref|XP_003690373.1| PREDICTED: 60S ribosomal protein L35a-like [Apis florea]

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 76/112 (67%), Positives = 92/112 (82%), Gaps = 1/112 (0%)

Query: 77  RHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKP 136
           RHGRLYA+AIFTG+KRG RNQH +T+LL +E    K+D+ FYVGKRCV++YKAK K   P
Sbjct: 35  RHGRLYAKAIFTGYKRGLRNQHEHTALLKVEGARDKQDSNFYVGKRCVYVYKAKNKTPVP 94

Query: 137 HSK-RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             K RK+++RAIWGKVTRPHG+SGSVRAKF +NLPA  MG ++RIMLYPS I
Sbjct: 95  GKKSRKTKVRAIWGKVTRPHGTSGSVRAKFKKNLPAKAMGHRIRIMLYPSRI 146

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	187
FB|FBgn0037328	157	RpL35A "Ribosomal protein L35A	0.593	0.707	0.625	7.2e-36
WB|WBGene00004447	124	rpl-33 [Caenorhabditis elegans	0.582	0.879	0.605	2.9e-32
RGD|2318348	110	LOC100362338 "ribosomal protei	0.577	0.981	0.550	3.4e-29
RGD|2318932	110	LOC100362049 "ribosomal protei	0.577	0.981	0.550	5.6e-29
RGD|2323316	110	LOC100359825 "ribosomal protei	0.577	0.981	0.550	5.6e-29
UNIPROTKB|E2QYD8	110	RPL35A "Uncharacterized protei	0.577	0.981	0.541	1.2e-28
UNIPROTKB|P18077	110	RPL35A "60S ribosomal protein	0.577	0.981	0.541	1.2e-28
UNIPROTKB|F2Z5Q8	110	RPL35A "Uncharacterized protei	0.577	0.981	0.541	1.2e-28
UNIPROTKB|Q56JY1	110	RPL35A "60S ribosomal protein	0.577	0.981	0.532	1.5e-28
RGD|628793	110	Rpl35a "ribosomal protein L35a	0.577	0.981	0.541	1.5e-28

FB|FBgn0037328 RpL35A "Ribosomal protein L35A" [Drosophila melanogaster (taxid:7227)]

 Score = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 70/112 (62%), Positives = 91/112 (81%)

Query:    77 RHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKP 136
             RHGRL+A+A+FTG+KRG RNQH N ++L IE    KE   FYVGKRCV++YKA+TK+  P
Sbjct:    46 RHGRLFAKAVFTGYKRGLRNQHENQAILKIEGARRKEHGSFYVGKRCVYVYKAETKKCVP 105

Query:   137 -HSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
              H +RK+R+RA+WGKVTR HG++G+VRA+F+RNLP   MG ++RIMLYPS I
Sbjct:   106 QHPERKTRVRAVWGKVTRIHGNTGAVRARFNRNLPGHAMGHRIRIMLYPSRI 157

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

GO:0006412 "translation" evidence=ISS

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

GO:0005840 "ribosome" evidence=IDA

WB|WBGene00004447 rpl-33 [Caenorhabditis elegans (taxid:6239)]

 Score = 353 (129.3 bits), Expect = 2.9e-32, P = 2.9e-32
 Identities = 66/109 (60%), Positives = 82/109 (75%)

Query:    79 GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
             GRLY +AIFTGFKRG R Q  +TSLL +E    KEDA FY GKR V+LYKA  K LK   
Sbjct:    16 GRLYVKAIFTGFKRGLRTQSEHTSLLKLEGVFNKEDAGFYAGKRVVYLYKAHNKTLKTGH 75

Query:   139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
                +R RAIWGK+TRPHG++G+VRAKFH N+P   +G+++R++LYPSNI
Sbjct:    76 TVATRTRAIWGKITRPHGNAGAVRAKFHHNIPPSALGKRIRVLLYPSNI 124

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

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0040017 "positive regulation of locomotion" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

RGD|2318348 LOC100362338 "ribosomal protein L35a-like" [Rattus norvegicus (taxid:10116)]

 Score = 324 (119.1 bits), Expect = 3.4e-29, P = 3.4e-29
 Identities = 60/109 (55%), Positives = 79/109 (72%)

Query:    79 GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
             GRL+ +AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P  
Sbjct:     3 GRLWCKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGG 62

Query:   139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             K  ++ R IWGKVTR HG+SG VRAKF RNLPA  +G ++R+MLYPS I
Sbjct:    63 K-PNKTRVIWGKVTRAHGNSGMVRAKFRRNLPAKAIGHRIRVMLYPSRI 110

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

RGD|2318932 LOC100362049 "ribosomal protein L35a-like" [Rattus norvegicus (taxid:10116)]

 Score = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 60/109 (55%), Positives = 79/109 (72%)

Query:    79 GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
             GRL+ +AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P S
Sbjct:     3 GRLWCKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGS 62

Query:   139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             K  ++ R IWGKVTR HG+SG VRAKF  NLPA  +G ++R+MLYPS I
Sbjct:    63 K-PNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

RGD|2323316 LOC100359825 "ribosomal protein L35a-like" [Rattus norvegicus (taxid:10116)]

 Score = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 60/109 (55%), Positives = 79/109 (72%)

Query:    79 GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
             GRL+ +AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P S
Sbjct:     3 GRLWCKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGS 62

Query:   139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             K  ++ R IWGKVTR HG+SG VRAKF  NLPA  +G ++R+MLYPS I
Sbjct:    63 K-PNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|E2QYD8 RPL35A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 319 (117.4 bits), Expect = 1.2e-28, P = 1.2e-28
 Identities = 59/109 (54%), Positives = 79/109 (72%)

Query:    79 GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
             GRL+++AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P  
Sbjct:     3 GRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGG 62

Query:   139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             K  ++ R IWGKVTR HG+SG VRAKF  NLPA  +G ++R+MLYPS I
Sbjct:    63 K-PNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

UNIPROTKB|P18077 RPL35A "60S ribosomal protein L35a" [Homo sapiens (taxid:9606)]

 Score = 319 (117.4 bits), Expect = 1.2e-28, P = 1.2e-28
 Identities = 59/109 (54%), Positives = 79/109 (72%)

Query:    79 GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
             GRL+++AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P  
Sbjct:     3 GRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGG 62

Query:   139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             K  ++ R IWGKVTR HG+SG VRAKF  NLPA  +G ++R+MLYPS I
Sbjct:    63 K-PNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

GO:0000049 "tRNA binding" evidence=IEA

GO:0006364 "rRNA processing" evidence=IMP

GO:0042273 "ribosomal large subunit biogenesis" evidence=IMP

GO:0006412 "translation" evidence=NAS;TAS

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

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

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0006414 "translational elongation" evidence=TAS

GO:0006415 "translational termination" evidence=TAS

GO:0006614 "SRP-dependent cotranslational protein targeting to membrane" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0019083 "viral transcription" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

UNIPROTKB|F2Z5Q8 RPL35A "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 319 (117.4 bits), Expect = 1.2e-28, P = 1.2e-28
 Identities = 59/109 (54%), Positives = 79/109 (72%)

Query:    79 GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
             GRL+++AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P  
Sbjct:     3 GRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGG 62

Query:   139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             K  ++ R IWGKVTR HG+SG VRAKF  NLPA  +G ++R+MLYPS I
Sbjct:    63 K-PNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

UNIPROTKB|Q56JY1 RPL35A "60S ribosomal protein L35a" [Bos taurus (taxid:9913)]

 Score = 318 (117.0 bits), Expect = 1.5e-28, P = 1.5e-28
 Identities = 58/109 (53%), Positives = 79/109 (72%)

Query:    79 GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
             GRL+++AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P  
Sbjct:     3 GRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGG 62

Query:   139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             K  ++ R IWGK+TR HG+SG VRAKF  NLPA  +G ++R+MLYPS I
Sbjct:    63 K-PNKTRVIWGKITRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

GO:0005840 "ribosome" evidence=IEA

GO:0000049 "tRNA binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

RGD|628793 Rpl35a "ribosomal protein L35a" [Rattus norvegicus (taxid:10116)]

 Score = 318 (117.0 bits), Expect = 1.5e-28, P = 1.5e-28
 Identities = 59/109 (54%), Positives = 78/109 (71%)

Query:    79 GRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHS 138
             GRL+ +AIF G+KRG RNQ  +T+LL IE    +++  FY+GKRC ++YKAK   + P  
Sbjct:     3 GRLWCKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGG 62

Query:   139 KRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             K  ++ R IWGKVTR HG+SG VRAKF  NLPA  +G ++R+MLYPS I
Sbjct:    63 K-PNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI 110

GO:0000049 "tRNA binding" evidence=TAS

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

GO:0005739 "mitochondrion" evidence=ISO

GO:0005840 "ribosome" evidence=TAS

GO:0006364 "rRNA processing" evidence=ISO

GO:0006412 "translation" evidence=IEA

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

GO:0042273 "ribosomal large subunit biogenesis" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9C912	R35A3_ARATH	No assigned EC number	0.5648	0.5454	0.9107	yes	N/A
Q9LMK0	R35A1_ARATH	No assigned EC number	0.5555	0.5454	0.9107	yes	N/A
Q9USX4	RL33A_SCHPO	No assigned EC number	0.5092	0.5454	0.9444	yes	N/A
Q5R8K6	RL35A_PONAB	No assigned EC number	0.5412	0.5775	0.9818	yes	N/A
P49180	RL35A_CAEEL	No assigned EC number	0.6055	0.5828	0.8790	yes	N/A
P18077	RL35A_HUMAN	No assigned EC number	0.5412	0.5775	0.9818	yes	N/A
P04646	RL35A_RAT	No assigned EC number	0.5412	0.5775	0.9818	yes	N/A
O55142	RL35A_MOUSE	No assigned EC number	0.5412	0.5775	0.9818	yes	N/A
Q56JY1	RL35A_BOVIN	No assigned EC number	0.5321	0.5775	0.9818	yes	N/A
P51422	R35A4_ARATH	No assigned EC number	0.5555	0.5454	0.9189	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	187
pfam01247	95	pfam01247, Ribosomal_L35Ae, Ribosomal protein L35A	1e-47
PTZ00041	120	PTZ00041, PTZ00041, 60S ribosomal protein L35a; Pr	4e-43
COG2451	100	COG2451, COG2451, Ribosomal protein L35AE/L33A [Tr	4e-30
PRK04337	87	PRK04337, PRK04337, 50S ribosomal protein L35Ae; V	7e-12

>gnl|CDD|189906 pfam01247, Ribosomal_L35Ae, Ribosomal protein L35Ae

 Score =  150 bits (381), Expect = 1e-47
 Identities = 64/101 (63%), Positives = 78/101 (77%), Gaps = 6/101 (5%)

Query: 81  LYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKR 140
           LY +A+F G++RG+RNQHPNTSLL IE  NTKEDA+FY+GKR  ++YKAK K      K 
Sbjct: 1   LYVKAVFLGYRRGKRNQHPNTSLLKIEGVNTKEDAQFYLGKRVAYVYKAKKK------KN 54

Query: 141 KSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIM 181
            S++R IWGKVTRPHG+SG VRAKF RNLP   MG +VR+M
Sbjct: 55  GSKIRVIWGKVTRPHGNSGVVRAKFRRNLPPQAMGARVRVM 95

Length = 95

>gnl|CDD|240239 PTZ00041, PTZ00041, 60S ribosomal protein L35a; Provisional

 Score =  139 bits (353), Expect = 4e-43
 Identities = 64/125 (51%), Positives = 88/125 (70%), Gaps = 6/125 (4%)

Query: 63  KKVKKTKKHKRLRLRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKR 122
            ++ K KK    + +  RLY +A+F G+KR + NQ+PN +LL IE  NT+EDARFY+GKR
Sbjct: 2   HQLTKKKKKTNRKKKPVRLYVKAVFLGYKRSKVNQYPNVALLKIEGVNTREDARFYLGKR 61

Query: 123 CVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIML 182
             ++YKAK        K  ++ RAIWGK+TRPHG+SG VRA+F++NLP   +G +VR+ L
Sbjct: 62  VAYVYKAKKL------KNGTKFRAIWGKITRPHGNSGVVRARFNKNLPPKAIGSRVRVFL 115

Query: 183 YPSNI 187
           YPSNI
Sbjct: 116 YPSNI 120

Length = 120

>gnl|CDD|225295 COG2451, COG2451, Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]

 Score =  106 bits (265), Expect = 4e-30
 Identities = 46/108 (42%), Positives = 65/108 (60%), Gaps = 13/108 (12%)

Query: 80  RLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSK 139
           RL  + +   ++R +R QHPN SL+ IE  ++ E+A+FY+GKR  + Y++          
Sbjct: 6   RLRIKGVVLSYRRSKRTQHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYRSSG-------- 57

Query: 140 RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
                R I GKV R HG+SG+VRA+F RNLP   +G  V + LYPSNI
Sbjct: 58  -----RVIKGKVVRTHGNSGAVRARFERNLPGQALGTSVEVKLYPSNI 100

Length = 100

>gnl|CDD|179831 PRK04337, PRK04337, 50S ribosomal protein L35Ae; Validated

 Score = 58.5 bits (142), Expect = 7e-12
 Identities = 23/98 (23%), Positives = 43/98 (43%), Gaps = 14/98 (14%)

Query: 83  ARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKS 142
            + +   ++RG+  Q+    ++     + +E+A   +G++ +  +K  T           
Sbjct: 3   MKGVILSYRRGKNTQYNRQVIIKPLGVDDREEAAKLIGRKVI--WKDPTGNK-------- 52

Query: 143 RLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRI 180
                 GK+ R HG+ G VRA+F   LP   +G  V I
Sbjct: 53  ----YVGKIVRVHGNRGEVRARFKPGLPGQALGDYVEI 86

Length = 87

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	187
PTZ00041	120	60S ribosomal protein L35a; Provisional	100.0
KOG0887|consensus	111		100.0
PF01247	95	Ribosomal_L35Ae: Ribosomal protein L35Ae; InterPro	100.0
PRK04337	87	50S ribosomal protein L35Ae; Validated	100.0
COG2451	100	Ribosomal protein L35AE/L33A [Translation, ribosom	100.0
PF09853	53	DUF2080: Putative transposon-encoded protein (DUF2	94.79
PF01782	84	RimM: RimM N-terminal domain; InterPro: IPR002676	91.05
PRK14591	169	rimM 16S rRNA-processing protein RimM; Provisional	87.55
TIGR02273	165	16S_RimM 16S rRNA processing protein RimM. This fa	85.89
PRK14592	165	rimM 16S rRNA-processing protein RimM; Provisional	85.21
PRK13829	162	rimM 16S rRNA-processing protein RimM; Provisional	83.68
PF01782	84	RimM: RimM N-terminal domain; InterPro: IPR002676	82.77
PRK13828	161	rimM 16S rRNA-processing protein RimM; Provisional	81.72
PRK00122	172	rimM 16S rRNA-processing protein RimM; Provisional	80.19

>PTZ00041 60S ribosomal protein L35a; Provisional

Probab=100.00  E-value=1e-59  Score=370.58  Aligned_cols=112  Identities=55%  Similarity=0.985  Sum_probs=106.2

Q ss_pred             hccccccCCCceEEEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEe
Q psy4327          70 KHKRLRLRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWG  149 (187)
Q Consensus        70 k~~~~~~~~~RLyvKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWG  149 (187)
                      +..+....++|||++|+|+|||||++||+|||||||||||++++||+|||||||||||++++.      .+++++|+|||
T Consensus         9 ~~~~~~~~~~Rly~kgv~lgYkRg~~nQ~~~~aLlKieGV~~~~~a~fYlGKrvayvyka~~~------~~~~k~RviwG   82 (120)
T PTZ00041          9 KKTNRKKKPVRLYVKAVFLGYKRSKVNQYPNVALLKIEGVNTREDARFYLGKRVAYVYKAKKL------KNGTKFRAIWG   82 (120)
T ss_pred             ecccCCcCCcceEEEEEEEEeccccccCCCceEEEEecCcCChhhhHhhccceEEEEEcCccc------cCCcceeEEEE
Confidence            344566788899999999999999999999999999999999999999999999999999876      47899999999


Q ss_pred             EEEcccCCCceEEEEeCCCCCccCCCCeEEEEEeecCC
Q psy4327         150 KVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI  187 (187)
Q Consensus       150 KVtR~HGNSGvVRAKFk~NLPpqAiG~rVRVmLYPS~I  187 (187)
                      ||+|+|||||+|||+|++||||||||++||||||||+|
T Consensus        83 KVtR~HGnsGvVrAkF~~nLPp~A~G~~VrVmlyPs~i  120 (120)
T PTZ00041         83 KITRPHGNSGVVRARFNKNLPPKAIGSRVRVFLYPSNI  120 (120)
T ss_pred             EEEcccCCCcEEEEEeCCCCChHHcCCeEEEEEccCCC
Confidence            99999999999999999999999999999999999998

>KOG0887|consensus

Probab=100.00  E-value=2e-55  Score=342.03  Aligned_cols=105  Identities=66%  Similarity=1.137  Sum_probs=101.1

Q ss_pred             CCCceEEEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccC
Q psy4327          77 RHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHG  156 (187)
Q Consensus        77 ~~~RLyvKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HG  156 (187)
                      ..+|||++|+|+||+||+++|+||++|||||||+++|||+|||||||+||||++..      .+++++|+|||||||+||
T Consensus         7 e~~rl~vk~~~~~~kr~~r~~~~~t~llkIEGv~skeEa~fYlGkR~~yvYKa~~~------~~~~k~RvIWGkVTr~HG   80 (111)
T KOG0887|consen    7 ERGRLYVKGTFLGYKRGKRNQHPNTSLLKIEGVYSKEEASFYLGKRCVYVYKAKPE------VRGSKTRVIWGKVTRPHG   80 (111)
T ss_pred             ccceeEeeeEEeeeeecccccCCCcEEEEEecccchhhhheeecCcEEEEEecCCC------CCCceEEEEEEEEecccC
Confidence            34899999999999999999999999999999999999999999999999999743      478999999999999999


Q ss_pred             CCceEEEEeCCCCCccCCCCeEEEEEeecCC
Q psy4327         157 SSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI  187 (187)
Q Consensus       157 NSGvVRAKFk~NLPpqAiG~rVRVmLYPS~I  187 (187)
                      |||+|||+|.+||||+|||++||||||||+|
T Consensus        81 NsG~VrAkF~~Nlp~Ka~G~rvrVmLYps~i  111 (111)
T KOG0887|consen   81 NSGVVRAKFTSNLPPKAMGHRVRVMLYPSNI  111 (111)
T ss_pred             CcceEEEEeccCCChhHcCcEEEEEEecccC
Confidence            9999999999999999999999999999998

>PF01247 Ribosomal_L35Ae: Ribosomal protein L35Ae; InterPro: IPR001780 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=100.00  E-value=1e-52  Score=319.32  Aligned_cols=95  Identities=64%  Similarity=1.107  Sum_probs=86.9

Q ss_pred             eEEEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccCCCce
Q psy4327          81 LYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGS  160 (187)
Q Consensus        81 LyvKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HGNSGv  160 (187)
                      ||+||+|+|||||++||||||||||||||++++||+|||||||+|||++++.      .++++.|+|||||+|+|||||+
T Consensus         1 ly~kgv~~gykRg~~~Q~~~~aLlKiegV~~~~~a~fylGKrv~yvyk~~~~------~~~~k~r~iwGkV~r~HGnsGv   74 (95)
T PF01247_consen    1 LYVKGVFLGYKRGKRNQHPNTALLKIEGVNTKEDAQFYLGKRVAYVYKAKNK------KNGSKGRVIWGKVTRPHGNSGV   74 (95)
T ss_dssp             -EEEEEEEEEEEETSTTCEEEEEEEESS-STCHHHHTTTT-EEEEEECE-SS------STTECSEEEEEEEEEESTTTTE
T ss_pred             CeeeEEEEeecccccccCCCeeEEeecCccCHHHHHhhcCcEEEEEEecccc------cCCCcEeEEEEEEEeEEcCCCE
Confidence            8999999999999999999999999999999999999999999999999887      3689999999999999999999


Q ss_pred             EEEEeCCCCCccCCCCeEEEE
Q psy4327         161 VRAKFHRNLPAIYMGRKVRIM  181 (187)
Q Consensus       161 VRAKFk~NLPpqAiG~rVRVm  181 (187)
                      |||+|++||||||||++||||
T Consensus        75 VrAkF~~nLP~~a~G~~VrVm   95 (95)
T PF01247_consen   75 VRAKFKKNLPPQAIGSRVRVM   95 (95)
T ss_dssp             EEEEESS--STTGCSSEEEEE
T ss_pred             EEEEeCCCCChHHcCCEEEeC
Confidence            999999999999999999999

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 ribosomal L35A eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of: Vertebrate L35A. Caenorhabditis elegans L35A (F10E7.7). Saccharomyces cerevisiae L37A/L37B (Rp47). Plant L35A. Pyrococcus woesei L35A homologue []. These proteins have 87 to 110 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_j 2LP6_A 1SQR_A 4A18_H 4A1D_H 4A19_H 4A1B_H 3IZS_j.

>PRK04337 50S ribosomal protein L35Ae; Validated

Probab=100.00  E-value=1.6e-47  Score=287.70  Aligned_cols=85  Identities=25%  Similarity=0.503  Sum_probs=81.9

Q ss_pred             EEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccCCCceEE
Q psy4327          83 ARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSVR  162 (187)
Q Consensus        83 vKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HGNSGvVR  162 (187)
                      +||+|+|||||++||+|||||||||||++++||+|||||||+|||++       |       |+|||||||+|||||+||
T Consensus         3 ~kgv~~gykRg~~nQ~~~~aLlkiegv~~~~~a~fylGKrv~yvyk~-------g-------rviwGKItR~HGnsGvVr   68 (87)
T PRK04337          3 MKGVILSYRRGKNTQYNRQVIIKPLGVDDREEAAKLIGRKVIWKDPT-------G-------NKYVGKIVRVHGNRGEVR   68 (87)
T ss_pred             ceEEEEEeccccCccCCceEEEEEcCcCCHHHHHhhcCceEEEEeCC-------C-------CEEEEEEEeeeCCCceEE
Confidence            69999999999999999999999999999999999999999999975       1       799999999999999999


Q ss_pred             EEeCCCCCccCCCCeEEEE
Q psy4327         163 AKFHRNLPAIYMGRKVRIM  181 (187)
Q Consensus       163 AKFk~NLPpqAiG~rVRVm  181 (187)
                      |+|++||||||||++|||.
T Consensus        69 AkF~~nLP~~a~G~~vrv~   87 (87)
T PRK04337         69 ARFKPGLPGQALGDYVEII   87 (87)
T ss_pred             EEECCCCChHHcCCEEEeC
Confidence            9999999999999999983

>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1e-44  Score=277.91  Aligned_cols=97  Identities=47%  Similarity=0.846  Sum_probs=92.7

Q ss_pred             CCceEEEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccCC
Q psy4327          78 HGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGS  157 (187)
Q Consensus        78 ~~RLyvKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HGN  157 (187)
                      ..|++++|+|+|||||+++|||+++|||||||+|++||+|||||+|+|+|+..             .|||||+|+|+|||
T Consensus         4 ~~r~~ikgv~lsyrR~k~~q~P~~~liKi~gv~s~~eA~~y~gk~v~yk~~~~-------------G~Vi~G~V~R~HGn   70 (100)
T COG2451           4 GHRLRIKGVVLSYRRSKRTQHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYRSS-------------GRVIKGKVVRTHGN   70 (100)
T ss_pred             cceEEEeeEEEEEEecccccCCceEEEEEecCCCHHHHHhhhccEEEEEeCCC-------------CcEEEEEEEEecCC
Confidence            36999999999999999999999999999999999999999999999998641             28999999999999


Q ss_pred             CceEEEEeCCCCCccCCCCeEEEEEeecCC
Q psy4327         158 SGSVRAKFHRNLPAIYMGRKVRIMLYPSNI  187 (187)
Q Consensus       158 SGvVRAKFk~NLPpqAiG~rVRVmLYPS~I  187 (187)
                      ||+|||+|.+||||||+|..|+||||||+|
T Consensus        71 sGaVrarF~~~LP~qa~G~~v~v~ly~~~~  100 (100)
T COG2451          71 SGAVRARFERNLPGQALGTSVEVKLYPSNI  100 (100)
T ss_pred             cceEEEEecCCCCchhcCcEEEEEEccCCC
Confidence            999999999999999999999999999986

>PF09853 DUF2080: Putative transposon-encoded protein (DUF2080); InterPro: IPR019205 This entry, found in various hypothetical archaeal proteins, has no known function

Probab=94.79  E-value=0.051  Score=38.34  Aligned_cols=34  Identities=38%  Similarity=0.681  Sum_probs=27.2

Q ss_pred             eEEeEEEcccCCCceEEEEeCCCCCccCCCCeEEEEEee
Q psy4327         146 AIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYP  184 (187)
Q Consensus       146 vIWGKVtR~HGNSGvVRAKFk~NLPpqAiG~rVRVmLYP  184 (187)
                      +++|+|+ +||||    |++..+||+.-+|.++.|.+..
T Consensus        17 ~~~~~vk-~~Gns----a~v~p~lPkeyiGK~v~iiil~   50 (53)
T PF09853_consen   17 TFIGVVK-PFGNS----ARVYPSLPKEYIGKKVIIIILE   50 (53)
T ss_pred             EEEEEEE-ecCcc----eeEcCCCChHHcCcEEEEEEeC
Confidence            4555555 99999    4677999999999999987643

>PF01782 RimM: RimM N-terminal domain; InterPro: IPR002676 The RimM protein is essential for efficient processing of 16S rRNA []

Probab=91.05  E-value=0.66  Score=32.80  Aligned_cols=40  Identities=13%  Similarity=0.161  Sum_probs=28.3

Q ss_pred             eEEEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEE
Q psy4327          81 LYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVF  125 (187)
Q Consensus        81 LyvKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaY  125 (187)
                      .|..-.+.+++     .+.+..|++++||+|+++|+.|.|..+..
T Consensus        41 ~~~~~~v~~~~-----~~~~~~i~~~~gi~~r~~Ae~l~g~~l~v   80 (84)
T PF01782_consen   41 EWRPLKVESVR-----PHGKSLIVKFEGIDDREAAEALRGCELYV   80 (84)
T ss_dssp             EEEEEEEEEEE-----EETTEEEEEETT--SHHHHHTTTT-EEEE
T ss_pred             ceEEEEEEEEE-----EeCCEEEEEEcCCCCHHHHHhhCCCEEEE
Confidence            34445566665     33789999999999999999999987643

The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes [].; GO: 0006364 rRNA processing; PDB: 2QGG_A 3A1P_C 2DOG_A 2DYI_A 3H9N_A 2F1L_A.

>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional

Probab=87.55  E-value=0.84  Score=37.08  Aligned_cols=31  Identities=16%  Similarity=0.254  Sum_probs=25.8

Q ss_pred             CCCCeeEEeecCCCChhhhhhhccceEEEEEe
Q psy4327          97 QHPNTSLLAIEKCNTKEDARFYVGKRCVFLYK  128 (187)
Q Consensus        97 Q~pntALLKIEGV~tkedA~FYlGKRVaYVYK  128 (187)
                      ++.+..|++++||+++++|+.|.|..+. +.+
T Consensus        59 ~~~~~~lv~f~gi~dr~~Ae~l~g~~l~-v~~   89 (169)
T PRK14591         59 KRADKVYIKLANINNADTAKKYVNALIG-VPK   89 (169)
T ss_pred             EECCEEEEEEcCCCCHHHHHHhcCCEEE-EEH
Confidence            3457789999999999999999998774 444

>TIGR02273 16S_RimM 16S rRNA processing protein RimM

Probab=85.89  E-value=0.78  Score=36.74  Aligned_cols=28  Identities=18%  Similarity=0.232  Sum_probs=24.2

Q ss_pred             CCCeeEEeecCCCChhhhhhhccceEEE
Q psy4327          98 HPNTSLLAIEKCNTKEDARFYVGKRCVF  125 (187)
Q Consensus        98 ~pntALLKIEGV~tkedA~FYlGKRVaY  125 (187)
                      +.+..||+++|++|+++|+.+.|..+..
T Consensus        55 ~~~~~lv~f~gi~~~~~Ae~L~g~~l~i   82 (165)
T TIGR02273        55 QNNKLIVKFEGIDDREAAEALKGLELFV   82 (165)
T ss_pred             ECCEEEEEECCCCCHHHHHHhcCCEEEE
Confidence            3457899999999999999999987644

This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide.

>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional

Probab=85.21  E-value=1.5  Score=35.39  Aligned_cols=29  Identities=17%  Similarity=0.219  Sum_probs=24.9

Q ss_pred             CCCCeeEEeecCCCChhhhhhhccceEEE
Q psy4327          97 QHPNTSLLAIEKCNTKEDARFYVGKRCVF  125 (187)
Q Consensus        97 Q~pntALLKIEGV~tkedA~FYlGKRVaY  125 (187)
                      ++.+..|++++||+|+++|+.|.|..+..
T Consensus        51 ~~~~~~lv~f~gi~~~~~Ae~l~g~~l~v   79 (165)
T PRK14592         51 IGANLVIAKISGINSRTEAELLRNKKLYV   79 (165)
T ss_pred             ecCCEEEEEEcCCCCHHHHHHhcCCEEEE
Confidence            44567899999999999999999998754

>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional

Probab=83.68  E-value=1.1  Score=36.24  Aligned_cols=31  Identities=19%  Similarity=0.200  Sum_probs=25.9

Q ss_pred             CCCCeeEEeecCCCChhhhhhhccceEEEEEe
Q psy4327          97 QHPNTSLLAIEKCNTKEDARFYVGKRCVFLYK  128 (187)
Q Consensus        97 Q~pntALLKIEGV~tkedA~FYlGKRVaYVYK  128 (187)
                      .+.+..|++++||+|+++|+.|.|..+. +.+
T Consensus        48 ~~~~~~l~~f~gi~~r~~Ae~l~g~~l~-v~~   78 (162)
T PRK13829         48 RVGPELVLHLAGVTSREGAEALVGLRVY-ADD   78 (162)
T ss_pred             EECCEEEEEECCCCCHHHHHHhcCCEEE-EEH
Confidence            4456689999999999999999998764 444

>PF01782 RimM: RimM N-terminal domain; InterPro: IPR002676 The RimM protein is essential for efficient processing of 16S rRNA []

Probab=82.77  E-value=1.3  Score=31.30  Aligned_cols=28  Identities=25%  Similarity=0.627  Sum_probs=23.0

Q ss_pred             EeEEEcccCCCceEEEEeCCCCCccCCC
Q psy4327         148 WGKVTRPHGSSGSVRAKFHRNLPAIYMG  175 (187)
Q Consensus       148 WGKVtR~HGNSGvVRAKFk~NLPpqAiG  175 (187)
                      .|+|.++||-.|-|++..-.+.|.....
T Consensus         2 vG~I~~~hGlkG~vkv~~~td~~~~~~~   29 (84)
T PF01782_consen    2 VGRIGKPHGLKGEVKVRPFTDFPERLFN   29 (84)
T ss_dssp             EEEEEEEETTTTEEEEEE-SSSGGGGGG
T ss_pred             EEEECCCEecCEEEEEEEecCCHHHHcC
Confidence            4999999999999999999887765443

The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes [].; GO: 0006364 rRNA processing; PDB: 2QGG_A 3A1P_C 2DOG_A 2DYI_A 3H9N_A 2F1L_A.

>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional

Probab=81.72  E-value=1.4  Score=35.53  Aligned_cols=29  Identities=14%  Similarity=0.110  Sum_probs=24.8

Q ss_pred             CCCCeeEEeecCCCChhhhhhhccceEEE
Q psy4327          97 QHPNTSLLAIEKCNTKEDARFYVGKRCVF  125 (187)
Q Consensus        97 Q~pntALLKIEGV~tkedA~FYlGKRVaY  125 (187)
                      ++.+..|++++||+|+++|+.|.|..+..
T Consensus        39 ~~~~~~lv~f~gi~dr~~Ae~L~g~~l~i   67 (161)
T PRK13828         39 PAKDGLVARLKGVATREAAEALRGLELYV   67 (161)
T ss_pred             EECCEEEEEECCCCCHHHHHHhcCCEEEE
Confidence            34566899999999999999999987754

>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional

Probab=80.19  E-value=1.7  Score=35.14  Aligned_cols=28  Identities=14%  Similarity=0.197  Sum_probs=24.0

Q ss_pred             CCCeeEEeecCCCChhhhhhhccceEEE
Q psy4327          98 HPNTSLLAIEKCNTKEDARFYVGKRCVF  125 (187)
Q Consensus        98 ~pntALLKIEGV~tkedA~FYlGKRVaY  125 (187)
                      +.+..||+++|++++++|+.|.|..+..
T Consensus        60 ~~~~~lvkf~gi~~~~~Ae~l~g~~l~i   87 (172)
T PRK00122         60 HKGFLIVKFEGVDDRNAAEALKGCELFV   87 (172)
T ss_pred             ECCEEEEEECCCCCHHHHHHhCCCEEEE
Confidence            3456899999999999999999987644

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	187
3izr_j	111	Localization Of The Large Subunit Ribosomal Protein		1e-29
3zf7_l	149	High-resolution Cryo-electron Microscopy Structure		8e-24
3izs_j	107	Localization Of The Large Subunit Ribosomal Protein		9e-24
4a18_H	113	T.Thermophila 60s Ribosomal Subunit In Complex With		7e-21
1sqr_A	95	Solution Structure Of The 50s Ribosomal Protein L35		2e-07
3j21_c	87	Promiscuous Behavior Of Proteins In Archaeal Riboso		8e-07

>pdb|3IZR|JJ Chain j, Localization Of The Large Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 111

Iteration: 1
 Score =  125 bits (314), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 61/108 (56%), Positives = 74/108 (68%), Gaps = 6/108 (5%)
Query: 80  RLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSK 139
           RLY R    G+KR + NQ+ NTSLL IE  NTKE+  +Y GKR  ++YKAKTK       
Sbjct: 10  RLYVRGTILGYKRSKSNQYENTSLLQIEGVNTKEEVGWYAGKRIAYVYKAKTKS------ 63
Query: 140 RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
             S +R IWGKVTRPHG+SG VRAKF  NLP   MG+KVR+ +YPS+I
Sbjct: 64  NDSTIRCIWGKVTRPHGNSGVVRAKFRSNLPPTSMGKKVRVFMYPSSI 111

>pdb|3ZF7|LL Chain l, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 149

Iteration: 1
 Score =  106 bits (264), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 55/113 (48%), Positives = 76/113 (67%), Gaps = 5/113 (4%)
Query: 80  RLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKA-KTKELKPHS 138
           RLY +    G+ RG   Q+ NT+L+ IE  NT EDA++YVGKR  ++Y   K K     S
Sbjct: 37  RLYMKGTLAGYTRGLHGQNKNTALVRIENVNTTEDAKWYVGKRVCYVYHGYKIKRCVRWS 96
Query: 139 K---RKSRLRAIWGKVTRPHGSSGSVRAKFH-RNLPAIYMGRKVRIMLYPSNI 187
           K   R+S  RAIWG++TRPHG+SG+VR KF+  ++PA  +GR++R+ LYPS I
Sbjct: 97  KAPARRSNTRAIWGRITRPHGTSGTVRVKFNGSSVPASAIGRRIRVYLYPSRI 149

>pdb|3IZS|JJ Chain j, Localization Of The Large Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 107

Iteration: 1
 Score =  106 bits (264), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 54/108 (50%), Positives = 72/108 (66%), Gaps = 6/108 (5%)
Query: 80  RLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSK 139
           RLY +     ++R +R  +PN SL+ IE   T +DA+FY+GKR  ++Y+A +KE+     
Sbjct: 6   RLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRA-SKEV----- 59
Query: 140 RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
           R S++R +WGKVTR HG+SG VRA F  NLPA   G  VRI LYPSNI
Sbjct: 60  RGSKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 107

>pdb|4A18|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 1 Length = 113

Iteration: 1
 Score = 96.7 bits (239), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 45/106 (42%), Positives = 66/106 (62%), Gaps = 7/106 (6%)
Query: 80  RLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSK 139
           RL+ +A FTGF+R +  Q+ N +LL ++  NTKED  FY GKR V++YK + K       
Sbjct: 13  RLWVKAAFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQKKN------ 66
Query: 140 RKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPS 185
             S  R IWG++ + HG++G   A+F  NLP   +G  +R+MLYP+
Sbjct: 67  -GSNYRTIWGRIGKAHGNNGVAVARFAHNLPPQAIGSVLRVMLYPN 111

>pdb|1SQR|A Chain A, Solution Structure Of The 50s Ribosomal Protein L35ae From Pyrococcus Furiosus. Northeast Structural Genomics Consortium Target Pfr48. Length = 95

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/99 (27%), Positives = 53/99 (53%), Gaps = 14/99 (14%)
Query: 84  RAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSR 143
           + +   ++R + NQH N  ++     N++E+A   +G+  + L+K+ + ++         
Sbjct: 4   KGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGR--LVLWKSPSGKI--------- 52
Query: 144 LRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIML 182
              + GK+ R HG+ G+VRA+F + LP   +G  V I+L
Sbjct: 53  ---LKGKIVRVHGTKGAVRARFEKGLPGQALGDYVEIVL 88

>pdb|3J21|CC Chain c, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Proteins) Length = 87

Iteration: 1
 Score = 50.1 bits (118), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 26/98 (26%), Positives = 52/98 (53%), Gaps = 14/98 (14%)
Query: 84  RAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSR 143
           + +   ++R + NQH N  ++     N++E+A   +G+  + L+K+ + ++         
Sbjct: 4   KGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGR--LVLWKSPSGKI--------- 52
Query: 144 LRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIM 181
              + GK+ R HG+ G+VRA+F + LP   +G  V I+
Sbjct: 53  ---LKGKIVRVHGTKGAVRARFEKGLPGQALGDYVEIV 87

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	187
3izc_j	107	60S ribosomal protein RPL33 (L35AE); eukaryotic ri	7e-45
3iz5_J	166	60S ribosomal protein L12 (L11P); eukaryotic ribos	3e-44
4a18_H	113	RPL35A; ribosome, eukaryotic initiation factor 6,	1e-41
1sqr_A	95	50S ribosomal protein L35AE; PFR48, structure, aut	2e-39

>4a18_H RPL35A; ribosome, eukaryotic initiation factor 6, EIF6, transla large ribosomal subunit, rRNA; 3.52A {Tetrahymena thermophila} PDB: 4a19_H 4a1b_H 4a1d_H Length = 113

 Score =  135 bits (340), Expect = 1e-41
 Identities = 46/117 (39%), Positives = 68/117 (58%), Gaps = 7/117 (5%)

Query: 69  KKHKRLRLRHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYK 128
            K     +   RL+ +A FTGF+R +  Q+ N +LL ++  NTKED  FY GKR V++YK
Sbjct: 2   AKTSTSPVAPTRLWVKAAFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYK 61

Query: 129 AKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPS 185
            +        K  S  R IWG++ + HG++G   A+F  NLP   +G  +R+MLYP+
Sbjct: 62  GQ-------KKNGSNYRTIWGRIGKAHGNNGVAVARFAHNLPPQAIGSVLRVMLYPN 111

>1sqr_A 50S ribosomal protein L35AE; PFR48, structure, autostructure, northeast structural genomics consortium, beta-barrel; NMR {Pyrococcus furiosus} SCOP: b.43.3.3 PDB: 2lp6_A Length = 95

 Score =  128 bits (324), Expect = 2e-39
 Identities = 25/107 (23%), Positives = 51/107 (47%), Gaps = 14/107 (13%)

Query: 81  LYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKR 140
           +  + +   ++R + NQH N  ++     N++E+A   +G+  ++   +           
Sbjct: 1   MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSG---------- 50

Query: 141 KSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI 187
               + + GK+ R HG+ G+VRA+F + LP   +G  V I+L   + 
Sbjct: 51  ----KILKGKIVRVHGTKGAVRARFEKGLPGQALGDYVEIVLEHHHH 93

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	187
3iz5_j	111	60S ribosomal protein L35A (L35AE); eukaryotic rib	100.0
3izc_j	107	60S ribosomal protein RPL33 (L35AE); eukaryotic ri	100.0
4a18_H	113	RPL35A; ribosome, eukaryotic initiation factor 6,	100.0
1sqr_A	95	50S ribosomal protein L35AE; PFR48, structure, aut	100.0
3j21_c	87	50S ribosomal protein L35AE; archaea, archaeal, KI	100.0
1wb1_A	482	Translation elongation factor SELB; selenocysteine	88.17
3h9n_A	177	Ribosome maturation factor RIMM; structural genomi	82.26

>4a18_H RPL35A; ribosome, eukaryotic initiation factor 6, EIF6, transla large ribosomal subunit, rRNA; 3.52A {Tetrahymena thermophila} PDB: 4a19_H 4a1b_H 4a1d_H

Probab=100.00  E-value=7.9e-59  Score=361.34  Aligned_cols=104  Identities=43%  Similarity=0.848  Sum_probs=100.2

Q ss_pred             CCCceEEEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccC
Q psy4327          77 RHGRLYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHG  156 (187)
Q Consensus        77 ~~~RLyvKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HG  156 (187)
                      +++|||+||+|+|||||++||||||||||||||++++||+|||||||+||||++++       .++++|+|||||||+||
T Consensus        10 ~~~rly~Kgv~lgYkRg~~nQ~~~taLlKIeGV~~~~~a~fylGKrvayvykak~~-------~g~k~RviwGKVtR~HG   82 (113)
T 4a18_H           10 APTRLWVKAAFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQKK-------NGSNYRTIWGRIGKAHG   82 (113)
T ss_dssp             CSCCCCEEEEEEEEEEETTEEEEEEEEEEETTCCSHHHHHTTTTCEEEEEEEEEEE-------TTEEEEEEEEEEEEEET
T ss_pred             ccceeEEEEEEEecccccCCCCCCeEEEEEcCcCCHHHHHhhcCCeEEEEEecCCC-------CCCeEEEEEEEEEeeeC
Confidence            67899999999999999999999999999999999999999999999999999874       46899999999999999


Q ss_pred             CCceEEEEeCCCCCccCCCCeEEEEEeecCC
Q psy4327         157 SSGSVRAKFHRNLPAIYMGRKVRIMLYPSNI  187 (187)
Q Consensus       157 NSGvVRAKFk~NLPpqAiG~rVRVmLYPS~I  187 (187)
                      |||+|||+|++||||||||++||||||||+.
T Consensus        83 nsGvVrAkF~~nLP~kA~G~~VrVmLyPs~~  113 (113)
T 4a18_H           83 NNGVAVARFAHNLPPQAIGSVLRVMLYPNRA  113 (113)
T ss_dssp             TTTEEEEEESSCCCGGGGGSEEEEECCCCCC
T ss_pred             CCCeEEEEeCCCCChHHcCCeEEEEEecCCC
Confidence            9999999999999999999999999999973

>1sqr_A 50S ribosomal protein L35AE; PFR48, structure, autostructure, northeast structural genomics consortium, beta-barrel; NMR {Pyrococcus furiosus} SCOP: b.43.3.3 PDB: 2lp6_A

Probab=100.00  E-value=1.4e-50  Score=307.23  Aligned_cols=88  Identities=28%  Similarity=0.548  Sum_probs=84.3

Q ss_pred             EEEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccCCCceE
Q psy4327          82 YARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSV  161 (187)
Q Consensus        82 yvKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HGNSGvV  161 (187)
                      |+||+|+|||||++||+|||||||||||++++||+|||||||+|||+++              |+|||||||+|||||+|
T Consensus         2 ~~Kgv~lgYkRg~~nQ~~~~aLlkIegV~~k~~a~fYlGKrvayvyka~--------------rviwGKVtR~HGnsGvV   67 (95)
T 1sqr_A            2 RIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSG--------------KILKGKIVRVHGTKGAV   67 (95)
T ss_dssp             CCEEEEEEEECCSSSSSCCEEEEEESCCCCHHHHHHHTTCEEEECCSTT--------------CCEEEEEEEESSSSSCE
T ss_pred             eeeEEEEeeccccCcCCCceEEEEEcCCCCHHHHHhhcCCeEEEEECCC--------------CEEEEEEEeeeCCCCEE
Confidence            8999999999999999999999999999999999999999999999773              89999999999999999


Q ss_pred             EEEeCCCCCccCCCCeEEEEEe
Q psy4327         162 RAKFHRNLPAIYMGRKVRIMLY  183 (187)
Q Consensus       162 RAKFk~NLPpqAiG~rVRVmLY  183 (187)
                      ||+|++||||||||++|||||-
T Consensus        68 rAkF~~nLP~kA~G~~VrVml~   89 (95)
T 1sqr_A           68 RARFEKGLPGQALGDYVEIVLE   89 (95)
T ss_dssp             EEECSSCCSSSCTTCEEECC--
T ss_pred             EEEeCCCCChHHcCCEEEEEEe
Confidence            9999999999999999999984

>3j21_c 50S ribosomal protein L35AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} PDB: 1sqr_A 2lp6_A

Probab=100.00  E-value=1e-47  Score=287.55  Aligned_cols=84  Identities=29%  Similarity=0.568  Sum_probs=80.7

Q ss_pred             EEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccCCCceEE
Q psy4327          83 ARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSVR  162 (187)
Q Consensus        83 vKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HGNSGvVR  162 (187)
                      +||+|+|||||++||||||||||||||++++||+|||||||+|||++       |       ++|||||||+|||||+||
T Consensus         3 ~Kg~~~gykRg~~nQ~~~taLlkieGV~~~~~a~fylGKrvayv~~~-------g-------~~iwGKVtr~HGnsGvVr   68 (87)
T 3j21_c            3 IKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPS-------G-------KILKGKIVRVHGTKGAVR   68 (87)
T ss_dssp             EEEEEEEESCCSSCCCTTCEEEEESSCCSHHHHGGGTTCEEEECCSS-------S-------CCEEEEEEEECCSSSCEE
T ss_pred             eeEEEEecccccCcCCCCeEEEEEcCcCCHHHHHhhcCceEEEEeCC-------C-------CEEEEEEEeeeCCCCeEE
Confidence            79999999999999999999999999999999999999999999963       1       489999999999999999


Q ss_pred             EEeCCCCCccCCCCeEEE
Q psy4327         163 AKFHRNLPAIYMGRKVRI  180 (187)
Q Consensus       163 AKFk~NLPpqAiG~rVRV  180 (187)
                      |+|++||||||||++|||
T Consensus        69 AkF~~nLP~~a~G~~Vri   86 (87)
T 3j21_c           69 ARFEKGLPGQALGDYVEI   86 (87)
T ss_dssp             EEESSCCCSSCSCCEECC
T ss_pred             EEeCCCCChHHcCCeEEe
Confidence            999999999999999997

>1wb1_A Translation elongation factor SELB; selenocysteine, protein synthesis, selenium, ribosome; HET: GDP DXC; 3.0A {Methanococcus maripaludis} SCOP: b.43.3.1 b.43.3.1 b.44.1.1 c.37.1.8 PDB: 1wb2_A* 1wb3_A*

Probab=88.17  E-value=0.13  Score=45.87  Aligned_cols=68  Identities=19%  Similarity=0.218  Sum_probs=52.0

Q ss_pred             CCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccCCCceEEEEeCCCCCccCCCC
Q psy4327          97 QHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGR  176 (187)
Q Consensus        97 Q~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HGNSGvVRAKFk~NLPpqAiG~  176 (187)
                      ++.++++++=- ..+..|.++|+|.+|...+         |        -|+|.|-.+.|.||.+++.|.-+|.++   +
T Consensus       413 ~~~~~~i~~~l-f~~~~~~~~f~g~~v~~~~---------g--------~~~G~I~~~fg~~G~~~~~f~~~~~~~---d  471 (482)
T 1wb1_A          413 IDKGRTVIDGL-AQSKVAAEKLIGEEISIEG---------K--------DIVGKIKGTFGTKGLLTAEFSGNVENR---D  471 (482)
T ss_dssp             CCSSCCEETTS-CSSHHHHHHSCSCCCEETT---------T--------CCCBCCCCCBTTTTBBCCCBSSCCCSS---C
T ss_pred             EcCCEEEEEcC-ccchhhhHHhcCcEEEEcC---------C--------ceEEEEeccCCCCceEEEEecCCCCCC---C
Confidence            46778877622 4566789999999987721         2        256999999999999999999998764   5


Q ss_pred             eEEEEEeec
Q psy4327         177 KVRIMLYPS  185 (187)
Q Consensus       177 rVRVmLYPS  185 (187)
                      .|.+-||-.
T Consensus       472 ~v~~~~~~~  480 (482)
T 1wb1_A          472 KVILNRLRR  480 (482)
T ss_dssp             EEEEECCCS
T ss_pred             eeeeehhhc
Confidence            677667653

>3h9n_A Ribosome maturation factor RIMM; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.70A {Haemophilus influenzae}

Probab=82.26  E-value=1.8  Score=34.31  Aligned_cols=41  Identities=7%  Similarity=0.139  Sum_probs=31.5

Q ss_pred             EEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEecc
Q psy4327          84 RAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAK  130 (187)
Q Consensus        84 KgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK  130 (187)
                      .-.+.++|.     +.+..|++++||+++++|+.|.|..+ ||.+..
T Consensus        46 ~~~v~~~r~-----~~~~~lvkf~gi~dr~~Ae~L~G~~l-~v~~~~   86 (177)
T 3h9n_A           46 SIELENWRY-----HNHEIIVKLKGVDDREAAQILANVEI-GVDLSV   86 (177)
T ss_dssp             EECEEEEEE-----SSSCEEEEESSCCSHHHHHTTTTCEE-EEECCC
T ss_pred             EEEEEEEEE-----eCCEEEEEEcCCCCHHHHHHhcCCEE-EEEHHH
Confidence            334556664     34668999999999999999999987 666653

---

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	187
d1sqra_	87	b.43.3.3 (A:) Ribosomal protein L35ae {Pyrococcus	4e-37

>d1sqra_ b.43.3.3 (A:) Ribosomal protein L35ae {Pyrococcus furiosus [TaxId: 2261]} Length = 87

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Ribosomal protein L35ae
domain: Ribosomal protein L35ae
species: Pyrococcus furiosus [TaxId: 2261]

 Score =  121 bits (306), Expect = 4e-37
 Identities = 24/101 (23%), Positives = 49/101 (48%), Gaps = 14/101 (13%)

Query: 81  LYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKR 140
           +  + +   ++R + NQH N  ++     N++E+A   +G+  ++   +           
Sbjct: 1   MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSG---------- 50

Query: 141 KSRLRAIWGKVTRPHGSSGSVRAKFHRNLPAIYMGRKVRIM 181
               + + GK+ R HG+ G+VRA+F + LP   +G  V I+
Sbjct: 51  ----KILKGKIVRVHGTKGAVRARFEKGLPGQALGDYVEIV 87

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	187
d1sqra_	87	Ribosomal protein L35ae {Pyrococcus furiosus [TaxI	100.0
d2f1la2	89	16S rRNA processing protein RimM, N-terminal domai	93.32
d1wb1a2	79	Elongation factor SelB, domains 2 and 4 {Methanoco	87.67

>d1sqra_ b.43.3.3 (A:) Ribosomal protein L35ae {Pyrococcus furiosus [TaxId: 2261]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Ribosomal protein L35ae
domain: Ribosomal protein L35ae
species: Pyrococcus furiosus [TaxId: 2261]

Probab=100.00  E-value=8.7e-50  Score=296.84  Aligned_cols=87  Identities=28%  Similarity=0.547  Sum_probs=83.5

Q ss_pred             eEEEEEEEeeecccCCCCCCeeEEeecCCCChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccCCCce
Q psy4327          81 LYARAIFTGFKRGQRNQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGS  160 (187)
Q Consensus        81 LyvKgvflGYKRG~rnQ~pntALLKIEGV~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HGNSGv  160 (187)
                      ||+||+|+|||||++||+|||||||||||++++||+|||||||+|+|++              .|+|||||||+|||||+
T Consensus         1 lyvKgv~~gykRg~~nq~~~~~Llkiegv~~k~~a~fylGKrv~y~~~~--------------~r~iwGKVtr~HGnsGv   66 (87)
T d1sqra_           1 MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPS--------------GKILKGKIVRVHGTKGA   66 (87)
T ss_dssp             CCCEEEEEEEECCSSSSSCCEEEEEESCCCCHHHHHHHTTCEEEECCST--------------TCCEEEEEEEESSSSSC
T ss_pred             CeEEEEEEEeccccccCCCCEEEEEEcCcCCHHHHHhhcCcEEEEECCC--------------CcEEEeeEeeecCCCce
Confidence            8999999999999999999999999999999999999999999996643              27999999999999999


Q ss_pred             EEEEeCCCCCccCCCCeEEEE
Q psy4327         161 VRAKFHRNLPAIYMGRKVRIM  181 (187)
Q Consensus       161 VRAKFk~NLPpqAiG~rVRVm  181 (187)
                      |||+|++||||||||++||||
T Consensus        67 VrAkF~~nLP~qa~G~~VrVm   87 (87)
T d1sqra_          67 VRARFEKGLPGQALGDYVEIV   87 (87)
T ss_dssp             EEEECSSCCSSSCTTCEEECC
T ss_pred             EEEEecCCCChHHcCCEEEeC
Confidence            999999999999999999998

>d2f1la2 b.43.3.4 (A:7-95) 16S rRNA processing protein RimM, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: RimM N-terminal domain-like
domain: 16S rRNA processing protein RimM, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=93.32  E-value=0.02  Score=38.13  Aligned_cols=32  Identities=16%  Similarity=0.291  Sum_probs=26.8

Q ss_pred             CCCCCeeEEeecCCCChhhhhhhccceEEEEEe
Q psy4327          96 NQHPNTSLLAIEKCNTKEDARFYVGKRCVFLYK  128 (187)
Q Consensus        96 nQ~pntALLKIEGV~tkedA~FYlGKRVaYVYK  128 (187)
                      +++.+..+|+++||+|+++|+.++|+.+. +.+
T Consensus        53 ~~~~~~~~vk~~~i~~r~~Ae~l~g~~i~-i~~   84 (89)
T d2f1la2          53 RLHGKVLAAKLKGLDDREEARTFTGYEIC-IPR   84 (89)
T ss_dssp             EEETTEEEEEETTCCSHHHHHTTTTCEEE-EEG
T ss_pred             EecccEEEEEEcCCCCHHHHHHhCCCEEE-EEH
Confidence            35667899999999999999999999764 443

>d1wb1a2 b.43.3.1 (A:390-468) Elongation factor SelB, domains 2 and 4 {Methanococcus maripaludis [TaxId: 39152]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor SelB, domains 2 and 4
species: Methanococcus maripaludis [TaxId: 39152]

Probab=87.67  E-value=0.053  Score=38.22  Aligned_cols=50  Identities=24%  Similarity=0.391  Sum_probs=40.3

Q ss_pred             EeecCC-CChhhhhhhccceEEEEEeccccccCCCCCCCCceeeEEeEEEcccCCCceEEEEeCCCCC
Q psy4327         104 LAIEKC-NTKEDARFYVGKRCVFLYKAKTKELKPHSKRKSRLRAIWGKVTRPHGSSGSVRAKFHRNLP  170 (187)
Q Consensus       104 LKIEGV-~tkedA~FYlGKRVaYVYKaK~~~~~pg~~k~sk~RvIWGKVtR~HGNSGvVRAKFk~NLP  170 (187)
                      .=|||. .|+..|+.+||-+|-.          ||       .-|||||.-+||..|.+.|-|.-|.-
T Consensus        15 ~~IegLA~sK~~aEkLIGe~v~i----------~~-------k~i~Gkik~TfGTkG~l~adF~geV~   65 (79)
T d1wb1a2          15 TVIDGLAQSKVAAEKLIGEEISI----------EG-------KDIVGKIKGTFGTKGLLTAEFSGNVE   65 (79)
T ss_dssp             CEETTSCSSHHHHHHSCSCCCEE----------TT-------TCCCBCCCCCBTTTTBBCCCBSSCCC
T ss_pred             EEeeecccchhHHHhhcCcEEEe----------cC-------CceEEEEeccccCceEEEEEeccccC
Confidence            446776 5788899999998754          23       24799999999999999999998764