Query psy9119
Match_columns 250
No_of_seqs 171 out of 1254
Neff 3.8
Searched_HMMs 46136
Date Fri Aug 16 19:23:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9119.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9119hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0225 MsrA Peptide methionin 100.0 2.1E-44 4.6E-49 310.3 11.0 115 3-122 42-164 (174)
2 PRK14054 methionine sulfoxide 100.0 8.5E-43 1.8E-47 299.4 12.8 125 2-131 38-171 (172)
3 PRK13014 methionine sulfoxide 100.0 2.7E-42 5.8E-47 299.8 12.8 126 2-131 43-176 (186)
4 PF01625 PMSR: Peptide methion 100.0 1.4E-41 3E-46 287.1 9.9 113 2-119 35-154 (155)
5 PRK00058 methionine sulfoxide 100.0 3.5E-41 7.5E-46 298.1 12.5 115 2-121 80-204 (213)
6 PRK14018 trifunctional thiored 100.0 1E-40 2.2E-45 325.5 13.0 161 2-170 233-432 (521)
7 TIGR00401 msrA methionine-S-su 100.0 1.9E-40 4.1E-45 279.0 11.8 106 2-108 35-148 (149)
8 KOG1635|consensus 100.0 8.5E-40 1.8E-44 282.8 9.9 113 3-119 60-178 (191)
9 PRK05528 methionine sulfoxide 100.0 8.9E-39 1.9E-43 271.1 11.6 107 9-122 38-150 (156)
10 PRK05550 bifunctional methioni 100.0 1.5E-38 3.1E-43 291.2 11.9 114 3-121 163-282 (283)
11 cd04752 Commd4 COMM_Domain con 51.5 27 0.00059 30.1 4.5 34 203-242 55-88 (174)
12 COG0229 Conserved domain frequ 45.1 16 0.00036 31.5 2.2 20 124-143 4-24 (140)
13 PF01641 SelR: SelR domain; I 43.5 16 0.00035 30.6 1.9 19 125-143 1-19 (124)
14 cd04750 Commd2 COMM_Domain con 42.1 47 0.001 28.5 4.5 53 184-243 21-81 (166)
15 PF02617 ClpS: ATP-dependent C 39.9 1E+02 0.0022 23.2 5.6 62 24-88 10-82 (82)
16 KOG4309|consensus 38.0 34 0.00073 31.1 3.1 51 13-63 131-191 (217)
17 KOG0856|consensus 33.2 27 0.00059 30.3 1.7 24 121-144 14-37 (146)
18 PF04963 Sigma54_CBD: Sigma-54 31.2 72 0.0016 27.8 4.0 33 218-250 54-86 (194)
19 PF01402 RHH_1: Ribbon-helix-h 30.5 1E+02 0.0022 19.5 3.8 26 216-241 11-38 (39)
20 KOG0843|consensus 29.7 40 0.00086 30.6 2.2 28 203-234 120-147 (197)
21 PRK04758 hypothetical protein; 28.7 35 0.00075 30.2 1.6 38 199-241 96-133 (181)
22 COG2137 OraA Uncharacterized p 28.7 1.3E+02 0.0028 26.5 5.2 86 129-238 24-109 (174)
23 COG5053 CDC33 Translation init 28.4 1.8E+02 0.004 26.8 6.2 49 33-81 132-189 (217)
24 PRK02166 hypothetical protein; 26.3 39 0.00084 29.9 1.5 37 199-241 99-135 (184)
25 KOG1575|consensus 26.0 1.2E+02 0.0025 29.6 4.8 74 173-247 254-331 (336)
26 TIGR00357 methionine-R-sulfoxi 25.3 54 0.0012 28.0 2.1 45 125-171 4-55 (134)
27 PF13348 Y_phosphatase3C: Tyro 22.2 1.3E+02 0.0029 21.3 3.4 40 199-240 28-67 (68)
28 KOG0427|consensus 22.1 1.1E+02 0.0024 26.7 3.4 33 127-159 7-40 (161)
29 PF11491 DUF3213: Protein of u 21.1 60 0.0013 26.1 1.5 27 15-41 31-57 (88)
30 PRK14134 recX recombination re 21.1 1.8E+02 0.0038 27.1 4.8 45 187-236 103-147 (283)
31 KOG0608|consensus 20.7 1.1E+02 0.0023 33.4 3.6 48 198-245 569-616 (1034)
32 PRK00222 methionine sulfoxide 20.4 63 0.0014 27.9 1.6 45 125-171 7-58 (142)
No 1
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.1e-44 Score=310.27 Aligned_cols=115 Identities=38% Similarity=0.592 Sum_probs=107.5
Q ss_pred CCCCcccccccccCCeeEEEEEEEcCCCCCHHHHHHHHHhhCCCCCC------CCCCcceEEeeCCHhhHHHHHHHHHHH
Q psy9119 3 VISEHRGICTVYSGDHTEVTQVDFDPSVISYKEILRIFWKHHDPTVQ------MKTQYRSMILHVNPEDKEVAEKSLAEE 76 (250)
Q Consensus 3 ~~~tYe~VCsG~~GDHtEaVeV~YDP~vISYeeLLdiFw~~HDPT~~------~g~QYRSaIfy~deeQr~~Ae~s~~~~ 76 (250)
+-|||++||+|.+| |+|+|+|+|||++|||++||++||++||||+. +|+||||+|||+|++|+++|+++++++
T Consensus 42 ~nptY~~Vcsg~Tg-HaE~V~V~yDp~~isy~~LL~~ff~ihDPT~~nrQGnD~GtqYRs~Iy~~~~~q~~~a~~~~~~~ 120 (174)
T COG0225 42 PNPTYEEVCSGTTG-HAEAVEVTYDPKVISYEELLEVFFEIHDPTSLNRQGNDRGTQYRSAIYYTNEEQKAIAEASIEEL 120 (174)
T ss_pred CCCChhhccCCCCC-ceEEEEEEeCCccccHHHHHHHHheecCCCCCCccCCcccccceeEEEEcCHHHHHHHHHHHHHH
Confidence 56999999999875 99999999999999999999999999999987 489999999999999999999999999
Q ss_pred Hh-h-CCCCcEEEeecCcCceeCcccchhHHhhhhcCCCCCCCCcccc
Q psy9119 77 KT-K-HRKPITTLVVPFKRFYDAEEWPRRVSLRRRRNIGNPSPHLSYR 122 (250)
Q Consensus 77 q~-k-~~~~I~TEIepl~~FYpAEdYHQ~YL~K~~~~~p~~yChi~~~ 122 (250)
++ . ++++|+|||+|+++||+||||||+||+| ||++|||++..
T Consensus 121 q~~~~~~~~IvteI~p~~~Fy~AEeYHQ~Yl~K----NP~gY~~~~~~ 164 (174)
T COG0225 121 QASGYFKKPIVTEIEPAKNFYPAEEYHQDYLKK----NPNGYCHIGLT 164 (174)
T ss_pred HHhccCCCCeEEEeeccccCcccHHHHHHHHHh----CCCCceeeccc
Confidence 87 3 4569999999999999999999999999 89999998543
No 2
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=100.00 E-value=8.5e-43 Score=299.39 Aligned_cols=125 Identities=35% Similarity=0.542 Sum_probs=114.3
Q ss_pred CCCCCcccccccccCCeeEEEEEEEcCCCCCHHHHHHHHHhhCCCCCC------CCCCcceEEeeCCHhhHHHHHHHHHH
Q psy9119 2 SVISEHRGICTVYSGDHTEVTQVDFDPSVISYKEILRIFWKHHDPTVQ------MKTQYRSMILHVNPEDKEVAEKSLAE 75 (250)
Q Consensus 2 ~~~~tYe~VCsG~~GDHtEaVeV~YDP~vISYeeLLdiFw~~HDPT~~------~g~QYRSaIfy~deeQr~~Ae~s~~~ 75 (250)
.+-|||++||+|.+| |+|+|+|+|||++|||++||++||++||||+. .|+||||+|||+|++|+++|++++++
T Consensus 38 ~~~PtY~~Vcsg~tg-h~E~V~V~yDp~~isy~~Ll~~f~~~hDPt~~~~Qg~D~G~qYRS~If~~~~~q~~~a~~~~~~ 116 (172)
T PRK14054 38 VENPTYEQVCSGTTG-HAEAVEITYDPAVISYRELLELFFQIHDPTTLNRQGNDRGTQYRSAIFYHDEEQKEIAEASIAE 116 (172)
T ss_pred CCCCChhhcccCCCC-CeEEEEEEECCCcCCHHHHHHHHHHhCCCCccCCCCCCCCcCceeEEEeCCHHHHHHHHHHHHH
Confidence 357999999999875 99999999999999999999999999999986 47999999999999999999999999
Q ss_pred HHhh--CCCCcEEEeecCcCceeCcccchhHHhhhhcCCCCCCCCccccccchh-HHHh
Q psy9119 76 EKTK--HRKPITTLVVPFKRFYDAEEWPRRVSLRRRRNIGNPSPHLSYRSHDSM-TRKT 131 (250)
Q Consensus 76 ~q~k--~~~~I~TEIepl~~FYpAEdYHQ~YL~K~~~~~p~~yChi~~~~~dd~-lk~~ 131 (250)
++++ ++++|+|+|+|+.+||+||+|||+||.| ||++||++.+..+... ||++
T Consensus 117 ~~~~~~~~~~i~Tei~~~~~Fy~AEeyHQ~Yl~k----~p~~~~~~~~~~~~~~~~~~~ 171 (172)
T PRK14054 117 LQASGLFDKPIVTEVEPAETFYEAEEYHQDYLEK----NPNGYCCIFVIPPKVLKKREQ 171 (172)
T ss_pred HHHhcccCCCcEEEEecCCCceECHHHHHHHHHh----CCCCcceeeccCHHHHHHHhc
Confidence 9876 6789999999999999999999999999 6888999988887665 5543
No 3
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=100.00 E-value=2.7e-42 Score=299.78 Aligned_cols=126 Identities=32% Similarity=0.501 Sum_probs=111.6
Q ss_pred CCCCCcccccccccCCeeEEEEEEEcCCCCCHHHHHHHHHhhCCCCCC------CCCCcceEEeeCCHhhHHHHHHHHHH
Q psy9119 2 SVISEHRGICTVYSGDHTEVTQVDFDPSVISYKEILRIFWKHHDPTVQ------MKTQYRSMILHVNPEDKEVAEKSLAE 75 (250)
Q Consensus 2 ~~~~tYe~VCsG~~GDHtEaVeV~YDP~vISYeeLLdiFw~~HDPT~~------~g~QYRSaIfy~deeQr~~Ae~s~~~ 75 (250)
.+-|||++||+|.+| |+|+|+|+|||++|||++||++||++||||+. .|+||||+|||+|++|+++|++++++
T Consensus 43 ~~nPtY~~Vcsg~tg-H~E~V~V~yDp~~iSy~~LL~~Ff~~hDPt~~~~Qg~D~G~QYRS~If~~~~eQ~~~a~~~~~~ 121 (186)
T PRK13014 43 VDNPTYEQVCTGTTG-HAEAVQITYDPKQVSYENLLQIFFSTHDPTQLNRQGPDRGEQYRSAIFYHDEEQKKVAEAYIAQ 121 (186)
T ss_pred CCCCChhhhcCCCCC-ceEEEEEEECCCcCCHHHHHHHHHHhcCCCccCCCCCCCCCCceEEEEeCCHHHHHHHHHHHHH
Confidence 357999999999885 99999999999999999999999999999986 47999999999999999999999999
Q ss_pred HHhh--CCCCcEEEeecCcCceeCcccchhHHhhhhcCCCCCCCCccccccchhHHHh
Q psy9119 76 EKTK--HRKPITTLVVPFKRFYDAEEWPRRVSLRRRRNIGNPSPHLSYRSHDSMTRKT 131 (250)
Q Consensus 76 ~q~k--~~~~I~TEIepl~~FYpAEdYHQ~YL~K~~~~~p~~yChi~~~~~dd~lk~~ 131 (250)
++++ ++++|+|+|+|+.+||+||+|||+||+|+ |.+||||+......+.+++.
T Consensus 122 ~~~~~~~~~~i~Tei~p~~~Fy~AEeyHQ~Yl~k~---p~~~yc~~~~~~~~~~~~~~ 176 (186)
T PRK13014 122 LDEAGIFKKPIVTPIKPYKNFYPAEDYHQDYLKKN---PTHPYIVYNDLPKGSGLKAF 176 (186)
T ss_pred HHhccccCCCcEEEEecCCCeeeCHHHHHHHHHhC---CCCCccEEEeChhhhhHHHH
Confidence 8763 67899999999999999999999999995 56699999765433334443
No 4
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=100.00 E-value=1.4e-41 Score=287.13 Aligned_cols=113 Identities=40% Similarity=0.624 Sum_probs=100.2
Q ss_pred CCCCCcccccccccCCeeEEEEEEEcCCCCCHHHHHHHHHhhCCCCCC------CCCCcceEEeeCCHhhHHHHHHHHHH
Q psy9119 2 SVISEHRGICTVYSGDHTEVTQVDFDPSVISYKEILRIFWKHHDPTVQ------MKTQYRSMILHVNPEDKEVAEKSLAE 75 (250)
Q Consensus 2 ~~~~tYe~VCsG~~GDHtEaVeV~YDP~vISYeeLLdiFw~~HDPT~~------~g~QYRSaIfy~deeQr~~Ae~s~~~ 75 (250)
.+-|||++||+|.+ ||+|||+|+|||++|||++||++||++||||+. .|+||||+|||+|++|+++|++++++
T Consensus 35 ~~~PtY~~v~~g~t-gh~E~V~V~yD~~~is~~~Ll~~f~~~~dPt~~~~Qg~d~G~qYrs~If~~~~~q~~~a~~~~~~ 113 (155)
T PF01625_consen 35 TPNPTYRQVCSGRT-GHAEAVRVTYDPSVISYEELLDVFFRIHDPTQVNGQGNDRGTQYRSAIFYHDEEQKKIAEASIAE 113 (155)
T ss_dssp SSS--HHHHHTTTT-T-EEEEEEEEETTTS-HHHHHHHHHHHS-TTSTSEETTEESGGG-EEEEESSHHHHHHHHHHHHH
T ss_pred CCCCcceeeecCCC-CCeEEEEEEECCCcccHHHHHHHHHHhcCCcccccccCcccccceeEEecCCHHHHHHHHHHHHH
Confidence 35699999999986 599999999999999999999999999999984 58999999999999999999999999
Q ss_pred HHhh-CCCCcEEEeecCcCceeCcccchhHHhhhhcCCCCCCCCc
Q psy9119 76 EKTK-HRKPITTLVVPFKRFYDAEEWPRRVSLRRRRNIGNPSPHL 119 (250)
Q Consensus 76 ~q~k-~~~~I~TEIepl~~FYpAEdYHQ~YL~K~~~~~p~~yChi 119 (250)
++++ ++++|+|+|+|+++||+||+|||+||.| +|.+|||+
T Consensus 114 ~~~~~~~~~i~tei~p~~~Fy~AE~yHQ~Yl~k----~p~~yc~~ 154 (155)
T PF01625_consen 114 LQAKRFGRPIVTEIEPLKNFYPAEEYHQKYLEK----NPNGYCHY 154 (155)
T ss_dssp HHHHTTSSSBS-EEEECEEEEEHHGGGTTHHHH----STTSTTSS
T ss_pred HHHhcCCCCeEEEEecCCcEEECHHHHHHHHHh----CCcccEec
Confidence 9999 8899999999999999999999999999 67779997
No 5
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=100.00 E-value=3.5e-41 Score=298.12 Aligned_cols=115 Identities=37% Similarity=0.580 Sum_probs=106.4
Q ss_pred CCCCCcccccccccCCeeEEEEEEEcCCCCCHHHHHHHHHhhCCCCCC------CCCCcceEEeeCCHhhHHHHHHHHHH
Q psy9119 2 SVISEHRGICTVYSGDHTEVTQVDFDPSVISYKEILRIFWKHHDPTVQ------MKTQYRSMILHVNPEDKEVAEKSLAE 75 (250)
Q Consensus 2 ~~~~tYe~VCsG~~GDHtEaVeV~YDP~vISYeeLLdiFw~~HDPT~~------~g~QYRSaIfy~deeQr~~Ae~s~~~ 75 (250)
.+-|||++||+|.+| |+|+|+|+|||++|||++||++||++||||+. .|+||||+|||+|++|+++|++++++
T Consensus 80 ~~~PtY~~VcsG~tg-H~EaV~V~YDp~~ISy~~LL~~Ff~~hDPt~~n~QG~D~G~QYRS~Ify~~~eQ~~~a~~~~~~ 158 (213)
T PRK00058 80 TPNPTYREVCSGRTG-HAEVVRVVYDPAVISYEQLLQVFWENHDPTQGMRQGNDVGTQYRSAIYTLTPEQLAAAEASREA 158 (213)
T ss_pred CCCCChhhcccCCCC-CeEEEEEEECCccCCHHHHHHHHHHhcCCcccCCCCCCCCcCceEEEEeCCHHHHHHHHHHHHH
Confidence 357999999999875 99999999999999999999999999999986 47999999999999999999999999
Q ss_pred HHhhC----CCCcEEEeecCcCceeCcccchhHHhhhhcCCCCCCCCccc
Q psy9119 76 EKTKH----RKPITTLVVPFKRFYDAEEWPRRVSLRRRRNIGNPSPHLSY 121 (250)
Q Consensus 76 ~q~k~----~~~I~TEIepl~~FYpAEdYHQ~YL~K~~~~~p~~yChi~~ 121 (250)
+++++ .++|+|+|+|++.||+||+|||+||+| +|++||||+.
T Consensus 159 ~~~~~~~~~~~~i~TeI~~~~~Fy~AEeyHQ~Yl~k----~p~~yc~~~~ 204 (213)
T PRK00058 159 YQQALAAAGDGPITTEIAPAPPFYYAEDYHQQYLAK----NPNGYCGLGG 204 (213)
T ss_pred HHHHhhhccCCCeEEEEecCCCcccCHHHHHHHHHh----CCCCccccCC
Confidence 98765 247999999999999999999999999 6889999864
No 6
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=100.00 E-value=1e-40 Score=325.49 Aligned_cols=161 Identities=26% Similarity=0.348 Sum_probs=136.0
Q ss_pred CCCCCcccccccccCCeeEEEEEEEcCCCCCHHHHHHHHHhhCCCCCC------CCCCcceEEeeCCHhhHHHHHHHHHH
Q psy9119 2 SVISEHRGICTVYSGDHTEVTQVDFDPSVISYKEILRIFWKHHDPTVQ------MKTQYRSMILHVNPEDKEVAEKSLAE 75 (250)
Q Consensus 2 ~~~~tYe~VCsG~~GDHtEaVeV~YDP~vISYeeLLdiFw~~HDPT~~------~g~QYRSaIfy~deeQr~~Ae~s~~~ 75 (250)
.+-|||++||+| + ||+|+|+|+|||++|||++||++||++||||+. .|+||||+|||+|++|+++|++++++
T Consensus 233 ~~~PtY~~Vc~g-t-gH~E~V~V~yDp~~is~~~Ll~~f~~~~dPt~~~~Qg~d~G~qYrs~I~~~~~eq~~~a~~~~~~ 310 (521)
T PRK14018 233 TKNPSYEDVYRH-S-GHAETVKVTYDADKLSLDTILQYYFRVVDPTSLNKQGNDTGTQYRSGVYYTDPADKAVIAAALKR 310 (521)
T ss_pred CCCCChhhccCC-C-CcEEEEEEEECCCcCcHHHHHHHHHHhCCCccccccCCCCCCCceEEEEeCCHHHHHHHHHHHHH
Confidence 357999999999 5 599999999999999999999999999999975 57999999999999999999999999
Q ss_pred HHhhCCCCcEEEeecCcCceeCcccchhHHhhhhcCCCCCCCCcccccc-------------------------chh-HH
Q psy9119 76 EKTKHRKPITTLVVPFKRFYDAEEWPRRVSLRRRRNIGNPSPHLSYRSH-------------------------DSM-TR 129 (250)
Q Consensus 76 ~q~k~~~~I~TEIepl~~FYpAEdYHQ~YL~K~~~~~p~~yChi~~~~~-------------------------dd~-lk 129 (250)
++++++++|+|||+|+.+||+||+|||+||.| +|++|||+++... +++ +|
T Consensus 311 ~~~~~~~~i~tei~~~~~Fy~AE~yHQ~Yl~k----~p~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 386 (521)
T PRK14018 311 EQQKYQLPLVVENEPLKNFYDAEEYHQDYLIK----NPNGYCHIDLRKADEPLPGKTKTAPQGKGFDAATYKKPSDAELK 386 (521)
T ss_pred HHHHcCCCeEEEEecCCCeeecHHHHHHHHHh----CCCceeEeecccccccccccccccccccccchhhccCCChHHHh
Confidence 99989999999999999999999999999999 6889999966532 444 89
Q ss_pred HhhhHHHHHHHHHHHH-------hhcCCCCCCcchhhccccccccccc
Q psy9119 130 KTLRASAQVELQERRL-------LQNLPPSGTPERLCRGLNNRLLFSL 170 (250)
Q Consensus 130 ~~l~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~ 170 (250)
++||++|+.+|+|.-- +.+....|+ =.|++-++-|.-|-
T Consensus 387 ~~Lt~~~y~v~~~~gtE~~f~~~~~~~~~~G~--y~c~~c~~pLf~s~ 432 (521)
T PRK14018 387 RTLTEEQYQITQNAATERAFSHEYDHLFKPGI--YVDVVSGEPLFSSA 432 (521)
T ss_pred ccCCHHHHHHHHhcCCCCCCCCCCcCCCCCEE--EEecCCCCccccCc
Confidence 9999999999998631 112222222 35666666665543
No 7
>TIGR00401 msrA methionine-S-sulfoxide reductase. This model describes peptide methionine sulfoxide reductase (MsrA), a repair enzyme for proteins that have been inactivated by oxidation. The enzyme from E. coli is coextensive with this model and has enzymatic activity. However, in all completed genomes in which this module is present, a second protein module, described in TIGR00357, is also found, and in several cases as part of the same polypeptide chain: N-terminal to this module in Helicobacter pylori and Haemophilus influenzae (as in PilB of Neisseria gonorrhoeae) but C-terminal to it in Treponema pallidum. PilB, containing both domains, has been shown to be important for the expression of adhesins in certain pathogens.
Probab=100.00 E-value=1.9e-40 Score=279.01 Aligned_cols=106 Identities=35% Similarity=0.567 Sum_probs=99.8
Q ss_pred CCCCCcccccccccCCeeEEEEEEEcCCCCCHHHHHHHHHhhCCCCCC------CCCCcceEEeeCCHhhHHHHHHHHHH
Q psy9119 2 SVISEHRGICTVYSGDHTEVTQVDFDPSVISYKEILRIFWKHHDPTVQ------MKTQYRSMILHVNPEDKEVAEKSLAE 75 (250)
Q Consensus 2 ~~~~tYe~VCsG~~GDHtEaVeV~YDP~vISYeeLLdiFw~~HDPT~~------~g~QYRSaIfy~deeQr~~Ae~s~~~ 75 (250)
.+-|||++||+|.+ ||+|+|+|+|||++|||++||++||++||||+. .|+||||+|||+|++|+++|++++++
T Consensus 35 ~~~PtY~~Vc~g~t-gh~E~V~V~yDp~~is~~~Ll~~f~~~hdPt~~~~Qg~d~G~qYRs~If~~~~~q~~~a~~~~~~ 113 (149)
T TIGR00401 35 TPNPTYEEVCSGDT-GHAEAVQVTYDPKVISYEELLDVFWEIHDPTQGNRQGNDIGTQYRSGIYYHSDEQEKAARASKER 113 (149)
T ss_pred CCCCChhhcccCCC-CceEEEEEEECCCcCcHHHHHHHHHHhCCCCcCCCCCCCCCCCceEEEEeCCHHHHHHHHHHHHH
Confidence 46799999999987 599999999999999999999999999999975 47999999999999999999999999
Q ss_pred HHh--hCCCCcEEEeecCcCceeCcccchhHHhhh
Q psy9119 76 EKT--KHRKPITTLVVPFKRFYDAEEWPRRVSLRR 108 (250)
Q Consensus 76 ~q~--k~~~~I~TEIepl~~FYpAEdYHQ~YL~K~ 108 (250)
+++ .++++|+|+|+|+++||+||+|||+||+|+
T Consensus 114 ~~~~~~~~~~i~tei~~~~~Fy~AE~yHQ~Yl~k~ 148 (149)
T TIGR00401 114 LQAAANYGDPIVTEIEPAENFYYAEEYHQQYLKKN 148 (149)
T ss_pred HHHhcccCCCeEEEEecCCCeeecHHHHHHHHhhC
Confidence 987 567899999999999999999999999994
No 8
>KOG1635|consensus
Probab=100.00 E-value=8.5e-40 Score=282.75 Aligned_cols=113 Identities=36% Similarity=0.605 Sum_probs=105.7
Q ss_pred CCCCcccccccccCCeeEEEEEEEcCCCCCHHHHHHHHHhhCCCCCCC------CCCcceEEeeCCHhhHHHHHHHHHHH
Q psy9119 3 VISEHRGICTVYSGDHTEVTQVDFDPSVISYKEILRIFWKHHDPTVQM------KTQYRSMILHVNPEDKEVAEKSLAEE 76 (250)
Q Consensus 3 ~~~tYe~VCsG~~GDHtEaVeV~YDP~vISYeeLLdiFw~~HDPT~~~------g~QYRSaIfy~deeQr~~Ae~s~~~~ 76 (250)
.=|||++||+|.+ +|+|+|+|+|||++|||++||++||++||||+.+ |+||||+||+++++|.++|+.++++.
T Consensus 60 ~nPtYk~vc~~tT-~HaEvvrV~ydpk~~sy~~Lld~Fw~~HdPtt~n~QG~D~GtQYRS~I~~~s~eq~k~A~~s~e~~ 138 (191)
T KOG1635|consen 60 DNPTYKDVCSGTT-NHAEVVRVQYDPKVISYEELLDFFWSRHDPTTLNRQGNDVGTQYRSGIYTYSPEQEKLARESKERE 138 (191)
T ss_pred CCcchhhhccCCC-CcceEEEEEeCcccccHHHHHHHHHHcCCchhhhccCCcccceeeeeeeeCCHHHHHHHHHHHHHH
Confidence 4589999999987 5999999999999999999999999999999874 69999999999999999999999999
Q ss_pred HhhCCCCcEEEeecCcCceeCcccchhHHhhhhcCCCCCCCCc
Q psy9119 77 KTKHRKPITTLVVPFKRFYDAEEWPRRVSLRRRRNIGNPSPHL 119 (250)
Q Consensus 77 q~k~~~~I~TEIepl~~FYpAEdYHQ~YL~K~~~~~p~~yChi 119 (250)
|++..++|+|+|+|+++||.||||||+||.|+ ++.|||..
T Consensus 139 Q~k~~~kI~T~I~p~~kFY~AE~yHQqYl~K~---~~~Gy~~s 178 (191)
T KOG1635|consen 139 QKKWNGKIVTEILPAKKFYRAEEYHQQYLSKN---PRNGYAQS 178 (191)
T ss_pred HhccCCcceEEEeeccchhhchHHHHHHHhhC---CCCccccc
Confidence 99989999999999999999999999999994 44888765
No 9
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=100.00 E-value=8.9e-39 Score=271.06 Aligned_cols=107 Identities=16% Similarity=0.260 Sum_probs=98.0
Q ss_pred cccccccCCeeEEEEEEEcCCCCCHHHHHHHHHhhCCCCCC------CCCCcceEEeeCCHhhHHHHHHHHHHHHhhCCC
Q psy9119 9 GICTVYSGDHTEVTQVDFDPSVISYKEILRIFWKHHDPTVQ------MKTQYRSMILHVNPEDKEVAEKSLAEEKTKHRK 82 (250)
Q Consensus 9 ~VCsG~~GDHtEaVeV~YDP~vISYeeLLdiFw~~HDPT~~------~g~QYRSaIfy~deeQr~~Ae~s~~~~q~k~~~ 82 (250)
++|+|.+ ||+|+|+|+|||++|||++||++||++||||+. .|+||||+|||+|++|+++|+++++++++ .+
T Consensus 38 ~p~~~~t-gH~E~V~V~yDp~~isy~~LL~~f~~~hdPt~~~~Qg~D~G~QYRS~If~~d~eQ~~~a~~~~~~~~~--~~ 114 (156)
T PRK05528 38 TLDGPYD-GYAECVKTHFDPRMVSITDLMGYLFEIIDPYSVNKQGNDVGEKYRTGIYSEVDDHLIEARQFIERRED--AD 114 (156)
T ss_pred CCCCCCC-CcEEEEEEEECCCcCCHHHHHHHHHHhCCcccccccCCCCCCCceEEEEeCCHHHHHHHHHHHHHHhc--CC
Confidence 4677875 599999999999999999999999999999975 47999999999999999999999988765 46
Q ss_pred CcEEEeecCcCceeCcccchhHHhhhhcCCCCCCCCcccc
Q psy9119 83 PITTLVVPFKRFYDAEEWPRRVSLRRRRNIGNPSPHLSYR 122 (250)
Q Consensus 83 ~I~TEIepl~~FYpAEdYHQ~YL~K~~~~~p~~yChi~~~ 122 (250)
+|+|+|+|+.+||+||+|||+||+| +|.+|||++..
T Consensus 115 ~i~Tei~~~~~Fy~AE~yHQ~Yl~k----~p~~yc~~~~~ 150 (156)
T PRK05528 115 KIAVEVLPLTNYVKSAEEHQDRLEK----FPEDYCHIPKD 150 (156)
T ss_pred CeEEEEecCCCeeecHHHHHHHHHh----CCCCCcccChH
Confidence 8999999999999999999999999 68899999743
No 10
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=100.00 E-value=1.5e-38 Score=291.16 Aligned_cols=114 Identities=34% Similarity=0.537 Sum_probs=104.6
Q ss_pred CCCCcccccccccCCeeEEEEEEEcCCCCCHHHHHHHHHhhCCCCCC------CCCCcceEEeeCCHhhHHHHHHHHHHH
Q psy9119 3 VISEHRGICTVYSGDHTEVTQVDFDPSVISYKEILRIFWKHHDPTVQ------MKTQYRSMILHVNPEDKEVAEKSLAEE 76 (250)
Q Consensus 3 ~~~tYe~VCsG~~GDHtEaVeV~YDP~vISYeeLLdiFw~~HDPT~~------~g~QYRSaIfy~deeQr~~Ae~s~~~~ 76 (250)
+-|||++||+|.+ ||+|||+|+|||++|||++||++||++||||+. +|+||||+|||+|++|+++|+++++++
T Consensus 163 ~nPtY~~VcsG~t-gH~EaV~V~yDp~~isy~~LL~~F~~~hDPt~~~~Qg~D~G~QYRS~If~~d~eq~~~A~~~~~~~ 241 (283)
T PRK05550 163 KNPTYEQVCSGTT-GHAEAVRVEFDPAKISYETLLKVFFEIHDPTQLNRQGPDIGTQYRSAIFYHDDEQKQIAEKLIAEL 241 (283)
T ss_pred CCCChhhcccCCC-CCeEEEEEEECCccCCHHHHHHHHHhhcCCCccCCCCCCCCcCceEEEEeCCHHHHHHHHHHHHHH
Confidence 5699999999986 599999999999999999999999999999975 579999999999999999999999999
Q ss_pred HhhCCCCcEEEeecCcCceeCcccchhHHhhhhcCCCCCCCCccc
Q psy9119 77 KTKHRKPITTLVVPFKRFYDAEEWPRRVSLRRRRNIGNPSPHLSY 121 (250)
Q Consensus 77 q~k~~~~I~TEIepl~~FYpAEdYHQ~YL~K~~~~~p~~yChi~~ 121 (250)
+++. .+|+|+|+|+++||+||+|||+||.|+ |.++|||++.
T Consensus 242 ~~~~-~~i~TeI~~l~~Fy~AEeyHQ~Yl~k~---p~~~yc~~~~ 282 (283)
T PRK05550 242 TKKG-YPVVTEVEAAGPFYPAEDYHQDYYEKH---GKQPYCHIVV 282 (283)
T ss_pred HhcC-CceEEEEeeCCCeeECHHHHHHHHHhC---CCCCeeeeeC
Confidence 8753 489999999999999999999999995 4446999873
No 11
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=51.46 E-value=27 Score=30.06 Aligned_cols=34 Identities=24% Similarity=0.290 Sum_probs=28.7
Q ss_pred HHHHhccccccCChhhHHHHHHhcCCCHHHHHHHHHHHHh
Q psy9119 203 AARLNGYVVGFGGIKQFEEEADQLGLSEDVKNYVRKYVKR 242 (250)
Q Consensus 203 ~~~~n~~~~g~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 242 (250)
|+|.| -+.++|.+|+.++||+++..+.+.+....
T Consensus 55 A~k~n------~~~~~l~~eL~~lglp~e~~~~l~~~~~~ 88 (174)
T cd04752 55 AAKYN------VDGESLSSELQQLGLPKEHATSLCRSYEE 88 (174)
T ss_pred HHHcC------CCHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 56666 68999999999999999999988776654
No 12
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=45.07 E-value=16 Score=31.48 Aligned_cols=20 Identities=10% Similarity=0.036 Sum_probs=16.9
Q ss_pred cch-hHHHhhhHHHHHHHHHH
Q psy9119 124 HDS-MTRKTLRASAQVELQER 143 (250)
Q Consensus 124 ~dd-~lk~~l~~~~~~~~~~~ 143 (250)
+.| .+|++||++|+++||+.
T Consensus 4 ~sd~e~~~~Lt~~qy~Vtq~~ 24 (140)
T COG0229 4 PSDEELKEKLTPEQYRVTQNH 24 (140)
T ss_pred cchHHHHHhcCHHHHHHHHhc
Confidence 344 49999999999999985
No 13
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=43.48 E-value=16 Score=30.65 Aligned_cols=19 Identities=32% Similarity=0.307 Sum_probs=16.4
Q ss_pred chhHHHhhhHHHHHHHHHH
Q psy9119 125 DSMTRKTLRASAQVELQER 143 (250)
Q Consensus 125 dd~lk~~l~~~~~~~~~~~ 143 (250)
|+.+|++||++|+++|++.
T Consensus 1 d~ew~~~Lt~~qy~V~r~~ 19 (124)
T PF01641_consen 1 DEEWRKRLTPEQYRVLREK 19 (124)
T ss_dssp -HHHHHHSCHHHHHHHHHT
T ss_pred CHHHHhhCCHHHHHHHHhc
Confidence 4569999999999999985
No 14
>cd04750 Commd2 COMM_Domain containing protein 2. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=42.08 E-value=47 Score=28.55 Aligned_cols=53 Identities=17% Similarity=0.288 Sum_probs=39.1
Q ss_pred ccccccCCCChhhhhhh--------hHHHHHhccccccCChhhHHHHHHhcCCCHHHHHHHHHHHHhh
Q psy9119 184 ELQPKLNFKSEDCYKTS--------HLAARLNGYVVGFGGIKQFEEEADQLGLSEDVKNYVRKYVKRY 243 (250)
Q Consensus 184 ~~~~~~~~~~~~~~~~s--------~~~~~~n~~~~g~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 243 (250)
....+|++..+ .++.. .-|+|+| .+-.+|..++.++|++++.++.+-+....+
T Consensus 21 ~~A~~l~i~~~-~vk~~v~aL~~ll~~a~K~~------l~~~~~~~~L~~l~~~~e~~~~l~~~y~~~ 81 (166)
T cd04750 21 GAARKLEVEVE-TVQHGVEALVYLLIESTKLK------LSERDFQDSIEFLGFSDDLNEILLQLYESN 81 (166)
T ss_pred HHHHHhCCCHH-HHHHHHHHHHHHHHHHHhcc------CCHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 35567776544 44433 2367777 678999999999999999999988866543
No 15
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins []. ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
Probab=39.87 E-value=1e+02 Score=23.17 Aligned_cols=62 Identities=11% Similarity=0.243 Sum_probs=42.0
Q ss_pred EEEcCCCCCHHHHHHHHHhhCCCCCC-----------CCCCcceEEeeCCHhhHHHHHHHHHHHHhhCCCCcEEEe
Q psy9119 24 VDFDPSVISYKEILRIFWKHHDPTVQ-----------MKTQYRSMILHVNPEDKEVAEKSLAEEKTKHRKPITTLV 88 (250)
Q Consensus 24 V~YDP~vISYeeLLdiFw~~HDPT~~-----------~g~QYRSaIfy~deeQr~~Ae~s~~~~q~k~~~~I~TEI 88 (250)
|.||.++-||+..+.......+.+.. .| |++|+..+.++.+.....+.+.....+.|+.+.|
T Consensus 10 vL~NDe~ht~~~Vi~~L~~~~~~s~~~A~~~a~~v~~~G---~avv~~~~~e~ae~~~~~l~~~g~~~~~PL~~ti 82 (82)
T PF02617_consen 10 VLWNDEVHTFEQVIDVLRRVFGCSEEQARQIAMEVHREG---RAVVGTGSREEAEEYAEKLQRAGRDSGHPLRATI 82 (82)
T ss_dssp EEE--SSSBHHHHHHHHHHHC---HHHHHHHHHHHHHHS---EEEEEEEEHHHHHHHHHHHHHHHHHTT---EEEE
T ss_pred EEEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhHcC---CEeeeeCCHHHHHHHHHHHHHHhhccCCCeEEeC
Confidence 78999999999999999998876643 24 3888888888777777777776655667777665
No 16
>KOG4309|consensus
Probab=38.01 E-value=34 Score=31.14 Aligned_cols=51 Identities=20% Similarity=0.348 Sum_probs=34.4
Q ss_pred cccCCee--EEEEEEEcCCCCC------HHHHHHHHHhhCCCCCC--CCCCcceEEeeCCH
Q psy9119 13 VYSGDHT--EVTQVDFDPSVIS------YKEILRIFWKHHDPTVQ--MKTQYRSMILHVNP 63 (250)
Q Consensus 13 G~~GDHt--EaVeV~YDP~vIS------YeeLLdiFw~~HDPT~~--~g~QYRSaIfy~de 63 (250)
..+|-|. =+|+|+|||.+|- ..+.|.-||..|-|+.+ .|.+=...||---|
T Consensus 131 vTmg~tvKGi~vEIEY~pcvI~~~Cw~M~~Eflqsflg~~~p~aP~~fg~t~h~~~y~p~D 191 (217)
T KOG4309|consen 131 VTMGPTVKGISVEIEYGPCVIASDCWSMLLEFLQSFLGSHTPGAPAVFGNTRHDAVYGPAD 191 (217)
T ss_pred eEeccccceEEEEEeeCCEEEhHHHHHHHHHHHHHHhcccCCCchHhhcCccCccccCcHH
Confidence 3444444 5789999999985 35778888888888854 55554455554433
No 17
>KOG0856|consensus
Probab=33.15 E-value=27 Score=30.33 Aligned_cols=24 Identities=25% Similarity=0.244 Sum_probs=19.9
Q ss_pred ccccchhHHHhhhHHHHHHHHHHH
Q psy9119 121 YRSHDSMTRKTLRASAQVELQERR 144 (250)
Q Consensus 121 ~~~~dd~lk~~l~~~~~~~~~~~~ 144 (250)
..+.++..|+.|||+|+++|+|.-
T Consensus 14 v~k~~~EWr~~LsPeQ~~v~Rekg 37 (146)
T KOG0856|consen 14 VQKNDEEWRKVLSPEQFRVLREKG 37 (146)
T ss_pred cccCHHHHHhhcCHHHhhhhHhhc
Confidence 345667799999999999999863
No 18
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=31.17 E-value=72 Score=27.78 Aligned_cols=33 Identities=27% Similarity=0.415 Sum_probs=25.8
Q ss_pred hHHHHHHhcCCCHHHHHHHHHHHHhhCCCCccC
Q psy9119 218 QFEEEADQLGLSEDVKNYVRKYVKRYEGSGMMC 250 (250)
Q Consensus 218 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 250 (250)
..++-++.+|+|++....+.+.+..-+-.|+.|
T Consensus 54 ~~~eia~~l~~~~~~v~~~l~~lQ~leP~GigA 86 (194)
T PF04963_consen 54 SLEEIAEELGVSEEEVEKALELLQSLEPAGIGA 86 (194)
T ss_dssp -HHHHHHHCTS-HHHHHHHHHHHHTTSS--TTT
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHcCCCCccCc
Confidence 567778999999999999999999999888764
No 19
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=30.54 E-value=1e+02 Score=19.51 Aligned_cols=26 Identities=27% Similarity=0.615 Sum_probs=17.9
Q ss_pred hhhHHHHHHhcCCCHH--HHHHHHHHHH
Q psy9119 216 IKQFEEEADQLGLSED--VKNYVRKYVK 241 (250)
Q Consensus 216 ~~~~~~~~~~~~l~~~--~~~~~~~~~~ 241 (250)
.+.|++.+...|+|-. +...|+.|++
T Consensus 11 ~~~l~~~a~~~g~s~s~~ir~ai~~~l~ 38 (39)
T PF01402_consen 11 YERLDELAKELGRSRSELIREAIREYLE 38 (39)
T ss_dssp HHHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHHHHh
Confidence 3567888888888765 4555666654
No 20
>KOG0843|consensus
Probab=29.69 E-value=40 Score=30.61 Aligned_cols=28 Identities=39% Similarity=0.401 Sum_probs=22.2
Q ss_pred HHHHhccccccCChhhHHHHHHhcCCCHHHHH
Q psy9119 203 AARLNGYVVGFGGIKQFEEEADQLGLSEDVKN 234 (250)
Q Consensus 203 ~~~~n~~~~g~~~~~~~~~~~~~~~l~~~~~~ 234 (250)
|-.=|+|||| ..-++.|..|||||.+..
T Consensus 120 ~F~~~~Yvvg----~eR~~LA~~L~LsetQVk 147 (197)
T KOG0843|consen 120 AFEGNQYVVG----AERKQLAQSLSLSETQVK 147 (197)
T ss_pred HHhcCCeeec----hHHHHHHHHcCCChhHhh
Confidence 4445999999 467788999999998654
No 21
>PRK04758 hypothetical protein; Validated
Probab=28.71 E-value=35 Score=30.17 Aligned_cols=38 Identities=21% Similarity=0.323 Sum_probs=26.0
Q ss_pred hhhHHHHHhccccccCChhhHHHHHHhcCCCHHHHHHHHHHHH
Q psy9119 199 TSHLAARLNGYVVGFGGIKQFEEEADQLGLSEDVKNYVRKYVK 241 (250)
Q Consensus 199 ~s~~~~~~n~~~~g~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 241 (250)
...|+...|||+.|||-... +.-.+|+++++.++.+.+
T Consensus 96 a~AL~~W~~gFL~G~Gl~~~-----~~~~~s~e~~E~L~Dl~~ 133 (181)
T PRK04758 96 ADALFDWCRAFLGGFGLAAQ-----QRPALSEEGEEALQDLAR 133 (181)
T ss_pred HHHHHHHHHHHHHHHHhhcc-----ccccCCHHHHHHHHHHHH
Confidence 45677788999999986542 333466777777766654
No 22
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=28.65 E-value=1.3e+02 Score=26.46 Aligned_cols=86 Identities=14% Similarity=0.272 Sum_probs=58.3
Q ss_pred HHhhhHHHHHHHHHHHHhhcCCCCCCcchhhcccccccccccccccccchhccccccccccCCCChhhhhhhhHHHHHhc
Q psy9119 129 RKTLRASAQVELQERRLLQNLPPSGTPERLCRGLNNRLLFSLHSYHQKYRLRQHSELQPKLNFKSEDCYKTSHLAARLNG 208 (250)
Q Consensus 129 k~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~hqk~~l~~~~~~~~~~~~~~~~~~~~s~~~~~~n~ 208 (250)
..-|....+++.-|..|-..|-+-|.++.+-.-.= .-+...|+-++..|..+-+..|.+.
T Consensus 24 ~~Al~~Ls~R~rse~ELr~kL~k~~~~~~~Ie~Vi--------------------~~l~~~~~ldD~~fAe~~i~~r~~~ 83 (174)
T COG2137 24 NRALRLLSRRDRSEKELRRKLAKKEFSEEIIEEVI--------------------DRLAEEGYLDDTRFAEAYIRSRSRK 83 (174)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHH--------------------HHHHHcCcccHHHHHHHHHHHHHhc
Confidence 44566666666666666666666666655411110 1123456667778989999888874
Q ss_pred cccccCChhhHHHHHHhcCCCHHHHHHHHH
Q psy9119 209 YVVGFGGIKQFEEEADQLGLSEDVKNYVRK 238 (250)
Q Consensus 209 ~~~g~~~~~~~~~~~~~~~l~~~~~~~~~~ 238 (250)
| .|+..+..|+.+.|++++....+..
T Consensus 84 ---g-~G~~rl~qeL~qkGi~~~~Ie~aL~ 109 (174)
T COG2137 84 ---G-KGPARLKQELKQKGIDDEIIEEALE 109 (174)
T ss_pred ---c-cChHHHHHHHHHcCCCHHHHHHHHh
Confidence 6 6889999999999999998776554
No 23
>COG5053 CDC33 Translation initiation factor 4E (eIF-4E) [Translation, ribosomal structure and biogenesis]
Probab=28.40 E-value=1.8e+02 Score=26.76 Aligned_cols=49 Identities=24% Similarity=0.179 Sum_probs=39.2
Q ss_pred HHHHHHHHHhhCCCCCC---------CCCCcceEEeeCCHhhHHHHHHHHHHHHhhCC
Q psy9119 33 YKEILRIFWKHHDPTVQ---------MKTQYRSMILHVNPEDKEVAEKSLAEEKTKHR 81 (250)
Q Consensus 33 YeeLLdiFw~~HDPT~~---------~g~QYRSaIfy~deeQr~~Ae~s~~~~q~k~~ 81 (250)
...||-..++..|||.. ++.-|+-+|+..+...++...+...++.+.++
T Consensus 132 l~tlla~igeT~Dp~~~ei~GvV~n~rkgfyKlAiWtr~~~n~dvl~~ig~efk~vl~ 189 (217)
T COG5053 132 LRTLLAAIGETLDPTGSEIGGVVGNMRKGFYKLAIWTRNCNNKDVLGAIGNEFKQVLE 189 (217)
T ss_pred HHHHHHHHhhccCCCCCeeccEEEEeecCceEEEEEecCCCcHHHHHHHHHHHHhccc
Confidence 34567778899999753 35789999999999999999998888776543
No 24
>PRK02166 hypothetical protein; Reviewed
Probab=26.26 E-value=39 Score=29.90 Aligned_cols=37 Identities=22% Similarity=0.321 Sum_probs=27.0
Q ss_pred hhhHHHHHhccccccCChhhHHHHHHhcCCCHHHHHHHHHHHH
Q psy9119 199 TSHLAARLNGYVVGFGGIKQFEEEADQLGLSEDVKNYVRKYVK 241 (250)
Q Consensus 199 ~s~~~~~~n~~~~g~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 241 (250)
...|+...|||+.|||-.... -.+|+++++.++.+.+
T Consensus 99 a~AL~~W~~gFL~G~Gl~~~~------~~~s~e~~E~l~Dl~~ 135 (184)
T PRK02166 99 AAALGQWCQGFLAGFGLNAGG------KDLSGEAKEVLQDLAA 135 (184)
T ss_pred HHHHHHHHHHHHHHHHhccCc------cCCCHHHHHHHHHHHH
Confidence 456778889999999976321 1478888888877654
No 25
>KOG1575|consensus
Probab=25.99 E-value=1.2e+02 Score=29.60 Aligned_cols=74 Identities=16% Similarity=0.152 Sum_probs=53.6
Q ss_pred ccccchhccccccccccCCCChhhhhhhhHHHHHhcc--ccccCChhhHHHHHH--hcCCCHHHHHHHHHHHHhhCCCC
Q psy9119 173 YHQKYRLRQHSELQPKLNFKSEDCYKTSHLAARLNGY--VVGFGGIKQFEEEAD--QLGLSEDVKNYVRKYVKRYEGSG 247 (250)
Q Consensus 173 ~hqk~~l~~~~~~~~~~~~~~~~~~~~s~~~~~~n~~--~~g~~~~~~~~~~~~--~~~l~~~~~~~~~~~~~~~~~~~ 247 (250)
.|||--|++-+++.++.|.... .+.=+-+.++=|+. +.|-+.++++++-++ .+-|+++..+++.+.++...+.|
T Consensus 254 ~~~~~~~~~~~~iA~k~g~T~~-qlALawv~~~~~v~~pIpG~s~ve~l~eni~Al~~~Lt~e~~~~l~~~~~~~~~~~ 331 (336)
T KOG1575|consen 254 DKQKPILEALSKIAEKHGCTVP-QLALAWVLSNGKVSSPIPGASKIEQLKENIGALSVKLTPEEIKELEEIIDKILGFG 331 (336)
T ss_pred hhHHHHHHHHHHHHHHcCCCHH-HHHHHHHHHhCCCEEecCCCCcHHHHHHHHhhhhccCCHHHHHHHHHhhccccCcC
Confidence 6777777778888888874322 34333333333332 358889999999999 78899999999999998776655
No 26
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=25.29 E-value=54 Score=28.02 Aligned_cols=45 Identities=16% Similarity=0.003 Sum_probs=27.6
Q ss_pred chhHHHhhhHHHHHHHHHHHH-------hhcCCCCCCcchhhcccccccccccc
Q psy9119 125 DSMTRKTLRASAQVELQERRL-------LQNLPPSGTPERLCRGLNNRLLFSLH 171 (250)
Q Consensus 125 dd~lk~~l~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~ 171 (250)
++.+|++||+.|+.+|++.-- +.+....|+ -.|++-++-|.-|-|
T Consensus 4 ~~ewr~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~--Y~C~~Cg~pLF~S~~ 55 (134)
T TIGR00357 4 DEELKKKLTPLQYEVTQNAGTEPPFTNEYWDNKEEGI--YVDITCGEPLFSSED 55 (134)
T ss_pred HHHHHHhCCHHHHHHHHHhCCCCCCCCCCCCCCCCeE--EEccCCCCccccccc
Confidence 344999999999999998721 112222222 246666666655544
No 27
>PF13348 Y_phosphatase3C: Tyrosine phosphatase family C-terminal region; PDB: 1YWF_A 2OZ5_B.
Probab=22.21 E-value=1.3e+02 Score=21.34 Aligned_cols=40 Identities=25% Similarity=0.444 Sum_probs=27.2
Q ss_pred hhhHHHHHhccccccCChhhHHHHHHhcCCCHHHHHHHHHHH
Q psy9119 199 TSHLAARLNGYVVGFGGIKQFEEEADQLGLSEDVKNYVRKYV 240 (250)
Q Consensus 199 ~s~~~~~~n~~~~g~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 240 (250)
.+.+.+-|.-.-..|||++.+=. +.||||++..+.+|...
T Consensus 28 ~e~l~~~l~~i~~~yGs~e~Yl~--~~lgl~~~~i~~Lr~~l 67 (68)
T PF13348_consen 28 PEYLEAALDAIDERYGSVENYLR--EELGLSEEDIERLRERL 67 (68)
T ss_dssp HHHHHHHHHHHHHHHSSHHHHHH--HT-T--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCHHHHHH--HcCCCCHHHHHHHHHHc
Confidence 34555666666668999998843 67999999999998753
No 28
>KOG0427|consensus
Probab=22.07 E-value=1.1e+02 Score=26.69 Aligned_cols=33 Identities=39% Similarity=0.451 Sum_probs=26.8
Q ss_pred hHHHhhhHHHHHHHH-HHHHhhcCCCCCCcchhh
Q psy9119 127 MTRKTLRASAQVELQ-ERRLLQNLPPSGTPERLC 159 (250)
Q Consensus 127 ~lk~~l~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 159 (250)
..||.|+..+++.+| |---+|+-||.|---+.-
T Consensus 7 ~~rk~ls~~at~RLqKEl~e~q~~pP~G~~~~v~ 40 (161)
T KOG0427|consen 7 PSRKALSKIATNRLQKELSEWQNNPPTGFKHRVT 40 (161)
T ss_pred chHHHHHHHHHHHHHHHHHHHhcCCCCcceeecc
Confidence 379999999999988 456689999999766543
No 29
>PF11491 DUF3213: Protein of unknown function (DUF3213) ; InterPro: IPR021583 The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold []. ; PDB: 2F40_A.
Probab=21.07 E-value=60 Score=26.10 Aligned_cols=27 Identities=26% Similarity=0.224 Sum_probs=13.1
Q ss_pred cCCeeEEEEEEEcCCCCCHHHHHHHHH
Q psy9119 15 SGDHTEVTQVDFDPSVISYKEILRIFW 41 (250)
Q Consensus 15 ~GDHtEaVeV~YDP~vISYeeLLdiFw 41 (250)
+.+.+-.-.|.|||+++|=++||..+=
T Consensus 31 iNgYar~g~VifDe~kl~~e~lL~~le 57 (88)
T PF11491_consen 31 INGYARNGFVIFDESKLSKEELLEMLE 57 (88)
T ss_dssp --TTSS--EEE--B-S-SHHHH---HH
T ss_pred ecccccceEEEECcccCCHHHHHHHHH
Confidence 334566778999999999999998763
No 30
>PRK14134 recX recombination regulator RecX; Provisional
Probab=21.05 E-value=1.8e+02 Score=27.10 Aligned_cols=45 Identities=18% Similarity=0.307 Sum_probs=36.6
Q ss_pred cccCCCChhhhhhhhHHHHHhccccccCChhhHHHHHHhcCCCHHHHHHH
Q psy9119 187 PKLNFKSEDCYKTSHLAARLNGYVVGFGGIKQFEEEADQLGLSEDVKNYV 236 (250)
Q Consensus 187 ~~~~~~~~~~~~~s~~~~~~n~~~~g~~~~~~~~~~~~~~~l~~~~~~~~ 236 (250)
...|+-++..|..+-+-.++|+ . |+..+..|+.+-|++++..+.+
T Consensus 103 ~e~~yldD~ryA~~yv~~~~~~----~-G~~~I~~eL~qKGI~~~iIe~a 147 (283)
T PRK14134 103 KEYNFIDDDKYCDMYIREKINS----Y-GRNKIKYTLLNKGIKENIIIEK 147 (283)
T ss_pred HHCCCCCHHHHHHHHHHHHHHh----h-hHHHHHHHHHHCCCCHHHHHHH
Confidence 4567888889999999888884 3 5789999999999999876544
No 31
>KOG0608|consensus
Probab=20.71 E-value=1.1e+02 Score=33.40 Aligned_cols=48 Identities=27% Similarity=0.343 Sum_probs=36.1
Q ss_pred hhhhHHHHHhccccccCChhhHHHHHHhcCCCHHHHHHHHHHHHhhCC
Q psy9119 198 KTSHLAARLNGYVVGFGGIKQFEEEADQLGLSEDVKNYVRKYVKRYEG 245 (250)
Q Consensus 198 ~~s~~~~~~n~~~~g~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 245 (250)
..-|+---|--|---.--.+|||+|+-..||++...+.+||++-..|.
T Consensus 569 MEQHVEnvlksyqqr~~Rk~QLEkEM~kagLpd~~q~qMrkmL~QKES 616 (1034)
T KOG0608|consen 569 MEQHVENVLKSYQQREKRKKQLEKEMVKAGLPDIMQNQMRKMLQQKES 616 (1034)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhhh
Confidence 344554444444444446789999999999999999999999877653
No 32
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=20.42 E-value=63 Score=27.88 Aligned_cols=45 Identities=18% Similarity=0.086 Sum_probs=28.9
Q ss_pred chhHHHhhhHHHHHHHHHHHH-------hhcCCCCCCcchhhcccccccccccc
Q psy9119 125 DSMTRKTLRASAQVELQERRL-------LQNLPPSGTPERLCRGLNNRLLFSLH 171 (250)
Q Consensus 125 dd~lk~~l~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~ 171 (250)
|+..|++||+.|+.+|++.-- +.+....|+ =.|++-++-|.-|-+
T Consensus 7 ~~ew~~~Lt~~qy~V~r~~gTE~pftg~~~~~~~~G~--Y~C~~Cg~pLF~S~~ 58 (142)
T PRK00222 7 KEEWKKQLTPEQYRVTQEHGTERPFTGEYLDNKEKGI--YVCIVCGEPLFSSDT 58 (142)
T ss_pred HHHHHhhCCHHHHHHHHhcCCCCCCCCCCCCCCCCeE--EEecCCCchhcCCcc
Confidence 444999999999999998631 222233332 257776766665544
Done!