Query 033801
Match_columns 111
No_of_seqs 110 out of 1083
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 06:26:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033801.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033801hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05591 rplQ 50S ribosomal pr 100.0 1.4E-57 3E-62 322.5 12.7 111 1-111 1-111 (113)
2 COG0203 RplQ Ribosomal protein 100.0 2.4E-57 5.2E-62 321.3 11.6 109 3-111 6-114 (116)
3 TIGR00059 L17 ribosomal protei 100.0 5.1E-57 1.1E-61 319.2 12.5 109 3-111 1-109 (112)
4 PTZ00076 60S ribosomal protein 100.0 1.6E-50 3.6E-55 316.4 12.2 109 3-111 18-127 (253)
5 PF01196 Ribosomal_L17: Riboso 100.0 3.3E-50 7.1E-55 278.1 8.7 95 17-111 1-95 (97)
6 KOG3280 Mitochondrial/chloropl 100.0 5.7E-47 1.2E-51 282.1 9.0 106 6-111 16-124 (171)
7 PRK13266 Thf1-like protein; Re 59.5 15 0.00033 29.0 3.9 78 9-98 68-147 (225)
8 PRK13848 conjugal transfer pro 59.4 21 0.00045 25.0 4.1 46 42-93 24-69 (98)
9 PF02082 Rrf2: Transcriptional 57.6 28 0.00062 22.3 4.4 46 47-92 13-66 (83)
10 PF04079 DUF387: Putative tran 53.6 31 0.00068 25.5 4.6 46 45-92 3-48 (159)
11 PF05598 DUF772: Transposase d 50.6 59 0.0013 20.1 5.9 72 8-81 1-77 (77)
12 PLN00047 photosystem II biogen 45.3 45 0.00098 27.3 4.6 78 9-98 119-197 (283)
13 COG1775 HgdB Benzoyl-CoA reduc 44.2 54 0.0012 28.0 5.1 81 27-107 161-251 (379)
14 PF07820 TraC: TraC-like prote 43.9 59 0.0013 22.5 4.4 41 43-89 24-64 (92)
15 PRK00135 scpB segregation and 43.8 83 0.0018 23.9 5.6 51 41-91 5-55 (188)
16 cd00491 4Oxalocrotonate_Tautom 38.0 43 0.00094 19.4 2.7 21 8-28 10-30 (58)
17 COG5095 TAF6 Transcription ini 37.7 45 0.00098 28.4 3.6 40 38-77 192-232 (450)
18 PRK00745 4-oxalocrotonate taut 34.9 50 0.0011 19.6 2.7 21 8-28 11-31 (62)
19 TIGR00013 taut 4-oxalocrotonat 34.0 53 0.0012 19.5 2.7 21 8-28 11-31 (63)
20 PRK02220 4-oxalocrotonate taut 33.5 55 0.0012 19.3 2.7 21 8-28 11-31 (61)
21 COG1959 Predicted transcriptio 33.0 1E+02 0.0023 22.2 4.6 46 47-92 13-66 (150)
22 COG2257 Uncharacterized homolo 32.5 41 0.00088 23.3 2.2 42 43-84 32-79 (92)
23 PRK01964 4-oxalocrotonate taut 32.4 58 0.0013 19.7 2.7 21 8-28 11-31 (64)
24 COG4463 CtsR Transcriptional r 29.7 32 0.00069 25.8 1.4 13 88-100 64-76 (153)
25 PF03127 GAT: GAT domain; Int 29.5 1.5E+02 0.0033 19.6 4.6 62 15-81 20-88 (100)
26 PF14552 Tautomerase_2: Tautom 27.9 56 0.0012 21.5 2.2 21 7-27 38-58 (82)
27 TIGR02573 LcrG_PcrG type III s 27.9 47 0.001 22.9 1.8 18 9-26 16-33 (90)
28 PF06858 NOG1: Nucleolar GTP-b 26.1 54 0.0012 20.8 1.7 18 71-88 32-49 (58)
29 PLN03060 inositol phosphatase- 25.8 97 0.0021 24.2 3.5 74 9-97 66-143 (206)
30 PF05848 CtsR: Firmicute trans 24.5 38 0.00083 25.2 1.0 36 62-100 31-76 (152)
31 PRK02289 4-oxalocrotonate taut 24.0 99 0.0021 18.6 2.7 21 8-28 11-31 (60)
32 PRK11920 rirA iron-responsive 23.6 2.1E+02 0.0046 20.6 4.8 45 48-92 14-65 (153)
33 PRK09778 putative antitoxin of 23.3 1.3E+02 0.0029 21.0 3.4 30 29-58 64-93 (97)
34 PF10341 TPP1: Shelterin compl 23.2 41 0.0009 22.6 0.9 29 82-110 19-47 (106)
35 cd00580 CHMI 5-carboxymethyl-2 22.5 1E+02 0.0022 20.9 2.7 21 8-28 70-90 (113)
36 PF03979 Sigma70_r1_1: Sigma-7 20.6 1.4E+02 0.0031 19.2 3.1 40 42-81 6-49 (82)
37 smart00751 BSD domain in trans 20.3 73 0.0016 18.8 1.5 27 60-86 9-35 (51)
No 1
>PRK05591 rplQ 50S ribosomal protein L17; Validated
Probab=100.00 E-value=1.4e-57 Score=322.53 Aligned_cols=111 Identities=52% Similarity=0.826 Sum_probs=109.5
Q ss_pred CCcCCCCCCCchHHHHHHHHHHHHHHhcccceecHHhHHHHhhhHHHHHHhhccCChhHHHHHHhhcCChhHHHHHHHHH
Q 033801 1 MTKFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTEL 80 (111)
Q Consensus 1 ~~~~~klgr~~~hR~~llrnl~t~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~~r~a~~~L~~~~~v~KLf~~l 80 (111)
+.+++||||+++||++|||||+||||+||+|+||++||||+|+|||+|||+||+||+|++|++.+||.|+++++|||++|
T Consensus 1 ~~~~rkl~r~~~hR~allrnl~tsLi~herI~TT~~KAKelr~~aEklIt~aK~~~~~~rR~~~~~L~~~~~v~KLf~~l 80 (113)
T PRK05591 1 RKKGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHARRQAFARLRDKEAVHKLFDEI 80 (113)
T ss_pred CCCCCCCCCChHHHHHHHHHHHHHHHHcCeEEecHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHhCCHHHHHHHHHHH
Confidence 46889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhccCCCCeeEEEcccCCCCCCCcccccC
Q 033801 81 AYRYKDRAGGYTRLLRSRIRVGDAAPMAYIE 111 (111)
Q Consensus 81 ~pRy~~r~GGYTRi~kl~~R~GD~A~maiiE 111 (111)
+|||+||+||||||+|+++|.||+|||||||
T Consensus 81 apry~~R~GGYTRI~k~~~R~gD~A~ma~iE 111 (113)
T PRK05591 81 APRYADRNGGYTRILKLGFRRGDNAPMAIIE 111 (113)
T ss_pred HHHhCcCCCCeEEEEECCCCCCCCCCeEEEE
Confidence 9999999999999999999999999999998
No 2
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.4e-57 Score=321.27 Aligned_cols=109 Identities=51% Similarity=0.815 Sum_probs=108.0
Q ss_pred cCCCCCCCchHHHHHHHHHHHHHHhcccceecHHhHHHHhhhHHHHHHhhccCChhHHHHHHhhcCChhHHHHHHHHHHH
Q 033801 3 KFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAY 82 (111)
Q Consensus 3 ~~~klgr~~~hR~~llrnl~t~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~~r~a~~~L~~~~~v~KLf~~l~p 82 (111)
++++|||+++||++||+||++|||+||+|+||++||||+|+++|+|||+||.||++++|+|.++|.|++++.|||++|+|
T Consensus 6 ~~rkl~rtsshR~amlrnla~sLi~he~I~TT~~KAKelr~~vEkLITlaK~~~l~~RR~a~~~l~d~~~v~kLF~~iap 85 (116)
T COG0203 6 KGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLANRRLAFARLRDKDAVKKLFDEIAP 85 (116)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHcCceeecHHHHHHHHHHHHHHHHHhhcccHHHHHHHHHHcccHHHHHHHHHHhCh
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCCCeeEEEcccCCCCCCCcccccC
Q 033801 83 RYKDRAGGYTRLLRSRIRVGDAAPMAYIE 111 (111)
Q Consensus 83 Ry~~r~GGYTRi~kl~~R~GD~A~maiiE 111 (111)
||.+||||||||+|+|+|.||+|||||||
T Consensus 86 ry~~R~GGYtRIlK~g~R~GD~A~maiiE 114 (116)
T COG0203 86 RYAERNGGYTRILKLGFRRGDNAPMAIIE 114 (116)
T ss_pred hhcCCCCCeeEEEecCCCCCCCCceEEEE
Confidence 99999999999999999999999999998
No 3
>TIGR00059 L17 ribosomal protein L17. Eubacterial and mitochondrial. The mitochondrial form, from yeast, contains an additional 110 amino acids C-terminal to the region found by this model.
Probab=100.00 E-value=5.1e-57 Score=319.23 Aligned_cols=109 Identities=48% Similarity=0.827 Sum_probs=107.6
Q ss_pred cCCCCCCCchHHHHHHHHHHHHHHhcccceecHHhHHHHhhhHHHHHHhhccCChhHHHHHHhhcCChhHHHHHHHHHHH
Q 033801 3 KFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAY 82 (111)
Q Consensus 3 ~~~klgr~~~hR~~llrnl~t~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~~r~a~~~L~~~~~v~KLf~~l~p 82 (111)
+++||||+++||++|||||++|||+||+|+||++||||+|+|||+|||+||+||+|++|++.+||.|+++++|||++|+|
T Consensus 1 ~~~klgr~~~hR~allrnl~tsLi~herI~TT~~KAKelr~~aEklIt~AK~~~~~~rR~~~~~l~~~~~v~KLf~~lap 80 (112)
T TIGR00059 1 SYRKLGRTSAHRKALLRNLASALIRHEKIKTTLAKAKELRRVVEKLITLAKVDNFNNRREAKAYIRNKEIVHKLFSEIAP 80 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHCCeEEECHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 46999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCCCeeEEEcccCCCCCCCcccccC
Q 033801 83 RYKDRAGGYTRLLRSRIRVGDAAPMAYIE 111 (111)
Q Consensus 83 Ry~~r~GGYTRi~kl~~R~GD~A~maiiE 111 (111)
||++||||||||+|+++|.||+|||||||
T Consensus 81 ry~~R~GGYTRI~kl~~R~gD~A~maiiE 109 (112)
T TIGR00059 81 RYAQRPGGYTRILKLGPRRGDAAEMAIIE 109 (112)
T ss_pred HhCCCCCCeEEEEECCCCCCCCCCeEEEE
Confidence 99999999999999999999999999998
No 4
>PTZ00076 60S ribosomal protein L17; Provisional
Probab=100.00 E-value=1.6e-50 Score=316.36 Aligned_cols=109 Identities=30% Similarity=0.523 Sum_probs=107.1
Q ss_pred cCCCCCCCchHHHHHHHHHHHHHHhcccceecHHhHHHHhhhHHHHHHhhccCChhHHHHHHhhcCChhHHHHHHHHHHH
Q 033801 3 KFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAY 82 (111)
Q Consensus 3 ~~~klgr~~~hR~~llrnl~t~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~~r~a~~~L~~~~~v~KLf~~l~p 82 (111)
+++||||+++||++|||||++|||+||||+||++||||+|+|||+|||+||++++|++|++.++|.|+++++|||++|+|
T Consensus 18 ~~rKLgR~ssHR~AlLRNLvtsLI~hERIeTTlaKAKELR~~AEKLITlAKk~tl~sRR~a~s~L~d~~av~KLF~eLAP 97 (253)
T PTZ00076 18 LFRRAHGQPHHRWDSIKNQLDELLRYGRLELTLPRAKELQQYAEELIYLAKKDTPESNLKVESMLRTPQGRRKLYEKYVP 97 (253)
T ss_pred ccCCCCCCHHHHHHHHHHHHHHHHHcCcEEecHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCHHHHHHHHHHhhh
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCCCeeEEEcc-cCCCCCCCcccccC
Q 033801 83 RYKDRAGGYTRLLRS-RIRVGDAAPMAYIE 111 (111)
Q Consensus 83 Ry~~r~GGYTRi~kl-~~R~GD~A~maiiE 111 (111)
||++|+||||||+|+ ++|.||+|||||||
T Consensus 98 RY~dR~GGYTRIlK~~g~R~GD~ApMAiIE 127 (253)
T PTZ00076 98 LYRDRPFFFTRVVNQWRLRLRDAAPMAYIE 127 (253)
T ss_pred HhcCCCCCeeEEEeCCCCCCCCCCCEEEEE
Confidence 999999999999997 69999999999998
No 5
>PF01196 Ribosomal_L17: Ribosomal protein L17; InterPro: IPR000456 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 [, ]. Ribosomal protein L17 is one of the proteins from the large ribosomal subunit. Bacterial L17 is a protein of 120 to 130 amino-acid residues while yeast YmL8 is twice as large (238 residues). The N-terminal half of YmL8 is colinear with the sequence of L17 from Escherichia coli.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3F1F_R 1VSP_L 3PYV_N 3PYR_N 3PYO_N 1VSA_L 3MS1_N 3F1H_R 3D5B_R 3MRZ_N ....
Probab=100.00 E-value=3.3e-50 Score=278.11 Aligned_cols=95 Identities=54% Similarity=0.881 Sum_probs=93.3
Q ss_pred HHHHHHHHHHhcccceecHHhHHHHhhhHHHHHHhhccCChhHHHHHHhhcCChhHHHHHHHHHHHhhccCCCCeeEEEc
Q 033801 17 MLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLR 96 (111)
Q Consensus 17 llrnl~t~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~~r~a~~~L~~~~~v~KLf~~l~pRy~~r~GGYTRi~k 96 (111)
|||||+|+||+||+|+||++||||+|+|||+|||+||+|++|+++++.+||.|+++++|||++|+|||++|+||||||+|
T Consensus 1 llrnlvt~Li~herI~TT~~KAke~r~~aErlIt~ak~~~~~~~r~~~~~l~~~~~v~KLf~~l~pRy~~r~GgYTRi~k 80 (97)
T PF01196_consen 1 LLRNLVTSLIRHERIETTLAKAKELRPYAERLITLAKKGDLHARRQALSWLRDKELVKKLFKELAPRYADRNGGYTRIIK 80 (97)
T ss_dssp HHHHHHHHHHHHSEEEEEHHHHHHHHHHHHHHHHHHTSSTHHHHHHHHHCSSSHHHHHHHHTTHHHHTTTSSS-SEEEEE
T ss_pred ChHHHHHHHHhCCeEEecHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHhcchHHHHHHHHHHHHHHccCCCCeEEEEe
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCcccccC
Q 033801 97 SRIRVGDAAPMAYIE 111 (111)
Q Consensus 97 l~~R~GD~A~maiiE 111 (111)
+++|.||+|||||||
T Consensus 81 l~~R~gD~A~maiiE 95 (97)
T PF01196_consen 81 LGPRRGDAAPMAIIE 95 (97)
T ss_dssp EEECSSSTCEEEEEE
T ss_pred CCCCCCCCCCEEEEE
Confidence 999999999999998
No 6
>KOG3280 consensus Mitochondrial/chloroplast ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.7e-47 Score=282.12 Aligned_cols=106 Identities=61% Similarity=0.933 Sum_probs=104.4
Q ss_pred CCCCCchHHHHHHHHHHHHHHhcccceecHHhHHHHhhhHHHHHHhh-ccCChhHH--HHHHhhcCChhHHHHHHHHHHH
Q 033801 6 KLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLG-KEGSLCAA--RRAAAFVRGDDVIHKLFTELAY 82 (111)
Q Consensus 6 klgr~~~hR~~llrnl~t~Li~herI~TT~~KAKelr~~aEklIt~A-K~~~~~~~--r~a~~~L~~~~~v~KLf~~l~p 82 (111)
|+||+++||.++||||||+|++||||+|||+||||+|+|||+|||+| |.|++|++ +++.+||..+++++|||++|+|
T Consensus 16 Klgr~~~~R~~lLR~lvt~LvkHErIe~t~ara~Ear~~aEklIt~~~k~g~~~~~~~~~a~~~l~ekdli~KlF~vl~p 95 (171)
T KOG3280|consen 16 KLGRPPAHRLALLRNLVTQLVKHERIETTWARAKEARRYAEKLITLGKKAGSLHERTARMADGWLREKDLLHKLFTVLAP 95 (171)
T ss_pred hcCCCcHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhcCcHhHHHHHHHhcccccchHHHHHHHHhch
Confidence 99999999999999999999999999999999999999999999999 78999988 9999999999999999999999
Q ss_pred hhccCCCCeeEEEcccCCCCCCCcccccC
Q 033801 83 RYKDRAGGYTRLLRSRIRVGDAAPMAYIE 111 (111)
Q Consensus 83 Ry~~r~GGYTRi~kl~~R~GD~A~maiiE 111 (111)
||+||+|||||+++++||.||+|||||||
T Consensus 96 RY~dr~ggYTRllrlppr~~d~apmavlE 124 (171)
T KOG3280|consen 96 RYKDRNGGYTRLLRLPPRRGDRAPMAVLE 124 (171)
T ss_pred hhccCCCCceehhccCcccccccCceeee
Confidence 99999999999999999999999999998
No 7
>PRK13266 Thf1-like protein; Reviewed
Probab=59.52 E-value=15 Score=29.02 Aligned_cols=78 Identities=19% Similarity=0.279 Sum_probs=56.5
Q ss_pred CCchHHHHHHHHHHHHHHhcccceecHHhHHHHhhhHHHHHHhhccCChhHHHHHHhhcCCh--hHHHHHHHHHHHhhcc
Q 033801 9 RPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGD--DVIHKLFTELAYRYKD 86 (111)
Q Consensus 9 r~~~hR~~llrnl~t~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~~r~a~~~L~~~--~~v~KLf~~l~pRy~~ 86 (111)
++.+|+..++..+|.++= --+.++|..|++|..+|+..+.. ...+||..+ .....|...+...=.+
T Consensus 68 ~Pee~~~~IF~Alc~a~~---------~dp~~~r~dA~~l~~~a~~~s~~---~i~~~l~~~~~~~~~~l~~~l~~ia~~ 135 (225)
T PRK13266 68 RPEEHKDSIFNALCQAVG---------FDPEQLRQDAERLLELAKGKSLK---EILSWLTQKALGEPGGLLATLLAIANN 135 (225)
T ss_pred CChHHHHHHHHHHHHHcC---------CCHHHHHHHHHHHHHHHhcCCHH---HHHHHHhccccccchhHHHHHHHHhcC
Confidence 478899999999999864 35889999999999999987665 344566643 2223355556555567
Q ss_pred CCCCeeEEEccc
Q 033801 87 RAGGYTRLLRSR 98 (111)
Q Consensus 87 r~GGYTRi~kl~ 98 (111)
.+--|.|++=+|
T Consensus 136 ~~f~YSRl~AIG 147 (225)
T PRK13266 136 SKFKYSRLFAIG 147 (225)
T ss_pred CCCchHHHHHHH
Confidence 777888876544
No 8
>PRK13848 conjugal transfer protein TraC; Provisional
Probab=59.45 E-value=21 Score=24.97 Aligned_cols=46 Identities=22% Similarity=0.323 Sum_probs=31.1
Q ss_pred hhhHHHHHHhhccCChhHHHHHHhhcCChhHHHHHHHHHHHhhccCCCCeeE
Q 033801 42 RRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYTR 93 (111)
Q Consensus 42 r~~aEklIt~AK~~~~~~~r~a~~~L~~~~~v~KLf~~l~pRy~~r~GGYTR 93 (111)
.+-+||+-.+|-+..+.. +=-+...+...|++|+.||.+..|+-|=
T Consensus 24 ~keAERigRiAlKAGLge------ieI~d~eL~~aFeeiAaRFR~g~~~~~g 69 (98)
T PRK13848 24 TREAERIGRIALKAGLGE------IEIEEAELQAAFEELAKRFRGGKGAATG 69 (98)
T ss_pred HHHHHHHHHHHHHcCccc------cccCHHHHHHHHHHHHHHHhcCCCcccc
Confidence 345666666665544431 1125667899999999999998887653
No 9
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=57.56 E-value=28 Score=22.25 Aligned_cols=46 Identities=17% Similarity=0.329 Sum_probs=32.5
Q ss_pred HHHHhhccCC---hhHHHHHHhhcCChhHHHHHHHHHHH-----hhccCCCCee
Q 033801 47 NMVQLGKEGS---LCAARRAAAFVRGDDVIHKLFTELAY-----RYKDRAGGYT 92 (111)
Q Consensus 47 klIt~AK~~~---~~~~r~a~~~L~~~~~v~KLf~~l~p-----Ry~~r~GGYT 92 (111)
=|+.+|..++ ......|...=-++..+.++++.|.. -...++|||.
T Consensus 13 ~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~ 66 (83)
T PF02082_consen 13 ILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYR 66 (83)
T ss_dssp HHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEE
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCcee
Confidence 3566776655 45667777777788899999999886 3456677775
No 10
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=53.65 E-value=31 Score=25.49 Aligned_cols=46 Identities=15% Similarity=0.299 Sum_probs=29.7
Q ss_pred HHHHHHhhccCChhHHHHHHhhcCChhHHHHHHHHHHHhhccCCCCee
Q 033801 45 ADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYT 92 (111)
Q Consensus 45 aEklIt~AK~~~~~~~r~a~~~L~~~~~v~KLf~~l~pRy~~r~GGYT 92 (111)
+|-++-.+-++ -+......++.+++.+.++.++|...|.+.++|+.
T Consensus 3 iEAlLF~s~~p--vs~~~La~~l~~~~~v~~~l~~L~~~y~~~~~gl~ 48 (159)
T PF04079_consen 3 IEALLFASGEP--VSIEELAEILGSEDEVEEALEELQEEYNEEDRGLE 48 (159)
T ss_dssp HHHHHHH-SS---B-HHHHHHHCT-HHHHHHHHHHHHHHHHHCT-SEE
T ss_pred hHhhHHHcCCC--CCHHHHHHHhCCHHHHHHHHHHHHHHhccCCCCEE
Confidence 45555554333 34445555666889999999999999988877764
No 11
>PF05598 DUF772: Transposase domain (DUF772); InterPro: IPR008490 This presumed domain is found at the N terminus of transposase insH and other related transposases.
Probab=50.55 E-value=59 Score=20.12 Aligned_cols=72 Identities=15% Similarity=0.175 Sum_probs=38.1
Q ss_pred CCCchHHHHHHHHHHHHHHhcc-cceecHHhHH---HHhhhHHHHHHh-hccCChhHHHHHHhhcCChhHHHHHHHHHH
Q 033801 8 NRPTGHRMSMLRTMVSQLVKHE-RIETTVAKAK---EVRRLADNMVQL-GKEGSLCAARRAAAFVRGDDVIHKLFTELA 81 (111)
Q Consensus 8 gr~~~hR~~llrnl~t~Li~he-rI~TT~~KAK---elr~~aEklIt~-AK~~~~~~~r~a~~~L~~~~~v~KLf~~l~ 81 (111)
||++-+-..|++-++-+-...- ...-....++ .++.++. +.. ....|..+-......+.++++.++||++++
T Consensus 1 GRp~~~~~~ml~~ll~~~~~~~~S~r~l~~~l~~~~~~r~~~g--~~~~~~~pd~stl~rfr~rl~~~~~~~~lf~~~v 77 (77)
T PF05598_consen 1 GRPAYPPRMMLKALLLKYLFGLRSDRELEERLRDNLSFRYFCG--LSLEEPVPDHSTLSRFRKRLIQHGLIEKLFDQVV 77 (77)
T ss_pred CcCCCCHHHHHHHHHHHHHHhcchHHHHHhhHhhhhHHHHHHh--cccCCCCCChHHHHHHHHHHhhccHHHHHHHHhC
Confidence 7888888888888887776643 2211111111 1111111 000 112222333444456788889999999864
No 12
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=45.33 E-value=45 Score=27.35 Aligned_cols=78 Identities=13% Similarity=0.226 Sum_probs=57.9
Q ss_pred CCchHHHHHHHHHHHHHHhcccceecHHhHHHHhhhHHHHHHhhccCChhHHHHHHhhcCChhHHHHHHHHHHHhhc-cC
Q 033801 9 RPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYK-DR 87 (111)
Q Consensus 9 r~~~hR~~llrnl~t~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~~r~a~~~L~~~~~v~KLf~~l~pRy~-~r 87 (111)
++.+|+..++..+|.++=. -+.++|..|++|..+|+..+.. .+..|+.....+...+..|+.+=+ +.
T Consensus 119 ~Pee~~~~IF~Alc~a~g~---------Dp~qyr~dA~~l~~~A~~~s~~---~l~~~l~~~~~l~~~l~~IA~~a~~~~ 186 (283)
T PLN00047 119 PSDEDRDAIFKAYIKALGE---------DPEQYRKDAAKLEEWARSQTGS---SLVDFSSKEGEIEGILKDIAERAGSKG 186 (283)
T ss_pred CChHHHHHHHHHHHHHcCC---------CHHHHHHHHHHHHHHHhcCCHH---HHHHHHhcchHHHHHHHHHHHhhccCC
Confidence 4678999999999998744 4789999999999999977654 445677777778888888875532 23
Q ss_pred CCCeeEEEccc
Q 033801 88 AGGYTRLLRSR 98 (111)
Q Consensus 88 ~GGYTRi~kl~ 98 (111)
.--|.|++=+|
T Consensus 187 ~f~YSRlfAIG 197 (283)
T PLN00047 187 KFSYSRFFAIG 197 (283)
T ss_pred CcchHHHHHHH
Confidence 44577765443
No 13
>COG1775 HgdB Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism]
Probab=44.21 E-value=54 Score=27.95 Aligned_cols=81 Identities=23% Similarity=0.346 Sum_probs=56.6
Q ss_pred hcccceecHHhHHHHhhhHHHHHHhhccCC------hhHHHHHHh-hcCChhHHHHHHHHHHHhhccC--CCCeeEEEcc
Q 033801 27 KHERIETTVAKAKEVRRLADNMVQLGKEGS------LCAARRAAA-FVRGDDVIHKLFTELAYRYKDR--AGGYTRLLRS 97 (111)
Q Consensus 27 ~herI~TT~~KAKelr~~aEklIt~AK~~~------~~~~r~a~~-~L~~~~~v~KLf~~l~pRy~~r--~GGYTRi~kl 97 (111)
..+..+=+.++.-++|..--+++.+++..+ -+...++.+ ++.|.+...-.++++..+++.| .|+=+||+-.
T Consensus 161 T~e~L~da~~r~N~~rea~~k~~kL~~~~P~plsg~D~~~~~~~~~~~~d~d~~~~~l~~l~eelekr~~eg~~~Ri~~~ 240 (379)
T COG1775 161 TEEKLRDAIARYNRLREALAKLYKLAKHKPSPLSGSDAFNVMAFAVFLRDKDAFIEELEELIEELEKRVEEGEGPRILIT 240 (379)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhHHHHHhhHHHHhcchHHHHHHHHHHHHHHHHHHhccCCceEEee
Confidence 345666677788888888888888888543 244556666 8888887777777776666655 2333999999
Q ss_pred cCC-CCCCCcc
Q 033801 98 RIR-VGDAAPM 107 (111)
Q Consensus 98 ~~R-~GD~A~m 107 (111)
|-| .+|+-+.
T Consensus 241 g~p~~~~~~~v 251 (379)
T COG1775 241 GIPILGDNPKV 251 (379)
T ss_pred cCcccCCCcch
Confidence 977 5577553
No 14
>PF07820 TraC: TraC-like protein; InterPro: IPR012930 The members of this family are sequences that are similar to TraC (Q84HT8 from SWISSPROT) from Rhizobium etli. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli (strain CFN 42/ATCC 51251) that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42d, the symbiotic plasmid which carries most of the genes required for nodulation and nitrogen fixation by this symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58 []. ; GO: 0000746 conjugation
Probab=43.94 E-value=59 Score=22.49 Aligned_cols=41 Identities=17% Similarity=0.305 Sum_probs=26.7
Q ss_pred hhHHHHHHhhccCChhHHHHHHhhcCChhHHHHHHHHHHHhhccCCC
Q 033801 43 RLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAG 89 (111)
Q Consensus 43 ~~aEklIt~AK~~~~~~~r~a~~~L~~~~~v~KLf~~l~pRy~~r~G 89 (111)
+-+||+-.+|-+.-+. .+--+.+.+.+.|++|+.||....+
T Consensus 24 keaERigr~AlKaGL~------eieI~d~eL~~~FeeIa~RFrk~~~ 64 (92)
T PF07820_consen 24 KEAERIGRIALKAGLG------EIEISDAELQAAFEEIAARFRKGKK 64 (92)
T ss_pred HHHHHHHHHHHHcccc------cccCCHHHHHHHHHHHHHHHhcccc
Confidence 4456665555443332 2223567899999999999988744
No 15
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=43.75 E-value=83 Score=23.90 Aligned_cols=51 Identities=16% Similarity=0.287 Sum_probs=34.7
Q ss_pred HhhhHHHHHHhhccCChhHHHHHHhhcCChhHHHHHHHHHHHhhccCCCCe
Q 033801 41 VRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGY 91 (111)
Q Consensus 41 lr~~aEklIt~AK~~~~~~~r~a~~~L~~~~~v~KLf~~l~pRy~~r~GGY 91 (111)
+...+|-++-.+-...+.-.+++.-+=.+++.|.++.++|...|.++++|+
T Consensus 5 ~~~~iEA~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi 55 (188)
T PRK00135 5 YKSIIEALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGL 55 (188)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCE
Confidence 455678888877665344444443322356789999999999999776664
No 16
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=37.96 E-value=43 Score=19.44 Aligned_cols=21 Identities=5% Similarity=0.224 Sum_probs=18.0
Q ss_pred CCCchHHHHHHHHHHHHHHhc
Q 033801 8 NRPTGHRMSMLRTMVSQLVKH 28 (111)
Q Consensus 8 gr~~~hR~~llrnl~t~Li~h 28 (111)
||+.+++.+|.+.+..+|.++
T Consensus 10 grt~eqk~~l~~~i~~~l~~~ 30 (58)
T cd00491 10 GRTDEQKRELIERVTEAVSEI 30 (58)
T ss_pred CCCHHHHHHHHHHHHHHHHHH
Confidence 788999999999998888765
No 17
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=37.67 E-value=45 Score=28.44 Aligned_cols=40 Identities=25% Similarity=0.316 Sum_probs=31.9
Q ss_pred HHHHhhhHHHHHH-hhccCChhHHHHHHhhcCChhHHHHHH
Q 033801 38 AKEVRRLADNMVQ-LGKEGSLCAARRAAAFVRGDDVIHKLF 77 (111)
Q Consensus 38 AKelr~~aEklIt-~AK~~~~~~~r~a~~~L~~~~~v~KLf 77 (111)
.||+|-|.||+|+ ++-..+.+.+.-|..-|++..-++.|.
T Consensus 192 sKELq~YF~kvisal~dEs~~~~r~aAl~sLr~dsGlhQLv 232 (450)
T COG5095 192 SKELQMYFDKVISALLDESDEQTRDAALESLRNDSGLHQLV 232 (450)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCccHHHHH
Confidence 5899999999995 777778888888899999866555443
No 18
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=34.95 E-value=50 Score=19.58 Aligned_cols=21 Identities=10% Similarity=0.246 Sum_probs=18.3
Q ss_pred CCCchHHHHHHHHHHHHHHhc
Q 033801 8 NRPTGHRMSMLRTMVSQLVKH 28 (111)
Q Consensus 8 gr~~~hR~~llrnl~t~Li~h 28 (111)
||+.+++.+|.+.+..+|.++
T Consensus 11 grs~eqk~~l~~~it~~l~~~ 31 (62)
T PRK00745 11 GRTVEQKRKLVEEITRVTVET 31 (62)
T ss_pred CCCHHHHHHHHHHHHHHHHHH
Confidence 789999999999998888775
No 19
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=33.99 E-value=53 Score=19.48 Aligned_cols=21 Identities=5% Similarity=0.273 Sum_probs=17.8
Q ss_pred CCCchHHHHHHHHHHHHHHhc
Q 033801 8 NRPTGHRMSMLRTMVSQLVKH 28 (111)
Q Consensus 8 gr~~~hR~~llrnl~t~Li~h 28 (111)
||+.+++.+|++.+..+|..+
T Consensus 11 grt~eqK~~l~~~it~~l~~~ 31 (63)
T TIGR00013 11 GRTDEQKRQLIEGVTEAMAET 31 (63)
T ss_pred CCCHHHHHHHHHHHHHHHHHH
Confidence 689999999999988888764
No 20
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=33.47 E-value=55 Score=19.33 Aligned_cols=21 Identities=10% Similarity=0.287 Sum_probs=18.4
Q ss_pred CCCchHHHHHHHHHHHHHHhc
Q 033801 8 NRPTGHRMSMLRTMVSQLVKH 28 (111)
Q Consensus 8 gr~~~hR~~llrnl~t~Li~h 28 (111)
||+.+++.+|++.+..+|.+.
T Consensus 11 Grs~eqk~~l~~~it~~l~~~ 31 (61)
T PRK02220 11 GRTEEQLKALVKDVTAAVSKN 31 (61)
T ss_pred CCCHHHHHHHHHHHHHHHHHH
Confidence 899999999999998888764
No 21
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=32.99 E-value=1e+02 Score=22.20 Aligned_cols=46 Identities=17% Similarity=0.245 Sum_probs=34.1
Q ss_pred HHHHhhccCC--h-hHHHHHHhhcCChhHHHHHHHHHHH-----hhccCCCCee
Q 033801 47 NMVQLGKEGS--L-CAARRAAAFVRGDDVIHKLFTELAY-----RYKDRAGGYT 92 (111)
Q Consensus 47 klIt~AK~~~--~-~~~r~a~~~L~~~~~v~KLf~~l~p-----Ry~~r~GGYT 92 (111)
=|+.+|+.++ . .....|...=-++.-+.|+|..|.. -.+..+|||.
T Consensus 13 ~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~ 66 (150)
T COG1959 13 ALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYR 66 (150)
T ss_pred HHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCcc
Confidence 3778898765 3 3566777777788899999998865 4667788884
No 22
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=32.46 E-value=41 Score=23.31 Aligned_cols=42 Identities=17% Similarity=0.380 Sum_probs=23.8
Q ss_pred hhHHHHHHhhccCChh---HHHHHHhhcC---ChhHHHHHHHHHHHhh
Q 033801 43 RLADNMVQLGKEGSLC---AARRAAAFVR---GDDVIHKLFTELAYRY 84 (111)
Q Consensus 43 ~~aEklIt~AK~~~~~---~~r~a~~~L~---~~~~v~KLf~~l~pRy 84 (111)
..||++|..||+.+.+ ..-++...+. +.+.=..||+.++.-|
T Consensus 32 ~iAe~II~~Ake~~Vpi~edp~Lv~~L~~lelg~~IPeelY~vVAEif 79 (92)
T COG2257 32 EIAEKIIEKAKEHGVPIQEDPLLVELLLKLELGDEIPEELYEVVAEIF 79 (92)
T ss_pred HHHHHHHHHHHHcCCCcccCHHHHHHHHhccccccCCHHHHHHHHHHH
Confidence 5799999999998753 2222222222 3333445555555544
No 23
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=32.45 E-value=58 Score=19.65 Aligned_cols=21 Identities=14% Similarity=0.357 Sum_probs=18.3
Q ss_pred CCCchHHHHHHHHHHHHHHhc
Q 033801 8 NRPTGHRMSMLRTMVSQLVKH 28 (111)
Q Consensus 8 gr~~~hR~~llrnl~t~Li~h 28 (111)
||+.++++++++.+..+|.++
T Consensus 11 grt~eqk~~l~~~it~~l~~~ 31 (64)
T PRK01964 11 GRPEEKIKNLIREVTEAISAT 31 (64)
T ss_pred CCCHHHHHHHHHHHHHHHHHH
Confidence 789999999999998888764
No 24
>COG4463 CtsR Transcriptional repressor of class III stress genes [Transcription]
Probab=29.70 E-value=32 Score=25.78 Aligned_cols=13 Identities=31% Similarity=0.830 Sum_probs=11.1
Q ss_pred CCCeeEEEcccCC
Q 033801 88 AGGYTRLLRSRIR 100 (111)
Q Consensus 88 ~GGYTRi~kl~~R 100 (111)
-|||-||.|..+.
T Consensus 64 GGGYIRI~Kv~~~ 76 (153)
T COG4463 64 GGGYIRIIKVEYS 76 (153)
T ss_pred CCceEEEEEeccc
Confidence 6899999998764
No 25
>PF03127 GAT: GAT domain; InterPro: IPR004152 The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 [] and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins [].; GO: 0006886 intracellular protein transport, 0005622 intracellular; PDB: 1YD8_H 1WR6_C 1WRD_A 1O3X_A 1J2J_B 1NWM_X 1X79_A 1OXZ_A 1NAF_A.
Probab=29.50 E-value=1.5e+02 Score=19.62 Aligned_cols=62 Identities=10% Similarity=0.200 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHhccccee-------cHHhHHHHhhhHHHHHHhhccCChhHHHHHHhhcCChhHHHHHHHHHH
Q 033801 15 MSMLRTMVSQLVKHERIET-------TVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELA 81 (111)
Q Consensus 15 ~~llrnl~t~Li~herI~T-------T~~KAKelr~~aEklIt~AK~~~~~~~r~a~~~L~~~~~v~KLf~~l~ 81 (111)
..+|.+|+..+-..+...- =...|+.+||-+-++|...-.++ .....|.-.+.+...|..+-
T Consensus 20 ~~lL~emL~~~~~~~~~~~~~el~~eL~~~ck~~r~~i~~li~~~~dee-----~l~~lL~~ND~L~~~l~~Y~ 88 (100)
T PF03127_consen 20 AKLLNEMLDNYDPGEESSSDNELIQELYESCKSMRPRIQRLIEEVEDEE-----LLGELLQANDELNQALERYD 88 (100)
T ss_dssp HHHHHHHHHHTTTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTCH-----HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHHHHHHHhhcCcHH-----HHHHHHHHHHHHHHHHHHHH
Confidence 3566677766655554322 25779999999999996644432 34445554455555554443
No 26
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=27.90 E-value=56 Score=21.54 Aligned_cols=21 Identities=19% Similarity=0.439 Sum_probs=15.7
Q ss_pred CCCCchHHHHHHHHHHHHHHh
Q 033801 7 LNRPTGHRMSMLRTMVSQLVK 27 (111)
Q Consensus 7 lgr~~~hR~~llrnl~t~Li~ 27 (111)
-||+.++.+++++.++..|-.
T Consensus 38 ~gRs~e~K~~ly~~l~~~L~~ 58 (82)
T PF14552_consen 38 AGRSTEQKKALYRALAERLAE 58 (82)
T ss_dssp S---HHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHH
Confidence 389999999999999998865
No 27
>TIGR02573 LcrG_PcrG type III secretion protein LcrG. This protein is found in type III secretion operons, along with LcrR, H and V. Also known as PcrG in Pseudomonas, the protein is believed to make a 1:1 complex with PcrV (LcrV). Mutants of LcrG cause premature secretion of effector proteins into the medium.
Probab=27.89 E-value=47 Score=22.91 Aligned_cols=18 Identities=28% Similarity=0.350 Sum_probs=15.4
Q ss_pred CCchHHHHHHHHHHHHHH
Q 033801 9 RPTGHRMSMLRTMVSQLV 26 (111)
Q Consensus 9 r~~~hR~~llrnl~t~Li 26 (111)
++++||.++|..|+.+|=
T Consensus 16 ~dsd~R~~llqEm~~gLg 33 (90)
T TIGR02573 16 RDSDERNDLLQEMWQGLG 33 (90)
T ss_pred hchHHHHHHHHHHHHHcC
Confidence 578999999999988763
No 28
>PF06858 NOG1: Nucleolar GTP-binding protein 1 (NOG1); InterPro: IPR010674 This domain represents a conserved region of approximately 60 residues in length within nucleolar GTP-binding protein 1 (NOG1). The NOG1 family includes eukaryotic, bacterial and archaeal proteins. In Saccharomyces cerevisiae, the NOG1 gene has been shown to be essential for cell viability, suggesting that NOG1 may play an important role in nucleolar functions. In particular, NOG1 is believed to be functionally linked to ribosome biogenesis, which occurs in the nucleolus. In eukaryotes, NOG1 mutants were found to disrupt the biogenesis of the 60S ribosomal subunit []. The DRG and OBG proteins as well as the prokaryotic NOG-like proteins are homologous throughout their length to the amino half of eukaryotic NOG1, which contains the GTP binding motifs (IPR006073 from INTERPRO); the N-terminal GTP-binding motif is required for function.; GO: 0005525 GTP binding; PDB: 2E87_A.
Probab=26.09 E-value=54 Score=20.76 Aligned_cols=18 Identities=17% Similarity=0.346 Sum_probs=14.2
Q ss_pred hHHHHHHHHHHHhhccCC
Q 033801 71 DVIHKLFTELAYRYKDRA 88 (111)
Q Consensus 71 ~~v~KLf~~l~pRy~~r~ 88 (111)
+.=-+||+++.|+|.++|
T Consensus 32 e~Q~~L~~~ik~~F~~~P 49 (58)
T PF06858_consen 32 EEQLSLFKEIKPLFPNKP 49 (58)
T ss_dssp HHHHHHHHHHHHHTTTS-
T ss_pred HHHHHHHHHHHHHcCCCC
Confidence 445689999999998765
No 29
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=25.80 E-value=97 Score=24.23 Aligned_cols=74 Identities=18% Similarity=0.259 Sum_probs=49.9
Q ss_pred CCchHHHHHHHHHHHHHHhcccceecHHhHHHHhhhHHHHHHhhccCChhHHHHHHhhcCCh----hHHHHHHHHHHHhh
Q 033801 9 RPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGD----DVIHKLFTELAYRY 84 (111)
Q Consensus 9 r~~~hR~~llrnl~t~Li~herI~TT~~KAKelr~~aEklIt~AK~~~~~~~r~a~~~L~~~----~~v~KLf~~l~pRy 84 (111)
++.+|+..++..+|.++= --+.++|..|++|..+|+.-+.. ...+||... +.+...+.-++
T Consensus 66 ~Pee~~~~IF~Alc~a~~---------~dp~~~r~dA~~l~~~a~~~s~~---~l~~~l~~~~~~~~~l~~~~~~~~--- 130 (206)
T PLN03060 66 PNATDRDAIFKAYIEALG---------EDPDQYRKDAKKLEEWASSQSAS---GIADFNSGDGEVEAVLKDIAERAA--- 130 (206)
T ss_pred CChHHHHHHHHHHHHHcC---------CCHHHHHHHHHHHHHHHhcCCHH---HHHHHHhcccccchHHHHHHHHhh---
Confidence 578899999999999874 35789999999999999976654 344556532 33444444333
Q ss_pred ccCCCCeeEEEcc
Q 033801 85 KDRAGGYTRLLRS 97 (111)
Q Consensus 85 ~~r~GGYTRi~kl 97 (111)
.+..--|.|++=+
T Consensus 131 ~~~~f~YSRl~AI 143 (206)
T PLN03060 131 GKTKFHYSRFFAI 143 (206)
T ss_pred cCCCcchHHHHHH
Confidence 3444557776543
No 30
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=24.47 E-value=38 Score=25.25 Aligned_cols=36 Identities=28% Similarity=0.433 Sum_probs=20.0
Q ss_pred HHHhhcCChhHHHHHHHHHHHhhccC----------CCCeeEEEcccCC
Q 033801 62 RAAAFVRGDDVIHKLFTELAYRYKDR----------AGGYTRLLRSRIR 100 (111)
Q Consensus 62 ~a~~~L~~~~~v~KLf~~l~pRy~~r----------~GGYTRi~kl~~R 100 (111)
+|..|=.-|.-+.= +|.-||--- -|||-||.|+...
T Consensus 31 LA~~F~CvPSQINY---Vl~TRFT~e~GY~VESrRGGGGyIRI~rv~~~ 76 (152)
T PF05848_consen 31 LAERFNCVPSQINY---VLSTRFTPERGYIVESRRGGGGYIRIVRVPLD 76 (152)
T ss_dssp HHHHTTS-THHHHH---HHHHHSSCCCTEEEEEE-STT-EEEEEEEEES
T ss_pred HHHHhCCchhhhhe---eeeccccCCCCeEEEeccCCCceEEEEEEccC
Confidence 33333333444443 445588543 5799999998754
No 31
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=24.01 E-value=99 Score=18.57 Aligned_cols=21 Identities=10% Similarity=0.245 Sum_probs=18.3
Q ss_pred CCCchHHHHHHHHHHHHHHhc
Q 033801 8 NRPTGHRMSMLRTMVSQLVKH 28 (111)
Q Consensus 8 gr~~~hR~~llrnl~t~Li~h 28 (111)
||+.+++.+|...+..++.+.
T Consensus 11 Grs~EqK~~L~~~it~a~~~~ 31 (60)
T PRK02289 11 GRSQEQKNALAREVTEVVSRI 31 (60)
T ss_pred CCCHHHHHHHHHHHHHHHHHH
Confidence 899999999999988888764
No 32
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=23.62 E-value=2.1e+02 Score=20.57 Aligned_cols=45 Identities=16% Similarity=0.213 Sum_probs=28.8
Q ss_pred HHHhhccCC--hhHHHHHHhhcCChhHHHHHHHHHHH-----hhccCCCCee
Q 033801 48 MVQLGKEGS--LCAARRAAAFVRGDDVIHKLFTELAY-----RYKDRAGGYT 92 (111)
Q Consensus 48 lIt~AK~~~--~~~~r~a~~~L~~~~~v~KLf~~l~p-----Ry~~r~GGYT 92 (111)
|+.+|...+ ..+...|...--++.-+.|++..|.. -...++|||.
T Consensus 14 L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~ 65 (153)
T PRK11920 14 LMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVR 65 (153)
T ss_pred HHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCee
Confidence 556665433 23455666666677778888887764 4567778875
No 33
>PRK09778 putative antitoxin of the YafO-YafN toxin-antitoxin system; Provisional
Probab=23.28 E-value=1.3e+02 Score=20.96 Aligned_cols=30 Identities=17% Similarity=0.293 Sum_probs=25.2
Q ss_pred ccceecHHhHHHHhhhHHHHHHhhccCChh
Q 033801 29 ERIETTVAKAKEVRRLADNMVQLGKEGSLC 58 (111)
Q Consensus 29 erI~TT~~KAKelr~~aEklIt~AK~~~~~ 58 (111)
+|-.-|-++-|++-..+|++|.-|+.+|++
T Consensus 64 ~R~~~~~~~~~~i~~~~~~~~~~~~~~d~~ 93 (97)
T PRK09778 64 ARFRPSAARLEEITRRAEKYLNDMTDDDFN 93 (97)
T ss_pred HHcCccHHHHHHHHHHHHHHHHHhhhhhhh
Confidence 344478899999999999999999988865
No 34
>PF10341 TPP1: Shelterin complex subunit, TPP1/ACD; InterPro: IPR019437 EST3 is a component of the telomerase holoenzyme, involved in telomere replication. It has been demonstrated that Est3 dimerises and binds to DNA and RNA. Furthermore, Est3 stimulates the dissociation of RNA/DNA hetero-duplexes [, ]. ; GO: 0042162 telomeric DNA binding, 0007004 telomere maintenance via telomerase, 0032508 DNA duplex unwinding, 0000781 chromosome, telomeric region, 0005697 telomerase holoenzyme complex; PDB: 2I46_B.
Probab=23.20 E-value=41 Score=22.59 Aligned_cols=29 Identities=21% Similarity=0.177 Sum_probs=16.0
Q ss_pred HhhccCCCCeeEEEcccCCCCCCCccccc
Q 033801 82 YRYKDRAGGYTRLLRSRIRVGDAAPMAYI 110 (111)
Q Consensus 82 pRy~~r~GGYTRi~kl~~R~GD~A~maii 110 (111)
.++..+++-|.||++......|++.+|+|
T Consensus 19 ~~~~~~~~q~~ri~~~~~~~~~~~i~a~l 47 (106)
T PF10341_consen 19 IRSNVNPPQLLRILKFAKSTSDGAITALL 47 (106)
T ss_dssp -----EEEEEEEEEE-S---TTS-EEEEE
T ss_pred cccccCCCeEEEEEEEecCCCCCcEEEEE
Confidence 56666788899999997777788888875
No 35
>cd00580 CHMI 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the homoprotocatechuate pathway, one of the microbial meta-fission pathways that degrade aromatic carbon sources to citric acid cycle intermediates. Despite the structural similarity of CHMI with 4-oxalocrotonate tautomerase (4-OT) and macrophage migration inhibitory factor (MIF), there is no significant sequence similarity among these protein families, and therefore, they are not combined in one hierarchy.
Probab=22.48 E-value=1e+02 Score=20.91 Aligned_cols=21 Identities=14% Similarity=0.358 Sum_probs=18.3
Q ss_pred CCCchHHHHHHHHHHHHHHhc
Q 033801 8 NRPTGHRMSMLRTMVSQLVKH 28 (111)
Q Consensus 8 gr~~~hR~~llrnl~t~Li~h 28 (111)
||+.++++++.+.++..|-.+
T Consensus 70 GRs~eqK~~l~~~i~~~l~~~ 90 (113)
T cd00580 70 GRSEEQKQELSEALLAALRAH 90 (113)
T ss_pred CCCHHHHHHHHHHHHHHHHHh
Confidence 899999999999999888554
No 36
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=20.58 E-value=1.4e+02 Score=19.19 Aligned_cols=40 Identities=10% Similarity=0.236 Sum_probs=24.0
Q ss_pred hhhHHHHHHhhccCChhHHHHHHhhcC----ChhHHHHHHHHHH
Q 033801 42 RRLADNMVQLGKEGSLCAARRAAAFVR----GDDVIHKLFTELA 81 (111)
Q Consensus 42 r~~aEklIt~AK~~~~~~~r~a~~~L~----~~~~v~KLf~~l~ 81 (111)
+..+.+||..||+...-+...+...|. +++.+..+|..|.
T Consensus 6 ~~~i~~Li~~gK~~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~ 49 (82)
T PF03979_consen 6 EEAIKKLIEKGKKKGYLTYDEINDALPEDDLDPEQIDEIYDTLE 49 (82)
T ss_dssp HHHHHHHHHHHHHHSS-BHHHHHHH-S-S---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhcCcCCHHHHHHHcCccCCCHHHHHHHHHHHH
Confidence 455678999997644445555555555 4566777766654
No 37
>smart00751 BSD domain in transcription factors and synapse-associated proteins.
Probab=20.29 E-value=73 Score=18.79 Aligned_cols=27 Identities=15% Similarity=0.378 Sum_probs=20.5
Q ss_pred HHHHHhhcCChhHHHHHHHHHHHhhcc
Q 033801 60 ARRAAAFVRGDDVIHKLFTELAYRYKD 86 (111)
Q Consensus 60 ~r~a~~~L~~~~~v~KLf~~l~pRy~~ 86 (111)
...+...|.....+.+++++++|..-+
T Consensus 9 ~~~i~~il~~~p~l~~~~~~lVP~~~s 35 (51)
T smart00751 9 KEEIESLLKENPLLKKLYNELVPKVLS 35 (51)
T ss_pred HHHHHHHHHHCHHHHHHHHHHCCCCCC
Confidence 345567777777899999999996544
Done!