Query 036289
Match_columns 149
No_of_seqs 271 out of 1564
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 11:12:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036289.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036289hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.5 2.8E-13 6.1E-18 85.0 8.5 58 32-89 1-62 (62)
2 KOG4656 Copper chaperone for s 99.5 1.7E-13 3.6E-18 104.5 6.6 95 28-122 6-101 (247)
3 COG2608 CopZ Copper chaperone 99.4 4.7E-12 1E-16 82.1 8.7 65 29-93 2-70 (71)
4 KOG1603 Copper chaperone [Inor 99.3 2.5E-11 5.5E-16 79.0 8.7 67 28-94 4-71 (73)
5 PLN02957 copper, zinc superoxi 98.7 3.2E-07 7E-12 72.3 11.0 72 28-99 5-76 (238)
6 PRK10671 copA copper exporting 98.4 1E-06 2.2E-11 80.3 8.2 63 29-93 3-66 (834)
7 COG2217 ZntA Cation transport 98.2 4.5E-06 9.7E-11 74.9 7.9 63 29-92 2-69 (713)
8 TIGR00003 copper ion binding p 98.0 0.00013 2.8E-09 42.7 8.6 60 30-89 3-66 (68)
9 KOG0207 Cation transport ATPas 97.8 6.7E-05 1.5E-09 68.2 7.3 68 29-96 146-217 (951)
10 PRK10671 copA copper exporting 97.4 0.00067 1.4E-08 62.0 8.2 65 30-94 100-165 (834)
11 KOG0207 Cation transport ATPas 97.3 0.00069 1.5E-08 61.8 7.2 69 27-95 67-139 (951)
12 PRK11033 zntA zinc/cadmium/mer 97.1 0.002 4.3E-08 58.4 7.9 66 28-93 52-119 (741)
13 TIGR02052 MerP mercuric transp 94.7 0.61 1.3E-05 29.4 9.5 63 30-92 24-90 (92)
14 PRK13748 putative mercuric red 90.8 2.1 4.5E-05 37.3 9.1 64 32-95 3-69 (561)
15 COG1888 Uncharacterized protei 90.7 2.6 5.5E-05 28.6 7.4 68 27-94 4-80 (97)
16 PF02680 DUF211: Uncharacteriz 89.5 3 6.5E-05 28.4 7.1 65 28-93 4-77 (95)
17 cd00371 HMA Heavy-metal-associ 88.3 2.3 4.9E-05 21.8 7.5 38 34-71 3-41 (63)
18 PF01206 TusA: Sulfurtransfera 87.6 2.3 4.9E-05 26.5 5.3 54 32-94 2-58 (70)
19 PRK11018 hypothetical protein; 80.1 11 0.00024 24.3 6.3 55 30-93 8-65 (78)
20 cd03421 SirA_like_N SirA_like_ 77.7 8.8 0.00019 23.7 5.1 52 33-94 2-56 (67)
21 PF01883 DUF59: Domain of unkn 74.1 7.4 0.00016 24.3 4.1 33 29-61 34-72 (72)
22 cd03420 SirA_RHOD_Pry_redox Si 72.4 16 0.00035 22.8 5.3 53 33-94 2-57 (69)
23 cd03422 YedF YedF is a bacteri 66.7 25 0.00054 21.9 5.3 53 33-94 2-57 (69)
24 cd03423 SirA SirA (also known 64.6 32 0.00068 21.4 5.8 53 33-94 2-57 (69)
25 PRK14054 methionine sulfoxide 63.7 25 0.00055 26.4 5.6 28 40-67 10-37 (172)
26 PRK11152 ilvM acetolactate syn 63.4 33 0.00072 22.2 5.5 55 5-61 15-75 (76)
27 cd00291 SirA_YedF_YeeD SirA, Y 61.4 34 0.00074 20.7 5.6 53 33-94 2-57 (69)
28 PRK10553 assembly protein for 61.1 46 0.001 22.1 6.0 45 40-84 16-61 (87)
29 PRK11198 LysM domain/BON super 59.1 44 0.00094 24.2 6.1 44 41-84 26-70 (147)
30 PF14437 MafB19-deam: MafB19-l 57.7 33 0.00071 25.2 5.1 40 29-69 100-141 (146)
31 PRK00299 sulfur transfer prote 56.5 52 0.0011 21.2 6.5 55 30-93 9-66 (81)
32 PF13732 DUF4162: Domain of un 51.5 57 0.0012 20.6 5.1 41 50-92 26-68 (84)
33 PRK00058 methionine sulfoxide 47.1 81 0.0017 24.6 6.1 34 28-66 45-78 (213)
34 TIGR03527 selenium_YedF seleni 47.0 59 0.0013 24.8 5.3 49 36-93 5-55 (194)
35 PRK13014 methionine sulfoxide 46.2 60 0.0013 24.8 5.2 36 27-67 7-42 (186)
36 TIGR03406 FeS_long_SufT probab 45.9 31 0.00067 26.0 3.6 35 30-64 114-154 (174)
37 COG0425 SirA Predicted redox p 45.2 83 0.0018 20.3 6.3 52 30-90 5-60 (78)
38 PF03927 NapD: NapD protein; 43.9 87 0.0019 20.2 6.3 44 42-86 16-60 (79)
39 COG2151 PaaD Predicted metal-s 42.8 47 0.001 23.2 3.8 21 43-63 69-89 (111)
40 PRK05528 methionine sulfoxide 42.3 36 0.00077 25.2 3.3 44 40-83 8-68 (156)
41 PF13740 ACT_6: ACT domain; PD 41.4 89 0.0019 19.5 5.5 56 30-85 2-64 (76)
42 PF09580 Spore_YhcN_YlaJ: Spor 38.8 1.1E+02 0.0024 22.3 5.6 33 39-71 73-105 (177)
43 PF08712 Nfu_N: Scaffold prote 36.7 1.2E+02 0.0025 20.0 4.9 40 44-85 37-78 (87)
44 PF13291 ACT_4: ACT domain; PD 35.2 1.1E+02 0.0024 18.9 5.2 56 5-60 18-79 (80)
45 TIGR02945 SUF_assoc FeS assemb 35.0 49 0.0011 21.9 2.9 35 30-64 40-78 (99)
46 PF13216 DUF4024: Protein of u 33.3 12 0.00026 20.1 -0.2 11 138-148 8-18 (35)
47 cd04888 ACT_PheB-BS C-terminal 32.2 1.2E+02 0.0026 18.3 5.0 33 29-61 41-74 (76)
48 COG4312 Uncharacterized protei 31.9 2.3E+02 0.005 22.5 6.4 59 25-90 73-137 (247)
49 KOG3411 40S ribosomal protein 31.4 42 0.00091 24.3 2.1 43 40-85 97-140 (143)
50 PF08821 CGGC: CGGC domain; I 31.3 1.3E+02 0.0029 20.6 4.7 58 33-92 38-104 (107)
51 PRK13562 acetolactate synthase 29.5 1.7E+02 0.0038 19.4 6.2 61 4-64 13-80 (84)
52 PHA01634 hypothetical protein 29.5 18 0.00039 26.4 0.0 17 33-49 93-110 (156)
53 COG2092 EFB1 Translation elong 29.3 98 0.0021 20.8 3.5 34 29-62 49-83 (88)
54 COG2761 FrnE Predicted dithiol 28.7 1.4E+02 0.0031 23.5 4.9 38 28-65 3-45 (225)
55 PF11150 DUF2927: Protein of u 27.9 35 0.00076 26.5 1.4 16 134-149 164-179 (213)
56 PF01625 PMSR: Peptide methion 27.7 71 0.0015 23.5 2.9 27 40-66 7-33 (155)
57 PF04972 BON: BON domain; Int 27.7 42 0.0009 20.0 1.5 29 45-74 3-34 (64)
58 PRK09577 multidrug efflux prot 27.0 1.9E+02 0.0042 27.6 6.3 46 43-88 158-211 (1032)
59 PF08777 RRM_3: RNA binding mo 26.6 2.1E+02 0.0046 19.4 6.3 55 32-86 3-60 (105)
60 TIGR00489 aEF-1_beta translati 26.1 1.3E+02 0.0028 20.1 3.7 23 40-62 61-83 (88)
61 PRK07334 threonine dehydratase 25.3 4.1E+02 0.0088 22.3 7.5 63 31-93 327-402 (403)
62 TIGR00401 msrA methionine-S-su 25.2 60 0.0013 23.8 2.1 28 40-67 7-34 (149)
63 PRK05550 bifunctional methioni 25.1 2.4E+02 0.0051 23.0 5.7 28 40-67 134-161 (283)
64 PRK10555 aminoglycoside/multid 25.1 2.1E+02 0.0045 27.5 6.1 44 43-86 159-210 (1037)
65 COG0225 MsrA Peptide methionin 24.0 1E+02 0.0023 23.3 3.2 35 28-67 6-40 (174)
66 PF13383 Methyltransf_22: Meth 23.5 1.6E+02 0.0034 23.3 4.4 56 32-97 167-229 (242)
67 PRK11023 outer membrane lipopr 22.8 2.2E+02 0.0047 21.4 4.9 47 38-84 46-95 (191)
68 PF08002 DUF1697: Protein of u 22.6 2.9E+02 0.0063 19.6 5.8 48 44-92 22-74 (137)
69 PRK11023 outer membrane lipopr 22.1 2.6E+02 0.0057 21.0 5.2 40 42-81 128-169 (191)
70 PF13192 Thioredoxin_3: Thiore 21.8 1.3E+02 0.0027 18.7 2.9 11 35-45 6-16 (76)
71 PRK11670 antiporter inner memb 21.2 3.9E+02 0.0084 22.3 6.5 58 43-100 67-149 (369)
72 COG2177 FtsX Cell division pro 21.0 2E+02 0.0044 23.5 4.6 31 31-62 63-93 (297)
No 1
>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=99.48 E-value=2.8e-13 Score=84.97 Aligned_cols=58 Identities=36% Similarity=0.619 Sum_probs=53.9
Q ss_pred EEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec---CCHHHHHHHHHhcCCc
Q 036289 32 DLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTGY---VEANKVLKKAKSTGKR 89 (149)
Q Consensus 32 ~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g~---~~~~~I~~~I~~~G~~ 89 (149)
+|+| +|+|++|+.+|+++|.+++||.++.+|+.+++++|.++ +++++|.++|+++||+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGYE 62 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTSE
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCcC
Confidence 4789 99999999999999999999999999999999999965 4569999999999985
No 2
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.45 E-value=1.7e-13 Score=104.53 Aligned_cols=95 Identities=28% Similarity=0.382 Sum_probs=81.9
Q ss_pred ceEEEEEEcCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecCCHHHHHHHHHhcCCceEEccCCCCCcccCCCcc
Q 036289 28 LQTVDLKVRMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTGYVEANKVLKKAKSTGKRAEIWPYVPYNLVAQPYIA 107 (149)
Q Consensus 28 ~~~v~l~Vgm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g~~~~~~I~~~I~~~G~~a~~~~~~~~~~~~~~~~~ 107 (149)
.-+.+|.|.|+|++|+..|++.|..++||.+|++|++++.|.|.+...+++|..+|+.+|.+|.+.+....++++....-
T Consensus 6 ~~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G~psaval~at~ 85 (247)
T KOG4656|consen 6 TYEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAGKPSAVALLATV 85 (247)
T ss_pred ceeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCCchhHHHHHHHH
Confidence 45678999999999999999999999999999999999999999999999999999999999999988766665544333
Q ss_pred cccC-CCCCCceeecC
Q 036289 108 GAYD-KRAPPGYVRKV 122 (149)
Q Consensus 108 ~~~~-~~~~~g~~~~~ 122 (149)
+.|. ..+++|++||.
T Consensus 86 a~~~~~~~v~GvvRf~ 101 (247)
T KOG4656|consen 86 AKYTGPQAVQGVVRFV 101 (247)
T ss_pred HHhcCCccceeEEEEE
Confidence 4443 34789999984
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.37 E-value=4.7e-12 Score=82.13 Aligned_cols=65 Identities=26% Similarity=0.473 Sum_probs=58.3
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEE--e-cCCHHHHHHHHHhcCCceEEc
Q 036289 29 QTVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVT--G-YVEANKVLKKAKSTGKRAEIW 93 (149)
Q Consensus 29 ~~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~--g-~~~~~~I~~~I~~~G~~a~~~ 93 (149)
.+..|.| +|+|.+|+..|+++|.+++||.++++++..+.+.|. + .++.++|.++|+.+||++..+
T Consensus 2 ~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~~ 70 (71)
T COG2608 2 MKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEEI 70 (71)
T ss_pred ceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeeec
Confidence 4678999 999999999999999999999999999999777665 4 479999999999999988754
No 4
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.30 E-value=2.5e-11 Score=79.02 Aligned_cols=67 Identities=55% Similarity=0.885 Sum_probs=62.0
Q ss_pred ceEEEEEEcCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecCCHHHHHHHHHhcC-CceEEcc
Q 036289 28 LQTVDLKVRMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTGYVEANKVLKKAKSTG-KRAEIWP 94 (149)
Q Consensus 28 ~~~v~l~Vgm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g~~~~~~I~~~I~~~G-~~a~~~~ 94 (149)
+.+.++.+.|+|.+|..+|++.|..++||.++.+|...++++|.|.+++..|++.|++.| .++.+|.
T Consensus 4 ~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 4 IKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred ccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEec
Confidence 456778889999999999999999999999999999999999999999999999999988 7777775
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.67 E-value=3.2e-07 Score=72.25 Aligned_cols=72 Identities=29% Similarity=0.444 Sum_probs=63.5
Q ss_pred ceEEEEEEcCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecCCHHHHHHHHHhcCCceEEccCCCCC
Q 036289 28 LQTVDLKVRMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTGYVEANKVLKKAKSTGKRAEIWPYVPYN 99 (149)
Q Consensus 28 ~~~v~l~Vgm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g~~~~~~I~~~I~~~G~~a~~~~~~~~~ 99 (149)
.+++++.++|.|..|+.+|++.|.+++||..+.+++..++++|.......++.+.|++.||.+++++..+.+
T Consensus 5 ~~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 5 ELLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQGDPE 76 (238)
T ss_pred cEEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCCCcc
Confidence 345667889999999999999999999999999999999999987778899999999999999988764443
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.40 E-value=1e-06 Score=80.26 Aligned_cols=63 Identities=25% Similarity=0.480 Sum_probs=56.5
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecCCHHHHHHHHHhcCCceEEc
Q 036289 29 QTVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTGYVEANKVLKKAKSTGKRAEIW 93 (149)
Q Consensus 29 ~~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g~~~~~~I~~~I~~~G~~a~~~ 93 (149)
+++++.| ||+|.+|+.+|+++|.+++||.++++++. +.++.+..+.+.+.+.+++.||+++..
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~ 66 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVS 66 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCccccc
Confidence 5688999 99999999999999999999999999994 556666678999999999999999875
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.22 E-value=4.5e-06 Score=74.87 Aligned_cols=63 Identities=22% Similarity=0.487 Sum_probs=56.4
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec---CC-HHHHHHHHHhcCCceEE
Q 036289 29 QTVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTGY---VE-ANKVLKKAKSTGKRAEI 92 (149)
Q Consensus 29 ~~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g~---~~-~~~I~~~I~~~G~~a~~ 92 (149)
.+..+.| ||+|..|+.+|| +|.+++||..+.+|+.++++.|..+ .+ .+++...++..||.+..
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 3567999 999999999999 9999999999999999999998843 44 78999999999998765
No 8
>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=97.97 E-value=0.00013 Score=42.69 Aligned_cols=60 Identities=22% Similarity=0.343 Sum_probs=50.1
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEe---cCCHHHHHHHHHhcCCc
Q 036289 30 TVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTG---YVEANKVLKKAKSTGKR 89 (149)
Q Consensus 30 ~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g---~~~~~~I~~~I~~~G~~ 89 (149)
+..+.+ ++.|..|...+++.+...+++....+++...++.+.. ..+...+...+...|+.
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 66 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYE 66 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCC
Confidence 456889 9999999999999999999999999999999988763 24667777777777764
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.80 E-value=6.7e-05 Score=68.17 Aligned_cols=68 Identities=28% Similarity=0.460 Sum_probs=62.2
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEe---cCCHHHHHHHHHhcCCceEEccCC
Q 036289 29 QTVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTG---YVEANKVLKKAKSTGKRAEIWPYV 96 (149)
Q Consensus 29 ~~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g---~~~~~~I~~~I~~~G~~a~~~~~~ 96 (149)
.++.|.| ||.|.+|+.+|++.|.+++||.++++++.++++.|.. .+.+.++++.|+.+|+.+.+.++.
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~~~ 217 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRPYG 217 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeeecc
Confidence 6889999 9999999999999999999999999999999999873 378999999999999998877643
No 10
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.40 E-value=0.00067 Score=62.05 Aligned_cols=65 Identities=25% Similarity=0.445 Sum_probs=57.2
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecCCHHHHHHHHHhcCCceEEcc
Q 036289 30 TVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTGYVEANKVLKKAKSTGKRAEIWP 94 (149)
Q Consensus 30 ~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g~~~~~~I~~~I~~~G~~a~~~~ 94 (149)
++.+.+ ||+|..|...+++.+..++||.++.+++..+++.+.+..+.+++.+.+++.||.+.++.
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~~~ 165 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEAIE 165 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCccccc
Confidence 567889 99999999999999999999999999999999888765678888888999999876543
No 11
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.32 E-value=0.00069 Score=61.80 Aligned_cols=69 Identities=19% Similarity=0.298 Sum_probs=61.3
Q ss_pred cceEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec---CCHHHHHHHHHhcCCceEEccC
Q 036289 27 QLQTVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTGY---VEANKVLKKAKSTGKRAEIWPY 95 (149)
Q Consensus 27 ~~~~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g~---~~~~~I~~~I~~~G~~a~~~~~ 95 (149)
...+..+.+ ||+|..|+..+++.|++++||.++.+.+...+..+..+ +.++.+.+.+++.|+.+++...
T Consensus 67 ~~~~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~ 139 (951)
T KOG0207|consen 67 TASKCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIES 139 (951)
T ss_pred ccceeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhc
Confidence 344678999 99999999999999999999999999999999998733 7889999999999999987653
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.11 E-value=0.002 Score=58.39 Aligned_cols=66 Identities=29% Similarity=0.319 Sum_probs=54.3
Q ss_pred ceEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec-CCHHHHHHHHHhcCCceEEc
Q 036289 28 LQTVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTGY-VEANKVLKKAKSTGKRAEIW 93 (149)
Q Consensus 28 ~~~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g~-~~~~~I~~~I~~~G~~a~~~ 93 (149)
..+..+.+ +|+|.+|..++++.+.+++||..+.+++..+++.+..+ ...+++.+.++..||.+..+
T Consensus 52 ~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~~~ 119 (741)
T PRK11033 52 GTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLRDE 119 (741)
T ss_pred CceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccccccc
Confidence 44667889 99999999999999999999999999999999877632 12267777888899987644
No 13
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=94.72 E-value=0.61 Score=29.38 Aligned_cols=63 Identities=25% Similarity=0.422 Sum_probs=47.0
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEe---cCCHHHHHHHHHhcCCceEE
Q 036289 30 TVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTG---YVEANKVLKKAKSTGKRAEI 92 (149)
Q Consensus 30 ~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g---~~~~~~I~~~I~~~G~~a~~ 92 (149)
+..+.+ ++.|..|...++..+...+++....++.......+.. ......+...+...|+.+++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 456778 9999999999999999999988888888777755541 23555555566677776544
No 14
>PRK13748 putative mercuric reductase; Provisional
Probab=90.85 E-value=2.1 Score=37.29 Aligned_cols=64 Identities=23% Similarity=0.408 Sum_probs=50.3
Q ss_pred EEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEe--cCCHHHHHHHHHhcCCceEEccC
Q 036289 32 DLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTG--YVEANKVLKKAKSTGKRAEIWPY 95 (149)
Q Consensus 32 ~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g--~~~~~~I~~~I~~~G~~a~~~~~ 95 (149)
.+.+ ++.|..|..+++..+...+++....+++......+.. ......+...++..|+..+....
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~~~ 69 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLADA 69 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeeccCc
Confidence 3567 9999999999999999999999888998888866652 24556666667788887766654
No 15
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=90.67 E-value=2.6 Score=28.58 Aligned_cols=68 Identities=16% Similarity=0.260 Sum_probs=44.9
Q ss_pred cceEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEec-----C--CCEEEEEec-CCHHHHHHHHHhcCCceEEcc
Q 036289 27 QLQTVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINR-----K--QQKVSVTGY-VEANKVLKKAKSTGKRAEIWP 94 (149)
Q Consensus 27 ~~~~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl-----~--~~~v~V~g~-~~~~~I~~~I~~~G~~a~~~~ 94 (149)
..+++.+.+ .-+-.--.--+-+.|.+++||..|++.+ + +-+++|.|. ++.++|.+.|++.|....-..
T Consensus 4 ~iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHSiD 80 (97)
T COG1888 4 GIRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHSID 80 (97)
T ss_pred cceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeeehh
Confidence 345566666 4443333345566788888888777532 3 334556664 899999999999998765543
No 16
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=89.54 E-value=3 Score=28.41 Aligned_cols=65 Identities=17% Similarity=0.320 Sum_probs=43.5
Q ss_pred ceEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEe-----cCCCEE--EEEec-CCHHHHHHHHHhcCCceEEc
Q 036289 28 LQTVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEIN-----RKQQKV--SVTGY-VEANKVLKKAKSTGKRAEIW 93 (149)
Q Consensus 28 ~~~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vd-----l~~~~v--~V~g~-~~~~~I~~~I~~~G~~a~~~ 93 (149)
.+++.|.| ..+-+.- -.+-+.|.+++||..|++. .....+ +|+|. ++.++|.++|++.|-.+.-.
T Consensus 4 irRlVLDVlKP~~p~i-~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHSI 77 (95)
T PF02680_consen 4 IRRLVLDVLKPHEPSI-VELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHSI 77 (95)
T ss_dssp EEEEEEEEEEESSS-H-HHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEEE
T ss_pred eeEEEEEeecCCCCCH-HHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEee
Confidence 45677777 4444443 4566779999999988754 333433 45565 89999999999999766543
No 17
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=88.30 E-value=2.3 Score=21.83 Aligned_cols=38 Identities=39% Similarity=0.712 Sum_probs=30.0
Q ss_pred EE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEE
Q 036289 34 KV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVT 71 (149)
Q Consensus 34 ~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~ 71 (149)
.+ ++.|..|...++..+....++.....++......+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVE 41 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEE
Confidence 35 788999999999988888898777777766665554
No 18
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=87.58 E-value=2.3 Score=26.53 Aligned_cols=54 Identities=17% Similarity=0.166 Sum_probs=39.2
Q ss_pred EEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEe--cCCHHHHHHHHHhcCCceEEcc
Q 036289 32 DLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTG--YVEANKVLKKAKSTGKRAEIWP 94 (149)
Q Consensus 32 ~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g--~~~~~~I~~~I~~~G~~a~~~~ 94 (149)
++.+ |+.|+...-+++++|.+++. .+.+.|.. ......|...++..|+...-+.
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~---------G~~l~v~~d~~~~~~di~~~~~~~g~~~~~~~ 58 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPP---------GEVLEVLVDDPAAVEDIPRWCEENGYEVVEVE 58 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGT---------T-EEEEEESSTTHHHHHHHHHHHHTEEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCC---------CCEEEEEECCccHHHHHHHHHHHCCCEEEEEE
Confidence 5778 99999999999999998743 23444442 3456889999999999865543
No 19
>PRK11018 hypothetical protein; Provisional
Probab=80.14 E-value=11 Score=24.28 Aligned_cols=55 Identities=15% Similarity=0.079 Sum_probs=41.0
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEE--ecCCHHHHHHHHHhcCCceEEc
Q 036289 30 TVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVT--GYVEANKVLKKAKSTGKRAEIW 93 (149)
Q Consensus 30 ~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~--g~~~~~~I~~~I~~~G~~a~~~ 93 (149)
..++.+ |..|+.-.-+.+++|.+++.- +.+.|. .......|...+++.|+++...
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~~G---------~~L~V~~d~~~a~~di~~~~~~~G~~v~~~ 65 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLKKG---------EILEVVSDCPQSINNIPLDARNHGYTVLDI 65 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCCCC---------CEEEEEeCCccHHHHHHHHHHHcCCEEEEE
Confidence 356888 999999999999999988532 233333 3356678888999999987643
No 20
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=77.68 E-value=8.8 Score=23.67 Aligned_cols=52 Identities=21% Similarity=0.294 Sum_probs=36.8
Q ss_pred EEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEE--ecCCHHHHHHHHHhcCCceEEcc
Q 036289 33 LKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVT--GYVEANKVLKKAKSTGKRAEIWP 94 (149)
Q Consensus 33 l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~--g~~~~~~I~~~I~~~G~~a~~~~ 94 (149)
+.+ |+.|+.-.-+++++| ++.. .+.+.|. .......|...+++.|+......
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~~~s~~~i~~~~~~~G~~~~~~~ 56 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEA---------GGEIEVLVDNEVAKENVSRFAESRGYEVSVEE 56 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCC---------CCEEEEEEcChhHHHHHHHHHHHcCCEEEEEe
Confidence 456 899999999999999 5532 2233333 23455789999999999885443
No 21
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=74.13 E-value=7.4 Score=24.29 Aligned_cols=33 Identities=27% Similarity=0.590 Sum_probs=21.6
Q ss_pred eEEEEEEcCcChhH------HHHHHHHHhCCCCeeEEEE
Q 036289 29 QTVDLKVRMDCDGC------ELKVKNAVSSLSGVKSVEI 61 (149)
Q Consensus 29 ~~v~l~Vgm~C~~C------~~kV~k~L~~~~GV~~v~v 61 (149)
.++.+.+.+..++| ...++++|..++||.+++|
T Consensus 34 ~~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 34 GKVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp CEEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred CEEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 45555554455444 4778899999999998875
No 22
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=72.43 E-value=16 Score=22.81 Aligned_cols=53 Identities=23% Similarity=0.264 Sum_probs=39.2
Q ss_pred EEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEE--ecCCHHHHHHHHHhcCCceEEcc
Q 036289 33 LKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVT--GYVEANKVLKKAKSTGKRAEIWP 94 (149)
Q Consensus 33 l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~--g~~~~~~I~~~I~~~G~~a~~~~ 94 (149)
+.+ |+.|+.=.-+.+++|.+++. .+.+.|. .......|....+..|++.....
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~---------G~~l~V~~d~~~a~~di~~~~~~~G~~~~~~~ 57 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQD---------GEQLEVKASDPGFARDAQAWCKSTGNTLISLE 57 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHHHcCCEEEEEE
Confidence 456 89999999999999998752 2233443 33567889999999999887443
No 23
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=66.75 E-value=25 Score=21.93 Aligned_cols=53 Identities=17% Similarity=0.138 Sum_probs=38.6
Q ss_pred EEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEE--ecCCHHHHHHHHHhcCCceEEcc
Q 036289 33 LKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVT--GYVEANKVLKKAKSTGKRAEIWP 94 (149)
Q Consensus 33 l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~--g~~~~~~I~~~I~~~G~~a~~~~ 94 (149)
+.+ |..|+.=.-+.+++|++++.- +.+.|. .......|...++..|+++....
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~~G---------~~l~V~~d~~~s~~ni~~~~~~~g~~v~~~~ 57 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLKPG---------EILEVISDCPQSINNIPIDARNHGYKVLAIE 57 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCC---------CEEEEEecCchHHHHHHHHHHHcCCEEEEEE
Confidence 345 889999999999999988522 223333 33567888899999999886443
No 24
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=64.56 E-value=32 Score=21.39 Aligned_cols=53 Identities=11% Similarity=0.101 Sum_probs=38.8
Q ss_pred EEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEE--ecCCHHHHHHHHHhcCCceEEcc
Q 036289 33 LKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVT--GYVEANKVLKKAKSTGKRAEIWP 94 (149)
Q Consensus 33 l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~--g~~~~~~I~~~I~~~G~~a~~~~ 94 (149)
+.+ |..|+.=.-+++++|.+++- .+.+.|. .......|...+++.|+++....
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~~---------G~~l~V~~dd~~s~~di~~~~~~~g~~~~~~~ 57 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMKP---------GDTLLVLATDPSTTRDIPKFCTFLGHELLAQE 57 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCCC---------CCEEEEEeCCCchHHHHHHHHHHcCCEEEEEE
Confidence 345 88999999999999998742 2233333 33567889999999999886543
No 25
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=63.72 E-value=25 Score=26.41 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=24.5
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCCE
Q 036289 40 DGCELKVKNAVSSLSGVKSVEINRKQQK 67 (149)
Q Consensus 40 ~~C~~kV~k~L~~~~GV~~v~vdl~~~~ 67 (149)
.+|-+-++..+..++||.++.+-...+.
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~ 37 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGH 37 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCC
Confidence 6788889999999999999999877664
No 26
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=63.37 E-value=33 Score=22.19 Aligned_cols=55 Identities=20% Similarity=0.225 Sum_probs=38.1
Q ss_pred cchhHHHhhhccCC-Ccc-----ccccCcceEEEEEEcCcChhHHHHHHHHHhCCCCeeEEEE
Q 036289 5 GTLEYLSDLMGSSG-HKH-----KKKKKQLQTVDLKVRMDCDGCELKVKNAVSSLSGVKSVEI 61 (149)
Q Consensus 5 ~~~~~~s~~~~~~~-~~~-----~~~~~~~~~v~l~Vgm~C~~C~~kV~k~L~~~~GV~~v~v 61 (149)
|+|+.++++|.-++ +.. ........++++.++ -+.....+.+.|.++..|..|++
T Consensus 15 GVL~Ri~~lf~rRGfnI~sl~v~~t~~~~~sriti~v~--~~~~i~ql~kQL~KL~dV~~V~~ 75 (76)
T PRK11152 15 EVLERVLRVVRHRGFQVCSMNMTQNTDAQNINIELTVA--SERPIDLLSSQLNKLVDVAHVEI 75 (76)
T ss_pred cHHHHHHHHHhcCCeeeeeEEeeecCCCCEEEEEEEEC--CCchHHHHHHHHhcCcCeEEEEE
Confidence 78888999885321 111 112344566666664 58889999999999999988876
No 27
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=61.43 E-value=34 Score=20.75 Aligned_cols=53 Identities=23% Similarity=0.172 Sum_probs=38.3
Q ss_pred EEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEe--cCCHHHHHHHHHhcCCceEEcc
Q 036289 33 LKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTG--YVEANKVLKKAKSTGKRAEIWP 94 (149)
Q Consensus 33 l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g--~~~~~~I~~~I~~~G~~a~~~~ 94 (149)
+.+ |+.|+.=..++.++|.+++. .+.+.|.. ......|.+.++..|++.....
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~~---------g~~l~v~~d~~~~~~~i~~~~~~~g~~~~~~~ 57 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLKS---------GEVLEVLLDDPGAVEDIPAWAKETGHEVLEVE 57 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCCC---------CCEEEEEecCCcHHHHHHHHHHHcCCEEEEEE
Confidence 456 89999999999999988643 23334432 2457889999999999876543
No 28
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=61.13 E-value=46 Score=22.14 Aligned_cols=45 Identities=7% Similarity=0.142 Sum_probs=31.3
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCCEEEEE-ecCCHHHHHHHHH
Q 036289 40 DGCELKVKNAVSSLSGVKSVEINRKQQKVSVT-GYVEANKVLKKAK 84 (149)
Q Consensus 40 ~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~-g~~~~~~I~~~I~ 84 (149)
+.=...+.+.|..++|+.-.-.|...+|+.|+ ...+..++.+.|.
T Consensus 16 Pe~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 16 SERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred hHHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 34467889999999999766677778887766 2335555555554
No 29
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=59.08 E-value=44 Score=24.19 Aligned_cols=44 Identities=18% Similarity=0.230 Sum_probs=27.5
Q ss_pred hHHHHHHHHHhCC-CCeeEEEEecCCCEEEEEecCCHHHHHHHHH
Q 036289 41 GCELKVKNAVSSL-SGVKSVEINRKQQKVSVTGYVEANKVLKKAK 84 (149)
Q Consensus 41 ~C~~kV~k~L~~~-~GV~~v~vdl~~~~v~V~g~~~~~~I~~~I~ 84 (149)
.-...|.+.|.+. -+...++|....+.|++.|.+.......++.
T Consensus 26 ~~~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~~~~~ 70 (147)
T PRK11198 26 DAADALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAKEKIL 70 (147)
T ss_pred HHHHHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHHHHHH
Confidence 3446677777543 2344566777799999998865444444443
No 30
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=57.71 E-value=33 Score=25.24 Aligned_cols=40 Identities=28% Similarity=0.446 Sum_probs=30.9
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecC-CCEEE
Q 036289 29 QTVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRK-QQKVS 69 (149)
Q Consensus 29 ~~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~-~~~v~ 69 (149)
..+++.| .-.|..|..-|.....++ |+.++.|... ++++.
T Consensus 100 ~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~ 141 (146)
T PF14437_consen 100 RSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVY 141 (146)
T ss_pred CeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEE
Confidence 4567888 888999998888877766 8888888766 55443
No 31
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=56.49 E-value=52 Score=21.25 Aligned_cols=55 Identities=7% Similarity=0.099 Sum_probs=40.3
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEE--ecCCHHHHHHHHHhcCCceEEc
Q 036289 30 TVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVT--GYVEANKVLKKAKSTGKRAEIW 93 (149)
Q Consensus 30 ~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~--g~~~~~~I~~~I~~~G~~a~~~ 93 (149)
..++.+ |+.|+.=.-+++++|.+++. .+.+.|. .....+.|....+..|++....
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~~---------G~~l~V~~dd~~~~~di~~~~~~~G~~~~~~ 66 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQP---------GETLLIIADDPATTRDIPSFCRFMDHELLAQ 66 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCCC---------CCEEEEEeCCccHHHHHHHHHHHcCCEEEEE
Confidence 356788 99999999999999998842 2233333 3356778888889999988643
No 32
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=51.52 E-value=57 Score=20.56 Aligned_cols=41 Identities=27% Similarity=0.353 Sum_probs=30.1
Q ss_pred HhCCCCeeEEEEecCCCEEE--EEecCCHHHHHHHHHhcCCceEE
Q 036289 50 VSSLSGVKSVEINRKQQKVS--VTGYVEANKVLKKAKSTGKRAEI 92 (149)
Q Consensus 50 L~~~~GV~~v~vdl~~~~v~--V~g~~~~~~I~~~I~~~G~~a~~ 92 (149)
|..++||..+...- .+.+. +.......+|++.|...|. +.-
T Consensus 26 l~~~~~v~~v~~~~-~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~ 68 (84)
T PF13732_consen 26 LEELPGVESVEQDG-DGKLRIKLEDEETANELLQELIEKGI-IRS 68 (84)
T ss_pred HhhCCCeEEEEEeC-CcEEEEEECCcccHHHHHHHHHhCCC-eeE
Confidence 77889999988643 44344 4455678999999999998 553
No 33
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=47.13 E-value=81 Score=24.62 Aligned_cols=34 Identities=18% Similarity=0.220 Sum_probs=27.1
Q ss_pred ceEEEEEEcCcChhHHHHHHHHHhCCCCeeEEEEecCCC
Q 036289 28 LQTVDLKVRMDCDGCELKVKNAVSSLSGVKSVEINRKQQ 66 (149)
Q Consensus 28 ~~~v~l~Vgm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~ 66 (149)
+.++.|. .+|-+-++..+.+++||.++.+-...+
T Consensus 45 ~~~a~fa-----gGCFWg~E~~F~~l~GV~~t~vGYagG 78 (213)
T PRK00058 45 MEQAIFG-----MGCFWGAERLFWQLPGVYSTAVGYAGG 78 (213)
T ss_pred ccEEEEE-----ccCcchhHHHHhcCCCEEEEEeeecCC
Confidence 4455554 778888999999999999999987744
No 34
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=47.02 E-value=59 Score=24.81 Aligned_cols=49 Identities=22% Similarity=0.245 Sum_probs=36.8
Q ss_pred cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEE--ecCCHHHHHHHHHhcCCceEEc
Q 036289 36 RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVT--GYVEANKVLKKAKSTGKRAEIW 93 (149)
Q Consensus 36 gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~--g~~~~~~I~~~I~~~G~~a~~~ 93 (149)
|+.|+.-.-+.+++|.+++. .+.++|. .....+.|.+.++..|+++...
T Consensus 5 Gl~CP~Pvi~tKkal~~l~~---------g~~L~VlvD~~~a~~nV~~~~~~~G~~v~~~ 55 (194)
T TIGR03527 5 GLACPQPVILTKKALDELGE---------EGVLTVIVDNEAAKENVSKFATSLGYEVEVE 55 (194)
T ss_pred CCCCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHHHcCCEEEEE
Confidence 88999999999999998852 1223332 3456778999999999988754
No 35
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=46.22 E-value=60 Score=24.77 Aligned_cols=36 Identities=22% Similarity=0.326 Sum_probs=27.9
Q ss_pred cceEEEEEEcCcChhHHHHHHHHHhCCCCeeEEEEecCCCE
Q 036289 27 QLQTVDLKVRMDCDGCELKVKNAVSSLSGVKSVEINRKQQK 67 (149)
Q Consensus 27 ~~~~v~l~Vgm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~ 67 (149)
.++++.|. .+|-+-++....+++||.++.+-...+.
T Consensus 7 ~~~~a~~a-----gGCFWg~E~~f~~l~GV~~t~vGYagG~ 42 (186)
T PRK13014 7 GMETATFA-----GGCFWGVEGVFQHVPGVVSVVSGYSGGH 42 (186)
T ss_pred CccEEEEe-----cCCceeeHHHHccCCCEEEEEeeecCCC
Confidence 34555554 6788888899999999999999877664
No 36
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=45.94 E-value=31 Score=25.96 Aligned_cols=35 Identities=26% Similarity=0.500 Sum_probs=23.1
Q ss_pred EEEEEEcCcChhH------HHHHHHHHhCCCCeeEEEEecC
Q 036289 30 TVDLKVRMDCDGC------ELKVKNAVSSLSGVKSVEINRK 64 (149)
Q Consensus 30 ~v~l~Vgm~C~~C------~~kV~k~L~~~~GV~~v~vdl~ 64 (149)
++.+.+.+..++| ...|+.+|..++||.+++|++.
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l~ 154 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVELV 154 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEEE
Confidence 3444444444444 3458889999999998888653
No 37
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=45.22 E-value=83 Score=20.30 Aligned_cols=52 Identities=19% Similarity=0.266 Sum_probs=36.7
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEe--cCCHHHHHHHHHhcC-Cce
Q 036289 30 TVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVTG--YVEANKVLKKAKSTG-KRA 90 (149)
Q Consensus 30 ~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~g--~~~~~~I~~~I~~~G-~~a 90 (149)
..++.+ |+.|+.=...++++|.+++- .+.+.|.. ....++|...+++.| +..
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~---------Ge~LeV~~ddp~~~~dIp~~~~~~~~~~l 60 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLKP---------GEILEVIADDPAAKEDIPAWAKKEGGHEL 60 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCCC---------CCEEEEEecCcchHHHHHHHHHHcCCcEE
Confidence 457889 99999999999999998842 33344442 245677888887555 443
No 38
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=43.87 E-value=87 Score=20.19 Aligned_cols=44 Identities=16% Similarity=0.218 Sum_probs=30.0
Q ss_pred HHHHHHHHHhCCCCeeEEEEecCCCEEEEE-ecCCHHHHHHHHHhc
Q 036289 42 CELKVKNAVSSLSGVKSVEINRKQQKVSVT-GYVEANKVLKKAKST 86 (149)
Q Consensus 42 C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~-g~~~~~~I~~~I~~~ 86 (149)
=...+..+|..++|+.-...+-. +|+.|+ ...+..++.+.+...
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~i 60 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDAI 60 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHHH
Confidence 35678899999999955556555 787665 334666666666543
No 39
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=42.84 E-value=47 Score=23.21 Aligned_cols=21 Identities=29% Similarity=0.479 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCCCeeEEEEec
Q 036289 43 ELKVKNAVSSLSGVKSVEINR 63 (149)
Q Consensus 43 ~~kV~k~L~~~~GV~~v~vdl 63 (149)
...++.+|..++||.++++++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 678899999999999888864
No 40
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=42.30 E-value=36 Score=25.22 Aligned_cols=44 Identities=23% Similarity=0.315 Sum_probs=32.4
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCCE--------------EEEEe---cCCHHHHHHHH
Q 036289 40 DGCELKVKNAVSSLSGVKSVEINRKQQK--------------VSVTG---YVEANKVLKKA 83 (149)
Q Consensus 40 ~~C~~kV~k~L~~~~GV~~v~vdl~~~~--------------v~V~g---~~~~~~I~~~I 83 (149)
.+|-+-++..+.+++||.++.+-...+. |.|+- .++.++|++..
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f 68 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYL 68 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHH
Confidence 6788889999999999999998766543 33332 26777777754
No 41
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=41.38 E-value=89 Score=19.55 Aligned_cols=56 Identities=7% Similarity=0.012 Sum_probs=35.6
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCC-eeEEEEecCCCEEEEE----ec-CCHHHHHHHHHh
Q 036289 30 TVDLKV-RMDCDGCELKVKNAVSSLSG-VKSVEINRKQQKVSVT----GY-VEANKVLKKAKS 85 (149)
Q Consensus 30 ~v~l~V-gm~C~~C~~kV~k~L~~~~G-V~~v~vdl~~~~v~V~----g~-~~~~~I~~~I~~ 85 (149)
.+.+.+ |.+.++....+.+.|....+ +.+++.....+..+.. .. .+.+++.+.|++
T Consensus 2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~~~~~~~l~~~L~~ 64 (76)
T PF13740_consen 2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIPEDSLERLESALEE 64 (76)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEESHHHHHHHHHHHHH
T ss_pred EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeCcccHHHHHHHHHH
Confidence 466788 99999999999999998865 5566666556655432 22 244555555543
No 42
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=38.81 E-value=1.1e+02 Score=22.32 Aligned_cols=33 Identities=15% Similarity=0.225 Sum_probs=27.9
Q ss_pred ChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEE
Q 036289 39 CDGCELKVKNAVSSLSGVKSVEINRKQQKVSVT 71 (149)
Q Consensus 39 C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~ 71 (149)
-..=+..|.+.+.+++||.++.+-.....+.|.
T Consensus 73 ~~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 73 RQQLADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 355678999999999999999998888887764
No 43
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=36.67 E-value=1.2e+02 Score=19.96 Aligned_cols=40 Identities=23% Similarity=0.268 Sum_probs=28.3
Q ss_pred HHHHHHHhCCCCeeEEEEecCCCEEEEE--ecCCHHHHHHHHHh
Q 036289 44 LKVKNAVSSLSGVKSVEINRKQQKVSVT--GYVEANKVLKKAKS 85 (149)
Q Consensus 44 ~kV~k~L~~~~GV~~v~vdl~~~~v~V~--g~~~~~~I~~~I~~ 85 (149)
.-+-+.|-.++||.+|-+. ..=++|+ ...+++.|...|..
T Consensus 37 spLA~~Lf~i~gV~~Vf~~--~dfItVtK~~~~~W~~l~~~I~~ 78 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFIG--DDFITVTKNPDADWEDLKPEIRE 78 (87)
T ss_dssp -HHHHHHHTSTTEEEEEEE--TTEEEEEE-TTS-HHHHHHHHHH
T ss_pred CHHHHHhcCCCCEeEEEEE--CCEEEEeeCCCCCHHHHHHHHHH
Confidence 4455566799999988775 5667776 55899999887764
No 44
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=35.18 E-value=1.1e+02 Score=18.95 Aligned_cols=56 Identities=16% Similarity=0.227 Sum_probs=34.1
Q ss_pred cchhHHHhhhccC-CCcc----ccc-cCcceEEEEEEcCcChhHHHHHHHHHhCCCCeeEEE
Q 036289 5 GTLEYLSDLMGSS-GHKH----KKK-KKQLQTVDLKVRMDCDGCELKVKNAVSSLSGVKSVE 60 (149)
Q Consensus 5 ~~~~~~s~~~~~~-~~~~----~~~-~~~~~~v~l~Vgm~C~~C~~kV~k~L~~~~GV~~v~ 60 (149)
|+|.-++..+... .+.. ... ......+.|.+...-..-...+-+.|++++||.+|.
T Consensus 18 GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 18 GLLADITSVISENGVNIRSINARTNKDDGTARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp THHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred CHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 5666777766442 1111 111 234555666665555666677888899999998774
No 45
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=35.00 E-value=49 Score=21.87 Aligned_cols=35 Identities=26% Similarity=0.420 Sum_probs=23.0
Q ss_pred EEEEEE-cCcChhH---HHHHHHHHhCCCCeeEEEEecC
Q 036289 30 TVDLKV-RMDCDGC---ELKVKNAVSSLSGVKSVEINRK 64 (149)
Q Consensus 30 ~v~l~V-gm~C~~C---~~kV~k~L~~~~GV~~v~vdl~ 64 (149)
.+.+.+ .-.|... ...++.+|..++|+.++++++.
T Consensus 40 ~i~l~l~~p~~~~~~~l~~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 40 DIQMTLTAPNCPVAGSMPGEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred EEEEEECCCCCChHHHHHHHHHHHHHhCCCCceEEEEEE
Confidence 344444 3444443 3457788889999999888764
No 46
>PF13216 DUF4024: Protein of unknown function (DUF4024)
Probab=33.29 E-value=12 Score=20.11 Aligned_cols=11 Identities=27% Similarity=0.637 Sum_probs=9.0
Q ss_pred CCCCCCCCCCC
Q 036289 138 YISMFSDDNPN 148 (149)
Q Consensus 138 ~~~~fsd~np~ 148 (149)
..++|-|||.|
T Consensus 8 ~lhlfrde~vn 18 (35)
T PF13216_consen 8 NLHLFRDEKVN 18 (35)
T ss_pred EEEEeecCCcc
Confidence 46789999987
No 47
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=32.15 E-value=1.2e+02 Score=18.31 Aligned_cols=33 Identities=15% Similarity=0.247 Sum_probs=23.8
Q ss_pred eEEEEEEcCcChh-HHHHHHHHHhCCCCeeEEEE
Q 036289 29 QTVDLKVRMDCDG-CELKVKNAVSSLSGVKSVEI 61 (149)
Q Consensus 29 ~~v~l~Vgm~C~~-C~~kV~k~L~~~~GV~~v~v 61 (149)
..+.|.+...-.. --..+-+.|++++||.+|.+
T Consensus 41 ~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 41 ANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 4455555434444 77888899999999998875
No 48
>COG4312 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.93 E-value=2.3e+02 Score=22.52 Aligned_cols=59 Identities=12% Similarity=0.260 Sum_probs=36.0
Q ss_pred cCcceEEEEEEc----CcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEE--EecCCHHHHHHHHHhcCCce
Q 036289 25 KKQLQTVDLKVR----MDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSV--TGYVEANKVLKKAKSTGKRA 90 (149)
Q Consensus 25 ~~~~~~v~l~Vg----m~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V--~g~~~~~~I~~~I~~~G~~a 90 (149)
++++..+.|..+ -.|++|...... +......+....+++ ......++|+..=++.|.+.
T Consensus 73 rsqLIvYhfmF~P~~~~~C~gCS~laD~-------~dGa~~HL~~~dv~lv~VsRAPl~~l~~~k~rmGW~f 137 (247)
T COG4312 73 RSQLIVYHFMFGPGWDHGCPGCSFLADH-------WDGAVAHLEHHDVTLVAVSRAPLEELVAYKRRMGWQF 137 (247)
T ss_pred CceEEEEEEecCCCccCCCCchhhHHhh-------hhhhhhhHhhcCceEEEEecCcHHHHHHHHHhcCCcc
Confidence 355666666662 359999754432 222233444444443 35678888888888899773
No 49
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=31.38 E-value=42 Score=24.34 Aligned_cols=43 Identities=19% Similarity=0.242 Sum_probs=27.5
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCCEE-EEEecCCHHHHHHHHHh
Q 036289 40 DGCELKVKNAVSSLSGVKSVEINRKQQKV-SVTGYVEANKVLKKAKS 85 (149)
Q Consensus 40 ~~C~~kV~k~L~~~~GV~~v~vdl~~~~v-~V~g~~~~~~I~~~I~~ 85 (149)
.+|.+++-++|+ .+.-|+.+...++. +-.|.-+.++|...|..
T Consensus 97 ~~i~rkvlQ~Le---~~~~ve~hp~gGR~lt~~GqrdldrIa~~i~~ 140 (143)
T KOG3411|consen 97 GGIARKVLQALE---KMGIVEKHPKGGRRLTEQGQRDLDRIAGQIRE 140 (143)
T ss_pred cHHHHHHHHHHH---hCCceeeCCCCcceeCcccchhHHHHHHHHHh
Confidence 556666655555 45556666666553 34477888888887754
No 50
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=31.28 E-value=1.3e+02 Score=20.61 Aligned_cols=58 Identities=16% Similarity=0.323 Sum_probs=30.0
Q ss_pred EEE-cC-cChhHH-HHHHHHHhC--CCCeeEEEEecCCCEEEEE--ec-CCHHHHHHHHHhc-CCceEE
Q 036289 33 LKV-RM-DCDGCE-LKVKNAVSS--LSGVKSVEINRKQQKVSVT--GY-VEANKVLKKAKST-GKRAEI 92 (149)
Q Consensus 33 l~V-gm-~C~~C~-~kV~k~L~~--~~GV~~v~vdl~~~~v~V~--g~-~~~~~I~~~I~~~-G~~a~~ 92 (149)
+.+ +| +|.+|- .++...+.. ..|+..+-+. +-...-. +. -..+++.+.|++. |+++..
T Consensus 38 ~elvgf~~CgGCpg~~~~~~~~~l~~~~~d~IHls--sC~~~~~~~~~CP~~~~~~~~I~~~~gi~VV~ 104 (107)
T PF08821_consen 38 VELVGFFTCGGCPGRKLVRRIKKLKKNGADVIHLS--SCMVKGNPHGPCPHIDEIKKIIEEKFGIEVVE 104 (107)
T ss_pred eEEEEEeeCCCCChhHHHHHHHHHHHCCCCEEEEc--CCEecCCCCCCCCCHHHHHHHHHHHhCCCEee
Confidence 555 66 899873 222222222 3556533332 2211101 11 3578899999876 887654
No 51
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=29.47 E-value=1.7e+02 Score=19.35 Aligned_cols=61 Identities=11% Similarity=0.122 Sum_probs=39.2
Q ss_pred ccchhHHHhhhccC-CCcc-----ccccCcceEEEEEEcCcChhHHHHHHHHHhCCCCeeEEE-EecC
Q 036289 4 AGTLEYLSDLMGSS-GHKH-----KKKKKQLQTVDLKVRMDCDGCELKVKNAVSSLSGVKSVE-INRK 64 (149)
Q Consensus 4 ~~~~~~~s~~~~~~-~~~~-----~~~~~~~~~v~l~Vgm~C~~C~~kV~k~L~~~~GV~~v~-vdl~ 64 (149)
-|+|..++.+|+-+ -+.. -...+...++++-+....+.-...|.+.|.++-.|..|. +|+.
T Consensus 13 ~GVL~Rit~lFsRRg~NI~SLtvg~Te~~~iSRmtivv~~~d~~~ieqI~kQL~KlidVikV~~~~~~ 80 (84)
T PRK13562 13 VSTLNRITSAFVRLQYNIDTLHVTHSEQPGISNMEIQVDIQDDTSLHILIKKLKQQINVLTVECYDLV 80 (84)
T ss_pred CCHHHHHHHHHhccCcCeeeEEecccCCCCceEEEEEEeCCCHHHHHHHHHHHhCCccEEEEEEeecc
Confidence 47899999998543 1111 122345566666654356677788888999998887765 4543
No 52
>PHA01634 hypothetical protein
Probab=29.47 E-value=18 Score=26.39 Aligned_cols=17 Identities=41% Similarity=0.984 Sum_probs=13.0
Q ss_pred EEE-cCcChhHHHHHHHH
Q 036289 33 LKV-RMDCDGCELKVKNA 49 (149)
Q Consensus 33 l~V-gm~C~~C~~kV~k~ 49 (149)
+.| -|+|++|+.++.-.
T Consensus 93 ~Di~~iDCeGCE~~l~v~ 110 (156)
T PHA01634 93 VDIFVMDCEGCEEKLNVS 110 (156)
T ss_pred cceEEEEccchHHhcCHH
Confidence 456 79999999887543
No 53
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=29.28 E-value=98 Score=20.78 Aligned_cols=34 Identities=29% Similarity=0.445 Sum_probs=25.2
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEe
Q 036289 29 QTVDLKV-RMDCDGCELKVKNAVSSLSGVKSVEIN 62 (149)
Q Consensus 29 ~~v~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vd 62 (149)
..+.+.+ --+-.+-...++++|..++||.++++-
T Consensus 49 kal~l~vvv~D~Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 49 KALKLYVVVEDKEGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred eeEEEEEEEcccccCcHHHHHHHhhccCcceEEEE
Confidence 3444444 344566789999999999999998874
No 54
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=28.71 E-value=1.4e+02 Score=23.49 Aligned_cols=38 Identities=18% Similarity=0.394 Sum_probs=27.6
Q ss_pred ceEEEEEE--cCcChhH---HHHHHHHHhCCCCeeEEEEecCC
Q 036289 28 LQTVDLKV--RMDCDGC---ELKVKNAVSSLSGVKSVEINRKQ 65 (149)
Q Consensus 28 ~~~v~l~V--gm~C~~C---~~kV~k~L~~~~GV~~v~vdl~~ 65 (149)
+.++++.| +.-|+-| ..++++++...++-..+++....
T Consensus 3 ~~~i~I~v~sD~vCPwC~ig~~rL~ka~~~~~~~~~v~i~w~p 45 (225)
T COG2761 3 PMKIEIDVFSDVVCPWCYIGKRRLEKALAEYPQEVRVEIRWRP 45 (225)
T ss_pred CceEEEEEEeCCcCchhhcCHHHHHHHHHhcCcceeEEEEecc
Confidence 34566666 9999999 68899999988865466665433
No 55
>PF11150 DUF2927: Protein of unknown function (DUF2927); InterPro: IPR021323 This family is conserved in Proteobacteria. Several members are described as being putative lipoproteins, but otherwise the function is not known.
Probab=27.86 E-value=35 Score=26.50 Aligned_cols=16 Identities=38% Similarity=0.368 Sum_probs=12.7
Q ss_pred CCCCCCCCCCCCCCCC
Q 036289 134 LEDPYISMFSDDNPNA 149 (149)
Q Consensus 134 ~~~~~~~~fsd~np~a 149 (149)
.+.-.++.|+|||+++
T Consensus 164 s~~~~pSIFNDd~~~~ 179 (213)
T PF11150_consen 164 SPRARPSIFNDDNEFA 179 (213)
T ss_pred CCcCCCceeeCCCccc
Confidence 3556789999999875
No 56
>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=27.73 E-value=71 Score=23.52 Aligned_cols=27 Identities=30% Similarity=0.410 Sum_probs=23.6
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCC
Q 036289 40 DGCELKVKNAVSSLSGVKSVEINRKQQ 66 (149)
Q Consensus 40 ~~C~~kV~k~L~~~~GV~~v~vdl~~~ 66 (149)
.+|-+-++..+.+++||.++.+-...+
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG 33 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGG 33 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESS
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCC
Confidence 578889999999999999999987655
No 57
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=27.71 E-value=42 Score=20.05 Aligned_cols=29 Identities=24% Similarity=0.444 Sum_probs=12.8
Q ss_pred HHHHHHhC---CCCeeEEEEecCCCEEEEEecC
Q 036289 45 KVKNAVSS---LSGVKSVEINRKQQKVSVTGYV 74 (149)
Q Consensus 45 kV~k~L~~---~~GV~~v~vdl~~~~v~V~g~~ 74 (149)
+|+..|.. +++- .+.+....+.+++.|.+
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v 34 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSVENGVVTLSGEV 34 (64)
T ss_dssp ----------CTT-T-TEEEEEECTEEEEEEEE
T ss_pred ccccccccccccCCC-eEEEEEECCEEEEEeeC
Confidence 34455544 2333 45666677777777764
No 58
>PRK09577 multidrug efflux protein; Reviewed
Probab=26.96 E-value=1.9e+02 Score=27.63 Aligned_cols=46 Identities=13% Similarity=0.151 Sum_probs=35.2
Q ss_pred HHHHHHHHhCCCCeeEEEEecCCCEEEEE--------ecCCHHHHHHHHHhcCC
Q 036289 43 ELKVKNAVSSLSGVKSVEINRKQQKVSVT--------GYVEANKVLKKAKSTGK 88 (149)
Q Consensus 43 ~~kV~k~L~~~~GV~~v~vdl~~~~v~V~--------g~~~~~~I~~~I~~~G~ 88 (149)
.+.++..|++++||.+|+++-....+.|. ..++..+|.++|+....
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n~ 211 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAHNA 211 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhCC
Confidence 46789999999999999998655555553 23778889999986543
No 59
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=26.57 E-value=2.1e+02 Score=19.39 Aligned_cols=55 Identities=25% Similarity=0.225 Sum_probs=32.0
Q ss_pred EEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEE--ecCCHHHHHHHHHhc
Q 036289 32 DLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVSVT--GYVEANKVLKKAKST 86 (149)
Q Consensus 32 ~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~V~--g~~~~~~I~~~I~~~ 86 (149)
.+++ |+.-+-+...|+..+.....|.-|++........|. ..-....+++.+...
T Consensus 3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhc
Confidence 3556 666566688999999999889999988878777776 334567777777655
No 60
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=26.05 E-value=1.3e+02 Score=20.09 Aligned_cols=23 Identities=30% Similarity=0.562 Sum_probs=19.8
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEe
Q 036289 40 DGCELKVKNAVSSLSGVKSVEIN 62 (149)
Q Consensus 40 ~~C~~kV~k~L~~~~GV~~v~vd 62 (149)
.+-...++.++++++||+++++-
T Consensus 61 ~g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 61 EGGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred CcChHHHHHHHhcCCCccEEEEE
Confidence 35569999999999999999874
No 61
>PRK07334 threonine dehydratase; Provisional
Probab=25.31 E-value=4.1e+02 Score=22.28 Aligned_cols=63 Identities=16% Similarity=0.220 Sum_probs=41.8
Q ss_pred EEEEE-cCcChhHHHHHHHHHhCCC-CeeEEEEecC-----CCEEEEE------ecCCHHHHHHHHHhcCCceEEc
Q 036289 31 VDLKV-RMDCDGCELKVKNAVSSLS-GVKSVEINRK-----QQKVSVT------GYVEANKVLKKAKSTGKRAEIW 93 (149)
Q Consensus 31 v~l~V-gm~C~~C~~kV~k~L~~~~-GV~~v~vdl~-----~~~v~V~------g~~~~~~I~~~I~~~G~~a~~~ 93 (149)
+.|.| ..+-.+=-..|-+.|...+ .|.+++.... .+...+. .....+.|++.|++.||++.+.
T Consensus 327 v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~~~L~~vi~~Lr~~g~~~~~~ 402 (403)
T PRK07334 327 ARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDAAHLQEVIAALRAAGFEARLV 402 (403)
T ss_pred EEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCHHHHHHHHHHHHHcCCeeEeC
Confidence 56777 6777777888888887552 3566665432 3443332 1234568999999999998864
No 62
>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=25.22 E-value=60 Score=23.75 Aligned_cols=28 Identities=21% Similarity=0.256 Sum_probs=23.2
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCCE
Q 036289 40 DGCELKVKNAVSSLSGVKSVEINRKQQK 67 (149)
Q Consensus 40 ~~C~~kV~k~L~~~~GV~~v~vdl~~~~ 67 (149)
.+|-+-++.....++||.++.+-...+.
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG~ 34 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGGY 34 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCCC
Confidence 5788888999999999999998766553
No 63
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=25.12 E-value=2.4e+02 Score=23.03 Aligned_cols=28 Identities=32% Similarity=0.367 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCCE
Q 036289 40 DGCELKVKNAVSSLSGVKSVEINRKQQK 67 (149)
Q Consensus 40 ~~C~~kV~k~L~~~~GV~~v~vdl~~~~ 67 (149)
.+|-+-++..+.+++||.++.+-...+.
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG~ 161 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGGD 161 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCCC
Confidence 6788889999999999999998766553
No 64
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=25.08 E-value=2.1e+02 Score=27.46 Aligned_cols=44 Identities=14% Similarity=0.212 Sum_probs=33.7
Q ss_pred HHHHHHHHhCCCCeeEEEEecCCCEEEEE--------ecCCHHHHHHHHHhc
Q 036289 43 ELKVKNAVSSLSGVKSVEINRKQQKVSVT--------GYVEANKVLKKAKST 86 (149)
Q Consensus 43 ~~kV~k~L~~~~GV~~v~vdl~~~~v~V~--------g~~~~~~I~~~I~~~ 86 (149)
++.++..|+.++||.+|++.-....+.|. ..++..+|..+|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 46789999999999999998654445554 237888899999743
No 65
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=23.96 E-value=1e+02 Score=23.27 Aligned_cols=35 Identities=17% Similarity=0.240 Sum_probs=27.2
Q ss_pred ceEEEEEEcCcChhHHHHHHHHHhCCCCeeEEEEecCCCE
Q 036289 28 LQTVDLKVRMDCDGCELKVKNAVSSLSGVKSVEINRKQQK 67 (149)
Q Consensus 28 ~~~v~l~Vgm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~ 67 (149)
++++.|. .+|-+=+++...+++||.++.+-...+.
T Consensus 6 ~~~a~fa-----gGCFWg~E~~f~~i~GV~~t~~GYagG~ 40 (174)
T COG0225 6 MEKAYFA-----GGCFWGVEAYFEQIPGVLSTVSGYAGGH 40 (174)
T ss_pred cEEEEEe-----ccCccchHHHHhhCCCeEEEeeeEcCCC
Confidence 4555554 6788888999999999999988766554
No 66
>PF13383 Methyltransf_22: Methyltransferase domain
Probab=23.51 E-value=1.6e+02 Score=23.26 Aligned_cols=56 Identities=25% Similarity=0.402 Sum_probs=35.8
Q ss_pred EEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEE--EEecC----CHHHHHHHHHhcCCceEEccCCC
Q 036289 32 DLKV-RMDCDGCELKVKNAVSSLSGVKSVEINRKQQKVS--VTGYV----EANKVLKKAKSTGKRAEIWPYVP 97 (149)
Q Consensus 32 ~l~V-gm~C~~C~~kV~k~L~~~~GV~~v~vdl~~~~v~--V~g~~----~~~~I~~~I~~~G~~a~~~~~~~ 97 (149)
.+.| .|+|++|+..+-..+.. .++ ..+. |.+.. ...++++.|++.||..--..+++
T Consensus 167 ~idiLKiDIEG~Ew~~L~~~l~-~~~---------~Qi~iEiH~~~~~~~~~~~~l~~l~~~gfr~F~~e~N~ 229 (242)
T PF13383_consen 167 EIDILKIDIEGAEWTVLEPLLE-SGV---------CQILIEIHGWPSEHREWYKLLQELEKAGFRLFNVEPNP 229 (242)
T ss_pred cccEEEEEcCccHHHHHHHHHh-cCC---------cEEEEEEEeCccchhHHHHHHHHHHHCCcEEEEecCCh
Confidence 3556 78999999998776643 244 2333 33321 23468999999998765555444
No 67
>PRK11023 outer membrane lipoprotein; Provisional
Probab=22.81 E-value=2.2e+02 Score=21.42 Aligned_cols=47 Identities=32% Similarity=0.382 Sum_probs=34.3
Q ss_pred cChhHHHHHHHHHhCCCCee---EEEEecCCCEEEEEecCCHHHHHHHHH
Q 036289 38 DCDGCELKVKNAVSSLSGVK---SVEINRKQQKVSVTGYVEANKVLKKAK 84 (149)
Q Consensus 38 ~C~~C~~kV~k~L~~~~GV~---~v~vdl~~~~v~V~g~~~~~~I~~~I~ 84 (149)
+-..=..+|+.+|...+.+. .+++....+.|++.|.++.++......
T Consensus 46 dD~~i~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~V~~~~~k~~A~ 95 (191)
T PRK11023 46 DDGTLELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQSPNAELSERAK 95 (191)
T ss_pred hhHHHHHHHHHHHhhCcccCcCceEEEEEECCEEEEEEEeCCHHHHHHHH
Confidence 45566788999998877764 578888999999999866554444333
No 68
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=22.58 E-value=2.9e+02 Score=19.61 Aligned_cols=48 Identities=15% Similarity=0.223 Sum_probs=32.4
Q ss_pred HHHHHHHhCCCCeeEEEEecCCCEEEEEecCCHHHHHHHHH-----hcCCceEE
Q 036289 44 LKVKNAVSSLSGVKSVEINRKQQKVSVTGYVEANKVLKKAK-----STGKRAEI 92 (149)
Q Consensus 44 ~kV~k~L~~~~GV~~v~vdl~~~~v~V~g~~~~~~I~~~I~-----~~G~~a~~ 92 (149)
..++..|.++ |-.+|+.-+.++-+..+...+.+++...|+ ..|+.+.+
T Consensus 22 aeLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~fG~~v~v 74 (137)
T PF08002_consen 22 AELREALEDL-GFTNVRTYIQSGNVVFESDRDPAELAAKIEKALEERFGFDVPV 74 (137)
T ss_dssp HHHHHHHHHC-T-EEEEEETTTTEEEEEESS-HHHHHHHHHHHHHHH-TT---E
T ss_pred HHHHHHHHHc-CCCCceEEEeeCCEEEecCCChHHHHHHHHHHHHHhcCCCeEE
Confidence 4566667666 899999999999999997777777766664 56887654
No 69
>PRK11023 outer membrane lipoprotein; Provisional
Probab=22.11 E-value=2.6e+02 Score=20.97 Aligned_cols=40 Identities=23% Similarity=0.304 Sum_probs=25.2
Q ss_pred HHHHHHHHHhCCCCeeE--EEEecCCCEEEEEecCCHHHHHH
Q 036289 42 CELKVKNAVSSLSGVKS--VEINRKQQKVSVTGYVEANKVLK 81 (149)
Q Consensus 42 C~~kV~k~L~~~~GV~~--v~vdl~~~~v~V~g~~~~~~I~~ 81 (149)
=..+|+.+|...+.+.. +++...++.|++.|.++.++...
T Consensus 128 It~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~~~ 169 (191)
T PRK11023 128 ITTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREAKA 169 (191)
T ss_pred HHHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHHHH
Confidence 56677777776666654 34445577777777766555433
No 70
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=21.79 E-value=1.3e+02 Score=18.74 Aligned_cols=11 Identities=18% Similarity=0.319 Sum_probs=8.3
Q ss_pred EcCcChhHHHH
Q 036289 35 VRMDCDGCELK 45 (149)
Q Consensus 35 Vgm~C~~C~~k 45 (149)
++..|+.|...
T Consensus 6 ~~~~C~~C~~~ 16 (76)
T PF13192_consen 6 FSPGCPYCPEL 16 (76)
T ss_dssp ECSSCTTHHHH
T ss_pred eCCCCCCcHHH
Confidence 47789999743
No 71
>PRK11670 antiporter inner membrane protein; Provisional
Probab=21.16 E-value=3.9e+02 Score=22.30 Aligned_cols=58 Identities=14% Similarity=0.215 Sum_probs=37.6
Q ss_pred HHHHHHHHhCCCCeeEEEEecCCC------------------EEEEE------ec-CCHHHHHHHHHhcCCceEEccCCC
Q 036289 43 ELKVKNAVSSLSGVKSVEINRKQQ------------------KVSVT------GY-VEANKVLKKAKSTGKRAEIWPYVP 97 (149)
Q Consensus 43 ~~kV~k~L~~~~GV~~v~vdl~~~------------------~v~V~------g~-~~~~~I~~~I~~~G~~a~~~~~~~ 97 (149)
...++.+|..++|+..+.+.+... .+.|. |+ ...--+...+.+.|+++-+....+
T Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avNLA~aLA~~G~rVlLID~D~ 146 (369)
T PRK11670 67 KEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVNLALALAAEGAKVGILDADI 146 (369)
T ss_pred HHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCC
Confidence 456888999999998877654331 12232 11 223445667788999999987766
Q ss_pred CCc
Q 036289 98 YNL 100 (149)
Q Consensus 98 ~~~ 100 (149)
+..
T Consensus 147 qgp 149 (369)
T PRK11670 147 YGP 149 (369)
T ss_pred CCC
Confidence 653
No 72
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=20.97 E-value=2e+02 Score=23.47 Aligned_cols=31 Identities=29% Similarity=0.413 Sum_probs=24.8
Q ss_pred EEEEEcCcChhHHHHHHHHHhCCCCeeEEEEe
Q 036289 31 VDLKVRMDCDGCELKVKNAVSSLSGVKSVEIN 62 (149)
Q Consensus 31 v~l~Vgm~C~~C~~kV~k~L~~~~GV~~v~vd 62 (149)
+.+..+.+ +.|...+++.+.+.+||.++++-
T Consensus 63 vyL~~~~~-~~~~~~v~~~i~~~~gV~~v~~~ 93 (297)
T COG2177 63 VYLQIDAD-QDDAALVREKIEGIPGVKSVRFI 93 (297)
T ss_pred EEEecCCC-hHHHHHHHHHHhcCCCcceEEEe
Confidence 34444555 89999999999999999988774
Done!