Psyllid ID: psy4238

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60-------
Protein Sequence
LGIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE
Secondary Structure (PSIPRED)
ccEEEEEEEEccEEEEEccEEEEEccccEEEEEcccccccccccHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEccccEEEEccEEEEEEcccccEEEccccccccccccHHHHHHHHHHccccccccccccc
Coil and Loop (DISEMBL)
LGIVWEIGRVRKQVvnipsfvvrldsqkhidfslnspfggggagrvkRKNLRKAAssaaapaeedee
Flexible Loop (DISEMBL)
lgivweigrvrkqvvnIPSFVVRldsqkhidfslnspfggggagrvkRKNLRKaassaaapaeedee
Low Complexity Region (SEG)
LGIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKaassaaapaeedee
Disordered region (IsUnstruct)
**IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSL*********************************
Disordered Region (DISOPRED)
*****E*GRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG*************************
Disordered Region (DISEMBL)
LGIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVK********************
Disordered Region (DISPRO)
LGIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAG**K********************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
LGIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	67	2.2.26 [Sep-21-2011]
P55935	195	40S ribosomal protein S9	yes	N/A	0.671	0.230	0.911	8e-17
P29314	194	40S ribosomal protein S9	yes	N/A	0.880	0.304	0.711	1e-15
A9L913	194	40S ribosomal protein S9	N/A	N/A	0.880	0.304	0.711	1e-15
Q6ZWN5	194	40S ribosomal protein S9	yes	N/A	0.880	0.304	0.711	1e-15
P46781	194	40S ribosomal protein S9	yes	N/A	0.880	0.304	0.711	1e-15
A6QLG5	194	40S ribosomal protein S9	yes	N/A	0.880	0.304	0.711	1e-15
Q20228	189	40S ribosomal protein S9	yes	N/A	0.820	0.291	0.644	5e-15
Q9LXG1	198	40S ribosomal protein S9-	yes	N/A	0.761	0.257	0.705	3e-14
Q09757	191	40S ribosomal protein S9-	yes	N/A	0.656	0.230	0.75	2e-13
Q9FLF0	197	40S ribosomal protein S9-	no	N/A	0.761	0.258	0.666	3e-13

>sp|P55935|RS9_DROME 40S ribosomal protein S9 OS=Drosophila melanogaster GN=RpS9 PE=2 SV=2

 Score = 85.5 bits (210), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 41/45 (91%), Positives = 42/45 (93%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
           RVRKQVVNIPSFVVRLDSQKHIDFSL SPFGGG  GRVKRKNL+K
Sbjct: 137 RVRKQVVNIPSFVVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLKK 181

Drosophila melanogaster (taxid: 7227)

>sp|P29314|RS9_RAT 40S ribosomal protein S9 OS=Rattus norvegicus GN=Rps9 PE=1 SV=4

 Score = 81.6 bits (200), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 48/59 (81%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
           RVRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct: 136 RVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

Rattus norvegicus (taxid: 10116)

>sp|A9L913|RS9_PAPAN 40S ribosomal protein S9 OS=Papio anubis GN=RPS9 PE=3 SV=1

 Score = 81.6 bits (200), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 48/59 (81%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
           RVRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct: 136 RVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

Papio anubis (taxid: 9555)

>sp|Q6ZWN5|RS9_MOUSE 40S ribosomal protein S9 OS=Mus musculus GN=Rps9 PE=2 SV=3

 Score = 81.6 bits (200), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 48/59 (81%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
           RVRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct: 136 RVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

Mus musculus (taxid: 10090)

>sp|P46781|RS9_HUMAN 40S ribosomal protein S9 OS=Homo sapiens GN=RPS9 PE=1 SV=3

 Score = 81.6 bits (200), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 48/59 (81%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
           RVRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct: 136 RVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

Homo sapiens (taxid: 9606)

>sp|A6QLG5|RS9_BOVIN 40S ribosomal protein S9 OS=Bos taurus GN=RPS9 PE=2 SV=1

 Score = 81.6 bits (200), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 48/59 (81%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
           RVRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct: 136 RVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

Bos taurus (taxid: 9913)

>sp|Q20228|RS9_CAEEL 40S ribosomal protein S9 OS=Caenorhabditis elegans GN=rps-9 PE=3 SV=1

 Score = 79.7 bits (195), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 38/59 (64%), Positives = 46/59 (77%), Gaps = 4/59 (6%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
           RVR+QVV++PSF+VRLDSQKHIDFSL SP+GGG  GRVKR+ LRK   +      +DEE
Sbjct: 135 RVRRQVVDVPSFIVRLDSQKHIDFSLQSPYGGGRPGRVKRRTLRKGDGAGG----DDEE 189

Caenorhabditis elegans (taxid: 6239)

>sp|Q9LXG1|RS91_ARATH 40S ribosomal protein S9-1 OS=Arabidopsis thaliana GN=RPS9B PE=1 SV=1

 Score = 77.4 bits (189), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/51 (70%), Positives = 43/51 (84%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAA 59
           RV KQ+VNIPSF+VRLDSQKHIDF+L SPFGGG  GRVKR+N + A+  A+
Sbjct: 137 RVGKQLVNIPSFMVRLDSQKHIDFALTSPFGGGRPGRVKRRNEKSASKKAS 187

Arabidopsis thaliana (taxid: 3702)

>sp|Q09757|RS9A_SCHPO 40S ribosomal protein S9-A OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rps9a PE=1 SV=2

 Score = 74.3 bits (181), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 33/44 (75%), Positives = 39/44 (88%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLR 52
           RV KQ+VN+PSFVVRLD+QKHIDF+L+SP+GGG  GR KRK LR
Sbjct: 135 RVGKQIVNVPSFVVRLDTQKHIDFALSSPYGGGRPGRCKRKRLR 178

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q9FLF0|RS92_ARATH 40S ribosomal protein S9-2 OS=Arabidopsis thaliana GN=RPS9C PE=2 SV=1

 Score = 73.9 bits (180), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 34/51 (66%), Positives = 42/51 (82%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAA 59
           RV +Q+VNIPSF+VR++SQKH+DFSL SPFGGG  GRVKR+N R  A  A+
Sbjct: 137 RVGRQLVNIPSFMVRVESQKHVDFSLTSPFGGGRPGRVKRRNERAGAKKAS 187

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	67
110671456	195	putative ribosomal protein S9 [Diaphorin	0.880	0.302	1.0	8e-26
291242674	190	PREDICTED: ribosomal protein S9-like [Sa	0.880	0.310	0.779	1e-18
332374562	194	unknown [Dendroctonus ponderosae]	0.865	0.298	0.810	1e-18
125977176	195	GA28351 [Drosophila pseudoobscura pseudo	0.880	0.302	0.796	5e-18
70909509	193	ribosomal protein S9e [Sphaerius sp. APV	0.850	0.295	0.807	5e-18
307202013	193	40S ribosomal protein S9 [Harpegnathos s	0.850	0.295	0.807	6e-18
340724942	193	PREDICTED: 40S ribosomal protein S9-like	0.850	0.295	0.807	7e-18
307182078	193	40S ribosomal protein S9 [Camponotus flo	0.850	0.295	0.807	7e-18
355428300	193	hypothetical protein [Triatoma rubida]	0.850	0.295	0.789	7e-18
62083481	194	ribosomal protein S9 [Lysiphlebus testac	0.865	0.298	0.775	7e-18

>gi|110671456|gb|ABG81979.1| putative ribosomal protein S9 [Diaphorina citri]

 Score =  120 bits (302), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 59/59 (100%), Positives = 59/59 (100%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
           RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE
Sbjct: 137 RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 195

Source: Diaphorina citri

Species: Diaphorina citri

Genus: Diaphorina

Family: Psyllidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|291242674|ref|XP_002741225.1| PREDICTED: ribosomal protein S9-like [Saccoglossus kowalevskii]

 Score = 97.4 bits (241), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 51/59 (86%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
           RVRKQVVNIPSFVVRLDSQKHIDFSL SP+GGG  GRVKRKN+RKA ++ A   EEDE+
Sbjct: 132 RVRKQVVNIPSFVVRLDSQKHIDFSLKSPYGGGRPGRVKRKNMRKAQNAGAVEEEEDED 190

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|332374562|gb|AEE62422.1| unknown [Dendroctonus ponderosae]

 Score = 97.1 bits (240), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 47/58 (81%), Positives = 50/58 (86%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDE 66
           RVRKQVVNIPSF+VRLDSQKHIDFSL SPFGGG  GRVKRKNLRK AS  AA  EE++
Sbjct: 137 RVRKQVVNIPSFIVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLRKGASGGAAAEEEED 194

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125977176|ref|XP_001352621.1| GA28351 [Drosophila pseudoobscura pseudoobscura] gi|195168054|ref|XP_002024847.1| GL17960 [Drosophila persimilis] gi|195178296|ref|XP_002029028.1| GL20135 [Drosophila persimilis] gi|195191346|ref|XP_002029552.1| GL21280 [Drosophila persimilis] gi|54641369|gb|EAL30119.1| GA28351 [Drosophila pseudoobscura pseudoobscura] gi|194103695|gb|EDW25738.1| GL21280 [Drosophila persimilis] gi|194108277|gb|EDW30320.1| GL17960 [Drosophila persimilis] gi|194117383|gb|EDW39426.1| GL20135 [Drosophila persimilis]

 Score = 95.1 bits (235), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 49/59 (83%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
           RVRKQVVNIPSFVVRLDSQKHIDFSL SPFGGG  GRVKRKNL+K     AA  EEDE+
Sbjct: 137 RVRKQVVNIPSFVVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLKKNLGGGAAAPEEDED 195

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|70909509|emb|CAJ17220.1| ribosomal protein S9e [Sphaerius sp. APV-2005]

 Score = 95.1 bits (235), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 47/57 (82%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEED 65
           RVRKQVVNIPSF+VRLDSQKHIDFSL SPFGGG  GRVKRKNLRK A    A  EED
Sbjct: 137 RVRKQVVNIPSFIVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLRKGAKGETAEEEED 193

Source: Sphaerius sp. APV-2005

Species: Sphaerius sp. APV-2005

Genus: Sphaerius

Family: Sphaeriusidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307202013|gb|EFN81577.1| 40S ribosomal protein S9 [Harpegnathos saltator]

 Score = 94.7 bits (234), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 48/57 (84%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEED 65
           RVRKQVVNIPSF+VRLDSQKHIDFSL SPFGGG  GRVKRKNLRK +  AA   EED
Sbjct: 137 RVRKQVVNIPSFIVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLRKGSGGAAPEEEED 193

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340724942|ref|XP_003400837.1| PREDICTED: 40S ribosomal protein S9-like [Bombus terrestris] gi|350422075|ref|XP_003493048.1| PREDICTED: 40S ribosomal protein S9-like [Bombus impatiens] gi|380027607|ref|XP_003697513.1| PREDICTED: 40S ribosomal protein S9-like isoform 1 [Apis florea] gi|383854712|ref|XP_003702864.1| PREDICTED: 40S ribosomal protein S9-like [Megachile rotundata]

 Score = 94.7 bits (234), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 48/57 (84%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEED 65
           RVRKQVVNIPSF+VRLDSQKHIDFSL SPFGGG  GRVKRKNLRK +  AA   EED
Sbjct: 137 RVRKQVVNIPSFIVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLRKGSGGAAPEEEED 193

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307182078|gb|EFN69456.1| 40S ribosomal protein S9 [Camponotus floridanus] gi|322799909|gb|EFZ21050.1| hypothetical protein SINV_10506 [Solenopsis invicta] gi|332017469|gb|EGI58192.1| 40S ribosomal protein S9 [Acromyrmex echinatior]

 Score = 94.7 bits (234), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 48/57 (84%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEED 65
           RVRKQVVNIPSF+VRLDSQKHIDFSL SPFGGG  GRVKRKNLRK +  AA   EED
Sbjct: 137 RVRKQVVNIPSFIVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLRKGSGGAAPEEEED 193

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|355428300|gb|AER92466.1| hypothetical protein [Triatoma rubida]

 Score = 94.7 bits (234), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 45/57 (78%), Positives = 49/57 (85%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEED 65
           RVRKQVVNIPSF+VRLDSQKHIDFSL SPFGGG  GRVKRKN RK  ++AAA  +ED
Sbjct: 137 RVRKQVVNIPSFIVRLDSQKHIDFSLKSPFGGGRHGRVKRKNSRKGTTAAAAEEDED 193

Source: Triatoma rubida

Species: Triatoma rubida

Genus: Triatoma

Family: Reduviidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|62083481|gb|AAX62465.1| ribosomal protein S9 [Lysiphlebus testaceipes] gi|62083483|gb|AAX62466.1| ribosomal protein S9 variant 1 [Lysiphlebus testaceipes]

 Score = 94.4 bits (233), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 45/58 (77%), Positives = 50/58 (86%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDE 66
           RVRKQVVNIPSFVVRLDSQKHIDFSL SPFGGG  GRVKRKN++K  +S AA  EE++
Sbjct: 137 RVRKQVVNIPSFVVRLDSQKHIDFSLKSPFGGGRPGRVKRKNMKKGTNSGAAEEEEED 194

Source: Lysiphlebus testaceipes

Species: Lysiphlebus testaceipes

Genus: Lysiphlebus

Family: Braconidae

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	67
FB|FBgn0010408	195	RpS9 "Ribosomal protein S9" [D	0.671	0.230	0.911	8.6e-17
ZFIN|ZDB-GENE-010724-15	194	rps9 "ribosomal protein S9" [D	0.671	0.231	0.866	6e-16
UNIPROTKB|A6QLG5	194	RPS9 "40S ribosomal protein S9	0.671	0.231	0.844	7.7e-16
UNIPROTKB|E2R8R8	194	RPS9 "Uncharacterized protein"	0.671	0.231	0.844	7.7e-16
UNIPROTKB|P46781	194	RPS9 "40S ribosomal protein S9	0.671	0.231	0.844	7.7e-16
UNIPROTKB|I3LEX0	193	RPS9 "40S ribosomal protein S9	0.671	0.233	0.844	7.7e-16
UNIPROTKB|A9L913	194	RPS9 "40S ribosomal protein S9	0.671	0.231	0.844	7.7e-16
MGI|MGI:1924096	194	Rps9 "ribosomal protein S9" [M	0.671	0.231	0.844	7.7e-16
RGD|619889	194	Rps9 "ribosomal protein S9" [R	0.671	0.231	0.844	7.7e-16
WB|WBGene00004478	189	rps-9 [Caenorhabditis elegans	0.671	0.238	0.777	8.8e-15

FB|FBgn0010408 RpS9 "Ribosomal protein S9" [Drosophila melanogaster (taxid:7227)]

 Score = 207 (77.9 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 41/45 (91%), Positives = 42/45 (93%)

Query:     9 RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
             RVRKQVVNIPSFVVRLDSQKHIDFSL SPFGGG  GRVKRKNL+K
Sbjct:   137 RVRKQVVNIPSFVVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLKK 181

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISS;NAS

GO:0006412 "translation" evidence=ISS;NAS

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

GO:0005840 "ribosome" evidence=IDA;NAS

GO:0019843 "rRNA binding" evidence=IEA

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0000022 "mitotic spindle elongation" evidence=IMP

ZFIN|ZDB-GENE-010724-15 rps9 "ribosomal protein S9" [Danio rerio (taxid:7955)]

 Score = 199 (75.1 bits), Expect = 6.0e-16, P = 6.0e-16
 Identities = 39/45 (86%), Positives = 41/45 (91%)

Query:     9 RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
             RVRKQVVNIPSFVVRLDSQKHIDFSL SP+GGG  GRVKRKN +K
Sbjct:   136 RVRKQVVNIPSFVVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK 180

GO:0019843 "rRNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0006412 "translation" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

UNIPROTKB|A6QLG5 RPS9 "40S ribosomal protein S9" [Bos taurus (taxid:9913)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 38/45 (84%), Positives = 41/45 (91%)

Query:     9 RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
             RVRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K
Sbjct:   136 RVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK 180

GO:0030529 "ribonucleoprotein complex" evidence=ISS

GO:0045182 "translation regulator activity" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|E2R8R8 RPS9 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 38/45 (84%), Positives = 41/45 (91%)

Query:     9 RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
             RVRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K
Sbjct:   136 RVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK 180

GO:0045182 "translation regulator activity" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|P46781 RPS9 "40S ribosomal protein S9" [Homo sapiens (taxid:9606)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 38/45 (84%), Positives = 41/45 (91%)

Query:     9 RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
             RVRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K
Sbjct:   136 RVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK 180

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

GO:0019843 "rRNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0008284 "positive regulation of cell proliferation" evidence=IMP

GO:0006412 "translation" evidence=IC;IMP;TAS

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0045182 "translation regulator activity" evidence=IMP

GO:0005840 "ribosome" evidence=NAS

GO:0030529 "ribonucleoprotein complex" 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

GO:0006417 "regulation of translation" evidence=IMP

UNIPROTKB|I3LEX0 RPS9 "40S ribosomal protein S9" [Sus scrofa (taxid:9823)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 38/45 (84%), Positives = 41/45 (91%)

Query:     9 RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
             RVRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K
Sbjct:   135 RVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK 179

GO:0045182 "translation regulator activity" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|A9L913 RPS9 "40S ribosomal protein S9" [Papio anubis (taxid:9555)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 38/45 (84%), Positives = 41/45 (91%)

Query:     9 RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
             RVRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K
Sbjct:   136 RVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK 180

GO:0030529 "ribonucleoprotein complex" evidence=ISS

MGI|MGI:1924096 Rps9 "ribosomal protein S9" [Mus musculus (taxid:10090)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 38/45 (84%), Positives = 41/45 (91%)

Query:     9 RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
             RVRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K
Sbjct:   136 RVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK 180

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005622 "intracellular" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=ISO

GO:0006417 "regulation of translation" evidence=ISO

GO:0008284 "positive regulation of cell proliferation" evidence=ISO

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=ISO

GO:0045182 "translation regulator activity" evidence=ISO

RGD|619889 Rps9 "ribosomal protein S9" [Rattus norvegicus (taxid:10116)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 38/45 (84%), Positives = 41/45 (91%)

Query:     9 RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
             RVRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K
Sbjct:   136 RVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK 180

GO:0003674 "molecular_function" evidence=ND

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

GO:0005730 "nucleolus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006412 "translation" evidence=IEA;ISO

GO:0006417 "regulation of translation" evidence=ISO

GO:0008150 "biological_process" evidence=ND

GO:0008284 "positive regulation of cell proliferation" evidence=ISO

GO:0019843 "rRNA binding" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISO;IDA

GO:0030529 "ribonucleoprotein complex" evidence=ISO;ISS

GO:0045182 "translation regulator activity" evidence=ISO

WB|WBGene00004478 rps-9 [Caenorhabditis elegans (taxid:6239)]

 Score = 188 (71.2 bits), Expect = 8.8e-15, P = 8.8e-15
 Identities = 35/45 (77%), Positives = 41/45 (91%)

Query:     9 RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
             RVR+QVV++PSF+VRLDSQKHIDFSL SP+GGG  GRVKR+ LRK
Sbjct:   135 RVRRQVVDVPSFIVRLDSQKHIDFSLQSPYGGGRPGRVKRRTLRK 179

GO:0005622 "intracellular" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0006412 "translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0000003 "reproduction" evidence=IMP

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

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

GO:0008340 "determination of adult lifespan" evidence=IMP

GO:0010171 "body morphogenesis" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0032502 "developmental process" evidence=IMP

GO:0006915 "apoptotic process" evidence=IMP

---

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)
P29314	RS9_RAT	No assigned EC number	0.7118	0.8805	0.3041	yes	N/A
P55935	RS9_DROME	No assigned EC number	0.9111	0.6716	0.2307	yes	N/A
Q20228	RS9_CAEEL	No assigned EC number	0.6440	0.8208	0.2910	yes	N/A
A6QLG5	RS9_BOVIN	No assigned EC number	0.7118	0.8805	0.3041	yes	N/A
P46781	RS9_HUMAN	No assigned EC number	0.7118	0.8805	0.3041	yes	N/A
Q9LXG1	RS91_ARATH	No assigned EC number	0.7058	0.7611	0.2575	yes	N/A
Q6ZWN5	RS9_MOUSE	No assigned EC number	0.7118	0.8805	0.3041	yes	N/A
O13516	RS9A_YEAST	No assigned EC number	0.6808	0.6865	0.2335	yes	N/A
P05755	RS9B_YEAST	No assigned EC number	0.7179	0.5820	0.2	yes	N/A
Q09757	RS9A_SCHPO	No assigned EC number	0.75	0.6567	0.2303	yes	N/A
O59675	RS9B_SCHPO	No assigned EC number	0.75	0.6567	0.2291	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	67
PLN00189	194	PLN00189, PLN00189, 40S ribosomal protein S9; Prov	1e-24
PTZ00155	181	PTZ00155, PTZ00155, 40S ribosomal protein S9; Prov	3e-21
TIGR01018	162	TIGR01018, rpsD_arch, ribosomal protein S4(archaea	1e-10
COG0522	205	COG0522, RpsD, Ribosomal protein S4 and related pr	0.003

>gnl|CDD|177783 PLN00189, PLN00189, 40S ribosomal protein S9; Provisional

 Score = 90.2 bits (224), Expect = 1e-24
 Identities = 42/59 (71%), Positives = 46/59 (77%), Gaps = 1/59 (1%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
           RV KQ+VN+PSF+VR+DSQKHIDFSL SP GGG  GRVKRKN  KAAS      EEDEE
Sbjct: 137 RVGKQIVNVPSFMVRVDSQKHIDFSLTSPLGGGRPGRVKRKNQ-KAASGGGDGDEEDEE 194

Length = 194

>gnl|CDD|185484 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provisional

 Score = 80.9 bits (200), Expect = 3e-21
 Identities = 30/47 (63%), Positives = 37/47 (78%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAA 55
           RV KQ+V+IPSF+VR+DS+KHIDF+  SPFG G  GRVKRK  + A 
Sbjct: 135 RVGKQIVDIPSFLVRVDSEKHIDFADTSPFGNGRPGRVKRKAAKAAK 181

Length = 181

>gnl|CDD|213577 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type)

 Score = 52.8 bits (127), Expect = 1e-10
 Identities = 13/31 (41%), Positives = 20/31 (64%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFG 39
            V  + V  PS++VR + +K IDF+ +SPF 
Sbjct: 132 AVDGRRVTSPSYIVRREEEKKIDFAPSSPFK 162

This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 162

>gnl|CDD|223596 COG0522, RpsD, Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]

 Score = 33.4 bits (77), Expect = 0.003
 Identities = 10/42 (23%), Positives = 17/42 (40%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKN 50
            V  + VNIPS++V    +  +     SP     A  +  + 
Sbjct: 122 LVNGKRVNIPSYLVSPGDEISVREKSKSPIKIKEALELAAQR 163

Length = 205

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	67
PLN00189	194	40S ribosomal protein S9; Provisional	99.89
KOG3301|consensus	183		99.87
PTZ00155	181	40S ribosomal protein S9; Provisional	99.81
TIGR01018	162	rpsD_arch ribosomal protein S4(archaeal type)/S9(e	99.58
PRK04051	177	rps4p 30S ribosomal protein S4P; Validated	99.45
COG0522	205	RpsD Ribosomal protein S4 and related proteins [Tr	99.38
CHL00113	201	rps4 ribosomal protein S4; Reviewed	97.5
TIGR01017	200	rpsD_bact ribosomal protein S4, bacterial/organell	97.27
PRK05327	203	rpsD 30S ribosomal protein S4; Validated	97.17
PF01479	48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	96.99
KOG4655|consensus	181		96.7
cd00165	70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	96.17
smart00363	60	S4 S4 RNA-binding domain.	95.38
TIGR02988	59	YaaA_near_RecF S4 domain protein YaaA. This small	95.38
PF11736	146	DUF3299: Protein of unknown function (DUF3299); In	93.12
COG1188	100	Ribosome-associated heat shock protein implicated	92.89
TIGR00478	228	tly hemolysin TlyA family protein. Hemolysins are	90.17
PRK10348	133	ribosome-associated heat shock protein Hsp15; Prov	89.22
TIGR03069	257	PS_II_S4 photosystem II S4 domain protein. Members	85.12
COG1189	245	Predicted rRNA methylase [Translation, ribosomal s	81.17

>PLN00189 40S ribosomal protein S9; Provisional

Probab=99.89  E-value=1.4e-23  Score=148.87  Aligned_cols=64  Identities=56%  Similarity=0.828  Sum_probs=57.6

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCCcchhhhhhhhhhhccCCCCCCcc
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEED   65 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~pgRvkrk~~k~~~~~~~~~~~~~   65 (67)
                      .|+||||+|||++||+|||+|++++|++|+|+.+|||+++.|+|+|||+++++++++++++|||
T Consensus       130 lI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~~~Sp~~~~~p~r~~~k~~~~~~~~~~~~~~~~  193 (194)
T PLN00189        130 LIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSLTSPLGGGRPGRVKRKNQKAASGGGDGDEEDE  193 (194)
T ss_pred             heeCCCEeECCEEEecCcEEEecCCEEEEEEecCCcccCCChhHHHHHHHHhccCCCCcccccc
Confidence            5999999999999999999999999999999999999997799999999999877655555443

>KOG3301|consensus

Probab=99.87  E-value=6.1e-23  Score=144.73  Aligned_cols=66  Identities=61%  Similarity=0.818  Sum_probs=58.4

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCCcchhhhhhhhhhhccCCCCCCcccC
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE   67 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~pgRvkrk~~k~~~~~~~~~~~~~~~   67 (67)
                      .|.|+||+|++|+||+|||||+.|+|++|||+++|||++++|+|+|+|+++++.++.++.+++||+
T Consensus       118 Li~~rhI~V~~qiV~IPsf~vrldsqk~iD~s~~s~~g~~~pg~~krk~~~k~~~~~g~~~~~Ee~  183 (183)
T KOG3301|consen  118 LIRQRHIRVGKQIVNIPSFMVRLDSQKHIDFSLPSPYGGARPGRVKRKNNQKADAKGGGLDENEEE  183 (183)
T ss_pred             HhcCccEEecCeEeeccceeEeechhhhccccccccCCCCCcchhhhhhhhhhhcccCCccccccC
Confidence            588999999999999999999999999999999999999999999999877776666655555543

>PTZ00155 40S ribosomal protein S9; Provisional

Probab=99.81  E-value=1.5e-20  Score=131.98  Aligned_cols=53  Identities=58%  Similarity=0.834  Sum_probs=50.0

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCCcchhhhhhhhhh
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKA   54 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~pgRvkrk~~k~~   54 (67)
                      .|+||||+|||++||+|||+|++++|++|+|+.+|||+++.|+|++||+++++
T Consensus       128 lI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~~S~~~~~~~~r~~~~~~~~~  180 (181)
T PTZ00155        128 LIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADTSPFGNGRPGRVKRKAAKAA  180 (181)
T ss_pred             heeCCCEEECCEEeccCceEeccCccCceeeecCCCccCCChHHHHHHhhhhc
Confidence            59999999999999999999999999999999999999977999999988764

>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type)

Probab=99.58  E-value=1.1e-15  Score=105.81  Aligned_cols=38  Identities=39%  Similarity=0.537  Sum_probs=36.7

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCC
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFG   39 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~   39 (67)
                      .|+||||+|||++||+|||+|++++|++|+|+.+|||+
T Consensus       125 lI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~~S~~~  162 (162)
T TIGR01018       125 LIVHGHIAVDGRRVTSPSYIVRREEEKKIDFAPSSPFK  162 (162)
T ss_pred             HhhCCCeeECCEEeccCceEecCCCCCeeeeecCCCCC
Confidence            58999999999999999999999999999999999985

This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.

>PRK04051 rps4p 30S ribosomal protein S4P; Validated

Probab=99.45  E-value=4.4e-14  Score=98.90  Aligned_cols=47  Identities=26%  Similarity=0.318  Sum_probs=43.2

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCC-cchhhh
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG-AGRVKR   48 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~-pgRvkr   48 (67)
                      .|.||||+|||++|+.|||+|+.++|++|+|+++||++... |+|..-
T Consensus       124 lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~S~i~~~~~~~r~~~  171 (177)
T PRK04051        124 FIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSPLADELHPERAEA  171 (177)
T ss_pred             HHHcCCEEECCEEeCCCCeECCCCCcceEEEeCCCCCCCCCCcchhhh
Confidence            48999999999999999999999999999999999999855 887654

>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]

Probab=99.38  E-value=1.7e-13  Score=97.53  Aligned_cols=44  Identities=20%  Similarity=0.115  Sum_probs=40.7

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCC-cch
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG-AGR   45 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~-pgR   45 (67)
                      .|+||||+|||++||+|||+|+.+.|..|.+..+||+.... +++
T Consensus       115 lV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~s~~~~~~~~~~  159 (205)
T COG0522         115 LVSHGHILVNGKRVNIPSYLVSPGDEISVREKSKSPIKIKEALEL  159 (205)
T ss_pred             HhhcceEEECCEEeccCcEEecCCCEEEeeecccchhhhhhhhhh
Confidence            48999999999999999999999999999999999999876 544

>CHL00113 rps4 ribosomal protein S4; Reviewed

Probab=97.50  E-value=5.2e-05  Score=53.91  Aligned_cols=33  Identities=18%  Similarity=0.165  Sum_probs=28.1

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCC
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNS   36 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~S   36 (67)
                      .|.||||.|||++|++|||.|..+  +.|.+...|
T Consensus       110 lI~~G~V~VNGk~v~~ps~~Vk~G--D~I~V~~~~  142 (201)
T CHL00113        110 LVNHGHILVNGRIVDIPSYRCKPK--DIITVKDKQ  142 (201)
T ss_pred             HHHCCcEEECCEEecCccccCCCC--CEEEEcccc
Confidence            378999999999999999999876  788886544

>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type

Probab=97.27  E-value=0.00015  Score=50.97  Aligned_cols=33  Identities=27%  Similarity=0.230  Sum_probs=28.1

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCC
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNS   36 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~S   36 (67)
                      .|.||||.|||++|+.|||.|..+  +.|.+...+
T Consensus       111 lI~~G~V~VNgk~v~~ps~~V~~G--D~I~V~~~~  143 (200)
T TIGR01017       111 LVSHGHILVNGKKVDIPSYQVRPG--DIISIKEKS  143 (200)
T ss_pred             HHHCCCEEECCEEeCCCCCCCCCC--CEEEEeeCc
Confidence            378999999999999999999866  678887554

This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.

>PRK05327 rpsD 30S ribosomal protein S4; Validated

Probab=97.17  E-value=0.00021  Score=50.42  Aligned_cols=32  Identities=25%  Similarity=0.217  Sum_probs=27.4

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecC
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLN   35 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~   35 (67)
                      .|.||||.|||+.|++|||.|..+  +.|.+...
T Consensus       114 lI~~G~V~VNgk~v~~ps~~v~~G--D~I~v~~~  145 (203)
T PRK05327        114 LVSHGHILVNGKKVNIPSYRVKPG--DVIEVREK  145 (203)
T ss_pred             HHHCCcEEECCEEECCCCcCCCCC--CEEEECCc
Confidence            378999999999999999998765  66888765

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

Probab=96.99  E-value=0.0002  Score=39.00  Aligned_cols=23  Identities=30%  Similarity=0.372  Sum_probs=20.8

Q ss_pred             eeeeeEEECCEEeccCCeeEEcC
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLD   25 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~d   25 (67)
                      |-+|+|.|||++|+-|+|.|..+
T Consensus        23 I~~g~V~VNg~~v~~~~~~v~~~   45 (48)
T PF01479_consen   23 IKQGRVKVNGKVVKDPSYIVKPG   45 (48)
T ss_dssp             HHTTTEEETTEEESSTTSBESTT
T ss_pred             cCCCEEEECCEEEcCCCCCCCCc
Confidence            67899999999999999999754

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 ....

>KOG4655|consensus

Probab=96.70  E-value=0.00021  Score=51.06  Aligned_cols=35  Identities=23%  Similarity=0.265  Sum_probs=32.3

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEeecCCC
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSP   37 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SP   37 (67)
                      |=|||++||-.+||=|+|||.+..|+.|.+-.+|-
T Consensus       129 vEqGHVRvGp~~vtDPa~lvtr~mEDfvtWvd~SK  163 (181)
T KOG4655|consen  129 VEQGHVRVGPKVVTDPAFLVTRSMEDFVTWVDSSK  163 (181)
T ss_pred             HHcCceeeCCeeccCchHHhhhhhhhhhhhhhhHH
Confidence            56999999999999999999999999999887774

>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=96.17  E-value=0.0039  Score=33.65  Aligned_cols=31  Identities=26%  Similarity=0.234  Sum_probs=25.7

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEeecC
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLN   35 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~   35 (67)
                      |-+|+|.|||++++.|++.|..+  +.|.+...
T Consensus        23 i~~g~V~vn~~~~~~~~~~v~~~--d~i~i~~~   53 (70)
T cd00165          23 IKHGHVLVNGKVVTKPSYKVKPG--DVIEVDGK   53 (70)
T ss_pred             HHcCCEEECCEEccCCccCcCCC--CEEEEcCC
Confidence            67899999999998899998876  56777753

>smart00363 S4 S4 RNA-binding domain

Probab=95.38  E-value=0.019  Score=30.12  Aligned_cols=30  Identities=23%  Similarity=0.214  Sum_probs=24.1

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEeec
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSL   34 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~   34 (67)
                      |-+|+|.|||+.++.|++.|..  .+.|.+..
T Consensus        23 i~~g~i~vng~~~~~~~~~l~~--gd~i~~~~   52 (60)
T smart00363       23 IEQGRVKVNGKKVTKPSYIVKP--GDVISVRG   52 (60)
T ss_pred             HHcCCEEECCEEecCCCeEeCC--CCEEEEcc
Confidence            5689999999999779988754  46777765

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA

Probab=95.38  E-value=0.0061  Score=34.74  Aligned_cols=24  Identities=8%  Similarity=-0.162  Sum_probs=20.6

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCC
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDS   26 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~de   26 (67)
                      |-.|+|.|||++|+.|+|.|...+
T Consensus        31 i~~G~V~VNg~~~~~~~~~l~~Gd   54 (59)
T TIGR02988        31 LQENEVLVNGELENRRGKKLYPGD   54 (59)
T ss_pred             HHcCCEEECCEEccCCCCCCCCCC
Confidence            678999999999999999877654

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.

>PF11736 DUF3299: Protein of unknown function (DUF3299); InterPro: IPR021727 This is a family of bacterial proteins of unknown function

Probab=93.12  E-value=0.063  Score=36.59  Aligned_cols=25  Identities=28%  Similarity=0.636  Sum_probs=20.1

Q ss_pred             EECCEEeccCCeeEEcCCCC-ce-Eee
Q psy4238           9 RVRKQVVNIPSFVVRLDSQK-HI-DFS   33 (67)
Q Consensus         9 aV~gq~V~~PsylVr~deE~-~I-df~   33 (67)
                      +++||.|.+|||||.++.+. .| +|-
T Consensus        52 ~L~Gk~V~i~Gf~vPle~~~~~v~eFl   78 (146)
T PF11736_consen   52 ALDGKQVRIPGFMVPLEQEEGKVTEFL   78 (146)
T ss_pred             HhCCCEEEEeeEEEeeccCCCcEEEEE
Confidence            46899999999999999864 34 553

>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]

Probab=92.89  E-value=0.076  Score=34.83  Aligned_cols=29  Identities=24%  Similarity=0.134  Sum_probs=24.8

Q ss_pred             eeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238           4 VWEIGRVRKQVVNIPSFVVRLDSQKHIDFS   33 (67)
Q Consensus         4 vHGHIaV~gq~V~~PsylVr~deE~~Idf~   33 (67)
                      -=|||.|||+++ .||+.|+.+..=.|.|.
T Consensus        32 ~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~   60 (100)
T COG1188          32 EGGRVKVNGQRA-KPSKEVKVGDILTIRFG   60 (100)
T ss_pred             HCCeEEECCEEc-ccccccCCCCEEEEEeC
Confidence            359999999998 69999999988777765

>TIGR00478 tly hemolysin TlyA family protein

Probab=90.17  E-value=0.16  Score=36.36  Aligned_cols=34  Identities=29%  Similarity=0.355  Sum_probs=27.1

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCC
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPF   38 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl   38 (67)
                      |..|+|.|||++++.|++.|..+  +.|.+....+|
T Consensus        22 I~~G~V~Vng~~v~k~s~~V~~~--d~I~v~~~~~~   55 (228)
T TIGR00478        22 ILKGFVLVNGKKVDKPSALVDFD--AKIELLQNPLF   55 (228)
T ss_pred             HHCCcEEECCEEeCCCCCCCCCC--CEEeccCccch
Confidence            67899999999999999988654  67877654333

Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).

>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional

Probab=89.22  E-value=0.19  Score=34.07  Aligned_cols=29  Identities=21%  Similarity=0.098  Sum_probs=23.8

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEe
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDF   32 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf   32 (67)
                      |-.|+|.|||++ ..||..|..+.+=.|.|
T Consensus        31 I~~G~V~vnG~~-~Kps~~V~~gd~l~v~~   59 (133)
T PRK10348         31 IEGGKVHYNGQR-SKPSKIVELNATLTLRQ   59 (133)
T ss_pred             HHCCCEEECCEE-CCCCCccCCCCEEEEEE
Confidence            667999999999 78999998776655544

>TIGR03069 PS_II_S4 photosystem II S4 domain protein

Probab=85.12  E-value=0.62  Score=33.96  Aligned_cols=29  Identities=17%  Similarity=0.181  Sum_probs=23.7

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS   33 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~   33 (67)
                      |-.|+|.|||+.|+.|++.|...  +.|.+.
T Consensus       205 I~~G~V~VNg~~v~~~s~~v~~g--D~Isvr  233 (257)
T TIGR03069       205 IKAGRLRLNWKTVTQPSRELKVG--DRLQLR  233 (257)
T ss_pred             HHCCeEEECCEEcCCCCCcCCCC--CEEEEc
Confidence            66899999999999999988544  566665

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.

>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]

Probab=81.17  E-value=0.98  Score=33.65  Aligned_cols=36  Identities=25%  Similarity=0.307  Sum_probs=27.0

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEee-cCCCCCC
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS-LNSPFGG   40 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~-~~SPl~~   40 (67)
                      |--|-+.|||++|+.||++|..+.  .|+.. +-.||-.
T Consensus        25 I~~G~V~Vng~~v~KP~~~V~~~~--~i~v~~~~~~yVS   61 (245)
T COG1189          25 ILAGNVLVNGEKVTKPSQLVDIDD--EIEVKGEEQPYVS   61 (245)
T ss_pred             HHcCeEEECCEEecCcceecCCCc--eEEEcccCcCccc
Confidence            556899999999999999998554  45555 5555543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	67
3iz6_C	195	Localization Of The Small Subunit Ribosomal Protein		8e-14
3izb_C	197	Localization Of The Small Subunit Ribosomal Protein		9e-12
1s1h_D	179	Structure Of The Ribosomal 80s-Eef2-Sordarin Comple		1e-11
2xzm_D	181	Crystal Structure Of The Eukaryotic 40s Ribosomal S		7e-10
3zey_6	190	High-resolution Cryo-electron Microscopy Structure		1e-07
3jyv_D	158	Structure Of The 40s Rrna And Proteins And PE TRNA		7e-07

>pdb|3IZ6|C Chain C, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 195

Iteration: 1
 Score = 72.0 bits (175), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 33/45 (73%), Positives = 40/45 (88%)
Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
           RV +Q+VNIPSF+VR++S+KHIDFSL SPFGGG  GRVKRKN +K
Sbjct: 137 RVGRQIVNIPSFMVRVESEKHIDFSLTSPFGGGPPGRVKRKNQKK 181

>pdb|3IZB|C Chain C, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 197

Iteration: 1
 Score = 65.1 bits (157), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 28/39 (71%), Positives = 33/39 (84%)
Query: 12  KQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKN 50
           KQ+VNIPSF+VRLDS+KHIDF+  SPFGG   GRV R+N
Sbjct: 138 KQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRN 176

>pdb|1S1H|D Chain D, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From Yeast Obtained By Docking Atomic Models For Rna And Protein Components Into A 11.7 A Cryo-Em Map. This File, 1s1h, Contains 40s Subunit. The 60s Ribosomal Subunit Is In File 1s1i Length = 179

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 28/39 (71%), Positives = 33/39 (84%)
Query: 12  KQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKN 50
           KQ+VNIPSF+VRLDS+KHIDF+  SPFGG   GRV R+N
Sbjct: 120 KQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRN 158

>pdb|2XZM|D Chain D, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit In Complex With Initiation Factor 1. This File Contains The 40s Subunit And Initiation Factor For Molecule 1 Length = 181

Iteration: 1
 Score = 58.9 bits (141), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 27/45 (60%), Positives = 34/45 (75%)
Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 53
           +V K +VN+PSF+VR DS+K IDF+  SP GGG  GR KRKN +K
Sbjct: 135 KVGKNLVNVPSFMVRTDSEKSIDFASTSPLGGGREGRTKRKNAKK 179

>pdb|3ZEY|6 Chain 6, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 190

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 29/39 (74%)
Query: 10  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKR 48
           V KQ+V IPSF+VR+ S+ HI F+  SPFG G  GRVKR
Sbjct: 135 VAKQIVTIPSFIVRVSSEHHIAFADASPFGNGRPGRVKR 173

>pdb|3JYV|D Chain D, Structure Of The 40s Rrna And Proteins And PE TRNA FOR EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 158

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 20/26 (76%), Positives = 24/26 (92%)
Query: 12  KQVVNIPSFVVRLDSQKHIDFSLNSP 37
           KQ+VNIPSF+VRLDS+KHIDF+  SP
Sbjct: 133 KQIVNIPSFMVRLDSEKHIDFAPTSP 158
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	67
3u5c_J	197	40S ribosomal protein S9-A; translation, ribosome,	3e-17
3iz6_C	195	40S ribosomal protein S9 (S4P); eukaryotic ribosom	5e-17
2xzm_D	181	Ribosomal protein S4 containing protein; ribosome,	4e-14
2cqj_A	71	BRMS2, U3 small nucleolar ribonucleoprotein protei	3e-09

>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D* Length = 197

 Score = 70.5 bits (172), Expect = 3e-17
 Identities = 33/59 (55%), Positives = 43/59 (72%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
            V KQ+VNIPSF+VRLDS+KHIDF+  SPFGG   GRV R+N  + A ++   A+E +E
Sbjct: 135 AVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKAEASGEAADEADE 193

>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Length = 195

 Score = 69.7 bits (170), Expect = 5e-17
 Identities = 39/59 (66%), Positives = 47/59 (79%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
           RV +Q+VNIPSF+VR++S+KHIDFSL SPFGGG  GRVKRKN +KA+       EEDEE
Sbjct: 137 RVGRQIVNIPSFMVRVESEKHIDFSLTSPFGGGPPGRVKRKNQKKASGGGGDGEEEDEE 195

>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D Length = 181

 Score = 62.0 bits (150), Expect = 4e-14
 Identities = 28/47 (59%), Positives = 36/47 (76%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAA 55
           +V K +VN+PSF+VR DS+K IDF+  SP GGG  GR KRKN +K+A
Sbjct: 135 KVGKNLVNVPSFMVRTDSEKSIDFASTSPLGGGREGRTKRKNAKKSA 181

>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71

 Score = 46.9 bits (112), Expect = 3e-09
 Identities = 10/36 (27%), Positives = 17/36 (47%)

Query: 9  RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAG 44
          RV   VV  P+F+V    +  + +  +S   G  +G
Sbjct: 36 RVGPDVVTDPAFLVTRSMEDFVTWVDSSKISGPSSG 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	67
3iz6_C	195	40S ribosomal protein S9 (S4P); eukaryotic ribosom	99.84
3u5c_J	197	40S ribosomal protein S9-A; translation, ribosome,	99.81
2xzm_D	181	Ribosomal protein S4 containing protein; ribosome,	99.55
3j20_D	180	30S ribosomal protein S4P; archaea, archaeal, KINK	99.12
2cqj_A	71	BRMS2, U3 small nucleolar ribonucleoprotein protei	99.01
3bbn_D	201	Ribosomal protein S4; small ribosomal subunit, spi	97.55
1c05_A	159	Ribosomal protein S4 delta 41; two subdomains, uni	97.1
2vqe_D	209	30S ribosomal protein S4; tRNA-binding, rRNA-bindi	97.09
3r8n_D	205	30S ribosomal protein S4; protein biosynthesis, RN	96.92
1dm9_A	133	Hypothetical 15.5 KD protein in MRCA-PCKA intergen	92.51
3j20_E	243	30S ribosomal protein S4E; archaea, archaeal, KINK	92.36
3kbg_A	213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	91.79
2k6p_A	92	Uncharacterized protein HP_1423; alpha-L motif, RN	90.68
4hsp_A	150	Hypothetical protein; PF11736 family protein, DUF3	89.92
1p9k_A	79	ORF, hypothetical protein; alfal motif, RNA-bindin	89.24
1ksk_A	234	Ribosomal small subunit pseudouridine synthase A;	86.15
3hp7_A	291	Hemolysin, putative; structural genomics, APC64019	85.47
1vio_A	243	Ribosomal small subunit pseudouridine synthase A;	85.32

>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=99.84  E-value=8.5e-23  Score=143.59  Aligned_cols=66  Identities=61%  Similarity=0.876  Sum_probs=60.2

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCCcchhhhhhhhhhhccCCCCCCcccC
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE   67 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~pgRvkrk~~k~~~~~~~~~~~~~~~   67 (67)
                      .|.||||.|||++|++|||+|+.++|.+|+|+.+|||++++|||+|||+++++++++++++|||||
T Consensus       130 lI~~GhV~VNG~~V~~Ps~~V~~gde~~I~~~~~spyv~~~~gr~~rk~~~~~~~~~~~~~~~~~~  195 (195)
T 3iz6_C          130 LIRQRHIRVGRQIVNIPSFMVRVESEKHIDFSLTSPFGGGPPGRVKRKNQKKASGGGGDGEEEDEE  195 (195)
T ss_dssp             HHHHHSTTTSCCCCCCCCCCCSSSCSSSSCSSSCCCCCCCCCCHHHHHHHHTTTSSSSCCCCCCCC
T ss_pred             HHHcCCEEECCEEeCCCCcCcCCCCEEEEEecCCCCCCCCCchhHHHHHHhhccCCCCCccccccC
Confidence            488999999999999999999999999999999999999999999999999987776666666654

>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D*

Probab=99.81  E-value=1.6e-21  Score=137.22  Aligned_cols=54  Identities=57%  Similarity=0.827  Sum_probs=51.6

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCCcchhhhhhhhhhh
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAA   55 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~pgRvkrk~~k~~~   55 (67)
                      .|.||||.|||++|+.|||+|+.++|++|.|..+|||.+++|||+|||++|+++
T Consensus       128 LI~~GhV~VNG~~V~~Ps~~V~~g~ed~I~~~~~spyvs~~~gr~~rk~~~~~~  181 (197)
T 3u5c_J          128 LITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKA  181 (197)
T ss_dssp             HHHTSCCBSSSCBCCCTTCCCCSTTGGGCBCCSSSSSSSSCCCHHHHHHHHHHH
T ss_pred             HHHcCCEEECCEEeCCCccccCCCCccEEEEcCCCCCcCCCchhHHHHHHHhhc
Confidence            488999999999999999999999999999999999999999999999999864

>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D

Probab=99.55  E-value=1e-15  Score=105.78  Aligned_cols=53  Identities=53%  Similarity=0.782  Sum_probs=49.7

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCCcchhhhhhhhhh
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKA   54 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~pgRvkrk~~k~~   54 (67)
                      .|.||||.|||++|+.|||+|..+.++.|.|...|||.+++|||+||||++++
T Consensus       128 LI~~G~V~VNg~~V~~Ps~~V~~~d~~~I~v~~~s~~~~~~~~r~~~~~~~~~  180 (181)
T 2xzm_D          128 LIRQRHIKVGKNLVNVPSFMVRTDSEKSIDFASTSPLGGGREGRTKRKNAKKS  180 (181)
T ss_dssp             HTTTTCCEETTEECCCSCCBCCSTTSSCEECTTSTTTTTCCSHHHHHHHHHC-
T ss_pred             HHHCCEEEECCEEECCCCcCCCCCCceEEEEeCCCccCCCCCchhhhhhhccC
Confidence            37899999999999999999999999999999999999999999999998865

>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=99.12  E-value=4.4e-12  Score=87.89  Aligned_cols=51  Identities=24%  Similarity=0.359  Sum_probs=46.6

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCC-cchhhhhhhh
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG-AGRVKRKNLR   52 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~-pgRvkrk~~k   52 (67)
                      .|.||||.|||++|+.|||+|..++|+.|.|..+|||.++. |+|.-.-++|
T Consensus       124 LI~~G~V~VNg~~V~~Ps~~V~~~~eD~I~v~~~s~i~~~~~~~~~~~~~~~  175 (180)
T 3j20_D          124 LIVHGHIEVNGQIIRSPSYLVLKEEEDTITYARTSPFANPQHPERMMIEKAK  175 (180)
T ss_dssp             HHHHTCCEESSSBCCCSSCCCCTGGGGCEECSSCSSSSSSCCHHHHHHHHCC
T ss_pred             HHHcCCeEECCEEeCCCCcccCCCCCCEEEEeCCCcccCCCCCcchhHHHHh
Confidence            47899999999999999999999999999999999999988 9998776544

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

Probab=99.01  E-value=5.7e-11  Score=70.90  Aligned_cols=41  Identities=22%  Similarity=0.234  Sum_probs=37.9

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCCCCCCC
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG   42 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SPl~~~~   42 (67)
                      .|.||||.|||++|+.|||+|..++++.|.|...||+....
T Consensus        29 lI~~G~V~Vng~~v~kps~~V~~~~~d~I~~~~~~~~~~~~   69 (71)
T 2cqj_A           29 FVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWVDSSKISGPS   69 (71)
T ss_dssp             HHHTTCEEETTBCCCCTTCEEEHHHHTTEEESCCSSSCCCC
T ss_pred             HHHCCcEEECCEEECCCCCCCCCCCCcEEEEECCceecccc
Confidence            47899999999999999999999999999999999998653

>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=97.55  E-value=1.8e-05  Score=55.25  Aligned_cols=33  Identities=18%  Similarity=0.143  Sum_probs=27.4

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCC
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNS   36 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~S   36 (67)
                      .|.||||.|||++|++|||.|..+  +.|.+...+
T Consensus       110 LI~~G~V~VNG~~V~~pS~~V~~g--D~I~V~~~~  142 (201)
T 3bbn_D          110 LVNHRHILVNGRIVDIPSYRCKPQ--DTIMARDEQ  142 (201)
T ss_dssp             HHHTTCEEETTEECCCTTCBCCTT--EEEEECSST
T ss_pred             HHhCCcEEeCCEEEeecceecCCC--CEEEEcccc
Confidence            378999999999999999999764  578776543

>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=97.10  E-value=0.00012  Score=48.68  Aligned_cols=32  Identities=28%  Similarity=0.259  Sum_probs=27.2

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEeecCC
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNS   36 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~S   36 (67)
                      |.||||.|||++|+.|+|.|..  .+.|.+...|
T Consensus        73 I~~G~V~VNG~~v~~ps~~V~~--gD~I~V~~~~  104 (159)
T 1c05_A           73 VTHGHILVDGSRVNIPSYRVKP--GQTIAVREKS  104 (159)
T ss_dssp             HHTTCEEETTEECCCSSCBCCT--TCEEEECGGG
T ss_pred             HHCCCEEECCEEeCcCCcEeCC--CCEEEEeCce
Confidence            7899999999999999999876  4578887654

>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=97.09  E-value=0.00012  Score=50.76  Aligned_cols=32  Identities=25%  Similarity=0.281  Sum_probs=27.5

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEeecCC
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNS   36 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~S   36 (67)
                      |.||||.|||++|+.|||.|..  .+.|.+...|
T Consensus       121 I~~G~V~VNG~~v~~ps~~V~~--gD~I~V~~~~  152 (209)
T 2vqe_D          121 VRHGHITVNGRRVDLPSYRVRP--GDEIAVAEKS  152 (209)
T ss_dssp             HHTTCEEETTEECCCTTCBCCT--TCEEEECGGG
T ss_pred             HHCCCEEECCEEeCcCCcCcCC--CCEEEEcCcc
Confidence            7899999999999999999875  5678887664

>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=92.51  E-value=0.03  Score=36.01  Aligned_cols=24  Identities=25%  Similarity=0.126  Sum_probs=20.2

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCC
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQ   27 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE   27 (67)
                      |-+|+|.|||+++ .|++.|....+
T Consensus        31 i~~G~V~VNG~~v-k~s~~V~~GD~   54 (133)
T 1dm9_A           31 IEGGKVHYNGQRS-KPSKIVELNAT   54 (133)
T ss_dssp             HHTTCEEETTEEC-CTTCBCCTTCE
T ss_pred             HHCCcEEECCEEc-CCCCEeCCCCE
Confidence            5689999999998 79999877644

>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=92.36  E-value=0.033  Score=40.09  Aligned_cols=22  Identities=18%  Similarity=-0.068  Sum_probs=19.8

Q ss_pred             eeeeeEEECCEEeccCCeeEEc
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRL   24 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~   24 (67)
                      +.||||.|||++++.|+|-|..
T Consensus        66 v~~~~I~VdGKvr~d~~ypvG~   87 (243)
T 3j20_E           66 LNEGKFLVDGRVRKDYKFPVGI   87 (243)
T ss_dssp             HHHCSCEETTEECCCSSCEECT
T ss_pred             HHCCcEEECCEEeccccCCccc
Confidence            5699999999999999998765

>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum}

Probab=91.79  E-value=0.046  Score=38.66  Aligned_cols=23  Identities=17%  Similarity=0.193  Sum_probs=19.9

Q ss_pred             eeeeeEEECCEEeccCCeeEEcC
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLD   25 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~d   25 (67)
                      +.||||.|||++++.|+|-|..-
T Consensus        31 v~~~~I~VDGKvr~d~~ypvG~m   53 (213)
T 3kbg_A           31 LANGLVKVDGKTVREKKFAVGFM   53 (213)
T ss_dssp             HHTTCEEETTEECCCTTCEECTT
T ss_pred             HHCCCEEECCEEecccCCCccce
Confidence            56999999999999999976653

>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori}

Probab=90.68  E-value=0.034  Score=32.78  Aligned_cols=29  Identities=10%  Similarity=-0.048  Sum_probs=22.7

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEeec
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSL   34 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~   34 (67)
                      |-+|.|.|||+.+ .|+|.|...  +.|.+..
T Consensus        23 i~~G~V~VNg~~~-~~~~~v~~g--d~I~v~~   51 (92)
T 2k6p_A           23 CNVGAVWLNGSCA-KASKEVKAG--DTISLHY   51 (92)
T ss_dssp             HHHTCCEETTEEC-CTTCBCCTT--CEEEECC
T ss_pred             HHCCcEEECCEEc-CCCCCcCCC--CEEEEEe
Confidence            5689999999998 699998755  4566653

>4hsp_A Hypothetical protein; PF11736 family protein, DUF3299, structural genomics, joint for structural genomics, JCSG; HET: MSE; 2.45A {Pseudomonas aeruginosa}

Probab=89.92  E-value=0.11  Score=35.08  Aligned_cols=31  Identities=23%  Similarity=0.493  Sum_probs=21.8

Q ss_pred             EECCEEeccCCeeEEcCCC--Cc-eEeecCCCCCC
Q psy4238           9 RVRKQVVNIPSFVVRLDSQ--KH-IDFSLNSPFGG   40 (67)
Q Consensus         9 aV~gq~V~~PsylVr~deE--~~-Idf~~~SPl~~   40 (67)
                      ++||+.|.+|+|+|.++..  .. -+|.. .|+.+
T Consensus        51 ~LdGk~VripGfvvPLe~~~~~~vteFlL-VPy~G   84 (150)
T 4hsp_A           51 ALDGIEAKLPGYIVPLEISEAGLVTEFLL-VPYYG   84 (150)
T ss_dssp             GGTTEEEEEEEEEEEEEECTTSEEEEEEE-ESSTT
T ss_pred             hhCCCEEEeccEEEEeccCCCCcEEEEEE-eCCCC
Confidence            3689999999999999954  33 55543 34443

>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=89.24  E-value=0.037  Score=32.11  Aligned_cols=29  Identities=14%  Similarity=0.089  Sum_probs=22.7

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS   33 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~   33 (67)
                      |-.|.|.|||++++.|++.|..+  +.|.+.
T Consensus        43 I~~G~V~VNG~~v~~~~~~v~~g--d~I~v~   71 (79)
T 1p9k_A           43 IAEGQVKVDGAVETRKRCKIVAG--QTVSFA   71 (79)
T ss_dssp             HHHHHHEETTBCCCCSSCCCCSS--EEEEET
T ss_pred             HHCCEEEECCEEecCCCCCCCCC--CEEEEC
Confidence            55799999999999999988633  456553

>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A*

Probab=86.15  E-value=0.33  Score=32.69  Aligned_cols=29  Identities=14%  Similarity=0.195  Sum_probs=23.3

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS   33 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~   33 (67)
                      |-.|.|.|||++|+.|++.|...  +.|.+.
T Consensus        25 i~~G~V~VNG~~v~~~~~~v~~g--D~I~v~   53 (234)
T 1ksk_A           25 IRGNRVTVDGEIVRNAAFKLLPE--HDVAYD   53 (234)
T ss_dssp             HHTTCEEETTEECCCTTCEECTT--CCEEET
T ss_pred             HHcCeEEECCEEeCCCCCCCCCC--CEEEEe
Confidence            55799999999999899998755  466664

>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein STR initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.53A {Streptococcus thermophilus}

Probab=85.47  E-value=0.21  Score=35.64  Aligned_cols=36  Identities=3%  Similarity=-0.086  Sum_probs=28.0

Q ss_pred             eeeeeEEECC-E-EeccCCeeEEcCCCCceEeecC-CCCCC
Q psy4238           3 IVWEIGRVRK-Q-VVNIPSFVVRLDSQKHIDFSLN-SPFGG   40 (67)
Q Consensus         3 IvHGHIaV~g-q-~V~~PsylVr~deE~~Idf~~~-SPl~~   40 (67)
                      |-.|+|.||| + +|+.|++.|..+  +.|.+... .||-.
T Consensus        29 I~~G~V~Vng~~~~v~kp~~~V~~~--d~I~v~g~~~~yvs   67 (291)
T 3hp7_A           29 VMAGLVVNVINGERYDKPGEKIDDG--TELKLKGEKLRYVS   67 (291)
T ss_dssp             HHTTCEEETTTCCBCCCTTCEEETT--CCEEETTCCCCSSS
T ss_pred             HHCCeEEECCeEEEEccCCCCCCCC--CEEEEccccccccc
Confidence            6789999999 8 899999999876  56777644 35554

>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5

Probab=85.32  E-value=0.38  Score=32.69  Aligned_cols=29  Identities=17%  Similarity=0.233  Sum_probs=23.1

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS   33 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~   33 (67)
                      |-.|.|.|||++|+.|++.|....  .|.+.
T Consensus        24 I~~G~V~VNG~~v~~~~~~v~~gD--~I~v~   52 (243)
T 1vio_A           24 IRQSAVKINGEIVKSGSVQISQED--EIYFE   52 (243)
T ss_dssp             HHTTCEEETTEECCCTTCEECTTS--CEEET
T ss_pred             HHcCcEEECCEEeCCCCCCcCCCC--EEEEe
Confidence            457899999999988999887654  66664

---

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	67
d1c06a_	159	Ribosomal protein S4 {Bacillus stearothermophilus	98.5
d2uubd1	208	Ribosomal protein S4 {Thermus thermophilus [TaxId:	98.35
d2gy9d1	204	Ribosomal protein S4 {Escherichia coli [TaxId: 562	98.32
d1kska3	59	Pseudouridine synthase RsuA N-terminal domain {Esc	96.85
d1dm9a_	104	Heat shock protein 15 kD {Escherichia coli [TaxId:	96.56
d1vioa2	58	Pseudouridine synthase RsuA N-terminal domain {Hae	96.41
d1p9ka_	79	Hypothetical protein YbcJ {Escherichia coli [TaxId	93.88

>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=98.50  E-value=1e-08  Score=68.08  Aligned_cols=33  Identities=27%  Similarity=0.218  Sum_probs=27.8

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCC
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNS   36 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~S   36 (67)
                      .|.||||.|||++||+|||+|+..  +-|.+.+.|
T Consensus        72 ~v~Hghi~vNgk~v~iPSy~vk~G--DvIsvkeks  104 (159)
T d1c06a_          72 LVTHGHILVDGSRVNIPSYRVKPG--QTIAVREKS  104 (159)
T ss_dssp             HHHTSCEEETTEECCCSSCCCCSS--CEEEECGGG
T ss_pred             HHHhcceEccceEEEecceeecCC--cEEeecccc
Confidence            478999999999999999999887  467776543

>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Thermus thermophilus [TaxId: 274]

Probab=98.35  E-value=3.7e-08  Score=67.84  Aligned_cols=34  Identities=24%  Similarity=0.223  Sum_probs=28.6

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCCC
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNSP   37 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~SP   37 (67)
                      .|.||||.|||++||+|||+|+..  +-|.+.+.|.
T Consensus       119 ~v~Hg~i~vNg~~v~ips~~~~~g--d~I~vreksk  152 (208)
T d2uubd1         119 LVRHGHITVNGRRVDLPSYRVRPG--DEIAVAEKSR  152 (208)
T ss_dssp             HHHTTCEEETTEECCCTTCBCCTT--CEEEECGGGT
T ss_pred             HHHhcCeecCCeEEEeccEEecCC--ceeehhhccc
Confidence            478999999999999999999876  6677766553

>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Escherichia coli [TaxId: 562]

Probab=98.32  E-value=2.5e-08  Score=68.43  Aligned_cols=33  Identities=21%  Similarity=0.214  Sum_probs=27.6

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEeecCC
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFSLNS   36 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~~~S   36 (67)
                      .|.||||.|||++||+|||.|+..  +.|.+-+.|
T Consensus       115 ~v~Hghi~VNgk~VnIPSy~vk~G--DvIsvkeks  147 (204)
T d2gy9d1         115 LVSHKAIMVNGRVVNIASYQVSPN--DVVSIREKA  147 (204)
T ss_dssp             HHHTTCEEESSSBCCCTTCBCCTT--CBEEECTTG
T ss_pred             HHHhcceecCCEEEEeccEeecCC--CEEEeccch
Confidence            378999999999999999998865  557776655

>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=96.85  E-value=0.00019  Score=39.33  Aligned_cols=30  Identities=13%  Similarity=0.180  Sum_probs=25.4

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS   33 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~   33 (67)
                      .|-+|+|.|||++|+.|+|.|.-+  +.|.|.
T Consensus        21 lI~~g~V~Vng~~v~~~~~~V~~~--d~I~~d   50 (59)
T d1kska3          21 EIRGNRVTVDGEIVRNAAFKLLPE--HDVAYD   50 (59)
T ss_dssp             HHHTTCEEETTEECCCTTCEECTT--CCEEET
T ss_pred             HHHcCcEEECCEEeecCCcCcCCC--CEEEEC
Confidence            367899999999999999999754  668875

>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Heat shock protein 15 kD
domain: Heat shock protein 15 kD
species: Escherichia coli [TaxId: 562]

Probab=96.56  E-value=0.00023  Score=43.48  Aligned_cols=26  Identities=23%  Similarity=0.123  Sum_probs=21.2

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCc
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKH   29 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~   29 (67)
                      |-||||.|||++|. |||.|+....=.
T Consensus        27 i~~G~V~vNg~~vK-ps~~vk~GDvI~   52 (104)
T d1dm9a_          27 IEGGKVHYNGQRSK-PSKIVELNATLT   52 (104)
T ss_dssp             HHTTCEEETTEECC-TTCBCCTTCEEE
T ss_pred             HHcCCeeeCCeecc-ccccCCCCCEEE
Confidence            67999999999986 999987665433

>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=96.41  E-value=0.00047  Score=37.57  Aligned_cols=30  Identities=17%  Similarity=0.231  Sum_probs=25.0

Q ss_pred             ceeeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238           2 GIVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS   33 (67)
Q Consensus         2 ~IvHGHIaV~gq~V~~PsylVr~deE~~Idf~   33 (67)
                      .|-+|+|.|||++|+.|+|.|.-+  +.|.|.
T Consensus        22 lI~~g~V~Vng~~v~~~~~~v~~~--d~I~~~   51 (58)
T d1vioa2          22 AIRQSAVKINGEIVKSGSVQISQE--DEIYFE   51 (58)
T ss_dssp             HHHTTCEEETTEECCCTTCEECTT--SCEEET
T ss_pred             HHHcCeEEECCEEeCCCCCCCCCC--CEEEEC
Confidence            367899999999999999998665  567774

>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: YbcJ-like
domain: Hypothetical protein YbcJ
species: Escherichia coli [TaxId: 562]

Probab=93.88  E-value=0.0021  Score=37.08  Aligned_cols=29  Identities=14%  Similarity=0.089  Sum_probs=24.3

Q ss_pred             eeeeeEEECCEEeccCCeeEEcCCCCceEee
Q psy4238           3 IVWEIGRVRKQVVNIPSFVVRLDSQKHIDFS   33 (67)
Q Consensus         3 IvHGHIaV~gq~V~~PsylVr~deE~~Idf~   33 (67)
                      |-.|+|.|||++++.|+|.|..+  +.|.|.
T Consensus        43 I~~G~V~VNG~~~~~p~~~V~~~--d~I~vd   71 (79)
T d1p9ka_          43 IAEGQVKVDGAVETRKRCKIVAG--QTVSFA   71 (79)
T ss_dssp             HHHHHHEETTBCCCCSSCCCCSS--EEEEET
T ss_pred             HHhCCcccCCEEeccccccCCCC--CEEEEC
Confidence            56799999999999999988864  567775