Query 035036
Match_columns 75
No_of_seqs 115 out of 1019
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 08:41:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035036.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035036hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1584 Sulfotransferase [Gene 99.9 6.4E-24 1.4E-28 151.4 5.5 73 1-73 31-108 (297)
2 PLN02164 sulfotransferase 99.9 2.3E-22 4.9E-27 145.8 4.6 55 2-56 72-130 (346)
3 PF00685 Sulfotransfer_1: Sulf 98.4 2.4E-07 5.3E-12 61.8 3.5 26 9-34 1-26 (267)
4 PF13469 Sulfotransfer_3: Sulf 96.8 0.0011 2.4E-08 41.8 2.7 19 11-29 2-21 (215)
5 PF09037 Sulphotransf: Stf0 su 88.6 0.48 1E-05 33.1 2.8 26 13-38 3-28 (245)
6 COG4424 Uncharacterized protei 84.5 1.1 2.3E-05 31.7 2.7 27 12-38 8-34 (250)
7 COG1158 Rho Transcription term 77.4 2.7 5.8E-05 31.8 2.9 22 13-34 177-199 (422)
8 KOG3988 Protein-tyrosine sulfo 75.7 2.3 5E-05 31.5 2.1 19 12-30 73-91 (378)
9 PF10589 NADH_4Fe-4S: NADH-ubi 55.9 9.6 0.00021 20.0 1.6 18 19-36 23-40 (46)
10 PF10922 DUF2745: Protein of u 51.4 11 0.00023 22.8 1.4 27 2-32 55-81 (85)
11 PF11880 DUF3400: Domain of un 51.3 16 0.00035 19.6 2.0 26 11-36 12-39 (45)
12 TIGR03715 KxYKxGKxW KxYKxGKxW 46.8 18 0.00038 17.1 1.6 13 19-31 8-20 (29)
13 PRK04290 30S ribosomal protein 46.6 9.3 0.0002 24.2 0.7 17 12-28 5-21 (115)
14 PF09538 FYDLN_acid: Protein o 43.2 9.2 0.0002 23.8 0.3 11 17-27 29-39 (108)
15 PF01092 Ribosomal_S6e: Riboso 42.7 3.3 7.3E-05 26.6 -1.8 17 13-29 3-19 (127)
16 PRK15078 polysaccharide export 41.5 46 0.001 24.7 3.8 30 2-33 331-360 (379)
17 PRK09907 toxin MazF; Provision 40.9 33 0.00072 21.0 2.6 22 2-23 2-24 (111)
18 smart00425 TBOX Domain first f 37.2 10 0.00023 25.7 -0.1 15 17-31 88-102 (190)
19 PRK15175 Vi polysaccharide exp 36.2 39 0.00086 25.0 2.7 25 2-27 316-340 (355)
20 cd00182 TBOX T-box DNA binding 35.9 11 0.00025 25.5 -0.1 14 17-30 89-102 (188)
21 PHA02325 hypothetical protein 34.8 9.7 0.00021 22.1 -0.5 10 17-26 6-15 (72)
22 cd04459 Rho_CSD Rho_CSD: Rho p 33.9 32 0.00069 19.7 1.5 13 4-16 21-33 (68)
23 cd04120 Rab12 Rab12 subfamily. 33.2 66 0.0014 21.4 3.2 13 59-71 185-197 (202)
24 TIGR02300 FYDLN_acid conserved 32.6 17 0.00037 23.6 0.3 11 17-27 29-39 (129)
25 PF12197 lci: Bacillus cereus 31.7 10 0.00022 20.3 -0.7 17 8-24 7-23 (45)
26 COG2125 RPS6A Ribosomal protei 31.4 15 0.00032 23.6 -0.1 20 10-29 3-22 (120)
27 PF08675 RNA_bind: RNA binding 31.2 66 0.0014 19.5 2.7 29 4-35 3-31 (87)
28 PF02452 PemK: PemK-like prote 30.2 34 0.00073 19.8 1.3 16 8-23 1-16 (110)
29 PF13481 AAA_25: AAA domain; P 30.0 93 0.002 19.7 3.5 25 11-35 34-59 (193)
30 COG4088 Predicted nucleotide k 29.3 70 0.0015 22.9 2.9 26 12-37 4-30 (261)
31 COG3257 GlxB Uncharacterized p 26.9 33 0.00071 24.5 1.0 30 9-38 44-75 (264)
32 PF01555 N6_N4_Mtase: DNA meth 26.5 79 0.0017 20.2 2.7 24 8-34 190-213 (231)
33 PRK06851 hypothetical protein; 26.5 92 0.002 23.3 3.3 25 12-36 33-58 (367)
34 KOG3586 TBX1 and related T-box 26.2 34 0.00075 26.2 1.0 15 17-31 169-183 (437)
35 COG0863 DNA modification methy 25.1 54 0.0012 22.3 1.8 19 7-25 220-238 (302)
36 PTZ00028 40S ribosomal protein 24.7 40 0.00087 23.7 1.0 16 13-28 3-18 (218)
37 PF07497 Rho_RNA_bind: Rho ter 24.6 57 0.0012 19.2 1.6 14 3-16 22-35 (78)
38 PF06950 DUF1293: Protein of u 24.1 50 0.0011 20.9 1.3 12 12-23 10-21 (115)
39 PF14511 RE_EcoO109I: Type II 23.7 65 0.0014 22.3 1.9 25 7-32 100-126 (200)
40 PF05708 DUF830: Orthopoxvirus 23.4 92 0.002 19.3 2.5 15 6-20 1-15 (158)
41 PRK09488 sdhD succinate dehydr 23.4 80 0.0017 19.7 2.2 19 14-32 5-24 (115)
42 PRK03803 murD UDP-N-acetylmura 22.0 55 0.0012 24.1 1.4 16 7-23 411-426 (448)
43 PHA02290 hypothetical protein 21.7 72 0.0016 22.1 1.8 17 7-23 73-91 (234)
44 PRK09812 toxin ChpB; Provision 21.6 1.1E+02 0.0023 18.8 2.5 22 2-23 2-24 (116)
45 cd00984 DnaB_C DnaB helicase C 21.6 1.5E+02 0.0032 19.6 3.3 29 7-35 10-40 (242)
46 PRK15321 putative type III sec 20.8 58 0.0013 20.5 1.1 14 22-38 101-114 (120)
47 PF06656 Tenui_PVC2: Tenuiviru 20.8 1.1E+02 0.0023 25.2 2.8 30 4-34 723-763 (785)
48 PF13671 AAA_33: AAA domain; P 20.6 1.4E+02 0.003 17.8 2.8 20 12-31 2-22 (143)
49 COG4004 Uncharacterized protei 20.6 68 0.0015 19.8 1.3 12 8-19 30-41 (96)
50 PF07136 DUF1385: Protein of u 20.5 63 0.0014 22.8 1.4 12 15-26 137-148 (236)
51 COG2209 NqrE Na+-transporting 20.3 83 0.0018 21.5 1.8 28 2-32 131-158 (198)
No 1
>KOG1584 consensus Sulfotransferase [General function prediction only]
Probab=99.89 E-value=6.4e-24 Score=151.36 Aligned_cols=73 Identities=37% Similarity=0.499 Sum_probs=57.3
Q ss_pred CCcCCccCCCCEEEEecCCCchhHHHHHHHHHhcCCCCCCccccCCccccccccccc-----CCCCCCCCCCCCCCCC
Q 035036 1 MQQHFQARPTDVYLTSKPKSGTTWLKALVFSTMNRSSAPLCLTISPHECVPFPEHLF-----RTTPIPEHLFKPSVPG 73 (75)
Q Consensus 1 ~~~~f~~r~dDV~i~syPKsGTtW~q~Iv~~i~~~~~~~~~~~~~~~~~~P~lE~~~-----~~~~~~~~~~~p~~~~ 73 (75)
+|++|++|||||+|||||||||||+|+|+++|+++++.+.+...++..+.|++|+.. ..-...+++.|||+|+
T Consensus 31 ~~~~Fq~r~dDiiiaTyPKsGTTWlkel~~~i~~~~d~~~~~~~pL~~~~P~~e~p~~e~~~~~~~~~~~l~SPRl~k 108 (297)
T KOG1584|consen 31 VQKHFQARPDDVIIATYPKSGTTWLQELTFLILNRGDFEKAKRHPLLERNPHLEVPFLELQLYGNDSAPDLPSPRLFK 108 (297)
T ss_pred HHhcCCCCCCCEEEEecCCCchHHHHHHHHHHHcCCCcccccCCchhhcCCceeecccccccccccccccCCCCccee
Confidence 367899999999999999999999999999999999987766667777888887642 2222335555666664
No 2
>PLN02164 sulfotransferase
Probab=99.86 E-value=2.3e-22 Score=145.79 Aligned_cols=55 Identities=53% Similarity=0.772 Sum_probs=46.5
Q ss_pred CcCCccCCCCEEEEecCCCchhHHHHHHHHHhcCCCCCCc----cccCCcccccccccc
Q 035036 2 QQHFQARPTDVYLTSKPKSGTTWLKALVFSTMNRSSAPLC----LTISPHECVPFPEHL 56 (75)
Q Consensus 2 ~~~f~~r~dDV~i~syPKsGTtW~q~Iv~~i~~~~~~~~~----~~~~~~~~~P~lE~~ 56 (75)
|++|++|+|||||||||||||||||+|+++|+++++.+.. ...++++++||+|..
T Consensus 72 ~~~f~~r~~DV~laSyPKsGTTWlq~iv~~i~~~~~~~~~~~pl~~~~p~~~vP~lE~~ 130 (346)
T PLN02164 72 QEFFQARPNDFLVCSYPKTGTTWLKALTFAIANRSRFDDSSNPLLKRNPHEFVPYIEID 130 (346)
T ss_pred HHcCCCCCCCEEEEcCCCchhHHHHHHHHHHHcCCCcccccCcccccCccccCCceecc
Confidence 5789999999999999999999999999999987664331 234568899999975
No 3
>PF00685 Sulfotransfer_1: Sulfotransferase domain; InterPro: IPR000863 This family includes a range of sulphotransferase proteins including flavonyl 3-sulphotransferase, aryl sulphotransferase, alcohol sulphotransferase, oestrogen sulphotransferase and phenol-sulphating phenol sulphotransferase. These enzymes are responsible for the transfer of sulphate groups to specific compounds.; GO: 0008146 sulfotransferase activity; PDB: 3MGC_A 3MGB_A 3MG9_A 1G3M_B 1HY3_B 2QP4_A 3F3Y_C 1EFH_A 1OV4_A 1J99_A ....
Probab=98.42 E-value=2.4e-07 Score=61.81 Aligned_cols=26 Identities=38% Similarity=0.864 Sum_probs=23.5
Q ss_pred CCCEEEEecCCCchhHHHHHHHHHhc
Q 035036 9 PTDVYLTSKPKSGTTWLKALVFSTMN 34 (75)
Q Consensus 9 ~dDV~i~syPKsGTtW~q~Iv~~i~~ 34 (75)
|.+|||+++|||||||+++++....+
T Consensus 1 ~~~i~I~g~prSGTt~l~~lL~~h~~ 26 (267)
T PF00685_consen 1 PPPIFIVGAPRSGTTWLRELLNSHPD 26 (267)
T ss_dssp TTSEEEEESTTSSHHHHHHHHHHHHT
T ss_pred CCCEEEECCCCCcHHHHHHHHHhCcc
Confidence 57999999999999999999998654
No 4
>PF13469 Sulfotransfer_3: Sulfotransferase family; PDB: 3AP1_B 3AP3_B 3AP2_B 3RNL_A 2Z6V_A 2ZQ5_A.
Probab=96.82 E-value=0.0011 Score=41.80 Aligned_cols=19 Identities=42% Similarity=0.742 Sum_probs=16.7
Q ss_pred CEEEEecCCCchhHHH-HHH
Q 035036 11 DVYLTSKPKSGTTWLK-ALV 29 (75)
Q Consensus 11 DV~i~syPKsGTtW~q-~Iv 29 (75)
=|||++.|||||||+. .+.
T Consensus 2 pvfI~G~~RSGTTlL~~~Ll 21 (215)
T PF13469_consen 2 PVFIVGMPRSGTTLLSRRLL 21 (215)
T ss_dssp CEEEECSTTSSHHHHH-HHH
T ss_pred eEEEECCCCCcHHHHHHHHH
Confidence 3899999999999999 665
No 5
>PF09037 Sulphotransf: Stf0 sulphotransferase; InterPro: IPR024628 Members of this family are essential for the biosynthesis of sulpholipid-1 in prokaryotes. They adopt a structure that belongs to the sulphotransferase superfamily, consisting of a single domain with a core four-stranded parallel beta-sheet flanked by alpha-helices []. ; PDB: 1TEX_B.
Probab=88.61 E-value=0.48 Score=33.07 Aligned_cols=26 Identities=27% Similarity=0.259 Sum_probs=18.2
Q ss_pred EEEecCCCchhHHHHHHHHHhcCCCC
Q 035036 13 YLTSKPKSGTTWLKALVFSTMNRSSA 38 (75)
Q Consensus 13 ~i~syPKsGTtW~q~Iv~~i~~~~~~ 38 (75)
+||+-|+||+||+-+.+..--.-|.+
T Consensus 3 ii~~t~RSGStlL~~~L~~tg~~G~p 28 (245)
T PF09037_consen 3 IICSTQRSGSTLLCELLRATGVAGRP 28 (245)
T ss_dssp EEEE-TTSSHHHHHHHHHHCTSS---
T ss_pred EEEeCCCCcHHHHHHHHHhCcCCCCc
Confidence 57888999999999998776554544
No 6
>COG4424 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.52 E-value=1.1 Score=31.69 Aligned_cols=27 Identities=26% Similarity=0.343 Sum_probs=21.8
Q ss_pred EEEEecCCCchhHHHHHHHHHhcCCCC
Q 035036 12 VYLTSKPKSGTTWLKALVFSTMNRSSA 38 (75)
Q Consensus 12 V~i~syPKsGTtW~q~Iv~~i~~~~~~ 38 (75)
-+|++-||||+||+-.++..--+.|++
T Consensus 8 Ylilt~pRSGStlLckllaatG~sG~p 34 (250)
T COG4424 8 YLILTTPRSGSTLLCKLLAATGCSGEP 34 (250)
T ss_pred eeEecCCCCcchHHHHHHHhcCCCCCc
Confidence 467888999999999988776666655
No 7
>COG1158 Rho Transcription termination factor [Transcription]
Probab=77.45 E-value=2.7 Score=31.79 Aligned_cols=22 Identities=27% Similarity=0.478 Sum_probs=18.1
Q ss_pred EEEecCCCc-hhHHHHHHHHHhc
Q 035036 13 YLTSKPKSG-TTWLKALVFSTMN 34 (75)
Q Consensus 13 ~i~syPKsG-TtW~q~Iv~~i~~ 34 (75)
.||+.||+| |+.+|+|.+.|-.
T Consensus 177 LIVAPPkaGKT~lLq~IA~aIt~ 199 (422)
T COG1158 177 LIVAPPKAGKTTLLQNIANAITT 199 (422)
T ss_pred eEecCCCCCchHHHHHHHHHHhc
Confidence 789999999 5578888888875
No 8
>KOG3988 consensus Protein-tyrosine sulfotransferase TPST1/TPST2 [Posttranslational modification, protein turnover, chaperones]
Probab=75.66 E-value=2.3 Score=31.51 Aligned_cols=19 Identities=32% Similarity=0.702 Sum_probs=16.9
Q ss_pred EEEEecCCCchhHHHHHHH
Q 035036 12 VYLTSKPKSGTTWLKALVF 30 (75)
Q Consensus 12 V~i~syPKsGTtW~q~Iv~ 30 (75)
|||-.-||||||.|.+|+.
T Consensus 73 IFiGGVPRSGTTLMRAmLD 91 (378)
T KOG3988|consen 73 IFIGGVPRSGTTLMRAMLD 91 (378)
T ss_pred EEEcCCCCCchHHHHHHHh
Confidence 7999999999999998864
No 9
>PF10589 NADH_4Fe-4S: NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; InterPro: IPR019575 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the F subunit of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoF. This family does not have any members in chloroplast or cyanobacteria, where the quinone may be plastoquinone and NADH may be replaced by NADPH, nor in Methanosarcina, where NADH is replaced by F420H2. This entry represents the iron-sulphur binding domain of the F subunit.; GO: 0055114 oxidation-reduction process; PDB: 3IAS_S 2FUG_A 3I9V_A 3M9S_1 3IAM_A 2YBB_1.
Probab=55.90 E-value=9.6 Score=20.00 Aligned_cols=18 Identities=17% Similarity=0.261 Sum_probs=14.7
Q ss_pred CCchhHHHHHHHHHhcCC
Q 035036 19 KSGTTWLKALVFSTMNRS 36 (75)
Q Consensus 19 KsGTtW~q~Iv~~i~~~~ 36 (75)
|=||.|+.+++..|.++.
T Consensus 23 R~Gt~~l~~~l~~i~~G~ 40 (46)
T PF10589_consen 23 REGTRQLAEILEKIVRGE 40 (46)
T ss_dssp HCCCCHHHHHHHHHTBT-
T ss_pred HhHHHHHHHHHHHHHcCC
Confidence 459999999999998753
No 10
>PF10922 DUF2745: Protein of unknown function (DUF2745); InterPro: IPR020147 The T7-like bacteriophage gene 1.2 protein is an inhibitor of the Escherichia coli dGTP triphosphohydrolase (dGTPase) and is implicated in DNA replication.
Probab=51.39 E-value=11 Score=22.84 Aligned_cols=27 Identities=22% Similarity=0.389 Sum_probs=21.1
Q ss_pred CcCCccCCCCEEEEecCCCchhHHHHHHHHH
Q 035036 2 QQHFQARPTDVYLTSKPKSGTTWLKALVFST 32 (75)
Q Consensus 2 ~~~f~~r~dDV~i~syPKsGTtW~q~Iv~~i 32 (75)
.+.|+-.++||+.. ++|.|+-.+-.++
T Consensus 55 ~~tf~h~DeDV~~n----~~T~WLnk~~~qL 81 (85)
T PF10922_consen 55 SKTFEHHDEDVLYN----MCTEWLNKMYDQL 81 (85)
T ss_pred eeeEEeeCCceeeh----HHHHHHHHHHHHh
Confidence 45788899999887 4799998876554
No 11
>PF11880 DUF3400: Domain of unknown function (DUF3400); InterPro: IPR021817 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 50 amino acids in length. This domain is found associated with PF02754 from PFAM, PF02913 from PFAM, PF01565 from PFAM.
Probab=51.32 E-value=16 Score=19.56 Aligned_cols=26 Identities=19% Similarity=0.336 Sum_probs=17.6
Q ss_pred CEEEEecCC--CchhHHHHHHHHHhcCC
Q 035036 11 DVYLTSKPK--SGTTWLKALVFSTMNRS 36 (75)
Q Consensus 11 DV~i~syPK--sGTtW~q~Iv~~i~~~~ 36 (75)
|-+++-..| =|-+|+++.+...-++|
T Consensus 12 DYIVVEmA~~lLGe~W~~~~v~~a~~GG 39 (45)
T PF11880_consen 12 DYIVVEMARHLLGENWQQDYVERANNGG 39 (45)
T ss_pred ceehHHHHHHHhhhhHHHHHHHHHHcCC
Confidence 333443444 48999999999887654
No 12
>TIGR03715 KxYKxGKxW KxYKxGKxW signal peptide. This model describes a novel form of signal peptide that occurs as an N-terminal domain with a recognizable motif, reminiscent of the YSIRK and PEP-CTERM forms of signal peptide. This domain tends to occur on long, low-complexity (usually Serine-rich and heavily glycosylated) proteins of the Firmicutes, and (as with YSIRK) the majority of these proteins have the LPXTG cell wall-anchoring motif at the C-terminus.
Probab=46.78 E-value=18 Score=17.12 Aligned_cols=13 Identities=38% Similarity=0.728 Sum_probs=10.2
Q ss_pred CCchhHHHHHHHH
Q 035036 19 KSGTTWLKALVFS 31 (75)
Q Consensus 19 KsGTtW~q~Iv~~ 31 (75)
|||-+|+..-+..
T Consensus 8 KsGK~Wv~a~~~~ 20 (29)
T TIGR03715 8 KSGKQWVFAAITT 20 (29)
T ss_pred ecccHHHHHHHHH
Confidence 8999999866443
No 13
>PRK04290 30S ribosomal protein S6e; Validated
Probab=46.63 E-value=9.3 Score=24.23 Aligned_cols=17 Identities=24% Similarity=0.481 Sum_probs=14.7
Q ss_pred EEEEecCCCchhHHHHH
Q 035036 12 VYLTSKPKSGTTWLKAL 28 (75)
Q Consensus 12 V~i~syPKsGTtW~q~I 28 (75)
-+++|+|++|+++.-+|
T Consensus 5 Kl~IsdP~tG~~~~~ei 21 (115)
T PRK04290 5 KVVVSDPKTGKAYQIEI 21 (115)
T ss_pred EEEEEcCCCCeEEEEEe
Confidence 47899999999998866
No 14
>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. The function of members of this family is unknown.
Probab=43.21 E-value=9.2 Score=23.80 Aligned_cols=11 Identities=36% Similarity=0.540 Sum_probs=9.1
Q ss_pred cCCCchhHHHH
Q 035036 17 KPKSGTTWLKA 27 (75)
Q Consensus 17 yPKsGTtW~q~ 27 (75)
-|||||.|--+
T Consensus 29 CP~CG~~~~~~ 39 (108)
T PF09538_consen 29 CPKCGTEFPPE 39 (108)
T ss_pred CCCCCCccCcc
Confidence 49999998766
No 15
>PF01092 Ribosomal_S6e: Ribosomal protein S6e; InterPro: IPR001377 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins have been grouped on the basis of sequence similarities. Ribosomal protein S6 is the major substrate of protein kinases in eukaryotic ribosomes [] and may play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZM_Y 2XZN_Y 3U5C_G 3U5G_G 3J16_C.
Probab=42.66 E-value=3.3 Score=26.62 Aligned_cols=17 Identities=24% Similarity=0.214 Sum_probs=13.2
Q ss_pred EEEecCCCchhHHHHHH
Q 035036 13 YLTSKPKSGTTWLKALV 29 (75)
Q Consensus 13 ~i~syPKsGTtW~q~Iv 29 (75)
+.+|||++|+++..+|=
T Consensus 3 l~isdP~tG~~~~iei~ 19 (127)
T PF01092_consen 3 LNISDPKTGKQKQIEID 19 (127)
T ss_dssp EEEEETTTTEEEEEE--
T ss_pred EEEEcCCCCEEEEEEeC
Confidence 57899999999887774
No 16
>PRK15078 polysaccharide export protein Wza; Provisional
Probab=41.49 E-value=46 Score=24.71 Aligned_cols=30 Identities=13% Similarity=0.359 Sum_probs=19.9
Q ss_pred CcCCccCCCCEEEEecCCCchhHHHHHHHHHh
Q 035036 2 QQHFQARPTDVYLTSKPKSGTTWLKALVFSTM 33 (75)
Q Consensus 2 ~~~f~~r~dDV~i~syPKsGTtW~q~Iv~~i~ 33 (75)
..+|+.+|+||+.++.-+ -+.|- .++.+++
T Consensus 331 a~~f~Lqp~DiVyV~~s~-~~~~~-~~i~~ll 360 (379)
T PRK15078 331 GTEFRLQPYDIVYVTTAP-VARWN-RVISQLV 360 (379)
T ss_pred ccCCccCCCCEEEECCCc-hHHHH-HHHHHHh
Confidence 357999999999997532 24454 4545444
No 17
>PRK09907 toxin MazF; Provisional
Probab=40.88 E-value=33 Score=21.01 Aligned_cols=22 Identities=14% Similarity=0.267 Sum_probs=17.9
Q ss_pred CcCCccCCCCEEEEec-CCCchh
Q 035036 2 QQHFQARPTDVYLTSK-PKSGTT 23 (75)
Q Consensus 2 ~~~f~~r~dDV~i~sy-PKsGTt 23 (75)
-.+|.++.+|||.+-+ |-.|.-
T Consensus 2 ~~~~~~~rGdI~~vdl~P~~G~E 24 (111)
T PRK09907 2 VSRYVPDMGDLIWVDFDPTKGSE 24 (111)
T ss_pred CcccCCCCCcEEEEECCCCCCcc
Confidence 4578899999999998 777764
No 18
>smart00425 TBOX Domain first found in the mice T locus (Brachyury) protein.
Probab=37.21 E-value=10 Score=25.66 Aligned_cols=15 Identities=33% Similarity=0.694 Sum_probs=12.3
Q ss_pred cCCCchhHHHHHHHH
Q 035036 17 KPKSGTTWLKALVFS 31 (75)
Q Consensus 17 yPKsGTtW~q~Iv~~ 31 (75)
-|++|..||.+.|..
T Consensus 88 sp~tG~~wM~~~v~F 102 (190)
T smart00425 88 SPATGAHWMKQPVSF 102 (190)
T ss_pred CccCHHHHhhCcccc
Confidence 478999999988743
No 19
>PRK15175 Vi polysaccharide export protein VexA; Provisional
Probab=36.15 E-value=39 Score=25.04 Aligned_cols=25 Identities=28% Similarity=0.211 Sum_probs=18.6
Q ss_pred CcCCccCCCCEEEEecCCCchhHHHH
Q 035036 2 QQHFQARPTDVYLTSKPKSGTTWLKA 27 (75)
Q Consensus 2 ~~~f~~r~dDV~i~syPKsGTtW~q~ 27 (75)
.++|++||+||+-++ ...-|-|-.-
T Consensus 316 A~~F~l~~~DvVyV~-~a~~~~~~k~ 340 (355)
T PRK15175 316 AQAIRVDNGDVIYIS-NASLTDFAKV 340 (355)
T ss_pred hhCCcCCCCCEEEEc-CCchHHHHHH
Confidence 478999999999998 4444666553
No 20
>cd00182 TBOX T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors.
Probab=35.90 E-value=11 Score=25.52 Aligned_cols=14 Identities=36% Similarity=0.809 Sum_probs=12.0
Q ss_pred cCCCchhHHHHHHH
Q 035036 17 KPKSGTTWLKALVF 30 (75)
Q Consensus 17 yPKsGTtW~q~Iv~ 30 (75)
-|++|..||.+.|.
T Consensus 89 sp~tG~~wM~~~is 102 (188)
T cd00182 89 SPATGAHWMKQPVS 102 (188)
T ss_pred CCcCHHHHhhCccc
Confidence 48999999998874
No 21
>PHA02325 hypothetical protein
Probab=34.82 E-value=9.7 Score=22.08 Aligned_cols=10 Identities=50% Similarity=1.125 Sum_probs=8.7
Q ss_pred cCCCchhHHH
Q 035036 17 KPKSGTTWLK 26 (75)
Q Consensus 17 yPKsGTtW~q 26 (75)
-||||..|+.
T Consensus 6 CPkC~A~Wld 15 (72)
T PHA02325 6 CPKCGARWLD 15 (72)
T ss_pred cCccCCEeEc
Confidence 5999999986
No 22
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=33.86 E-value=32 Score=19.67 Aligned_cols=13 Identities=23% Similarity=0.792 Sum_probs=10.9
Q ss_pred CCccCCCCEEEEe
Q 035036 4 HFQARPTDVYLTS 16 (75)
Q Consensus 4 ~f~~r~dDV~i~s 16 (75)
+|.+.++||+|..
T Consensus 21 ~y~~~~~DvyVs~ 33 (68)
T cd04459 21 NYLPGPDDIYVSP 33 (68)
T ss_pred CCCCCCCCEEECH
Confidence 7789999999863
No 23
>cd04120 Rab12 Rab12 subfamily. Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic
Probab=33.19 E-value=66 Score=21.37 Aligned_cols=13 Identities=31% Similarity=0.416 Sum_probs=10.4
Q ss_pred CCCCCCCCCCCCC
Q 035036 59 TTPIPEHLFKPSV 71 (75)
Q Consensus 59 ~~~~~~~~~~p~~ 71 (75)
...||+++++||-
T Consensus 185 ~~~~~~~~~~~~~ 197 (202)
T cd04120 185 EPEIPPELPPPRP 197 (202)
T ss_pred CCCCCcCCCCCCC
Confidence 4578999999983
No 24
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. 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. The function of members of this family is unknown.
Probab=32.58 E-value=17 Score=23.56 Aligned_cols=11 Identities=18% Similarity=0.434 Sum_probs=9.0
Q ss_pred cCCCchhHHHH
Q 035036 17 KPKSGTTWLKA 27 (75)
Q Consensus 17 yPKsGTtW~q~ 27 (75)
-||||+.|--.
T Consensus 29 cP~cg~~~~~~ 39 (129)
T TIGR02300 29 SPYTGEQFPPE 39 (129)
T ss_pred CCCcCCccCcc
Confidence 49999998665
No 25
>PF12197 lci: Bacillus cereus group antimicrobial protein; InterPro: IPR020976 This entry represents antimicrobial peptides from bacteria of approximately 40 amino acids in length.; PDB: 2B9K_A.
Probab=31.66 E-value=10 Score=20.33 Aligned_cols=17 Identities=29% Similarity=0.620 Sum_probs=9.9
Q ss_pred CCCCEEEEecCCCchhH
Q 035036 8 RPTDVYLTSKPKSGTTW 24 (75)
Q Consensus 8 r~dDV~i~syPKsGTtW 24 (75)
.+++||-.+|-..|++|
T Consensus 7 ~~nGvFAN~F~~~GitW 23 (45)
T PF12197_consen 7 SSNGVFANSFSDDGITW 23 (45)
T ss_dssp ETT-----EEEETTEEE
T ss_pred cCCCceEEEEEcCCcEE
Confidence 46788888888889888
No 26
>COG2125 RPS6A Ribosomal protein S6E (S10) [Translation, ribosomal structure and biogenesis]
Probab=31.45 E-value=15 Score=23.56 Aligned_cols=20 Identities=25% Similarity=0.293 Sum_probs=15.9
Q ss_pred CCEEEEecCCCchhHHHHHH
Q 035036 10 TDVYLTSKPKSGTTWLKALV 29 (75)
Q Consensus 10 dDV~i~syPKsGTtW~q~Iv 29 (75)
+-.+++|+||+|.+...+|-
T Consensus 3 ~~kvvisdp~~G~~~~~ei~ 22 (120)
T COG2125 3 TFKVVISDPKTGRAYQFEID 22 (120)
T ss_pred ccEEEEeccCcceeeeeeec
Confidence 45688999999999777654
No 27
>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN). ; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.
Probab=31.19 E-value=66 Score=19.49 Aligned_cols=29 Identities=17% Similarity=0.362 Sum_probs=17.1
Q ss_pred CCccCCCCEEEEecCCCchhHHHHHHHHHhcC
Q 035036 4 HFQARPTDVYLTSKPKSGTTWLKALVFSTMNR 35 (75)
Q Consensus 4 ~f~~r~dDV~i~syPKsGTtW~q~Iv~~i~~~ 35 (75)
+-++..|.||-+||||. |=+.=+.+++..
T Consensus 3 d~~P~RdHVFhltFPke---WK~~DI~qlFsp 31 (87)
T PF08675_consen 3 DPQPSRDHVFHLTFPKE---WKTSDIYQLFSP 31 (87)
T ss_dssp ----SGCCEEEEE--TT-----HHHHHHHCCC
T ss_pred CCCCCcceEEEEeCchH---hhhhhHHHHhcc
Confidence 34677899999999998 888777777654
No 28
>PF02452 PemK: PemK-like protein; InterPro: IPR003477 PemK is a growth inhibitor in Escherichia coli known to bind to the promoter region of the Pem operon, auto-regulating synthesis. It is responsible for mediating cell death through inhibiting protein synthesis through the cleavage of single-stranded RNA. PemK is part of the PemK-PemI system, where PemI is an antitoxin that inhibits the action of the PemK toxin []. PemK homologues have been found in a wide range of bacteria, which together form an endonuclease family that interfere with mRNA function. This family consists of the PemK protein in addition to ChpA, ChpB, Kid and MazF.; GO: 0003677 DNA binding; PDB: 1M1F_A 2C06_A 3NFC_F 1UB4_B 1NE8_A.
Probab=30.22 E-value=34 Score=19.82 Aligned_cols=16 Identities=19% Similarity=0.360 Sum_probs=10.2
Q ss_pred CCCCEEEEecCCCchh
Q 035036 8 RPTDVYLTSKPKSGTT 23 (75)
Q Consensus 8 r~dDV~i~syPKsGTt 23 (75)
+.+||+.+-||-.|+.
T Consensus 1 k~GdI~~v~~p~~~~e 16 (110)
T PF02452_consen 1 KRGDIVWVDFPDFGSE 16 (110)
T ss_dssp STTEEEEEE-S--TTS
T ss_pred CCceEEEEECCCCCcc
Confidence 5789999999855654
No 29
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=29.96 E-value=93 Score=19.69 Aligned_cols=25 Identities=20% Similarity=0.179 Sum_probs=18.2
Q ss_pred CEEEEecCCCchh-HHHHHHHHHhcC
Q 035036 11 DVYLTSKPKSGTT-WLKALVFSTMNR 35 (75)
Q Consensus 11 DV~i~syPKsGTt-W~q~Iv~~i~~~ 35 (75)
=++++.-|++|-| ++.+++..+..+
T Consensus 34 l~~i~g~~g~GKT~~~~~l~~~~~~g 59 (193)
T PF13481_consen 34 LTLIAGPPGSGKTTLALQLAAALATG 59 (193)
T ss_dssp EEEEEECSTSSHHHHHHHHHHHHHT-
T ss_pred EEEEEeCCCCCHHHHHHHHHHHHHhC
Confidence 3688889999955 566888777753
No 30
>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=29.34 E-value=70 Score=22.93 Aligned_cols=26 Identities=35% Similarity=0.349 Sum_probs=19.5
Q ss_pred EEEEecCCCc-hhHHHHHHHHHhcCCC
Q 035036 12 VYLTSKPKSG-TTWLKALVFSTMNRSS 37 (75)
Q Consensus 12 V~i~syPKsG-TtW~q~Iv~~i~~~~~ 37 (75)
|+++.||=|| ||...+++..+..++.
T Consensus 4 iIlTGyPgsGKTtfakeLak~L~~~i~ 30 (261)
T COG4088 4 IILTGYPGSGKTTFAKELAKELRQEIW 30 (261)
T ss_pred EEEecCCCCCchHHHHHHHHHHHHhhh
Confidence 6788999999 5577788777766544
No 31
>COG3257 GlxB Uncharacterized protein, possibly involved in glyoxylate utilization [General function prediction only]
Probab=26.93 E-value=33 Score=24.53 Aligned_cols=30 Identities=30% Similarity=0.409 Sum_probs=24.4
Q ss_pred CCCEEEEecCCCc--hhHHHHHHHHHhcCCCC
Q 035036 9 PTDVYLTSKPKSG--TTWLKALVFSTMNRSSA 38 (75)
Q Consensus 9 ~dDV~i~syPKsG--TtW~q~Iv~~i~~~~~~ 38 (75)
..+++|.+-|++| -|..|.|+..--++|+.
T Consensus 44 ~tr~wilsrP~~Gf~~tF~qyive~~p~GGs~ 75 (264)
T COG3257 44 NTRAWILSRPLSGFAATFVQYIVELHPNGGSQ 75 (264)
T ss_pred CceEEEEeccccchhhhhhhheEEECCCCCCC
Confidence 5688999999999 99999998876665443
No 32
>PF01555 N6_N4_Mtase: DNA methylase; InterPro: IPR002941 This domain is found in DNA methylases. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. This family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases. N-4 cytosine-specific DNA methylases (2.1.1.113 from EC) [] are enzymes that specifically methylate the amino group at the C-4 position of cytosines in DNA. Such enzymes are found as components of type II restriction-modification systems in prokaryotes. Such enzymes recognise a specific sequence in DNA and methylate a cytosine in that sequence. By this action they protect DNA from cleavage by type II restriction enzymes that recognise the same sequence. N-6 adenine-specific DNA methylases (2.1.1.72 from EC) (A-Mtase) are enzymes that specifically methylate the amino group at the C-6 position of adenines in DNA. Such enzymes are found in the three existing types of bacterial restriction-modification systems (in type I system the A-Mtase is the product of the hsdM gene, and in type III it is the product of the mod gene). All of these enzymes recognise a specific sequence in DNA and methylate an adenine in that sequence.; GO: 0003677 DNA binding, 0008170 N-methyltransferase activity, 0006306 DNA methylation; PDB: 2ZIF_A 2ZIE_A 2ZIG_A 1NW6_A 1NW8_A 1NW7_A 1NW5_A 1EG2_A 1BOO_A 1G60_B ....
Probab=26.54 E-value=79 Score=20.18 Aligned_cols=24 Identities=33% Similarity=0.458 Sum_probs=15.8
Q ss_pred CCCCEEEEecCCCchhHHHHHHHHHhc
Q 035036 8 RPTDVYLTSKPKSGTTWLKALVFSTMN 34 (75)
Q Consensus 8 r~dDV~i~syPKsGTtW~q~Iv~~i~~ 34 (75)
.++|+++-.|-=|||| .++...++
T Consensus 190 ~~gdiVlDpF~GSGTT---~~aa~~l~ 213 (231)
T PF01555_consen 190 NPGDIVLDPFAGSGTT---AVAAEELG 213 (231)
T ss_dssp -TT-EEEETT-TTTHH---HHHHHHTT
T ss_pred ccceeeehhhhccChH---HHHHHHcC
Confidence 6899999999999999 44444443
No 33
>PRK06851 hypothetical protein; Provisional
Probab=26.45 E-value=92 Score=23.26 Aligned_cols=25 Identities=20% Similarity=0.357 Sum_probs=20.6
Q ss_pred EEEEecCCCc-hhHHHHHHHHHhcCC
Q 035036 12 VYLTSKPKSG-TTWLKALVFSTMNRS 36 (75)
Q Consensus 12 V~i~syPKsG-TtW~q~Iv~~i~~~~ 36 (75)
++|...|-+| ||++++|...+...|
T Consensus 33 ~il~G~pGtGKStl~~~i~~~~~~~g 58 (367)
T PRK06851 33 FILKGGPGTGKSTLMKKIGEEFLEKG 58 (367)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHHcC
Confidence 5677789999 999999998887654
No 34
>KOG3586 consensus TBX1 and related T-box transcription factors [Transcription]
Probab=26.18 E-value=34 Score=26.20 Aligned_cols=15 Identities=40% Similarity=0.813 Sum_probs=12.6
Q ss_pred cCCCchhHHHHHHHH
Q 035036 17 KPKSGTTWLKALVFS 31 (75)
Q Consensus 17 yPKsGTtW~q~Iv~~ 31 (75)
-|-+|.+||.|||..
T Consensus 169 SP~sGe~wmkqiVSF 183 (437)
T KOG3586|consen 169 SPASGEQWMKQIVSF 183 (437)
T ss_pred CCCCHHHHHHhhhch
Confidence 377999999999854
No 35
>COG0863 DNA modification methylase [DNA replication, recombination, and repair]
Probab=25.14 E-value=54 Score=22.34 Aligned_cols=19 Identities=37% Similarity=0.422 Sum_probs=16.1
Q ss_pred cCCCCEEEEecCCCchhHH
Q 035036 7 ARPTDVYLTSKPKSGTTWL 25 (75)
Q Consensus 7 ~r~dDV~i~syPKsGTtW~ 25 (75)
..++|+++-.|..||||=+
T Consensus 220 s~~~diVlDpf~GsGtt~~ 238 (302)
T COG0863 220 SFPGDIVLDPFAGSGTTGI 238 (302)
T ss_pred CCCCCEEeecCCCCChHHH
Confidence 3589999999999999933
No 36
>PTZ00028 40S ribosomal protein S6e; Provisional
Probab=24.67 E-value=40 Score=23.67 Aligned_cols=16 Identities=13% Similarity=0.108 Sum_probs=13.1
Q ss_pred EEEecCCCchhHHHHH
Q 035036 13 YLTSKPKSGTTWLKAL 28 (75)
Q Consensus 13 ~i~syPKsGTtW~q~I 28 (75)
+.+|||++|++-.-+|
T Consensus 3 lnIsdP~tG~qk~iEi 18 (218)
T PTZ00028 3 LNIANPFTGLQKCIEI 18 (218)
T ss_pred EEEecCCCCeeEEEEe
Confidence 5789999999976655
No 37
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=24.62 E-value=57 Score=19.17 Aligned_cols=14 Identities=29% Similarity=0.778 Sum_probs=9.1
Q ss_pred cCCccCCCCEEEEe
Q 035036 3 QHFQARPTDVYLTS 16 (75)
Q Consensus 3 ~~f~~r~dDV~i~s 16 (75)
.+|.+.++||+|..
T Consensus 22 ~~y~~~~~DvYVs~ 35 (78)
T PF07497_consen 22 NNYLPSPDDVYVSP 35 (78)
T ss_dssp GTTS-STTSEEE-C
T ss_pred cCCCCCCCCEEECH
Confidence 37788888888864
No 38
>PF06950 DUF1293: Protein of unknown function (DUF1293); InterPro: IPR009712 This entry is represented by Vibrio phage Vf33, Vpf117. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial and phage proteins of around 115 residues in length. The function of this family is unknown.
Probab=24.10 E-value=50 Score=20.92 Aligned_cols=12 Identities=33% Similarity=0.490 Sum_probs=10.1
Q ss_pred EEEEecCCCchh
Q 035036 12 VYLTSKPKSGTT 23 (75)
Q Consensus 12 V~i~syPKsGTt 23 (75)
|-|..|||||++
T Consensus 10 I~i~~fp~sg~~ 21 (115)
T PF06950_consen 10 IDIKWFPKSGES 21 (115)
T ss_pred EEEEEcCCCCce
Confidence 457889999988
No 39
>PF14511 RE_EcoO109I: Type II restriction endonuclease EcoO109I; PDB: 1WTD_A 1WTE_A.
Probab=23.68 E-value=65 Score=22.27 Aligned_cols=25 Identities=20% Similarity=0.233 Sum_probs=15.7
Q ss_pred cCCCCEEEEecCCCchhHHH--HHHHHH
Q 035036 7 ARPTDVYLTSKPKSGTTWLK--ALVFST 32 (75)
Q Consensus 7 ~r~dDV~i~syPKsGTtW~q--~Iv~~i 32 (75)
.+|+...+|+ =|||++|+. ++..+.
T Consensus 100 ~~Dg~~~~~~-iKSGpNt~N~~qi~~~~ 126 (200)
T PF14511_consen 100 ERDGRRYICQ-IKSGPNTINSDQIKKMK 126 (200)
T ss_dssp -TTS-EEEEE-EESSTTS--HHHHHHHH
T ss_pred EECCeEEEEE-EecCCCcCCHHHHHHHH
Confidence 4678888888 699999987 444433
No 40
>PF05708 DUF830: Orthopoxvirus protein of unknown function (DUF830); PDB: 2IF6_B 3KW0_C.
Probab=23.45 E-value=92 Score=19.34 Aligned_cols=15 Identities=27% Similarity=0.330 Sum_probs=8.0
Q ss_pred ccCCCCEEEEecCCC
Q 035036 6 QARPTDVYLTSKPKS 20 (75)
Q Consensus 6 ~~r~dDV~i~syPKs 20 (75)
+.+++||++....-.
T Consensus 1 ~l~~GDIil~~~~~~ 15 (158)
T PF05708_consen 1 KLQTGDIILTRGKSS 15 (158)
T ss_dssp ---TT-EEEEEE-SC
T ss_pred CCCCeeEEEEECCch
Confidence 468999999986533
No 41
>PRK09488 sdhD succinate dehydrogenase cytochrome b556 small membrane subunit; Provisional
Probab=23.39 E-value=80 Score=19.68 Aligned_cols=19 Identities=5% Similarity=0.151 Sum_probs=12.9
Q ss_pred EEecCCCch-hHHHHHHHHH
Q 035036 14 LTSKPKSGT-TWLKALVFST 32 (75)
Q Consensus 14 i~syPKsGT-tW~q~Iv~~i 32 (75)
.+|.-|+|| +|..|-+..+
T Consensus 5 ~~~~~~~G~~~w~~QRvTAv 24 (115)
T PRK09488 5 ASALGRNGVHDFILVRATAI 24 (115)
T ss_pred ccccCcCcHHHHHHHHHHHH
Confidence 457789999 6776655444
No 42
>PRK03803 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=22.03 E-value=55 Score=24.14 Aligned_cols=16 Identities=31% Similarity=0.474 Sum_probs=12.9
Q ss_pred cCCCCEEEEecCCCchh
Q 035036 7 ARPTDVYLTSKPKSGTT 23 (75)
Q Consensus 7 ~r~dDV~i~syPKsGTt 23 (75)
++++|+++.| |.||+-
T Consensus 411 a~~gdvVL~S-Pa~aSf 426 (448)
T PRK03803 411 AQAGDIVLLS-PACASL 426 (448)
T ss_pred CCCCCEEEeC-chhhcc
Confidence 4789998887 999873
No 43
>PHA02290 hypothetical protein
Probab=21.68 E-value=72 Score=22.11 Aligned_cols=17 Identities=29% Similarity=0.626 Sum_probs=13.7
Q ss_pred cCCCCEEEEecCC--Cchh
Q 035036 7 ARPTDVYLTSKPK--SGTT 23 (75)
Q Consensus 7 ~r~dDV~i~syPK--sGTt 23 (75)
..++|.||||-|| -||+
T Consensus 73 ~~~N~L~I~TiP~~~~~T~ 91 (234)
T PHA02290 73 YEPNKLYICTIPKGYQSTE 91 (234)
T ss_pred cCCCceEEEECCCCCccce
Confidence 4578999999999 4665
No 44
>PRK09812 toxin ChpB; Provisional
Probab=21.65 E-value=1.1e+02 Score=18.84 Aligned_cols=22 Identities=23% Similarity=0.286 Sum_probs=16.9
Q ss_pred CcCCccCCCCEEEEec-CCCchh
Q 035036 2 QQHFQARPTDVYLTSK-PKSGTT 23 (75)
Q Consensus 2 ~~~f~~r~dDV~i~sy-PKsGTt 23 (75)
-+.+.++.+|||.+-+ |-.|+-
T Consensus 2 ~~~~~~~rGdI~~v~l~P~~G~E 24 (116)
T PRK09812 2 VKRSKFERGDIVLVGFDPASGHE 24 (116)
T ss_pred CccccCCCCcEEEEECCCCCccc
Confidence 3567789999999998 656664
No 45
>cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=21.60 E-value=1.5e+02 Score=19.60 Aligned_cols=29 Identities=17% Similarity=0.385 Sum_probs=19.6
Q ss_pred cCCCCE-EEEecCCCchhHH-HHHHHHHhcC
Q 035036 7 ARPTDV-YLTSKPKSGTTWL-KALVFSTMNR 35 (75)
Q Consensus 7 ~r~dDV-~i~syPKsGTtW~-q~Iv~~i~~~ 35 (75)
.+++++ .|+..|.+|-|++ .+++.....+
T Consensus 10 l~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~ 40 (242)
T cd00984 10 LQPGDLIIIAARPSMGKTAFALNIAENIAKK 40 (242)
T ss_pred CCCCeEEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence 355655 6688999997765 5777666544
No 46
>PRK15321 putative type III secretion system effector protein OrgC; Provisional
Probab=20.78 E-value=58 Score=20.46 Aligned_cols=14 Identities=14% Similarity=0.748 Sum_probs=9.8
Q ss_pred hhHHHHHHHHHhcCCCC
Q 035036 22 TTWLKALVFSTMNRSSA 38 (75)
Q Consensus 22 TtW~q~Iv~~i~~~~~~ 38 (75)
|.|||+++ +++|..
T Consensus 101 ~sWMQe~i---LS~G~~ 114 (120)
T PRK15321 101 TSWMQEII---LSGGEN 114 (120)
T ss_pred HHHHHHHH---hcCCCc
Confidence 57999984 455654
No 47
>PF06656 Tenui_PVC2: Tenuivirus PVC2 protein; InterPro: IPR009547 This family consists of several Tenuivirus PVC2 proteins from Rice grassy stunt virus, Maize stripe virus and Rice hoja blanca virus. The function of this family is unknown.
Probab=20.77 E-value=1.1e+02 Score=25.17 Aligned_cols=30 Identities=27% Similarity=0.573 Sum_probs=23.2
Q ss_pred CCccCCCCEEEEecCC-----------CchhHHHHHHHHHhc
Q 035036 4 HFQARPTDVYLTSKPK-----------SGTTWLKALVFSTMN 34 (75)
Q Consensus 4 ~f~~r~dDV~i~syPK-----------sGTtW~q~Iv~~i~~ 34 (75)
.+.++|=||.++| || |+++|+.-|+..|..
T Consensus 723 kydvsp~~I~Vvs-p~~d~~s~~~vk~s~qnw~~fl~~~ird 763 (785)
T PF06656_consen 723 KYDVSPIEITVVS-PKLDLSSFEAVKESTQNWMKFLMEIIRD 763 (785)
T ss_pred eeccCceEEEEec-CCccccccceeeecCCcHHHHHHHHHhc
Confidence 4667888888776 54 799999998887753
No 48
>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B ....
Probab=20.63 E-value=1.4e+02 Score=17.75 Aligned_cols=20 Identities=35% Similarity=0.439 Sum_probs=14.4
Q ss_pred EEEEecCCCc-hhHHHHHHHH
Q 035036 12 VYLTSKPKSG-TTWLKALVFS 31 (75)
Q Consensus 12 V~i~syPKsG-TtW~q~Iv~~ 31 (75)
|+++..|=|| |||.+++...
T Consensus 2 ii~~G~pgsGKSt~a~~l~~~ 22 (143)
T PF13671_consen 2 IILCGPPGSGKSTLAKRLAKR 22 (143)
T ss_dssp EEEEESTTSSHHHHHHHHHHH
T ss_pred EEEECCCCCCHHHHHHHHHHH
Confidence 5778888888 5677777643
No 49
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.56 E-value=68 Score=19.75 Aligned_cols=12 Identities=25% Similarity=0.335 Sum_probs=9.9
Q ss_pred CCCCEEEEecCC
Q 035036 8 RPTDVYLTSKPK 19 (75)
Q Consensus 8 r~dDV~i~syPK 19 (75)
+.+|.+++|||=
T Consensus 30 ~eGD~ivas~pg 41 (96)
T COG4004 30 EEGDRIVASSPG 41 (96)
T ss_pred ecccEEEEecCC
Confidence 478999999983
No 50
>PF07136 DUF1385: Protein of unknown function (DUF1385); InterPro: IPR010787 This family contains a number of hypothetical bacterial proteins of unknown function approximately 300 residues in length. Some family members are predicted to be metal-dependent.
Probab=20.47 E-value=63 Score=22.85 Aligned_cols=12 Identities=33% Similarity=0.689 Sum_probs=9.3
Q ss_pred EecCCCchhHHH
Q 035036 15 TSKPKSGTTWLK 26 (75)
Q Consensus 15 ~syPKsGTtW~q 26 (75)
..-|+|||+.+-
T Consensus 137 r~HpRCGTsFl~ 148 (236)
T PF07136_consen 137 RLHPRCGTSFLL 148 (236)
T ss_pred CcCCCcchhHHH
Confidence 346999999775
No 51
>COG2209 NqrE Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrE [Energy production and conversion]
Probab=20.33 E-value=83 Score=21.45 Aligned_cols=28 Identities=29% Similarity=0.438 Sum_probs=18.5
Q ss_pred CcCCccCCCCEEEEecCCCchhHHHHHHHHH
Q 035036 2 QQHFQARPTDVYLTSKPKSGTTWLKALVFST 32 (75)
Q Consensus 2 ~~~f~~r~dDV~i~syPKsGTtW~q~Iv~~i 32 (75)
|++|..-+.-|+=.. ||.-|+..|+.+.
T Consensus 131 qR~Y~f~es~vyg~G---sG~gW~LAIvalA 158 (198)
T COG2209 131 QRDYNFAESVVYGFG---SGLGWMLAIVALA 158 (198)
T ss_pred eecCCCchhhheecC---CchHHHHHHHHHH
Confidence 445555555444333 8999999998775
Done!