Query 030161
Match_columns 182
No_of_seqs 113 out of 1084
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 09:29:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030161.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030161hhsearch_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 2.4E-69 5.2E-74 438.9 13.4 143 40-182 3-150 (174)
2 TIGR00401 msrA methionine-S-su 100.0 2.1E-65 4.6E-70 408.8 14.2 139 44-182 1-144 (149)
3 PRK13014 methionine sulfoxide 100.0 5.1E-65 1.1E-69 419.2 14.3 144 39-182 4-152 (186)
4 PRK14054 methionine sulfoxide 100.0 6.3E-65 1.4E-69 414.4 14.0 141 42-182 2-147 (172)
5 KOG1635 Peptide methionine sul 100.0 7.8E-64 1.7E-68 406.0 11.9 145 37-182 18-166 (191)
6 PRK00058 methionine sulfoxide 100.0 4.1E-63 8.9E-68 414.9 14.6 143 40-182 42-191 (213)
7 PF01625 PMSR: Peptide methion 100.0 7.1E-64 1.5E-68 402.2 9.1 139 44-182 1-143 (155)
8 PRK05528 methionine sulfoxide 100.0 2E-62 4.3E-67 394.3 13.7 136 43-182 1-136 (156)
9 PRK05550 bifunctional methioni 100.0 9.2E-60 2E-64 408.9 14.1 140 41-182 125-268 (283)
10 PRK14018 trifunctional thiored 100.0 3.7E-57 7.9E-62 419.5 14.2 143 39-182 194-339 (521)
11 PF00403 HMA: Heavy-metal-asso 95.1 0.036 7.8E-07 36.7 3.9 48 49-111 9-56 (62)
12 COG2608 CopZ Copper chaperone 88.3 0.87 1.9E-05 31.7 4.0 48 49-111 13-60 (71)
13 PF07172 GRP: Glycine rich pro 83.4 1.2 2.5E-05 33.3 2.8 24 1-25 1-25 (95)
14 PF08098 ATX_III: Anemonia sul 80.0 0.66 1.4E-05 26.9 0.3 9 48-56 11-19 (27)
15 PF02682 AHS1: Allophanate hyd 80.0 2.8 6.1E-05 35.0 4.2 68 54-140 28-97 (202)
16 COG2049 DUR1 Allophanate hydro 78.1 3.1 6.6E-05 35.8 3.9 41 54-111 26-68 (223)
17 PF03852 Vsr: DNA mismatch end 75.4 1.4 3.1E-05 31.8 1.0 15 41-55 54-68 (75)
18 TIGR02712 urea_carbox urea car 65.4 23 0.0005 37.1 7.6 65 63-147 842-909 (1201)
19 COG2217 ZntA Cation transport 61.4 10 0.00022 37.7 3.9 46 50-111 14-60 (713)
20 smart00796 AHS1 Allophanate hy 60.7 15 0.00033 30.5 4.4 68 54-140 28-98 (201)
21 COG3727 Vsr DNA G:T-mismatch r 58.5 8 0.00017 31.1 2.2 18 40-57 54-71 (150)
22 TIGR00003 copper ion binding p 58.1 35 0.00075 19.7 5.3 47 50-111 14-60 (68)
23 PHA03303 envelope glycoprotein 50.7 5.5 0.00012 32.4 0.2 17 47-63 141-157 (159)
24 PF11491 DUF3213: Protein of u 40.5 20 0.00042 26.6 1.7 29 88-117 33-61 (88)
25 PF03622 IBV_3B: IBV 3B protei 39.7 17 0.00037 25.3 1.2 19 41-59 35-53 (64)
26 COG3458 Acetyl esterase (deace 38.6 40 0.00086 30.4 3.6 71 44-118 148-238 (321)
27 TIGR00370 conserved hypothetic 38.4 43 0.00094 28.0 3.7 40 54-111 23-62 (202)
28 PRK15266 subtilase cytotoxin s 37.9 35 0.00075 27.2 2.8 107 5-111 2-115 (135)
29 PRK12386 fumarate reductase ir 37.4 1.5E+02 0.0033 25.6 7.0 78 89-173 18-95 (251)
30 KOG4309 Transcription mediator 35.6 32 0.0007 29.0 2.5 44 91-138 140-189 (217)
31 COG5053 CDC33 Translation init 35.3 77 0.0017 27.1 4.7 50 104-153 132-184 (217)
32 COG3017 LolB Outer membrane li 34.1 43 0.00094 28.5 3.0 31 1-31 1-32 (206)
33 KOG2003 TPR repeat-containing 33.8 14 0.0003 35.8 0.0 15 47-61 397-411 (840)
34 PF02083 Urotensin_II: Urotens 33.8 13 0.00029 17.9 -0.0 6 50-55 4-9 (12)
35 KOG0207 Cation transport ATPas 33.4 47 0.001 34.1 3.6 53 46-113 74-129 (951)
36 PF15240 Pro-rich: Proline-ric 30.6 45 0.00097 27.8 2.5 21 5-25 1-21 (179)
37 TIGR00632 vsr DNA mismatch end 29.7 31 0.00068 26.7 1.4 19 37-55 50-68 (117)
38 COG3045 CreA Uncharacterized p 28.8 48 0.001 27.2 2.3 23 1-23 1-23 (165)
39 PRK10614 multidrug efflux syst 27.3 67 0.0015 32.9 3.6 48 54-115 160-212 (1025)
40 PF09299 Mu-transpos_C: Mu tra 26.5 34 0.00074 22.7 1.0 13 91-103 36-48 (62)
41 PRK14624 hypothetical protein; 25.0 47 0.001 25.7 1.6 17 87-103 48-64 (115)
42 PF00873 ACR_tran: AcrB/AcrD/A 23.8 71 0.0015 32.5 3.0 46 54-113 159-209 (1021)
43 PF04990 RNA_pol_Rpb1_7: RNA p 22.2 42 0.00092 26.5 0.9 27 90-116 7-38 (135)
44 PRK15265 subtilase cytotoxin s 21.0 1.2E+02 0.0026 24.2 3.2 21 91-111 91-111 (134)
No 1
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.4e-69 Score=438.91 Aligned_cols=143 Identities=41% Similarity=0.651 Sum_probs=137.4
Q ss_pred CCCccEEEEcCCcccchhhhhcccCCeEEEeeeecCCCCCCCCccccC----CceeEEEEEEcCCCCCHHHHHHHHHhcC
Q 030161 40 GRPLKAAVFALGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLG----DHAESVQVEYDPRVINFRQLLEVFWTSH 115 (182)
Q Consensus 40 ~~~~~~a~fagGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~----gH~EaV~V~yDp~~is~~~LL~~F~~~h 115 (182)
...|++|+||||||||+|+.|+++|||++|+|||+||+++||||++|| ||+|+|+|+|||++|||++||++||++|
T Consensus 3 ~~~~~~a~fagGCFWg~E~~f~~i~GV~~t~~GYagG~~~nptY~~Vcsg~TgHaE~V~V~yDp~~isy~~LL~~ff~ih 82 (174)
T COG0225 3 PAGMEKAYFAGGCFWGVEAYFEQIPGVLSTVSGYAGGHTPNPTYEEVCSGTTGHAEAVEVTYDPKVISYEELLEVFFEIH 82 (174)
T ss_pred cCCcEEEEEeccCccchHHHHhhCCCeEEEeeeEcCCCCCCCChhhccCCCCCceEEEEEEeCCccccHHHHHHHHheec
Confidence 356899999999999999999999999999999999999999999997 8999999999999999999999999999
Q ss_pred CCCcCCCCCCCCCCCceeeeccCCHHHHHHHHHHHHHHHh-hcCCCceEEEEeeCCCcccCcccccCC
Q 030161 116 DCRQVFGQGPDVGNQYRSIIFTNGTEESRLAAHSKEREQM-KSKSSIVTTQIQQLVAFYPAEPEHQVL 182 (182)
Q Consensus 116 dPt~~~~Qg~d~G~QYRSaIf~~~~~q~~~a~~~~~~~~~-~~~~~~i~TeI~p~~~Fy~AEeyHQ~Y 182 (182)
|||+.||||||+|+||||+||++|++|+++|+++++++++ +.+.++|+|||+|+++||+||||||+|
T Consensus 83 DPT~~nrQGnD~GtqYRs~Iy~~~~~q~~~a~~~~~~~q~~~~~~~~IvteI~p~~~Fy~AEeYHQ~Y 150 (174)
T COG0225 83 DPTSLNRQGNDRGTQYRSAIYYTNEEQKAIAEASIEELQASGYFKKPIVTEIEPAKNFYPAEEYHQDY 150 (174)
T ss_pred CCCCCCccCCcccccceeEEEEcCHHHHHHHHHHHHHHHHhccCCCCeEEEeeccccCcccHHHHHHH
Confidence 9999999999999999999999999999999999998887 455669999999999999999999997
No 2
>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=2.1e-65 Score=408.84 Aligned_cols=139 Identities=44% Similarity=0.693 Sum_probs=133.1
Q ss_pred cEEEEcCCcccchhhhhcccCCeEEEeeeecCCCCCCCCccccC----CceeEEEEEEcCCCCCHHHHHHHHHhcCCCCc
Q 030161 44 KAAVFALGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLG----DHAESVQVEYDPRVINFRQLLEVFWTSHDCRQ 119 (182)
Q Consensus 44 ~~a~fagGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~----gH~EaV~V~yDp~~is~~~LL~~F~~~hdPt~ 119 (182)
++|+||||||||+|+.|++++||++|+|||+||+++||||++|| ||+|+|+|+|||++|||++||++||++||||+
T Consensus 1 ~~~~~agGCFWg~E~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~g~tgh~E~V~V~yDp~~is~~~Ll~~f~~~hdPt~ 80 (149)
T TIGR00401 1 EIATFAGGCFWGVEKYFWLIPGVYSTAVGYTGGYTPNPTYEEVCSGDTGHAEAVQVTYDPKVISYEELLDVFWEIHDPTQ 80 (149)
T ss_pred CEEEEecCCchhhHHHHhcCCCEEEEEEeeCCCCCCCCChhhcccCCCCceEEEEEEECCCcCcHHHHHHHHHHhCCCCc
Confidence 47999999999999999999999999999999999999999995 89999999999999999999999999999999
Q ss_pred CCCCCCCCCCCceeeeccCCHHHHHHHHHHHHHHHhh-cCCCceEEEEeeCCCcccCcccccCC
Q 030161 120 VFGQGPDVGNQYRSIIFTNGTEESRLAAHSKEREQMK-SKSSIVTTQIQQLVAFYPAEPEHQVL 182 (182)
Q Consensus 120 ~~~Qg~d~G~QYRSaIf~~~~~q~~~a~~~~~~~~~~-~~~~~i~TeI~p~~~Fy~AEeyHQ~Y 182 (182)
.||||+|+|+||||+||++|++|+++|+.+++++++. ...++|+|+|+|+++||+||+|||+|
T Consensus 81 ~~~Qg~d~G~qYRs~If~~~~~q~~~a~~~~~~~~~~~~~~~~i~tei~~~~~Fy~AE~yHQ~Y 144 (149)
T TIGR00401 81 GNRQGNDIGTQYRSGIYYHSDEQEKAARASKERLQAAANYGDPIVTEIEPAENFYYAEEYHQQY 144 (149)
T ss_pred CCCCCCCCCCCceEEEEeCCHHHHHHHHHHHHHHHHhcccCCCeEEEEecCCCeeecHHHHHHH
Confidence 9999999999999999999999999999999888764 24568999999999999999999998
No 3
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=100.00 E-value=5.1e-65 Score=419.22 Aligned_cols=144 Identities=38% Similarity=0.661 Sum_probs=137.1
Q ss_pred CCCCccEEEEcCCcccchhhhhcccCCeEEEeeeecCCCCCCCCccccC----CceeEEEEEEcCCCCCHHHHHHHHHhc
Q 030161 39 LGRPLKAAVFALGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLG----DHAESVQVEYDPRVINFRQLLEVFWTS 114 (182)
Q Consensus 39 ~~~~~~~a~fagGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~----gH~EaV~V~yDp~~is~~~LL~~F~~~ 114 (182)
....+++|+||||||||+|+.|++++||++|+|||+||.++||||++|| ||+|+|+|+|||++|||++||++||++
T Consensus 4 ~~~~~~~a~~agGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff~~ 83 (186)
T PRK13014 4 AADGMETATFAGGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFFST 83 (186)
T ss_pred CCCCccEEEEecCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHHHh
Confidence 4566899999999999999999999999999999999999999999997 899999999999999999999999999
Q ss_pred CCCCcCCCCCCCCCCCceeeeccCCHHHHHHHHHHHHHHHhhc-CCCceEEEEeeCCCcccCcccccCC
Q 030161 115 HDCRQVFGQGPDVGNQYRSIIFTNGTEESRLAAHSKEREQMKS-KSSIVTTQIQQLVAFYPAEPEHQVL 182 (182)
Q Consensus 115 hdPt~~~~Qg~d~G~QYRSaIf~~~~~q~~~a~~~~~~~~~~~-~~~~i~TeI~p~~~Fy~AEeyHQ~Y 182 (182)
||||+.||||+|+|+||||+||++|++|+++|++++++++++. ..++|+|+|+|+++||+||+|||+|
T Consensus 84 hDPt~~~~Qg~D~G~QYRS~If~~~~eQ~~~a~~~~~~~~~~~~~~~~i~Tei~p~~~Fy~AEeyHQ~Y 152 (186)
T PRK13014 84 HDPTQLNRQGPDRGEQYRSAIFYHDEEQKKVAEAYIAQLDEAGIFKKPIVTPIKPYKNFYPAEDYHQDY 152 (186)
T ss_pred cCCCccCCCCCCCCCCceEEEEeCCHHHHHHHHHHHHHHHhccccCCCcEEEEecCCCeeeCHHHHHHH
Confidence 9999999999999999999999999999999999998876642 4678999999999999999999998
No 4
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=100.00 E-value=6.3e-65 Score=414.41 Aligned_cols=141 Identities=40% Similarity=0.657 Sum_probs=135.2
Q ss_pred CccEEEEcCCcccchhhhhcccCCeEEEeeeecCCCCCCCCccccC----CceeEEEEEEcCCCCCHHHHHHHHHhcCCC
Q 030161 42 PLKAAVFALGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLG----DHAESVQVEYDPRVINFRQLLEVFWTSHDC 117 (182)
Q Consensus 42 ~~~~a~fagGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~----gH~EaV~V~yDp~~is~~~LL~~F~~~hdP 117 (182)
++++|+||||||||+|+.|+++|||++|+|||+||.++||||++|| ||+|+|+|+|||++|||++||++||++|||
T Consensus 2 ~~~~a~fagGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~~~hDP 81 (172)
T PRK14054 2 MMETAVLAGGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFFQIHDP 81 (172)
T ss_pred CceEEEEEcCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHHHhCCC
Confidence 5789999999999999999999999999999999999999999996 899999999999999999999999999999
Q ss_pred CcCCCCCCCCCCCceeeeccCCHHHHHHHHHHHHHHHhhc-CCCceEEEEeeCCCcccCcccccCC
Q 030161 118 RQVFGQGPDVGNQYRSIIFTNGTEESRLAAHSKEREQMKS-KSSIVTTQIQQLVAFYPAEPEHQVL 182 (182)
Q Consensus 118 t~~~~Qg~d~G~QYRSaIf~~~~~q~~~a~~~~~~~~~~~-~~~~i~TeI~p~~~Fy~AEeyHQ~Y 182 (182)
|+.||||+|+|+||||+|||+|++|+++|+.++++++.+. ..++|+|+|+|+++||+||+|||+|
T Consensus 82 t~~~~Qg~D~G~qYRS~If~~~~~q~~~a~~~~~~~~~~~~~~~~i~Tei~~~~~Fy~AEeyHQ~Y 147 (172)
T PRK14054 82 TTLNRQGNDRGTQYRSAIFYHDEEQKEIAEASIAELQASGLFDKPIVTEVEPAETFYEAEEYHQDY 147 (172)
T ss_pred CccCCCCCCCCcCceeEEEeCCHHHHHHHHHHHHHHHHhcccCCCcEEEEecCCCceECHHHHHHH
Confidence 9999999999999999999999999999999998887653 4678999999999999999999997
No 5
>KOG1635 consensus Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.8e-64 Score=405.96 Aligned_cols=145 Identities=46% Similarity=0.746 Sum_probs=139.6
Q ss_pred CCCCCCccEEEEcCCcccchhhhhcccCCeEEEeeeecCCCCCCCCccccCC----ceeEEEEEEcCCCCCHHHHHHHHH
Q 030161 37 DELGRPLKAAVFALGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLGD----HAESVQVEYDPRVINFRQLLEVFW 112 (182)
Q Consensus 37 ~~~~~~~~~a~fagGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~g----H~EaV~V~yDp~~is~~~LL~~F~ 112 (182)
+.|...++.|+||+|||||+|..|+++|||++|+|||+||.+.||||++||+ |+|+|+|.|||..|||++||++||
T Consensus 18 d~~~~g~q~a~fg~GCFWg~E~a~~~l~gV~~T~vGYagG~~~nPtYk~vc~~tT~HaEvvrV~ydpk~~sy~~Lld~Fw 97 (191)
T KOG1635|consen 18 DVPAPGLQFATFGAGCFWGVELAYQRLPGVVRTEVGYAGGITDNPTYKDVCSGTTNHAEVVRVQYDPKVISYEELLDFFW 97 (191)
T ss_pred CCCCCccceeeeeccchhhHHHHHhhcCCeEEEeecccCCccCCcchhhhccCCCCcceEEEEEeCcccccHHHHHHHHH
Confidence 5567789999999999999999999999999999999999999999999985 999999999999999999999999
Q ss_pred hcCCCCcCCCCCCCCCCCceeeeccCCHHHHHHHHHHHHHHHhhcCCCceEEEEeeCCCcccCcccccCC
Q 030161 113 TSHDCRQVFGQGPDVGNQYRSIIFTNGTEESRLAAHSKEREQMKSKSSIVTTQIQQLVAFYPAEPEHQVL 182 (182)
Q Consensus 113 ~~hdPt~~~~Qg~d~G~QYRSaIf~~~~~q~~~a~~~~~~~~~~~~~~~i~TeI~p~~~Fy~AEeyHQ~Y 182 (182)
++||||+.||||+|+|+||||+||+++++|.++|+.++++.|.+ ..++|+|+|+|+++||.||||||+|
T Consensus 98 ~~HdPtt~n~QG~D~GtQYRS~I~~~s~eq~k~A~~s~e~~Q~k-~~~kI~T~I~p~~kFY~AE~yHQqY 166 (191)
T KOG1635|consen 98 SRHDPTTLNRQGNDVGTQYRSGIYTYSPEQEKLARESKEREQKK-WNGKIVTEILPAKKFYRAEEYHQQY 166 (191)
T ss_pred HcCCchhhhccCCcccceeeeeeeeCCHHHHHHHHHHHHHHHhc-cCCcceEEEeeccchhhchHHHHHH
Confidence 99999999999999999999999999999999999999998887 4678999999999999999999997
No 6
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=100.00 E-value=4.1e-63 Score=414.87 Aligned_cols=143 Identities=45% Similarity=0.698 Sum_probs=135.3
Q ss_pred CCCccEEEEcCCcccchhhhhcccCCeEEEeeeecCCCCCCCCccccC----CceeEEEEEEcCCCCCHHHHHHHHHhcC
Q 030161 40 GRPLKAAVFALGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLG----DHAESVQVEYDPRVINFRQLLEVFWTSH 115 (182)
Q Consensus 40 ~~~~~~a~fagGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~----gH~EaV~V~yDp~~is~~~LL~~F~~~h 115 (182)
...++.|+||||||||+|+.|++++||++|+|||+||.++||||++|| ||+|+|+|+|||++|||++||++||++|
T Consensus 42 ~~~~~~a~fagGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff~~h 121 (213)
T PRK00058 42 PEGMEQAIFGMGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFWENH 121 (213)
T ss_pred CCCccEEEEEccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHHHhc
Confidence 456899999999999999999999999999999999999999999995 8999999999999999999999999999
Q ss_pred CCCcCCCCCCCCCCCceeeeccCCHHHHHHHHHHHHHHHhhc---CCCceEEEEeeCCCcccCcccccCC
Q 030161 116 DCRQVFGQGPDVGNQYRSIIFTNGTEESRLAAHSKEREQMKS---KSSIVTTQIQQLVAFYPAEPEHQVL 182 (182)
Q Consensus 116 dPt~~~~Qg~d~G~QYRSaIf~~~~~q~~~a~~~~~~~~~~~---~~~~i~TeI~p~~~Fy~AEeyHQ~Y 182 (182)
|||+.||||+|+|+||||+|||+|++|+++|++++++++.+. +.++|+|+|+|+++||+||+|||+|
T Consensus 122 DPt~~n~QG~D~G~QYRS~Ify~~~eQ~~~a~~~~~~~~~~~~~~~~~~i~TeI~~~~~Fy~AEeyHQ~Y 191 (213)
T PRK00058 122 DPTQGMRQGNDVGTQYRSAIYTLTPEQLAAAEASREAYQQALAAAGDGPITTEIAPAPPFYYAEDYHQQY 191 (213)
T ss_pred CCcccCCCCCCCCcCceEEEEeCCHHHHHHHHHHHHHHHHHhhhccCCCeEEEEecCCCcccCHHHHHHH
Confidence 999999999999999999999999999999999888776643 1358999999999999999999998
No 7
>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=7.1e-64 Score=402.22 Aligned_cols=139 Identities=47% Similarity=0.760 Sum_probs=127.8
Q ss_pred cEEEEcCCcccchhhhhcccCCeEEEeeeecCCCCCCCCcccc----CCceeEEEEEEcCCCCCHHHHHHHHHhcCCCCc
Q 030161 44 KAAVFALGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNL----GDHAESVQVEYDPRVINFRQLLEVFWTSHDCRQ 119 (182)
Q Consensus 44 ~~a~fagGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v----~gH~EaV~V~yDp~~is~~~LL~~F~~~hdPt~ 119 (182)
++|+||||||||+|+.|++++||++|+|||+||+.+||||++| +||+|+|+|+|||++|||++||++||++||||+
T Consensus 1 e~a~fa~GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~is~~~Ll~~f~~~~dPt~ 80 (155)
T PF01625_consen 1 EKAYFAGGCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVISYEELLDVFFRIHDPTQ 80 (155)
T ss_dssp EEEEEEESSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS-HHHHHHHHHHHS-TTS
T ss_pred CEEEEecCCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcccHHHHHHHHHHhcCCcc
Confidence 5799999999999999999999999999999999999999999 589999999999999999999999999999999
Q ss_pred CCCCCCCCCCCceeeeccCCHHHHHHHHHHHHHHHhhcCCCceEEEEeeCCCcccCcccccCC
Q 030161 120 VFGQGPDVGNQYRSIIFTNGTEESRLAAHSKEREQMKSKSSIVTTQIQQLVAFYPAEPEHQVL 182 (182)
Q Consensus 120 ~~~Qg~d~G~QYRSaIf~~~~~q~~~a~~~~~~~~~~~~~~~i~TeI~p~~~Fy~AEeyHQ~Y 182 (182)
.||||+|+|+||||+||++|++|+++|+.++++++++...++|+|+|+|+++||+||+|||+|
T Consensus 81 ~~~Qg~d~G~qYrs~If~~~~~q~~~a~~~~~~~~~~~~~~~i~tei~p~~~Fy~AE~yHQ~Y 143 (155)
T PF01625_consen 81 VNGQGNDRGTQYRSAIFYHDEEQKKIAEASIAELQAKRFGRPIVTEIEPLKNFYPAEEYHQKY 143 (155)
T ss_dssp TSEETTEESGGG-EEEEESSHHHHHHHHHHHHHHHHHTTSSSBS-EEEECEEEEEHHGGGTTH
T ss_pred cccccCcccccceeEEecCCHHHHHHHHHHHHHHHHhcCCCCeEEEEecCCcEEECHHHHHHH
Confidence 999999999999999999999999999999998888745679999999999999999999998
No 8
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=100.00 E-value=2e-62 Score=394.28 Aligned_cols=136 Identities=27% Similarity=0.436 Sum_probs=128.4
Q ss_pred ccEEEEcCCcccchhhhhcccCCeEEEeeeecCCCCCCCCccccCCceeEEEEEEcCCCCCHHHHHHHHHhcCCCCcCCC
Q 030161 43 LKAAVFALGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLGDHAESVQVEYDPRVINFRQLLEVFWTSHDCRQVFG 122 (182)
Q Consensus 43 ~~~a~fagGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~gH~EaV~V~yDp~~is~~~LL~~F~~~hdPt~~~~ 122 (182)
|++|+||||||||+|+.|+++|||++|+|||+||.++||++.. +||+|+|+|+|||++|||++||++||++||||+.||
T Consensus 1 ~~~a~fagGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~-tgH~E~V~V~yDp~~isy~~LL~~f~~~hdPt~~~~ 79 (156)
T PRK05528 1 METVYFAGGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPY-DGYAECVKTHFDPRMVSITDLMGYLFEIIDPYSVNK 79 (156)
T ss_pred CCEEEEecCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCC-CCcEEEEEEEECCCcCCHHHHHHHHHHhCCcccccc
Confidence 5789999999999999999999999999999999999998433 799999999999999999999999999999999999
Q ss_pred CCCCCCCCceeeeccCCHHHHHHHHHHHHHHHhhcCCCceEEEEeeCCCcccCcccccCC
Q 030161 123 QGPDVGNQYRSIIFTNGTEESRLAAHSKEREQMKSKSSIVTTQIQQLVAFYPAEPEHQVL 182 (182)
Q Consensus 123 Qg~d~G~QYRSaIf~~~~~q~~~a~~~~~~~~~~~~~~~i~TeI~p~~~Fy~AEeyHQ~Y 182 (182)
||+|+|+||||+||++|++|+++|++++++++. .++|+|+|+|+.+||+||+|||+|
T Consensus 80 Qg~D~G~QYRS~If~~d~eQ~~~a~~~~~~~~~---~~~i~Tei~~~~~Fy~AE~yHQ~Y 136 (156)
T PRK05528 80 QGNDVGEKYRTGIYSEVDDHLIEARQFIERRED---ADKIAVEVLPLTNYVKSAEEHQDR 136 (156)
T ss_pred cCCCCCCCceEEEEeCCHHHHHHHHHHHHHHhc---CCCeEEEEecCCCeeecHHHHHHH
Confidence 999999999999999999999999998876643 358999999999999999999997
No 9
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=100.00 E-value=9.2e-60 Score=408.85 Aligned_cols=140 Identities=40% Similarity=0.662 Sum_probs=134.0
Q ss_pred CCccEEEEcCCcccchhhhhcccCCeEEEeeeecCCCCCCCCccccC----CceeEEEEEEcCCCCCHHHHHHHHHhcCC
Q 030161 41 RPLKAAVFALGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLG----DHAESVQVEYDPRVINFRQLLEVFWTSHD 116 (182)
Q Consensus 41 ~~~~~a~fagGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~----gH~EaV~V~yDp~~is~~~LL~~F~~~hd 116 (182)
..+++|+||||||||+|+.|++++||++|+|||+||.++||||++|| ||+|+|+|+|||++|||++||++||++||
T Consensus 125 ~~~~~~~fagGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~VcsG~tgH~EaV~V~yDp~~isy~~LL~~F~~~hD 204 (283)
T PRK05550 125 YDTEEAIFAGGCFWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEFDPAKISYETLLKVFFEIHD 204 (283)
T ss_pred ccceEEEEecCCchhhhhhHhhCcCEEEEEEeeCCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHHhhcC
Confidence 34899999999999999999999999999999999999999999995 89999999999999999999999999999
Q ss_pred CCcCCCCCCCCCCCceeeeccCCHHHHHHHHHHHHHHHhhcCCCceEEEEeeCCCcccCcccccCC
Q 030161 117 CRQVFGQGPDVGNQYRSIIFTNGTEESRLAAHSKEREQMKSKSSIVTTQIQQLVAFYPAEPEHQVL 182 (182)
Q Consensus 117 Pt~~~~Qg~d~G~QYRSaIf~~~~~q~~~a~~~~~~~~~~~~~~~i~TeI~p~~~Fy~AEeyHQ~Y 182 (182)
||+.||||+|+|+||||+||++|++|+++|++++++++++. .+|+|+|+|+++||+||+|||+|
T Consensus 205 Pt~~~~Qg~D~G~QYRS~If~~d~eq~~~A~~~~~~~~~~~--~~i~TeI~~l~~Fy~AEeyHQ~Y 268 (283)
T PRK05550 205 PTQLNRQGPDIGTQYRSAIFYHDDEQKQIAEKLIAELTKKG--YPVVTEVEAAGPFYPAEDYHQDY 268 (283)
T ss_pred CCccCCCCCCCCcCceEEEEeCCHHHHHHHHHHHHHHHhcC--CceEEEEeeCCCeeECHHHHHHH
Confidence 99999999999999999999999999999999998877653 28999999999999999999998
No 10
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=100.00 E-value=3.7e-57 Score=419.51 Aligned_cols=143 Identities=31% Similarity=0.507 Sum_probs=136.5
Q ss_pred CCCCccEEEEcCCcccchhhhhcccCCeEEEeeeecCCCCCCCCcccc---CCceeEEEEEEcCCCCCHHHHHHHHHhcC
Q 030161 39 LGRPLKAAVFALGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNL---GDHAESVQVEYDPRVINFRQLLEVFWTSH 115 (182)
Q Consensus 39 ~~~~~~~a~fagGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v---~gH~EaV~V~yDp~~is~~~LL~~F~~~h 115 (182)
...++++|+||||||||+|+.|++++||++|+|||+||.++||||++| +||+|+|+|+|||++|||++||++||++|
T Consensus 194 ~~~~~~~~~~agGCFWg~e~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~gtgH~E~V~V~yDp~~is~~~Ll~~f~~~~ 273 (521)
T PRK14018 194 KIMNTRTIYLAGGCFWGLEAYFQRIDGVVDAVSGYANGNTKNPSYEDVYRHSGHAETVKVTYDADKLSLDTILQYYFRVV 273 (521)
T ss_pred CCCCccEEEEecCCchhhHHHHccCCCEEEEEEeeCCCCCCCCChhhccCCCCcEEEEEEEECCCcCcHHHHHHHHHHhC
Confidence 455789999999999999999999999999999999999999999999 58999999999999999999999999999
Q ss_pred CCCcCCCCCCCCCCCceeeeccCCHHHHHHHHHHHHHHHhhcCCCceEEEEeeCCCcccCcccccCC
Q 030161 116 DCRQVFGQGPDVGNQYRSIIFTNGTEESRLAAHSKEREQMKSKSSIVTTQIQQLVAFYPAEPEHQVL 182 (182)
Q Consensus 116 dPt~~~~Qg~d~G~QYRSaIf~~~~~q~~~a~~~~~~~~~~~~~~~i~TeI~p~~~Fy~AEeyHQ~Y 182 (182)
|||+.||||+|+|+||||+|||+|++|+++|+.+++.++.+ ..++|+|+|+|+++||+||+|||+|
T Consensus 274 dPt~~~~Qg~d~G~qYrs~I~~~~~eq~~~a~~~~~~~~~~-~~~~i~tei~~~~~Fy~AE~yHQ~Y 339 (521)
T PRK14018 274 DPTSLNKQGNDTGTQYRSGVYYTDPADKAVIAAALKREQQK-YQLPLVVENEPLKNFYDAEEYHQDY 339 (521)
T ss_pred CCccccccCCCCCCCceEEEEeCCHHHHHHHHHHHHHHHHH-cCCCeEEEEecCCCeeecHHHHHHH
Confidence 99999999999999999999999999999999998887765 4568999999999999999999998
No 11
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=95.11 E-value=0.036 Score=36.74 Aligned_cols=48 Identities=25% Similarity=0.387 Sum_probs=41.2
Q ss_pred cCCcccchhhhhcccCCeEEEeeeecCCCCCCCCccccCCceeEEEEEEcCCCCCHHHHHHHH
Q 030161 49 ALGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLGDHAESVQVEYDPRVINFRQLLEVF 111 (182)
Q Consensus 49 agGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~gH~EaV~V~yDp~~is~~~LL~~F 111 (182)
-.+|-+.++..+.++|||.++.+=+..+ .|.|.||+..++.++|.+..
T Consensus 9 C~~C~~~v~~~l~~~~GV~~v~vd~~~~---------------~v~v~~~~~~~~~~~i~~~i 56 (62)
T PF00403_consen 9 CEGCAKKVEKALSKLPGVKSVKVDLETK---------------TVTVTYDPDKTSIEKIIEAI 56 (62)
T ss_dssp SHHHHHHHHHHHHTSTTEEEEEEETTTT---------------EEEEEESTTTSCHHHHHHHH
T ss_pred cHHHHHHHHHHHhcCCCCcEEEEECCCC---------------EEEEEEecCCCCHHHHHHHH
Confidence 3578888999999999999999988755 57899999999999988764
No 12
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=88.32 E-value=0.87 Score=31.65 Aligned_cols=48 Identities=17% Similarity=0.315 Sum_probs=42.3
Q ss_pred cCCcccchhhhhcccCCeEEEeeeecCCCCCCCCccccCCceeEEEEEEcCCCCCHHHHHHHH
Q 030161 49 ALGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLGDHAESVQVEYDPRVINFRQLLEVF 111 (182)
Q Consensus 49 agGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~gH~EaV~V~yDp~~is~~~LL~~F 111 (182)
.++|.=-++..+.+++||.++.+-...|. +.|+||+..++-++|.+..
T Consensus 13 C~~C~~~V~~al~~v~gv~~v~v~l~~~~---------------~~V~~d~~~~~~~~i~~ai 60 (71)
T COG2608 13 CGHCVKTVEKALEEVDGVASVDVDLEKGT---------------ATVTFDSNKVDIEAIIEAI 60 (71)
T ss_pred cHHHHHHHHHHHhcCCCeeEEEEEcccCe---------------EEEEEcCCcCCHHHHHHHH
Confidence 56788888999999999999999988763 7899999999999999883
No 13
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=83.35 E-value=1.2 Score=33.32 Aligned_cols=24 Identities=33% Similarity=0.560 Sum_probs=15.9
Q ss_pred CcchhhHHHHHHHHH-HHhhcccccc
Q 030161 1 MVLSKRYLFFSVLHL-LLLTDTALCI 25 (182)
Q Consensus 1 ~~~~~~~~~~~~~~~-~~~~~~~~~~ 25 (182)
|- ||.+|||.++++ +|++.+..+.
T Consensus 1 Ma-SK~~llL~l~LA~lLlisSevaa 25 (95)
T PF07172_consen 1 MA-SKAFLLLGLLLAALLLISSEVAA 25 (95)
T ss_pred Cc-hhHHHHHHHHHHHHHHHHhhhhh
Confidence 44 999999998874 4444444443
No 14
>PF08098 ATX_III: Anemonia sulcata toxin III family; InterPro: IPR012509 This entry occurs within the Anemonia sulcata toxin III (ATX III) neurotoxin family. ATX III is a neurotoxin that is produced by sea anemone; it adopts a compact structure containing four reverse turns and two other chain reversals, but no regular alpha-helix or beta-sheet. A hydrophobic patch found on the surface of the peptide may constitute part of the sodium channel binding surface [].; GO: 0019871 sodium channel inhibitor activity, 0009405 pathogenesis, 0042151 nematocyst; PDB: 1ANS_A.
Probab=80.02 E-value=0.66 Score=26.94 Aligned_cols=9 Identities=22% Similarity=0.652 Sum_probs=5.5
Q ss_pred EcCCcccch
Q 030161 48 FALGSFWRS 56 (182)
Q Consensus 48 fagGCFWg~ 56 (182)
+-+|||||-
T Consensus 11 ~~~gC~WGQ 19 (27)
T PF08098_consen 11 YTGGCPWGQ 19 (27)
T ss_dssp TTTT-SSS-
T ss_pred eecCCcccc
Confidence 457899983
No 15
>PF02682 AHS1: Allophanate hydrolase subunit 1; InterPro: IPR003833 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 1 of allophanate hydrolase (AHS1), which is found in urea carboxylase.; PDB: 3VA7_A 3MML_H 3OEP_A 3OPF_C 3ORE_A 2ZP2_A 2KWA_A 2PHC_B.
Probab=79.98 E-value=2.8 Score=35.00 Aligned_cols=68 Identities=18% Similarity=0.182 Sum_probs=43.9
Q ss_pred cchhhhhcc--cCCeEEEeeeecCCCCCCCCccccCCceeEEEEEEcCCCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCc
Q 030161 54 WRSEAVFGC--LNGVVRTTVGYAGGSKTNPEFRNLGDHAESVQVEYDPRVINFRQLLEVFWTSHDCRQVFGQGPDVGNQY 131 (182)
Q Consensus 54 Wg~E~~F~~--~~GV~~t~vGYagG~~~nPtY~~v~gH~EaV~V~yDp~~is~~~LL~~F~~~hdPt~~~~Qg~d~G~QY 131 (182)
|.....+.+ ++||++++.+|. .|-|.|||..+++.+|.+..-+...-... .-...++..
T Consensus 28 ~al~~~l~~~~~~gi~e~vp~~~-----------------sllV~fdp~~~~~~~l~~~l~~~~~~~~~--~~~~~~r~~ 88 (202)
T PF02682_consen 28 LALARALRAAPLPGIVEVVPAYR-----------------SLLVHFDPLRIDRAALRAALEELLASPQP--SEKPPSRLI 88 (202)
T ss_dssp HHHHHHHHHHT-TTEEEEEEESS-----------------EEEEEESTTTSHHHHHHHHHHHHHCCCCS--SCCCCEEEE
T ss_pred HHHHHHHhcCCCCCeEEeecccc-----------------EEEEEEcCCcCCHHHHHHHHHHhhhhccc--cccCCCceE
Confidence 455555666 899999998885 67899999999999998877554322110 001122345
Q ss_pred eeeeccCCH
Q 030161 132 RSIIFTNGT 140 (182)
Q Consensus 132 RSaIf~~~~ 140 (182)
+==|.|.++
T Consensus 89 ~iPV~Y~~~ 97 (202)
T PF02682_consen 89 EIPVCYDGE 97 (202)
T ss_dssp EEEEEESTT
T ss_pred EEEEEECCC
Confidence 666677754
No 16
>COG2049 DUR1 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]
Probab=78.10 E-value=3.1 Score=35.77 Aligned_cols=41 Identities=37% Similarity=0.629 Sum_probs=30.8
Q ss_pred cchhhhhcc--cCCeEEEeeeecCCCCCCCCccccCCceeEEEEEEcCCCCCHHHHHHHH
Q 030161 54 WRSEAVFGC--LNGVVRTTVGYAGGSKTNPEFRNLGDHAESVQVEYDPRVINFRQLLEVF 111 (182)
Q Consensus 54 Wg~E~~F~~--~~GV~~t~vGYagG~~~nPtY~~v~gH~EaV~V~yDp~~is~~~LL~~F 111 (182)
|.+...+.+ ++||++++.||. .+.|.||+.+++..+|++..
T Consensus 26 ~al~~~l~~~~~~gvve~vP~~~-----------------sllv~~d~~~~~~~~l~~~L 68 (223)
T COG2049 26 WALARALEAAPLPGVVEIVPGYR-----------------SLLVIYDPPRLDPQELLERL 68 (223)
T ss_pred HHHHHHHHhcCCCCeEEecccce-----------------eEEEEecccccCHHHHHHHH
Confidence 334444444 469999999986 57899999999988877653
No 17
>PF03852 Vsr: DNA mismatch endonuclease Vsr; InterPro: IPR004603 This entry represents VSR (very short patch repair) endonucleases, which occur in a variety of bacteria. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine []. GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine []. The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer alpha/beta/alpha topology []. ; GO: 0004519 endonuclease activity, 0006298 mismatch repair; PDB: 1ODG_A 1VSR_A 1CW0_A.
Probab=75.44 E-value=1.4 Score=31.78 Aligned_cols=15 Identities=40% Similarity=0.844 Sum_probs=12.3
Q ss_pred CCccEEEEcCCcccc
Q 030161 41 RPLKAAVFALGSFWR 55 (182)
Q Consensus 41 ~~~~~a~fagGCFWg 55 (182)
...+.|+|--||||+
T Consensus 54 ~~~k~aIFVdGCFWH 68 (75)
T PF03852_consen 54 PKYKIAIFVDGCFWH 68 (75)
T ss_dssp GGGTEEEEEE-TTTT
T ss_pred CCCCEEEEEecceeC
Confidence 456899999999998
No 18
>TIGR02712 urea_carbox urea carboxylase. Members of this family are ATP-dependent urea carboxylase, including characterized members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae. The allophanate hydrolase domain of the yeast enzyme is not included in this model and is represented by an adjacent gene in Oleomonas sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated urea amidolyase. The enzyme from Oleomonas sagaranensis was shown to be highly active on acetamide and formamide as well as urea.
Probab=65.43 E-value=23 Score=37.14 Aligned_cols=65 Identities=25% Similarity=0.252 Sum_probs=40.6
Q ss_pred cCCeEEEeeeecCCCCCCCCccccCCceeEEEEEEcCCCCCHHHHHHHHHhcC---CCCcCCCCCCCCCCCceeeeccCC
Q 030161 63 LNGVVRTTVGYAGGSKTNPEFRNLGDHAESVQVEYDPRVINFRQLLEVFWTSH---DCRQVFGQGPDVGNQYRSIIFTNG 139 (182)
Q Consensus 63 ~~GV~~t~vGYagG~~~nPtY~~v~gH~EaV~V~yDp~~is~~~LL~~F~~~h---dPt~~~~Qg~d~G~QYRSaIf~~~ 139 (182)
++||++++.||. .+.|.|||.+++..+|++..-... ++.. .. ...++..+-=|.|.+
T Consensus 842 ~~gi~e~vP~~~-----------------Sl~v~~dp~~~~~~~l~~~l~~~~~~~~~~~-~~--~~~~r~v~iPv~y~~ 901 (1201)
T TIGR02712 842 LPGIIDLTPGIR-----------------SLQIHYDPRVISQSELLEVLVAIEEQLPAAE-DL--QVPSRIVHLPLSWED 901 (1201)
T ss_pred CCCeEEeccccE-----------------EEEEEECCCCCCHHHHHHHHHHHHhhccccc-cc--CCCCcEEEEEeEECC
Confidence 689999988874 688999999999999887653322 2211 10 112234455567777
Q ss_pred HHHHHHHH
Q 030161 140 TEESRLAA 147 (182)
Q Consensus 140 ~~q~~~a~ 147 (182)
+.-++..+
T Consensus 902 ~~~~~~~~ 909 (1201)
T TIGR02712 902 PATLLAVE 909 (1201)
T ss_pred HHHHHHHH
Confidence 65444333
No 19
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=61.37 E-value=10 Score=37.71 Aligned_cols=46 Identities=26% Similarity=0.356 Sum_probs=39.8
Q ss_pred CCcccchhhhhcccCCeEEEeeeecCCCCCCCCccccCCceeEEEEEEcCCCCC-HHHHHHHH
Q 030161 50 LGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLGDHAESVQVEYDPRVIN-FRQLLEVF 111 (182)
Q Consensus 50 gGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~gH~EaV~V~yDp~~is-~~~LL~~F 111 (182)
..|-|.+| .+.+++||.+.+|-++ +|.+.|.||++.++ .+++....
T Consensus 14 a~C~~~ie-~l~~~~gV~~~~vn~~---------------t~~~~v~~~~~~~~~~~~~~~~v 60 (713)
T COG2217 14 AACASRIE-ALNKLPGVEEARVNLA---------------TERATVVYDPEEVDLPADIVAAV 60 (713)
T ss_pred HHHHHHHH-HHhcCCCeeEEEeecc---------------cceEEEEecccccccHHHHHHHH
Confidence 46889999 9999999999999888 67889999998887 67777665
No 20
>smart00796 AHS1 Allophanate hydrolase subunit 1. This domain represents subunit 1 of allophanate hydrolase (AHS1).
Probab=60.72 E-value=15 Score=30.55 Aligned_cols=68 Identities=24% Similarity=0.196 Sum_probs=41.8
Q ss_pred cchhhhhc--ccCCeEEEeeeecCCCCCCCCccccCCceeEEEEEEcCCCCCHHHHHHHHHhc-CCCCcCCCCCCCCCCC
Q 030161 54 WRSEAVFG--CLNGVVRTTVGYAGGSKTNPEFRNLGDHAESVQVEYDPRVINFRQLLEVFWTS-HDCRQVFGQGPDVGNQ 130 (182)
Q Consensus 54 Wg~E~~F~--~~~GV~~t~vGYagG~~~nPtY~~v~gH~EaV~V~yDp~~is~~~LL~~F~~~-hdPt~~~~Qg~d~G~Q 130 (182)
|.....+. ..+||++++.+|. .|-|.|||.+++..+|++..=+. .++.. ......++.
T Consensus 28 ~~l~~~l~~~~~~gi~e~vp~~~-----------------sllv~fdp~~~~~~~l~~~l~~~~~~~~~--~~~~~~~r~ 88 (201)
T smart00796 28 LALARALRAAPLPGVVELVPGYR-----------------SLLVHFDPLVIDPAALLARLRALEALPLA--EALEVPGRI 88 (201)
T ss_pred HHHHHHHHhcCCCCeEEccccce-----------------EEEEEEcCCCCCHHHHHHHHHHHHhcccc--cccCCCCcE
Confidence 44444444 3689999987763 67899999999999887754221 12111 111223456
Q ss_pred ceeeeccCCH
Q 030161 131 YRSIIFTNGT 140 (182)
Q Consensus 131 YRSaIf~~~~ 140 (182)
++==|.|.++
T Consensus 89 ~~IPV~Y~~~ 98 (201)
T smart00796 89 IEIPVCYGGE 98 (201)
T ss_pred EEEeeEeCCC
Confidence 6666777754
No 21
>COG3727 Vsr DNA G:T-mismatch repair endonuclease [DNA replication, recombination, and repair]
Probab=58.51 E-value=8 Score=31.14 Aligned_cols=18 Identities=22% Similarity=0.648 Sum_probs=14.6
Q ss_pred CCCccEEEEcCCcccchh
Q 030161 40 GRPLKAAVFALGSFWRSE 57 (182)
Q Consensus 40 ~~~~~~a~fagGCFWg~E 57 (182)
....+.++|--||||+--
T Consensus 54 l~~y~~viFvHGCFWh~H 71 (150)
T COG3727 54 LPKYRCVIFVHGCFWHGH 71 (150)
T ss_pred ecCceEEEEEeeeeccCC
Confidence 356788999999999843
No 22
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=58.10 E-value=35 Score=19.73 Aligned_cols=47 Identities=26% Similarity=0.266 Sum_probs=37.4
Q ss_pred CCcccchhhhhcccCCeEEEeeeecCCCCCCCCccccCCceeEEEEEEcCCCCCHHHHHHHH
Q 030161 50 LGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLGDHAESVQVEYDPRVINFRQLLEVF 111 (182)
Q Consensus 50 gGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~gH~EaV~V~yDp~~is~~~LL~~F 111 (182)
..|-|.++..+...+||..+.+...++ .+.|.||+...+-..+....
T Consensus 14 ~~c~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~ 60 (68)
T TIGR00003 14 QHCVDKIEKFVGELEGVSKVQVKLEKA---------------SVKVEFDAPQATEICIAEAI 60 (68)
T ss_pred HHHHHHHHHHHhcCCCEEEEEEEcCCC---------------EEEEEeCCCCCCHHHHHHHH
Confidence 478999999999999999888877755 36688888877777776554
No 23
>PHA03303 envelope glycoprotein L; Provisional
Probab=50.73 E-value=5.5 Score=32.44 Aligned_cols=17 Identities=18% Similarity=0.477 Sum_probs=14.5
Q ss_pred EEcCCcccchhhhhccc
Q 030161 47 VFALGSFWRSEAVFGCL 63 (182)
Q Consensus 47 ~fagGCFWg~E~~F~~~ 63 (182)
.-..||+||.+.+|+++
T Consensus 141 pp~~GCV~g~~~~~~~~ 157 (159)
T PHA03303 141 IPDIGCVFGADNLFQRL 157 (159)
T ss_pred CCCCCccccHHHHHHHh
Confidence 33789999999999875
No 24
>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=40.50 E-value=20 Score=26.63 Aligned_cols=29 Identities=21% Similarity=0.171 Sum_probs=14.6
Q ss_pred CceeEEEEEEcCCCCCHHHHHHHHHhcCCC
Q 030161 88 DHAESVQVEYDPRVINFRQLLEVFWTSHDC 117 (182)
Q Consensus 88 gH~EaV~V~yDp~~is~~~LL~~F~~~hdP 117 (182)
|.+-.=.|.|||++++-++||+.+= -..|
T Consensus 33 gYar~g~VifDe~kl~~e~lL~~le-~~kp 61 (88)
T PF11491_consen 33 GYARNGFVIFDESKLSKEELLEMLE-EFKP 61 (88)
T ss_dssp TTSS--EEE--B-S-SHHHH---HH-HTTT
T ss_pred ccccceEEEECcccCCHHHHHHHHH-hcCh
Confidence 4556667999999999999997653 3345
No 25
>PF03622 IBV_3B: IBV 3B protein ; InterPro: IPR005295 These proteins are the product of ORF 3B from Infectious bronchitis virus). Currently, the function of this protein remains unknown [].
Probab=39.67 E-value=17 Score=25.28 Aligned_cols=19 Identities=32% Similarity=0.763 Sum_probs=16.0
Q ss_pred CCccEEEEcCCcccchhhh
Q 030161 41 RPLKAAVFALGSFWRSEAV 59 (182)
Q Consensus 41 ~~~~~a~fagGCFWg~E~~ 59 (182)
.+.+..|.-+|+||-.|..
T Consensus 35 DPFE~cyyrgGsfwEieSa 53 (64)
T PF03622_consen 35 DPFEVCYYRGGSFWEIESA 53 (64)
T ss_pred CCeeEEEEecCcEEEeecc
Confidence 3478999999999998863
No 26
>COG3458 Acetyl esterase (deacetylase) [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=38.59 E-value=40 Score=30.43 Aligned_cols=71 Identities=20% Similarity=0.455 Sum_probs=53.7
Q ss_pred cEEEEcCCcc---cchhhhhcccCCeEEEeeeecCCCCC----------C-------CCccccCCceeEEEEEEcCCCCC
Q 030161 44 KAAVFALGSF---WRSEAVFGCLNGVVRTTVGYAGGSKT----------N-------PEFRNLGDHAESVQVEYDPRVIN 103 (182)
Q Consensus 44 ~~a~fagGCF---Wg~E~~F~~~~GV~~t~vGYagG~~~----------n-------PtY~~v~gH~EaV~V~yDp~~is 103 (182)
+.-|+=.||| |-.=....+++-|-..++|++||+-. + |.|--.|+..-+|++ +..=+
T Consensus 148 kd~yyyr~v~~D~~~ave~~~sl~~vde~Ri~v~G~SqGGglalaaaal~~rik~~~~~~Pfl~df~r~i~~---~~~~~ 224 (321)
T COG3458 148 KDTYYYRGVFLDAVRAVEILASLDEVDEERIGVTGGSQGGGLALAAAALDPRIKAVVADYPFLSDFPRAIEL---ATEGP 224 (321)
T ss_pred CCceEEeeehHHHHHHHHHHhccCccchhheEEeccccCchhhhhhhhcChhhhcccccccccccchhheee---cccCc
Confidence 4567778998 55556677889999999999988632 2 334445777888888 67779
Q ss_pred HHHHHHHHHhcCCCC
Q 030161 104 FRQLLEVFWTSHDCR 118 (182)
Q Consensus 104 ~~~LL~~F~~~hdPt 118 (182)
|.+|- .||+.|||.
T Consensus 225 ydei~-~y~k~h~~~ 238 (321)
T COG3458 225 YDEIQ-TYFKRHDPK 238 (321)
T ss_pred HHHHH-HHHHhcCch
Confidence 99986 789999984
No 27
>TIGR00370 conserved hypothetical protein TIGR00370.
Probab=38.44 E-value=43 Score=28.03 Aligned_cols=40 Identities=23% Similarity=0.414 Sum_probs=26.9
Q ss_pred cchhhhhcccCCeEEEeeeecCCCCCCCCccccCCceeEEEEEEcCCCCCHHHHHHHH
Q 030161 54 WRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLGDHAESVQVEYDPRVINFRQLLEVF 111 (182)
Q Consensus 54 Wg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~gH~EaV~V~yDp~~is~~~LL~~F 111 (182)
|.+-..+.+.+||++++.||. .|-|.|||..+ ..+|+...
T Consensus 23 ~~l~~~l~~~~gi~e~vP~~~-----------------sllv~fdp~~~-~~~l~~~l 62 (202)
T TIGR00370 23 WAAAAYLEEQPGFVECIPGMN-----------------NLTVFYDMYEV-YKHLPQRL 62 (202)
T ss_pred HHHHHHHhcCCCcEEeecccE-----------------EEEEEECchhh-HHHHHHHH
Confidence 333334443489999887774 67799999987 66666543
No 28
>PRK15266 subtilase cytotoxin subunit B; Provisional
Probab=37.91 E-value=35 Score=27.17 Aligned_cols=107 Identities=16% Similarity=0.217 Sum_probs=49.0
Q ss_pred hhHHHHHHHHHHHhhcccccccCCCCCCCCCCCCCCCCccEEEEcCCcccchhhhhcccCCeEEEeeeecCCCCCCCCcc
Q 030161 5 KRYLFFSVLHLLLLTDTALCIRFPDRVSTSINDELGRPLKAAVFALGSFWRSEAVFGCLNGVVRTTVGYAGGSKTNPEFR 84 (182)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~fagGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~ 84 (182)
||++....+++|+....++..=..+...+.-++..-.++..-..-++-|.|+++.=..--+...+-+-=..-..=.|+|+
T Consensus 2 k~~~~~~~~~~~~~~~~a~aewtgd~~~~y~Snv~In~f~~G~id~~~yFCI~~~~~~Gs~~~~iaC~V~~~s~w~~sf~ 81 (135)
T PRK15266 2 KKFVPVYTLLILIYSFNASAEWTGDNTNAYYSDEVISELHVGQIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFK 81 (135)
T ss_pred cEeehhhhHHHhhhcCcchhhhcCCcccceecceEEeecceeeEcCCceEEEEEEecCCCCCceEEEEEeccccchhhHH
Confidence 56666666666666665554333232222111111122333344457777765432111011111111111111224555
Q ss_pred ccC-------CceeEEEEEEcCCCCCHHHHHHHH
Q 030161 85 NLG-------DHAESVQVEYDPRVINFRQLLEVF 111 (182)
Q Consensus 85 ~v~-------gH~EaV~V~yDp~~is~~~LL~~F 111 (182)
..- ---+.|||.|+|++-++....+.|
T Consensus 82 ~l~~qA~YyYtTG~~VRiYy~~nVWt~p~F~~af 115 (135)
T PRK15266 82 ELLDQARYFYSTGQSVRIHVQKNIWTYPLFVNTF 115 (135)
T ss_pred HHHHhhheeEecCceEEEEEcCCcccCchhhhhc
Confidence 432 123789999999987776655554
No 29
>PRK12386 fumarate reductase iron-sulfur subunit; Provisional
Probab=37.37 E-value=1.5e+02 Score=25.61 Aligned_cols=78 Identities=12% Similarity=0.037 Sum_probs=51.0
Q ss_pred ceeEEEEEEcCCCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCceeeeccCCHHHHHHHHHHHHHHHhhcCCCceEEEEee
Q 030161 89 HAESVQVEYDPRVINFRQLLEVFWTSHDCRQVFGQGPDVGNQYRSIIFTNGTEESRLAAHSKEREQMKSKSSIVTTQIQQ 168 (182)
Q Consensus 89 H~EaV~V~yDp~~is~~~LL~~F~~~hdPt~~~~Qg~d~G~QYRSaIf~~~~~q~~~a~~~~~~~~~~~~~~~i~TeI~p 168 (182)
|-|.++|.++|. .|.-++|+..-...||+..-|.|+..|-==.-++.+.... . .+.+.....- ..+. +++|+|
T Consensus 18 ~~q~y~v~~~~~-~tvLd~L~~i~~~~d~~l~~r~~C~~g~CGsCa~~InG~p--~--laC~t~~~~~-~~~~-~itiep 90 (251)
T PRK12386 18 ELQDYTVEVNEG-EVVLDVIHRLQATQAPDLAVRWNCKAGKCGSCSAEINGRP--R--LMCMTRMSTF-DEDE-TVTVTP 90 (251)
T ss_pred ceEEEEEeCCCC-CCHHHHHHHhccccCCCCcccCCCCCCcCCCCEEEECccE--e--ccHHhHHHHh-CCCC-eEEEcc
Confidence 578999999875 5676666665556799999999998887777788887632 1 1111111111 1112 368999
Q ss_pred CCCcc
Q 030161 169 LVAFY 173 (182)
Q Consensus 169 ~~~Fy 173 (182)
+.+|-
T Consensus 91 l~~fp 95 (251)
T PRK12386 91 MRTFP 95 (251)
T ss_pred CCCCC
Confidence 98763
No 30
>KOG4309 consensus Transcription mediator-related factor [Transcription]
Probab=35.65 E-value=32 Score=28.98 Aligned_cols=44 Identities=30% Similarity=0.454 Sum_probs=29.6
Q ss_pred eEEEEEEcCCCCC------HHHHHHHHHhcCCCCcCCCCCCCCCCCceeeeccC
Q 030161 91 ESVQVEYDPRVIN------FRQLLEVFWTSHDCRQVFGQGPDVGNQYRSIIFTN 138 (182)
Q Consensus 91 EaV~V~yDp~~is------~~~LL~~F~~~hdPt~~~~Qg~d~G~QYRSaIf~~ 138 (182)
=+|+|+|||.+|- ..+.|+-||..|-|+.. .-.|.+=...||--
T Consensus 140 i~vEIEY~pcvI~~~Cw~M~~Eflqsflg~~~p~aP----~~fg~t~h~~~y~p 189 (217)
T KOG4309|consen 140 ISVEIEYGPCVIASDCWSMLLEFLQSFLGSHTPGAP----AVFGNTRHDAVYGP 189 (217)
T ss_pred EEEEEeeCCEEEhHHHHHHHHHHHHHHhcccCCCch----HhhcCccCccccCc
Confidence 4689999999984 25677778888888743 23344445566643
No 31
>COG5053 CDC33 Translation initiation factor 4E (eIF-4E) [Translation, ribosomal structure and biogenesis]
Probab=35.27 E-value=77 Score=27.07 Aligned_cols=50 Identities=16% Similarity=0.086 Sum_probs=35.0
Q ss_pred HHHHHHHHHhcCCCCcCCC---CCCCCCCCceeeeccCCHHHHHHHHHHHHHH
Q 030161 104 FRQLLEVFWTSHDCRQVFG---QGPDVGNQYRSIIFTNGTEESRLAAHSKERE 153 (182)
Q Consensus 104 ~~~LL~~F~~~hdPt~~~~---Qg~d~G~QYRSaIf~~~~~q~~~a~~~~~~~ 153 (182)
+..||-.+++..|||...- -++.+..-||-|||+.+...++...+...+.
T Consensus 132 l~tlla~igeT~Dp~~~ei~GvV~n~rkgfyKlAiWtr~~~n~dvl~~ig~ef 184 (217)
T COG5053 132 LRTLLAAIGETLDPTGSEIGGVVGNMRKGFYKLAIWTRNCNNKDVLGAIGNEF 184 (217)
T ss_pred HHHHHHHHhhccCCCCCeeccEEEEeecCceEEEEEecCCCcHHHHHHHHHHH
Confidence 3556677899999974321 2467778999999999976666665544433
No 32
>COG3017 LolB Outer membrane lipoprotein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]
Probab=34.13 E-value=43 Score=28.54 Aligned_cols=31 Identities=26% Similarity=0.259 Sum_probs=19.6
Q ss_pred CcchhhHHHHHHHHHHHhhccccc-ccCCCCC
Q 030161 1 MVLSKRYLFFSVLHLLLLTDTALC-IRFPDRV 31 (182)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 31 (182)
|+++||..++.+++++++..+|+. ...|..+
T Consensus 1 ~~~~~~~~~~l~~~As~LL~aC~~~~~~~~~~ 32 (206)
T COG3017 1 MPMMKRLLFLLLALASLLLTACTLTASRPPNN 32 (206)
T ss_pred CchHHHHHHHHHHHHHHHHHhccCcCCCCCCC
Confidence 788888888877776555555533 3444433
No 33
>KOG2003 consensus TPR repeat-containing protein [General function prediction only]
Probab=33.84 E-value=14 Score=35.76 Aligned_cols=15 Identities=33% Similarity=0.470 Sum_probs=12.5
Q ss_pred EEcCCcccchhhhhc
Q 030161 47 VFALGSFWRSEAVFG 61 (182)
Q Consensus 47 ~fagGCFWg~E~~F~ 61 (182)
-||.||-||+|.+=.
T Consensus 397 ~fa~g~dwcle~lk~ 411 (840)
T KOG2003|consen 397 DFAAGCDWCLESLKA 411 (840)
T ss_pred chhcccHHHHHHHHH
Confidence 479999999998754
No 34
>PF02083 Urotensin_II: Urotensin II; InterPro: IPR001483 Urotensin II, a small peptide that contains a disulphide bridge, was originally isolated from the caudal portion of the spinal cord of teleost and elasmobranch fish []. The peptide has also been found in the brain of frogs []. Urotensin II seems to be involved in smooth muscle stimulation.; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=33.81 E-value=13 Score=17.90 Aligned_cols=6 Identities=33% Similarity=1.171 Sum_probs=4.4
Q ss_pred CCcccc
Q 030161 50 LGSFWR 55 (182)
Q Consensus 50 gGCFWg 55 (182)
.-|||.
T Consensus 4 ~~CFWK 9 (12)
T PF02083_consen 4 SECFWK 9 (12)
T ss_pred cchhhh
Confidence 469995
No 35
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=33.40 E-value=47 Score=34.14 Aligned_cols=53 Identities=21% Similarity=0.221 Sum_probs=41.7
Q ss_pred EEEcCCcccch---hhhhcccCCeEEEeeeecCCCCCCCCccccCCceeEEEEEEcCCCCCHHHHHHHHHh
Q 030161 46 AVFALGSFWRS---EAVFGCLNGVVRTTVGYAGGSKTNPEFRNLGDHAESVQVEYDPRVINFRQLLEVFWT 113 (182)
Q Consensus 46 a~fagGCFWg~---E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~gH~EaV~V~yDp~~is~~~LL~~F~~ 113 (182)
-.-||+|-=|+ |...++..||.+..|--..+ .-+|.|||+++|.+.+++.+=+
T Consensus 74 ~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~---------------~~~v~~dp~v~s~~~~~e~ie~ 129 (951)
T KOG0207|consen 74 SVNGMTCASCVATIERNLRKIEGVESAVVALSAS---------------KAEVIYDPAVTSPDSIAESIED 129 (951)
T ss_pred EecCceeHHHHHHHHHHhhccCCcceEEEEeecc---------------ceeEEECCcccCchhHHHHHHh
Confidence 45589999887 56677789999887766533 4469999999999999988754
No 36
>PF15240 Pro-rich: Proline-rich
Probab=30.58 E-value=45 Score=27.84 Aligned_cols=21 Identities=19% Similarity=0.074 Sum_probs=13.3
Q ss_pred hhHHHHHHHHHHHhhcccccc
Q 030161 5 KRYLFFSVLHLLLLTDTALCI 25 (182)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~ 25 (182)
|+.+||||.||.|+++-...-
T Consensus 1 MLlVLLSvALLALSSAQ~~dE 21 (179)
T PF15240_consen 1 MLLVLLSVALLALSSAQSTDE 21 (179)
T ss_pred ChhHHHHHHHHHhhhcccccc
Confidence 456788888876655544433
No 37
>TIGR00632 vsr DNA mismatch endonuclease Vsr. All proteins in this family for which functions are known are G:T mismatch endonucleases that function in a specialized mismatch repair process used usually to repair G:T mismatches in specific sections of the genome. This family was based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Members of this family typically are found near to a DNA cytosine methyltransferase.
Probab=29.67 E-value=31 Score=26.74 Aligned_cols=19 Identities=26% Similarity=0.649 Sum_probs=14.9
Q ss_pred CCCCCCccEEEEcCCcccc
Q 030161 37 DELGRPLKAAVFALGSFWR 55 (182)
Q Consensus 37 ~~~~~~~~~a~fagGCFWg 55 (182)
|.--...+.|+|--||||+
T Consensus 50 D~~~~~~klaIfVDGcfWH 68 (117)
T TIGR00632 50 DIVFDEYRCVIFIHGCFWH 68 (117)
T ss_pred cEEecCCCEEEEEcccccc
Confidence 3333567899999999999
No 38
>COG3045 CreA Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.77 E-value=48 Score=27.22 Aligned_cols=23 Identities=39% Similarity=0.505 Sum_probs=17.3
Q ss_pred CcchhhHHHHHHHHHHHhhcccc
Q 030161 1 MVLSKRYLFFSVLHLLLLTDTAL 23 (182)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~ 23 (182)
|.|..|.++|+.++|++++..+.
T Consensus 1 ~~~~~~~~ll~~~~~~~l~~~a~ 23 (165)
T COG3045 1 MLMKIRLLLLAGLLLLLLVGLAH 23 (165)
T ss_pred CcchHHHHHHHHHHHHHhccccc
Confidence 78899999999986665555544
No 39
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=27.28 E-value=67 Score=32.94 Aligned_cols=48 Identities=17% Similarity=0.347 Sum_probs=37.1
Q ss_pred cchhhhhcccCCeEEEeeeecCCCCCCCCccccCCceeEEEEEEcCCC-----CCHHHHHHHHHhcC
Q 030161 54 WRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLGDHAESVQVEYDPRV-----INFRQLLEVFWTSH 115 (182)
Q Consensus 54 Wg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~gH~EaV~V~yDp~~-----is~~~LL~~F~~~h 115 (182)
|-++..+.++|||.++.++ |+ .-+.++|..||++ +|..++.+..=...
T Consensus 160 ~~l~~~L~~i~GV~~V~~~--G~------------~~~ei~V~vd~~kl~~~gls~~dV~~al~~~~ 212 (1025)
T PRK10614 160 TQLAQTISQIDGVGDVDVG--GS------------SLPAVRVGLNPQALFNQGVSLDDVRQAISNAN 212 (1025)
T ss_pred HHHHHHhcCCCCceEEEec--CC------------CceEEEEEeCHHHHHHcCCCHHHHHHHHHHhC
Confidence 4466677889999999885 33 2588999999987 68888888776544
No 40
>PF09299 Mu-transpos_C: Mu transposase, C-terminal; InterPro: IPR015378 This domain is found in various prokaryotic integrases and transposases. It adopts a beta-barrel structure with Greek-key topology []. ; PDB: 1BCO_A 1BCM_B.
Probab=26.49 E-value=34 Score=22.68 Aligned_cols=13 Identities=38% Similarity=0.797 Sum_probs=9.7
Q ss_pred eEEEEEEcCCCCC
Q 030161 91 ESVQVEYDPRVIN 103 (182)
Q Consensus 91 EaV~V~yDp~~is 103 (182)
+.|.|.|||..++
T Consensus 36 ~~V~vryDp~dl~ 48 (62)
T PF09299_consen 36 QKVRVRYDPDDLS 48 (62)
T ss_dssp SEEEEEE-GGGTT
T ss_pred CEEEEEECcccCC
Confidence 5599999998764
No 41
>PRK14624 hypothetical protein; Provisional
Probab=24.99 E-value=47 Score=25.67 Aligned_cols=17 Identities=6% Similarity=0.147 Sum_probs=14.9
Q ss_pred CCceeEEEEEEcCCCCC
Q 030161 87 GDHAESVQVEYDPRVIN 103 (182)
Q Consensus 87 ~gH~EaV~V~yDp~~is 103 (182)
.|.-|.+.|..||+.+.
T Consensus 48 nG~~~i~~i~Idp~lld 64 (115)
T PRK14624 48 TGEGQITNVFINKQLFD 64 (115)
T ss_pred EcCccEEEEEECHHHcC
Confidence 47789999999999884
No 42
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=23.76 E-value=71 Score=32.51 Aligned_cols=46 Identities=20% Similarity=0.433 Sum_probs=33.2
Q ss_pred cchhhhhcccCCeEEEeeeecCCCCCCCCccccCCceeEEEEEEcCCC-----CCHHHHHHHHHh
Q 030161 54 WRSEAVFGCLNGVVRTTVGYAGGSKTNPEFRNLGDHAESVQVEYDPRV-----INFRQLLEVFWT 113 (182)
Q Consensus 54 Wg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~v~gH~EaV~V~yDp~~-----is~~~LL~~F~~ 113 (182)
|-++..+.++|||.++.+. ||. .+.|+|.+||++ +|..++.+..=.
T Consensus 159 ~~l~~~L~~i~gV~~v~~~--G~~------------~~ei~i~~d~~kl~~~gls~~~v~~~l~~ 209 (1021)
T PF00873_consen 159 EQLKPRLERIPGVARVDIS--GGR------------EREIQIELDPEKLAAYGLSLSDVAQALQA 209 (1021)
T ss_dssp HCTHHHHHTSTTEEEEEES--SS--------------EEEEEEE-HHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHhccceeEEEEEEec--cch------------hhhhhheechhhhhhhCCCHHHHHHHHHH
Confidence 4566678889999999873 553 799999999987 688998887654
No 43
>PF04990 RNA_pol_Rpb1_7: RNA polymerase Rpb1, domain 7; InterPro: IPR007073 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 interacts with the lobe domain of Rpb2 (IPR007642 from INTERPRO) [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 1Y77_A 3CQZ_A 3GTM_A 1TWA_A 4A3I_A 2NVY_A 2NVT_A 1I6H_A 1TWF_A ....
Probab=22.23 E-value=42 Score=26.46 Aligned_cols=27 Identities=30% Similarity=0.560 Sum_probs=20.7
Q ss_pred eeEEEEEEcCCCCCH-----HHHHHHHHhcCC
Q 030161 90 AESVQVEYDPRVINF-----RQLLEVFWTSHD 116 (182)
Q Consensus 90 ~EaV~V~yDp~~is~-----~~LL~~F~~~hd 116 (182)
+...+|.|||..-+= .++++.||..-|
T Consensus 7 t~~teIyYDPdp~~Tvi~eD~e~V~~y~e~pd 38 (135)
T PF04990_consen 7 TASTEIYYDPDPRNTVIEEDREFVESYFEIPD 38 (135)
T ss_dssp ECEEEEEE-SSTTSSSSSTTHCHHHHCCCTT-
T ss_pred hhheeEEECCCCCCCcchhhHHHHHHHHhCCC
Confidence 578899999987644 779999998866
No 44
>PRK15265 subtilase cytotoxin subunit B-like protein; Provisional
Probab=20.98 E-value=1.2e+02 Score=24.23 Aligned_cols=21 Identities=19% Similarity=0.428 Sum_probs=16.8
Q ss_pred eEEEEEEcCCCCCHHHHHHHH
Q 030161 91 ESVQVEYDPRVINFRQLLEVF 111 (182)
Q Consensus 91 EaV~V~yDp~~is~~~LL~~F 111 (182)
+-|+|.|+|++-+.-..-+.|
T Consensus 91 ~~vRiy~~~nVWTdp~F~~~f 111 (134)
T PRK15265 91 KRIRVYYAPDVWTNNSFVRAL 111 (134)
T ss_pred CcEEEEEcCCcccCcHHHhhh
Confidence 678888888888777777666
Done!