Psyllid ID: psy15072

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------
Protein Sequence
MSNEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTASFLVSYPVLLFDSDFTFLIL
Secondary Structure (PSIPRED)
cccccEEEEEcccccEEEEEccccccccccEEEEEEEccccccccccEEEEEEcHHHcccccccccccEEEEEEccEEEEEEEEEEEEEccEEEEEc
Secondary Structure Prediction (SSPRO)
cccEEEEEEEcccccEEEcccccccccccccEEEEccccccccccccEEEEEccHHHHHHccccccccHHHHHHHHHHHHccccEEEEccccEEEEc
Coil and Loop (DISEMBL)
msnewqvcnvdengkihrlrrectseqcgAGVFMAAMsdrhycgnkfSSLSVELKSArsqvrfppganflTFVLGTASFlvsypvllfdsdftflil
Flexible Loop (DISEMBL)
msnewqvcnvdengkihrlrrECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTASFLVSYPVLLFDSDFTFLIL
Low Complexity Region (SEG)
MSNEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTASFLVSYPVLLFDSDFTFLIL
Disordered region (IsUnstruct)
****WQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTASFLVSYPVLLFDSDFTFLI*
Disordered Region (DISOPRED)
***EWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVE************GANFLTFVLGTASFLVSYPVLLFDSDFTFLIL
Disordered Region (DISEMBL)
MSNEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTASFLVSYPVLLFDSDFTFLIL
Disordered Region (DISPRO)
*SNEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTASFLVSYPVLLFDSDFTFLIL
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSNEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTASFLVSYPVLLFDSDFTFLIL
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	97	2.2.26 [Sep-21-2011]
P68202	155	Ubiquitin-40S ribosomal p	N/A	N/A	0.381	0.238	0.891	8e-15
P29504	155	Ubiquitin-40S ribosomal p	N/A	N/A	0.432	0.270	0.785	1e-14
P68203	156	Ubiquitin-40S ribosomal p	N/A	N/A	0.432	0.269	0.785	1e-14
P15357	156	Ubiquitin-40S ribosomal p	yes	N/A	0.381	0.237	0.810	1e-12
P68200	156	Ubiquitin-40S ribosomal p	N/A	N/A	0.381	0.237	0.756	8e-12
P79781	156	Ubiquitin-40S ribosomal p	yes	N/A	0.381	0.237	0.783	2e-11
P62979	156	Ubiquitin-40S ribosomal p	yes	N/A	0.381	0.237	0.756	5e-11
P62978	156	Ubiquitin-40S ribosomal p	yes	N/A	0.381	0.237	0.756	5e-11
P62992	156	Ubiquitin-40S ribosomal p	yes	N/A	0.381	0.237	0.756	5e-11
P14799	154	Ubiquitin-40S ribosomal p	N/A	N/A	0.371	0.233	0.75	1e-10

>sp|P68202|RS27A_PLUXY Ubiquitin-40S ribosomal protein S27a OS=Plutella xylostella PE=2 SV=2

 Score = 79.0 bits (193), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 33/37 (89%), Positives = 33/37 (89%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VDENGKIHRLRRECTSEQCGAGVFMA M DRHYCG 
Sbjct: 107 KVDENGKIHRLRRECTSEQCGAGVFMAVMEDRHYCGK 143

Ribosomal protein S27a is a component of the 40S subunit of the ribosome.
Plutella xylostella (taxid: 51655)

>sp|P29504|RS27A_MANSE Ubiquitin-40S ribosomal protein S27a OS=Manduca sexta PE=2 SV=2

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 35/42 (83%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSL 50
            VDENGKIHRLRRECT EQCGAGVFMA M DRHYCG   S++
Sbjct: 107 KVDENGKIHRLRRECTGEQCGAGVFMAVMEDRHYCGKCHSTM 148

Ribosomal protein S27a is a component of the 40S subunit of the ribosome.

Manduca sexta (taxid: 7130)

>sp|P68203|RS27A_SPOFR Ubiquitin-40S ribosomal protein S27a OS=Spodoptera frugiperda PE=2 SV=2

 Score = 78.2 bits (191), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 35/42 (83%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSL 50
            VDENGKIHRLRRECT EQCGAGVFMA M DRHYCG   S++
Sbjct: 107 KVDENGKIHRLRRECTGEQCGAGVFMAVMEDRHYCGKCHSTM 148

Ribosomal protein S27a is a component of the 40S subunit of the ribosome.

Spodoptera frugiperda (taxid: 7108)

>sp|P15357|RS27A_DROME Ubiquitin-40S ribosomal protein S27a OS=Drosophila melanogaster GN=RpS27A PE=1 SV=2

 Score = 72.0 bits (175), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 30/37 (81%), Positives = 30/37 (81%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VDENGKIHRLRREC  E CGAGVFMAA  DRHYCG 
Sbjct: 107 KVDENGKIHRLRRECPGENCGAGVFMAAHEDRHYCGK 143

Ribosomal protein S27a is a component of the 40S subunit of the ribosome.

Drosophila melanogaster (taxid: 7227)

>sp|P68200|RS27A_ICTPU Ubiquitin-40S ribosomal protein S27a OS=Ictalurus punctatus GN=rps27a PE=2 SV=2

 Score = 68.9 bits (167), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 28/37 (75%), Positives = 32/37 (86%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VDENGKIHRLRREC +++CGAGVFMA+  DRHYCG 
Sbjct: 107 KVDENGKIHRLRRECPADECGAGVFMASHFDRHYCGK 143

Ribosomal protein S27a is a component of the 40S subunit of the ribosome.

Ictalurus punctatus (taxid: 7998)

>sp|P79781|RS27A_CHICK Ubiquitin-40S ribosomal protein S27a OS=Gallus gallus GN=RPS27A PE=2 SV=3

 Score = 67.8 bits (164), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/37 (78%), Positives = 31/37 (83%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VDENGKI RLRREC SE+CGAGVFMA+  DRHYCG 
Sbjct: 107 KVDENGKISRLRRECPSEECGAGVFMASHFDRHYCGK 143

Ribosomal protein S27a is a component of the 40S subunit of the ribosome.

Gallus gallus (taxid: 9031)

>sp|P62979|RS27A_HUMAN Ubiquitin-40S ribosomal protein S27a OS=Homo sapiens GN=RPS27A PE=1 SV=2

 Score = 66.6 bits (161), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 28/37 (75%), Positives = 31/37 (83%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VDENGKI RLRREC S++CGAGVFMA+  DRHYCG 
Sbjct: 107 KVDENGKISRLRRECPSDECGAGVFMASHFDRHYCGK 143

Ribosomal protein S27a is a component of the 40S subunit of the ribosome.

Homo sapiens (taxid: 9606)

>sp|P62978|RS27A_CAVPO Ubiquitin-40S ribosomal protein S27a OS=Cavia porcellus GN=RPS27A PE=1 SV=2

 Score = 66.6 bits (161), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 28/37 (75%), Positives = 31/37 (83%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VDENGKI RLRREC S++CGAGVFMA+  DRHYCG 
Sbjct: 107 KVDENGKISRLRRECPSDECGAGVFMASHFDRHYCGK 143

Ribosomal protein S27a is a component of the 40S subunit of the ribosome.

Cavia porcellus (taxid: 10141)

>sp|P62992|RS27A_BOVIN Ubiquitin-40S ribosomal protein S27a OS=Bos taurus GN=RPS27A PE=1 SV=2

 Score = 66.6 bits (161), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 28/37 (75%), Positives = 31/37 (83%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VDENGKI RLRREC S++CGAGVFMA+  DRHYCG 
Sbjct: 107 KVDENGKISRLRRECPSDECGAGVFMASHFDRHYCGK 143

Ribosomal protein S27a is a component of the 40S subunit of the ribosome.

Bos taurus (taxid: 9913)

>sp|P14799|RS27A_NEUCR Ubiquitin-40S ribosomal protein S27a OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=ubi-3 PE=1 SV=4

 Score = 65.5 bits (158), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 27/36 (75%), Positives = 29/36 (80%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
            VD +GKI RLRREC +E CGAGVFMAAM DR YCG
Sbjct: 107 KVDSDGKIERLRRECPNETCGAGVFMAAMQDRQYCG 142

Ribosomal protein S27a is a component of the 40S subunit of the ribosome.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

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	97
110671414	156	putative ubiquitin/ribosomal protein S27	0.381	0.237	0.945	3e-14
407080727	155	ubiquitin ribosomal protein RpS27a [Plut	0.381	0.238	0.891	3e-13
302393756	155	RecName: Full=Ubiquitin-40S ribosomal pr	0.381	0.238	0.891	3e-13
39840928	155	ubiquitin [Antheraea yamamai]	0.432	0.270	0.785	5e-13
50284394	155	ubiquitin/ribosomal protein S27Ae fusion	0.432	0.270	0.785	5e-13
357627500	155	Ubiquitin-40S ribosomal protein S27a [Da	0.432	0.270	0.785	5e-13
345480443	160	PREDICTED: ubiquitin-40S ribosomal prote	0.381	0.231	0.891	5e-13
156551219	156	PREDICTED: ubiquitin-40S ribosomal prote	0.381	0.237	0.891	5e-13
302393750	155	RecName: Full=Ubiquitin-40S ribosomal pr	0.432	0.270	0.785	5e-13
148298787	155	ubiquitin and ribosomal protein S27a [Bo	0.432	0.270	0.785	5e-13

>gi|110671414|gb|ABG81958.1| putative ubiquitin/ribosomal protein S27Ae fusion protein [Diaphorina citri]

 Score = 82.4 bits (202), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 35/37 (94%), Positives = 35/37 (94%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 
Sbjct: 107 KVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGK 143

Source: Diaphorina citri

Species: Diaphorina citri

Genus: Diaphorina

Family: Psyllidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|407080727|gb|AFS89619.1| ubiquitin ribosomal protein RpS27a [Plutella xylostella]

 Score = 79.0 bits (193), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 33/37 (89%), Positives = 33/37 (89%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VDENGKIHRLRRECTSEQCGAGVFMA M DRHYCG 
Sbjct: 107 KVDENGKIHRLRRECTSEQCGAGVFMAVMEDRHYCGK 143

Source: Plutella xylostella

Species: Plutella xylostella

Genus: Plutella

Family: Plutellidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|302393756|sp|P68202.2|RS27A_PLUXY RecName: Full=Ubiquitin-40S ribosomal protein S27a; Contains: RecName: Full=Ubiquitin; Contains: RecName: Full=40S ribosomal protein S27a; Flags: Precursor gi|49532928|dbj|BAD26699.1| Ribosomal protein S27A [Plutella xylostella] gi|440552733|gb|AGC11974.1| ubiquitin ribosomal protein RpS27a [Plutella xylostella]

 Score = 79.0 bits (193), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 33/37 (89%), Positives = 33/37 (89%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VDENGKIHRLRRECTSEQCGAGVFMA M DRHYCG 
Sbjct: 107 KVDENGKIHRLRRECTSEQCGAGVFMAVMEDRHYCGK 143

Source: Plutella xylostella

Species: Plutella xylostella

Genus: Plutella

Family: Plutellidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|39840928|dbj|BAD05031.1| ubiquitin [Antheraea yamamai]

 Score = 78.6 bits (192), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 35/42 (83%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSL 50
            VDENGKIHRLRRECT EQCGAGVFMA M DRHYCG   S++
Sbjct: 107 KVDENGKIHRLRRECTGEQCGAGVFMAVMEDRHYCGKCHSTM 148

Source: Antheraea yamamai

Species: Antheraea yamamai

Genus: Antheraea

Family: Saturniidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|50284394|emb|CAH04128.1| ubiquitin/ribosomal protein S27Ae fusion protein [Papilio dardanus]

 Score = 78.6 bits (192), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 35/42 (83%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSL 50
            VDENGKIHRLRRECT EQCGAGVFMA M DRHYCG   S++
Sbjct: 107 KVDENGKIHRLRRECTGEQCGAGVFMAVMEDRHYCGKCHSTM 148

Source: Papilio dardanus

Species: Papilio dardanus

Genus: Papilio

Family: Papilionidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357627500|gb|EHJ77179.1| Ubiquitin-40S ribosomal protein S27a [Danaus plexippus]

 Score = 78.6 bits (192), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 35/42 (83%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSL 50
            VDENGKIHRLRRECT EQCGAGVFMA M DRHYCG   S++
Sbjct: 107 KVDENGKIHRLRRECTGEQCGAGVFMAVMDDRHYCGKCHSTM 148

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345480443|ref|XP_003424147.1| PREDICTED: ubiquitin-40S ribosomal protein S27a-like isoform 2 [Nasonia vitripennis]

 Score = 78.6 bits (192), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 33/37 (89%), Positives = 33/37 (89%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VDENGKIHRLRREC SEQCGAGVFMAAM DRHYCG 
Sbjct: 111 KVDENGKIHRLRRECPSEQCGAGVFMAAMEDRHYCGK 147

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156551219|ref|XP_001602185.1| PREDICTED: ubiquitin-40S ribosomal protein S27a-like isoform 1 [Nasonia vitripennis]

 Score = 78.6 bits (192), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 33/37 (89%), Positives = 33/37 (89%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VDENGKIHRLRREC SEQCGAGVFMAAM DRHYCG 
Sbjct: 107 KVDENGKIHRLRRECPSEQCGAGVFMAAMEDRHYCGK 143

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|302393750|sp|P29504.2|RS27A_MANSE RecName: Full=Ubiquitin-40S ribosomal protein S27a; Contains: RecName: Full=Ubiquitin; Contains: RecName: Full=40S ribosomal protein S27a; Flags: Precursor gi|9725|emb|CAA37599.1| unnamed protein product [Manduca sexta] gi|268306492|gb|ACY95367.1| ribosomal protein S27A [Manduca sexta] gi|315115365|gb|ADT80655.1| ribosomal protein S27A [Euphydryas aurinia] gi|342356355|gb|AEL28836.1| ribosomal protein S27A [Heliconius melpomene cythera] gi|389608233|dbj|BAM17728.1| ribosomal protein S27A [Papilio xuthus] gi|389610663|dbj|BAM18943.1| ribosomal protein S27A [Papilio polytes]

 Score = 78.6 bits (192), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 35/42 (83%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSL 50
            VDENGKIHRLRRECT EQCGAGVFMA M DRHYCG   S++
Sbjct: 107 KVDENGKIHRLRRECTGEQCGAGVFMAVMEDRHYCGKCHSTM 148

Source: Manduca sexta

Species: Manduca sexta

Genus: Manduca

Family: Sphingidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|148298787|ref|NP_001091826.1| ubiquitin and ribosomal protein S27a [Bombyx mori] gi|4587234|dbj|BAA76675.1| ubiquitin/79aa fusion protein [Bombyx mori] gi|54609339|gb|AAV34885.1| ribosomal protein S27A [Bombyx mori] gi|75266796|gb|ABA18643.1| ubiquitin/ribosomal protein S27Ae fusion [Bombyx mori] gi|124365247|gb|ABN09652.1| ubiquitin-ribosomal protein S27a fusion [Bombyx mori]

 Score = 78.6 bits (192), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 35/42 (83%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSL 50
            VDENGKIHRLRRECT EQCGAGVFMA M DRHYCG   S++
Sbjct: 107 KVDENGKIHRLRRECTGEQCGAGVFMAVMEDRHYCGKCHSTM 148

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	97
FB|FBgn0003942	156	RpS27A "Ribosomal protein S27A	0.360	0.224	0.857	1.2e-12
ZFIN|ZDB-GENE-030131-10018	172	rps27a "ribosomal protein S27a	0.360	0.203	0.8	3.9e-12
UNIPROTKB|F1P0H5	179	RPS27A "Ubiquitin-40S ribosoma	0.360	0.195	0.828	8.2e-12
UNIPROTKB|F1P0H6	157	RPS27A "Ubiquitin-40S ribosoma	0.360	0.222	0.828	8.2e-12
UNIPROTKB|G1K315	80	RPS27A "Ubiquitin-40S ribosoma	0.360	0.437	0.828	8.2e-12
UNIPROTKB|P79781	156	RPS27A "Ubiquitin-40S ribosoma	0.360	0.224	0.828	8.2e-12
UNIPROTKB|P62992	156	RPS27A "Ubiquitin-40S ribosoma	0.360	0.224	0.8	1.7e-11
UNIPROTKB|F1PEZ4	156	RPS27A "Uncharacterized protei	0.360	0.224	0.8	1.7e-11
UNIPROTKB|J9P601	156	J9P601 "Uncharacterized protei	0.360	0.224	0.8	1.7e-11
UNIPROTKB|P62979	156	RPS27A "Ubiquitin-40S ribosoma	0.360	0.224	0.8	1.7e-11

FB|FBgn0003942 RpS27A "Ribosomal protein S27A" [Drosophila melanogaster (taxid:7227)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 30/35 (85%), Positives = 30/35 (85%)

Query:    10 VDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
             VDENGKIHRLRREC  E CGAGVFMAA  DRHYCG
Sbjct:   108 VDENGKIHRLRRECPGENCGAGVFMAAHEDRHYCG 142

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

GO:0006412 "translation" evidence=ISS

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

GO:0005840 "ribosome" evidence=NAS

GO:0005875 "microtubule associated complex" evidence=IDA

ZFIN|ZDB-GENE-030131-10018 rps27a "ribosomal protein S27a" [Danio rerio (taxid:7955)]

 Score = 163 (62.4 bits), Expect = 3.9e-12, P = 3.9e-12
 Identities = 28/35 (80%), Positives = 32/35 (91%)

Query:    10 VDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
             VDENGKIHRLRREC +++CGAGVFMA+  DRHYCG
Sbjct:   124 VDENGKIHRLRRECPADECGAGVFMASHFDRHYCG 158

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

GO:0006412 "translation" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

UNIPROTKB|F1P0H5 RPS27A "Ubiquitin-40S ribosomal protein S27a" [Gallus gallus (taxid:9031)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 29/35 (82%), Positives = 31/35 (88%)

Query:    10 VDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
             VDENGKI RLRREC SE+CGAGVFMA+  DRHYCG
Sbjct:   131 VDENGKISRLRRECPSEECGAGVFMASHFDRHYCG 165

GO:0006412 "translation" evidence=IEA

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

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

UNIPROTKB|F1P0H6 RPS27A "Ubiquitin-40S ribosomal protein S27a" [Gallus gallus (taxid:9031)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 29/35 (82%), Positives = 31/35 (88%)

Query:    10 VDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
             VDENGKI RLRREC SE+CGAGVFMA+  DRHYCG
Sbjct:   109 VDENGKISRLRRECPSEECGAGVFMASHFDRHYCG 143

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|G1K315 RPS27A "Ubiquitin-40S ribosomal protein S27a" [Gallus gallus (taxid:9031)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 29/35 (82%), Positives = 31/35 (88%)

Query:    10 VDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
             VDENGKI RLRREC SE+CGAGVFMA+  DRHYCG
Sbjct:    32 VDENGKISRLRRECPSEECGAGVFMASHFDRHYCG 66

GO:0006412 "translation" evidence=IEA

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

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

UNIPROTKB|P79781 RPS27A "Ubiquitin-40S ribosomal protein S27a" [Gallus gallus (taxid:9031)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 29/35 (82%), Positives = 31/35 (88%)

Query:    10 VDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
             VDENGKI RLRREC SE+CGAGVFMA+  DRHYCG
Sbjct:   108 VDENGKISRLRRECPSEECGAGVFMASHFDRHYCG 142

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

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0002218 "activation of innate immune response" evidence=TAS

GO:0002224 "toll-like receptor signaling pathway" evidence=TAS

GO:0002755 "MyD88-dependent toll-like receptor signaling pathway" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0007250 "activation of NF-kappaB-inducing kinase activity" evidence=TAS

GO:0019985 "translesion synthesis" evidence=TAS

GO:0034134 "toll-like receptor 2 signaling pathway" evidence=TAS

GO:0034138 "toll-like receptor 3 signaling pathway" evidence=TAS

GO:0034142 "toll-like receptor 4 signaling pathway" evidence=TAS

GO:0034146 "toll-like receptor 5 signaling pathway" evidence=TAS

GO:0034154 "toll-like receptor 7 signaling pathway" evidence=TAS

GO:0035419 "activation of MAPK activity involved in innate immune response" evidence=TAS

GO:0035681 "toll-like receptor 15 signaling pathway" evidence=TAS

GO:0035682 "toll-like receptor 21 signaling pathway" evidence=TAS

UNIPROTKB|P62992 RPS27A "Ubiquitin-40S ribosomal protein S27a" [Bos taurus (taxid:9913)]

 Score = 157 (60.3 bits), Expect = 1.7e-11, P = 1.7e-11
 Identities = 28/35 (80%), Positives = 31/35 (88%)

Query:    10 VDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
             VDENGKI RLRREC S++CGAGVFMA+  DRHYCG
Sbjct:   108 VDENGKISRLRRECPSDECGAGVFMASHFDRHYCG 142

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|F1PEZ4 RPS27A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 157 (60.3 bits), Expect = 1.7e-11, P = 1.7e-11
 Identities = 28/35 (80%), Positives = 31/35 (88%)

Query:    10 VDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
             VDENGKI RLRREC S++CGAGVFMA+  DRHYCG
Sbjct:   108 VDENGKISRLRRECPSDECGAGVFMASHFDRHYCG 142

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

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

GO:0006412 "translation" evidence=IEA

UNIPROTKB|J9P601 J9P601 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 157 (60.3 bits), Expect = 1.7e-11, P = 1.7e-11
 Identities = 28/35 (80%), Positives = 31/35 (88%)

Query:    10 VDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
             VDENGKI RLRREC S++CGAGVFMA+  DRHYCG
Sbjct:   108 VDENGKISRLRRECPSDECGAGVFMASHFDRHYCG 142

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

UNIPROTKB|P62979 RPS27A "Ubiquitin-40S ribosomal protein S27a" [Homo sapiens (taxid:9606)]

 Score = 157 (60.3 bits), Expect = 1.7e-11, P = 1.7e-11
 Identities = 28/35 (80%), Positives = 31/35 (88%)

Query:    10 VDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
             VDENGKI RLRREC S++CGAGVFMA+  DRHYCG
Sbjct:   108 VDENGKISRLRRECPSDECGAGVFMASHFDRHYCG 142

GO:0046872 "metal ion binding" evidence=IEA

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

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

GO:0015935 "small ribosomal subunit" evidence=IDA

GO:0006412 "translation" evidence=IC;TAS

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0000080 "G1 phase of mitotic cell cycle" evidence=TAS

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=TAS

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

GO:0000187 "activation of MAPK activity" evidence=TAS

GO:0000209 "protein polyubiquitination" evidence=TAS

GO:0000216 "M/G1 transition of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0002224 "toll-like receptor signaling pathway" evidence=TAS

GO:0002474 "antigen processing and presentation of peptide antigen via MHC class I" evidence=TAS

GO:0002479 "antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent" evidence=TAS

GO:0002755 "MyD88-dependent toll-like receptor signaling pathway" evidence=TAS

GO:0002756 "MyD88-independent toll-like receptor signaling pathway" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0005886 "plasma membrane" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006351 "transcription, DNA-dependent" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" 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:0006915 "apoptotic process" evidence=TAS

GO:0006977 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" evidence=TAS

GO:0007173 "epidermal growth factor receptor signaling pathway" evidence=TAS

GO:0007179 "transforming growth factor beta receptor signaling pathway" evidence=TAS

GO:0007219 "Notch signaling pathway" evidence=TAS

GO:0007220 "Notch receptor processing" evidence=TAS

GO:0007249 "I-kappaB kinase/NF-kappaB cascade" evidence=TAS

GO:0007254 "JNK cascade" evidence=TAS

GO:0008063 "Toll signaling pathway" evidence=TAS

GO:0008543 "fibroblast growth factor receptor signaling pathway" evidence=TAS

GO:0010008 "endosome membrane" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016044 "cellular membrane organization" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0016197 "endosomal transport" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0019083 "viral transcription" evidence=TAS

GO:0019221 "cytokine-mediated signaling pathway" evidence=TAS

GO:0030512 "negative regulation of transforming growth factor beta receptor signaling pathway" evidence=TAS

GO:0030666 "endocytic vesicle membrane" evidence=TAS

GO:0031145 "anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process" evidence=TAS

GO:0032480 "negative regulation of type I interferon production" evidence=TAS

GO:0033554 "cellular response to stress" evidence=TAS

GO:0034130 "toll-like receptor 1 signaling pathway" evidence=TAS

GO:0034134 "toll-like receptor 2 signaling pathway" evidence=TAS

GO:0034138 "toll-like receptor 3 signaling pathway" evidence=TAS

GO:0034142 "toll-like receptor 4 signaling pathway" evidence=TAS

GO:0035666 "TRIF-dependent toll-like receptor signaling pathway" evidence=TAS

GO:0035872 "nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway" evidence=TAS

GO:0042059 "negative regulation of epidermal growth factor receptor signaling pathway" evidence=TAS

GO:0042590 "antigen processing and presentation of exogenous peptide antigen via MHC class I" evidence=TAS

GO:0042981 "regulation of apoptotic process" evidence=TAS

GO:0043123 "positive regulation of I-kappaB kinase/NF-kappaB cascade" evidence=TAS

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

GO:0045087 "innate immune response" evidence=TAS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=TAS

GO:0046788 "egress of virus within host cell" evidence=TAS

GO:0048011 "neurotrophin TRK receptor signaling pathway" evidence=TAS

GO:0050852 "T cell receptor signaling pathway" evidence=TAS

GO:0051092 "positive regulation of NF-kappaB transcription factor activity" evidence=TAS

GO:0051403 "stress-activated MAPK cascade" evidence=TAS

GO:0051436 "negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051437 "positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051439 "regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0061418 "regulation of transcription from RNA polymerase II promoter in response to hypoxia" evidence=TAS

GO:0070423 "nucleotide-binding oligomerization domain containing signaling pathway" evidence=TAS

GO:0071456 "cellular response to hypoxia" evidence=TAS

---

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)
P14797	RS27A_DICDI	No assigned EC number	0.625	0.4123	0.2597	yes	N/A
P37165	RS27A_CAEEL	No assigned EC number	0.5306	0.5051	0.3006	yes	N/A
P59233	R27AC_ARATH	No assigned EC number	0.55	0.4123	0.2547	yes	N/A
P59232	R27AB_ARATH	No assigned EC number	0.575	0.4123	0.2547	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	97
pfam01599	47	pfam01599, Ribosomal_S27, Ribosomal protein S27a	4e-19
COG1998	51	COG1998, RPS31, Ribosomal protein S27AE [Translati	4e-07

>gnl|CDD|110592 pfam01599, Ribosomal_S27, Ribosomal protein S27a

 Score = 73.3 bits (180), Expect = 4e-19
 Identities = 23/36 (63%), Positives = 26/36 (72%)

Query: 9  NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
           VD  GK+ RLRREC + +CGAGVFMA   DR YCG
Sbjct: 7  KVDGEGKVVRLRRECPNPRCGAGVFMAEHKDRQYCG 42

This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesised as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins. Length = 47

>gnl|CDD|224909 COG1998, RPS31, Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]

 Score = 42.8 bits (101), Expect = 4e-07
 Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 2/34 (5%)

Query: 11 DENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
           ++ K+ R  R C   +CG GVFMA   DR  CG
Sbjct: 10 VDDEKVKRKNRFCP--RCGPGVFMADHKDRWACG 41

Length = 51

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	97
PF01599	47	Ribosomal_S27: Ribosomal protein S27a; InterPro: I	99.97
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	99.94
PRK00432	50	30S ribosomal protein S27ae; Validated	99.77
KOG0004|consensus	156		99.72
smart00661	52	RPOL9 RNA polymerase subunit 9.	94.74
PF08646	146	Rep_fac-A_C: Replication factor-A C terminal domai	94.59
PHA00626	59	hypothetical protein	94.47
KOG0004|consensus	156		94.36
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	93.12
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	92.34
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	91.28
smart00647	64	IBR In Between Ring fingers. the domains occurs be	91.23
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	90.62
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	89.42
PF13248	26	zf-ribbon_3: zinc-ribbon domain	89.07
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	88.75
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	88.59
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	87.59
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	86.78
KOG0003|consensus	128		86.65
PRK00241	256	nudC NADH pyrophosphatase; Reviewed	86.41
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	85.91
cd04476	166	RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds cor	85.29
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	84.79
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	84.58
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	83.93
KOG0005|consensus	70		83.34
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	82.06
PRK05978	148	hypothetical protein; Provisional	81.02
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	80.46
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	80.28
PRK09710	64	lar restriction alleviation and modification prote	80.15

>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.97  E-value=3.8e-33  Score=173.48  Aligned_cols=47  Identities=55%  Similarity=0.978  Sum_probs=39.2

Q ss_pred             ccceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeE
Q psy15072          3 NEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSS   49 (97)
Q Consensus         3 ~~LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T   49 (97)
                      |+|||||||+||||+|+|++||+|+||+|||||+|+||+||||||+|
T Consensus         1 AvlkyYkvd~~Gkv~r~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~T   47 (47)
T PF01599_consen    1 AVLKYYKVDENGKVKRLRKECPSPRCGAGVFMAEHKDRHYCGKCGYT   47 (47)
T ss_dssp             S----CEEETTTEEEESSEE-TSTTTTSSSEEEE-SSEEEETTTSS-
T ss_pred             CcceEEEECCCCcEEEhhhcCCCcccCCceEeeecCCCccCCCcccC
Confidence            68999999999999999999999999999999999999999999997

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 [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.

>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]

Probab=99.94  E-value=4.6e-28  Score=153.62  Aligned_cols=50  Identities=34%  Similarity=0.524  Sum_probs=46.5

Q ss_pred             CCccceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeEEEee
Q psy15072          1 MSNEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVE   53 (97)
Q Consensus         1 M~~~LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~   53 (97)
                      +.++++||+||+ +||+|+++.||+  ||+|||||+|.||++|||||||++++
T Consensus         1 ~~~~~~yY~v~~-~kv~rk~~~CPr--CG~gvfmA~H~dR~~CGkCgyTe~~~   50 (51)
T COG1998           1 KMAVLKYYEVDD-EKVKRKNRFCPR--CGPGVFMADHKDRWACGKCGYTEFKK   50 (51)
T ss_pred             CccceeEEEEcC-CcEEEccccCCC--CCCcchhhhcCceeEeccccceEeec
Confidence            357899999995 679999999999  99999999999999999999999875

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=99.77  E-value=2.1e-19  Score=111.54  Aligned_cols=47  Identities=34%  Similarity=0.557  Sum_probs=43.9

Q ss_pred             CccceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeEEEe
Q psy15072          2 SNEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSV   52 (97)
Q Consensus         2 ~~~LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~   52 (97)
                      .++|+||+||+ +||+++++.||+  ||+| |||.|.+|++||+||+|++.
T Consensus         3 ~~~~~~y~v~~-~~v~~~~~fCP~--Cg~~-~m~~~~~r~~C~~Cgyt~~~   49 (50)
T PRK00432          3 MAKREYYEVDG-GKVKRKNKFCPR--CGSG-FMAEHLDRWHCGKCGYTEFK   49 (50)
T ss_pred             cceeeeEEECC-CEEEEccCcCcC--CCcc-hheccCCcEECCCcCCEEec
Confidence            57899999985 699999999999  9999 99999999999999999975

>KOG0004|consensus

Probab=99.72  E-value=1.7e-18  Score=129.37  Aligned_cols=53  Identities=49%  Similarity=0.915  Sum_probs=50.2

Q ss_pred             ccceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeEEEeecc
Q psy15072          3 NEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELK   55 (97)
Q Consensus         3 ~~LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~   55 (97)
                      ++++||+||+||+|++++++||+++||+|||||+|+||+|||||.+|+.+.+.
T Consensus       101 ~~~~y~kvd~ngkiq~l~~~~~~~~~~~~v~~a~~~~r~y~gkc~~~~~~~~~  153 (156)
T KOG0004|consen  101 AVLKYYKVDENGKVQRLRRECPNPACGAGVFMASHADRHYCGKCLLTYKFKKA  153 (156)
T ss_pred             CCccceeeccCcchhhhhhhcCCcccccceecccccccccccccceeehhhhc
Confidence            57899999999999999999999999999999999999999999999987654

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=94.74  E-value=0.021  Score=33.50  Aligned_cols=33  Identities=21%  Similarity=0.326  Sum_probs=22.6

Q ss_pred             ccCCCCcCCceEEeceeC--CccccCCceeEEEeecc
Q psy15072         21 RECTSEQCGAGVFMAAMS--DRHYCGNKFSSLSVELK   55 (97)
Q Consensus        21 keCP~~eCGaGVFMA~H~--DR~yCGKCg~T~~~~~~   55 (97)
                      +.||.  ||.=++.-.-.  +|+.|.+||+.+..+..
T Consensus         1 ~FCp~--Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~~   35 (52)
T smart00661        1 KFCPK--CGNMLIPKEGKEKRRFVCRKCGYEEPIEQK   35 (52)
T ss_pred             CCCCC--CCCccccccCCCCCEEECCcCCCeEECCCc
Confidence            46998  99844443322  38999999998765533

>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing

Probab=94.59  E-value=0.17  Score=35.23  Aligned_cols=64  Identities=19%  Similarity=0.216  Sum_probs=37.8

Q ss_pred             CeEEEecc------cCCCCcCCceEEeceeCCccccCCceeEEEeecccccccccCCCCceEEEEEecceeeeeeeeeEE
Q psy15072         14 GKIHRLRR------ECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTASFLVSYPVLL   87 (97)
Q Consensus        14 GKI~rlrk------eCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l~~~~~~~~~~~~~~~~~   87 (97)
                      |+|..+..      .||++.|+..|-.- -.+.++|.||+.+.             +....+.++-+..+-.--+-.+.+
T Consensus         6 a~I~~I~~~~~~Y~aC~~~~C~kKv~~~-~~~~y~C~~C~~~~-------------~~~~~ry~l~~~i~D~tg~~~~~~   71 (146)
T PF08646_consen    6 ATIVEIKSDNWYYPACPNEKCNKKVTEN-GDGSYRCEKCNKTV-------------ENPKYRYRLSLKISDGTGSIWVTL   71 (146)
T ss_dssp             EEEEEEETTTTEEEE-TSTTTS-B-EEE-TTTEEEETTTTEEE-------------SS-EEEEEEEEEEEETTEEEEEEE
T ss_pred             EEEEEEECCCcEECCCCCccCCCEeecC-CCcEEECCCCCCcC-------------CCeeEEEEEEEEEEeCCCeEEEEE
Confidence            45555544      59966699865432 24689999999764             233456666665555555666777


Q ss_pred             Eecc
Q psy15072         88 FDSD   91 (97)
Q Consensus        88 ~~~~   91 (97)
                      ||..
T Consensus        72 F~~~   75 (146)
T PF08646_consen   72 FDEE   75 (146)
T ss_dssp             EHHH
T ss_pred             EhHH
Confidence            7754

It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.

>PHA00626 hypothetical protein

Probab=94.47  E-value=0.025  Score=37.18  Aligned_cols=31  Identities=26%  Similarity=0.419  Sum_probs=24.4

Q ss_pred             cCCCCcCCceEEec-----eeCCccccCCceeEEEeec
Q psy15072         22 ECTSEQCGAGVFMA-----AMSDRHYCGNKFSSLSVEL   54 (97)
Q Consensus        22 eCP~~eCGaGVFMA-----~H~DR~yCGKCg~T~~~~~   54 (97)
                      .||+  ||.+-.+-     .|.+|+-|-+|||.+.++.
T Consensus         2 ~CP~--CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~   37 (59)
T PHA00626          2 SCPK--CGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDA   37 (59)
T ss_pred             CCCC--CCCceeeeeceecccCcceEcCCCCCeechhh
Confidence            5998  99963333     6789999999999987654

>KOG0004|consensus

Probab=94.36  E-value=0.011  Score=44.84  Aligned_cols=19  Identities=32%  Similarity=0.403  Sum_probs=16.3

Q ss_pred             ccccc--ccCCCCceEEEEEe
Q psy15072         56 SARSQ--VRFPPGANFLTFVL   74 (97)
Q Consensus        56 ~a~~q--~~~p~~~~~l~~~~   74 (97)
                      +|++|  ++||||||+|||+-
T Consensus        27 Kakiq~~egIp~dqqrlifag   47 (156)
T KOG0004|consen   27 KAKIQDKEGIPPDQQRLIFAG   47 (156)
T ss_pred             HHhhhcccCCCchhhhhhhhh
Confidence            66666  99999999999973

>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins

Probab=93.12  E-value=0.08  Score=34.53  Aligned_cols=19  Identities=16%  Similarity=0.022  Sum_probs=15.0

Q ss_pred             ccccCCceeEEEeeccccc
Q psy15072         40 RHYCGNKFSSLSVELKSAR   58 (97)
Q Consensus        40 R~yCGKCg~T~~~~~~~a~   58 (97)
                      -.+|-+|||||+++.+...
T Consensus        36 ~v~C~~CGYTE~Y~~~~~~   54 (64)
T PF09855_consen   36 TVSCTNCGYTEFYKAKTSN   54 (64)
T ss_pred             EEECCCCCCEEEEeecCcc
Confidence            3489999999999866443

>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=92.34  E-value=0.071  Score=31.47  Aligned_cols=35  Identities=11%  Similarity=0.114  Sum_probs=21.9

Q ss_pred             ecccCCCCcCCceEEeceeCCc--cccCCceeEEEee
Q psy15072         19 LRRECTSEQCGAGVFMAAMSDR--HYCGNKFSSLSVE   53 (97)
Q Consensus        19 lrkeCP~~eCGaGVFMA~H~DR--~yCGKCg~T~~~~   53 (97)
                      ..+.||++.|+.++......+.  ..|..|+..+.+.
T Consensus        17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~   53 (64)
T PF01485_consen   17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFK   53 (64)
T ss_dssp             -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSS
T ss_pred             CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccc
Confidence            3469999999988877777666  7999999876554

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=91.28  E-value=0.094  Score=34.93  Aligned_cols=28  Identities=18%  Similarity=0.343  Sum_probs=23.1

Q ss_pred             ccCCCCcCCceEEeceeCCccccCCceeEEEe
Q psy15072         21 RECTSEQCGAGVFMAAMSDRHYCGNKFSSLSV   52 (97)
Q Consensus        21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~   52 (97)
                      +.||+  ||.  .|....++++|..|++++..
T Consensus         1 ~fC~~--Cg~--~l~~~~~~~~C~~C~~~~~~   28 (104)
T TIGR01384         1 KFCPK--CGS--LMTPKNGVYVCPSCGYEKEK   28 (104)
T ss_pred             CCCcc--cCc--ccccCCCeEECcCCCCcccc
Confidence            36998  987  77777889999999988654

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>smart00647 IBR In Between Ring fingers

Probab=91.23  E-value=0.19  Score=29.74  Aligned_cols=35  Identities=17%  Similarity=0.294  Sum_probs=26.3

Q ss_pred             ecccCCCCcCCceEEece--eCCccccCCceeEEEee
Q psy15072         19 LRRECTSEQCGAGVFMAA--MSDRHYCGNKFSSLSVE   53 (97)
Q Consensus        19 lrkeCP~~eCGaGVFMA~--H~DR~yCGKCg~T~~~~   53 (97)
                      ..+.||++.|+..+....  ......|.+||+.+.+.
T Consensus        17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~   53 (64)
T smart00647       17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFR   53 (64)
T ss_pred             CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCC
Confidence            457899888999887753  55677898998776543

the domains occurs between pairs og RING fingers

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=90.62  E-value=0.18  Score=29.25  Aligned_cols=27  Identities=19%  Similarity=0.262  Sum_probs=15.2

Q ss_pred             ccCCCCcCCceEEec----eeCCccccCCceeE
Q psy15072         21 RECTSEQCGAGVFMA----AMSDRHYCGNKFSS   49 (97)
Q Consensus        21 keCP~~eCGaGVFMA----~H~DR~yCGKCg~T   49 (97)
                      |.||.  ||.-+-.+    ++..|+.|..||+.
T Consensus         1 kfC~~--CG~~l~~~ip~gd~r~R~vC~~Cg~I   31 (34)
T PF14803_consen    1 KFCPQ--CGGPLERRIPEGDDRERLVCPACGFI   31 (34)
T ss_dssp             -B-TT--T--B-EEE--TT-SS-EEEETTTTEE
T ss_pred             Ccccc--ccChhhhhcCCCCCccceECCCCCCE
Confidence            46888  99865443    45679999999975

>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

Probab=89.42  E-value=0.44  Score=33.51  Aligned_cols=47  Identities=13%  Similarity=0.191  Sum_probs=31.6

Q ss_pred             ccCCCCcCCceEEece----eCCccccCCceeEEEeecc---cccccccCCCCceEEE
Q psy15072         21 RECTSEQCGAGVFMAA----MSDRHYCGNKFSSLSVELK---SARSQVRFPPGANFLT   71 (97)
Q Consensus        21 keCP~~eCGaGVFMA~----H~DR~yCGKCg~T~~~~~~---~a~~q~~~p~~~~~l~   71 (97)
                      +.||.  ||+  .|=.    =..+..|.||||.+-...+   .-......|+.+....
T Consensus         3 ~FCp~--Cgs--ll~p~~~~~~~~l~C~kCgye~~~~~~~~~~~~~~~~~~~~~~~~~   56 (113)
T COG1594           3 RFCPK--CGS--LLYPKKDDEGGKLVCRKCGYEEEASNKKVYRYSVKEAVEKKKEVVL   56 (113)
T ss_pred             cccCC--ccC--eeEEeEcCCCcEEECCCCCcchhccccceeEEEEeeccCCcceeee
Confidence            67998  997  5544    2458899999999877753   2223366666665443

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=89.07  E-value=0.14  Score=27.48  Aligned_cols=23  Identities=30%  Similarity=0.579  Sum_probs=17.1

Q ss_pred             ccCCCCcCCceEEeceeCCccccCCceeE
Q psy15072         21 RECTSEQCGAGVFMAAMSDRHYCGNKFSS   49 (97)
Q Consensus        21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T   49 (97)
                      +.||+  ||+.    ...+-.+|.+||..
T Consensus         3 ~~Cp~--Cg~~----~~~~~~fC~~CG~~   25 (26)
T PF13248_consen    3 MFCPN--CGAE----IDPDAKFCPNCGAK   25 (26)
T ss_pred             CCCcc--cCCc----CCcccccChhhCCC
Confidence            57998  9982    24567789999963

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=88.75  E-value=0.54  Score=27.37  Aligned_cols=29  Identities=21%  Similarity=0.347  Sum_probs=19.5

Q ss_pred             cCCCCcCCceEEeceeC-CccccCCceeEEEe
Q psy15072         22 ECTSEQCGAGVFMAAMS-DRHYCGNKFSSLSV   52 (97)
Q Consensus        22 eCP~~eCGaGVFMA~H~-DR~yCGKCg~T~~~   52 (97)
                      .||.  ||+..+.-++. .-..|..||...-.
T Consensus         2 ~Cp~--Cg~~~~~~D~~~g~~vC~~CG~Vl~e   31 (43)
T PF08271_consen    2 KCPN--CGSKEIVFDPERGELVCPNCGLVLEE   31 (43)
T ss_dssp             SBTT--TSSSEEEEETTTTEEEETTT-BBEE-
T ss_pred             CCcC--CcCCceEEcCCCCeEECCCCCCEeec
Confidence            5998  99977555544 34599999976543

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains

Probab=88.59  E-value=0.28  Score=27.19  Aligned_cols=30  Identities=23%  Similarity=0.172  Sum_probs=17.2

Q ss_pred             ecccCCCCcCCceEEeceeCCccccCCceeEE
Q psy15072         19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSSL   50 (97)
Q Consensus        19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~   50 (97)
                      ..+.||+  ||+-...+.-.-...|..||..+
T Consensus         2 ~~rfC~~--CG~~t~~~~~g~~r~C~~Cg~~~   31 (32)
T PF09297_consen    2 NHRFCGR--CGAPTKPAPGGWARRCPSCGHEH   31 (32)
T ss_dssp             TTSB-TT--T--BEEE-SSSS-EEESSSS-EE
T ss_pred             CCcccCc--CCccccCCCCcCEeECCCCcCEe
Confidence            3578998  99877766555556788888764

; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=87.59  E-value=0.75  Score=27.05  Aligned_cols=32  Identities=16%  Similarity=0.288  Sum_probs=22.3

Q ss_pred             cCCCCcCCceEEeceeCCccccCCceeEEEeecc
Q psy15072         22 ECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELK   55 (97)
Q Consensus        22 eCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~   55 (97)
                      .||+  ||+-+-.-....-..|..||........
T Consensus         5 ~C~~--CG~~~~~~~~~~~~~Cp~CG~~~~~~~~   36 (46)
T PRK00398          5 KCAR--CGREVELDEYGTGVRCPYCGYRILFKER   36 (46)
T ss_pred             ECCC--CCCEEEECCCCCceECCCCCCeEEEccC
Confidence            5888  9985544444446789999987776544

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=86.78  E-value=0.53  Score=34.76  Aligned_cols=39  Identities=18%  Similarity=0.322  Sum_probs=31.7

Q ss_pred             EecccCCCCcCCceEEeceeCCccccCCceeEEEeeccccccc
Q psy15072         18 RLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQ   60 (97)
Q Consensus        18 rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~q   60 (97)
                      .+...||.  ||.=-|  .|..+.+|.-||++.......++++
T Consensus        26 ML~~hCp~--Cg~PLF--~KdG~v~CPvC~~~~~~v~~e~~~~   64 (131)
T COG1645          26 MLAKHCPK--CGTPLF--RKDGEVFCPVCGYREVVVEEEEEEV   64 (131)
T ss_pred             HHHhhCcc--cCCcce--eeCCeEECCCCCceEEEeecccccc
Confidence            46678999  998777  5888999999999888877765555

>KOG0003|consensus

Probab=86.65  E-value=0.097  Score=38.66  Aligned_cols=19  Identities=32%  Similarity=0.403  Sum_probs=16.2

Q ss_pred             ccccc--ccCCCCceEEEEEe
Q psy15072         56 SARSQ--VRFPPGANFLTFVL   74 (97)
Q Consensus        56 ~a~~q--~~~p~~~~~l~~~~   74 (97)
                      +|+.|  +++||++++|+|+-
T Consensus        27 KA~i~~~~Gi~~~~~~L~~~~   47 (128)
T KOG0003|consen   27 KAKIQDKEGIPPDQQRLIFAG   47 (128)
T ss_pred             HHHhccccCCCHHHHHHHhcc
Confidence            66666  99999999999974

>PRK00241 nudC NADH pyrophosphatase; Reviewed

Probab=86.41  E-value=0.46  Score=36.98  Aligned_cols=38  Identities=16%  Similarity=0.226  Sum_probs=27.2

Q ss_pred             EecccCCCCcCCceEEeceeCCccccCCceeEEEeecccc
Q psy15072         18 RLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSA   57 (97)
Q Consensus        18 rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a   57 (97)
                      +..+.||+  ||.=.......-+..|++|+..++.+...+
T Consensus        97 ~~~~fC~~--CG~~~~~~~~~~~~~C~~c~~~~yp~~~pa  134 (256)
T PRK00241         97 RSHRFCGY--CGHPMHPSKTEWAMLCPHCRERYYPRIAPC  134 (256)
T ss_pred             hcCccccc--cCCCCeecCCceeEECCCCCCEECCCCCCE
Confidence            34688999  998655555556779999998776654433

>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors []

Probab=85.91  E-value=0.82  Score=26.25  Aligned_cols=30  Identities=23%  Similarity=0.399  Sum_probs=22.7

Q ss_pred             cccCCCCcCCceEEeceeCCccccCCceeEEE
Q psy15072         20 RRECTSEQCGAGVFMAAMSDRHYCGNKFSSLS   51 (97)
Q Consensus        20 rkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~   51 (97)
                      .+.|+.  ||....+-.-.|...|..||.++.
T Consensus         3 ~~~C~~--C~~~~i~~~~~~~~~C~~Cg~~~~   32 (33)
T PF08792_consen    3 LKKCSK--CGGNGIVNKEDDYEVCIFCGSSFP   32 (33)
T ss_pred             ceEcCC--CCCCeEEEecCCeEEcccCCcEee
Confidence            367888  987666645577888999998864

>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70)

Probab=85.29  E-value=2.9  Score=29.57  Aligned_cols=66  Identities=20%  Similarity=0.236  Sum_probs=39.8

Q ss_pred             EEEECCCCeEEEecc------cCCCCcCCceEEeceeC-CccccCCceeEEEeecccccccccCCCCceEEEEEecceee
Q psy15072          7 VCNVDENGKIHRLRR------ECTSEQCGAGVFMAAMS-DRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTASF   79 (97)
Q Consensus         7 yYkVdenGKI~rlrk------eCP~~eCGaGVFMA~H~-DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l~~~~~~~~~   79 (97)
                      +|.|.  |+|.....      .||.  |..-|.  ... ++++|.||+.+.             +....+..+-+..+-.
T Consensus        17 ~~~v~--a~I~~I~~~~~~Y~aC~~--C~kkv~--~~~~~~~~C~~C~~~~-------------~~~~~ry~l~~~i~D~   77 (166)
T cd04476          17 YFTVK--ATIVFIKPDNWWYPACPG--CNKKVV--EEGNGTYRCEKCNKSV-------------PNPEYRYILSLNVADH   77 (166)
T ss_pred             EEEEE--EEEEEEcCCCeEEccccc--cCcccE--eCCCCcEECCCCCCcC-------------CCccEEEEEEEEEEeC
Confidence            44443  45555544      4997  987543  334 799999998653             3344555555544444


Q ss_pred             eeeeeeEEEecc
Q psy15072         80 LVSYPVLLFDSD   91 (97)
Q Consensus        80 ~~~~~~~~~~~~   91 (97)
                      --+..+.+||..
T Consensus        78 Tg~~~~~~F~~~   89 (166)
T cd04476          78 TGEAWLTLFDEV   89 (166)
T ss_pred             CCCEEEEEehHH
Confidence            455667777753

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=84.79  E-value=0.94  Score=25.34  Aligned_cols=29  Identities=14%  Similarity=0.298  Sum_probs=18.2

Q ss_pred             ccCCCCcCCceEEece-----eCCccccCCceeEEE
Q psy15072         21 RECTSEQCGAGVFMAA-----MSDRHYCGNKFSSLS   51 (97)
Q Consensus        21 keCP~~eCGaGVFMA~-----H~DR~yCGKCg~T~~   51 (97)
                      -+||+  ||+=..+..     ...+..|++||.++.
T Consensus         3 ~~CP~--C~~~~~v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         3 IQCPN--CKTSFRVVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             EECCC--CCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence            46888  987444432     122468999987653

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2

Probab=84.58  E-value=0.63  Score=26.77  Aligned_cols=31  Identities=19%  Similarity=0.352  Sum_probs=18.2

Q ss_pred             ccCCCCcCCceEEeceeCC-ccccCCceeEEEee
Q psy15072         21 RECTSEQCGAGVFMAAMSD-RHYCGNKFSSLSVE   53 (97)
Q Consensus        21 keCP~~eCGaGVFMA~H~D-R~yCGKCg~T~~~~   53 (97)
                      +-||.  ||.=-.-.+... +..|-+|+|.+-.+
T Consensus         2 ~FCp~--C~nlL~p~~~~~~~~~C~~C~Y~~~~~   33 (35)
T PF02150_consen    2 RFCPE--CGNLLYPKEDKEKRVACRTCGYEEPIS   33 (35)
T ss_dssp             -BETT--TTSBEEEEEETTTTEEESSSS-EEE-S
T ss_pred             eeCCC--CCccceEcCCCccCcCCCCCCCccCCC
Confidence            46887  998444444332 22599999987543

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=83.93  E-value=0.59  Score=32.94  Aligned_cols=32  Identities=31%  Similarity=0.537  Sum_probs=22.3

Q ss_pred             ecccCCCCcCCceEEeceeCCccccCCceeEEEee
Q psy15072         19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVE   53 (97)
Q Consensus        19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~   53 (97)
                      .+|.||+  ||+= |---.++--.|-|||.++...
T Consensus         8 tKR~Cp~--CG~k-FYDLnk~PivCP~CG~~~~~~   39 (108)
T PF09538_consen    8 TKRTCPS--CGAK-FYDLNKDPIVCPKCGTEFPPE   39 (108)
T ss_pred             CcccCCC--Ccch-hccCCCCCccCCCCCCccCcc
Confidence            4689998  9983 322223555799999887666

The function of members of this family is unknown.

>KOG0005|consensus

Probab=83.34  E-value=0.23  Score=33.47  Aligned_cols=19  Identities=16%  Similarity=0.279  Sum_probs=15.4

Q ss_pred             cccccccCCCCceEEEEEe
Q psy15072         56 SARSQVRFPPGANFLTFVL   74 (97)
Q Consensus        56 ~a~~q~~~p~~~~~l~~~~   74 (97)
                      ..++.++|||-+|+|+|+-
T Consensus        29 rvEEkeGIPp~qqrli~~g   47 (70)
T KOG0005|consen   29 RVEEKEGIPPQQQRLIYAG   47 (70)
T ss_pred             HhhhhcCCCchhhhhhhcc
Confidence            3455599999999999973

>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]

Probab=82.06  E-value=0.98  Score=31.73  Aligned_cols=33  Identities=15%  Similarity=0.323  Sum_probs=22.0

Q ss_pred             EEecccCCCCcCCceEEeceeCCccccCCceeEEE
Q psy15072         17 HRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLS   51 (97)
Q Consensus        17 ~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~   51 (97)
                      .+..-.||.  ||.=..=-.-..-|.|.|||+++-
T Consensus        32 ~~~~~~Cp~--C~~~~VkR~a~GIW~C~kCg~~fA   64 (89)
T COG1997          32 QRAKHVCPF--CGRTTVKRIATGIWKCRKCGAKFA   64 (89)
T ss_pred             HhcCCcCCC--CCCcceeeeccCeEEcCCCCCeec
Confidence            345567998  987422222235789999999863

>PRK05978 hypothetical protein; Provisional

Probab=81.02  E-value=0.75  Score=34.22  Aligned_cols=33  Identities=21%  Similarity=0.513  Sum_probs=24.6

Q ss_pred             ecccCCCCcCCceEEecee-CCccccCCceeEEEee
Q psy15072         19 LRRECTSEQCGAGVFMAAM-SDRHYCGNKFSSLSVE   53 (97)
Q Consensus        19 lrkeCP~~eCGaGVFMA~H-~DR~yCGKCg~T~~~~   53 (97)
                      ++..||+  ||.|=.+..- +-+..|-.||..+...
T Consensus        32 l~grCP~--CG~G~LF~g~Lkv~~~C~~CG~~~~~~   65 (148)
T PRK05978         32 FRGRCPA--CGEGKLFRAFLKPVDHCAACGEDFTHH   65 (148)
T ss_pred             HcCcCCC--CCCCcccccccccCCCccccCCccccC
Confidence            4667999  9998765543 3477999999877443

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=80.46  E-value=0.65  Score=25.49  Aligned_cols=24  Identities=25%  Similarity=0.578  Sum_probs=16.8

Q ss_pred             ccCCCCcCCceEEeceeCCccccCCceeEE
Q psy15072         21 RECTSEQCGAGVFMAAMSDRHYCGNKFSSL   50 (97)
Q Consensus        21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T~   50 (97)
                      |.||.  |++-|=.+    -..|-.||+.+
T Consensus         1 K~CP~--C~~~V~~~----~~~Cp~CG~~F   24 (26)
T PF10571_consen    1 KTCPE--CGAEVPES----AKFCPHCGYDF   24 (26)
T ss_pred             CcCCC--CcCCchhh----cCcCCCCCCCC
Confidence            57888  99866333    45688888754

Several members are annotated as putative helicases.

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=80.28  E-value=2  Score=25.96  Aligned_cols=14  Identities=14%  Similarity=0.026  Sum_probs=6.4

Q ss_pred             CCccccCCceeEEE
Q psy15072         38 SDRHYCGNKFSSLS   51 (97)
Q Consensus        38 ~DR~yCGKCg~T~~   51 (97)
                      .|-..|-.||+-..
T Consensus        17 ~~~irC~~CG~rIl   30 (44)
T smart00659       17 KDVVRCRECGYRIL   30 (44)
T ss_pred             CCceECCCCCceEE
Confidence            34444555554443

present in RNA polymerase I, II and III

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=80.15  E-value=1.5  Score=29.09  Aligned_cols=28  Identities=21%  Similarity=0.411  Sum_probs=23.8

Q ss_pred             cccCCCCcCCceEEeceeCCccc---cCCceeE
Q psy15072         20 RRECTSEQCGAGVFMAAMSDRHY---CGNKFSS   49 (97)
Q Consensus        20 rkeCP~~eCGaGVFMA~H~DR~y---CGKCg~T   49 (97)
                      -|-||-  ||--+....|.++++   |.+|+-.
T Consensus         6 lKPCPF--CG~~~~~v~~~~g~~~v~C~~CgA~   36 (64)
T PRK09710          6 VKPCPF--CGCPSVTVKAISGYYRAKCNGCESR   36 (64)
T ss_pred             ccCCCC--CCCceeEEEecCceEEEEcCCCCcC
Confidence            478999  999999999998776   9999864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	97
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		1e-07
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		1e-07
3zey_9	153	High-resolution Cryo-electron Microscopy Structure		5e-05
2xzm_9	189	Crystal Structure Of The Eukaryotic 40s Ribosomal S		2e-04

>pdb|3U5C|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 40s Subunit, Ribosome A Length = 152

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 26/37 (70%)
Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VD  GK+ +LRREC++  CGAGVF+A   DR YCG 
Sbjct: 107 KVDAEGKVTKLRRECSNPTCGAGVFLANHKDRLYCGK 143

>pdb|3U5G|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 40s Subunit, Ribosome B Length = 152

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 26/37 (70%)
Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
            VD  GK+ +LRREC++  CGAGVF+A   DR YCG 
Sbjct: 107 KVDAEGKVTKLRRECSNPTCGAGVFLANHKDRLYCGK 143

>pdb|3ZEY|9 Chain 9, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 153

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 22/37 (59%)
Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN 45
           N D + K+ R R EC +  CGAGVFMA    R YCG 
Sbjct: 109 NDDGSFKVERTRDECPNPNCGAGVFMAQHKGRKYCGK 145

>pdb|2XZM|9 Chain 9, 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 = 189

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 2/44 (4%)
Query: 10  VDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVE 53
           ++ NGK+   ++ C   +CG G+FMA   DRHYCG    +L ++
Sbjct: 103 LENNGKVSLQQKGC--PKCGPGIFMAKHYDRHYCGKCHLTLKID 144

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	97
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	7e-19
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	4e-12
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	2e-11

>3u5c_F RP14, S2, YS8, 40S ribosomal protein S5; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_F 3o30_D 3o2z_D 3u5g_F 3jyv_G* 2noq_F 1s1h_G 3iz6_F Length = 225

 Score = 74.8 bits (184), Expect = 7e-19
 Identities = 1/36 (2%), Positives = 6/36 (16%)

Query: 9   NVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
            +     I               + +   +  +   
Sbjct: 107 KLKAVRIIKHTLDIINVLTDQNPIQVVVDAITNTGP 142

>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8 Length = 55

 Score = 54.8 bits (132), Expect = 4e-12
 Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 2/33 (6%)

Query: 12 ENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
           +GK+ R  R C   +CG GVF+A  +DR+ CG
Sbjct: 10 ADGKLVRKHRFC--PRCGPGVFLAEHADRYSCG 40

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9 Length = 189

 Score = 56.3 bits (135), Expect = 2e-11
 Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 2/40 (5%)

Query: 5   WQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
                ++ NGK+   ++ C    CG G+FMA   DRHYCG
Sbjct: 98  LAFYKLENNGKVSLQQKGCPK--CGPGIFMAKHYDRHYCG 135

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	97
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	99.96
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	99.91
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.91
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	99.89
2zkr_2	97	60S ribosomal protein L37E; protein-RNA complex, 6	97.78
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	94.04
1l1o_C	181	Replication protein A 70 kDa DNA-binding subunit;	93.09
4gop_C	444	Putative uncharacterized protein; OB fold, ssDNA b	89.46
3u50_C	172	Telomerase-associated protein 82; TEB1, processivi	89.3
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	88.77
2jmo_A	80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	86.91
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	83.59
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	83.04
1vk6_A	269	NADH pyrophosphatase; 1790429, structural genomics	81.29
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	80.52

>3u5c_f 40S ribosomal protein S31; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_f

Probab=99.96  E-value=1.7e-30  Score=186.39  Aligned_cols=51  Identities=45%  Similarity=0.845  Sum_probs=49.4

Q ss_pred             ccceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeEEEee
Q psy15072          3 NEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVE   53 (97)
Q Consensus         3 ~~LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~   53 (97)
                      ++|+||+||+||||+|+|++||+++||+|||||+|+||+||||||+||+++
T Consensus       101 ~~~~~~~~~~~~~~~~~~~~c~~~~cg~g~fma~h~~r~~cgkc~~t~~~~  151 (152)
T 3u5c_f          101 XVLSYYKVDAEGKVTKLRRECSNPTCGAGVFLANHKDRLYCGKCHSVYKVN  151 (152)
T ss_dssp             CCCCCSEECSSSCEECCSCBCCSTTSCSSSBEEECSSCEEESSSSSCCEEC
T ss_pred             ceeeEEEEccCCeEEECcCcCCCccCCCceEecccCCCcccCCCceEEEec
Confidence            679999999999999999999999999999999999999999999999876

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=99.91  E-value=3.8e-25  Score=136.18  Aligned_cols=49  Identities=35%  Similarity=0.708  Sum_probs=47.2

Q ss_pred             CCccceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeEEEe
Q psy15072          1 MSNEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSV   52 (97)
Q Consensus         1 M~~~LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~   52 (97)
                      |+.+|+||+|| ||||+|++++||+  ||+|+|||+|.||++|||||+|++.
T Consensus         1 m~~~l~~y~v~-~~kv~~~~k~CP~--CG~~~fm~~~~~R~~C~kCG~t~~~   49 (50)
T 3j20_Y            1 MGQKWKLYEIK-DGKVIRKNKFCPR--CGPGVFMADHGDRWACGKCGYTEWK   49 (50)
T ss_dssp             CCCCCCCCEEC-SSCEECSSEECSS--SCSSCEEEECSSEEECSSSCCEEEC
T ss_pred             CCcceeEEEEE-CCEEEEecccCCC--CCCceEEecCCCeEECCCCCCEEEC
Confidence            88999999999 7999999999998  9999999999999999999999975

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9

Probab=99.91  E-value=1.3e-25  Score=168.10  Aligned_cols=56  Identities=30%  Similarity=0.708  Sum_probs=51.6

Q ss_pred             ccceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeEEEeeccccccc
Q psy15072          3 NEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQ   60 (97)
Q Consensus         3 ~~LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~q   60 (97)
                      ++|+||+||+||||+|+|++||+  ||+|||||+|+||+||||||+||++++...+++
T Consensus        96 ~~Lk~y~Vd~~Gkv~~~~~~Cp~--Cg~g~fma~h~dR~~CGkC~~t~~~~~~~~~~~  151 (189)
T 2xzm_9           96 GALAFYKLENNGKVSLQQKGCPK--CGPGIFMAKHYDRHYCGKCHLTLKIDXXXXXXX  151 (189)
T ss_dssp             SCCCCEEEETTTEEEECSEECST--TCSSCEEEECSSCEEETTTCCCBCCHHHHHHHH
T ss_pred             ceeeEEEECCCceEEEccccCCc--cCCCccccCccCCCccCCceeEEEeeccccccc
Confidence            57999999999999999999999  999999999999999999999999887655544

>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8

Probab=99.89  E-value=3.8e-25  Score=138.39  Aligned_cols=54  Identities=31%  Similarity=0.577  Sum_probs=50.3

Q ss_pred             ccceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeEEEeecccccc
Q psy15072          3 NEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARS   59 (97)
Q Consensus         3 ~~LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~   59 (97)
                      ++|+||+||+ |||+|++++||+  ||+|+|||+|+||++|||||||++.+++++++
T Consensus         2 ~~~~~y~v~~-gki~~~~~fCPk--CG~~~~ma~~~dr~~C~kCgyt~~~~~~~~~~   55 (55)
T 2k4x_A            2 QKRELYEIAD-GKLVRKHRFCPR--CGPGVFLAEHADRYSCGRCGYTEFKKAKKSKS   55 (55)
T ss_dssp             CCCCCCCCCC-CCCCCSSCCCTT--TTTTCCCEECSSEEECTTTCCCEECCCCCCCC
T ss_pred             ceEEEEEEcC-CEEEEccccCcC--CCCceeEeccCCEEECCCCCCEEEeCccccCC
Confidence            4899999997 999999999998  99999999999999999999999988777764

>2zkr_2 60S ribosomal protein L37E; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} SCOP: i.1.1.1

Probab=97.78  E-value=4.2e-06  Score=58.05  Aligned_cols=31  Identities=16%  Similarity=0.420  Sum_probs=26.5

Q ss_pred             EecccCCCCcCCceEEeceeCCccccCCceeEEEee
Q psy15072         18 RLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVE   53 (97)
Q Consensus        18 rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~   53 (97)
                      +.+..||+  ||.++|   |.++.+||+|||+....
T Consensus        14 KtH~lCrR--CG~~sf---H~qK~~CgkCGYpa~k~   44 (97)
T 2zkr_2           14 KTHTLCRR--CGSKAY---HLQKSTCGKCGYPAKRK   44 (97)
T ss_dssp             CCEECCTT--TCSSCE---ETTSCCBTTTCTTTSSC
T ss_pred             CCCCcCCC--CCCccC---cCccccCcccCCchHhc
Confidence            35668999  999998   99999999999986543

>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=94.04  E-value=0.017  Score=35.51  Aligned_cols=27  Identities=19%  Similarity=0.193  Sum_probs=22.3

Q ss_pred             ecccCCCCcCCceEEeceeCCccccCCceeEEE
Q psy15072         19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLS   51 (97)
Q Consensus        19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~   51 (97)
                      ....||+  ||+=    ++..-|.|.|||++..
T Consensus        13 ~k~iCpk--C~a~----~~~gaw~CrKCG~~~l   39 (51)
T 3j21_g           13 KKYVCLR--CGAT----NPWGAKKCRKCGYKRL   39 (51)
T ss_dssp             SEEECTT--TCCE----ECTTCSSCSSSSSCCC
T ss_pred             CCccCCC--CCCc----CCCCceecCCCCCccc
Confidence            4567999  9983    7889999999999944

>1l1o_C Replication protein A 70 kDa DNA-binding subunit; eukaryotic SSB, ssDNA binding protein, OB-fold; 2.80A {Homo sapiens} SCOP: b.40.4.3

Probab=93.09  E-value=0.38  Score=34.23  Aligned_cols=70  Identities=16%  Similarity=0.201  Sum_probs=44.8

Q ss_pred             ceEEEECCCCeEEEecc------cCCCCcCCceEEeceeCCccccCCceeEEEeecccccccccCCCCceEEEEEeccee
Q psy15072          5 WQVCNVDENGKIHRLRR------ECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTAS   78 (97)
Q Consensus         5 LkyYkVdenGKI~rlrk------eCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l~~~~~~~~   78 (97)
                      =.||.|-  +.|...+.      .||.+.|.-=|-- ...++|.|-||+.++             |....+.++-+..+-
T Consensus        24 ~~~f~v~--atI~~i~~d~~~Y~aC~~~~CnKKv~~-~~~g~~~CekC~~~~-------------~~~~~ry~l~~~i~D   87 (181)
T 1l1o_C           24 PDYFSSV--ATVVYLRKENCMYQACPTQDCNKKVID-QQNGLYRCEKCDTEF-------------PNFKYRMILSVNIAD   87 (181)
T ss_dssp             CEEEEEE--EEEEEECCSTTEEEBCCSTTCCCBCEE-ETTTEEEETTTTEEE-------------SSCCEEEEEEEEEEC
T ss_pred             CcEEEEE--EEEEEEeCCCEEECCCCchhcCCcccc-CCCCeEECCCCCCcC-------------CCceEEEEEEEEEEe
Confidence            3577775  67777765      5999899885541 245689999998653             455666666554443


Q ss_pred             eeeeeeeEEEec
Q psy15072         79 FLVSYPVLLFDS   90 (97)
Q Consensus        79 ~~~~~~~~~~~~   90 (97)
                      .--+--+.+||.
T Consensus        88 ~Tg~~~~t~F~~   99 (181)
T 1l1o_C           88 FQENQWVTCFQE   99 (181)
T ss_dssp             SSCEEEEEEEHH
T ss_pred             CCCCEEEEEEhH
Confidence            333445556654

>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=89.46  E-value=0.95  Score=35.61  Aligned_cols=41  Identities=22%  Similarity=0.391  Sum_probs=29.8

Q ss_pred             eEEEECCCCeEEEecc------cCCCCcCCceEEeceeCCccccCCceeE
Q psy15072          6 QVCNVDENGKIHRLRR------ECTSEQCGAGVFMAAMSDRHYCGNKFSS   49 (97)
Q Consensus         6 kyYkVdenGKI~rlrk------eCP~~eCGaGVFMA~H~DR~yCGKCg~T   49 (97)
                      .||.|-  +.|...+.      .||.+.|+--|-- ...++|.|.||+.+
T Consensus       290 ~~~~v~--atI~~i~~~~~~Y~aC~~~~C~kkv~~-~~~g~~~C~~C~~~  336 (444)
T 4gop_C          290 DYFNVR--ATVVYIKQENLYYTACASEGCNKKVNL-DHENNWRCEKCDRS  336 (444)
T ss_dssp             EEEEEE--EEEEEECCTTCEEEECCSTTCCCBEEE-CTTSCEEETTTTEE
T ss_pred             cEEEEE--EEEEEEcCCceEEccCCcccCCCcccc-CCCccEECCCCCCc
Confidence            567664  67777664      4998889986653 24568999999865

>1vq8_Z 50S ribosomal protein L37AE; 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: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=88.77  E-value=0.31  Score=32.01  Aligned_cols=30  Identities=13%  Similarity=0.262  Sum_probs=22.5

Q ss_pred             cccCCCCcCCceEEeceeCCccccCCceeEEE
Q psy15072         20 RRECTSEQCGAGVFMAAMSDRHYCGNKFSSLS   51 (97)
Q Consensus        20 rkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~   51 (97)
                      +-.||.  ||....-..=..-|.|.+||+++.
T Consensus        27 ~y~Cp~--CG~~~v~r~atGiW~C~~Cg~~~a   56 (83)
T 1vq8_Z           27 DHACPN--CGEDRVDRQGTGIWQCSYCDYKFT   56 (83)
T ss_dssp             CEECSS--SCCEEEEEEETTEEEETTTCCEEE
T ss_pred             cCcCCC--CCCcceeccCCCeEECCCCCCEec
Confidence            456999  998555444467899999999864

>2jmo_A Parkin; IBR, E3 ligase, zinc binding domain, RBR; NMR {Homo sapiens}

Probab=86.91  E-value=0.22  Score=31.56  Aligned_cols=34  Identities=21%  Similarity=0.332  Sum_probs=25.6

Q ss_pred             cccCCCCcCCceEEeceeCCccccC-----CceeEEEee
Q psy15072         20 RRECTSEQCGAGVFMAAMSDRHYCG-----NKFSSLSVE   53 (97)
Q Consensus        20 rkeCP~~eCGaGVFMA~H~DR~yCG-----KCg~T~~~~   53 (97)
                      .+-||++.|+.++....-..+..|.     +||+.+.+.
T Consensus        25 ~~~CP~p~C~~~v~~~~~~~~v~C~~~~~~~C~~~FC~~   63 (80)
T 2jmo_A           25 GVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRE   63 (80)
T ss_dssp             SCCCCSSSCCCCCCCCSCTTSBCTTSSSTTCCSCCEETT
T ss_pred             cEECCCCCCCcccEECCCCCcCCCCCCCCCCCCCeeccc
Confidence            6789999999877654433456897     899887765

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=83.59  E-value=0.67  Score=31.13  Aligned_cols=32  Identities=19%  Similarity=0.169  Sum_probs=22.5

Q ss_pred             ccCCCCcCCceEEecee----CCccccCCceeEEEeec
Q psy15072         21 RECTSEQCGAGVFMAAM----SDRHYCGNKFSSLSVEL   54 (97)
Q Consensus        21 keCP~~eCGaGVFMA~H----~DR~yCGKCg~T~~~~~   54 (97)
                      +-||.  ||.-...-.-    ..|+.|.+|+|.+..+.
T Consensus         5 ~FCp~--Cgn~L~~~~~~~~~~~~~~C~~C~y~~~~~~   40 (113)
T 3h0g_I            5 QYCIE--CNNMLYPREDKVDRVLRLACRNCDYSEIAAT   40 (113)
T ss_dssp             CCCSS--SCCCCEECCCTTTCCCCEECSSSCCEECCSC
T ss_pred             eeCcC--CCCEeeEcccCCCCeeEEECCCCCCeEEcCC
Confidence            57998  9985444332    23899999999876543

>3plu_A Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-1, SNU66, peptide binding protein; 1.40A {Saccharomyces cerevisiae} PDB: 3plv_A 1m94_A 1p0r_A

Probab=83.04  E-value=0.26  Score=33.02  Aligned_cols=17  Identities=18%  Similarity=0.071  Sum_probs=14.7

Q ss_pred             cccccccCCCCceEEEE
Q psy15072         56 SARSQVRFPPGANFLTF   72 (97)
Q Consensus        56 ~a~~q~~~p~~~~~l~~   72 (97)
                      .+.+++++||.+|+|+|
T Consensus        50 ~I~~k~Gip~~qQrLif   66 (93)
T 3plu_A           50 VLSLQIGTQPNKIVLQK   66 (93)
T ss_dssp             HHHHHHTCCGGGEEEEE
T ss_pred             HHHHHhCCCHHHEEEEe
Confidence            55566999999999999

>1vk6_A NADH pyrophosphatase; 1790429, structural genomics, JCSG, PS protein structure initiative, joint center for structural G hydrolase; HET: MSE; 2.20A {Escherichia coli} SCOP: d.113.1.4 d.113.1.4 g.41.14.1 PDB: 2gb5_A

Probab=81.29  E-value=0.98  Score=33.86  Aligned_cols=35  Identities=11%  Similarity=0.273  Sum_probs=27.7

Q ss_pred             ecccCCCCcCCceEEeceeCCccccCCceeEEEeecc
Q psy15072         19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELK   55 (97)
Q Consensus        19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~   55 (97)
                      ..+.||.  ||.-..+....-|.+|..||...+.+..
T Consensus       106 ~~~fC~~--CG~~~~~~~~~~~~~C~~C~~~~yp~~~  140 (269)
T 1vk6_A          106 SHKYCGY--CGHEMYPSKTEWAMLCSHCRERYYPQIA  140 (269)
T ss_dssp             TTSBCTT--TCCBEEECSSSSCEEESSSSCEECCCCE
T ss_pred             cCCcccc--CCCcCccCCCceeeeCCCCCCEecCCCC
Confidence            3578999  9998888776778899999987764433

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...

Probab=80.52  E-value=0.43  Score=32.47  Aligned_cols=31  Identities=13%  Similarity=0.132  Sum_probs=22.5

Q ss_pred             ccCCCCcCCceEEec----eeCCccccCCceeEEEee
Q psy15072         21 RECTSEQCGAGVFMA----AMSDRHYCGNKFSSLSVE   53 (97)
Q Consensus        21 keCP~~eCGaGVFMA----~H~DR~yCGKCg~T~~~~   53 (97)
                      +-||.  ||.=...-    .+..++.|.+|+|.+..+
T Consensus         5 ~FCp~--CgnlL~~~~~~~~~~~~~~C~~C~y~~~~~   39 (122)
T 1twf_I            5 RFCRD--CNNMLYPREDKENNRLLFECRTCSYVEEAG   39 (122)
T ss_dssp             CBCSS--SCCBCEEEEETTTTEEEEECSSSSCEEECS
T ss_pred             Ccccc--cCccCcccccCcCCCCEEECCcCCCeeecC
Confidence            67998  99844333    334689999999988654

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	97
d2k4xa1	55	g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermop	5e-12

>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]} Length = 55

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27a
domain: Ribosomal protein S27ae
species: Thermoplasma acidophilum [TaxId: 2303]

 Score = 53.6 bits (129), Expect = 5e-12
 Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 2/33 (6%)

Query: 12 ENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCG 44
           +GK+ R  R C   +CG GVF+A  +DR+ CG
Sbjct: 10 ADGKLVRKHRFC--PRCGPGVFLAEHADRYSCG 40

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	97
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	99.95
d1l1oc_	178	Replication protein A 70 KDa subunit (RPA70) {Huma	95.31
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	92.96
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	80.24

>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27a
domain: Ribosomal protein S27ae
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=99.95  E-value=7.4e-30  Score=161.27  Aligned_cols=54  Identities=31%  Similarity=0.574  Sum_probs=50.2

Q ss_pred             ccceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeEEEeecccccc
Q psy15072          3 NEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARS   59 (97)
Q Consensus         3 ~~LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~   59 (97)
                      ++++||+|| ||||+|++++||+  ||+|||||+|+||+||||||||++++.++++|
T Consensus         2 kk~~~Y~vd-~gkv~r~~k~CP~--CG~GvFmA~H~dR~~CGKCgyTefkk~~k~~s   55 (55)
T d2k4xa1           2 QKRELYEIA-DGKLVRKHRFCPR--CGPGVFLAEHADRYSCGRCGYTEFKKAKKSKS   55 (55)
T ss_dssp             CCCCCCCCC-CCCCCCSSCCCTT--TTTTCCCEECSSEEECTTTCCCEECCCCCCCC
T ss_pred             cceeEEEEc-CCEEEEecCcCcC--CCCcEEeeecCCCccccCCcccEEecccccCC
Confidence            468999998 6999999999998  99999999999999999999999998887764

>d1l1oc_ b.40.4.3 (C:) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 70 KDa subunit (RPA70)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.31  E-value=0.03  Score=38.63  Aligned_cols=72  Identities=15%  Similarity=0.224  Sum_probs=48.8

Q ss_pred             ccceEEEECCCCeEEEecc------cCCCCcCCceEEeceeCCccccCCceeEEEeecccccccccCCCCceEEEEEecc
Q psy15072          3 NEWQVCNVDENGKIHRLRR------ECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGT   76 (97)
Q Consensus         3 ~~LkyYkVdenGKI~rlrk------eCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l~~~~~~   76 (97)
                      .+-.||.|.  |.|..++.      .||.+.|.--|. ....+++.|-||+.++             |..+.+.++-+..
T Consensus        19 ~k~d~f~v~--a~I~~i~~~~~~Y~aCp~~~C~KKv~-~~~~g~~~C~kC~~~~-------------~~~~~ry~l~~~i   82 (178)
T d1l1oc_          19 DKPDYFSSV--ATVVYLRKENCMYQACPTQDCNKKVI-DQQNGLYRCEKCDTEF-------------PNFKYRMILSVNI   82 (178)
T ss_dssp             SSCEEEEEE--EEEEEECCSTTEEEBCCSTTCCCBCE-EETTTEEEETTTTEEE-------------SSCCEEEEEEEEE
T ss_pred             CCCCEEEEE--EEEEEEeCCCeEEcCCCCcccCCccc-cCCCCcEECCCCCCcC-------------CCceEEEEEEEEE
Confidence            345678776  67887775      499878987653 2344679999998764             3445666666655


Q ss_pred             eeeeeeeeeEEEec
Q psy15072         77 ASFLVSYPVLLFDS   90 (97)
Q Consensus        77 ~~~~~~~~~~~~~~   90 (97)
                      +-.--+..+.+||.
T Consensus        83 ~D~Tg~~~~~~F~~   96 (178)
T d1l1oc_          83 ADFQENQWVTCFQE   96 (178)
T ss_dssp             ECSSCEEEEEEEHH
T ss_pred             ecCCCCEEEEEehh
Confidence            55555667777775

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.96  E-value=0.023  Score=34.01  Aligned_cols=32  Identities=16%  Similarity=0.276  Sum_probs=27.7

Q ss_pred             cccCCCCcCCceEEeceeCCccccCCceeEEEee
Q psy15072         20 RRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVE   53 (97)
Q Consensus        20 rkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~   53 (97)
                      -+-||+  |+.+|.....-.+..|.+||..+.+.
T Consensus        18 ~k~CP~--C~~~~~~~~~~~~~~C~~C~~~fC~~   49 (73)
T d2ct7a1          18 FLWCAQ--CSFGFIYEREQLEATCPQCHQTFCVR   49 (73)
T ss_dssp             EECCSS--SCCCEECCCSCSCEECTTTCCEECSS
T ss_pred             CCCCCC--CCCEeEECCCCCEEEcCCCCCeECcc
Confidence            467998  99999988888899999999988765

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.24  E-value=0.35  Score=28.38  Aligned_cols=30  Identities=10%  Similarity=0.169  Sum_probs=21.8

Q ss_pred             ecccCCCCcCCceEEeceeCC-ccccCCceeEE
Q psy15072         19 LRRECTSEQCGAGVFMAAMSD-RHYCGNKFSSL   50 (97)
Q Consensus        19 lrkeCP~~eCGaGVFMA~H~D-R~yCGKCg~T~   50 (97)
                      .+-.||.  ||.--+.-++.+ -..|..||+..
T Consensus        10 ~~~~Cp~--Cgs~~ii~D~~~Ge~vC~~CG~Vl   40 (58)
T d1dl6a_          10 PRVTCPN--HPDAILVEDYRAGDMICPECGLVV   40 (58)
T ss_dssp             SCCSBTT--BSSSCCEECSSSCCEECTTTCCEE
T ss_pred             cccCCCC--CCCCCEEEECCCCcEecccCCCEe
Confidence            3567998  998766555543 46899999875