Query 025343
Match_columns 254
No_of_seqs 293 out of 2421
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 04:53:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025343.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025343hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK14018 trifunctional thiored 100.0 9.4E-73 2E-77 553.1 18.5 197 47-249 286-506 (521)
2 COG0229 Conserved domain frequ 100.0 4E-67 8.7E-72 435.8 11.8 126 123-250 2-131 (140)
3 TIGR00357 methionine-R-sulfoxi 100.0 1.4E-65 3E-70 426.7 12.6 123 125-249 2-127 (134)
4 PRK00222 methionine sulfoxide 100.0 3.2E-65 6.9E-70 427.9 13.0 126 122-249 2-130 (142)
5 PRK05508 methionine sulfoxide 100.0 6.3E-65 1.4E-69 415.1 12.0 117 132-249 2-118 (119)
6 PF01641 SelR: SelR domain; I 100.0 1.1E-64 2.3E-69 416.9 9.5 121 127-248 1-124 (124)
7 KOG0856 Predicted pilin-like t 100.0 1.5E-63 3.2E-68 415.3 11.5 136 116-251 7-145 (146)
8 PRK05550 bifunctional methioni 100.0 6.6E-58 1.4E-62 420.0 10.3 121 129-250 2-122 (283)
9 COG0225 MsrA Peptide methionin 99.7 3.7E-17 7.9E-22 141.7 5.9 70 47-119 95-168 (174)
10 PRK14054 methionine sulfoxide 99.6 1.1E-15 2.5E-20 132.2 4.1 72 46-120 91-165 (172)
11 PRK13014 methionine sulfoxide 99.5 6.4E-15 1.4E-19 129.1 6.0 72 46-120 96-170 (186)
12 TIGR00401 msrA methionine-S-su 99.5 1.6E-14 3.6E-19 122.4 5.1 59 46-107 88-149 (149)
13 PF01625 PMSR: Peptide methion 99.5 2.8E-14 6E-19 121.6 4.6 65 45-113 87-154 (155)
14 PRK05528 methionine sulfoxide 99.5 7.1E-14 1.5E-18 119.5 5.4 60 47-113 85-147 (156)
15 PRK00058 methionine sulfoxide 99.4 2.8E-13 6.1E-18 121.0 4.4 64 46-112 133-201 (213)
16 KOG1635 Peptide methionine sul 99.3 1.2E-12 2.6E-17 114.0 5.1 58 48-110 114-174 (191)
17 PRK05550 bifunctional methioni 99.3 2E-12 4.3E-17 119.8 5.9 61 46-112 215-278 (283)
18 PF03226 Yippee-Mis18: Yippee 90.8 0.13 2.8E-06 39.9 1.6 79 163-243 2-92 (96)
19 COG1645 Uncharacterized Zn-fin 70.3 1.4 3.1E-05 37.3 0.0 23 164-186 29-52 (131)
20 PF09855 DUF2082: Nucleic-acid 58.0 6.2 0.00013 29.5 1.4 43 164-216 1-43 (64)
21 PRK00420 hypothetical protein; 55.5 5.9 0.00013 32.7 1.1 23 164-186 24-48 (112)
22 TIGR01384 TFS_arch transcripti 51.8 18 0.00038 28.2 3.2 68 152-223 6-76 (104)
23 PF11781 RRN7: RNA polymerase 51.7 7.6 0.00016 25.7 0.9 21 152-172 14-34 (36)
24 PF03811 Zn_Tnp_IS1: InsA N-te 49.2 20 0.00044 23.8 2.7 27 207-236 3-30 (36)
25 PF06677 Auto_anti-p27: Sjogre 49.0 6.7 0.00014 26.9 0.3 13 165-177 19-31 (41)
26 smart00778 Prim_Zn_Ribbon Zinc 40.8 18 0.0004 24.3 1.5 16 155-170 17-32 (37)
27 PF08271 TF_Zn_Ribbon: TFIIB z 38.1 18 0.0004 24.2 1.2 28 159-188 15-42 (43)
28 PRK04351 hypothetical protein; 37.9 49 0.0011 28.2 4.0 15 208-222 131-145 (149)
29 PF04828 GFA: Glutathione-depe 37.5 22 0.00048 25.9 1.7 33 207-245 46-78 (92)
30 PF03119 DNA_ligase_ZBD: NAD-d 32.3 29 0.00064 21.7 1.3 23 211-240 1-23 (28)
31 PF06170 DUF983: Protein of un 32.1 24 0.00052 27.6 1.1 20 208-227 7-26 (86)
32 PRK12495 hypothetical protein; 31.7 18 0.00038 33.4 0.3 13 162-174 41-53 (226)
33 PHA02540 61 DNA primase; Provi 31.1 24 0.00053 34.1 1.2 17 155-171 45-63 (337)
34 PF04502 DUF572: Family of unk 30.9 43 0.00093 31.8 2.8 71 147-247 35-110 (324)
35 COG1405 SUA7 Transcription ini 29.5 41 0.00089 31.7 2.4 29 159-189 16-44 (285)
36 PRK00423 tfb transcription ini 29.4 45 0.00098 31.3 2.6 32 159-192 26-57 (310)
37 PF07295 DUF1451: Protein of u 29.2 27 0.00059 29.9 1.1 40 124-173 83-122 (146)
38 COG3791 Uncharacterized conser 29.0 23 0.0005 29.3 0.6 21 157-177 63-83 (133)
39 PF15288 zf-CCHC_6: Zinc knuck 27.4 23 0.00051 24.4 0.3 15 210-225 2-16 (40)
40 PRK04179 rpl37e 50S ribosomal 25.3 38 0.00082 25.4 1.1 28 162-189 16-44 (62)
41 PRK08624 hypothetical protein; 24.4 59 0.0013 32.1 2.5 20 158-177 54-76 (373)
42 KOG2691 RNA polymerase II subu 23.6 65 0.0014 26.8 2.2 34 202-235 65-99 (113)
43 PTZ00073 60S ribosomal protein 23.3 43 0.00093 26.9 1.1 29 162-190 15-43 (91)
44 TIGR03655 anti_R_Lar restricti 22.7 66 0.0014 22.4 1.9 18 155-172 18-35 (53)
45 PF13248 zf-ribbon_3: zinc-rib 22.2 42 0.00092 20.3 0.7 21 165-186 4-24 (26)
46 PRK13130 H/ACA RNA-protein com 22.2 51 0.0011 24.1 1.2 12 165-176 19-30 (56)
47 COG3634 AhpF Alkyl hydroperoxi 22.2 55 0.0012 32.9 1.8 35 159-193 337-371 (520)
48 PF01352 KRAB: KRAB box; Inte 22.2 99 0.0021 20.9 2.6 22 122-144 7-28 (41)
49 cd04984 IgV_L_lambda Immunoglo 21.7 49 0.0011 24.8 1.1 13 157-169 71-83 (98)
50 cd04983 IgV_TCR_alpha_like Imm 21.6 59 0.0013 24.4 1.6 14 158-171 79-92 (109)
51 PF09965 DUF2199: Uncharacteri 21.3 30 0.00065 29.7 -0.1 25 164-198 1-25 (148)
52 COG1885 Uncharacterized protei 21.3 37 0.0008 28.2 0.4 14 160-173 46-59 (115)
53 cd04980 IgV_L_kappa Immunoglob 20.1 48 0.001 25.2 0.8 12 158-169 80-91 (106)
No 1
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=100.00 E-value=9.4e-73 Score=553.08 Aligned_cols=197 Identities=29% Similarity=0.466 Sum_probs=177.5
Q ss_pred ccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCceeeeccceeecccceechhhcc---ccccccCceeeeccCC-C--
Q 025343 47 SSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGVVLAVASG-P-- 120 (254)
Q Consensus 47 s~~~~~aIFy~neeQk~~A~~~l~~l~~s~~~~k~I~vTe~~I~p~~~Fy~AEeYHQ---~KNP~~ggVVlaAaPk-~-- 120 (254)
-.||+++|||+|++|+++|+++++.+++ .+.++| +|+ |.|+++||+||+||| .|||.++..+....-. .
T Consensus 286 G~qYrs~I~~~~~eq~~~a~~~~~~~~~--~~~~~i-~te--i~~~~~Fy~AE~yHQ~Yl~k~p~~yc~~~~~~~~~~~~ 360 (521)
T PRK14018 286 GTQYRSGVYYTDPADKAVIAAALKREQQ--KYQLPL-VVE--NEPLKNFYDAEEYHQDYLIKNPNGYCHIDLRKADEPLP 360 (521)
T ss_pred CCCceEEEEeCCHHHHHHHHHHHHHHHH--HcCCCe-EEE--EecCCCeeecHHHHHHHHHhCCCceeEeeccccccccc
Confidence 4799999999999999999999999886 478899 999 999999999999999 8999988776554211 0
Q ss_pred ---------------CCCCCCHHHHHhcCCHHHHHHhhhCCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCccCCCC
Q 025343 121 ---------------ASVNKSEEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCG 185 (254)
Q Consensus 121 ---------------~~~~~s~~ewr~~Ltp~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~G 185 (254)
....++++|||+.|||+||+|||++|||+||||+||+++++|+|+|++||+|||+|++|||||||
T Consensus 361 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~Lt~~~y~v~~~~gtE~~f~~~~~~~~~~G~y~c~~c~~pLf~s~~Kf~sg~G 440 (521)
T PRK14018 361 GKTKTAPQGKGFDAATYKKPSDAELKRTLTEEQYQITQNAATERAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGCG 440 (521)
T ss_pred ccccccccccccchhhccCCChHHHhccCCHHHHHHHHhcCCCCCCCCCCcCCCCCEEEEecCCCCccccCcccccCCCC
Confidence 12356999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccccC-CCeeeecCC-CCC-eeEEEccccCCCcccccCCCCCCCCCCceeeecccceeeeeCC
Q 025343 186 WPAFYEGLP-GAINCSPDP-DGL-RIEITCAACGGHLGHVFKGEGFPTPTDERHCVNSISLKFVPAN 249 (254)
Q Consensus 186 WPSF~~~i~-~~v~~~~d~-~g~-RtEv~C~~Cg~HLGHVF~d~G~P~ptg~RyCINs~aL~F~p~~ 249 (254)
||||++||+ ++|....|. +|| ||||+|++||+||||||+| |+++|||+||||||+||+|+|.+
T Consensus 441 WPsF~~~i~~~~v~~~~d~s~g~~R~Ev~c~~c~~HLGHvf~d-gp~~~~g~RyCiNs~~l~f~~~~ 506 (521)
T PRK14018 441 WPSFTRPIDAKVVTEHDDFSYNMRRTEVRSRAADSHLGHVFPD-GPRDKGGLRYCINGASLKFIPLE 506 (521)
T ss_pred CcccCcccCcCceEEeeccCCCceEEEEEECCCCCcCCcccCC-CCCCCCCCEeeeceeEEEeecch
Confidence 999999995 678888886 677 9999999999999999986 43357999999999999999985
No 2
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4e-67 Score=435.75 Aligned_cols=126 Identities=48% Similarity=0.962 Sum_probs=119.2
Q ss_pred CCCCHHHHHhcCCHHHHHHhhhCCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCccCCCCCccccccc-CCCeeeec
Q 025343 123 VNKSEEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGL-PGAINCSP 201 (254)
Q Consensus 123 ~~~s~~ewr~~Ltp~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~~i-~~~v~~~~ 201 (254)
+.++|++||+.|||+||+|||++|||+||+|+||+++++|+|+|++||+|||+|++|||||||||||++|| +++|..++
T Consensus 2 ~~~sd~e~~~~Lt~~qy~Vtq~~gTE~pft~~y~~~~~~GiY~c~~cg~pLF~S~~KfdSgcGWPSF~~pi~~~~I~~~~ 81 (140)
T COG0229 2 IKPSDEELKEKLTPEQYRVTQNHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSEDKFDSGCGWPSFTKPISPDAITYKE 81 (140)
T ss_pred CccchHHHHHhcCHHHHHHHHhcCCCCCCCChhhcccCCceEEeecCCCccccccccccCCCCCccccccCCcccceEee
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999 66999998
Q ss_pred CC-CCC-eeEEEccccCCCcccccCCCCCCCCCC-ceeeecccceeeeeCCC
Q 025343 202 DP-DGL-RIEITCAACGGHLGHVFKGEGFPTPTD-ERHCVNSISLKFVPANS 250 (254)
Q Consensus 202 d~-~g~-RtEv~C~~Cg~HLGHVF~d~G~P~ptg-~RyCINs~aL~F~p~~~ 250 (254)
|. +|| ||||+|++||+||||||+| ||.||| +|||||||||+|+|.+.
T Consensus 82 D~S~gM~RtEVrc~~c~sHLGHVF~D--GP~~tgglRYCINSasL~Fip~~~ 131 (140)
T COG0229 82 DRSHGMVRTEVRCANCDSHLGHVFPD--GPPPTGGLRYCINSASLRFIPKEE 131 (140)
T ss_pred ccCCCcEEEEEEecCCCCccccccCC--CCCCCCCeeEeecchheeecchhh
Confidence 86 688 9999999999999999997 588887 99999999999999853
No 3
>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=100.00 E-value=1.4e-65 Score=426.67 Aligned_cols=123 Identities=45% Similarity=0.869 Sum_probs=118.1
Q ss_pred CCHHHHHhcCCHHHHHHhhhCCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCccCCCCCccccccc-CCCeeeecCC
Q 025343 125 KSEEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGL-PGAINCSPDP 203 (254)
Q Consensus 125 ~s~~ewr~~Ltp~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~~i-~~~v~~~~d~ 203 (254)
++++|||+.|||+||+|||++|||+||||+||+++++|+|+|++||+|||+|++|||||||||||+++| +++|.++.|.
T Consensus 2 ~~~~ewr~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~~V~~~~D~ 81 (134)
T TIGR00357 2 PSDEELKKKLTPLQYEVTQNAGTEPPFTNEYWDNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAYERDE 81 (134)
T ss_pred CCHHHHHHhCCHHHHHHHHHhCCCCCCCCCCCCCCCCeEEEccCCCCccccccchhcCCCCCcCcCcccCCCceEEeecC
Confidence 589999999999999999999999999999999999999999999999999999999999999999999 7899999886
Q ss_pred -CCC-eeEEEccccCCCcccccCCCCCCCCCCceeeecccceeeeeCC
Q 025343 204 -DGL-RIEITCAACGGHLGHVFKGEGFPTPTDERHCVNSISLKFVPAN 249 (254)
Q Consensus 204 -~g~-RtEv~C~~Cg~HLGHVF~d~G~P~ptg~RyCINs~aL~F~p~~ 249 (254)
.|| ||||+|++||+||||||+| ||+|||+||||||+||+|+|.+
T Consensus 82 s~gm~RtEv~C~~Cg~HLGHVF~D--GP~ptg~RyCINs~sL~F~p~~ 127 (134)
T TIGR00357 82 SHGMIRTEVRCRNCDAHLGHVFDD--GPEPTGLRYCINSAALKFIPLE 127 (134)
T ss_pred CCCcEEEEEEecCCCCccCcccCC--CCCCCCceEeecceeEecccch
Confidence 587 9999999999999999986 4899999999999999999975
No 4
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=3.2e-65 Score=427.94 Aligned_cols=126 Identities=51% Similarity=0.986 Sum_probs=120.1
Q ss_pred CCCCCHHHHHhcCCHHHHHHhhhCCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCccCCCCCccccccc-CCCeeee
Q 025343 122 SVNKSEEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGL-PGAINCS 200 (254)
Q Consensus 122 ~~~~s~~ewr~~Ltp~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~~i-~~~v~~~ 200 (254)
++.++++|||+.|||+||+|||++||||||||+||+++++|+|+|++||+|||+|++|||||||||||+++| +++|+.+
T Consensus 2 ~~~~~~~ew~~~Lt~~qy~V~r~~gTE~pftg~~~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~~V~~~ 81 (142)
T PRK00222 2 KIEKSKEEWKKQLTPEQYRVTQEHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKPIDEEAIREL 81 (142)
T ss_pred CccCCHHHHHhhCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEecCCCchhcCCcccccCCCCCcCcCcccCCCceEEe
Confidence 456899999999999999999999999999999999999999999999999999999999999999999999 5799999
Q ss_pred cCC-CCC-eeEEEccccCCCcccccCCCCCCCCCCceeeecccceeeeeCC
Q 025343 201 PDP-DGL-RIEITCAACGGHLGHVFKGEGFPTPTDERHCVNSISLKFVPAN 249 (254)
Q Consensus 201 ~d~-~g~-RtEv~C~~Cg~HLGHVF~d~G~P~ptg~RyCINs~aL~F~p~~ 249 (254)
.|. +|| ||||+|++||+||||||+| ||+|||+||||||+||+|+|++
T Consensus 82 ~D~s~gm~RtEv~C~~Cg~HLGHVF~D--GP~ptg~RyCINs~sL~F~p~~ 130 (142)
T PRK00222 82 RDTSHGMVRTEVRCANCDSHLGHVFPD--GPKPTGLRYCINSASLKFIPKD 130 (142)
T ss_pred eccCCCceEEEEEeCCCCCccCcccCC--CCCCCCCEeeeceeeEEeeccc
Confidence 886 687 9999999999999999986 4899999999999999999985
No 5
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=6.3e-65 Score=415.10 Aligned_cols=117 Identities=57% Similarity=1.098 Sum_probs=112.5
Q ss_pred hcCCHHHHHHhhhCCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCccCCCCCcccccccCCCeeeecCCCCCeeEEE
Q 025343 132 AILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGLPGAINCSPDPDGLRIEIT 211 (254)
Q Consensus 132 ~~Ltp~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~~i~~~v~~~~d~~g~RtEv~ 211 (254)
++|||+||+|||++||||||+|+||+++++|+|+|++||+|||+|++|||||||||||++||+++|..+.|..|+||||+
T Consensus 2 ~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~v~~~~D~~~~RtEv~ 81 (119)
T PRK05508 2 NELTPEEEAVILRKGTEPPFSGEYNDFFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDDEIKGAVKRIPDADGRRTEIV 81 (119)
T ss_pred CcCCHHHHHHHHhcCCCCCCCCCCcCcCCCeEEEecCCCCccccccccccCCCCCcccCcccccceEEEecCCCcEEEEE
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999888899999
Q ss_pred ccccCCCcccccCCCCCCCCCCceeeecccceeeeeCC
Q 025343 212 CAACGGHLGHVFKGEGFPTPTDERHCVNSISLKFVPAN 249 (254)
Q Consensus 212 C~~Cg~HLGHVF~d~G~P~ptg~RyCINs~aL~F~p~~ 249 (254)
|++||+||||||+|| ||+|||+|||||||||+|+|+.
T Consensus 82 C~~C~~HLGHVF~d~-gp~ptg~RyCINS~sL~F~p~~ 118 (119)
T PRK05508 82 CANCGGHLGHVFEGE-GFTPKNTRHCVNSISLKFVPDK 118 (119)
T ss_pred eCCCCCccCcccCCC-CCCCCCCEEeecceeEEeecCC
Confidence 999999999999975 5889999999999999999975
No 6
>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=100.00 E-value=1.1e-64 Score=416.85 Aligned_cols=121 Identities=59% Similarity=1.159 Sum_probs=110.3
Q ss_pred HHHHHhcCCHHHHHHhhhCCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCccCCCCCcccccccCC-CeeeecCC-C
Q 025343 127 EEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGLPG-AINCSPDP-D 204 (254)
Q Consensus 127 ~~ewr~~Ltp~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~~i~~-~v~~~~d~-~ 204 (254)
|+|||++|||+||+|||++|||+||||+|++++++|+|+|++||+|||+|++|||||||||||+++|++ +|....|. .
T Consensus 1 d~ew~~~Lt~~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~~v~~~~D~s~ 80 (124)
T PF01641_consen 1 DEEWRKRLTPEQYRVLREKGTERPFSGEYWDHKEEGIYVCAVCGTPLFSSDTKFDSGCGWPSFWQPIPGDAVKEREDFSH 80 (124)
T ss_dssp -HHHHHHSCHHHHHHHHHTTSSSTTSSGGCCTTSSEEEEETTTS-EEEEGGGEETSSSSSSEESSCSSTTSEEEEEEECT
T ss_pred CHHHHhhCCHHHHHHHHhcCCCCCCccCCcCCCCCEEEEcCCCCCccccCcccccCCcCCccccCcCChHHEEEeccccC
Confidence 689999999999999999999999999999999999999999999999999999999999999999965 99998886 5
Q ss_pred CC-eeEEEccccCCCcccccCCCCCCCCCCceeeecccceeeeeC
Q 025343 205 GL-RIEITCAACGGHLGHVFKGEGFPTPTDERHCVNSISLKFVPA 248 (254)
Q Consensus 205 g~-RtEv~C~~Cg~HLGHVF~d~G~P~ptg~RyCINs~aL~F~p~ 248 (254)
|| ||||+|++||+||||||+| |+++|||+||||||+||+|+|+
T Consensus 81 g~~R~Ev~C~~Cg~HLGHVF~D-Gp~~~tg~RyCINS~sL~F~p~ 124 (124)
T PF01641_consen 81 GMVRTEVRCARCGSHLGHVFDD-GPPPPTGLRYCINSASLKFIPK 124 (124)
T ss_dssp SSEEEEEEETTTCCEEEEEEST-SSTTCTSCEEEE-GGGEEEEE-
T ss_pred CceEEEEEecCCCCccccEeCC-CCCCCCCcEEEeeeeeEEEecC
Confidence 77 9999999999999999995 5334579999999999999995
No 7
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.5e-63 Score=415.27 Aligned_cols=136 Identities=72% Similarity=1.338 Sum_probs=127.8
Q ss_pred ccCCCCCCCCCHHHHHhcCCHHHHHHhhhCCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCccCCCCCccccccc-C
Q 025343 116 VASGPASVNKSEEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGL-P 194 (254)
Q Consensus 116 AaPk~~~~~~s~~ewr~~Ltp~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~~i-~ 194 (254)
.+|...+++++++|||++||||||+|||++|||+||+|+|++++++|+|+|++|++|||+|.+|||||||||||++.| +
T Consensus 7 ~~~~~~~v~k~~~EWr~~LsPeQ~~v~RekgTE~p~tGey~~~~e~GvY~C~~C~~pLykS~tKfdsgcGWPAF~e~i~~ 86 (146)
T KOG0856|consen 7 VAPKTGSVQKNDEEWRKVLSPEQFRVLREKGTERPGTGEYTKHFEEGVYVCAGCGTPLYKSTTKFDSGCGWPAFFEAIGP 86 (146)
T ss_pred ccCCCcccccCHHHHHhhcCHHHhhhhHhhcccCCCCcccccccCCceEEEeecCCccccccccccCCCCCchhhhccCC
Confidence 346678899999999999999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred CCeeeecCC--CCCeeEEEccccCCCcccccCCCCCCCCCCceeeecccceeeeeCCCC
Q 025343 195 GAINCSPDP--DGLRIEITCAACGGHLGHVFKGEGFPTPTDERHCVNSISLKFVPANSG 251 (254)
Q Consensus 195 ~~v~~~~d~--~g~RtEv~C~~Cg~HLGHVF~d~G~P~ptg~RyCINs~aL~F~p~~~~ 251 (254)
++|++++|. .|+|+||+|++||+||||||.+||+..||++|||||||||+|.|++++
T Consensus 87 gaI~r~~d~s~~~~R~Ev~Ca~C~~HLGHVF~~eG~~~Pt~~R~CiNS~sL~F~~~~~s 145 (146)
T KOG0856|consen 87 GAITRTPDNSRGGRRTEVSCATCGGHLGHVFKGEGPKTPTDERHCINSVSLKFVPADSS 145 (146)
T ss_pred CceeeccccCCCCcceEEEEeecCCceeeeecCCCCCCCCCceeEeeeeeeeeccCCCC
Confidence 999999995 356999999999999999999777555999999999999999999865
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=100.00 E-value=6.6e-58 Score=420.02 Aligned_cols=121 Identities=55% Similarity=1.060 Sum_probs=115.9
Q ss_pred HHHhcCCHHHHHHhhhCCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCccCCCCCcccccccCCCeeeecCCCCCee
Q 025343 129 EWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGLPGAINCSPDPDGLRI 208 (254)
Q Consensus 129 ewr~~Ltp~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~~i~~~v~~~~d~~g~Rt 208 (254)
.||++|||+||+|||++||||||+|+||+++++|+|+|++||+|||+|++|||||||||||+++|+++|..+.|..||||
T Consensus 2 ~~~~~Lt~~~y~v~r~~gTE~pf~g~~~~~~~~G~y~c~~c~~~LF~s~~Kf~sg~GWPsF~~~~~~~~~~~~d~~~~R~ 81 (283)
T PRK05550 2 DKMKSLTPFEYRVIEDKGTERPFSGEYYDHDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDDEIPGAVKRLPDADGRRT 81 (283)
T ss_pred hhhhhCCHHHHHHHHhcCCCCCCCCcCcCCCCCcEEEcCCCCchhcCChhhccCCCCCcCcCcccCCccEEEEcCCCceE
Confidence 69999999999999999999999999999999999999999999999999999999999999999998988888778999
Q ss_pred EEEccccCCCcccccCCCCCCCCCCceeeecccceeeeeCCC
Q 025343 209 EITCAACGGHLGHVFKGEGFPTPTDERHCVNSISLKFVPANS 250 (254)
Q Consensus 209 Ev~C~~Cg~HLGHVF~d~G~P~ptg~RyCINs~aL~F~p~~~ 250 (254)
||+|++||+||||||+|| ||+|||+||||||+||+|+|.+.
T Consensus 82 Ev~c~~c~~HLGHvF~dd-gp~ptg~RyCiNs~sL~f~p~~~ 122 (283)
T PRK05550 82 EIVCANCGAHLGHVFEGE-GLTPKNTRHCVNSASLDFVPAEE 122 (283)
T ss_pred EEEecCCCCccCcccCCC-CCCCCCccccccccccccCcccc
Confidence 999999999999999976 48899999999999999999854
No 9
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=99.68 E-value=3.7e-17 Score=141.71 Aligned_cols=70 Identities=17% Similarity=0.181 Sum_probs=63.1
Q ss_pred ccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCceeeeccceeecccceechhhcc---ccccccCcee-eeccCC
Q 025343 47 SSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGVV-LAVASG 119 (254)
Q Consensus 47 s~~~~~aIFy~neeQk~~A~~~l~~l~~s~~~~k~I~vTe~~I~p~~~Fy~AEeYHQ---~KNP~~ggVV-laAaPk 119 (254)
-.||+|+|||+|++|+++|+++++++++++.++++| ||| |+|+++||+|||||| +|||.++..+ ....++
T Consensus 95 GtqYRs~Iy~~~~~q~~~a~~~~~~~q~~~~~~~~I-vte--I~p~~~Fy~AEeYHQ~Yl~KNP~gY~~~~~~~~~~ 168 (174)
T COG0225 95 GTQYRSAIYYTNEEQKAIAEASIEELQASGYFKKPI-VTE--IEPAKNFYPAEEYHQDYLKKNPNGYCHIGLTGAPK 168 (174)
T ss_pred cccceeEEEEcCHHHHHHHHHHHHHHHHhccCCCCe-EEE--eeccccCcccHHHHHHHHHhCCCCceeeccccccc
Confidence 358999999999999999999999999987888899 999 999999999999999 9999999987 333443
No 10
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=99.57 E-value=1.1e-15 Score=132.24 Aligned_cols=72 Identities=18% Similarity=0.221 Sum_probs=64.6
Q ss_pred cccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCceeeeccceeecccceechhhcc---ccccccCceeeeccCCC
Q 025343 46 FSSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGVVLAVASGP 120 (254)
Q Consensus 46 ~s~~~~~aIFy~neeQk~~A~~~l~~l~~s~~~~k~I~vTe~~I~p~~~Fy~AEeYHQ---~KNP~~ggVVlaAaPk~ 120 (254)
--.||+++|||+|++|+++|+++++++++.+.+.++| +|+ |+|+++||+||+||| +|||.++.++....|+.
T Consensus 91 ~G~qYRS~If~~~~~q~~~a~~~~~~~~~~~~~~~~i-~Te--i~~~~~Fy~AEeyHQ~Yl~k~p~~~~~~~~~~~~~ 165 (172)
T PRK14054 91 RGTQYRSAIFYHDEEQKEIAEASIAELQASGLFDKPI-VTE--VEPAETFYEAEEYHQDYLEKNPNGYCCIFVIPPKV 165 (172)
T ss_pred CCcCceeEEEeCCHHHHHHHHHHHHHHHHhcccCCCc-EEE--EecCCCceECHHHHHHHHHhCCCCcceeeccCHHH
Confidence 3579999999999999999999999998765578899 999 999999999999999 89999999988776643
No 11
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=99.54 E-value=6.4e-15 Score=129.09 Aligned_cols=72 Identities=17% Similarity=0.169 Sum_probs=62.9
Q ss_pred cccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCceeeeccceeecccceechhhcc---ccccccCceeeeccCCC
Q 025343 46 FSSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGVVLAVASGP 120 (254)
Q Consensus 46 ~s~~~~~aIFy~neeQk~~A~~~l~~l~~s~~~~k~I~vTe~~I~p~~~Fy~AEeYHQ---~KNP~~ggVVlaAaPk~ 120 (254)
-..||+++|||+|++|+++|+++++.+++++.+.++| +|+ |+|+++||+||+||| .|||.++++-....|+.
T Consensus 96 ~G~QYRS~If~~~~eQ~~~a~~~~~~~~~~~~~~~~i-~Te--i~p~~~Fy~AEeyHQ~Yl~k~p~~~yc~~~~~~~~ 170 (186)
T PRK13014 96 RGEQYRSAIFYHDEEQKKVAEAYIAQLDEAGIFKKPI-VTP--IKPYKNFYPAEDYHQDYLKKNPTHPYIVYNDLPKG 170 (186)
T ss_pred CCCCceEEEEeCCHHHHHHHHHHHHHHHhccccCCCc-EEE--EecCCCeeeCHHHHHHHHHhCCCCCccEEEeChhh
Confidence 3579999999999999999999999998765678899 999 999999999999999 89999877755555543
No 12
>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=99.50 E-value=1.6e-14 Score=122.44 Aligned_cols=59 Identities=17% Similarity=0.211 Sum_probs=54.2
Q ss_pred cccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCceeeeccceeecccceechhhcc---cccc
Q 025343 46 FSSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRS 107 (254)
Q Consensus 46 ~s~~~~~aIFy~neeQk~~A~~~l~~l~~s~~~~k~I~vTe~~I~p~~~Fy~AEeYHQ---~KNP 107 (254)
--.||+|+|||+|++|+++|+++++++++++.+.++| +|+ |+|+++||+||+||| +|||
T Consensus 88 ~G~qYRs~If~~~~~q~~~a~~~~~~~~~~~~~~~~i-~te--i~~~~~Fy~AE~yHQ~Yl~k~p 149 (149)
T TIGR00401 88 IGTQYRSGIYYHSDEQEKAARASKERLQAAANYGDPI-VTE--IEPAENFYYAEEYHQQYLKKNP 149 (149)
T ss_pred CCCCceEEEEeCCHHHHHHHHHHHHHHHHhcccCCCe-EEE--EecCCCeeecHHHHHHHHhhCc
Confidence 3579999999999999999999999998865678899 999 999999999999999 7887
No 13
>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=99.48 E-value=2.8e-14 Score=121.62 Aligned_cols=65 Identities=15% Similarity=0.163 Sum_probs=57.2
Q ss_pred ccccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCceeeeccceeecccceechhhcc---ccccccCcee
Q 025343 45 TFSSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGVV 113 (254)
Q Consensus 45 ~~s~~~~~aIFy~neeQk~~A~~~l~~l~~s~~~~k~I~vTe~~I~p~~~Fy~AEeYHQ---~KNP~~ggVV 113 (254)
....||+++|||+|++|+++|++++++++.+ .+.++| +|+ |+|++.||+||+||| .|||.++..+
T Consensus 87 d~G~qYrs~If~~~~~q~~~a~~~~~~~~~~-~~~~~i-~te--i~p~~~Fy~AE~yHQ~Yl~k~p~~yc~~ 154 (155)
T PF01625_consen 87 DRGTQYRSAIFYHDEEQKKIAEASIAELQAK-RFGRPI-VTE--IEPLKNFYPAEEYHQKYLEKNPNGYCHY 154 (155)
T ss_dssp EESGGG-EEEEESSHHHHHHHHHHHHHHHHH-TTSSSB-S-E--EEECEEEEEHHGGGTTHHHHSTTSTTSS
T ss_pred cccccceeEEecCCHHHHHHHHHHHHHHHHh-cCCCCe-EEE--EecCCcEEECHHHHHHHHHhCCcccEec
Confidence 4568999999999999999999999999985 478899 999 999999999999999 8999997654
No 14
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=99.45 E-value=7.1e-14 Score=119.50 Aligned_cols=60 Identities=5% Similarity=-0.074 Sum_probs=53.8
Q ss_pred ccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCceeeeccceeecccceechhhcc---ccccccCcee
Q 025343 47 SSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGVV 113 (254)
Q Consensus 47 s~~~~~aIFy~neeQk~~A~~~l~~l~~s~~~~k~I~vTe~~I~p~~~Fy~AEeYHQ---~KNP~~ggVV 113 (254)
-.||+++|||+|++|+++|+++++.++. .++| +|+ |.|+.+||+||+||| +|||.+++.+
T Consensus 85 G~QYRS~If~~d~eQ~~~a~~~~~~~~~----~~~i-~Te--i~~~~~Fy~AE~yHQ~Yl~k~p~~yc~~ 147 (156)
T PRK05528 85 GEKYRTGIYSEVDDHLIEARQFIERRED----ADKI-AVE--VLPLTNYVKSAEEHQDRLEKFPEDYCHI 147 (156)
T ss_pred CCCceEEEEeCCHHHHHHHHHHHHHHhc----CCCe-EEE--EecCCCeeecHHHHHHHHHhCCCCCccc
Confidence 4699999999999999999999988765 3589 999 999999999999999 8999987654
No 15
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=99.38 E-value=2.8e-13 Score=120.99 Aligned_cols=64 Identities=13% Similarity=0.109 Sum_probs=54.5
Q ss_pred cccccceEEEeCCHHHHHHHHHHHHHHccCCCC--CCceeeeccceeecccceechhhcc---ccccccCce
Q 025343 46 FSSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLK--LKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGV 112 (254)
Q Consensus 46 ~s~~~~~aIFy~neeQk~~A~~~l~~l~~s~~~--~k~I~vTe~~I~p~~~Fy~AEeYHQ---~KNP~~ggV 112 (254)
-..||+++|||+|++|+++|+++++.+++.... .++| +|+ |+|++.||+||+||| +|||.+++.
T Consensus 133 ~G~QYRS~Ify~~~eQ~~~a~~~~~~~~~~~~~~~~~~i-~Te--I~~~~~Fy~AEeyHQ~Yl~k~p~~yc~ 201 (213)
T PRK00058 133 VGTQYRSAIYTLTPEQLAAAEASREAYQQALAAAGDGPI-TTE--IAPAPPFYYAEDYHQQYLAKNPNGYCG 201 (213)
T ss_pred CCcCceEEEEeCCHHHHHHHHHHHHHHHHHhhhccCCCe-EEE--EecCCCcccCHHHHHHHHHhCCCCccc
Confidence 347999999999999999999999888763211 3479 998 999999999999999 899987654
No 16
>KOG1635 consensus Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=99.33 E-value=1.2e-12 Score=113.99 Aligned_cols=58 Identities=19% Similarity=0.244 Sum_probs=52.4
Q ss_pred cccceEEEeCCHHHHHHHHHHHHHHccCCCCCCceeeeccceeecccceechhhcc---ccccccC
Q 025343 48 SVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRG 110 (254)
Q Consensus 48 ~~~~~aIFy~neeQk~~A~~~l~~l~~s~~~~k~I~vTe~~I~p~~~Fy~AEeYHQ---~KNP~~g 110 (254)
.||+|+||+++++|+++|+.++++.++. ..++| +|+ |+|++.||.|||||| .|||..|
T Consensus 114 tQYRS~I~~~s~eq~k~A~~s~e~~Q~k--~~~kI-~T~--I~p~~kFY~AE~yHQqYl~K~~~~G 174 (191)
T KOG1635|consen 114 TQYRSGIYTYSPEQEKLARESKEREQKK--WNGKI-VTE--ILPAKKFYRAEEYHQQYLSKNPRNG 174 (191)
T ss_pred ceeeeeeeeCCHHHHHHHHHHHHHHHhc--cCCcc-eEE--EeeccchhhchHHHHHHHhhCCCCc
Confidence 6999999999999999999999888873 67899 999 999999999999999 7888433
No 17
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=99.31 E-value=2e-12 Score=119.75 Aligned_cols=61 Identities=16% Similarity=0.229 Sum_probs=54.3
Q ss_pred cccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCceeeeccceeecccceechhhcc---ccccccCce
Q 025343 46 FSSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGV 112 (254)
Q Consensus 46 ~s~~~~~aIFy~neeQk~~A~~~l~~l~~s~~~~k~I~vTe~~I~p~~~Fy~AEeYHQ---~KNP~~ggV 112 (254)
-..||+++|||+|++|+++|+++++++++.+ ++| +|+ |+|+++||+||+||| .|||.++++
T Consensus 215 ~G~QYRS~If~~d~eq~~~A~~~~~~~~~~~---~~i-~Te--I~~l~~Fy~AEeyHQ~Yl~k~p~~~yc 278 (283)
T PRK05550 215 IGTQYRSAIFYHDDEQKQIAEKLIAELTKKG---YPV-VTE--VEAAGPFYPAEDYHQDYYEKHGKQPYC 278 (283)
T ss_pred CCcCceEEEEeCCHHHHHHHHHHHHHHHhcC---Cce-EEE--EeeCCCeeECHHHHHHHHHhCCCCCee
Confidence 3579999999999999999999999988753 289 998 999999999999999 899988443
No 18
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=90.85 E-value=0.13 Score=39.87 Aligned_cols=79 Identities=18% Similarity=0.456 Sum_probs=46.2
Q ss_pred EEEeccCCCCCCCCCCCcc-CCCCCcccc-cccCCCeeeec-----CCCC--CeeEEEccccCCCcccccCCCCCCCC--
Q 025343 163 IYNCSACGTPLYKSTTKFN-SGCGWPAFY-EGLPGAINCSP-----DPDG--LRIEITCAACGGHLGHVFKGEGFPTP-- 231 (254)
Q Consensus 163 ~Y~C~~Cg~pLF~S~~KFd-Sg~GWPSF~-~~i~~~v~~~~-----d~~g--~RtEv~C~~Cg~HLGHVF~d~G~P~p-- 231 (254)
+|.|+.|.++|=+|.+-.. .|..=++|- ..+...+...+ ...+ .-..+.|+.|+.+||=.+.-. |+.
T Consensus 2 vf~C~~C~t~l~ds~~lvs~~g~~~~a~l~~~v~~~~~~~~~~~t~~~~~~~~~~~l~C~~C~~~lGwkY~~a--~~~~~ 79 (96)
T PF03226_consen 2 VFQCKNCKTILADSNELVSFHGREGKAYLFNNVSNGVPVDRELMTGETGGDHTVRDLFCSGCNTILGWKYESA--PEEQK 79 (96)
T ss_pred EEECCCCCCCcCCHHHheecCCCCccEEEEeeeeecccccceEEEeeCCCCEEEEEeEcccCChhHCcEEEEc--CHhHh
Confidence 7999999999987777666 442223332 22221111110 0111 157899999999999998741 222
Q ss_pred -CCceeeecccce
Q 025343 232 -TDERHCVNSISL 243 (254)
Q Consensus 232 -tg~RyCINs~aL 243 (254)
.--+|++.-++|
T Consensus 80 ~k~g~file~~~i 92 (96)
T PF03226_consen 80 YKEGKFILEKASI 92 (96)
T ss_pred hhCCEEEEEhhHE
Confidence 334566665554
No 19
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=70.31 E-value=1.4 Score=37.30 Aligned_cols=23 Identities=39% Similarity=1.090 Sum_probs=16.7
Q ss_pred EEeccCCCCCCCCCCC-ccCCCCC
Q 025343 164 YNCSACGTPLYKSTTK-FNSGCGW 186 (254)
Q Consensus 164 Y~C~~Cg~pLF~S~~K-FdSg~GW 186 (254)
+||..||.|||.=+-+ |=+-||.
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCGY 52 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCCc
Confidence 7999999999982222 5555665
No 20
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=57.98 E-value=6.2 Score=29.48 Aligned_cols=43 Identities=26% Similarity=0.675 Sum_probs=31.9
Q ss_pred EEeccCCCCCCCCCCCccCCCCCcccccccCCCeeeecCCCCCeeEEEccccC
Q 025343 164 YNCSACGTPLYKSTTKFNSGCGWPAFYEGLPGAINCSPDPDGLRIEITCAACG 216 (254)
Q Consensus 164 Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~~i~~~v~~~~d~~g~RtEv~C~~Cg 216 (254)
|.|.-||..-|.++.--.+|.||-.+++- .+..=+-|.|.+||
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFdv----------q~~~f~~v~C~~CG 43 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFDV----------QNKKFTTVSCTNCG 43 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEEe----------cCcEEEEEECCCCC
Confidence 78999999999998888888888653311 11234678899997
No 21
>PRK00420 hypothetical protein; Validated
Probab=55.53 E-value=5.9 Score=32.68 Aligned_cols=23 Identities=26% Similarity=0.589 Sum_probs=16.1
Q ss_pred EEeccCCCCCCC--CCCCccCCCCC
Q 025343 164 YNCSACGTPLYK--STTKFNSGCGW 186 (254)
Q Consensus 164 Y~C~~Cg~pLF~--S~~KFdSg~GW 186 (254)
-+|..||.|||. ....|=+.||=
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCC
Confidence 478888888885 55556666665
No 22
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=51.82 E-value=18 Score=28.25 Aligned_cols=68 Identities=16% Similarity=0.362 Sum_probs=34.3
Q ss_pred CCCCCCCCCCeEEEeccCCCCCCCC-CCCccCCCCCcccccccCCCeeeecCC--CCCeeEEEccccCCCccccc
Q 025343 152 TGEYDKHFEEGIYNCSACGTPLYKS-TTKFNSGCGWPAFYEGLPGAINCSPDP--DGLRIEITCAACGGHLGHVF 223 (254)
Q Consensus 152 sg~y~~~~~~G~Y~C~~Cg~pLF~S-~~KFdSg~GWPSF~~~i~~~v~~~~d~--~g~RtEv~C~~Cg~HLGHVF 223 (254)
.|.++.. ..|.|.|..||...... +.++..- -.+...+.+.+....|. ...++++.|.+||.+-...|
T Consensus 6 Cg~~l~~-~~~~~~C~~C~~~~~~~~~~~~v~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~~~a~f~ 76 (104)
T TIGR01384 6 CGSLMTP-KNGVYVCPSCGYEKEKKPEDDYKVT---EKVKHKIKETIIIREEDSETLPTTRVECPKCGHKEAYYW 76 (104)
T ss_pred cCccccc-CCCeEECcCCCCccccccccccEEE---EEeccccccceeeccccccCCCcccCCCCCCCCCeeEEE
Confidence 4444433 34789999999875442 1122110 00111111222222222 23588999999986655555
No 23
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=51.73 E-value=7.6 Score=25.75 Aligned_cols=21 Identities=29% Similarity=0.626 Sum_probs=17.1
Q ss_pred CCCCCCCCCCeEEEeccCCCC
Q 025343 152 TGEYDKHFEEGIYNCSACGTP 172 (254)
Q Consensus 152 sg~y~~~~~~G~Y~C~~Cg~p 172 (254)
.|..+...++|.|.|+.||.-
T Consensus 14 C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 14 CGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCCeEeEccCCEEEhhhCceE
Confidence 566677789999999999864
No 24
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=49.24 E-value=20 Score=23.80 Aligned_cols=27 Identities=26% Similarity=0.652 Sum_probs=18.1
Q ss_pred eeEEEccccCCCcccccCCCCCCCCC-Ccee
Q 025343 207 RIEITCAACGGHLGHVFKGEGFPTPT-DERH 236 (254)
Q Consensus 207 RtEv~C~~Cg~HLGHVF~d~G~P~pt-g~Ry 236 (254)
-|+|+|..|++..+=+=.+ ..+. ..||
T Consensus 3 ~i~v~CP~C~s~~~v~k~G---~~~~G~qry 30 (36)
T PF03811_consen 3 KIDVHCPRCQSTEGVKKNG---KSPSGHQRY 30 (36)
T ss_pred cEeeeCCCCCCCCcceeCC---CCCCCCEeE
Confidence 5899999999998544332 3333 3676
No 25
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=49.01 E-value=6.7 Score=26.88 Aligned_cols=13 Identities=46% Similarity=1.232 Sum_probs=10.8
Q ss_pred EeccCCCCCCCCC
Q 025343 165 NCSACGTPLYKST 177 (254)
Q Consensus 165 ~C~~Cg~pLF~S~ 177 (254)
+|..||.|||.+.
T Consensus 19 ~Cp~C~~PL~~~k 31 (41)
T PF06677_consen 19 HCPDCGTPLMRDK 31 (41)
T ss_pred ccCCCCCeeEEec
Confidence 6889999999743
No 26
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=40.83 E-value=18 Score=24.25 Aligned_cols=16 Identities=38% Similarity=0.935 Sum_probs=13.8
Q ss_pred CCCCCCCeEEEeccCC
Q 025343 155 YDKHFEEGIYNCSACG 170 (254)
Q Consensus 155 y~~~~~~G~Y~C~~Cg 170 (254)
|.+.+..|.|+|..|+
T Consensus 17 ~~d~~g~G~~~C~~Cg 32 (37)
T smart00778 17 FDDKDGRGTWFCSVCG 32 (37)
T ss_pred cccCCCCcCEEeCCCC
Confidence 6777788999999996
No 27
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=38.07 E-value=18 Score=24.15 Aligned_cols=28 Identities=29% Similarity=0.601 Sum_probs=17.0
Q ss_pred CCCeEEEeccCCCCCCCCCCCccCCCCCcc
Q 025343 159 FEEGIYNCSACGTPLYKSTTKFNSGCGWPA 188 (254)
Q Consensus 159 ~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPS 188 (254)
...|.++|..||.-| .+...+++--|-+
T Consensus 15 ~~~g~~vC~~CG~Vl--~e~~i~~~~e~r~ 42 (43)
T PF08271_consen 15 PERGELVCPNCGLVL--EENIIDEGPEWRE 42 (43)
T ss_dssp TTTTEEEETTT-BBE--E-TTBSCCCSCCH
T ss_pred CCCCeEECCCCCCEe--ecccccCCccccc
Confidence 578999999999876 2233344444433
No 28
>PRK04351 hypothetical protein; Provisional
Probab=37.86 E-value=49 Score=28.25 Aligned_cols=15 Identities=27% Similarity=0.685 Sum_probs=11.2
Q ss_pred eEEEccccCCCcccc
Q 025343 208 IEITCAACGGHLGHV 222 (254)
Q Consensus 208 tEv~C~~Cg~HLGHV 222 (254)
..-+|.+|++.|-.+
T Consensus 131 ~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 131 KRYRCGKCRGKLKLI 145 (149)
T ss_pred CcEEeCCCCcEeeec
Confidence 345699999998654
No 29
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=37.53 E-value=22 Score=25.90 Aligned_cols=33 Identities=24% Similarity=0.203 Sum_probs=22.1
Q ss_pred eeEEEccccCCCcccccCCCCCCCCCCceeeecccceee
Q 025343 207 RIEITCAACGGHLGHVFKGEGFPTPTDERHCVNSISLKF 245 (254)
Q Consensus 207 RtEv~C~~Cg~HLGHVF~d~G~P~ptg~RyCINs~aL~F 245 (254)
..-..|++||++|.....+ .| ..+-|+..+|+-
T Consensus 46 ~~r~FC~~CGs~l~~~~~~--~~----~~~~V~~g~ld~ 78 (92)
T PF04828_consen 46 VERYFCPTCGSPLFSEDER--DP----DLVGVNAGTLDD 78 (92)
T ss_dssp CEEEEETTT--EEEEEESS--TT----TEEEEEGGGBTT
T ss_pred CcCcccCCCCCeeecccCC--CC----CEEEEEeEeeCC
Confidence 4558999999999977432 23 378888888763
No 30
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=32.28 E-value=29 Score=21.68 Aligned_cols=23 Identities=35% Similarity=0.761 Sum_probs=11.4
Q ss_pred EccccCCCcccccCCCCCCCCCCceeeecc
Q 025343 211 TCAACGGHLGHVFKGEGFPTPTDERHCVNS 240 (254)
Q Consensus 211 ~C~~Cg~HLGHVF~d~G~P~ptg~RyCINs 240 (254)
.|..||++|=+. +| .-..||+|+
T Consensus 1 ~CP~C~s~l~~~-~~------ev~~~C~N~ 23 (28)
T PF03119_consen 1 TCPVCGSKLVRE-EG------EVDIRCPNP 23 (28)
T ss_dssp B-TTT--BEEE--CC------TTCEEE--C
T ss_pred CcCCCCCEeEcC-CC------CEeEECCCC
Confidence 489999998744 22 125899998
No 31
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=32.10 E-value=24 Score=27.62 Aligned_cols=20 Identities=25% Similarity=0.629 Sum_probs=16.6
Q ss_pred eEEEccccCCCcccccCCCC
Q 025343 208 IEITCAACGGHLGHVFKGEG 227 (254)
Q Consensus 208 tEv~C~~Cg~HLGHVF~d~G 227 (254)
+.-+|..||--++|.=.|||
T Consensus 7 ~~~~C~~CG~d~~~~~adDg 26 (86)
T PF06170_consen 7 VAPRCPHCGLDYSHARADDG 26 (86)
T ss_pred CCCcccccCCccccCCcCcc
Confidence 34469999999999987776
No 32
>PRK12495 hypothetical protein; Provisional
Probab=31.74 E-value=18 Score=33.41 Aligned_cols=13 Identities=31% Similarity=1.042 Sum_probs=11.5
Q ss_pred eEEEeccCCCCCC
Q 025343 162 GIYNCSACGTPLY 174 (254)
Q Consensus 162 G~Y~C~~Cg~pLF 174 (254)
.-++|..||.|||
T Consensus 41 sa~hC~~CG~PIp 53 (226)
T PRK12495 41 TNAHCDECGDPIF 53 (226)
T ss_pred chhhcccccCccc
Confidence 3479999999999
No 33
>PHA02540 61 DNA primase; Provisional
Probab=31.11 E-value=24 Score=34.06 Aligned_cols=17 Identities=18% Similarity=0.419 Sum_probs=12.2
Q ss_pred CCCCCCCe--EEEeccCCC
Q 025343 155 YDKHFEEG--IYNCSACGT 171 (254)
Q Consensus 155 y~~~~~~G--~Y~C~~Cg~ 171 (254)
++-..++| +|+|=+||.
T Consensus 45 F~V~p~k~~~~yhCFgCGa 63 (337)
T PHA02540 45 GWIYEKKDGGVFKCHNCGY 63 (337)
T ss_pred EEEeccCCceEEEecCCCC
Confidence 34444555 999999996
No 34
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=30.91 E-value=43 Score=31.79 Aligned_cols=71 Identities=24% Similarity=0.461 Sum_probs=43.7
Q ss_pred CCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCccCCCCCcccccccCCCeeeecC--CCCC---eeEEEccccCCCccc
Q 025343 147 TEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGLPGAINCSPD--PDGL---RIEITCAACGGHLGH 221 (254)
Q Consensus 147 TE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~~i~~~v~~~~d--~~g~---RtEv~C~~Cg~HLGH 221 (254)
-|.||+ -.|..||..++.. .||++- ...+.+ +.|. |--++|..|++++
T Consensus 35 f~~Pf~-----------i~C~~C~~~I~kG-~rFNA~-------------Ke~v~~E~Yls~~I~rF~~kC~~C~~~i-- 87 (324)
T PF04502_consen 35 FMMPFN-----------IWCNTCGEYIYKG-VRFNAR-------------KEKVGNEKYLSTPIYRFYIKCPRCSNEI-- 87 (324)
T ss_pred EcCCcc-----------CcCCCCccccccc-eeeeee-------------eEecCCCccccceEEEEEEEcCCCCCEE--
Confidence 367996 4799999997764 566542 111222 4564 8899999999976
Q ss_pred ccCCCCCCCCCCceeeecccceeeee
Q 025343 222 VFKGEGFPTPTDERHCVNSISLKFVP 247 (254)
Q Consensus 222 VF~d~G~P~ptg~RyCINs~aL~F~p 247 (254)
+|.-| |. .+---|+-+|-=.|.+
T Consensus 88 ~~kTD--Pk-n~dY~~~~Ga~R~~~~ 110 (324)
T PF04502_consen 88 EFKTD--PK-NTDYVVESGARRNFEP 110 (324)
T ss_pred eeecC--CC-CCCeeeecCeeecCCc
Confidence 56642 43 2333455555444444
No 35
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=29.48 E-value=41 Score=31.71 Aligned_cols=29 Identities=34% Similarity=0.804 Sum_probs=24.6
Q ss_pred CCCeEEEeccCCCCCCCCCCCccCCCCCccc
Q 025343 159 FEEGIYNCSACGTPLYKSTTKFNSGCGWPAF 189 (254)
Q Consensus 159 ~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF 189 (254)
.+.|-++|+.||.-| -+.-+|.|..|=.|
T Consensus 16 ~~~ge~VC~~CG~Vi--~~~~id~gpewr~f 44 (285)
T COG1405 16 YERGEIVCADCGLVL--EDSLIDPGPEWRAF 44 (285)
T ss_pred ccCCeEEeccCCEEe--ccccccCCCCcccc
Confidence 357999999999876 45568999999999
No 36
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=29.39 E-value=45 Score=31.27 Aligned_cols=32 Identities=28% Similarity=0.661 Sum_probs=27.0
Q ss_pred CCCeEEEeccCCCCCCCCCCCccCCCCCcccccc
Q 025343 159 FEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEG 192 (254)
Q Consensus 159 ~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~~ 192 (254)
.+.|.++|..||.-| .+.-.|.|.-|-+|...
T Consensus 26 ~~~Ge~vC~~CG~Vl--~e~~iD~g~EWR~f~~~ 57 (310)
T PRK00423 26 YERGEIVCADCGLVI--EENIIDQGPEWRAFDPE 57 (310)
T ss_pred CCCCeEeecccCCcc--cccccccCCCccCCCcc
Confidence 579999999999876 56678889999999863
No 37
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=29.18 E-value=27 Score=29.86 Aligned_cols=40 Identities=25% Similarity=0.556 Sum_probs=24.2
Q ss_pred CCCHHHHHhcCCHHHHHHhhhCCCCCCCCCCCCCCCCCeEEEeccCCCCC
Q 025343 124 NKSEEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPL 173 (254)
Q Consensus 124 ~~s~~ewr~~Ltp~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pL 173 (254)
.+|.-||.+... =++.+| ---+|+. -..|+|+|..||..+
T Consensus 83 DkTqvEw~el~~-----d~~h~g--~Y~sGE~---~g~G~l~C~~Cg~~~ 122 (146)
T PF07295_consen 83 DKTQVEWAELAQ-----DLEHHG--VYHSGEV---VGPGTLVCENCGHEV 122 (146)
T ss_pred chhHHHHHHHHH-----HHHhcC--CeecCcE---ecCceEecccCCCEE
Confidence 466677765532 234455 2223332 378999999999764
No 38
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=28.98 E-value=23 Score=29.27 Aligned_cols=21 Identities=29% Similarity=0.572 Sum_probs=15.9
Q ss_pred CCCCCeEEEeccCCCCCCCCC
Q 025343 157 KHFEEGIYNCSACGTPLYKST 177 (254)
Q Consensus 157 ~~~~~G~Y~C~~Cg~pLF~S~ 177 (254)
.....+.+.|..||.+||...
T Consensus 63 ~s~~~~r~FC~~CGs~l~~~~ 83 (133)
T COG3791 63 SSGSAGRGFCPTCGSPLFWRG 83 (133)
T ss_pred ecCCCCCeecccCCCceEEec
Confidence 344566679999999998653
No 39
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=27.44 E-value=23 Score=24.36 Aligned_cols=15 Identities=33% Similarity=1.023 Sum_probs=12.0
Q ss_pred EEccccCCCcccccCC
Q 025343 210 ITCAACGGHLGHVFKG 225 (254)
Q Consensus 210 v~C~~Cg~HLGHVF~d 225 (254)
|+|.+||+ +||.=.+
T Consensus 2 ~kC~~CG~-~GH~~t~ 16 (40)
T PF15288_consen 2 VKCKNCGA-FGHMRTN 16 (40)
T ss_pred cccccccc-ccccccC
Confidence 57999997 6998654
No 40
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=25.27 E-value=38 Score=25.44 Aligned_cols=28 Identities=25% Similarity=0.666 Sum_probs=24.5
Q ss_pred eEEEeccCCCCCCCCCCCccCCCCC-ccc
Q 025343 162 GIYNCSACGTPLYKSTTKFNSGCGW-PAF 189 (254)
Q Consensus 162 G~Y~C~~Cg~pLF~S~~KFdSg~GW-PSF 189 (254)
=.-.|..||.--|....+.=+.||+ ||=
T Consensus 16 tHt~CrRCG~~syh~qK~~CasCGygps~ 44 (62)
T PRK04179 16 THIRCRRCGRHSYNVRKKYCAACGFGRSK 44 (62)
T ss_pred ccchhcccCcccccccccchhhcCCCccc
Confidence 3457999999999999999999999 763
No 41
>PRK08624 hypothetical protein; Provisional
Probab=24.35 E-value=59 Score=32.06 Aligned_cols=20 Identities=20% Similarity=0.634 Sum_probs=14.8
Q ss_pred CCCCeEEEec-cCCC--CCCCCC
Q 025343 158 HFEEGIYNCS-ACGT--PLYKST 177 (254)
Q Consensus 158 ~~~~G~Y~C~-~Cg~--pLF~S~ 177 (254)
+.+.++|+|- +||. -.|.-=
T Consensus 54 ~pekq~yhCF~GCGa~GDVf~Fv 76 (373)
T PRK08624 54 YIENDNFHCYTRCGDIFDVFELL 76 (373)
T ss_pred cCCCCEEEEeCCCCCCCceeeeh
Confidence 4588899999 9998 555443
No 42
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=23.63 E-value=65 Score=26.81 Aligned_cols=34 Identities=24% Similarity=0.403 Sum_probs=22.0
Q ss_pred CCCCCe-eEEEccccCCCcccccCCCCCCCCCCce
Q 025343 202 DPDGLR-IEITCAACGGHLGHVFKGEGFPTPTDER 235 (254)
Q Consensus 202 d~~g~R-tEv~C~~Cg~HLGHVF~d~G~P~ptg~R 235 (254)
|+.-.| ....|.+||.|-+=.|.--++-..+.+|
T Consensus 65 DPTLPrts~~~C~~C~~~eavffQ~~~~r~d~~m~ 99 (113)
T KOG2691|consen 65 DPTLPRTSDKHCPKCGHREAVFFQAQTRRADEAMR 99 (113)
T ss_pred CCCcCccccccCCccCCcceEEEecccccccceEE
Confidence 333356 7789999999999888743323334444
No 43
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=23.26 E-value=43 Score=26.90 Aligned_cols=29 Identities=24% Similarity=0.560 Sum_probs=25.5
Q ss_pred eEEEeccCCCCCCCCCCCccCCCCCcccc
Q 025343 162 GIYNCSACGTPLYKSTTKFNSGCGWPAFY 190 (254)
Q Consensus 162 G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~ 190 (254)
=.-.|..||.--|.-..+.=+.||+||=.
T Consensus 15 tHtlCrRCG~~syH~qK~~CasCGypsak 43 (91)
T PTZ00073 15 THTLCRRCGKRSFHVQKKRCASCGYPSAK 43 (91)
T ss_pred CcchhcccCccccccccccchhcCCchhh
Confidence 44679999999999999999999999753
No 44
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=22.74 E-value=66 Score=22.45 Aligned_cols=18 Identities=28% Similarity=0.695 Sum_probs=13.6
Q ss_pred CCCCCCCeEEEeccCCCC
Q 025343 155 YDKHFEEGIYNCSACGTP 172 (254)
Q Consensus 155 y~~~~~~G~Y~C~~Cg~p 172 (254)
+.+....|+|.|..||.-
T Consensus 18 ~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 18 FDPLDLSHYFECSTCGAS 35 (53)
T ss_pred cCCCCCEEEEECCCCCCC
Confidence 345567888999999864
No 45
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.21 E-value=42 Score=20.31 Aligned_cols=21 Identities=33% Similarity=0.868 Sum_probs=14.1
Q ss_pred EeccCCCCCCCCCCCccCCCCC
Q 025343 165 NCSACGTPLYKSTTKFNSGCGW 186 (254)
Q Consensus 165 ~C~~Cg~pLF~S~~KFdSg~GW 186 (254)
.|..||.++ ..+++|=+.||=
T Consensus 4 ~Cp~Cg~~~-~~~~~fC~~CG~ 24 (26)
T PF13248_consen 4 FCPNCGAEI-DPDAKFCPNCGA 24 (26)
T ss_pred CCcccCCcC-CcccccChhhCC
Confidence 577777743 667777766663
No 46
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=22.19 E-value=51 Score=24.10 Aligned_cols=12 Identities=25% Similarity=0.650 Sum_probs=8.4
Q ss_pred EeccCCCCCCCC
Q 025343 165 NCSACGTPLYKS 176 (254)
Q Consensus 165 ~C~~Cg~pLF~S 176 (254)
.|..||.++.++
T Consensus 19 ~CP~CG~~t~~~ 30 (56)
T PRK13130 19 ICPVCGGKTKNP 30 (56)
T ss_pred cCcCCCCCCCCC
Confidence 477888887544
No 47
>COG3634 AhpF Alkyl hydroperoxide reductase, large subunit [Posttranslational modification, protein turnover, chaperones]
Probab=22.17 E-value=55 Score=32.90 Aligned_cols=35 Identities=23% Similarity=0.458 Sum_probs=24.0
Q ss_pred CCCeEEEeccCCCCCCCCCCCccCCCCCccccccc
Q 025343 159 FEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGL 193 (254)
Q Consensus 159 ~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~~i 193 (254)
+.+|+=.|..|+-|||.-++-=-=|-|=--.-.+|
T Consensus 337 rnKGVayCPHCDGPLF~gK~VAVIGGGNSGvEAAI 371 (520)
T COG3634 337 RNKGVAYCPHCDGPLFKGKRVAVIGGGNSGVEAAI 371 (520)
T ss_pred hhCCeeeCCCCCCcccCCceEEEECCCcchHHHHH
Confidence 35789999999999999877644444433333444
No 48
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box []. The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ]. KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1V65_A.
Probab=22.17 E-value=99 Score=20.92 Aligned_cols=22 Identities=41% Similarity=0.735 Sum_probs=13.4
Q ss_pred CCCCCHHHHHhcCCHHHHHHhhh
Q 025343 122 SVNKSEEEWRAILSPEQFRILRQ 144 (254)
Q Consensus 122 ~~~~s~~ewr~~Ltp~qy~Vlr~ 144 (254)
.+..|.+||. .|.|.|...-|+
T Consensus 7 av~fs~eEW~-~L~~~Qk~ly~d 28 (41)
T PF01352_consen 7 AVYFSQEEWE-LLDPAQKNLYRD 28 (41)
T ss_dssp TT---HHHHH-TS-HHHHHHHHH
T ss_pred EEEcChhhcc-cccceecccchh
Confidence 4578999997 799999765543
No 49
>cd04984 IgV_L_lambda Immunoglobulin (Ig) lambda light chain variable (V) domain. IgV_L_lambda: Immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.
Probab=21.73 E-value=49 Score=24.78 Aligned_cols=13 Identities=23% Similarity=0.450 Sum_probs=10.2
Q ss_pred CCCCCeEEEeccC
Q 025343 157 KHFEEGIYNCSAC 169 (254)
Q Consensus 157 ~~~~~G~Y~C~~C 169 (254)
...+.|+|.|+.-
T Consensus 71 ~~~Dsg~Y~C~~~ 83 (98)
T cd04984 71 QTEDEADYYCQVW 83 (98)
T ss_pred ChhhCEEEEEEEc
Confidence 3458999999874
No 50
>cd04983 IgV_TCR_alpha_like Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins. IgV_TCR_alpha: immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens; they recognize proteins antigens directly and without antigen processing, and MHC independently of the bound peptide.
Probab=21.62 E-value=59 Score=24.40 Aligned_cols=14 Identities=14% Similarity=0.446 Sum_probs=10.9
Q ss_pred CCCCeEEEeccCCC
Q 025343 158 HFEEGIYNCSACGT 171 (254)
Q Consensus 158 ~~~~G~Y~C~~Cg~ 171 (254)
..+.|+|.|++...
T Consensus 79 ~~DsG~Y~C~~~~~ 92 (109)
T cd04983 79 LSDSAVYFCALSES 92 (109)
T ss_pred HHHCEEEEEEEecC
Confidence 35789999998753
No 51
>PF09965 DUF2199: Uncharacterized protein conserved in bacteria (DUF2199); InterPro: IPR018697 This domain has no known function.
Probab=21.28 E-value=30 Score=29.73 Aligned_cols=25 Identities=32% Similarity=0.615 Sum_probs=19.6
Q ss_pred EEeccCCCCCCCCCCCccCCCCCcccccccCCCee
Q 025343 164 YNCSACGTPLYKSTTKFNSGCGWPAFYEGLPGAIN 198 (254)
Q Consensus 164 Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~~i~~~v~ 198 (254)
|.|.+||..- -|||||.-..|+.+.
T Consensus 1 y~C~~Cg~~h----------~~~P~~~~~~Pd~~~ 25 (148)
T PF09965_consen 1 YTCSCCGEEH----------EGLPSLGFDAPDYYY 25 (148)
T ss_pred CCCCcCCccC----------CCCcccccCCChhhh
Confidence 7899999874 689998877776544
No 52
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.26 E-value=37 Score=28.18 Aligned_cols=14 Identities=43% Similarity=1.061 Sum_probs=12.9
Q ss_pred CCeEEEeccCCCCC
Q 025343 160 EEGIYNCSACGTPL 173 (254)
Q Consensus 160 ~~G~Y~C~~Cg~pL 173 (254)
+-|.+.|..||+++
T Consensus 46 e~G~t~CP~Cg~~~ 59 (115)
T COG1885 46 EVGSTSCPKCGEPF 59 (115)
T ss_pred ecccccCCCCCCcc
Confidence 78999999999986
No 53
>cd04980 IgV_L_kappa Immunoglobulin (Ig) light chain, kappa type, variable (V) domain. IgV_L_kappa: Immunoglobulin (Ig) light chain, kappa type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.
Probab=20.10 E-value=48 Score=25.20 Aligned_cols=12 Identities=17% Similarity=0.520 Sum_probs=9.6
Q ss_pred CCCCeEEEeccC
Q 025343 158 HFEEGIYNCSAC 169 (254)
Q Consensus 158 ~~~~G~Y~C~~C 169 (254)
..+.|+|.|+.-
T Consensus 80 ~~Dsg~Y~Ca~~ 91 (106)
T cd04980 80 PEDAAVYYCQQY 91 (106)
T ss_pred hHHCEEEEEEEe
Confidence 358999999873
Done!