Psyllid ID: psy1800

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80-
Protein Sequence
MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCPTIAD
Secondary Structure (PSIPRED)
cccccEEEEEcccccccEEEEEEEEEccccEEEEEEEcccccEEEEEEcEEEEEEcccccEEEcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccEEEEEccccccEEEEEEEcccccccEEEEEEEEccccEEEEEcccEEEEEcccccEEEcccccccccccccccccc
Coil and Loop (DISEMBL)
mfpgnlcmitggrnlgrvgtvvnrerhpgsfdivhvkdgnghvfATRLNNVFIIGkgtkafcskpkrnfvsprqtcptiad
Flexible Loop (DISEMBL)
mfpgnlcmitggrnlgrVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGtkafcskpkrnfvsprqtcptiad
Low Complexity Region (SEG)
MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCPTIAD
Disordered region (IsUnstruct)
****NLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS******************
Disordered Region (DISOPRED)
MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCP****
Disordered Region (DISEMBL)
MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCPTIAD
Disordered Region (DISPRO)
MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCPTIA*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCPTIAD
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	81	2.2.26 [Sep-21-2011]
Q5UAP0	263	40S ribosomal protein S4	N/A	N/A	0.777	0.239	0.841	4e-26
Q95V34	263	40S ribosomal protein S4	N/A	N/A	0.777	0.239	0.841	5e-26
Q4GXU6	261	40S ribosomal protein S4	N/A	N/A	0.777	0.241	0.841	7e-26
P41042	261	40S ribosomal protein S4	yes	N/A	0.777	0.241	0.857	9e-26
Q56FH2	262	40S ribosomal protein S4	N/A	N/A	0.777	0.240	0.809	8e-25
Q6PBC4	263	40S ribosomal protein S4	yes	N/A	0.777	0.239	0.698	1e-21
Q90YS0	263	40S ribosomal protein S4	N/A	N/A	0.777	0.239	0.698	1e-21
P47836	263	40S ribosomal protein S4	yes	N/A	0.777	0.239	0.698	1e-21
P47961	263	40S ribosomal protein S4	yes	N/A	0.777	0.239	0.698	1e-21
P79103	263	40S ribosomal protein S4	yes	N/A	0.777	0.239	0.698	1e-21

>sp|Q5UAP0|RS4_BOMMO 40S ribosomal protein S4 OS=Bombyx mori GN=RpS4 PE=2 SV=1

 Score =  116 bits (291), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 53/63 (84%), Positives = 58/63 (92%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCMITGGRNLGRVGT+V+RERHPGSFDIVH+KD  GH FATRLNNVFIIGKGTKA+ S
Sbjct: 178 GNLCMITGGRNLGRVGTIVSRERHPGSFDIVHIKDSTGHTFATRLNNVFIIGKGTKAYIS 237

Query: 64  KPK 66
            P+
Sbjct: 238 LPR 240

Bombyx mori (taxid: 7091)

>sp|Q95V34|RS4_SPOFR 40S ribosomal protein S4 OS=Spodoptera frugiperda GN=RpS4 PE=2 SV=1

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 53/63 (84%), Positives = 58/63 (92%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCMITGGRNLGRVGT+V+RERHPGSFDIVH+KD  GH FATRLNNVFIIGKGTKA+ S
Sbjct: 178 GNLCMITGGRNLGRVGTIVSRERHPGSFDIVHIKDSTGHTFATRLNNVFIIGKGTKAYIS 237

Query: 64  KPK 66
            P+
Sbjct: 238 LPR 240

Spodoptera frugiperda (taxid: 7108)

>sp|Q4GXU6|RS4_CARGR 40S ribosomal protein S4 OS=Carabus granulatus GN=RpS4 PE=2 SV=1

 Score =  115 bits (289), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 53/63 (84%), Positives = 57/63 (90%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCMITGGRNLGRVGTVVNRERHPGSFDIVH+KD  GH FA RLNNVFIIGKG+KA+ S
Sbjct: 178 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHIKDSQGHTFANRLNNVFIIGKGSKAYVS 237

Query: 64  KPK 66
            P+
Sbjct: 238 LPR 240

Carabus granulatus (taxid: 118799)

>sp|P41042|RS4_DROME 40S ribosomal protein S4 OS=Drosophila melanogaster GN=RpS4 PE=2 SV=2

 Score =  115 bits (288), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 54/63 (85%), Positives = 56/63 (88%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCMITGGRNLGRVGTVVNRERHPGSFDIVH+KD  GHVFATRL NVFIIGKG K + S
Sbjct: 178 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHIKDSQGHVFATRLTNVFIIGKGNKPYIS 237

Query: 64  KPK 66
            PK
Sbjct: 238 LPK 240

Drosophila melanogaster (taxid: 7227)

>sp|Q56FH2|RS4_LYSTE 40S ribosomal protein S4 OS=Lysiphlebus testaceipes GN=RpS4 PE=2 SV=1

 Score =  112 bits (279), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 51/63 (80%), Positives = 57/63 (90%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCMITGGRNLGRVGTVV+RERHPGSFDI H+KD  GH FATR+NNVFIIGKG+KA+ S
Sbjct: 178 GNLCMITGGRNLGRVGTVVSRERHPGSFDICHIKDSQGHTFATRMNNVFIIGKGSKAYVS 237

Query: 64  KPK 66
            P+
Sbjct: 238 LPR 240

Lysiphlebus testaceipes (taxid: 77504)

>sp|Q6PBC4|RS4_XENTR 40S ribosomal protein S4 OS=Xenopus tropicalis GN=rps4 PE=2 SV=3

 Score =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD NG+ FATRL+N+F+IGKG K + S
Sbjct: 178 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWIS 237

Query: 64  KPK 66
            P+
Sbjct: 238 LPR 240

Xenopus tropicalis (taxid: 8364)

>sp|Q90YS0|RS4_ICTPU 40S ribosomal protein S4 OS=Ictalurus punctatus GN=rps4 PE=2 SV=3

 Score =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD  G+ FATRL+N+F+IGKG KA+ S
Sbjct: 178 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDSTGNSFATRLSNIFVIGKGNKAWVS 237

Query: 64  KPK 66
            P+
Sbjct: 238 IPR 240

Ictalurus punctatus (taxid: 7998)

>sp|P47836|RS4_CHICK 40S ribosomal protein S4 OS=Gallus gallus GN=RPS4 PE=2 SV=2

 Score =  101 bits (251), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD NG+ FATRL+N+F+IGKG K + S
Sbjct: 178 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWIS 237

Query: 64  KPK 66
            P+
Sbjct: 238 LPR 240

Gallus gallus (taxid: 9031)

>sp|P47961|RS4_CRIGR 40S ribosomal protein S4 OS=Cricetulus griseus GN=RPS4 PE=2 SV=2

 Score =  101 bits (251), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD NG+ FATRL+N+F+IGKG K + S
Sbjct: 178 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWIS 237

Query: 64  KPK 66
            P+
Sbjct: 238 LPR 240

Cricetulus griseus (taxid: 10029)

>sp|P79103|RS4_BOVIN 40S ribosomal protein S4 OS=Bos taurus GN=RPS4 PE=2 SV=3

 Score =  101 bits (251), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD NG+ FATRL+N+F+IGKG K + S
Sbjct: 178 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWIS 237

Query: 64  KPK 66
            P+
Sbjct: 238 LPR 240

Bos taurus (taxid: 9913)

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	81
110456358	104	ribosomal protein S4-like protein [Diaph	0.777	0.605	0.952	3e-27
355428416	133	hypothetical protein, partial [Triatoma	0.814	0.496	0.863	7e-26
342906104	132	ribosomal protein S4e [Rhodnius prolixus	0.814	0.5	0.863	1e-25
70909485	261	ribosomal protein S4e [Julodis onopordi]	0.765	0.237	0.903	2e-25
146285351	263	ribosomal protein S4e [Lygus lineolaris]	0.814	0.250	0.863	2e-25
264667395	261	ribosomal protein S4 [Chrysomela tremula	0.777	0.241	0.888	2e-25
70909489	262	ribosomal protein S4e [Sphaerius sp. APV	0.777	0.240	0.857	3e-25
332376168	261	unknown [Dendroctonus ponderosae]	0.777	0.241	0.873	9e-25
242024748	245	40S ribosomal protein S4, putative [Pedi	0.777	0.257	0.857	1e-24
112984078	263	40S ribosomal protein S4 [Bombyx mori] g	0.777	0.239	0.841	2e-24

>gi|110456358|gb|ABG74702.1| ribosomal protein S4-like protein [Diaphorina citri]

 Score =  125 bits (315), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 60/63 (95%), Positives = 61/63 (96%)

Query: 4  GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
          GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKA+ S
Sbjct: 19 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAYIS 78

Query: 64 KPK 66
           PK
Sbjct: 79 LPK 81

Source: Diaphorina citri

Species: Diaphorina citri

Genus: Diaphorina

Family: Psyllidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|355428416|gb|AER92524.1| hypothetical protein, partial [Triatoma rubida]

 Score =  120 bits (302), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 57/66 (86%), Positives = 61/66 (92%)

Query: 1   MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKA 60
           M  GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD +GH+FATRLNNVFIIGKG+KA
Sbjct: 45  MDSGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDASGHMFATRLNNVFIIGKGSKA 104

Query: 61  FCSKPK 66
           + S PK
Sbjct: 105 YVSLPK 110

Source: Triatoma rubida

Species: Triatoma rubida

Genus: Triatoma

Family: Reduviidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|342906104|gb|AEL79335.1| ribosomal protein S4e [Rhodnius prolixus]

 Score =  120 bits (301), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 57/66 (86%), Positives = 61/66 (92%)

Query: 1   MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKA 60
           M  GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD +GH+FATRLNNVFIIGKG+KA
Sbjct: 52  MDSGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDASGHMFATRLNNVFIIGKGSKA 111

Query: 61  FCSKPK 66
           + S PK
Sbjct: 112 YVSLPK 117

Source: Rhodnius prolixus

Species: Rhodnius prolixus

Genus: Rhodnius

Family: Reduviidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|70909485|emb|CAJ17167.1| ribosomal protein S4e [Julodis onopordi]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 56/62 (90%), Positives = 59/62 (95%)

Query: 5   NLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSK 64
           NLCMITGGRNLGRVGTVVNRERHPGSFDIVH+KD NGHVFATRLNNVFIIGKG+KAF S 
Sbjct: 179 NLCMITGGRNLGRVGTVVNRERHPGSFDIVHIKDANGHVFATRLNNVFIIGKGSKAFVSL 238

Query: 65  PK 66
           P+
Sbjct: 239 PR 240

Source: Julodis onopordi

Species: Julodis onopordi

Genus: Julodis

Family: Buprestidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|146285351|gb|ABQ18253.1| ribosomal protein S4e [Lygus lineolaris]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 57/66 (86%), Positives = 59/66 (89%)

Query: 1   MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKA 60
           M  GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD  GH FATRLNNVFIIGKG+KA
Sbjct: 175 MDSGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDATGHTFATRLNNVFIIGKGSKA 234

Query: 61  FCSKPK 66
           + S PK
Sbjct: 235 YVSIPK 240

Source: Lygus lineolaris

Species: Lygus lineolaris

Genus: Lygus

Family: Miridae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|264667395|gb|ACY71283.1| ribosomal protein S4 [Chrysomela tremula]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 56/63 (88%), Positives = 59/63 (93%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCMITGGRNLGRVGTV+NRERHPGSFDIVHVKD NGHVFATRL+NVFIIGKG KAF S
Sbjct: 178 GNLCMITGGRNLGRVGTVMNRERHPGSFDIVHVKDANGHVFATRLHNVFIIGKGAKAFVS 237

Query: 64  KPK 66
            P+
Sbjct: 238 LPR 240

Source: Chrysomela tremula

Species: Chrysomela tremula

Genus: Chrysomela

Family: Chrysomelidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|70909489|emb|CAJ17169.1| ribosomal protein S4e [Sphaerius sp. APV-2005]

 Score =  118 bits (296), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 54/63 (85%), Positives = 59/63 (93%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCMITGGRNLGRVGTVVNRERHPGSFDIVH+KD  GH+FATRLNNVFIIGKG+KA+ S
Sbjct: 178 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHIKDSQGHIFATRLNNVFIIGKGSKAYVS 237

Query: 64  KPK 66
            P+
Sbjct: 238 LPR 240

Source: Sphaerius sp. APV-2005

Species: Sphaerius sp. APV-2005

Genus: Sphaerius

Family: Sphaeriusidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332376168|gb|AEE63224.1| unknown [Dendroctonus ponderosae]

 Score =  117 bits (293), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 55/63 (87%), Positives = 58/63 (92%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLC ITGGRNLGRVGTVVNRERHPGSFDIVH+KD N HVFATRLNNVFIIGKG+KAF S
Sbjct: 178 GNLCQITGGRNLGRVGTVVNRERHPGSFDIVHIKDANEHVFATRLNNVFIIGKGSKAFVS 237

Query: 64  KPK 66
            P+
Sbjct: 238 LPR 240

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242024748|ref|XP_002432788.1| 40S ribosomal protein S4, putative [Pediculus humanus corporis] gi|212518297|gb|EEB20050.1| 40S ribosomal protein S4, putative [Pediculus humanus corporis]

 Score =  117 bits (292), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 54/63 (85%), Positives = 58/63 (92%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCMITGGRNLGRVGTVVNRERHPGSFDIVH+KD  GH FATRLNNVFIIGKG+KA+ S
Sbjct: 160 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHIKDTQGHTFATRLNNVFIIGKGSKAYVS 219

Query: 64  KPK 66
            P+
Sbjct: 220 LPR 222

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|112984078|ref|NP_001037257.1| 40S ribosomal protein S4 [Bombyx mori] gi|74782218|sp|Q5UAP0.1|RS4_BOMMO RecName: Full=40S ribosomal protein S4 gi|54609289|gb|AAV34860.1| ribosomal protein S4 [Bombyx mori]

 Score =  116 bits (291), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 53/63 (84%), Positives = 58/63 (92%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNLCMITGGRNLGRVGT+V+RERHPGSFDIVH+KD  GH FATRLNNVFIIGKGTKA+ S
Sbjct: 178 GNLCMITGGRNLGRVGTIVSRERHPGSFDIVHIKDSTGHTFATRLNNVFIIGKGTKAYIS 237

Query: 64  KPK 66
            P+
Sbjct: 238 LPR 240

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

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	81
FB|FBgn0011284	261	RpS4 "Ribosomal protein S4" [D	0.777	0.241	0.857	1.1e-25
UNIPROTKB|P47836	263	RPS4 "40S ribosomal protein S4	0.777	0.239	0.698	2.1e-22
UNIPROTKB|A2VE06	263	RPS4Y1 "Ribosomal protein S4,	0.777	0.239	0.698	2.1e-22
UNIPROTKB|G3N0K3	262	G3N0K3 "Uncharacterized protei	0.777	0.240	0.698	2.1e-22
UNIPROTKB|P79103	263	RPS4 "40S ribosomal protein S4	0.777	0.239	0.698	2.1e-22
UNIPROTKB|F2Z4Q1	263	RPS4X "Uncharacterized protein	0.777	0.239	0.698	2.1e-22
UNIPROTKB|P62701	263	RPS4X "40S ribosomal protein S	0.777	0.239	0.698	2.1e-22
UNIPROTKB|F1RQ91	263	RPS4X "Uncharacterized protein	0.777	0.239	0.698	2.1e-22
UNIPROTKB|P62704	263	RPS4X "40S ribosomal protein S	0.777	0.239	0.698	2.1e-22
UNIPROTKB|P62705	263	RPS4X "40S ribosomal protein S	0.777	0.239	0.698	2.1e-22

FB|FBgn0011284 RpS4 "Ribosomal protein S4" [Drosophila melanogaster (taxid:7227)]

 Score = 291 (107.5 bits), Expect = 1.1e-25, P = 1.1e-25
 Identities = 54/63 (85%), Positives = 56/63 (88%)

Query:     4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
             GNLCMITGGRNLGRVGTVVNRERHPGSFDIVH+KD  GHVFATRL NVFIIGKG K + S
Sbjct:   178 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHIKDSQGHVFATRLTNVFIIGKGNKPYIS 237

Query:    64 KPK 66
              PK
Sbjct:   238 LPK 240

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

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

GO:0006412 "translation" evidence=ISS;NAS

GO:0005840 "ribosome" evidence=IDA;NAS

GO:0003723 "RNA binding" evidence=IEA

GO:0005811 "lipid particle" evidence=IDA

GO:0000022 "mitotic spindle elongation" evidence=IMP

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0051297 "centrosome organization" evidence=IMP

GO:0051298 "centrosome duplication" evidence=IMP

UNIPROTKB|P47836 RPS4 "40S ribosomal protein S4" [Gallus gallus (taxid:9031)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query:     4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
             GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD NG+ FATRL+N+F+IGKG K + S
Sbjct:   178 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWIS 237

Query:    64 KPK 66
              P+
Sbjct:   238 LPR 240

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

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

UNIPROTKB|A2VE06 RPS4Y1 "Ribosomal protein S4, Y-linked 1" [Bos taurus (taxid:9913)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query:     4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
             GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD NG+ FATRL+N+F+IGKG K + S
Sbjct:   178 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWIS 237

Query:    64 KPK 66
              P+
Sbjct:   238 LPR 240

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|G3N0K3 G3N0K3 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query:     4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
             GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD NG+ FATRL+N+F+IGKG K + S
Sbjct:   177 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWIS 236

Query:    64 KPK 66
              P+
Sbjct:   237 LPR 239

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P79103 RPS4 "40S ribosomal protein S4" [Bos taurus (taxid:9913)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query:     4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
             GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD NG+ FATRL+N+F+IGKG K + S
Sbjct:   178 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWIS 237

Query:    64 KPK 66
              P+
Sbjct:   238 LPR 240

GO:0019843 "rRNA binding" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|F2Z4Q1 RPS4X "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query:     4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
             GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD NG+ FATRL+N+F+IGKG K + S
Sbjct:   178 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWIS 237

Query:    64 KPK 66
              P+
Sbjct:   238 LPR 240

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P62701 RPS4X "40S ribosomal protein S4, X isoform" [Homo sapiens (taxid:9606)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query:     4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
             GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD NG+ FATRL+N+F+IGKG K + S
Sbjct:   178 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWIS 237

Query:    64 KPK 66
              P+
Sbjct:   238 LPR 240

GO:0019843 "rRNA binding" evidence=IEA

GO:0005840 "ribosome" evidence=IDA

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

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

GO:0045727 "positive regulation of translation" evidence=IMP

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

GO:0007275 "multicellular organismal development" evidence=IMP

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

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0005844 "polysome" evidence=IDA

GO:0015935 "small ribosomal subunit" evidence=IDA

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

GO:0005829 "cytosol" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0006414 "translational elongation" evidence=TAS

GO:0006415 "translational termination" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0019083 "viral transcription" evidence=TAS

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

UNIPROTKB|F1RQ91 RPS4X "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query:     4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
             GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD NG+ FATRL+N+F+IGKG K + S
Sbjct:   178 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWIS 237

Query:    64 KPK 66
              P+
Sbjct:   238 LPR 240

GO:0045727 "positive regulation of translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005844 "polysome" evidence=IEA

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

GO:0006412 "translation" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P62704 RPS4X "40S ribosomal protein S4, X isoform" [Mesocricetus auratus (taxid:10036)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query:     4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
             GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD NG+ FATRL+N+F+IGKG K + S
Sbjct:   178 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWIS 237

Query:    64 KPK 66
              P+
Sbjct:   238 LPR 240

GO:0005840 "ribosome" evidence=ISS

GO:0030529 "ribonucleoprotein complex" evidence=ISS

UNIPROTKB|P62705 RPS4X "40S ribosomal protein S4, X isoform" [Felis catus (taxid:9685)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 44/63 (69%), Positives = 54/63 (85%)

Query:     4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
             GNLCM+TGG NLGR+G + NRERHPGSFD+VHVKD NG+ FATRL+N+F+IGKG K + S
Sbjct:   178 GNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWIS 237

Query:    64 KPK 66
              P+
Sbjct:   238 LPR 240

GO:0005840 "ribosome" evidence=ISS

GO:0030529 "ribonucleoprotein complex" evidence=ISS

---

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)
Q9N3X2	RS4_CAEEL	No assigned EC number	0.6349	0.7777	0.2432	yes	N/A
P47836	RS4_CHICK	No assigned EC number	0.6984	0.7777	0.2395	yes	N/A
O59950	RS4_YARLI	No assigned EC number	0.6190	0.7777	0.2423	yes	N/A
Q8VYK6	RS43_ARATH	No assigned EC number	0.6190	0.7777	0.2404	yes	N/A
P49204	RS42_ARATH	No assigned EC number	0.6190	0.7777	0.2404	yes	N/A
Q9P4W9	RS4C_SCHPO	No assigned EC number	0.6166	0.7407	0.2290	yes	N/A
Q9USW5	RS4B_SCHPO	No assigned EC number	0.6166	0.7407	0.2290	yes	N/A
P79103	RS4_BOVIN	No assigned EC number	0.6984	0.7777	0.2395	yes	N/A
P47961	RS4_CRIGR	No assigned EC number	0.6984	0.7777	0.2395	yes	N/A
O62739	RS4Y1_MONDO	No assigned EC number	0.6825	0.7777	0.2395	yes	N/A
O62738	RS4X_MONDO	No assigned EC number	0.6666	0.7777	0.2395	yes	N/A
P49398	RS4_ORYSJ	No assigned EC number	0.6349	0.7777	0.2377	yes	N/A
Q93VH9	RS41_ARATH	No assigned EC number	0.6190	0.7777	0.2413	yes	N/A
P41042	RS4_DROME	No assigned EC number	0.8571	0.7777	0.2413	yes	N/A
Q6PBC4	RS4_XENTR	No assigned EC number	0.6984	0.7777	0.2395	yes	N/A
P62703	RS4X_RAT	No assigned EC number	0.6984	0.7777	0.2395	yes	N/A
P62702	RS4X_MOUSE	No assigned EC number	0.6984	0.7777	0.2395	yes	N/A
P87158	RS4A_SCHPO	No assigned EC number	0.6166	0.7407	0.2290	yes	N/A
P0CX36	RS4B_YEAST	No assigned EC number	0.5873	0.7777	0.2413	yes	N/A
P62701	RS4X_HUMAN	No assigned EC number	0.6984	0.7777	0.2395	yes	N/A
P0CX35	RS4A_YEAST	No assigned EC number	0.5873	0.7777	0.2413	yes	N/A
Q642H9	RS4X_DANRE	No assigned EC number	0.6507	0.7777	0.2395	yes	N/A
P51405	RS4_DICDI	No assigned EC number	0.7213	0.7530	0.2284	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	81
PLN00036	261	PLN00036, PLN00036, 40S ribosomal protein S4; Prov	1e-29
cd06087	55	cd06087, KOW_RPS4, KOW motif of Ribosomal Protein	8e-28
PTZ00118	262	PTZ00118, PTZ00118, 40S ribosomal protein S4; Prov	5e-27
PTZ00223	273	PTZ00223, PTZ00223, 40S ribosomal protein S4; Prov	2e-18
COG1471	241	COG1471, RPS4A, Ribosomal protein S4E [Translation	3e-17
PRK04313	237	PRK04313, PRK04313, 30S ribosomal protein S4e; Val	3e-12
pfam00467	32	pfam00467, KOW, KOW motif	0.003

>gnl|CDD|177670 PLN00036, PLN00036, 40S ribosomal protein S4; Provisional

 Score =  104 bits (262), Expect = 1e-29
 Identities = 44/63 (69%), Positives = 51/63 (80%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GNL M+TGGRN GRVG + NRE+H GSF+I+HVKD  GH FATRL NVF+IGKGTK + S
Sbjct: 178 GNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWIS 237

Query: 64  KPK 66
            PK
Sbjct: 238 LPK 240

Length = 261

>gnl|CDD|240511 cd06087, KOW_RPS4, KOW motif of Ribosomal Protein S4 (RPS4)

 Score = 94.5 bits (236), Expect = 8e-28
 Identities = 37/53 (69%), Positives = 43/53 (81%)

Query: 3  PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIG 55
           GNL M+TGGRN+GRVG +   ERH GSFDIVHVKD  G+ FATRL+NVF+IG
Sbjct: 3  EGNLAMVTGGRNVGRVGVIKEIERHKGSFDIVHVKDAAGNEFATRLSNVFVIG 55

RPS4 plays a critical role in the core assembly of the small ribosomal subunit with a KOW motif at its C-terminal. RPS4 also acts as a general transcription antiterminator factor and regulates ribosomal RNA expression level. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. RPS4 deficiency in human has been associated with Turner syndrome. Archeae RPS4 (RPS4e) showed substantial identity to the eukaryotic equivalents RPS4, but the archaeal proteins formed a different complex from the eukaryotic proteins. Length = 55

>gnl|CDD|240277 PTZ00118, PTZ00118, 40S ribosomal protein S4; Provisional

 Score = 98.4 bits (245), Expect = 5e-27
 Identities = 42/64 (65%), Positives = 53/64 (82%)

Query: 3   PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFC 62
            GNL MITGG N+GRVGT+V++E+HPGSFD++HVKD  G  FATRL+NVF+IG GTK + 
Sbjct: 177 VGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYV 236

Query: 63  SKPK 66
           S P+
Sbjct: 237 SLPR 240

Length = 262

>gnl|CDD|140250 PTZ00223, PTZ00223, 40S ribosomal protein S4; Provisional

 Score = 75.8 bits (186), Expect = 2e-18
 Identities = 31/53 (58%), Positives = 41/53 (77%)

Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGK 56
           G + M+TGG N GR+G +V+ ERHPG+FDI  +KD +GH FATR  N+F+IGK
Sbjct: 175 GKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGK 227

Length = 273

>gnl|CDD|224388 COG1471, RPS4A, Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]

 Score = 72.3 bits (178), Expect = 3e-17
 Identities = 24/56 (42%), Positives = 35/56 (62%), Gaps = 1/56 (1%)

Query: 3   PGNLCMITGGRNLGRVGTVVNRERHPGS-FDIVHVKDGNGHVFATRLNNVFIIGKG 57
            G L  +TGGR++GRVGT+V  E    S  ++V V+D  G+ F T  + VF+IG+ 
Sbjct: 176 EGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGED 231

Length = 241

>gnl|CDD|179820 PRK04313, PRK04313, 30S ribosomal protein S4e; Validated

 Score = 58.7 bits (143), Expect = 3e-12
 Identities = 23/56 (41%), Positives = 35/56 (62%), Gaps = 1/56 (1%)

Query: 3   PGNLCMITGGRNLGRVGTVVNRERHPGSF-DIVHVKDGNGHVFATRLNNVFIIGKG 57
            GNL +ITGG+++G +G +   E    S  +IV ++D +G  F T L+ VF+IGK 
Sbjct: 174 EGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGKE 229

Length = 237

>gnl|CDD|144165 pfam00467, KOW, KOW motif

 Score = 32.0 bits (74), Expect = 0.003
 Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 3/35 (8%)

Query: 3  PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVK 37
           G++  +  G   G+ G VV  +        VHV+
Sbjct: 1  KGDVVRVISGPFKGKKGKVVEVDDSKA---RVHVE 32

This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG. Length = 32

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	81
PLN00036	261	40S ribosomal protein S4; Provisional	99.97
PTZ00118	262	40S ribosomal protein S4; Provisional	99.97
PTZ00223	273	40S ribosomal protein S4; Provisional	99.96
KOG0378|consensus	263		99.95
PRK04313	237	30S ribosomal protein S4e; Validated	99.93
COG1471	241	RPS4A Ribosomal protein S4E [Translation, ribosoma	99.91
PF00467	32	KOW: KOW motif; InterPro: IPR005824 Ribosomes are	97.82
smart00739	28	KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif i	97.67
TIGR01080	114	rplX_A_E ribosomal protein L24p/L26e, archaeal/euk	95.66
PRK12281	76	rplX 50S ribosomal protein L24; Reviewed	94.72
CHL00141	83	rpl24 ribosomal protein L24; Validated	94.61
PRK00004	105	rplX 50S ribosomal protein L24; Reviewed	94.34
PRK01191	120	rpl24p 50S ribosomal protein L24P; Validated	94.27
TIGR01079	104	rplX_bact ribosomal protein L24, bacterial/organel	93.14
PF13051	68	DUF3912: Protein of unknown function (DUF3912)	91.49
COG2163	125	RPL14A Ribosomal protein L14E/L6E/L27E [Translatio	88.87
PTZ00194	143	60S ribosomal protein L26; Provisional	87.6
PF01588	95	tRNA_bind: Putative tRNA binding domain; InterPro:	84.15
PTZ00065	130	60S ribosomal protein L14; Provisional	83.87
PF14001	64	YdfZ: YdfZ protein	82.39
TIGR03784	174	marine_sortase sortase, marine proteobacterial typ	81.91
TIGR01076	136	sortase_fam LPXTG-site transpeptidase (sortase) fa	80.26

>PLN00036 40S ribosomal protein S4; Provisional

Probab=99.97  E-value=1.1e-30  Score=195.79  Aligned_cols=74  Identities=59%  Similarity=0.937  Sum_probs=72.2

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeee
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQ   74 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~   74 (81)
                      ||+||+||||||+|+||+|+|.+|+++++++|+||++|++|++|+|+++||||||++++|||+||++|||||++
T Consensus       175 fe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~vfvIG~~~kp~isLp~~~gi~~~~  248 (261)
T PLN00036        175 FDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPKGKGIKLSI  248 (261)
T ss_pred             cCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCCCCcccch
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999875

>PTZ00118 40S ribosomal protein S4; Provisional

Probab=99.97  E-value=1.2e-30  Score=195.59  Aligned_cols=74  Identities=57%  Similarity=0.979  Sum_probs=72.2

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeee
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQ   74 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~   74 (81)
                      ||+||+||||||+|+||+|+|.+++++++++|+||++|++|++|+|+++||||||++++|||+||++||||||+
T Consensus       175 fe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~vfvIG~~~kp~islp~~kgi~~~~  248 (262)
T PTZ00118        175 FEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLPRERGIKKDI  248 (262)
T ss_pred             cCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCCCCccccH
Confidence            89999999999999999999999999999999999999999999999999999999899999999999999875

>PTZ00223 40S ribosomal protein S4; Provisional

Probab=99.96  E-value=6.2e-30  Score=192.66  Aligned_cols=74  Identities=45%  Similarity=0.759  Sum_probs=71.7

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecC-CcceEecCCCceeeeee
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKG-TKAFCSKPKRNFVSPRQ   74 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~-~kp~IsLp~~kgi~~~~   74 (81)
                      |++||+||||||+|+||+|+|.+|++|++++|+||++|++|++|+|+++||||||++ ++|||+||++||||||+
T Consensus       172 fe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~VfvIG~~~~kp~IsLp~~kgi~~~~  246 (273)
T PTZ00223        172 NRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVPVTLPKQQGLRINV  246 (273)
T ss_pred             cCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEeCCCCCcceECcCCCCccccH
Confidence            899999999999999999999999999999999999999999999999999999995 69999999999999975

>KOG0378|consensus

Probab=99.95  E-value=2.1e-28  Score=182.67  Aligned_cols=74  Identities=59%  Similarity=1.029  Sum_probs=72.3

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeee
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQ   74 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~   74 (81)
                      |++|++||++||+|+||+|+|.+.|+|+|+||+||++|++|++|+|+++|+|+||+|+|||||||++|||++++
T Consensus       175 f~~~~~~~vtgg~n~gRig~i~~rerh~G~f~vvhvkdt~gnsFatrLsNifvIgkgnKpwisLPkgkgi~~si  248 (263)
T KOG0378|consen  175 FDTGNLCMVTGGANLGRIGVIKNRERHPGSFDVVHVKDTNGNSFATRLSNIFVIGEGNKPWISLPKGKGIALSI  248 (263)
T ss_pred             cCccceeeeeccccccccccccccccCCCceEEEEEEecCCcEeeeeeccEEEEecCCCccccCccccCccchh
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999875

>PRK04313 30S ribosomal protein S4e; Validated

Probab=99.93  E-value=9.5e-26  Score=167.25  Aligned_cols=65  Identities=37%  Similarity=0.646  Sum_probs=63.1

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCC
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPK   66 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~   66 (81)
                      |++||+||||||+|+||+|+|.+|+++++ ++|+|+++|++|++|+|+++||||||+ ++|+|+||.
T Consensus       172 fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvIG~-~kp~isl~~  237 (237)
T PRK04313        172 FEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGK-EKPVIKLPE  237 (237)
T ss_pred             cCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEEcC-CCcceeCCC
Confidence            89999999999999999999999999995 999999999999999999999999999 999999984

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

Probab=99.91  E-value=1.8e-24  Score=160.46  Aligned_cols=67  Identities=40%  Similarity=0.657  Sum_probs=65.2

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCc
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRN   68 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~k   68 (81)
                      |++|++|||+||+|+|++|+|.+|+++++ ++|+|+++|.+|+.|+|+++||||||+ ++|+|+||+|+
T Consensus       174 fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~yVfvIG~-~k~~i~l~~e~  241 (241)
T COG1471         174 FEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGE-DKPVISLPKEK  241 (241)
T ss_pred             cCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeEEEEEcC-CCceEeCCCCC
Confidence            79999999999999999999999999996 999999999999999999999999999 99999999985

>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.82  E-value=3.6e-05  Score=40.87  Aligned_cols=31  Identities=26%  Similarity=0.427  Sum_probs=26.4

Q ss_pred             CCcEEEEECCCCcceEEEEEEEEEecCCCcEEEE
Q psy1800           3 PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHV   36 (81)
Q Consensus         3 ~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~i   36 (81)
                      +|+.|+|+.|++.|+.|+|.++.++.   +.|++
T Consensus         1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~---~~V~v   31 (32)
T PF00467_consen    1 VGDTVKVISGPFKGKIGKIVEIDRSK---VRVTV   31 (32)
T ss_dssp             TTSEEEESSSTTTTEEEEEEEEETTT---TEEEE
T ss_pred             CCCEEEEeEcCCCCceEEEEEEECCC---CEEEE
Confidence            59999999999999999999998664   45554

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 KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....

>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif

Probab=97.67  E-value=7e-05  Score=37.46  Aligned_cols=26  Identities=23%  Similarity=0.391  Sum_probs=24.1

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEE
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRER   26 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~   26 (81)
                      |++|+.++|++|.+.|+.|+|.+++.
T Consensus         2 ~~~G~~V~I~~G~~~g~~g~i~~i~~   27 (28)
T smart00739        2 FEVGDTVRVIAGPFKGKVGKVLEVDG   27 (28)
T ss_pred             CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence            68999999999999999999999864

Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.

>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic

Probab=95.66  E-value=0.039  Score=37.33  Aligned_cols=36  Identities=19%  Similarity=0.126  Sum_probs=29.3

Q ss_pred             CCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCC
Q psy1800           2 FPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGN   40 (81)
Q Consensus         2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~   40 (81)
                      ..|+.+.|++|++-|..|+|.++...   .+.|.|+.-+
T Consensus        43 kkGD~V~Vi~Gk~KGk~GkV~~V~~~---~~~V~Vegvn   78 (114)
T TIGR01080        43 RKGDKVRIMRGDFKGHEGKVSKVDLK---RYRIYVEGVT   78 (114)
T ss_pred             ecCCEEEEecCCCCCCEEEEEEEEcC---CCEEEEcCeE
Confidence            46999999999999999999999743   3467776544

This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.

>PRK12281 rplX 50S ribosomal protein L24; Reviewed

Probab=94.72  E-value=0.092  Score=33.00  Aligned_cols=37  Identities=19%  Similarity=0.299  Sum_probs=30.5

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCC
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGN   40 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~   40 (81)
                      +..|+.+.|+.|+.-|+.|+|.++.+.   .+.|.+++-+
T Consensus         7 I~kGD~V~Vi~G~dKGK~G~V~~V~~~---~~~V~Vegvn   43 (76)
T PRK12281          7 VKKGDMVKVIAGDDKGKTGKVLAVLPK---KNRVIVEGVK   43 (76)
T ss_pred             ccCCCEEEEeEcCCCCcEEEEEEEEcC---CCEEEEcCcE
Confidence            357999999999999999999999764   4467787644

>CHL00141 rpl24 ribosomal protein L24; Validated

Probab=94.61  E-value=0.099  Score=33.33  Aligned_cols=36  Identities=25%  Similarity=0.334  Sum_probs=30.0

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcC
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDG   39 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~   39 (81)
                      +..|+.++|+.|+.-|+.|+|.++.+.   .+.|++++-
T Consensus         9 I~~GD~V~Vi~G~dKGK~G~V~~V~~~---~~~V~Vegv   44 (83)
T CHL00141          9 VKIGDTVKIISGSDKGKIGEVLKIIKK---SNKVIVKGI   44 (83)
T ss_pred             ccCCCEEEEeEcCCCCcEEEEEEEEcC---CCEEEEcCc
Confidence            357999999999999999999999754   356778654

>PRK00004 rplX 50S ribosomal protein L24; Reviewed

Probab=94.34  E-value=0.11  Score=34.25  Aligned_cols=76  Identities=18%  Similarity=0.230  Sum_probs=48.6

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCC--------------CC----EEEEeeccEEEEecC-Ccc-
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGN--------------GH----VFATRLNNVFIIGKG-TKA-   60 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~--------------g~----~F~T~~~nVfvIGk~-~kp-   60 (81)
                      +..|+.++|+.|++-|..|+|.++.+.   .+.|++++-+              |.    +..-..|||+.+-.. .+| 
T Consensus         5 i~kGD~V~Vi~G~dKGk~G~V~~V~~~---~~~V~Vegvn~~k~h~k~~~~~~~G~i~~~e~pI~~SnV~lv~p~~~~~~   81 (105)
T PRK00004          5 IKKGDTVIVIAGKDKGKRGKVLKVLPK---KNKVIVEGVNIVKKHQKPNQENPQGGIIEKEAPIHISNVALVDPKTGKAT   81 (105)
T ss_pred             ccCCCEEEEeEcCCCCcEEEEEEEEcC---CCEEEEcCcEEEEEecCCCCCCCCCceEEEECCcCHHHEEEEeCcCCCCe
Confidence            467999999999999999999999654   3456665422              21    112234888888632 333 


Q ss_pred             eEe--c-CCCceeeeeeeeccc
Q psy1800          61 FCS--K-PKRNFVSPRQTCPTI   79 (81)
Q Consensus        61 ~Is--L-p~~kgi~~~~~~~~~   79 (81)
                      -+.  + ..++-+|.+.-|-..
T Consensus        82 rv~~~~~~~g~kvRv~k~~g~~  103 (105)
T PRK00004         82 RVGFKFLEDGKKVRVAKKSGEV  103 (105)
T ss_pred             EEEEEEccCCcEEEEEecCCCC
Confidence            222  2 245667777776543

>PRK01191 rpl24p 50S ribosomal protein L24P; Validated

Probab=94.27  E-value=0.22  Score=34.10  Aligned_cols=34  Identities=21%  Similarity=0.233  Sum_probs=28.0

Q ss_pred             CCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEc
Q psy1800           2 FPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD   38 (81)
Q Consensus         2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd   38 (81)
                      ..|+.++|+.|+.-|..|+|.++.+.   .+.|.|+.
T Consensus        47 kkGD~V~VisG~~KGk~GkV~~V~~~---~~~V~VeG   80 (120)
T PRK01191         47 RKGDTVKVMRGDFKGEEGKVVEVDLK---RGRIYVEG   80 (120)
T ss_pred             eCCCEEEEeecCCCCceEEEEEEEcC---CCEEEEeC
Confidence            57999999999999999999999654   34566654

>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle

Probab=93.14  E-value=0.22  Score=32.94  Aligned_cols=74  Identities=18%  Similarity=0.247  Sum_probs=46.5

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcC---------------CCCE----EEEeeccEEEEecC-Ccc
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDG---------------NGHV----FATRLNNVFIIGKG-TKA   60 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~---------------~g~~----F~T~~~nVfvIGk~-~kp   60 (81)
                      +..|+.+.|+.|+.-|..|+|.++.+..   +.|.+++-               .|..    ..-..|||+.+-.. .+|
T Consensus         4 ikkGD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~VegvN~~kkh~k~~~~~~~~g~i~~~e~pI~~SnV~lv~p~~~k~   80 (104)
T TIGR01079         4 IKKGDTVKVISGKDKGKRGKVLKVLPKT---NKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEAPIHISNVMLFDPKTGKA   80 (104)
T ss_pred             ccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEECCcEEEEEecCcccCCCCCCceEEEEccCCHHHeEEEcCcCCCC
Confidence            4679999999999999999999996542   34444322               1211    11234888888632 344


Q ss_pred             e-Ee---cCCCceeeeeeeec
Q psy1800          61 F-CS---KPKRNFVSPRQTCP   77 (81)
Q Consensus        61 ~-Is---Lp~~kgi~~~~~~~   77 (81)
                      . +.   +..++-+|.+.-|-
T Consensus        81 ~rv~~~~~~~g~kvRv~k~~g  101 (104)
T TIGR01079        81 TRVGIRFEEDGKKVRVFKKTG  101 (104)
T ss_pred             eEEEEEEccCCcEEEEEeccC
Confidence            2 22   33566777776664

This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.

>PF13051 DUF3912: Protein of unknown function (DUF3912)

Probab=91.49  E-value=0.69  Score=28.61  Aligned_cols=50  Identities=24%  Similarity=0.434  Sum_probs=38.0

Q ss_pred             CCcEEEEECCCCcceEEEEEEEEEecC-CCcEEEEEcCCCCEEEEeeccEEEEec
Q psy1800           3 PGNLCMITGGRNLGRVGTVVNRERHPG-SFDIVHVKDGNGHVFATRLNNVFIIGK   56 (81)
Q Consensus         3 ~G~~~mVtgG~n~GrvG~I~~ie~~~g-~~~iV~ikd~~g~~F~T~~~nVfvIGk   56 (81)
                      +|..|||-.|.+.-|+|.+++-|.... .|.+|.    ++...+--+..+..+|-
T Consensus         5 ~gqkayikdgp~rnrigivk~~e~q~~~~f~ivi----~~q~i~velkdivlvgv   55 (68)
T PF13051_consen    5 VGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIVI----GEQSIDVELKDIVLVGV   55 (68)
T ss_pred             cccEeeeccCCccceeEEEecchhhcCCcEEEEE----CCeEEEEEeeeEEEEEe
Confidence            588999999999999999999988866 665553    22456666677777764

>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]

Probab=88.87  E-value=1.1  Score=30.86  Aligned_cols=34  Identities=21%  Similarity=0.346  Sum_probs=28.1

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEc
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD   38 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd   38 (81)
                      +++|-.|+++.|+.+|+-.+|..+..+    +.+++-+
T Consensus         5 l~~GrVvvv~~GR~aGkk~VIv~~iDd----~~v~i~g   38 (125)
T COG2163           5 LEVGRVVVVTAGRFAGKKVVIVKIIDD----NFVLITG   38 (125)
T ss_pred             ccCCeEEEEecceeCCceEEEEEEccC----CEEEEeC
Confidence            579999999999999999999988654    3555554

>PTZ00194 60S ribosomal protein L26; Provisional

Probab=87.60  E-value=1.4  Score=30.97  Aligned_cols=51  Identities=25%  Similarity=0.384  Sum_probs=35.2

Q ss_pred             CCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEc-----CCCCEE--EEeeccEEEEe
Q psy1800           2 FPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD-----GNGHVF--ATRLNNVFIIG   55 (81)
Q Consensus         2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd-----~~g~~F--~T~~~nVfvIG   55 (81)
                      ..|+.++|+.|++-|..|+|..+.+..   +.|.|+.     .+|..+  --..+||+++-
T Consensus        48 kkGD~V~Vi~Gk~KGk~GkV~~V~~k~---~~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~  105 (143)
T PTZ00194         48 RKDDEVMVVRGHHKGREGKVTAVYRKK---WVIHIEKITREKANGEPVQIGIHPSNVIITK  105 (143)
T ss_pred             ecCCEEEEecCCCCCCceEEEEEEcCC---CEEEEeCeEEEecCCCEeecCcCchheEEEc
Confidence            469999999999999999999996543   3555543     333322  23346666664

>PF01588 tRNA_bind: Putative tRNA binding domain; InterPro: IPR002547 This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [], human tyrosyl-tRNA synthetase [], and endothelial-monocyte activating polypeptide II

Probab=84.15  E-value=3.1  Score=26.26  Aligned_cols=22  Identities=36%  Similarity=0.536  Sum_probs=17.7

Q ss_pred             eEEEEEEEEEecCCCcEEEEEc
Q psy1800          17 RVGTVVNRERHPGSFDIVHVKD   38 (81)
Q Consensus        17 rvG~I~~ie~~~g~~~iV~ikd   38 (81)
                      |+|+|.+.+.||++..+..++=
T Consensus         2 ~vg~I~~~~~hp~sdkL~~~~V   23 (95)
T PF01588_consen    2 RVGKILEVEPHPNSDKLYVLKV   23 (95)
T ss_dssp             EEEEEEEEEEETTSSSEEEEEE
T ss_pred             EEEEEEEEEECCCCCEEEEEEE
Confidence            6899999999999666665553

G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases []. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme []. This domain may perform a common function in tRNA aminoacylation [].; GO: 0000049 tRNA binding; PDB: 3BU2_C 1PYB_A 2Q2I_A 2Q2H_A 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 2CWP_A ....

>PTZ00065 60S ribosomal protein L14; Provisional

Probab=83.87  E-value=1.5  Score=30.36  Aligned_cols=31  Identities=32%  Similarity=0.518  Sum_probs=27.5

Q ss_pred             CCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEE
Q psy1800           2 FPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHV   36 (81)
Q Consensus         2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~i   36 (81)
                      |+|-+|++.-|.+.|+..+|.+|..+    |.|.+
T Consensus         9 EiGRVvli~~Gp~~GKL~vIVDIID~----nRvLV   39 (130)
T PTZ00065          9 EPGRLCLIQYGPDAGKLCFIVDIVTP----TRVLV   39 (130)
T ss_pred             eeceEEEEecCCCCCCEEEEEEEEcC----CeEEE
Confidence            78999999999999999999999876    56655

>PF14001 YdfZ: YdfZ protein

Probab=82.39  E-value=4.1  Score=25.24  Aligned_cols=40  Identities=25%  Similarity=0.351  Sum_probs=29.3

Q ss_pred             CCCcEEEEECCCCcceEEEEEEEEEe------cCCCcEEEEEcCCCCEEE
Q psy1800           2 FPGNLCMITGGRNLGRVGTVVNRERH------PGSFDIVHVKDGNGHVFA   45 (81)
Q Consensus         2 e~G~~~mVtgG~n~GrvG~I~~ie~~------~g~~~iV~ikd~~g~~F~   45 (81)
                      .+|+.+|+-|   .|.+|+|+.|.-.      -.....|.+++.+| .|+
T Consensus        11 ~~G~rVMiag---tG~~gvikAih~~gl~~eq~rR~kcVel~g~~g-~f~   56 (64)
T PF14001_consen   11 TTGSRVMIAG---TGATGVIKAIHADGLTAEQIRRAKCVELEGCEG-RFA   56 (64)
T ss_pred             CCCCEEEEcC---CCcccEEeeeecCCCCHHHhhhccEEEEeCCCc-eEc
Confidence            5799999977   6788889988544      12456888888776 465

>TIGR03784 marine_sortase sortase, marine proteobacterial type

Probab=81.91  E-value=3.7  Score=29.10  Aligned_cols=47  Identities=11%  Similarity=0.164  Sum_probs=35.6

Q ss_pred             CCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeeeeec
Q psy1800          30 SFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCP   77 (81)
Q Consensus        30 ~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~~~~   77 (81)
                      .-|.|.+++.+|..+.-+...+.++-. +...+..|.++-.-..+||-
T Consensus       111 ~GD~I~v~~~~g~~~~Y~V~~~~iV~~-~d~~v~~~~~~~~LtLiTC~  157 (174)
T TIGR03784       111 PGDVIRLQTPDGQWQSYQVTATRVVDE-SETGLDLPADDSQLVLITCY  157 (174)
T ss_pred             CCCEEEEEECCCeEEEEEEeEEEEECC-ccceeccCCCCCEEEEEeCC
Confidence            458999999999888888999999988 44455556555555667894

Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).

>TIGR01076 sortase_fam LPXTG-site transpeptidase (sortase) family protein

Probab=80.26  E-value=7.1  Score=26.00  Aligned_cols=65  Identities=12%  Similarity=0.088  Sum_probs=43.7

Q ss_pred             EEECCCCcce----EEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeeeeec
Q psy1800           8 MITGGRNLGR----VGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQTCP   77 (81)
Q Consensus         8 mVtgG~n~Gr----vG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~~~~   77 (81)
                      +|+.|+|.++    ...+.+.    ..-+.|.+++.+ ..|.-....+.++-+.+-+++..+.++..-..+||-
T Consensus        44 ~vIaGH~~~~~~~~F~~L~~l----~~GD~i~v~~~~-~~~~Y~V~~~~~v~~~d~~~l~~~~~~~~LtLiTC~  112 (136)
T TIGR01076        44 IVITGHRGLPTATMFTNLDKL----KKGDMLYLHVGN-EVLTYQVTSTKIVEPTDTEVLLIQHGKDYLTLITCT  112 (136)
T ss_pred             EEEEecCCCCCCCccCCHHHC----CCCCEEEEEECC-cEEEEEEEEEEEECcCcceeEeccCCCCEEEEEEeC
Confidence            4556666433    2233332    244688999876 579999999999998666677666666666678894

of an LPXTG motif to the cell wall. It also includes a protein required for correct assembly of an LPXTG-containing fimbrial protein, a set of homologous proteins from Streptococcus pneumoniae, in which LPXTG proteins are common. However, related proteins are found in Bacillus subtilis and Methanobacterium thermoautotrophicum, in which LPXTG-mediated cell wall attachment is not known.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	81
3iz6_D	265	Localization Of The Small Subunit Ribosomal Protein		2e-18
3izb_D	261	Localization Of The Small Subunit Ribosomal Protein		2e-17
2xzm_W	260	Crystal Structure Of The Eukaryotic 40s Ribosomal S		1e-15
3zey_1	273	High-resolution Cryo-electron Microscopy Structure		1e-14

>pdb|3IZ6|D Chain D, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 265

Iteration: 1
 Score = 87.4 bits (215), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 40/63 (63%), Positives = 48/63 (76%)
Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GN+ M+TGGRN GRVG + NRE+H GSF+ +HV+D  GH FATRL NVF IGKG K + S
Sbjct: 178 GNVVMVTGGRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRLGNVFTIGKGNKPWVS 237
Query: 64  KPK 66
            PK
Sbjct: 238 LPK 240

>pdb|3IZB|D Chain D, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 261

Iteration: 1
 Score = 83.6 bits (205), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 37/63 (58%), Positives = 48/63 (76%)
Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           G L  +TGGRNLGR+GT+V++ERH G FD+VH+KD   + F TRLNNVF+IG+  K + S
Sbjct: 178 GKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYIS 237
Query: 64  KPK 66
            PK
Sbjct: 238 LPK 240

>pdb|2XZM|W Chain W, 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 = 260

Iteration: 1
 Score = 78.2 bits (191), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 33/62 (53%), Positives = 45/62 (72%)
Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCS 63
           GN+C I  G N+GRVG + + E+H GSFDI HVKD  G+ FATRL N+F++G+G K++  
Sbjct: 180 GNVCYIQQGNNIGRVGIIQHIEKHQGSFDICHVKDAKGNAFATRLGNIFVLGQGKKSWIE 239
Query: 64  KP 65
            P
Sbjct: 240 LP 241

>pdb|3ZEY|1 Chain 1, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 273

Iteration: 1
 Score = 74.3 bits (181), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 31/53 (58%), Positives = 41/53 (77%)
Query: 4   GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGK 56
           G + M+TGG N GR+G +V+ ERHPG+FDI  +KD +GH FATR  N+F+IGK
Sbjct: 175 GKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRATNIFVIGK 227

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	81
3iz6_D	265	40S ribosomal protein S4 (S4E); eukaryotic ribosom	7e-25
2xzm_W	260	40S ribosomal protein S4; ribosome, translation; 3	3e-24
3u5c_E	261	RP5, S7, YS6, 40S ribosomal protein S4-A; translat	4e-24
3kbg_A	213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	2e-18

>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Length = 265

 Score = 92.5 bits (229), Expect = 7e-25
 Identities = 40/64 (62%), Positives = 48/64 (75%)

Query: 3   PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFC 62
            GN+ M+TGGRN GRVG + NRE+H GSF+ +HV+D  GH FATRL NVF IGKG K + 
Sbjct: 177 VGNVVMVTGGRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRLGNVFTIGKGNKPWV 236

Query: 63  SKPK 66
           S PK
Sbjct: 237 SLPK 240

>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W Length = 260

 Score = 90.5 bits (224), Expect = 3e-24
 Identities = 33/64 (51%), Positives = 45/64 (70%)

Query: 3   PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFC 62
            GN+C I  G N+GRVG + + E+H GSFDI HVKD  G+ FATRL N+F++G+G K++ 
Sbjct: 179 SGNVCYIQQGNNIGRVGIIQHIEKHQGSFDICHVKDAKGNAFATRLGNIFVLGQGKKSWI 238

Query: 63  SKPK 66
             P 
Sbjct: 239 ELPS 242

>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E Length = 261

 Score = 90.5 bits (224), Expect = 4e-24
 Identities = 37/64 (57%), Positives = 48/64 (75%)

Query: 3   PGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFC 62
            G L  +TGGRNLGR+GT+V++ERH G FD+VH+KD   + F TRLNNVF+IG+  K + 
Sbjct: 177 AGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYI 236

Query: 63  SKPK 66
           S PK
Sbjct: 237 SLPK 240

>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} Length = 213

 Score = 74.8 bits (183), Expect = 2e-18
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 5/65 (7%)

Query: 3   PGNLCMITGGRNLGRVGTVVNRERHPGS-FDIVHVKDGNGHVFATRLNNVFIIGKGTKAF 61
           PGN   IT G ++ + GT+   E   GS  ++VH ++G    F+T  ++VF+IG    +F
Sbjct: 141 PGNKAYITAGSHVNQTGTISKIEAKEGSSANLVHFQEG----FSTIKDHVFMIGSSKFSF 196

Query: 62  CSKPK 66
              P+
Sbjct: 197 VLSPE 201

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	81
3iz6_D	265	40S ribosomal protein S4 (S4E); eukaryotic ribosom	100.0
3u5c_E	261	RP5, S7, YS6, 40S ribosomal protein S4-A; translat	99.97
2xzm_W	260	40S ribosomal protein S4; ribosome, translation; 3	99.97
3j20_E	243	30S ribosomal protein S4E; archaea, archaeal, KINK	99.95
3kbg_A	213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	99.9
2do3_A	69	Transcription elongation factor SPT5; KOW motif, s	96.49
1vq8_T	120	50S ribosomal protein L24P; ribosome 50S, protein-	93.16
3v2d_Y	110	50S ribosomal protein L24; ribosome associated inh	92.11
1nz9_A	58	Transcription antitermination protein NUSG; transc	91.56
2zkr_t	145	60S ribosomal protein L26; protein-RNA complex, 60	91.09
2ckk_A	127	KIN17; beta barrel, ribosomal protein, ribonucleop	90.47
2ftc_N	96	Mitochondrial ribosomal protein L24; mitochondrial	90.09
3r8s_U	102	50S ribosomal protein L24; protein biosynthesis, R	89.64
3j21_U	121	50S ribosomal protein L24P; archaea, archaeal, KIN	89.05
2zjr_R	115	50S ribosomal protein L24; ribosome, large ribosom	88.94
4a18_F	126	RPL14; ribosome, eukaryotic initiation factor 6, E	85.75
3iz5_N	134	60S ribosomal protein L14 (L14E); eukaryotic ribos	85.62
3u5e_Y	127	L33, YL33, 60S ribosomal protein L26-A; translatio	83.84
3iz5_Y	150	60S ribosomal protein L26 (L24P); eukaryotic ribos	83.6
4a17_S	135	RPL26, 60S ribosomal protein L21; eukaryotic ribos	83.38
2e6z_A	59	Transcription elongation factor SPT5; KOW motif, s	83.11
3izc_N	138	60S ribosomal protein RPL14 (L14E); eukaryotic rib	82.39
3j21_5	83	50S ribosomal protein L14E; archaea, archaeal, KIN	81.88
4a18_N	144	RPL27, ribosomal protein L22; ribosome, eukaryotic	81.32
2joy_A	96	50S ribosomal protein L14E; protein solution struc	80.45

>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=100.00  E-value=2.6e-33  Score=209.15  Aligned_cols=74  Identities=54%  Similarity=0.867  Sum_probs=67.2

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeee
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQ   74 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~   74 (81)
                      ||+||+||||||+|+||+|+|++|++|+|+||+||++|++|++|+|+++||||||++++||||||++|||||++
T Consensus       175 fe~Gnl~mvtgG~n~GriG~I~~ie~~~gs~~iV~vkd~~g~~F~T~~~nvfvIGk~~kp~IsLp~~kg~~~~~  248 (265)
T 3iz6_D          175 FDVGNVVMVTGGRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRLGNVFTIGKGNKPWVSLPKGKGIKLSI  248 (265)
T ss_dssp             CSTTCEEEECSSSSCSCEEEEEEEECCSSSCCEEEECCCSSCCEEEEGGGEEEEECSSCCCCCCCCCC------
T ss_pred             ccCCCEEEEEcCCcceEEEEEEEEEEecCCCcEEEEEECCCCeEEEEeCeEEEEccCCCeeEeCCCCCceeeeh
Confidence            89999999999999999999999999999999999999999999999999999999889999999999999875

>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E

Probab=99.97  E-value=2.2e-33  Score=209.17  Aligned_cols=74  Identities=50%  Similarity=0.851  Sum_probs=72.2

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeee
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQ   74 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~   74 (81)
                      ||+||+||||||+|+||+|+|++|++|+|+||+||++|++|++|+|+++||||||++++||||||++|||||++
T Consensus       175 fe~Gnl~mvtgG~n~GriG~I~~ie~~~gs~~iV~vkd~~g~~F~T~~~nvfvIGk~~kp~IsLp~~kg~~~~~  248 (261)
T 3u5c_E          175 FDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKGKGIKLSI  248 (261)
T ss_dssp             CCSSCCEEECSSTTTTCBCCCCEEECCTTSCCEEEEECTTSCEEEEEGGGEEECCSSSCCSSCCCTTTTCCCCH
T ss_pred             ccCCCEEEEEcCCcceEEEEEEEEEEecCCCcEEEEEECCCCeEEEEeCeEEEEccCCCeeEeCCCCCceeeeh
Confidence            89999999999999999999999999999999999999999999999999999999889999999999999874

>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W

Probab=99.97  E-value=5.1e-32  Score=201.75  Aligned_cols=74  Identities=46%  Similarity=0.848  Sum_probs=71.9

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCceeeeee
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFVSPRQ   74 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi~~~~   74 (81)
                      |++||+||||||+|+||+|+|+++++|++++|+||++|++|++|+|+++||||||++++||||||++||||||+
T Consensus       177 fe~G~l~mvtgG~n~GriG~I~~~e~~~gs~~iV~vkd~~g~~F~T~~~~vfvIG~~~kp~Islp~~kgi~l~i  250 (260)
T 2xzm_W          177 LESGNVCYIQQGNNIGRVGIIQHIEKHQGSFDICHVKDAKGNAFATRLGNIFVLGQGKKSWIELPSGDGVRETI  250 (260)
T ss_dssp             CCSSCEEEECSSTTTTCEEEEEEEECCCSSCCEEEEECTTCCCEEEEGGGEEEEESTTCCSSCCSSSSSCCCCH
T ss_pred             ecCCCEEEEECCccceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEEeeEEEECCCCceeEecCCCCCeecch
Confidence            79999999999999999999999999999999999999999999999999999999779999999999999875

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

Probab=99.95  E-value=3.8e-28  Score=179.47  Aligned_cols=64  Identities=31%  Similarity=0.552  Sum_probs=62.7

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCC-CcEEEEEcCCCCEEEEeeccEEEEecCCcceEecC
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGS-FDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKP   65 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~-~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp   65 (81)
                      ||+||+||||||+|+||+|+|++|++|+|+ ||+||++|++|++|+|+++||||||+ ++||||||
T Consensus       179 f~~G~l~mvtgG~n~GriG~I~~ie~~~gs~~~~V~v~d~~g~~F~T~~~~vfvIGk-~kp~islp  243 (243)
T 3j20_E          179 FEKGAYVFVTQGKNVARKGRIVEIKRFPMGWPDVVTIEDEEGELFDTLKEYAFVVGT-DKPKISLP  243 (243)
T ss_dssp             CCTTCEEEECSSSSTTCEEEEEECCCCCSSSCCEEEEEESSCCCEEEETTTEEEEES-SCSCCSCC
T ss_pred             ccCCCEEEEECCccceEEEEEEEEEEecCCCceEEEEEcCCCCEEEEEeceEEEECC-CCccccCC
Confidence            899999999999999999999999999995 99999999999999999999999999 99999998

>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=99.90  E-value=2.2e-24  Score=156.93  Aligned_cols=65  Identities=32%  Similarity=0.522  Sum_probs=54.9

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCC-CcEEEEEcCCCCEEEEeeccEEEEecCCcceEecCCCcee
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGS-FDIVHVKDGNGHVFATRLNNVFIIGKGTKAFCSKPKRNFV   70 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~-~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kgi   70 (81)
                      |++||+||||||+|+||+|+|++|++|+|| +|+|+++    ++|+|+++||||||+ ++|||.+|.+.=|
T Consensus       139 f~~G~l~mvtgG~n~GriG~I~~ie~~~gs~~~iV~v~----~~F~T~~~~vfvIGk-~~p~i~~~p~~~~  204 (213)
T 3kbg_A          139 MQPGNKAYITAGSHVNQTGTISKIEAKEGSSANLVHFQ----EGFSTIKDHVFMIGS-SKFSFVLSPEEVI  204 (213)
T ss_dssp             CSTTCEEEECSSTTTTCEEEEEEECCCSCC--CEEEET----TTEEEEGGGEEEEEC-SSCBCC-------
T ss_pred             cCCCCEEEEECCCcceEEEEEEEEEEccCCCCCEEEEE----EEEEeeeceEEEEcC-CCccEEeChHHcc
Confidence            899999999999999999999999999997 7999998    679999999999999 7999987766544

>2do3_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: b.34.5.5

Probab=96.49  E-value=0.011  Score=36.15  Aligned_cols=46  Identities=20%  Similarity=0.205  Sum_probs=35.8

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeecc
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNN   50 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~n   50 (81)
                      |++|+-+-|++|+|.|..|.|.+++.    .-++.+-|...+++.-...+
T Consensus        18 F~~GDHVkVi~G~~~getGlVV~v~~----d~v~v~SD~t~~Ei~V~~~d   63 (69)
T 2do3_A           18 FKMGDHVKVIAGRFEGDTGLIVRVEE----NFVILFSDLTMHELKVLPRD   63 (69)
T ss_dssp             CCTTCEEEESSSTTTTCEEEEEEECS----SCEEEEESSSCSEEEECTTS
T ss_pred             ccCCCeEEEeccEEcCceEEEEEEeC----CEEEEEeCCCCCEEEEEhHH
Confidence            89999999999999999999999973    24556667776666544443

>1vq8_T 50S ribosomal protein L24P; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: b.34.5.1 PDB: 1vq4_T* 1vq5_T* 1vq6_T* 1vq7_T* 1s72_T* 1vq9_T* 1vqk_T* 1vql_T* 1vqm_T* 1vqn_T* 1vqo_T* 1vqp_T* 1yhq_T* 1yi2_T* 1yij_T* 1yit_T* 1yj9_T* 1yjn_T* 1yjw_T* 2otj_T* ...

Probab=93.16  E-value=0.2  Score=33.19  Aligned_cols=51  Identities=24%  Similarity=0.357  Sum_probs=36.8

Q ss_pred             CCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcC-----CCCEEEE--eeccEEEEe
Q psy1800           2 FPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDG-----NGHVFAT--RLNNVFIIG   55 (81)
Q Consensus         2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~-----~g~~F~T--~~~nVfvIG   55 (81)
                      ..|+.++|+.|+.-|..|+|..+..   ..+.|+|+.-     +|.+++-  ..+||+++-
T Consensus        44 kkGD~V~Vi~G~dKGk~GkV~~V~~---k~~~V~VEgvn~kK~~Gg~~e~pIh~SNV~i~~  101 (120)
T 1vq8_T           44 NAGDTVEVLRGDFAGEEGEVINVDL---DKAVIHVEDVTLEKTDGEEVPRPLDTSNVRVTD  101 (120)
T ss_dssp             CTTCEEEECSSTTTTCEEEEEEEET---TTTEEEETTCEEECSSSCEEECCBCGGGEEEEE
T ss_pred             cCCCEEEEEecCCCCCEEEEEEEEC---CCCEEEEeCeEeEcCCCCEEEeeechHHEEEEe
Confidence            5799999999999999999999863   3457777665     2333332  256777664

>3v2d_Y 50S ribosomal protein L24; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_S 2hgj_X 2hgq_X 2hgu_X 1vsa_S 2j03_Y 2jl6_Y 2jl8_Y 2v47_Y 2v49_Y 2wdi_Y 2wdj_Y 2wdl_Y 2wdn_Y 2wh2_Y 2wh4_Y 2wrj_Y 2wrl_Y 2wro_Y 2wrr_Y ...

Probab=92.11  E-value=0.95  Score=29.41  Aligned_cols=76  Identities=18%  Similarity=0.139  Sum_probs=50.0

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEc--------------CCCC----EEEEeeccEEEEe-cCCcc-
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD--------------GNGH----VFATRLNNVFIIG-KGTKA-   60 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd--------------~~g~----~F~T~~~nVfvIG-k~~kp-   60 (81)
                      +..|+.+.|+.|+.-|..|+|.++.+.   .+.|+++.              .+|.    +.--..|||+.+- +..+| 
T Consensus         7 IkkGD~V~Vi~GkdKGk~GkV~~V~~~---~~~ViVEGvN~~kkh~kp~~~~~~Ggi~~~E~PIh~SNV~lv~p~~~k~t   83 (110)
T 3v2d_Y            7 VKKGDTVLVASGKYKGRVGKVKEVLPK---KYAVIVEGVNIVKKAVRVSPKYPQGGFIEKEAPLHASKVRPICPACGKPT   83 (110)
T ss_dssp             CCTTSEEEECSSTTTTCEEEEEEEEGG---GTEEEETTSSEEEEECCSSSSSTTCCEEEEECCEEGGGEEEBCTTTCSBC
T ss_pred             cCCCCEEEEeEcCCCCeEeEEEEEECC---CCEEEEeCEEEEEEEeCCCccCCCCCEEEEECCcCHHHeEEEcCcCCCcc
Confidence            357999999999999999999998654   23444432              2341    2233448999985 22344 


Q ss_pred             --eEe-cCCCceeeeeeeeccc
Q psy1800          61 --FCS-KPKRNFVSPRQTCPTI   79 (81)
Q Consensus        61 --~Is-Lp~~kgi~~~~~~~~~   79 (81)
                        -+. +..++-+|.+-.|-.+
T Consensus        84 Rvg~~~~edG~kvRv~kk~g~~  105 (110)
T 3v2d_Y           84 RVRKKFLENGKKIRVCAKCGGA  105 (110)
T ss_dssp             CEEEEECSSCCEEEEESSSCCB
T ss_pred             EEEEEECCCCcEEEEEecCCCc
Confidence              233 4677788887776543

>1nz9_A Transcription antitermination protein NUSG; transcription elongation, riken structural genomics/proteomics initiative, RSGI; NMR {Thermus thermophilus} SCOP: b.34.5.4

Probab=91.56  E-value=0.67  Score=25.97  Aligned_cols=27  Identities=19%  Similarity=0.207  Sum_probs=24.5

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEe
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERH   27 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~   27 (81)
                      |++|+.+.|+.|.-.|..|+|.++..+
T Consensus         5 ~~~Gd~V~V~~Gpf~g~~g~v~~v~~~   31 (58)
T 1nz9_A            5 FREGDQVRVVSGPFADFTGTVTEINPE   31 (58)
T ss_dssp             CCTTCEEEECSGGGTTCEEEEEEEETT
T ss_pred             cCCCCEEEEeecCCCCcEEEEEEEcCC
Confidence            679999999999999999999999643

>2zkr_t 60S ribosomal protein L26; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}

Probab=91.09  E-value=0.26  Score=33.59  Aligned_cols=52  Identities=17%  Similarity=0.220  Sum_probs=36.4

Q ss_pred             CCCCcEEEEECCCCcceE-EEEEEEEEecCCCcEEEEEcCC-----CCEEE--EeeccEEEEe
Q psy1800           1 MFPGNLCMITGGRNLGRV-GTVVNRERHPGSFDIVHVKDGN-----GHVFA--TRLNNVFIIG   55 (81)
Q Consensus         1 fe~G~~~mVtgG~n~Grv-G~I~~ie~~~g~~~iV~ikd~~-----g~~F~--T~~~nVfvIG   55 (81)
                      +..|+.+.|+.|+.-|.. |+|..+..   ..+.|+|+.-+     |...+  -..+||+++-
T Consensus        49 IkkGD~V~Vi~GkdKGk~~GkV~~V~~---k~~~V~VEgvn~~Kp~G~~~e~PIh~SNV~lv~  108 (145)
T 2zkr_t           49 IRKDDEVQVVRGHYKGQQIGKVVQVYR---KKYVIYIERVQREKANGTTVHVGIHPSKVVITR  108 (145)
T ss_dssp             CCTTCEEEECSSTTTTCCSEEEEEEET---TTTEEEETTCEEECSSCCEEECCBCGGGEEECC
T ss_pred             cCCCCEEEEeecCCCCcceeEEEEEEC---CCCEEEEeeeEeEcCCCceEEeccCHHHEEEEc
Confidence            357999999999999999 99999863   34567776544     32222  1256777764

>2ckk_A KIN17; beta barrel, ribosomal protein, ribonucleoprotein, nuclear protein; 1.45A {Homo sapiens}

Probab=90.47  E-value=0.28  Score=32.32  Aligned_cols=25  Identities=24%  Similarity=0.404  Sum_probs=22.8

Q ss_pred             CCCcEEEEECCCCcceEEEEEEEEE
Q psy1800           2 FPGNLCMITGGRNLGRVGTVVNRER   26 (81)
Q Consensus         2 e~G~~~mVtgG~n~GrvG~I~~ie~   26 (81)
                      +.|+.+||..|++.|..|++.++..
T Consensus        72 ~~g~~V~Iv~G~~rG~~g~L~~id~   96 (127)
T 2ckk_A           72 APGKRILVLNGGYRGNEGTLESINE   96 (127)
T ss_dssp             CTTCEEEECSSTTTTCEEEEEEEEG
T ss_pred             CCCCEEEEEecccCCcEEEEEEEeC
Confidence            4699999999999999999999964

>2ftc_N Mitochondrial ribosomal protein L24; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_N

Probab=90.09  E-value=0.48  Score=30.10  Aligned_cols=71  Identities=21%  Similarity=0.203  Sum_probs=45.1

Q ss_pred             CcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcC-------------CCCEE---EE-eeccEEEEe-cCCcce---E
Q psy1800           4 GNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDG-------------NGHVF---AT-RLNNVFIIG-KGTKAF---C   62 (81)
Q Consensus         4 G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~-------------~g~~F---~T-~~~nVfvIG-k~~kp~---I   62 (81)
                      |+.++|+.|++-|..|+|.++.+.   .+.|+++.-             +|...   +. ..|||+.+- +..+|.   +
T Consensus         1 GD~V~Vi~GkdKGk~GkV~~V~~~---~~~ViVeGvN~~kkh~kp~~~~~Ggiv~~e~pIh~SNV~lv~p~~~k~tRvg~   77 (96)
T 2ftc_N            1 GDTVEILEGKDAGKQGKVVQVIRQ---RNWVVVGGLNTHYRYIGKTMDYRGTMIPSEAPLLHRQVKLVDPMDRKPTEIEW   77 (96)
T ss_pred             CCEEEEeEcCCCCcEEEEEEEECC---CCEEEEeCCEEEEEEcCCCCCCCCCEEEEecCcCHHHEEEEeCcCCCceEEEE
Confidence            789999999999999999998643   344555432             23211   22 268999885 223332   2


Q ss_pred             ec-CCCceeeeeeeec
Q psy1800          63 SK-PKRNFVSPRQTCP   77 (81)
Q Consensus        63 sL-p~~kgi~~~~~~~   77 (81)
                      .+ ..++-+|.+-.|-
T Consensus        78 ~~~~dg~kvR~~kk~g   93 (96)
T 2ftc_N           78 RFTEAGERVRVSTRSG   93 (96)
T ss_pred             EEccCCcEEEEEeccC
Confidence            33 5567777776664

>3r8s_U 50S ribosomal protein L24; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 2j28_U* 3fik_U 3j19_U 2wwq_U 3oat_U* 3oas_U* 3ofd_U 3ofc_U 3ofr_U* 3ofz_U* 3og0_U 3ofq_U 3r8t_U 3i1n_U 1vs8_U 1vs6_U 1vt2_U 3i1p_U 3i1r_U 3i1t_U ...

Probab=89.64  E-value=0.6  Score=29.95  Aligned_cols=72  Identities=21%  Similarity=0.093  Sum_probs=47.0

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCC--------------E-----EEEeeccEEEEec-CCcc
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGH--------------V-----FATRLNNVFIIGK-GTKA   60 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~--------------~-----F~T~~~nVfvIGk-~~kp   60 (81)
                      +..|+.++|+.|+.-|..|+|.++.+.    +.|+++.-+=.              .     .--..|||+.+-. ..+|
T Consensus         4 IkkGD~V~Vi~GkdKGk~GkV~~V~~~----~~ViVeGvN~~kkh~kp~~~~~~~Ggi~~~E~PIh~SNV~lv~p~~~k~   79 (102)
T 3r8s_U            4 IRRDDEVIVLTGKDKGKRGKVKNVLSS----GKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKA   79 (102)
T ss_dssp             SCSSCEEEECSSSSTTCEEEEEEEETT----TEEEETTCSEEEEEECCCSSSSCSCEEEEEECCEEGGGEEEEETTTTEE
T ss_pred             ccCCCEEEEeEcCCCCeeeEEEEEEeC----CEEEEeCeEEEEeccccCcccCCCCCEEEEECCcCHHHEEEEcCcCCCc
Confidence            357999999999999999999998642    56666543210              0     2223489998863 2344


Q ss_pred             ---eEecCCCceeeeeeee
Q psy1800          61 ---FCSKPKRNFVSPRQTC   76 (81)
Q Consensus        61 ---~IsLp~~kgi~~~~~~   76 (81)
                         -+.+..++-+|.+-.|
T Consensus        80 trvg~~~edG~kvRv~k~~   98 (102)
T 3r8s_U           80 DRVGFRFEDGKKVRFFKSN   98 (102)
T ss_dssp             ECEEEEEETTEEEEEETTT
T ss_pred             eEEEEEeCCCeEEEEEeec
Confidence               1335666667766555

>3j21_U 50S ribosomal protein L24P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=89.05  E-value=0.47  Score=31.37  Aligned_cols=35  Identities=23%  Similarity=0.219  Sum_probs=28.5

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEc
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD   38 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd   38 (81)
                      +..|+.++|+.|+.-|..|+|.++.+.   .+.|+++.
T Consensus        46 IkkGD~V~Vi~GkdKGk~GkV~~V~~k---~~~V~VEg   80 (121)
T 3j21_U           46 VRVGDKVRIMRGDYKGHEGKVVEVDLK---RYRIYVEG   80 (121)
T ss_dssp             CCSSSEEEECSSSCSSEEEEEEEEETT---TTEEEETT
T ss_pred             cccCCEEEEeecCCCCcEeEEEEEEec---CCEEEEeC
Confidence            357999999999999999999998633   35677764

>2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.34.5.1 PDB: 1nwx_S* 1nwy_S* 1sm1_S* 1xbp_S* 2d3o_S 2zjp_R* 2zjq_R 1nkw_S 3cf5_R* 3dll_R* 3pio_R* 3pip_R* 1pnu_S 1pny_S 1vor_V 1vou_V 1vow_V 1voy_V 1vp0_V

Probab=88.94  E-value=0.46  Score=31.06  Aligned_cols=74  Identities=19%  Similarity=0.171  Sum_probs=46.0

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCC--------------C----CEEEEeeccEEEEec-CCcc-
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGN--------------G----HVFATRLNNVFIIGK-GTKA-   60 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~--------------g----~~F~T~~~nVfvIGk-~~kp-   60 (81)
                      +..|+.+.|+.|+.-|..|+|.++...   .+.|+++.-+              |    .+.--..|||+++-. ..+| 
T Consensus        16 IkkGD~V~Vi~GkdKGk~GkV~~V~~~---~~~V~VEGvN~~kkh~kp~~~~~~Ggiv~~e~PIh~SNV~lv~p~~~k~t   92 (115)
T 2zjr_R           16 FKKGDTVIVLSGKHKGQTGKVLLALPR---DQKVVVEGVNVITKNVKPSMTNPQGGQEQRELALHASKVALVDPETGKAT   92 (115)
T ss_dssp             SCTTSEEECCSSSSTTCEEEEEEEETT---TTEEEESSSCBCCCCCCTTSSSCCCCCCCBCCCBCSSSEECBSSSSBCCC
T ss_pred             ccCCCEEEEeEcCCCCcEEEEEEEECC---CCEEEEeCcEeEEEecCCCcCCCCCCEEEEEcccCHHHEEEEeccCCCce
Confidence            357999999999999999999998633   4567776532              2    112223688888742 1222 


Q ss_pred             --eEecCCCceeeeeeeec
Q psy1800          61 --FCSKPKRNFVSPRQTCP   77 (81)
Q Consensus        61 --~IsLp~~kgi~~~~~~~   77 (81)
                        -+.+..++-+|.+-.|-
T Consensus        93 Rvg~~~~dG~kvR~~kk~g  111 (115)
T 2zjr_R           93 RVRKQIVDGKKVRVAVASG  111 (115)
T ss_dssp             CCCCCCSCTTSCCCCSSSC
T ss_pred             EEEEEEcCCCEEEEEeecC
Confidence              12334455566555543

>4a18_F RPL14; ribosome, eukaryotic initiation factor 6, EIF6, transla large ribosomal subunit, rRNA; 3.52A {Tetrahymena thermophila} PDB: 4a19_F 4a1b_F 4a1d_F 4adx_7

Probab=85.75  E-value=0.62  Score=31.12  Aligned_cols=31  Identities=19%  Similarity=0.357  Sum_probs=26.9

Q ss_pred             CCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEE
Q psy1800           2 FPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHV   36 (81)
Q Consensus         2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~i   36 (81)
                      |+|-+|++.-|++.|+..+|.+|..+    +.|.+
T Consensus         8 evGRVv~i~~G~~aGklavIVdIID~----nrvLV   38 (126)
T 4a18_F            8 QVGRVVYINYGADKGKLAVIVNIINQ----NRILI   38 (126)
T ss_dssp             ETTEEEEECSSTTTTEEEEEEEEETT----TEEEE
T ss_pred             ecceEEEEccCCccCCEEEEEEEecC----CeEEE
Confidence            78999999999999999999999754    45555

>3u5e_Y L33, YL33, 60S ribosomal protein L26-A; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 2wwa_L 2ww9_L 2wwb_L 3o5h_X 3o58_X 3u5i_Y 4b6a_Y 1s1i_U 3izc_Y 3izs_Y 3jyw_U

Probab=83.84  E-value=1.8  Score=28.88  Aligned_cols=34  Identities=18%  Similarity=0.196  Sum_probs=27.9

Q ss_pred             CCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEc
Q psy1800           2 FPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD   38 (81)
Q Consensus         2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd   38 (81)
                      ..|+.++|+.|+.-|..|+|..+.+.   .+.|+|+.
T Consensus        51 kkgD~V~Vi~GkdKGk~GkV~~V~~k---k~~V~VEg   84 (127)
T 3u5e_Y           51 RRDDEVLVVRGSKKGQEGKISSVYRL---KFAVQVDK   84 (127)
T ss_dssp             CTTCEEEECSSTTTTCEEEEEEEEGG---GTEEEEET
T ss_pred             cCCCEEEEeecCCCCccceEEEEECC---CCEEEEeC
Confidence            46999999999999999999998643   34677765

>4a17_S RPL26, 60S ribosomal protein L21; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_S 4a1c_S 4a1e_S

Probab=83.38  E-value=2.1  Score=28.89  Aligned_cols=34  Identities=24%  Similarity=0.263  Sum_probs=27.7

Q ss_pred             CCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEc
Q psy1800           2 FPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD   38 (81)
Q Consensus         2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd   38 (81)
                      ..|+.++|+.|+.-|..|+|..+.+   ..+.|+|+.
T Consensus        50 kkgD~V~Vi~GkdKGk~GkV~~V~~---kk~~V~VEg   83 (135)
T 4a17_S           50 RKDDEVLIVRGKFKGNKGKVTQVYR---KKWAIHVEK   83 (135)
T ss_dssp             CTTCEEEECSSTTTTCEEEEEEEET---TTTEEEETT
T ss_pred             cCCCEEEEeecCCCCceeeEEEEEc---CCCEEEEeC
Confidence            4699999999999999999999853   345677764

>2e6z_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=83.11  E-value=0.68  Score=26.51  Aligned_cols=25  Identities=16%  Similarity=0.387  Sum_probs=23.8

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEE
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRE   25 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie   25 (81)
                      |++|+.+-|+.|.=.|..|+|.+++
T Consensus         8 f~~GD~V~V~~Gpf~g~~G~V~evd   32 (59)
T 2e6z_A            8 FQPGDNVEVCEGELINLQGKILSVD   32 (59)
T ss_dssp             CCTTSEEEECSSTTTTCEEEECCCB
T ss_pred             CCCCCEEEEeecCCCCCEEEEEEEe
Confidence            7899999999999999999999986

>3j21_5 50S ribosomal protein L14E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=81.88  E-value=0.92  Score=27.98  Aligned_cols=26  Identities=23%  Similarity=0.362  Sum_probs=23.3

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEE
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRER   26 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~   26 (81)
                      +++|.+|++..|+..|+..+|.++..
T Consensus         4 ~~~Grvv~~~~Gr~~Gk~~vIv~iiD   29 (83)
T 3j21_5            4 IDVGRIAVVIAGRRAGQKVVVVDIID   29 (83)
T ss_dssp             CCTTEEEECSSSSSSCCCEEEEEECS
T ss_pred             cccCEEEEEeecCCCCCEEEEEEEcC
Confidence            58999999999999999999998743

>4a18_N RPL27, ribosomal protein L22; ribosome, eukaryotic initiation factor 6, EIF6, transla large ribosomal subunit, rRNA; 3.52A {Tetrahymena thermophila} PDB: 4a19_N 4a1b_N 4a1d_N

Probab=81.32  E-value=1.4  Score=30.03  Aligned_cols=27  Identities=19%  Similarity=0.388  Sum_probs=23.8

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEe
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERH   27 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~   27 (81)
                      +++|.+|+|..|+++|+-.+|.++...
T Consensus         5 ~kpGrVvivl~Gr~aGkkaVIvk~iD~   31 (144)
T 4a18_N            5 LKYGRVVILLQGRFAGKKAVIVKSSED   31 (144)
T ss_dssp             CCTTEEEEECSSTTTTCEEEEEEEESS
T ss_pred             ccCCeEEEEecCCcCCCEEEEEEecCC
Confidence            589999999999999999999987543

>2joy_A 50S ribosomal protein L14E; protein solution structure, structural genomics, PSI-2, protein structure initiative; NMR {Sulfolobus solfataricus} SCOP: b.34.5.7 PDB: 2kds_A

Probab=80.45  E-value=1.2  Score=27.87  Aligned_cols=25  Identities=24%  Similarity=0.450  Sum_probs=22.8

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEE
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRE   25 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie   25 (81)
                      +++|.+|++..|++.|+..+|.++.
T Consensus         4 v~~GrVv~~~~Gr~~Gk~~VIv~~i   28 (96)
T 2joy_A            4 IEVGRICVKVKGREAGSKCVIVDII   28 (96)
T ss_dssp             SSTTEEEECSSSSTTCCEEEEEEEC
T ss_pred             cccCEEEEEeecCCCCCEEEEEEEe
Confidence            4789999999999999999999884

---

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	81
d2do3a1	62	Transcription elongation factor SPT5 {Human (Homo	96.83
d1nz9a_	58	N-utilization substance G protein NusG, C-terminal	93.35
d1nppa2	58	N-utilization substance G protein NusG, C-terminal	92.78
d2joya1	96	Ribosomal protein L14e {Sulfolobus solfataricus [T	90.88
d1vqot1	119	Ribosomal proteins L24 (L24p) {Archaeon Haloarcula	90.49
d2zjrr1	110	Ribosomal proteins L24 (L24p) {Deinococcus radiodu	89.13
d1ci3m2	62	Cytochrome f, small domain {Phormidium laminosum [	82.58
d2gycs1	99	Ribosomal proteins L24 (L24p) {Escherichia coli [T	82.53

>d2do3a1 b.34.5.5 (A:462-523) Transcription elongation factor SPT5 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: SPT5 KOW domain-like
domain: Transcription elongation factor SPT5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.83  E-value=0.0016  Score=37.75  Aligned_cols=46  Identities=20%  Similarity=0.205  Sum_probs=36.7

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEcCCCCEEEEeecc
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKDGNGHVFATRLNN   50 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~T~~~n   50 (81)
                      |++|+-+-|++|+|.|..|.|.+++.    .-++.+.|...+++.-...+
T Consensus        11 F~~GDhVkVi~G~~~g~tGlVV~v~~----~~v~~~SD~t~~Ei~V~~~d   56 (62)
T d2do3a1          11 FKMGDHVKVIAGRFEGDTGLIVRVEE----NFVILFSDLTMHELKVLPRD   56 (62)
T ss_dssp             CCTTCEEEESSSTTTTCEEEEEEECS----SCEEEEESSSCSEEEECTTS
T ss_pred             cCCCCeEEEeccEEcCccEEEEEEeC----CEEEEEeCCCCCEEEEehHH
Confidence            78999999999999999999998853    24666777777777655444

>d1nz9a_ b.34.5.4 (A:) N-utilization substance G protein NusG, C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: N-utilization substance G protein NusG, C-terminal domain
domain: N-utilization substance G protein NusG, C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.35  E-value=0.042  Score=30.51  Aligned_cols=25  Identities=20%  Similarity=0.230  Sum_probs=23.8

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEE
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRE   25 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie   25 (81)
                      |++|+.+.|+.|.-.|..|+|.++.
T Consensus         5 F~~Gd~V~I~~GpF~g~~g~V~~i~   29 (58)
T d1nz9a_           5 FREGDQVRVVSGPFADFTGTVTEIN   29 (58)
T ss_dssp             CCTTCEEEECSGGGTTCEEEEEEEE
T ss_pred             ccCCCEEEEeccCCCCCEEEEEEEc
Confidence            8999999999999999999999984

>d1nppa2 b.34.5.4 (A:191-248) N-utilization substance G protein NusG, C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: N-utilization substance G protein NusG, C-terminal domain
domain: N-utilization substance G protein NusG, C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=92.78  E-value=0.071  Score=29.45  Aligned_cols=26  Identities=19%  Similarity=0.206  Sum_probs=24.3

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEE
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRER   26 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~   26 (81)
                      |++|+.+-|+.|.=.|..|+|.++..
T Consensus         5 f~~Gd~V~I~~GpF~g~~g~V~~i~~   30 (58)
T d1nppa2           5 FEKGDQVRVIEGPFMNFTGTVEEVHP   30 (58)
T ss_dssp             CCTTCEEEECSSTTTTCEEEEEEEEG
T ss_pred             ccCCCEEEEcccCCCCCEEEEEEEcC
Confidence            78999999999999999999999864

>d2joya1 b.34.5.7 (A:1-96) Ribosomal protein L14e {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal protein L14e
domain: Ribosomal protein L14e
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=90.88  E-value=0.075  Score=32.45  Aligned_cols=27  Identities=22%  Similarity=0.418  Sum_probs=24.3

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEe
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERH   27 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~   27 (81)
                      .|+|-+|++..|++.|+..+|.++..+
T Consensus         4 VevGrV~ii~~G~~~GK~~vIvdiid~   30 (96)
T d2joya1           4 IEVGRICVKVKGREAGSKCVIVDIIDD   30 (96)
T ss_dssp             SSTTEEEECSSSSTTCCEEEEEEECSS
T ss_pred             eeccEEEEEeecCCCCCEEEEEEEecC
Confidence            489999999999999999999998654

>d1vqot1 b.34.5.1 (T:1-119) Ribosomal proteins L24 (L24p) {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=90.49  E-value=0.24  Score=31.14  Aligned_cols=51  Identities=24%  Similarity=0.371  Sum_probs=35.3

Q ss_pred             CCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEc-----CCCCEEEE--eeccEEEEe
Q psy1800           2 FPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD-----GNGHVFAT--RLNNVFIIG   55 (81)
Q Consensus         2 e~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd-----~~g~~F~T--~~~nVfvIG   55 (81)
                      ..|+.|.|+.|++-|..|+|.++...   .+.|.|+.     .+|...+.  ..+||+++.
T Consensus        43 kkGD~V~Vi~Gk~KGk~GkV~~V~~k---~~~V~Vegin~~k~~~k~~~~pIh~SNv~i~~  100 (119)
T d1vqot1          43 NAGDTVEVLRGDFAGEEGEVINVDLD---KAVIHVEDVTLEKTDGEEVPRPLDTSNVRVTD  100 (119)
T ss_dssp             CTTCEEEECSSTTTTCEEEEEEEETT---TTEEEETTCEEECTTSCEEECCBCGGGEEEEE
T ss_pred             eCCCEEEEeecCCCCCcceEEEEECC---CCEEEEeCcEEEecCCceeeccCchHHEEEEe
Confidence            47999999999999999999998543   45566653     34433322  346666665

>d2zjrr1 b.34.5.1 (R:4-113) Ribosomal proteins L24 (L24p) {Deinococcus radiodurans [TaxId: 1299]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Deinococcus radiodurans [TaxId: 1299]

Probab=89.13  E-value=0.21  Score=31.02  Aligned_cols=35  Identities=20%  Similarity=0.306  Sum_probs=27.7

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEc
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD   38 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd   38 (81)
                      +..|+.++|+-|+.-|..|+|.++.+.   .+.|.++.
T Consensus        13 ikkGD~V~VisGkdKGk~G~Vl~V~~~---~~~ViVeG   47 (110)
T d2zjrr1          13 FKKGDTVIVLSGKHKGQTGKVLLALPR---DQKVVVEG   47 (110)
T ss_dssp             SCTTSEEECCSSSSTTCEEEEEEEETT---TTEEEESS
T ss_pred             eeCCCEEEEeecCCCCcceEEEEEECC---CCEEEEeC
Confidence            357999999999999999999998632   34555554

>d1ci3m2 b.84.2.2 (M:170-231) Cytochrome f, small domain {Phormidium laminosum [TaxId: 32059]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Rudiment single hybrid motif
family: Cytochrome f, small domain
domain: Cytochrome f, small domain
species: Phormidium laminosum [TaxId: 32059]

Probab=82.58  E-value=2  Score=23.23  Aligned_cols=30  Identities=10%  Similarity=0.240  Sum_probs=22.6

Q ss_pred             ceEEEEEEEEEecCCCcEEEEEcCCCCEEE
Q psy1800          16 GRVGTVVNRERHPGSFDIVHVKDGNGHVFA   45 (81)
Q Consensus        16 GrvG~I~~ie~~~g~~~iV~ikd~~g~~F~   45 (81)
                      =.-|+|.+|++.......|+|.+.+|+.++
T Consensus         6 ~~~G~V~~i~~~~~g~~~I~I~~~~G~~~~   35 (62)
T d1ci3m2           6 SAAGVITAIAKADDGSAEVKIRTEDGTTIV   35 (62)
T ss_dssp             SSCEEEEEEEECTTSCEEEEEECTTSCEEE
T ss_pred             ccCEEEEEeEeccCCCEEEEEECCCCCEEE
Confidence            345888999887765567888888987644

>d2gycs1 b.34.5.1 (S:3-101) Ribosomal proteins L24 (L24p) {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Escherichia coli [TaxId: 562]

Probab=82.53  E-value=0.49  Score=28.71  Aligned_cols=34  Identities=24%  Similarity=0.312  Sum_probs=27.3

Q ss_pred             CCCCcEEEEECCCCcceEEEEEEEEEecCCCcEEEEEc
Q psy1800           1 MFPGNLCMITGGRNLGRVGTVVNRERHPGSFDIVHVKD   38 (81)
Q Consensus         1 fe~G~~~mVtgG~n~GrvG~I~~ie~~~g~~~iV~ikd   38 (81)
                      +..|+.++|+-|+.-|..|+|..+.  + . +-|.++.
T Consensus         2 ikkGD~V~VisGkdKGK~G~V~~V~--~-~-~~viVeG   35 (99)
T d2gycs1           2 IRRDDEVIVLTGKDKGKRGKVKNVL--S-S-GKVIVEG   35 (99)
T ss_dssp             CCTTSEEECSSSTTTTCEEEEEEEC--T-T-SEEEETT
T ss_pred             ccCCCEEEEeeCCCCCCceEEEEEE--C-C-CeEEEeC
Confidence            4679999999999999999999983  2 2 4566654