Psyllid ID: psy7990

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70------
Protein Sequence
MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHccEEccEEEEcccEEEEEccccEEEEEcccccccccccHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHcccccccEEEEccEEEEEEcccccEEEccccccccccccHHHHHHHHHHccccccccccccc
Coil and Loop (DISEMBL)
MCSALFLSTQywehqgpgvrkqvvnipsfvvrldsqkhidfslnspfggggtgrvkrknlrkaassatapteedee
Flexible Loop (DISEMBL)
MCSALFLSTqywehqgpgvrKQVVNIPSFVVRLDSQkhidfslnspfggggtgrvkrknlrkaassatapteedee
Low Complexity Region (SEG)
MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE
Disordered region (IsUnstruct)
***ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSL*********************************
Disordered Region (DISOPRED)
********TQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGG***************************
Disordered Region (DISEMBL)
MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRV*********************
Disordered Region (DISPRO)
MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGR*KR*******************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE
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	76	2.2.26 [Sep-21-2011]
P55935	195	40S ribosomal protein S9	yes	N/A	0.578	0.225	0.909	2e-16
P29314	194	40S ribosomal protein S9	yes	N/A	0.763	0.298	0.706	3e-15
A9L913	194	40S ribosomal protein S9	N/A	N/A	0.763	0.298	0.706	3e-15
Q6ZWN5	194	40S ribosomal protein S9	yes	N/A	0.763	0.298	0.706	3e-15
P46781	194	40S ribosomal protein S9	yes	N/A	0.763	0.298	0.706	3e-15
A6QLG5	194	40S ribosomal protein S9	yes	N/A	0.763	0.298	0.706	3e-15
Q20228	189	40S ribosomal protein S9	yes	N/A	0.578	0.232	0.772	3e-14
Q9LXG1	198	40S ribosomal protein S9-	yes	N/A	0.631	0.242	0.708	9e-14
Q9FLF0	197	40S ribosomal protein S9-	no	N/A	0.631	0.243	0.666	7e-13
Q09757	191	40S ribosomal protein S9-	yes	N/A	0.539	0.214	0.756	9e-13

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

 Score = 84.0 bits (206), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 40/44 (90%), Positives = 41/44 (93%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRK 62
           VRKQVVNIPSFVVRLDSQKHIDFSL SPFGGG  GRVKRKNL+K
Sbjct: 138 VRKQVVNIPSFVVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLKK 181

Drosophila melanogaster (taxid: 7227)

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

 Score = 80.5 bits (197), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 41/58 (70%), Positives = 47/58 (81%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
           VRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct: 137 VRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

Rattus norvegicus (taxid: 10116)

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

 Score = 80.5 bits (197), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 41/58 (70%), Positives = 47/58 (81%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
           VRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct: 137 VRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

Papio anubis (taxid: 9555)

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

 Score = 80.5 bits (197), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 41/58 (70%), Positives = 47/58 (81%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
           VRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct: 137 VRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

Mus musculus (taxid: 10090)

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

 Score = 80.5 bits (197), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 41/58 (70%), Positives = 47/58 (81%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
           VRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct: 137 VRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

Homo sapiens (taxid: 9606)

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

 Score = 80.5 bits (197), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 41/58 (70%), Positives = 47/58 (81%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
           VRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct: 137 VRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

Bos taurus (taxid: 9913)

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

 Score = 77.4 bits (189), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 34/44 (77%), Positives = 40/44 (90%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRK 62
           VR+QVV++PSF+VRLDSQKHIDFSL SP+GGG  GRVKR+ LRK
Sbjct: 136 VRRQVVDVPSFIVRLDSQKHIDFSLQSPYGGGRPGRVKRRTLRK 179

Caenorhabditis elegans (taxid: 6239)

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

 Score = 75.5 bits (184), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 34/48 (70%), Positives = 41/48 (85%)

Query: 21  KQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSAT 68
           KQ+VNIPSF+VRLDSQKHIDF+L SPFGGG  GRVKR+N + A+  A+
Sbjct: 140 KQLVNIPSFMVRLDSQKHIDFALTSPFGGGRPGRVKRRNEKSASKKAS 187

Arabidopsis thaliana (taxid: 3702)

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

 Score = 72.4 bits (176), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 32/48 (66%), Positives = 40/48 (83%)

Query: 21  KQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSAT 68
           +Q+VNIPSF+VR++SQKH+DFSL SPFGGG  GRVKR+N R  A  A+
Sbjct: 140 RQLVNIPSFMVRVESQKHVDFSLTSPFGGGRPGRVKRRNERAGAKKAS 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 = 72.4 bits (176), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 31/41 (75%), Positives = 37/41 (90%)

Query: 21  KQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLR 61
           KQ+VN+PSFVVRLD+QKHIDF+L+SP+GGG  GR KRK LR
Sbjct: 138 KQIVNVPSFVVRLDTQKHIDFALSSPYGGGRPGRCKRKRLR 178

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

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	76
70909509	193	ribosomal protein S9e [Sphaerius sp. APV	0.736	0.290	0.821	4e-18
291242674	190	PREDICTED: ribosomal protein S9-like [Sa	0.763	0.305	0.758	7e-18
332374562	194	unknown [Dendroctonus ponderosae]	0.75	0.293	0.789	8e-18
125977176	195	GA28351 [Drosophila pseudoobscura pseudo	0.763	0.297	0.775	3e-17
110671456	195	putative ribosomal protein S9 [Diaphorin	0.578	0.225	0.977	4e-17
307202013	193	40S ribosomal protein S9 [Harpegnathos s	0.736	0.290	0.785	5e-17
307182078	193	40S ribosomal protein S9 [Camponotus flo	0.736	0.290	0.785	5e-17
340724942	193	PREDICTED: 40S ribosomal protein S9-like	0.736	0.290	0.785	5e-17
355428300	193	hypothetical protein [Triatoma rubida]	0.736	0.290	0.767	6e-17
62083481	194	ribosomal protein S9 [Lysiphlebus testac	0.75	0.293	0.754	6e-17

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

 Score = 95.5 bits (236), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 46/56 (82%), Positives = 47/56 (83%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEED 74
           VRKQVVNIPSF+VRLDSQKHIDFSL SPFGGG  GRVKRKNLRK A   TA  EED
Sbjct: 138 VRKQVVNIPSFIVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLRKGAKGETAEEEED 193

Source: Sphaerius sp. APV-2005

Species: Sphaerius sp. APV-2005

Genus: Sphaerius

Family: Sphaeriusidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 94.4 bits (233), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 44/58 (75%), Positives = 49/58 (84%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
           VRKQVVNIPSFVVRLDSQKHIDFSL SP+GGG  GRVKRKN+RKA ++     EEDE+
Sbjct: 133 VRKQVVNIPSFVVRLDSQKHIDFSLKSPYGGGRPGRVKRKNMRKAQNAGAVEEEEDED 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 = 94.4 bits (233), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 45/57 (78%), Positives = 48/57 (84%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDE 75
           VRKQVVNIPSF+VRLDSQKHIDFSL SPFGGG  GRVKRKNLRK AS   A  EE++
Sbjct: 138 VRKQVVNIPSFIVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLRKGASGGAAAEEEED 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 = 92.4 bits (228), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 45/58 (77%), Positives = 47/58 (81%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
           VRKQVVNIPSFVVRLDSQKHIDFSL SPFGGG  GRVKRKNL+K      A  EEDE+
Sbjct: 138 VRKQVVNIPSFVVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLKKNLGGGAAAPEEDED 195

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 92.0 bits (227), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 43/44 (97%), Positives = 43/44 (97%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRK 62
           VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG GRVKRKNLRK
Sbjct: 138 VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRK 181

Source: Diaphorina citri

Species: Diaphorina citri

Genus: Diaphorina

Family: Psyllidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 91.7 bits (226), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 44/56 (78%), Positives = 46/56 (82%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEED 74
           VRKQVVNIPSF+VRLDSQKHIDFSL SPFGGG  GRVKRKNLRK +  A    EED
Sbjct: 138 VRKQVVNIPSFIVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLRKGSGGAAPEEEED 193

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

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 = 91.7 bits (226), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 44/56 (78%), Positives = 46/56 (82%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEED 74
           VRKQVVNIPSF+VRLDSQKHIDFSL SPFGGG  GRVKRKNLRK +  A    EED
Sbjct: 138 VRKQVVNIPSFIVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLRKGSGGAAPEEEED 193

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

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 = 91.7 bits (226), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 44/56 (78%), Positives = 46/56 (82%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEED 74
           VRKQVVNIPSF+VRLDSQKHIDFSL SPFGGG  GRVKRKNLRK +  A    EED
Sbjct: 138 VRKQVVNIPSFIVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLRKGSGGAAPEEEED 193

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 91.3 bits (225), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 43/56 (76%), Positives = 47/56 (83%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEED 74
           VRKQVVNIPSF+VRLDSQKHIDFSL SPFGGG  GRVKRKN RK  ++A A  +ED
Sbjct: 138 VRKQVVNIPSFIVRLDSQKHIDFSLKSPFGGGRHGRVKRKNSRKGTTAAAAEEDED 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 = 91.3 bits (225), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 43/57 (75%), Positives = 48/57 (84%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDE 75
           VRKQVVNIPSFVVRLDSQKHIDFSL SPFGGG  GRVKRKN++K  +S  A  EE++
Sbjct: 138 VRKQVVNIPSFVVRLDSQKHIDFSLKSPFGGGRPGRVKRKNMKKGTNSGAAEEEEED 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	76
FB|FBgn0010408	195	RpS9 "Ribosomal protein S9" [D	0.763	0.297	0.741	1.2e-17
UNIPROTKB|A6QLG5	194	RPS9 "40S ribosomal protein S9	0.763	0.298	0.706	3.2e-17
UNIPROTKB|E2R8R8	194	RPS9 "Uncharacterized protein"	0.763	0.298	0.706	3.2e-17
UNIPROTKB|P46781	194	RPS9 "40S ribosomal protein S9	0.763	0.298	0.706	3.2e-17
UNIPROTKB|I3LEX0	193	RPS9 "40S ribosomal protein S9	0.763	0.300	0.706	3.2e-17
UNIPROTKB|A9L913	194	RPS9 "40S ribosomal protein S9	0.763	0.298	0.706	3.2e-17
MGI|MGI:1924096	194	Rps9 "ribosomal protein S9" [M	0.763	0.298	0.706	3.2e-17
RGD|619889	194	Rps9 "ribosomal protein S9" [R	0.763	0.298	0.706	3.2e-17
ZFIN|ZDB-GENE-010724-15	194	rps9 "ribosomal protein S9" [D	0.763	0.298	0.706	6.7e-17
RGD|1566136	194	RGD1566136 "similar to 40S rib	0.763	0.298	0.672	7.7e-16

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

 Score = 215 (80.7 bits), Expect = 1.2e-17, P = 1.2e-17
 Identities = 43/58 (74%), Positives = 46/58 (79%)

Query:    19 VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
             VRKQVVNIPSFVVRLDSQKHIDFSL SPFGGG  GRVKRKNL+K         EE+E+
Sbjct:   138 VRKQVVNIPSFVVRLDSQKHIDFSLKSPFGGGRPGRVKRKNLKKNQGGGGGAAEEEED 195

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

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

 Score = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 41/58 (70%), Positives = 47/58 (81%)

Query:    19 VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
             VRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct:   137 VRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

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 = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 41/58 (70%), Positives = 47/58 (81%)

Query:    19 VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
             VRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct:   137 VRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

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 = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 41/58 (70%), Positives = 47/58 (81%)

Query:    19 VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
             VRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct:   137 VRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

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 = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 41/58 (70%), Positives = 47/58 (81%)

Query:    19 VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
             VRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct:   136 VRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 193

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 = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 41/58 (70%), Positives = 47/58 (81%)

Query:    19 VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
             VRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct:   137 VRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

GO:0030529 "ribonucleoprotein complex" evidence=ISS

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

 Score = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 41/58 (70%), Positives = 47/58 (81%)

Query:    19 VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
             VRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct:   137 VRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

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 = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 41/58 (70%), Positives = 47/58 (81%)

Query:    19 VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
             VRKQVVNIPSF+VRLDSQKHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct:   137 VRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

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

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

 Score = 208 (78.3 bits), Expect = 6.7e-17, P = 6.7e-17
 Identities = 41/58 (70%), Positives = 46/58 (79%)

Query:    19 VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
             VRKQVVNIPSFVVRLDSQKHIDFSL SP+GGG  GRVKRKN +KA        +E+E+
Sbjct:   137 VRKQVVNIPSFVVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKAQGGGGGGDDEEED 194

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

RGD|1566136 RGD1566136 "similar to 40S ribosomal protein S9" [Rattus norvegicus (taxid:10116)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 39/58 (67%), Positives = 45/58 (77%)

Query:    19 VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
             VRKQVVNIPSF+V LDS KHIDFSL SP+GGG  GRVKRKN +K    A A  +E+E+
Sbjct:   137 VRKQVVNIPSFIVCLDSHKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED 194

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

GO:0006412 "translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P52810	RS9_PODAS	No assigned EC number	0.6964	0.7236	0.2894	yes	N/A
P29314	RS9_RAT	No assigned EC number	0.7068	0.7631	0.2989	yes	N/A
P55935	RS9_DROME	No assigned EC number	0.9090	0.5789	0.2256	yes	N/A
Q20228	RS9_CAEEL	No assigned EC number	0.7727	0.5789	0.2328	yes	N/A
A6QLG5	RS9_BOVIN	No assigned EC number	0.7068	0.7631	0.2989	yes	N/A
P46781	RS9_HUMAN	No assigned EC number	0.7068	0.7631	0.2989	yes	N/A
Q9LXG1	RS91_ARATH	No assigned EC number	0.7083	0.6315	0.2424	yes	N/A
Q6ZWN5	RS9_MOUSE	No assigned EC number	0.7068	0.7631	0.2989	yes	N/A
O13516	RS9A_YEAST	No assigned EC number	0.66	0.6447	0.2487	yes	N/A
P05755	RS9B_YEAST	No assigned EC number	0.6904	0.5526	0.2153	yes	N/A
Q09757	RS9A_SCHPO	No assigned EC number	0.7560	0.5394	0.2146	yes	N/A
O59675	RS9B_SCHPO	No assigned EC number	0.7560	0.5394	0.2135	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	76
PLN00189	194	PLN00189, PLN00189, 40S ribosomal protein S9; Prov	1e-24
PTZ00155	181	PTZ00155, PTZ00155, 40S ribosomal protein S9; Prov	2e-21
TIGR01018	162	TIGR01018, rpsD_arch, ribosomal protein S4(archaea	6e-11

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

 Score = 90.2 bits (224), Expect = 1e-24
 Identities = 41/58 (70%), Positives = 45/58 (77%), Gaps = 1/58 (1%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE 76
           V KQ+VN+PSF+VR+DSQKHIDFSL SP GGG  GRVKRKN  KAAS      EEDEE
Sbjct: 138 VGKQIVNVPSFMVRVDSQKHIDFSLTSPLGGGRPGRVKRKNQ-KAASGGGDGDEEDEE 194

Length = 194

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

 Score = 81.7 bits (202), Expect = 2e-21
 Identities = 29/46 (63%), Positives = 36/46 (78%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAA 64
           V KQ+V+IPSF+VR+DS+KHIDF+  SPFG G  GRVKRK  + A 
Sbjct: 136 VGKQIVDIPSFLVRVDSEKHIDFADTSPFGNGRPGRVKRKAAKAAK 181

Length = 181

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

 Score = 54.4 bits (131), Expect = 6e-11
 Identities = 13/30 (43%), Positives = 20/30 (66%)

Query: 19  VRKQVVNIPSFVVRLDSQKHIDFSLNSPFG 48
           V  + V  PS++VR + +K IDF+ +SPF 
Sbjct: 133 VDGRRVTSPSYIVRREEEKKIDFAPSSPFK 162

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	76
PLN00189	194	40S ribosomal protein S9; Provisional	99.95
PTZ00155	181	40S ribosomal protein S9; Provisional	99.91
KOG3301|consensus	183		99.91
COG0522	205	RpsD Ribosomal protein S4 and related proteins [Tr	99.81
TIGR01018	162	rpsD_arch ribosomal protein S4(archaeal type)/S9(e	99.81
PRK04051	177	rps4p 30S ribosomal protein S4P; Validated	99.72
CHL00113	201	rps4 ribosomal protein S4; Reviewed	98.99
PF01479	48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	98.93
TIGR01017	200	rpsD_bact ribosomal protein S4, bacterial/organell	98.88
PRK05327	203	rpsD 30S ribosomal protein S4; Validated	98.86
cd00165	70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	98.14
TIGR02988	59	YaaA_near_RecF S4 domain protein YaaA. This small	97.99
smart00363	60	S4 S4 RNA-binding domain.	97.83
PRK10348	133	ribosome-associated heat shock protein Hsp15; Prov	97.61
KOG4655|consensus	181		97.58
TIGR00478	228	tly hemolysin TlyA family protein. Hemolysins are	97.37
COG1188	100	Ribosome-associated heat shock protein implicated	97.36
TIGR03069	257	PS_II_S4 photosystem II S4 domain protein. Members	97.09
PLN00051	267	RNA-binding S4 domain-containing protein; Provisio	96.26
COG1189	245	Predicted rRNA methylase [Translation, ribosomal s	96.18
PRK10839	232	16S rRNA pseudouridylate synthase A; Provisional	96.11
PRK10700	289	23S rRNA pseudouridylate synthase B; Provisional	95.8
COG2302	257	Uncharacterized conserved protein, contains S4-lik	95.32
PRK11180	325	rluD 23S rRNA pseudouridine synthase D; Provisiona	95.28
TIGR00005	299	rluA_subfam pseudouridine synthase, RluA family. m	95.04
PRK10475	290	23S rRNA pseudouridine synthase F; Provisional	94.84
PRK11507	70	ribosome-associated protein; Provisional	94.06
PRK11025	317	23S rRNA pseudouridylate synthase C; Provisional	93.24
COG0564	289	RluA Pseudouridylate synthases, 23S RNA-specific [	92.87
PRK13354	410	tyrosyl-tRNA synthetase; Provisional	92.85
COG1187	248	RsuA 16S rRNA uridine-516 pseudouridylate synthase	92.54
PF13275	65	S4_2: S4 domain; PDB: 1P9K_A.	91.79
PRK05912	408	tyrosyl-tRNA synthetase; Validated	90.96
COG1471	241	RPS4A Ribosomal protein S4E [Translation, ribosoma	90.74
PF14451	81	Ub-Mut7C: Mut7-C ubiquitin	83.3
PLN02799	82	Molybdopterin synthase sulfur carrier subunit	82.55

>PLN00189 40S ribosomal protein S9; Provisional

Probab=99.95  E-value=1e-28  Score=179.38  Aligned_cols=73  Identities=48%  Similarity=0.756  Sum_probs=67.2

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCCcchhhhhhhhhhhccCCCCCCc
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEE   73 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~pgR~krk~~~~~~~~~~~~~~e   73 (76)
                      ||+|+.+|||||+||||.|||++||+|||+|++++|++|+|+.+|||+++.|||+|||+++++++++++|+|+
T Consensus       120 ~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~~~Sp~~~~~p~r~~~k~~~~~~~~~~~~~~~  192 (194)
T PLN00189        120 MAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSLTSPLGGGRPGRVKRKNQKAASGGGDGDEED  192 (194)
T ss_pred             CcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEEecCCcccCCChhHHHHHHHHhccCCCCccccc
Confidence            7999999999999999999999999999999999999999999999999789999999999997765554443

>PTZ00155 40S ribosomal protein S9; Provisional

Probab=99.91  E-value=2.1e-25  Score=160.28  Aligned_cols=63  Identities=46%  Similarity=0.741  Sum_probs=60.1

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCCcchhhhhhhhhh
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKA   63 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~pgR~krk~~~~~   63 (76)
                      ||+|+.+|||||+||||.|||++||+|||+|++++|++|+|+.+|||+++.|+|++||+++++
T Consensus       118 ~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~~S~~~~~~~~r~~~~~~~~~  180 (181)
T PTZ00155        118 LAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFADTSPFGNGRPGRVKRKAAKAA  180 (181)
T ss_pred             CcCCHHHhhhheeCCCEEECCEEeccCceEeccCccCceeeecCCCccCCChHHHHHHhhhhc
Confidence            799999999999999999999999999999999999999999999999877999999888754

>KOG3301|consensus

Probab=99.91  E-value=6.9e-25  Score=158.18  Aligned_cols=76  Identities=50%  Similarity=0.738  Sum_probs=67.1

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCCcchhhhhhhhhhhccCCCCCCcccC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE   76 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~pgR~krk~~~~~~~~~~~~~~e~~~   76 (76)
                      |.-|+.+|||||+|+||.|++|+||||||+|+.+++++|||+.+|||++++|||+|+|++++..++.++.+++||+
T Consensus       108 lAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrldsqk~iD~s~~s~~g~~~pg~~krk~~~k~~~~~g~~~~~Ee~  183 (183)
T KOG3301|consen  108 LAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRLDSQKHIDFSLPSPYGGARPGRVKRKNNQKADAKGGGLDENEEE  183 (183)
T ss_pred             hhhhhHHHHHHhcCccEEecCeEeeccceeEeechhhhccccccccCCCCCcchhhhhhhhhhhcccCCccccccC
Confidence            4568999999999999999999999999999999999999999999999999999999877776555555555543

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

Probab=99.81  E-value=6e-21  Score=138.96  Aligned_cols=54  Identities=20%  Similarity=0.133  Sum_probs=50.2

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCC-cch
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG-TGR   54 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~-pgR   54 (76)
                      |.+|+++|||||+||||+|||++||||||+|+++|+..|.+..+|++.... +.+
T Consensus       105 fA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~s~~~~~~~~~~  159 (205)
T COG0522         105 FAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKSKSPIKIKEALEL  159 (205)
T ss_pred             ccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeeecccchhhhhhhhhh
Confidence            578999999999999999999999999999999999999999999999766 443

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

Probab=99.81  E-value=2.1e-20  Score=132.57  Aligned_cols=48  Identities=31%  Similarity=0.509  Sum_probs=46.9

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFG   48 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~   48 (76)
                      ||+|+.+|||||+||||.|||++||+|||+|++++|++|+|+.+|||+
T Consensus       115 ~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~~S~~~  162 (162)
T TIGR01018       115 LARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFAPSSPFK  162 (162)
T ss_pred             CcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeeecCCCCC
Confidence            789999999999999999999999999999999999999999999985

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

>PRK04051 rps4p 30S ribosomal protein S4P; Validated

Probab=99.72  E-value=8e-18  Score=120.60  Aligned_cols=57  Identities=21%  Similarity=0.318  Sum_probs=53.1

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCC-cchhhh
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG-TGRVKR   57 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~-pgR~kr   57 (76)
                      ||.|+.+|||||.||||.|||++|++|||+|+.++|++|+|+.+||+.... |+|..-
T Consensus       114 la~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~S~i~~~~~~~r~~~  171 (177)
T PRK04051        114 LARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSPLADELHPERAEA  171 (177)
T ss_pred             CcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeCCCCCCCCCCcchhhh
Confidence            689999999999999999999999999999999999999999999999855 887543

>CHL00113 rps4 ribosomal protein S4; Reviewed

Probab=98.99  E-value=3.6e-10  Score=82.15  Aligned_cols=43  Identities=21%  Similarity=0.251  Sum_probs=37.8

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNS   45 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~S   45 (76)
                      +|+|+.+|||||.||||.|||++|++|||.|+.|  +.|.+...|
T Consensus       100 ~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~G--D~I~V~~~~  142 (201)
T CHL00113        100 MAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPK--DIITVKDKQ  142 (201)
T ss_pred             CCCCHHHHHHHHHCCcEEECCEEecCccccCCCC--CEEEEcccc
Confidence            3789999999999999999999999999999998  467776533

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

Probab=98.93  E-value=7.6e-10  Score=62.30  Aligned_cols=36  Identities=19%  Similarity=0.240  Sum_probs=33.7

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQ   36 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de   36 (76)
                      .|+|+.+|++||.||+|.|||++|+-|+|.|+.+|+
T Consensus        12 ~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~   47 (48)
T PF01479_consen   12 LASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPGDV   47 (48)
T ss_dssp             SSSSHHHHHHHHHTTTEEETTEEESSTTSBESTTEE
T ss_pred             CcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCcCC
Confidence            478999999999999999999999999999998874

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 ....

>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type

Probab=98.88  E-value=2e-09  Score=77.52  Aligned_cols=43  Identities=28%  Similarity=0.311  Sum_probs=37.9

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNS   45 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~S   45 (76)
                      +|+|+.+|||||.||||.|||++|++|||.|+.||  .|.+...+
T Consensus       101 ~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD--~I~V~~~~  143 (200)
T TIGR01017       101 FAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGD--IISIKEKS  143 (200)
T ss_pred             CCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCC--EEEEeeCc
Confidence            36899999999999999999999999999999995  67776543

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=98.86  E-value=1.8e-09  Score=77.93  Aligned_cols=41  Identities=24%  Similarity=0.216  Sum_probs=37.3

Q ss_pred             CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeC
Q psy7990           2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLN   44 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~   44 (76)
                      ++|+.+|||||.||||.|||++|++|||.|+.||.  |++...
T Consensus       105 ~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~--I~v~~~  145 (203)
T PRK05327        105 APTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDV--IEVREK  145 (203)
T ss_pred             cCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCE--EEECCc
Confidence            67999999999999999999999999999999965  777755

>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=98.14  E-value=3.6e-06  Score=47.03  Aligned_cols=40  Identities=23%  Similarity=0.189  Sum_probs=35.2

Q ss_pred             CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeee
Q psy7990           2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSL   43 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~   43 (76)
                      +.|..+|++++.+|+|.|||++++.|++.|..++  .|.+..
T Consensus        13 ~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d--~i~i~~   52 (70)
T cd00165          13 APSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGD--VIEVDG   52 (70)
T ss_pred             ccCHHHHHHHHHcCCEEECCEEccCCccCcCCCC--EEEEcC
Confidence            4688999999999999999999988999999985  477765

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA

Probab=97.99  E-value=4.7e-06  Score=49.00  Aligned_cols=35  Identities=6%  Similarity=-0.150  Sum_probs=32.3

Q ss_pred             ccchhhhhhhhcCCeEECCEEeCccceeeecCCCC
Q psy7990           3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQK   37 (76)
Q Consensus         3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~   37 (76)
                      +|.-.++++|..|+|.|||+.++-|+|.|+.||.=
T Consensus        22 ~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v   56 (59)
T TIGR02988        22 DSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVI   56 (59)
T ss_pred             cCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEE
Confidence            57889999999999999999999999999999863

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.

>smart00363 S4 S4 RNA-binding domain

Probab=97.83  E-value=2e-05  Score=42.88  Aligned_cols=40  Identities=18%  Similarity=0.177  Sum_probs=33.9

Q ss_pred             CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeee
Q psy7990           2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSL   43 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~   43 (76)
                      +.|..+|++++.+|+|.|||+.++-|++.|..+|.  |.+..
T Consensus        13 ~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~--i~~~~   52 (60)
T smart00363       13 APSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDV--ISVRG   52 (60)
T ss_pred             ccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCE--EEEcc
Confidence            36788999999999999999999779999988864  66544

>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional

Probab=97.61  E-value=5.4e-05  Score=52.59  Aligned_cols=41  Identities=17%  Similarity=0.124  Sum_probs=36.7

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      ++.|+..|.+||..|+|.|||++ ..||..|+++|+=.|.|.
T Consensus        20 l~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~   60 (133)
T PRK10348         20 FYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQG   60 (133)
T ss_pred             ccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEEC
Confidence            46799999999999999999999 789999999998777654

>KOG4655|consensus

Probab=97.58  E-value=1.4e-05  Score=58.36  Aligned_cols=46  Identities=20%  Similarity=0.271  Sum_probs=43.5

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSP   46 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP   46 (76)
                      ||+++-+|-.||.|||+.|+-.+|+=|+|+|....|+.|.+..+|.
T Consensus       118 m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr~mEDfvtWvd~SK  163 (181)
T KOG4655|consen  118 MAESVKEAVRFVEQGHVRVGPKVVTDPAFLVTRSMEDFVTWVDSSK  163 (181)
T ss_pred             hhhhHHHHHHHHHcCceeeCCeeccCchHHhhhhhhhhhhhhhhHH
Confidence            8999999999999999999999999999999999999999887764

>TIGR00478 tly hemolysin TlyA family protein

Probab=97.37  E-value=0.00017  Score=52.95  Aligned_cols=41  Identities=20%  Similarity=0.105  Sum_probs=36.0

Q ss_pred             CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeC
Q psy7990           2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLN   44 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~   44 (76)
                      ++|+.+|++||.+|.|.|||++++.|++.|..+  +.|.+...
T Consensus        12 ~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~--d~I~v~~~   52 (228)
T TIGR00478        12 FESREKAKRLILKGFVLVNGKKVDKPSALVDFD--AKIELLQN   52 (228)
T ss_pred             ccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCC--CEEeccCc
Confidence            578999999999999999999999999999887  46777644

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).

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

Probab=97.36  E-value=0.00014  Score=48.86  Aligned_cols=39  Identities=23%  Similarity=0.129  Sum_probs=35.4

Q ss_pred             cchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeee
Q psy7990           4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSL   43 (76)
Q Consensus         4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~   43 (76)
                      |+..|.-++.-|+|.|||+++ .||+.|++||+=.|.|..
T Consensus        23 rRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~~   61 (100)
T COG1188          23 RRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFGN   61 (100)
T ss_pred             hHHHHHHHHHCCeEEECCEEc-ccccccCCCCEEEEEeCC
Confidence            677899999999999999998 699999999998888863

>TIGR03069 PS_II_S4 photosystem II S4 domain protein

Probab=97.09  E-value=0.00035  Score=52.10  Aligned_cols=38  Identities=8%  Similarity=0.024  Sum_probs=33.6

Q ss_pred             ccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      -|+..|++||..|+|.|||+.|+.||+.|+.||  .|.+.
T Consensus       196 ~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD--~Isvr  233 (257)
T TIGR03069       196 LSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGD--RLQLR  233 (257)
T ss_pred             hhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCC--EEEEc
Confidence            478899999999999999999999999999986  55554

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.

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

Probab=96.26  E-value=0.0034  Score=47.42  Aligned_cols=38  Identities=5%  Similarity=-0.095  Sum_probs=33.4

Q ss_pred             ccchhhhhhhhcCCeEECCEEeCccceeeecCCCCcee
Q psy7990           3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHID   40 (76)
Q Consensus         3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~   40 (76)
                      -|+..|.+||..|+|.||++.|+-|||.|+.||.=.|.
T Consensus       204 ~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiR  241 (267)
T PLN00051        204 MSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVS  241 (267)
T ss_pred             cCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEe
Confidence            46788999999999999999999999999999864443

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

Probab=96.18  E-value=0.0046  Score=46.97  Aligned_cols=45  Identities=18%  Similarity=0.178  Sum_probs=36.8

Q ss_pred             CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee-eCCCCC
Q psy7990           2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS-LNSPFG   48 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~-~~SP~~   48 (76)
                      |.|+..|+-+|.-|.|.|||++|+.||+.|..+++  |+.. +..||-
T Consensus        15 ~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~--i~v~~~~~~yV   60 (245)
T COG1189          15 FESREKAKELILAGNVLVNGEKVTKPSQLVDIDDE--IEVKGEEQPYV   60 (245)
T ss_pred             hhhHHHHHHHHHcCeEEECCEEecCcceecCCCce--EEEcccCcCcc
Confidence            78999999999999999999999999999995554  5554 444443

>PRK10839 16S rRNA pseudouridylate synthase A; Provisional

Probab=96.11  E-value=0.0057  Score=43.73  Aligned_cols=37  Identities=8%  Similarity=0.146  Sum_probs=32.4

Q ss_pred             cchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      |...+++++..|.|.|||++++.|++.|+.+|.  |.++
T Consensus        14 Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~--I~l~   50 (232)
T PRK10839         14 SRAIAGRELRANRVTVDGEIVKNGAFKLLPEHD--VAYD   50 (232)
T ss_pred             CHHHHHHHHHcCeEEECCEEeccCCcCcCCCCE--EEEC
Confidence            577899999999999999999889999999875  5554

>PRK10700 23S rRNA pseudouridylate synthase B; Provisional

Probab=95.80  E-value=0.011  Score=44.55  Aligned_cols=39  Identities=10%  Similarity=-0.032  Sum_probs=33.8

Q ss_pred             ccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      .|+-+|++||..|.|.|||++++ |++.|.+++.+.|.+.
T Consensus        15 ~SRr~a~~lI~~G~V~VNG~~~~-~g~~V~~~~~d~I~v~   53 (289)
T PRK10700         15 GSRREIESIIEAGRVSVDGKIAT-LGDRVEVTPGLKIRID   53 (289)
T ss_pred             CCHHHHHHHHHcCCEEECCEecc-CCCEeCCCCCeEEEEC
Confidence            36788999999999999999985 9999998877777665

>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]

Probab=95.32  E-value=0.013  Score=44.93  Aligned_cols=36  Identities=22%  Similarity=0.121  Sum_probs=32.0

Q ss_pred             cchhhhhhhhcCCeEECCEEeCccceeeecCCCCce
Q psy7990           4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHI   39 (76)
Q Consensus         4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I   39 (76)
                      |+..|-|||.-|-+.||.+.|+-|||.|+.||-=.|
T Consensus       194 SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSi  229 (257)
T COG2302         194 SRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISI  229 (257)
T ss_pred             hHHHHHHHHHcCceEEeeEEeccccceeccCCEEEE
Confidence            577899999999999999999999999999875333

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional

Probab=95.28  E-value=0.017  Score=43.56  Aligned_cols=38  Identities=18%  Similarity=0.054  Sum_probs=33.0

Q ss_pred             ccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      .|+..++++|..|.|.|||++|+.|++.|+.+|.  |.++
T Consensus        31 ~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~--I~v~   68 (325)
T PRK11180         31 YSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQ--VAID   68 (325)
T ss_pred             cCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCE--EEEe
Confidence            4788899999999999999999889999998875  4444

>TIGR00005 rluA_subfam pseudouridine synthase, RluA family

Probab=95.04  E-value=0.018  Score=42.30  Aligned_cols=37  Identities=16%  Similarity=0.112  Sum_probs=31.2

Q ss_pred             cchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      |...++++|..|.|.|||+++.-|++.|+.+|.  |.++
T Consensus        20 Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~--I~i~   56 (299)
T TIGR00005        20 SRSRIQKLIENGQVKVNGKVTANPKLKVKDGDR--ITVR   56 (299)
T ss_pred             CHHHHHHHHHCCcEEECCEeccCcccCCCCCCE--EEEe
Confidence            678899999999999999877679999999864  5543

modifies uracil-65 in transfer RNAs to pseudouridine.

>PRK10475 23S rRNA pseudouridine synthase F; Provisional

Probab=94.84  E-value=0.022  Score=43.21  Aligned_cols=37  Identities=8%  Similarity=0.017  Sum_probs=30.9

Q ss_pred             ccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      .|+.+|++||..|.|.|||++++ |++.|..+|.  |.++
T Consensus        19 ~SRr~a~~lI~~G~V~VNGk~v~-~~~~V~~gD~--V~v~   55 (290)
T PRK10475         19 CSRREADRYIEQGNVFINGKRAT-IGDQVKAGDV--VKVN   55 (290)
T ss_pred             CCHHHHHHHHHCCcEEECCEEcc-CCCCcCCCCE--EEEC
Confidence            36889999999999999999985 9999988754  5554

>PRK11507 ribosome-associated protein; Provisional

Probab=94.06  E-value=0.061  Score=34.01  Aligned_cols=36  Identities=6%  Similarity=-0.171  Sum_probs=32.5

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQ   36 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de   36 (76)
                      .|+|=-+|.+||.-|.|.|||.+-+.-+-.+++||.
T Consensus        23 ~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~   58 (70)
T PRK11507         23 WSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQT   58 (70)
T ss_pred             cccChHHHHHHHHcCceEECCEEecccCCCCCCCCE
Confidence            367888999999999999999999999988888875

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional

Probab=93.24  E-value=0.068  Score=40.23  Aligned_cols=36  Identities=8%  Similarity=0.187  Sum_probs=31.0

Q ss_pred             cchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      +...+++++..|.|.|||++++ |++.|+.+|+  |.+.
T Consensus        34 sr~~i~~li~~G~V~VNg~~v~-~~~~v~~GD~--I~i~   69 (317)
T PRK11025         34 PKSMIYRILRKGEVRVNKKRIK-PEYKLEAGDE--VRIP   69 (317)
T ss_pred             CHHHHHHHHHcCCEEECCEEcC-cccccCCCCE--EEeC
Confidence            6778899999999999999996 9999999964  6553

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

Probab=92.87  E-value=0.1  Score=39.49  Aligned_cols=39  Identities=13%  Similarity=0.095  Sum_probs=33.9

Q ss_pred             cchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeee
Q psy7990           4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSL   43 (76)
Q Consensus         4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~   43 (76)
                      +.-+...++..|.|.|||++|+ |+|.|..||.=.|.+..
T Consensus        26 sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~   64 (289)
T COG0564          26 SRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPE   64 (289)
T ss_pred             CHHHHHHHHHCCCEEECCEEcc-CCeeeCCCCEEEEeccc
Confidence            3456678899999999999999 99999999998888765

>PRK13354 tyrosyl-tRNA synthetase; Provisional

Probab=92.85  E-value=0.086  Score=41.77  Aligned_cols=34  Identities=3%  Similarity=-0.015  Sum_probs=30.3

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLD   34 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~   34 (76)
                      +|+|--+||.||..|-|.|||.+|+-|.+.+..+
T Consensus       354 ~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~  387 (410)
T PRK13354        354 LEPSKREARRLIQNGAIKINGEKVTDVDAIINPE  387 (410)
T ss_pred             CCCCHHHHHHHHHcCCEEECCEEccCcccccChh
Confidence            5899999999999999999999998887777654

>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]

Probab=92.54  E-value=0.17  Score=38.11  Aligned_cols=33  Identities=18%  Similarity=0.126  Sum_probs=30.6

Q ss_pred             ccchhhhhhhhcCCeEECCEEeCccceeeecCC
Q psy7990           3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDS   35 (76)
Q Consensus         3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~d   35 (76)
                      -|+.+|.+||.-|.|.|||+++..+...|..++
T Consensus        15 ~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~   47 (248)
T COG1187          15 GSRREAEKLIEEGRVTVNGKVATLGGVVVDPDD   47 (248)
T ss_pred             CCHHHHHHHHHcCCEEECCEEeccCCeEeCCCC
Confidence            478899999999999999999999999998886

>PF13275 S4_2: S4 domain; PDB: 1P9K_A

Probab=91.79  E-value=0.043  Score=34.01  Aligned_cols=35  Identities=11%  Similarity=-0.100  Sum_probs=23.7

Q ss_pred             CccchhhhhhhhcCCeEECCEEeCccceeeecCCC
Q psy7990           2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQ   36 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de   36 (76)
                      ++|=-+|..||.-|.|.|||.+.+-.+-.+++||.
T Consensus        20 v~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~   54 (65)
T PF13275_consen   20 VSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDV   54 (65)
T ss_dssp             -SSSSTTSHHHHHHHHEETTB----SS----SSEE
T ss_pred             cccHHHHHHHHHcCceEECCEEccccCCcCCCCCE
Confidence            56778999999999999999999999998888875

>PRK05912 tyrosyl-tRNA synthetase; Validated

Probab=90.96  E-value=0.21  Score=39.45  Aligned_cols=33  Identities=9%  Similarity=0.148  Sum_probs=29.0

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeec
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRL   33 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~   33 (76)
                      +|+|--+||.||..|-|.|||.+|.-+.+.+..
T Consensus       354 ~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~  386 (408)
T PRK05912        354 LVPSKSEARRLIKQGGVKINGEKVSDENYVLTA  386 (408)
T ss_pred             CCCCHHHHHHHHHcCCEEECCEEecCccccccc
Confidence            489999999999999999999999877766654

>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]

Probab=90.74  E-value=0.29  Score=37.40  Aligned_cols=61  Identities=18%  Similarity=0.117  Sum_probs=49.3

Q ss_pred             ccchhhhhhhhcCCeEECCEE-------------eCcc----ceeeecCCCCceeeeeCCCCCCC-Ccchhhhhhhhhh
Q psy7990           3 SALFLSTQYWEHQGPGVRKQV-------------VNIP----SFVVRLDSQKHIDFSLNSPFGGG-GTGRVKRKNLRKA   63 (76)
Q Consensus         3 ~t~~~ARQ~V~HgHI~Vng~~-------------VniP----Sy~Vk~~de~~I~~~~~SP~~~~-~pgR~krk~~~~~   63 (76)
                      .+..+||-+++-|+|.|||++             |.||    +|+|=.++.....+.+-|-=... .+-|+++|..-++
T Consensus        55 d~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~tgE~yRvl~d~~grl~l~~is~EeA~~Kl~kV~nKt~vkg  133 (241)
T COG1471          55 DNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPKTGEHYRVLPDEKGRLVLHPISAEEASYKLCKVKNKTTVKG  133 (241)
T ss_pred             cchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECCCCceEEEEecCCccEEEEecChhhccceEEEEEeEEEecC
Confidence            466799999999999999985             6688    89999999999999987744444 4888888776433

>PF14451 Ub-Mut7C: Mut7-C ubiquitin

Probab=83.30  E-value=0.77  Score=29.18  Aligned_cols=26  Identities=8%  Similarity=-0.052  Sum_probs=20.4

Q ss_pred             CCeEECCEEeCccceeeecCCCCceeeee
Q psy7990          15 QGPGVRKQVVNIPSFVVRLDSQKHIDFSL   43 (76)
Q Consensus        15 gHI~Vng~~VniPSy~Vk~~de~~I~~~~   43 (76)
                      +-|+|||+.|+ ++|+++.||  .|.+++
T Consensus        50 ~~i~vNG~~v~-~~~~~~~Gd--~v~V~P   75 (81)
T PF14451_consen   50 GLILVNGRPVD-FDYRLKDGD--RVAVYP   75 (81)
T ss_pred             EEEEECCEECC-CcccCCCCC--EEEEEe
Confidence            56899999999 799988776  455554

>PLN02799 Molybdopterin synthase sulfur carrier subunit

Probab=82.55  E-value=2.4  Score=25.68  Aligned_cols=30  Identities=13%  Similarity=0.283  Sum_probs=21.7

Q ss_pred             CeEECCEEeCccceeeecCCCCceeeeeCCCCCCC
Q psy7990          16 GPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGG   50 (76)
Q Consensus        16 HI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~   50 (76)
                      -|.||++.|+ .++.|+  |-+.|.|.+  |++|+
T Consensus        53 ~vavN~~~v~-~~~~l~--dgDeVai~P--pvsGG   82 (82)
T PLN02799         53 VLALNEEYTT-ESAALK--DGDELAIIP--PISGG   82 (82)
T ss_pred             EEEECCEEcC-CCcCcC--CCCEEEEeC--CCCCC
Confidence            4899999987 776654  455677776  76664

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	76
3iz6_C	195	Localization Of The Small Subunit Ribosomal Protein		5e-14
3izb_C	197	Localization Of The Small Subunit Ribosomal Protein		3e-12
1s1h_D	179	Structure Of The Ribosomal 80s-Eef2-Sordarin Comple		4e-12
2xzm_D	181	Crystal Structure Of The Eukaryotic 40s Ribosomal S		3e-10
3zey_6	190	High-resolution Cryo-electron Microscopy Structure		9e-09
3jyv_D	158	Structure Of The 40s Rrna And Proteins And PE TRNA		8e-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 = 72.8 bits (177), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 32/44 (72%), Positives = 40/44 (90%)
Query: 21  KQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAA 64
           +Q+VNIPSF+VR++S+KHIDFSL SPFGGG  GRVKRKN +KA+
Sbjct: 140 RQIVNIPSFMVRVESEKHIDFSLTSPFGGGPPGRVKRKNQKKAS 183

>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 = 67.0 bits (162), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 33/50 (66%), Positives = 39/50 (78%), Gaps = 1/50 (2%)
Query: 18  GVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKN-LRKAASS 66
            V KQ+VNIPSF+VRLDS+KHIDF+  SPFGG   GRV R+N  RKA +S
Sbjct: 135 AVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKAEAS 184

>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 = 66.6 bits (161), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 33/50 (66%), Positives = 39/50 (78%), Gaps = 1/50 (2%)
Query: 18  GVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKN-LRKAASS 66
            V KQ+VNIPSF+VRLDS+KHIDF+  SPFGG   GRV R+N  RKA +S
Sbjct: 117 AVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKAEAS 166

>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 = 60.1 bits (144), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 27/44 (61%), Positives = 34/44 (77%)
Query: 21  KQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAA 64
           K +VN+PSF+VR DS+K IDF+  SP GGG  GR KRKN +K+A
Sbjct: 138 KNLVNVPSFMVRTDSEKSIDFASTSPLGGGREGRTKRKNAKKSA 181

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 18  GVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDE 75
            V KQ+V IPSF+VR+ S+ HI F+  SPFG G  GRVKR   R AA   +   ++DE
Sbjct: 134 AVAKQIVTIPSFIVRVSSEHHIAFADASPFGNGRPGRVKRVK-RNAAKKGSGGGDDDE 190

>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 = 48.5 bits (114), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 21/29 (72%), Positives = 25/29 (86%)
Query: 18  GVRKQVVNIPSFVVRLDSQKHIDFSLNSP 46
            V KQ+VNIPSF+VRLDS+KHIDF+  SP
Sbjct: 130 AVGKQIVNIPSFMVRLDSEKHIDFAPTSP 158

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	76
3u5c_J	197	40S ribosomal protein S9-A; translation, ribosome,	1e-18
3iz6_C	195	40S ribosomal protein S9 (S4P); eukaryotic ribosom	9e-18
2xzm_D	181	Ribosomal protein S4 containing protein; ribosome,	9e-16
2cqj_A	71	BRMS2, U3 small nucleolar ribonucleoprotein protei	8e-10

>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 = 74.8 bits (183), Expect = 1e-18
 Identities = 32/76 (42%), Positives = 47/76 (61%)

Query: 1   MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNL 60
           +  ++  +      +   V KQ+VNIPSF+VRLDS+KHIDF+  SPFGG   GRV R+N 
Sbjct: 118 LAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNA 177

Query: 61  RKAASSATAPTEEDEE 76
            + A ++    +E +E
Sbjct: 178 ARKAEASGEAADEADE 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 = 72.0 bits (176), Expect = 9e-18
 Identities = 39/76 (51%), Positives = 51/76 (67%)

Query: 1   MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNL 60
           M  ++  +      +   V +Q+VNIPSF+VR++S+KHIDFSL SPFGGG  GRVKRKN 
Sbjct: 120 MAKSIHHARVLIRQRHIRVGRQIVNIPSFMVRVESEKHIDFSLTSPFGGGPPGRVKRKNQ 179

Query: 61  RKAASSATAPTEEDEE 76
           +KA+       EEDEE
Sbjct: 180 KKASGGGGDGEEEDEE 195

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

 Score = 66.6 bits (162), Expect = 9e-16
 Identities = 29/64 (45%), Positives = 41/64 (64%)

Query: 1   MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNL 60
           + +++  S      +   V K +VN+PSF+VR DS+K IDF+  SP GGG  GR KRKN 
Sbjct: 118 LANSIHHSRVLIRQRHIKVGKNLVNVPSFMVRTDSEKSIDFASTSPLGGGREGRTKRKNA 177

Query: 61  RKAA 64
           +K+A
Sbjct: 178 KKSA 181

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

 Score = 48.9 bits (117), Expect = 8e-10
 Identities = 12/53 (22%), Positives = 21/53 (39%)

Query: 1  MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTG 53
          M   L  +  + E     V   VV  P+F+V    +  + +  +S   G  +G
Sbjct: 19 MAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWVDSSKISGPSSG 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	76
3iz6_C	195	40S ribosomal protein S9 (S4P); eukaryotic ribosom	99.93
3u5c_J	197	40S ribosomal protein S9-A; translation, ribosome,	99.91
2xzm_D	181	Ribosomal protein S4 containing protein; ribosome,	99.81
2cqj_A	71	BRMS2, U3 small nucleolar ribonucleoprotein protei	99.59
3j20_D	180	30S ribosomal protein S4P; archaea, archaeal, KINK	99.58
3bbn_D	201	Ribosomal protein S4; small ribosomal subunit, spi	99.13
2vqe_D	209	30S ribosomal protein S4; tRNA-binding, rRNA-bindi	98.9
3r8n_D	205	30S ribosomal protein S4; protein biosynthesis, RN	98.89
1c05_A	159	Ribosomal protein S4 delta 41; two subdomains, uni	98.87
3j20_E	243	30S ribosomal protein S4E; archaea, archaeal, KINK	98.27
3kbg_A	213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	98.25
2k6p_A	92	Uncharacterized protein HP_1423; alpha-L motif, RN	97.87
1p9k_A	79	ORF, hypothetical protein; alfal motif, RNA-bindin	97.78
1dm9_A	133	Hypothetical 15.5 KD protein in MRCA-PCKA intergen	97.78
3hp7_A	291	Hemolysin, putative; structural genomics, APC64019	97.19
1vio_A	243	Ribosomal small subunit pseudouridine synthase A;	97.03
1ksk_A	234	Ribosomal small subunit pseudouridine synthase A;	96.85
3dh3_A	290	Ribosomal large subunit pseudouridine synthase F;	95.8
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	95.77
1fm0_D	81	Molybdopterin convertin factor, subunit 1; molybde	92.9
2jan_A	432	Tyrosyl-tRNA synthetase; protein biosynthesis, ami	91.52
1h3f_A	432	Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy	91.2
1jil_A	420	Tyrrs, tyrosyl-tRNA synthetase; truncation, based	91.2
2q5w_D	77	Molybdopterin converting factor, subunit 1; MOCO,	91.05
2ts1_A	419	Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30	88.62
1vjk_A	98	Molybdopterin converting factor, subunit 1; struct	87.3
3dwg_C	93	9.5 kDa culture filtrate antigen CFP10A; sulfur ca	87.01
2g1e_A	90	Hypothetical protein TA0895; MOAD, molybdopterin,	83.84
3rpf_C	74	Molybdopterin converting factor, subunit 1 (MOAD);	83.19
2ktl_A	164	Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA s	82.09
2qjl_A	99	URM1, ubiquitin-related modifier 1; ubiquitin-like	81.51

>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=99.93  E-value=9.1e-28  Score=173.08  Aligned_cols=76  Identities=51%  Similarity=0.793  Sum_probs=70.2

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCCcchhhhhhhhhhhccCCCCCCcccC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKAASSATAPTEEDEE   76 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~pgR~krk~~~~~~~~~~~~~~e~~~   76 (76)
                      +|+|+.+|||||.||||.|||++|++|||+|+++++.+|+|..+|||+++.|||+|||+++++.+++++++|||||
T Consensus       120 ~a~SR~~ArqlI~~GhV~VNG~~V~~Ps~~V~~gde~~I~~~~~spyv~~~~gr~~rk~~~~~~~~~~~~~~~~~~  195 (195)
T 3iz6_C          120 MAKSIHHARVLIRQRHIRVGRQIVNIPSFMVRVESEKHIDFSLTSPFGGGPPGRVKRKNQKKASGGGGDGEEEDEE  195 (195)
T ss_dssp             CHHHHSCTTSHHHHHSTTTSCCCCCCCCCCCSSSCSSSSCSSSCCCCCCCCCCHHHHHHHHTTTSSSSCCCCCCCC
T ss_pred             ccCCHHHHHHHHHcCCEEECCEEeCCCCcCcCCCCEEEEEecCCCCCCCCCchhHHHHHHhhccCCCCCccccccC
Confidence            5789999999999999999999999999999999999999999999999999999999999987776676666664

>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=99.91  E-value=6.8e-26  Score=163.51  Aligned_cols=63  Identities=46%  Similarity=0.754  Sum_probs=61.2

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCCcchhhhhhhhhh
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKA   63 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~pgR~krk~~~~~   63 (76)
                      +|+|+.+|||||.||||.|||++|++|||+|++++++.|.|..+|||.+++|||+|||+++++
T Consensus       118 ~a~Sr~~ArqLI~~GhV~VNG~~V~~Ps~~V~~g~ed~I~~~~~spyvs~~~gr~~rk~~~~~  180 (197)
T 3u5c_J          118 LAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARK  180 (197)
T ss_dssp             TTSSHHHHHHHHHTSCCBSSSCBCCCTTCCCCSTTGGGCBCCSSSSSSSSCCCHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHcCCEEECCEEeCCCccccCCCCccEEEEcCCCCCcCCCchhHHHHHHHhh
Confidence            588999999999999999999999999999999999999999999999999999999999885

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

Probab=99.81  E-value=1.5e-20  Score=133.21  Aligned_cols=63  Identities=44%  Similarity=0.718  Sum_probs=59.9

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCCcchhhhhhhhhh
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGTGRVKRKNLRKA   63 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~pgR~krk~~~~~   63 (76)
                      +|+|+.+|||||.||||.|||++|++|||+|.++|++.|.|...|||.++.|||+|||+++++
T Consensus       118 ~a~SR~~Ar~LI~~G~V~VNg~~V~~Ps~~V~~~d~~~I~v~~~s~~~~~~~~r~~~~~~~~~  180 (181)
T 2xzm_D          118 LANSIHHSRVLIRQRHIKVGKNLVNVPSFMVRTDSEKSIDFASTSPLGGGREGRTKRKNAKKS  180 (181)
T ss_dssp             CSSSTTHHHHHTTTTCCEETTEECCCSCCBCCSTTSSCEECTTSTTTTTCCSHHHHHHHHHC-
T ss_pred             ccCCHHHHHHHHHCCEEEECCEEECCCCcCCCCCCceEEEEeCCCccCCCCCchhhhhhhccC
Confidence            578999999999999999999999999999999999999999999999999999999998864

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

Probab=99.59  E-value=2.8e-16  Score=96.41  Aligned_cols=51  Identities=22%  Similarity=0.291  Sum_probs=48.0

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG   51 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~   51 (76)
                      +|+|+.+|||||.||||.|||++|++|||+|++++++.|.|...|++....
T Consensus        19 la~SR~~A~~lI~~G~V~Vng~~v~kps~~V~~~~~d~I~~~~~~~~~~~~   69 (71)
T 2cqj_A           19 MAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWVDSSKISGPS   69 (71)
T ss_dssp             CSSSHHHHHHHHHTTCEEETTBCCCCTTCEEEHHHHTTEEESCCSSSCCCC
T ss_pred             CcCCHHHHHHHHHCCcEEECCEEECCCCCCCCCCCCcEEEEECCceecccc
Confidence            589999999999999999999999999999999999999999999997653

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

Probab=99.58  E-value=3e-16  Score=111.49  Aligned_cols=61  Identities=20%  Similarity=0.336  Sum_probs=55.8

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCCC-cchhhhhhhh
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGG-TGRVKRKNLR   61 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~~-pgR~krk~~~   61 (76)
                      +|.|+.+|||||.||||.|||++|++|||+|.+++++.|.|..+|||..+. |+|.-.-+++
T Consensus       114 ~a~SR~~Ar~LI~~G~V~VNg~~V~~Ps~~V~~~~eD~I~v~~~s~i~~~~~~~~~~~~~~~  175 (180)
T 3j20_D          114 LARTMRQARQLIVHGHIEVNGQIIRSPSYLVLKEEEDTITYARTSPFANPQHPERMMIEKAK  175 (180)
T ss_dssp             SSSSHHHHHHHHHHTCCEESSSBCCCSSCCCCTGGGGCEECSSCSSSSSSCCHHHHHHHHCC
T ss_pred             ccCcHHHHHHHHHcCCeEECCEEeCCCCcccCCCCCCEEEEeCCCcccCCCCCcchhHHHHh
Confidence            578999999999999999999999999999999999999999999999887 8887665444

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

Probab=99.13  E-value=2.7e-11  Score=86.97  Aligned_cols=43  Identities=21%  Similarity=0.220  Sum_probs=37.6

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNS   45 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~S   45 (76)
                      ++.|+.+|||||.||||.|||++|++|||.|+++|  .|.+...+
T Consensus       100 ~a~SR~~ArqLI~~G~V~VNG~~V~~pS~~V~~gD--~I~V~~~~  142 (201)
T 3bbn_D          100 MAPTIPGARQLVNHRHILVNGRIVDIPSYRCKPQD--TIMARDEQ  142 (201)
T ss_dssp             SSSSSHHHHHHHHTTCEEETTEECCCTTCBCCTTE--EEEECSST
T ss_pred             CcCCHHHHHHHHhCCcEEeCCEEEeecceecCCCC--EEEEcccc
Confidence            46899999999999999999999999999999986  56666443

>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=98.90  E-value=7.9e-10  Score=79.01  Aligned_cols=43  Identities=23%  Similarity=0.248  Sum_probs=37.7

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNS   45 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~S   45 (76)
                      ++.|+.+|||||.||||.|||++|++|||.|+++|  .|.+...|
T Consensus       110 ~~~SR~~arqLI~~G~V~VNG~~v~~ps~~V~~gD--~I~V~~~~  152 (209)
T 2vqe_D          110 FAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGD--EIAVAEKS  152 (209)
T ss_dssp             SSSSHHHHHHHHHTTCEEETTEECCCTTCBCCTTC--EEEECGGG
T ss_pred             CcCCHHHHHHHHHCCCEEECCEEeCcCCcCcCCCC--EEEEcCcc
Confidence            36799999999999999999999999999999976  57776553

>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=98.87  E-value=1.2e-09  Score=75.00  Aligned_cols=42  Identities=26%  Similarity=0.187  Sum_probs=37.3

Q ss_pred             CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCC
Q psy7990           2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNS   45 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~S   45 (76)
                      ++|+.+|||||.||||.|||++|+.|||.|+++|  .|.+...|
T Consensus        63 ~~SR~~ar~lI~~G~V~VNG~~v~~ps~~V~~gD--~I~V~~~~  104 (159)
T 1c05_A           63 ARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQ--TIAVREKS  104 (159)
T ss_dssp             CSSHHHHHHHHHTTCEEETTEECCCSSCBCCTTC--EEEECGGG
T ss_pred             cCCHHHHHHHHHCCCEEECCEEeCcCCcEeCCCC--EEEEeCce
Confidence            6799999999999999999999999999999986  57776553

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

Probab=98.27  E-value=3.4e-07  Score=67.77  Aligned_cols=39  Identities=13%  Similarity=-0.060  Sum_probs=35.3

Q ss_pred             CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCcee
Q psy7990           2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHID   40 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~   40 (76)
                      ..|..+|||++.||||.|||++++.|+|-|...|.-.|.
T Consensus        56 A~t~rEar~Iv~~~~I~VdGKvr~d~~ypvG~mDVIsI~   94 (243)
T 3j20_E           56 AKTAREARKILNEGKFLVDGRVRKDYKFPVGIMDVVSIP   94 (243)
T ss_dssp             CSSHHHHHHHHHHCSCEETTEECCCSSCEECTTCEEEET
T ss_pred             ccCHHHHHHHHHCCcEEECCEEeccccCCcccceEEEec
Confidence            357899999999999999999999999999999876664

>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=98.25  E-value=6.1e-07  Score=65.37  Aligned_cols=38  Identities=13%  Similarity=0.002  Sum_probs=34.5

Q ss_pred             CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCce
Q psy7990           2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHI   39 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I   39 (76)
                      ..|..+|||++.||||.|||++++.|+|.|...|.-.|
T Consensus        21 A~t~rEarkIv~~~~I~VDGKvr~d~~ypvG~mDVIsI   58 (213)
T 3kbg_A           21 SDKEREAARILANGLVKVDGKTVREKKFAVGFMDVIEI   58 (213)
T ss_dssp             TTCGGGHHHHHHTTCEEETTEECCCTTCEECTTCEEEE
T ss_pred             cccHHHHHHHHHCCCEEECCEEecccCCCccceeEEEe
Confidence            35789999999999999999999999999999987665

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

Probab=97.87  E-value=4.7e-06  Score=51.23  Aligned_cols=38  Identities=11%  Similarity=0.004  Sum_probs=32.3

Q ss_pred             CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCcee
Q psy7990           2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHID   40 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~   40 (76)
                      |+|...|++||.+|.|.|||+.+ .||+.|+.||+=.|.
T Consensus        13 ~~sR~~~~~li~~G~V~VNg~~~-~~~~~v~~gd~I~v~   50 (92)
T 2k6p_A           13 VKRRVLATDMCNVGAVWLNGSCA-KASKEVKAGDTISLH   50 (92)
T ss_dssp             CCCCCSSCCHHHHTCCEETTEEC-CTTCBCCTTCEEEEC
T ss_pred             CCCHHHHHHHHHCCcEEECCEEc-CCCCCcCCCCEEEEE
Confidence            46788899999999999999998 699999999754443

>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=97.78  E-value=3.9e-06  Score=50.75  Aligned_cols=39  Identities=8%  Similarity=-0.052  Sum_probs=34.3

Q ss_pred             CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      |+|+.+|++||..|.|.|||++++-|++.|..+|  .|.+.
T Consensus        33 ~~SR~~a~~lI~~G~V~VNG~~v~~~~~~v~~gd--~I~v~   71 (79)
T 1p9k_A           33 SESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQ--TVSFA   71 (79)
T ss_dssp             CSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSSE--EEEET
T ss_pred             CCCHHHHHHHHHCCEEEECCEEecCCCCCCCCCC--EEEEC
Confidence            6799999999999999999999999999998775  45553

>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=97.78  E-value=1.5e-05  Score=53.00  Aligned_cols=39  Identities=18%  Similarity=0.097  Sum_probs=33.7

Q ss_pred             CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceee
Q psy7990           2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDF   41 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~   41 (76)
                      +.|...|++||.+|+|.|||+.+ .||+.|+.||+=.|.+
T Consensus        21 ~~SRs~a~~li~~G~V~VNG~~v-k~s~~V~~GD~I~I~~   59 (133)
T 1dm9_A           21 YKTRALAREMIEGGKVHYNGQRS-KPSKIVELNATLTLRQ   59 (133)
T ss_dssp             SSSHHHHHHHHHTTCEEETTEEC-CTTCBCCTTCEEEEEE
T ss_pred             CCCHHHHHHHHHCCcEEECCEEc-CCCCEeCCCCEEEEEe
Confidence            35788999999999999999998 6999999998655554

>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=97.19  E-value=0.00016  Score=53.35  Aligned_cols=45  Identities=2%  Similarity=-0.219  Sum_probs=37.5

Q ss_pred             CccchhhhhhhhcCCeEECC-E-EeCccceeeecCCCCceeeeeC-CCCC
Q psy7990           2 CSALFLSTQYWEHQGPGVRK-Q-VVNIPSFVVRLDSQKHIDFSLN-SPFG   48 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng-~-~VniPSy~Vk~~de~~I~~~~~-SP~~   48 (76)
                      +.|+.+|++||..|+|.||| + +++.||+.|+.+++  |.+... .||-
T Consensus        19 ~~SR~~a~~lI~~G~V~Vng~~~~v~kp~~~V~~~d~--I~v~g~~~~yv   66 (291)
T 3hp7_A           19 FETREQAKRGVMAGLVVNVINGERYDKPGEKIDDGTE--LKLKGEKLRYV   66 (291)
T ss_dssp             SSSHHHHHHHHHTTCEEETTTCCBCCCTTCEEETTCC--EEETTCCCCSS
T ss_pred             cccHHHHHHHHHCCeEEECCeEEEEccCCCCCCCCCE--EEEcccccccc
Confidence            56899999999999999999 8 89999999999864  666543 3454

>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=97.03  E-value=0.00052  Score=48.32  Aligned_cols=38  Identities=13%  Similarity=0.128  Sum_probs=33.1

Q ss_pred             ccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      -|+.+|+++|..|.|.|||++|+.|++.|+.+|  .|.+.
T Consensus        15 ~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD--~I~v~   52 (243)
T 1vio_A           15 LTRSQATKAIRQSAVKINGEIVKSGSVQISQED--EIYFE   52 (243)
T ss_dssp             CCHHHHHHHHHTTCEEETTEECCCTTCEECTTS--CEEET
T ss_pred             CCHHHHHHHHHcCcEEECCEEeCCCCCCcCCCC--EEEEe
Confidence            367889999999999999999988999999987  55553

>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=96.85  E-value=0.00077  Score=47.02  Aligned_cols=38  Identities=8%  Similarity=0.127  Sum_probs=32.6

Q ss_pred             ccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      -|+..|+++|..|.|.|||++|+-|++.|+.+|  .|.+.
T Consensus        16 ~SR~~~~~li~~G~V~VNG~~v~~~~~~v~~gD--~I~v~   53 (234)
T 1ksk_A           16 VSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEH--DVAYD   53 (234)
T ss_dssp             CCHHHHHHHHHTTCEEETTEECCCTTCEECTTC--CEEET
T ss_pred             CCHHHHHHHHHcCeEEECCEEeCCCCCCCCCCC--EEEEe
Confidence            367889999999999999999988999999986  45543

>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli}

Probab=95.80  E-value=0.0056  Score=45.05  Aligned_cols=36  Identities=8%  Similarity=-0.020  Sum_probs=31.1

Q ss_pred             cchhhhhhhhcCCeEECCEEeCccceeeecCCCCcee
Q psy7990           4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHID   40 (76)
Q Consensus         4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~   40 (76)
                      |+.+|++||..|.|.|||++| -|++.|..+|.=.|+
T Consensus        20 SR~~a~~lI~~G~V~VNG~~v-~~~~~V~~gD~I~v~   55 (290)
T 3dh3_A           20 SRREADRYIEQGNVFLNGKRA-TIGDQVKPGDVVKVN   55 (290)
T ss_dssp             CHHHHHHHHHTTCEEETTEEC-CTTCEECTTCCEEET
T ss_pred             CHHHHHHHHHCCCEEECCEEc-cCCcCcCCCCEEEec
Confidence            778999999999999999999 699999998654443

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

Probab=95.77  E-value=0.0016  Score=47.70  Aligned_cols=39  Identities=18%  Similarity=-0.012  Sum_probs=0.0

Q ss_pred             ccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceee
Q psy7990           3 SALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDF   41 (76)
Q Consensus         3 ~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~   41 (76)
                      .|+.+|++||..|.|.|||++|..|++.|+.||.=.|.+
T Consensus        30 ~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~   68 (325)
T 1v9f_A           30 YSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA   68 (325)
T ss_dssp             ---------------------------------------
T ss_pred             cCHHHHHHHHHCCCEEECCEEccCCCCEeCCCCEEEEec
Confidence            467889999999999999999888999999998655544

>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} SCOP: d.15.3.1 PDB: 1fma_D 1jw9_D 1jwa_D* 1jwb_D* 3bii_D 1nvi_D

Probab=92.90  E-value=0.19  Score=29.16  Aligned_cols=30  Identities=20%  Similarity=0.300  Sum_probs=23.1

Q ss_pred             CeEECCEEeCccceeeecCCCCceeeeeCCCCCCC
Q psy7990          16 GPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGG   50 (76)
Q Consensus        16 HI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~   50 (76)
                      .|.|||+.|+ ++..++.+|+  |.|.+  |++|+
T Consensus        52 ~v~vN~~~v~-~~~~l~~gD~--V~i~P--pv~GG   81 (81)
T 1fm0_D           52 LAAVNQTLVS-FDHPLTDGDE--VAFFP--PVTGG   81 (81)
T ss_dssp             EEEETTEECC-TTCBCCTTCE--EEEEC--CCCCC
T ss_pred             EEEECCEECC-CCCCCCCCCE--EEEeC--CCCCC
Confidence            4999999997 6777776665  88877  77764

>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis}

Probab=91.52  E-value=0.084  Score=41.10  Aligned_cols=34  Identities=12%  Similarity=0.086  Sum_probs=30.2

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLD   34 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~   34 (76)
                      +|+|--+||.+|.-|-|.|||.+|+=|.+.+..+
T Consensus       367 l~~S~~earr~i~~ggv~in~~~v~d~~~~~~~~  400 (432)
T 2jan_A          367 LSASKGAARRTIHEGGVSVNNIRVDNEEWVPQSS  400 (432)
T ss_dssp             SCSSHHHHHHHHTTTCEEESSCEECCTTCCCCGG
T ss_pred             CcccHHHHHHHHHhCCEEECCEEccChhcccChh
Confidence            5889999999999999999999998888777644

>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYE; 2.00A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A*

Probab=91.20  E-value=0.17  Score=39.24  Aligned_cols=34  Identities=15%  Similarity=0.220  Sum_probs=31.2

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLD   34 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~   34 (76)
                      +|+|--+||.||.-|-|.|||.+|+=|.+.+..+
T Consensus       380 l~~S~~earr~i~~ggv~vn~~~v~d~~~~~~~~  413 (432)
T 1h3f_A          380 LTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLS  413 (432)
T ss_dssp             SSSSHHHHHHHHHTTCEEETTEECCCTTCEEECS
T ss_pred             CcccHHHHHHHHHhCCEEECCEEecCccceecCC
Confidence            5889999999999999999999999899888765

>1jil_A Tyrrs, tyrosyl-tRNA synthetase; truncation, based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A*

Probab=91.20  E-value=0.039  Score=42.51  Aligned_cols=35  Identities=0%  Similarity=-0.062  Sum_probs=0.0

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDS   35 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~d   35 (76)
                      +|+|--+||.+|.-|-|.|||.+|+-|.+.+..++
T Consensus       364 l~~SksEARRlI~~GgV~VNgekv~d~~~~l~~~d  398 (420)
T 1jil_A          364 ISPSKRQAREDVNNGAIYINGERQQDVNYALAPED  398 (420)
T ss_dssp             -----------------------------------
T ss_pred             CccCHHHHHHHHHhCCEEECCEEecccccccCccc
Confidence            48899999999999999999999998988887553

>2q5w_D Molybdopterin converting factor, subunit 1; MOCO, MPT synthase, MOAD, MOAE, transferase, molybdenum cofactor biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_B*

Probab=91.05  E-value=0.29  Score=28.17  Aligned_cols=30  Identities=20%  Similarity=0.361  Sum_probs=23.0

Q ss_pred             CeEECCEEeCccceeeecCCCCceeeeeCCCCCCC
Q psy7990          16 GPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGG   50 (76)
Q Consensus        16 HI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~   50 (76)
                      .|.|||+.|+ ++..++.+|  .|++.+  |++|+
T Consensus        48 ~v~vNg~~v~-~~~~L~~gD--~V~i~p--pv~GG   77 (77)
T 2q5w_D           48 QVAVNEEFVQ-KSDFIQPND--TVALIP--PVSGG   77 (77)
T ss_dssp             EEEETTEEEC-TTSEECTTC--EEEEEC--SCCCC
T ss_pred             EEEECCEECC-CCCCcCCCC--EEEEEC--CCCCC
Confidence            5999999998 577666665  488877  77764

>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A

Probab=88.62  E-value=0.084  Score=40.83  Aligned_cols=34  Identities=3%  Similarity=-0.051  Sum_probs=0.0

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLD   34 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~   34 (76)
                      +|+|--+||.+|.-|-|.|||.+|+=|.+.+..+
T Consensus       363 l~~S~~earr~i~~ggv~in~~~v~d~~~~~~~~  396 (419)
T 2ts1_A          363 ISPSKRQAREDIQNGAIYVNGERLQDVGAILTAE  396 (419)
T ss_dssp             ----------------------------------
T ss_pred             CCCCHHHHHHHHHhCCEEECCEEecCcccccChh
Confidence            4889999999999999999999998888777643

>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PSI, protein structure INI southeast collaboratory for structural genomics; 1.51A {Pyrococcus furiosus} SCOP: d.15.3.1

Probab=87.30  E-value=0.31  Score=29.83  Aligned_cols=32  Identities=16%  Similarity=0.141  Sum_probs=22.5

Q ss_pred             cCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCC
Q psy7990          14 HQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGG   50 (76)
Q Consensus        14 HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~   50 (76)
                      +--|.|||+.|. ++..|+.+|+  |.|.+  |++|+
T Consensus        67 ~v~v~VNg~~v~-~~~~L~dGDe--V~i~p--pv~GG   98 (98)
T 1vjk_A           67 DVNIAVNGRYVS-WDEELKDGDV--VGVFP--PVSGG   98 (98)
T ss_dssp             SBEEEETTBCCC-TTCBCCTTCE--EEEES--CC---
T ss_pred             cEEEEECCEECC-CCCCCCCCCE--EEEEC--CCCCC
Confidence            345999999998 6777777765  88876  77664

>3dwg_C 9.5 kDa culture filtrate antigen CFP10A; sulfur carrier protein complex, beta-grAsp fold, amino-acid biosynthesis; HET: PLP; 1.53A {Mycobacterium tuberculosis} PDB: 3dwm_A

Probab=87.01  E-value=0.6  Score=27.95  Aligned_cols=33  Identities=12%  Similarity=0.100  Sum_probs=24.4

Q ss_pred             cCCeEECCEEeCc---cceeeecCCCCceeeeeCCCCCCC
Q psy7990          14 HQGPGVRKQVVNI---PSFVVRLDSQKHIDFSLNSPFGGG   50 (76)
Q Consensus        14 HgHI~Vng~~Vni---PSy~Vk~~de~~I~~~~~SP~~~~   50 (76)
                      +-.|.|||+.|.-   +...|+.+|+  |.|.+  |++|+
T Consensus        58 ~~~v~VN~~~v~~~~~~~~~L~~gDe--V~i~P--pv~GG   93 (93)
T 3dwg_C           58 FVNIYVNDEDVRFSGGLATAIADGDS--VTILP--AVAGG   93 (93)
T ss_dssp             TEEEEETTEEGGGTTGGGCBCCTTCE--EEEEE--CCTTC
T ss_pred             CEEEEECCEEccCcCCCCcCCCCCCE--EEEEC--CCCCC
Confidence            3468999999875   5777776665  88887  77764

>2g1e_A Hypothetical protein TA0895; MOAD, molybdopterin, transferase; NMR {Thermoplasma acidophilum} PDB: 2k22_A

Probab=83.84  E-value=0.62  Score=27.33  Aligned_cols=34  Identities=21%  Similarity=0.217  Sum_probs=24.5

Q ss_pred             hcCCeEECCEEeCc---cceeeecCCCCceeeeeCCCCCCC
Q psy7990          13 EHQGPGVRKQVVNI---PSFVVRLDSQKHIDFSLNSPFGGG   50 (76)
Q Consensus        13 ~HgHI~Vng~~Vni---PSy~Vk~~de~~I~~~~~SP~~~~   50 (76)
                      .+-.|.|||+.|.-   +...++.+|+  |.|.+  |++|+
T Consensus        54 ~~v~v~vN~~~v~~~~~~~~~l~~gD~--V~i~p--pv~GG   90 (90)
T 2g1e_A           54 KNVIILVNGNNITSMKGLDTEIKDDDK--IDLFP--PVAGG   90 (90)
T ss_dssp             TTCEEEESSSBGGGTCSSSCBCCTTCE--EEEEC--CTTCC
T ss_pred             cceEEEECCEEccccCCCCcCCCCCCE--EEEeC--CCCCC
Confidence            34569999998863   5777776665  88876  77764

>3rpf_C Molybdopterin converting factor, subunit 1 (MOAD); MCSG, PSI-biology, structural genomics, midwest center for S genomics, transferase; 1.90A {Helicobacter pylori}

Probab=83.19  E-value=0.98  Score=26.16  Aligned_cols=34  Identities=12%  Similarity=0.159  Sum_probs=23.6

Q ss_pred             hcCCeEECCEEeCccceeeecCCCCceeeeeCCCCCCC
Q psy7990          13 EHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGG   50 (76)
Q Consensus        13 ~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~SP~~~~   50 (76)
                      .+-.|.|||+.|.-+...++.|  +.|.|.+  |++|+
T Consensus        41 ~~~~vavN~~~v~~~~~~l~~g--DeV~i~P--pvsGG   74 (74)
T 3rpf_C           41 GVCAIALNDHLIDNLNTPLKDG--DVISLLP--PVCGG   74 (74)
T ss_dssp             TTCEEEESSSEECCTTCCCCTT--CEEEEEC--CBCCC
T ss_pred             hccEEEECCEEcCCCCcCCCCC--CEEEEEC--CCCCC
Confidence            4566899999975466665555  5688877  67664

>2ktl_A Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA synthetase, ligase; NMR {Aspergillus nidulans fgsc A4}

Probab=82.09  E-value=0.3  Score=33.99  Aligned_cols=25  Identities=8%  Similarity=-0.009  Sum_probs=23.0

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVN   25 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~Vn   25 (76)
                      +|+|.-+||.||.-|-|.|||.+|.
T Consensus        61 La~SKsEARRlI~qGGv~VNg~kv~   85 (164)
T 2ktl_A           61 LVASKSEGQRIINNNGAYVGSRPGV   85 (164)
T ss_dssp             SCSTHHHHHHHHHHTCEEEEECCSC
T ss_pred             cccCHHHHHHHHHhCCEEECCEecc
Confidence            5899999999999999999998874

>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A

Probab=81.51  E-value=1.4  Score=26.88  Aligned_cols=31  Identities=13%  Similarity=0.191  Sum_probs=24.0

Q ss_pred             CeEECCEEeC---ccceeeecCCCCceeeeeCCCCCCC
Q psy7990          16 GPGVRKQVVN---IPSFVVRLDSQKHIDFSLNSPFGGG   50 (76)
Q Consensus        16 HI~Vng~~Vn---iPSy~Vk~~de~~I~~~~~SP~~~~   50 (76)
                      -|.||++-+.   =+.+.|+.+|+  |.|.+  |++|+
T Consensus        66 ~v~VN~~~~~~~~~~d~~L~dgDe--Va~~P--pv~GG   99 (99)
T 2qjl_A           66 ITLINDTDWELEGEKDYILEDGDI--ISFTS--TLHGG   99 (99)
T ss_dssp             EEEETTEEGGGGTGGGCBCCTTCE--EEEEE--CTTCC
T ss_pred             EEEECCEEccccCCCCcCcCCCCE--EEEEC--CCCCC
Confidence            4899999875   36788887776  88887  78764

---

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	76
d1c06a_	159	Ribosomal protein S4 {Bacillus stearothermophilus	99.71
d2gy9d1	204	Ribosomal protein S4 {Escherichia coli [TaxId: 562	99.7
d2uubd1	208	Ribosomal protein S4 {Thermus thermophilus [TaxId:	99.64
d1dm9a_	104	Heat shock protein 15 kD {Escherichia coli [TaxId:	98.76
d1vioa2	58	Pseudouridine synthase RsuA N-terminal domain {Hae	98.61
d1kska3	59	Pseudouridine synthase RsuA N-terminal domain {Esc	98.6
d1p9ka_	79	Hypothetical protein YbcJ {Escherichia coli [TaxId	98.28
d1h3fa2	81	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	97.18
d1jh3a_	99	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	96.98

>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=99.71  E-value=1.1e-18  Score=120.25  Aligned_cols=42  Identities=24%  Similarity=0.192  Sum_probs=37.8

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLN   44 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~   44 (76)
                      +++|+++|||||+||||+|||++||||||+|++||  .|++.+.
T Consensus        62 fa~t~~~arQ~v~Hghi~vNgk~v~iPSy~vk~GD--vIsvkek  103 (159)
T d1c06a_          62 LARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQ--TIAVREK  103 (159)
T ss_dssp             SSSSHHHHHHHHHTSCEEETTEECCCSSCCCCSSC--EEEECGG
T ss_pred             ccCCHHHHHHHHHhcceEccceEEEecceeecCCc--EEeeccc
Confidence            57999999999999999999999999999999998  5666543

>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=99.70  E-value=1.1e-18  Score=124.40  Aligned_cols=43  Identities=21%  Similarity=0.215  Sum_probs=38.2

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNS   45 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~S   45 (76)
                      +++|+++|||||+||||+|||++||||||+|++||.  |++.+.|
T Consensus       105 fa~t~~~ARQ~v~Hghi~VNgk~VnIPSy~vk~GDv--Isvkeks  147 (204)
T d2gy9d1         105 FGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDV--VSIREKA  147 (204)
T ss_dssp             SSSSHHHHHHHHHTTCEEESSSBCCCTTCBCCTTCB--EEECTTG
T ss_pred             ccccHHHHHHHHHhcceecCCEEEEeccEeecCCCE--EEeccch
Confidence            589999999999999999999999999999999986  5555433

>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=99.64  E-value=2.4e-17  Score=117.82  Aligned_cols=43  Identities=23%  Similarity=0.258  Sum_probs=38.2

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeeeeCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFSLNS   45 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~~~S   45 (76)
                      +++|+++|||||+||||+|||++||||||+|++||.  |.+.+.|
T Consensus       109 ~a~t~~~ARQ~v~Hg~i~vNg~~v~ips~~~~~gd~--I~vreks  151 (208)
T d2uubd1         109 FAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDE--IAVAEKS  151 (208)
T ss_dssp             SSSSHHHHHHHHHTTCEEETTEECCCTTCBCCTTCE--EEECGGG
T ss_pred             ccccHHHHHHHHHhcCeecCCeEEEeccEEecCCce--eehhhcc
Confidence            589999999999999999999999999999999975  6665544

>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=98.76  E-value=2e-09  Score=68.69  Aligned_cols=41  Identities=17%  Similarity=0.132  Sum_probs=36.1

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      ++.|+..|+|+|.||||.|||++|. |||.|++||.=.|.+.
T Consensus        16 ~~ktR~~A~~~i~~G~V~vNg~~vK-ps~~vk~GDvI~i~~~   56 (104)
T d1dm9a_          16 FYKTRALAREMIEGGKVHYNGQRSK-PSKIVELNATLTLRQG   56 (104)
T ss_dssp             SSSSHHHHHHHHHTTCEEETTEECC-TTCBCCTTCEEEEEET
T ss_pred             hHhhHHHHHHHHHcCCeeeCCeecc-ccccCCCCCEEEEEeC
Confidence            3679999999999999999999986 9999999998766554

>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=98.61  E-value=1.2e-08  Score=58.38  Aligned_cols=37  Identities=14%  Similarity=0.162  Sum_probs=33.3

Q ss_pred             cchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           4 ALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         4 t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      |+-+|++||.+|+|.|||++|+.|||.|..+|+  |.|.
T Consensus        15 SR~~a~~lI~~g~V~Vng~~v~~~~~~v~~~d~--I~~~   51 (58)
T d1vioa2          15 TRSQATKAIRQSAVKINGEIVKSGSVQISQEDE--IYFE   51 (58)
T ss_dssp             CHHHHHHHHHTTCEEETTEECCCTTCEECTTSC--EEET
T ss_pred             CHHHHHHHHHcCeEEECCEEeCCCCCCCCCCCE--EEEC
Confidence            788999999999999999999999999999864  6653

>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=98.60  E-value=1.5e-08  Score=57.98  Aligned_cols=38  Identities=8%  Similarity=0.140  Sum_probs=34.3

Q ss_pred             CccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           2 CSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         2 ~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      | |+-+|++||.+|.|+|||++|+.|+|.|.++|+  |.|.
T Consensus        13 ~-SR~~a~~lI~~g~V~Vng~~v~~~~~~V~~~d~--I~~d   50 (59)
T d1kska3          13 V-SRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHD--VAYD   50 (59)
T ss_dssp             C-CHHHHHHHHHTTCEEETTEECCCTTCEECTTCC--EEET
T ss_pred             C-CHHHHHHHHHcCcEEECCEEeecCCcCcCCCCE--EEEC
Confidence            5 789999999999999999999999999998754  7765

>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=98.28  E-value=2.9e-08  Score=60.24  Aligned_cols=40  Identities=8%  Similarity=-0.059  Sum_probs=36.4

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCCCceeee
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQKHIDFS   42 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de~~I~~~   42 (76)
                      +|+|+.+|++||..|+|.|||++++.|++.|.++|  .|.|.
T Consensus        32 l~~Sr~eAk~lI~~G~V~VNG~~~~~p~~~V~~~d--~I~vd   71 (79)
T d1p9ka_          32 WSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQ--TVSFA   71 (79)
T ss_dssp             SCSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSSE--EEEET
T ss_pred             CccCHHHHHHHHHhCCcccCCEEeccccccCCCCC--EEEEC
Confidence            48999999999999999999999999999999986  47664

>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
domain: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=97.18  E-value=0.00021  Score=42.44  Aligned_cols=36  Identities=14%  Similarity=0.205  Sum_probs=32.4

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDSQ   36 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~de   36 (76)
                      +|+|.-+||.||.-|-|.|||++|+=|.|.+..++.
T Consensus        29 l~~S~searRlI~~g~V~iN~~ki~d~~~~l~~~~~   64 (81)
T d1h3fa2          29 LTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRP   64 (81)
T ss_dssp             SSSSHHHHHHHHHTTCEEETTEECCCTTCEEECSSC
T ss_pred             CCcCHHHHHHHHHcCCEEECCEEecCccceecCCCe
Confidence            589999999999999999999999999998876653

>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
domain: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.98  E-value=0.00024  Score=43.49  Aligned_cols=35  Identities=3%  Similarity=-0.052  Sum_probs=32.2

Q ss_pred             CCccchhhhhhhhcCCeEECCEEeCccceeeecCC
Q psy7990           1 MCSALFLSTQYWEHQGPGVRKQVVNIPSFVVRLDS   35 (76)
Q Consensus         1 ~~~t~~~ARQ~V~HgHI~Vng~~VniPSy~Vk~~d   35 (76)
                      +|+|.-+||.||.-|-|.|||++|+=|.|.+..++
T Consensus        43 l~~S~seaRrlI~~ggv~iN~~kv~d~~~~l~~~~   77 (99)
T d1jh3a_          43 ISPSKRQAREDIQNGAIYVNGERLQDVGAILTAEH   77 (99)
T ss_dssp             SCCSHHHHHHHHHSTTEEETTEECCSTTTCCSSTT
T ss_pred             CCcCHHHHHHHHHcCCEEECCEEecCcccccCHhH
Confidence            58999999999999999999999999999887765