Query 032167
Match_columns 146
No_of_seqs 191 out of 1632
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 10:29:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032167.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032167hhsearch_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 99.4 1.1E-12 2.4E-17 79.6 8.8 58 27-84 1-62 (62)
2 KOG1603 Copper chaperone [Inor 99.3 1.8E-11 3.8E-16 77.0 9.0 67 23-89 4-71 (73)
3 COG2608 CopZ Copper chaperone 99.3 3.3E-11 7.1E-16 75.4 9.1 66 23-88 1-70 (71)
4 KOG4656 Copper chaperone for s 99.3 6.2E-12 1.4E-16 92.2 6.2 94 23-116 6-100 (247)
5 PLN02957 copper, zinc superoxi 98.5 1.9E-06 4.1E-11 65.7 10.6 72 23-94 5-76 (238)
6 PRK10671 copA copper exporting 98.2 4.7E-06 1E-10 73.6 8.3 64 24-89 3-67 (834)
7 COG2217 ZntA Cation transport 98.0 2.4E-05 5.1E-10 68.0 8.0 63 24-87 2-69 (713)
8 TIGR00003 copper ion binding p 97.8 0.00046 9.9E-09 39.4 8.7 61 24-84 2-66 (68)
9 KOG0207 Cation transport ATPas 97.6 0.00041 8.8E-09 61.1 8.5 69 24-92 146-218 (951)
10 PRK10671 copA copper exporting 97.1 0.0025 5.4E-08 56.6 8.1 64 25-88 100-164 (834)
11 KOG0207 Cation transport ATPas 97.0 0.0021 4.6E-08 56.8 6.5 62 31-92 2-65 (951)
12 PRK11033 zntA zinc/cadmium/mer 96.7 0.011 2.3E-07 52.0 8.5 66 23-88 52-119 (741)
13 TIGR02052 MerP mercuric transp 94.0 0.82 1.8E-05 28.0 9.6 63 25-87 24-90 (92)
14 COG1888 Uncharacterized protei 92.3 1.6 3.5E-05 28.3 7.4 66 23-88 5-79 (97)
15 PF02680 DUF211: Uncharacteriz 88.7 1.6 3.4E-05 28.6 5.0 64 23-87 4-76 (95)
16 PF01206 TusA: Sulfurtransfera 87.1 4.3 9.4E-05 24.4 6.2 54 27-89 2-58 (70)
17 PRK13748 putative mercuric red 85.8 7.6 0.00016 32.9 9.1 64 27-90 3-69 (561)
18 PRK11198 LysM domain/BON super 85.7 3.7 7.9E-05 28.9 6.0 69 1-81 1-72 (147)
19 cd00371 HMA Heavy-metal-associ 78.8 6.4 0.00014 19.5 7.3 38 29-66 3-41 (63)
20 PRK11152 ilvM acetolactate syn 77.3 11 0.00024 23.6 5.3 53 2-56 15-75 (76)
21 PRK11018 hypothetical protein; 74.8 18 0.00038 22.5 6.3 56 25-89 8-66 (78)
22 cd03421 SirA_like_N SirA_like_ 71.4 19 0.00041 21.4 5.7 52 28-89 2-56 (67)
23 PF01883 DUF59: Domain of unkn 70.5 10 0.00022 22.9 4.0 33 24-56 34-72 (72)
24 PRK14054 methionine sulfoxide 68.9 28 0.0006 25.3 6.5 45 35-79 10-76 (172)
25 cd03420 SirA_RHOD_Pry_redox Si 62.2 32 0.00069 20.6 5.8 53 28-89 2-57 (69)
26 PRK10553 assembly protein for 60.4 43 0.00092 21.5 6.0 45 35-79 16-61 (87)
27 PF14437 MafB19-deam: MafB19-l 58.3 34 0.00073 24.3 5.1 41 23-64 99-141 (146)
28 PRK00058 methionine sulfoxide 52.4 71 0.0015 24.1 6.3 52 23-79 45-118 (213)
29 cd00291 SirA_YedF_YeeD SirA, Y 52.1 47 0.001 19.4 6.0 53 28-89 2-57 (69)
30 PRK13014 methionine sulfoxide 51.6 54 0.0012 24.2 5.5 35 22-61 7-41 (186)
31 cd03422 YedF YedF is a bacteri 51.0 53 0.0011 19.7 5.8 53 28-89 2-57 (69)
32 cd04888 ACT_PheB-BS C-terminal 49.4 54 0.0012 19.3 5.8 34 23-56 40-74 (76)
33 PRK05528 methionine sulfoxide 48.5 25 0.00054 25.1 3.2 45 35-79 8-69 (156)
34 PF13732 DUF4162: Domain of un 48.4 61 0.0013 19.7 5.5 44 45-89 26-70 (84)
35 cd03423 SirA SirA (also known 46.7 62 0.0013 19.3 6.2 53 28-89 2-57 (69)
36 KOG3411 40S ribosomal protein 46.0 20 0.00042 25.0 2.2 44 35-81 97-141 (143)
37 PF13291 ACT_4: ACT domain; PD 44.8 69 0.0015 19.3 4.5 35 21-55 45-79 (80)
38 PF03927 NapD: NapD protein; 42.4 84 0.0018 19.6 6.5 44 37-81 16-60 (79)
39 PF08712 Nfu_N: Scaffold prote 42.4 74 0.0016 20.2 4.4 41 39-81 37-79 (87)
40 TIGR03406 FeS_long_SufT probab 39.9 47 0.001 24.2 3.6 22 39-60 134-155 (174)
41 PRK00299 sulfur transfer prote 39.9 92 0.002 19.3 7.0 56 25-89 9-67 (81)
42 PRK13562 acetolactate synthase 39.5 1E+02 0.0022 19.7 6.0 58 2-59 14-80 (84)
43 PF04972 BON: BON domain; Int 38.5 35 0.00075 19.7 2.3 30 40-70 3-35 (64)
44 PF09580 Spore_YhcN_YlaJ: Spor 37.9 1.4E+02 0.0031 21.0 6.0 32 35-66 74-105 (177)
45 PF01625 PMSR: Peptide methion 36.2 76 0.0016 22.6 4.1 27 35-61 7-33 (155)
46 TIGR03527 selenium_YedF seleni 32.6 2E+02 0.0044 21.1 6.4 50 31-89 5-56 (194)
47 TIGR02945 SUF_assoc FeS assemb 32.4 66 0.0014 20.5 3.1 36 24-59 39-78 (99)
48 PRK08178 acetolactate synthase 31.6 1.5E+02 0.0033 19.4 5.5 54 1-56 19-80 (96)
49 COG0425 SirA Predicted redox p 31.3 1.3E+02 0.0029 18.6 6.7 50 25-83 5-57 (78)
50 PRK04435 hypothetical protein; 30.5 1.9E+02 0.0041 20.1 5.6 33 24-56 110-143 (147)
51 PRK05550 bifunctional methioni 29.9 2.2E+02 0.0048 22.5 6.1 27 35-61 134-160 (283)
52 PF08256 Antimicrobial20: Aure 27.0 28 0.0006 14.3 0.4 8 2-9 1-8 (13)
53 PRK09577 multidrug efflux prot 26.2 2.2E+02 0.0048 26.5 6.3 45 38-82 158-210 (1032)
54 COG0225 MsrA Peptide methionin 25.5 1.2E+02 0.0025 22.2 3.6 35 22-61 5-39 (174)
55 PRK11023 outer membrane lipopr 25.2 2.3E+02 0.005 20.6 5.2 47 33-79 46-95 (191)
56 PRK10555 aminoglycoside/multid 24.9 2.2E+02 0.0048 26.5 6.1 43 38-80 159-209 (1037)
57 TIGR00401 msrA methionine-S-su 24.0 74 0.0016 22.5 2.3 27 35-61 7-33 (149)
58 PF04805 Pox_E10: E10-like pro 23.8 66 0.0014 19.7 1.7 21 31-51 15-35 (70)
59 PRK07334 threonine dehydratase 23.5 4.1E+02 0.0089 21.7 8.0 63 26-88 327-402 (403)
60 cd06167 LabA_like LabA_like pr 23.3 1.5E+02 0.0032 20.1 3.7 29 63-91 104-132 (149)
61 COG2092 EFB1 Translation elong 23.3 1.6E+02 0.0035 19.0 3.6 34 24-57 49-83 (88)
62 PF02672 CP12: CP12 domain; I 22.9 21 0.00045 22.1 -0.6 14 132-145 53-68 (71)
63 cd04902 ACT_3PGDH-xct C-termin 21.8 1.7E+02 0.0038 16.7 4.7 31 22-56 39-70 (73)
64 TIGR00489 aEF-1_beta translati 21.1 2.1E+02 0.0045 18.4 3.8 22 36-57 62-83 (88)
65 PRK15127 multidrug efflux syst 20.6 3.1E+02 0.0067 25.7 6.1 43 39-81 160-210 (1049)
66 PF13192 Thioredoxin_3: Thiore 20.1 1.5E+02 0.0032 17.8 2.9 11 30-40 6-16 (76)
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=99.45 E-value=1.1e-12 Score=79.62 Aligned_cols=58 Identities=34% Similarity=0.625 Sum_probs=54.2
Q ss_pred EEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee---CCHHHHHHHHHhcCCc
Q 032167 27 EIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH---VDPNKVLKKVRSTGKR 84 (146)
Q Consensus 27 ~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~---~~~~~i~~~l~~~G~~ 84 (146)
+|+| +|+|++|.++|+++|.+++||.++.+|+.+++++|.++ +++++|.++|+++||+
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 5889 99999999999999999999999999999999999976 4669999999999984
No 2
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.33 E-value=1.8e-11 Score=76.99 Aligned_cols=67 Identities=49% Similarity=0.941 Sum_probs=61.6
Q ss_pred ceEEEEEEcCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEeeCCHHHHHHHHHhcC-CceEEec
Q 032167 23 WQTVEIKVKMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGHVDPNKVLKKVRSTG-KRAEFWP 89 (146)
Q Consensus 23 ~~~~~l~V~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~l~~~G-~~a~~~~ 89 (146)
.++.++++.|+|++|..+|++.|..++||.++.+|...++++|.|.+++..|++.|++.+ .++.+|.
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 466788889999999999999999999999999999999999999999999999999988 6666664
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.30 E-value=3.3e-11 Score=75.39 Aligned_cols=66 Identities=27% Similarity=0.490 Sum_probs=58.4
Q ss_pred ceEEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEE--e-eCCHHHHHHHHHhcCCceEEe
Q 032167 23 WQTVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVT--G-HVDPNKVLKKVRSTGKRAEFW 88 (146)
Q Consensus 23 ~~~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~--g-~~~~~~i~~~l~~~G~~a~~~ 88 (146)
+.+.+|++ +|+|.+|+..|+++|.+++||.++.+++..+.+.|. + .++.++|.+++..+||.+..+
T Consensus 1 ~~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~~ 70 (71)
T COG2608 1 MMKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEEI 70 (71)
T ss_pred CceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeeec
Confidence 35678999 999999999999999999999999999999776665 4 379999999999999987654
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.29 E-value=6.2e-12 Score=92.17 Aligned_cols=94 Identities=28% Similarity=0.388 Sum_probs=76.8
Q ss_pred ceEEEEEEcCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEeeCCHHHHHHHHHhcCCceEEeccCCCCccCCCccc
Q 032167 23 WQTVEIKVKMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGHVDPNKVLKKVRSTGKRAEFWPYVPYNLVAYPYVA 102 (146)
Q Consensus 23 ~~~~~l~V~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~l~~~G~~a~~~~~~~~~~~~~~~~~ 102 (146)
.-+.+|.|.|+|++|+..|++.|..++||.++++|++.+.+.|.+...+.+|..+|+.+|++|.+.+.+..++..-...-
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 45678999999999999999999999999999999999999999999999999999999999999988766544322222
Q ss_pred ccc-cCCCCCCcccC
Q 032167 103 QAY-DKKAPSGYVRN 116 (146)
Q Consensus 103 ~~~-~~~~~~g~~~~ 116 (146)
+.| .+..++|++|+
T Consensus 86 a~~~~~~~v~GvvRf 100 (247)
T KOG4656|consen 86 AKYTGPQAVQGVVRF 100 (247)
T ss_pred HHhcCCccceeEEEE
Confidence 222 22255666665
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.49 E-value=1.9e-06 Score=65.66 Aligned_cols=72 Identities=25% Similarity=0.405 Sum_probs=64.4
Q ss_pred ceEEEEEEcCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEeeCCHHHHHHHHHhcCCceEEeccCCCC
Q 032167 23 WQTVEIKVKMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGHVDPNKVLKKVRSTGKRAEFWPYVPYN 94 (146)
Q Consensus 23 ~~~~~l~V~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~l~~~G~~a~~~~~~~~~ 94 (146)
.+++++.++|.|+.|..++++.|.+++||..+.+++..++++|........+.+.+++.|+.+++++....+
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 456778889999999999999999999999999999999999987778899999999999999988765544
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.23 E-value=4.7e-06 Score=73.63 Aligned_cols=64 Identities=19% Similarity=0.458 Sum_probs=57.3
Q ss_pred eEEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEeeCCHHHHHHHHHhcCCceEEec
Q 032167 24 QTVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGHVDPNKVLKKVRSTGKRAEFWP 89 (146)
Q Consensus 24 ~~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~l~~~G~~a~~~~ 89 (146)
++++++| +|+|.+|..+|+++|.+++||.++.+++. +.++.+..+.+.+.+.+++.||.++...
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 5789999 99999999999999999999999999994 5566666789999999999999998754
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.01 E-value=2.4e-05 Score=67.96 Aligned_cols=63 Identities=29% Similarity=0.550 Sum_probs=56.6
Q ss_pred eEEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee---CC-HHHHHHHHHhcCCceEE
Q 032167 24 QTVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH---VD-PNKVLKKVRSTGKRAEF 87 (146)
Q Consensus 24 ~~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~---~~-~~~i~~~l~~~G~~a~~ 87 (146)
.+.+|.+ ||+|..|.++|+ +|.+++||....+|+.++++.|..+ .+ .+++...+++.||.+..
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 4568999 999999999999 9999999999999999999998854 45 78999999999998876
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=97.79 E-value=0.00046 Score=39.36 Aligned_cols=61 Identities=20% Similarity=0.390 Sum_probs=50.0
Q ss_pred eEEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee---CCHHHHHHHHHhcCCc
Q 032167 24 QTVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH---VDPNKVLKKVRSTGKR 84 (146)
Q Consensus 24 ~~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~---~~~~~i~~~l~~~G~~ 84 (146)
.+..+.+ ++.|..|...+++.+....++....+++....+.+... .+...+...+...|+.
T Consensus 2 ~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 66 (68)
T TIGR00003 2 QKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYE 66 (68)
T ss_pred cEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCC
Confidence 3457899 99999999999999999999999999999998887642 4666776667776764
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.57 E-value=0.00041 Score=61.09 Aligned_cols=69 Identities=25% Similarity=0.484 Sum_probs=63.1
Q ss_pred eEEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee---CCHHHHHHHHHhcCCceEEeccCC
Q 032167 24 QTVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH---VDPNKVLKKVRSTGKRAEFWPYVP 92 (146)
Q Consensus 24 ~~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~---~~~~~i~~~l~~~G~~a~~~~~~~ 92 (146)
.++.|.| ||.|.+|+.++++.+.+++||.+.+++...+++.|..+ ..+.++.+.|..+|+.+.......
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~~~~ 218 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRPYGD 218 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeeeccc
Confidence 6889999 99999999999999999999999999999999998754 789999999999999988877533
No 10
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.08 E-value=0.0025 Score=56.59 Aligned_cols=64 Identities=27% Similarity=0.484 Sum_probs=56.4
Q ss_pred EEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEeeCCHHHHHHHHHhcCCceEEe
Q 032167 25 TVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGHVDPNKVLKKVRSTGKRAEFW 88 (146)
Q Consensus 25 ~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~l~~~G~~a~~~ 88 (146)
++.+.+ +|+|..|...+++.+..++||.++.+++..++..+.+..++.++.+.+++.|+.+.+.
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~~ 164 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEAI 164 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCcccc
Confidence 567889 9999999999999999999999999999999888875567888888899999987644
No 11
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.99 E-value=0.0021 Score=56.77 Aligned_cols=62 Identities=24% Similarity=0.459 Sum_probs=56.9
Q ss_pred cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHhcCCceEEeccCC
Q 032167 31 KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH--VDPNKVLKKVRSTGKRAEFWPYVP 92 (146)
Q Consensus 31 ~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~l~~~G~~a~~~~~~~ 92 (146)
||+|..|.+.+++++...+|+.+..+++..+...|..+ .+++.+.+.++..|+.+++.....
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ied~gf~~~~~~~~~ 65 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIEDMGFEASLLSDSE 65 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhhcccceeeecccCc
Confidence 79999999999999999999999999999999888755 899999999999999999987543
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.66 E-value=0.011 Score=52.05 Aligned_cols=66 Identities=26% Similarity=0.317 Sum_probs=53.5
Q ss_pred ceEEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee-CCHHHHHHHHHhcCCceEEe
Q 032167 23 WQTVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH-VDPNKVLKKVRSTGKRAEFW 88 (146)
Q Consensus 23 ~~~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~-~~~~~i~~~l~~~G~~a~~~ 88 (146)
..+..+.+ +|+|..|.+++++.+..++||..+.+++..+++.+..+ ....++.+.+++.|+.+...
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 45677889 99999999999999999999999999999988777633 12266677788888876543
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=94.01 E-value=0.82 Score=27.99 Aligned_cols=63 Identities=24% Similarity=0.360 Sum_probs=45.6
Q ss_pred EEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEe---eCCHHHHHHHHHhcCCceEE
Q 032167 25 TVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTG---HVDPNKVLKKVRSTGKRAEF 87 (146)
Q Consensus 25 ~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g---~~~~~~i~~~l~~~G~~a~~ 87 (146)
++.+.+ ++.|..|...++..+....++.....+.......+.. ..+...+...+.+.|+.+++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 456778 9999999999999999999988888877777655442 13555555555666766543
No 14
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=92.32 E-value=1.6 Score=28.31 Aligned_cols=66 Identities=14% Similarity=0.238 Sum_probs=43.6
Q ss_pred ceEEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEec-------cCCEEEEEee-CCHHHHHHHHHhcCCceEEe
Q 032167 23 WQTVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNR-------KQSRVTVTGH-VDPNKVLKKVRSTGKRAEFW 88 (146)
Q Consensus 23 ~~~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~-------~~~~v~V~g~-~~~~~i~~~l~~~G~~a~~~ 88 (146)
..++.|.+ --+-.--.-.+.+.|++++||+.|++.. .+-+++|.|. ++-++|.+.|++.|......
T Consensus 5 iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHSi 79 (97)
T COG1888 5 IRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHSI 79 (97)
T ss_pred ceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeeeh
Confidence 34556666 3332222334556688999988887753 2344567776 99999999999999765443
No 15
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=88.65 E-value=1.6 Score=28.62 Aligned_cols=64 Identities=16% Similarity=0.308 Sum_probs=42.7
Q ss_pred ceEEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEec-----cCC--EEEEEee-CCHHHHHHHHHhcCCceEE
Q 032167 23 WQTVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNR-----KQS--RVTVTGH-VDPNKVLKKVRSTGKRAEF 87 (146)
Q Consensus 23 ~~~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~-----~~~--~v~V~g~-~~~~~i~~~l~~~G~~a~~ 87 (146)
.+++.|.| --+-+.- -.+.+.|+.++||..+++.. ... +++|.|. ++.++|.+.|++.|.....
T Consensus 4 irRlVLDVlKP~~p~i-~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHS 76 (95)
T PF02680_consen 4 IRRLVLDVLKPHEPSI-VELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHS 76 (95)
T ss_dssp EEEEEEEEEEESSS-H-HHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEE
T ss_pred eeEEEEEeecCCCCCH-HHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEe
Confidence 45667777 3343433 45667799999999888753 223 3456687 9999999999999976543
No 16
>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=87.07 E-value=4.3 Score=24.37 Aligned_cols=54 Identities=7% Similarity=0.078 Sum_probs=39.1
Q ss_pred EEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHhcCCceEEec
Q 032167 27 EIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH--VDPNKVLKKVRSTGKRAEFWP 89 (146)
Q Consensus 27 ~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~l~~~G~~a~~~~ 89 (146)
++.+ |+.|+...-++.++|..++. .+.+.|..+ ....+|...++..|+....+.
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 99999999999999998732 234555544 455778888999999755553
No 17
>PRK13748 putative mercuric reductase; Provisional
Probab=85.84 E-value=7.6 Score=32.86 Aligned_cols=64 Identities=23% Similarity=0.440 Sum_probs=49.1
Q ss_pred EEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEe--eCCHHHHHHHHHhcCCceEEecc
Q 032167 27 EIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTG--HVDPNKVLKKVRSTGKRAEFWPY 90 (146)
Q Consensus 27 ~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g--~~~~~~i~~~l~~~G~~a~~~~~ 90 (146)
.+.+ ++.|..|..+++..+...+++....++.......+.. ..+...+...+...++..+....
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 4667 9999999999999999999998888888888766653 24556666667777877665554
No 18
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=85.73 E-value=3.7 Score=28.91 Aligned_cols=69 Identities=17% Similarity=0.283 Sum_probs=41.5
Q ss_pred Cchhhhhhhcccc--CccccCCCCceEEEEEEcCcChhhHHHHHHHHhCC-CCceEEEEeccCCEEEEEeeCCHHHHHHH
Q 032167 1 MGVLDHLFDLFEI--TPRRKRRKPWQTVEIKVKMDCDGCERRVRHAVSSM-KGAKSVEVNRKQSRVTVTGHVDPNKVLKK 77 (146)
Q Consensus 1 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~l~V~m~C~~C~~kv~k~l~~~-~GV~~v~vd~~~~~v~V~g~~~~~~i~~~ 77 (146)
||+|+|+..-=.+ +.... +. .-..-..+|.++|.+. -+...+++...++.|++.|.+......++
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~-~~-----------~~~~~~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~~~ 68 (147)
T PRK11198 1 MGLFSFVKEAGEKLFDAVTA-QA-----------DNEDAADALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAKEK 68 (147)
T ss_pred CcHHHHHHHHHHHhcCCCCc-cc-----------chHHHHHHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHHHH
Confidence 9999999874321 21111 10 1144556777777642 23445666677999999998666665665
Q ss_pred HHhc
Q 032167 78 VRST 81 (146)
Q Consensus 78 l~~~ 81 (146)
+...
T Consensus 69 ~~~a 72 (147)
T PRK11198 69 ILLA 72 (147)
T ss_pred HHHH
Confidence 5533
No 19
>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=78.79 E-value=6.4 Score=19.49 Aligned_cols=38 Identities=34% Similarity=0.685 Sum_probs=28.9
Q ss_pred EE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEE
Q 032167 29 KV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVT 66 (146)
Q Consensus 29 ~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~ 66 (146)
.+ ++.|..|...++..+....++.....+.......+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVE 41 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEE
Confidence 35 788999999999888888887776666666655444
No 20
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=77.31 E-value=11 Score=23.59 Aligned_cols=53 Identities=11% Similarity=0.143 Sum_probs=38.9
Q ss_pred chhhhhhhccccCcc------c--cCCCCceEEEEEEcCcChhhHHHHHHHHhCCCCceEEEE
Q 032167 2 GVLDHLFDLFEITPR------R--KRRKPWQTVEIKVKMDCDGCERRVRHAVSSMKGAKSVEV 56 (146)
Q Consensus 2 ~~~~~~~~~~~~~~~------~--~~~~~~~~~~l~V~m~C~~C~~kv~k~l~~~~GV~~v~v 56 (146)
|+++-+++|+..-.. . ..+....++++.++ .+.....+.+.|.++.+|..+++
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 788888888844221 1 12445677777774 58889999999999999988875
No 21
>PRK11018 hypothetical protein; Provisional
Probab=74.75 E-value=18 Score=22.51 Aligned_cols=56 Identities=13% Similarity=0.078 Sum_probs=40.8
Q ss_pred EEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHhcCCceEEec
Q 032167 25 TVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH--VDPNKVLKKVRSTGKRAEFWP 89 (146)
Q Consensus 25 ~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~l~~~G~~a~~~~ 89 (146)
..++.+ |..|+.-.-+.+++|.+++. .+.+.|..+ .....|..-+++.|+.+....
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~~---------G~~L~V~~d~~~a~~di~~~~~~~G~~v~~~~ 66 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLKK---------GEILEVVSDCPQSINNIPLDARNHGYTVLDIQ 66 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCCC---------CCEEEEEeCCccHHHHHHHHHHHcCCEEEEEE
Confidence 357888 99999999999999998742 223444433 456678888889999876443
No 22
>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=71.40 E-value=19 Score=21.36 Aligned_cols=52 Identities=15% Similarity=0.215 Sum_probs=36.4
Q ss_pred EEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHhcCCceEEec
Q 032167 28 IKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH--VDPNKVLKKVRSTGKRAEFWP 89 (146)
Q Consensus 28 l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~l~~~G~~a~~~~ 89 (146)
+.+ |+.|+.-.-+++++| .+.. .+.+.|..+ .....|..-+++.|+......
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 5522 223444433 445678888899999885544
No 23
>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=70.52 E-value=10 Score=22.85 Aligned_cols=33 Identities=27% Similarity=0.595 Sum_probs=20.3
Q ss_pred eEEEEEEcCcChhh------HHHHHHHHhCCCCceEEEE
Q 032167 24 QTVEIKVKMDCDGC------ERRVRHAVSSMKGAKSVEV 56 (146)
Q Consensus 24 ~~~~l~V~m~C~~C------~~kv~k~l~~~~GV~~v~v 56 (146)
.++.+.+.+..++| ...++++|..++||.++++
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 34455554444444 4677889999999998875
No 24
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=68.95 E-value=28 Score=25.32 Aligned_cols=45 Identities=20% Similarity=0.274 Sum_probs=33.7
Q ss_pred hhhHHHHHHHHhCCCCceEEEEeccCCE-------------------EEEEee---CCHHHHHHHHH
Q 032167 35 DGCERRVRHAVSSMKGAKSVEVNRKQSR-------------------VTVTGH---VDPNKVLKKVR 79 (146)
Q Consensus 35 ~~C~~kv~k~l~~~~GV~~v~vd~~~~~-------------------v~V~g~---~~~~~i~~~l~ 79 (146)
.+|-|-++..+.+++||.++.+-...+. |.|..+ ++.++|++..-
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~ 76 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFF 76 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHH
Confidence 7899999999999999999998765543 445433 67777776553
No 25
>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=62.20 E-value=32 Score=20.65 Aligned_cols=53 Identities=11% Similarity=0.206 Sum_probs=38.5
Q ss_pred EEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHhcCCceEEec
Q 032167 28 IKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH--VDPNKVLKKVRSTGKRAEFWP 89 (146)
Q Consensus 28 l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~l~~~G~~a~~~~ 89 (146)
+.+ |+.|+.=.-+++++|.+++. .+.+.|..+ .....|..-.+..|+......
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 89999999999999988742 223444433 556778888889999877544
No 26
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=60.38 E-value=43 Score=21.50 Aligned_cols=45 Identities=9% Similarity=0.194 Sum_probs=31.8
Q ss_pred hhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee-CCHHHHHHHHH
Q 032167 35 DGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH-VDPNKVLKKVR 79 (146)
Q Consensus 35 ~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~-~~~~~i~~~l~ 79 (146)
+.-...+.++|..++|++-...|...+|+.|+-. .+...+.+.+.
T Consensus 16 Pe~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 16 SERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred hHHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 3446788999999999987777777888766532 45555555554
No 27
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=58.28 E-value=34 Score=24.27 Aligned_cols=41 Identities=17% Similarity=0.359 Sum_probs=31.5
Q ss_pred ceEEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEecc-CCEEE
Q 032167 23 WQTVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRK-QSRVT 64 (146)
Q Consensus 23 ~~~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~-~~~v~ 64 (146)
-..+++.| .--|..|..-|.....++ |+.++.|... ++++.
T Consensus 99 g~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~ 141 (146)
T PF14437_consen 99 GRSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVY 141 (146)
T ss_pred CCeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEE
Confidence 35678888 888999998888877765 8988888766 55443
No 28
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=52.35 E-value=71 Score=24.10 Aligned_cols=52 Identities=15% Similarity=0.140 Sum_probs=37.3
Q ss_pred ceEEEEEEcCcChhhHHHHHHHHhCCCCceEEEEeccCC-------------------EEEEEee---CCHHHHHHHHH
Q 032167 23 WQTVEIKVKMDCDGCERRVRHAVSSMKGAKSVEVNRKQS-------------------RVTVTGH---VDPNKVLKKVR 79 (146)
Q Consensus 23 ~~~~~l~V~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~-------------------~v~V~g~---~~~~~i~~~l~ 79 (146)
+.++.|. .+|-|-++..+.+++||.++.+-...+ .|.|..+ ++.++|++..-
T Consensus 45 ~~~a~fa-----gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff 118 (213)
T PRK00058 45 MEQAIFG-----MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFW 118 (213)
T ss_pred ccEEEEE-----ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHH
Confidence 4555555 789999999999999999999976633 1444433 67777777654
No 29
>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=52.09 E-value=47 Score=19.44 Aligned_cols=53 Identities=11% Similarity=0.100 Sum_probs=37.9
Q ss_pred EEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHhcCCceEEec
Q 032167 28 IKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH--VDPNKVLKKVRSTGKRAEFWP 89 (146)
Q Consensus 28 l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~l~~~G~~a~~~~ 89 (146)
+.+ |+.|+.=..++.++|.+++. .+.+.|..+ .....|..-++..|+......
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 445 88999999999999987632 334444443 457788888999999866544
No 30
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=51.62 E-value=54 Score=24.16 Aligned_cols=35 Identities=20% Similarity=0.224 Sum_probs=27.5
Q ss_pred CceEEEEEEcCcChhhHHHHHHHHhCCCCceEEEEeccCC
Q 032167 22 PWQTVEIKVKMDCDGCERRVRHAVSSMKGAKSVEVNRKQS 61 (146)
Q Consensus 22 ~~~~~~l~V~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~ 61 (146)
.+.++.|. .+|-|-++..+.+++||.++.+-...+
T Consensus 7 ~~~~a~~a-----gGCFWg~E~~f~~l~GV~~t~vGYagG 41 (186)
T PRK13014 7 GMETATFA-----GGCFWGVEGVFQHVPGVVSVVSGYSGG 41 (186)
T ss_pred CccEEEEe-----cCCceeeHHHHccCCCEEEEEeeecCC
Confidence 35555655 788899999999999999999876544
No 31
>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=50.99 E-value=53 Score=19.69 Aligned_cols=53 Identities=15% Similarity=0.122 Sum_probs=37.7
Q ss_pred EEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHhcCCceEEec
Q 032167 28 IKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH--VDPNKVLKKVRSTGKRAEFWP 89 (146)
Q Consensus 28 l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~l~~~G~~a~~~~ 89 (146)
+.+ |..|+.=.-+.+++|.+++- .+.+.|..+ .....|..-++..|+......
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~~---------G~~l~V~~d~~~s~~ni~~~~~~~g~~v~~~~ 57 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLKP---------GEILEVISDCPQSINNIPIDARNHGYKVLAIE 57 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCC---------CCEEEEEecCchHHHHHHHHHHHcCCEEEEEE
Confidence 345 88999999999999998742 223344332 566778888889999886543
No 32
>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=49.36 E-value=54 Score=19.32 Aligned_cols=34 Identities=15% Similarity=0.221 Sum_probs=24.3
Q ss_pred ceEEEEEEcCcChh-hHHHHHHHHhCCCCceEEEE
Q 032167 23 WQTVEIKVKMDCDG-CERRVRHAVSSMKGAKSVEV 56 (146)
Q Consensus 23 ~~~~~l~V~m~C~~-C~~kv~k~l~~~~GV~~v~v 56 (146)
...+.|.+...-.. --..+.+.|.+++||.++.+
T Consensus 40 ~~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 40 RANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred eEEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 44555666444444 77888999999999998765
No 33
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=48.46 E-value=25 Score=25.13 Aligned_cols=45 Identities=20% Similarity=0.282 Sum_probs=32.5
Q ss_pred hhhHHHHHHHHhCCCCceEEEEeccCCE--------------EEEEee---CCHHHHHHHHH
Q 032167 35 DGCERRVRHAVSSMKGAKSVEVNRKQSR--------------VTVTGH---VDPNKVLKKVR 79 (146)
Q Consensus 35 ~~C~~kv~k~l~~~~GV~~v~vd~~~~~--------------v~V~g~---~~~~~i~~~l~ 79 (146)
.+|-|-++..+.+++||.++.+-...+. |.|..+ ++.++|++..-
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~ 69 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLF 69 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHH
Confidence 6899999999999999999998754422 334433 66677776553
No 34
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=48.40 E-value=61 Score=19.73 Aligned_cols=44 Identities=18% Similarity=0.340 Sum_probs=30.8
Q ss_pred HhCCCCceEEEEeccC-CEEEEEeeCCHHHHHHHHHhcCCceEEec
Q 032167 45 VSSMKGAKSVEVNRKQ-SRVTVTGHVDPNKVLKKVRSTGKRAEFWP 89 (146)
Q Consensus 45 l~~~~GV~~v~vd~~~-~~v~V~g~~~~~~i~~~l~~~G~~a~~~~ 89 (146)
|..++||..+...... -.+.+.......+|++.|...|. ..-..
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~f~ 70 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDEETANELLQELIEKGI-IRSFE 70 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHHhCCC-eeEEE
Confidence 7778999998865322 23444455678899999998887 55444
No 35
>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=46.74 E-value=62 Score=19.31 Aligned_cols=53 Identities=13% Similarity=0.094 Sum_probs=38.0
Q ss_pred EEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHhcCCceEEec
Q 032167 28 IKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH--VDPNKVLKKVRSTGKRAEFWP 89 (146)
Q Consensus 28 l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~l~~~G~~a~~~~ 89 (146)
+.. |..|+.=.-+++++|.+++- .+.+.|..+ .....|..-+++.|+......
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 88999999999999988732 223444332 566788888999999876544
No 36
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=45.98 E-value=20 Score=25.03 Aligned_cols=44 Identities=27% Similarity=0.416 Sum_probs=28.6
Q ss_pred hhhHHHHHHHHhCCCCceEEEEeccCCE-EEEEeeCCHHHHHHHHHhc
Q 032167 35 DGCERRVRHAVSSMKGAKSVEVNRKQSR-VTVTGHVDPNKVLKKVRST 81 (146)
Q Consensus 35 ~~C~~kv~k~l~~~~GV~~v~vd~~~~~-v~V~g~~~~~~i~~~l~~~ 81 (146)
.+|.+++.++| +.+.-|+.+...++ ++-.|.-+.+.|+..|+..
T Consensus 97 ~~i~rkvlQ~L---e~~~~ve~hp~gGR~lt~~GqrdldrIa~~i~~~ 141 (143)
T KOG3411|consen 97 GGIARKVLQAL---EKMGIVEKHPKGGRRLTEQGQRDLDRIAGQIREE 141 (143)
T ss_pred cHHHHHHHHHH---HhCCceeeCCCCcceeCcccchhHHHHHHHHHhc
Confidence 44555555555 55566677766554 5556878889998887643
No 37
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=44.77 E-value=69 Score=19.33 Aligned_cols=35 Identities=14% Similarity=0.152 Sum_probs=26.3
Q ss_pred CCceEEEEEEcCcChhhHHHHHHHHhCCCCceEEE
Q 032167 21 KPWQTVEIKVKMDCDGCERRVRHAVSSMKGAKSVE 55 (146)
Q Consensus 21 ~~~~~~~l~V~m~C~~C~~kv~k~l~~~~GV~~v~ 55 (146)
.....+.|.+...-..--..+.+.|.+++||.+|.
T Consensus 45 ~~~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 45 DGTARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp TTEEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred CCEEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 44566666666666677788888899999998764
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=42.41 E-value=84 Score=19.56 Aligned_cols=44 Identities=14% Similarity=0.215 Sum_probs=30.6
Q ss_pred hHHHHHHHHhCCCCceEEEEeccCCEEEEEe-eCCHHHHHHHHHhc
Q 032167 37 CERRVRHAVSSMKGAKSVEVNRKQSRVTVTG-HVDPNKVLKKVRST 81 (146)
Q Consensus 37 C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g-~~~~~~i~~~l~~~ 81 (146)
=...+.++|.+++|++-...+.. +++.|+- ..+...+.+.+...
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 45788899999999976666655 7766653 25666666666543
No 39
>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=42.36 E-value=74 Score=20.21 Aligned_cols=41 Identities=24% Similarity=0.317 Sum_probs=28.0
Q ss_pred HHHHHHHhCCCCceEEEEeccCCEEEEE--eeCCHHHHHHHHHhc
Q 032167 39 RRVRHAVSSMKGAKSVEVNRKQSRVTVT--GHVDPNKVLKKVRST 81 (146)
Q Consensus 39 ~kv~k~l~~~~GV~~v~vd~~~~~v~V~--g~~~~~~i~~~l~~~ 81 (146)
.-+-+.|-.++||.+|-+. .+=++|+ ..++++.|...|...
T Consensus 37 spLA~~Lf~i~gV~~Vf~~--~dfItVtK~~~~~W~~l~~~I~~~ 79 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFIG--DDFITVTKNPDADWEDLKPEIREV 79 (87)
T ss_dssp -HHHHHHHTSTTEEEEEEE--TTEEEEEE-TTS-HHHHHHHHHHH
T ss_pred CHHHHHhcCCCCEeEEEEE--CCEEEEeeCCCCCHHHHHHHHHHH
Confidence 3444556699999988775 5566666 458999998888643
No 40
>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=39.94 E-value=47 Score=24.17 Aligned_cols=22 Identities=23% Similarity=0.203 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCCceEEEEeccC
Q 032167 39 RRVRHAVSSMKGAKSVEVNRKQ 60 (146)
Q Consensus 39 ~kv~k~l~~~~GV~~v~vd~~~ 60 (146)
..++.+|..++||.++++++..
T Consensus 134 ~dV~~aL~~l~gV~~V~V~l~~ 155 (174)
T TIGR03406 134 EDVEDKVLAVPNVDEVEVELVF 155 (174)
T ss_pred HHHHHHHHhCCCceeEEEEEEe
Confidence 4578889999999988876543
No 41
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=39.90 E-value=92 Score=19.33 Aligned_cols=56 Identities=11% Similarity=0.099 Sum_probs=39.7
Q ss_pred EEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHhcCCceEEec
Q 032167 25 TVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH--VDPNKVLKKVRSTGKRAEFWP 89 (146)
Q Consensus 25 ~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~l~~~G~~a~~~~ 89 (146)
..++.. |+.|+.=.-+++++|.+++. .+.+.|..+ .....|..-.+..|+......
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~~---------G~~l~V~~dd~~~~~di~~~~~~~G~~~~~~~ 67 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQP---------GETLLIIADDPATTRDIPSFCRFMDHELLAQE 67 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCCC---------CCEEEEEeCCccHHHHHHHHHHHcCCEEEEEE
Confidence 356888 99999999999999998742 223344332 456677777788998776443
No 42
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=39.53 E-value=1e+02 Score=19.70 Aligned_cols=58 Identities=14% Similarity=0.129 Sum_probs=38.9
Q ss_pred chhhhhhhccccCccc--------cCCCCceEEEEEEcCcChhhHHHHHHHHhCCCCceEEE-Eecc
Q 032167 2 GVLDHLFDLFEITPRR--------KRRKPWQTVEIKVKMDCDGCERRVRHAVSSMKGAKSVE-VNRK 59 (146)
Q Consensus 2 ~~~~~~~~~~~~~~~~--------~~~~~~~~~~l~V~m~C~~C~~kv~k~l~~~~GV~~v~-vd~~ 59 (146)
|++--+++|+.+-..+ -......++++-+....+.-..++.|.|.++-.|..+. +|+.
T Consensus 14 GVL~Rit~lFsRRg~NI~SLtvg~Te~~~iSRmtivv~~~d~~~ieqI~kQL~KlidVikV~~~~~~ 80 (84)
T PRK13562 14 STLNRITSAFVRLQYNIDTLHVTHSEQPGISNMEIQVDIQDDTSLHILIKKLKQQINVLTVECYDLV 80 (84)
T ss_pred CHHHHHHHHHhccCcCeeeEEecccCCCCceEEEEEEeCCCHHHHHHHHHHHhCCccEEEEEEeecc
Confidence 7888888888653211 12344567777764456777789999999998887665 4443
No 43
>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=38.48 E-value=35 Score=19.74 Aligned_cols=30 Identities=27% Similarity=0.492 Sum_probs=15.1
Q ss_pred HHHHHHhC---CCCceEEEEeccCCEEEEEeeCC
Q 032167 40 RVRHAVSS---MKGAKSVEVNRKQSRVTVTGHVD 70 (146)
Q Consensus 40 kv~k~l~~---~~GV~~v~vd~~~~~v~V~g~~~ 70 (146)
+|+.+|.. +++. .+.+....+.+++.|.++
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v~ 35 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSVENGVVTLSGEVP 35 (64)
T ss_dssp ----------CTT-T-TEEEEEECTEEEEEEEES
T ss_pred ccccccccccccCCC-eEEEEEECCEEEEEeeCc
Confidence 45555555 3333 567777888999988753
No 44
>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=37.92 E-value=1.4e+02 Score=21.04 Aligned_cols=32 Identities=16% Similarity=0.232 Sum_probs=27.4
Q ss_pred hhhHHHHHHHHhCCCCceEEEEeccCCEEEEE
Q 032167 35 DGCERRVRHAVSSMKGAKSVEVNRKQSRVTVT 66 (146)
Q Consensus 35 ~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~ 66 (146)
..=+.+|.+.+.+++||.++.+=.....+.|-
T Consensus 74 ~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 74 QQLADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 55678899999999999999998888887765
No 45
>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=36.22 E-value=76 Score=22.58 Aligned_cols=27 Identities=26% Similarity=0.337 Sum_probs=23.3
Q ss_pred hhhHHHHHHHHhCCCCceEEEEeccCC
Q 032167 35 DGCERRVRHAVSSMKGAKSVEVNRKQS 61 (146)
Q Consensus 35 ~~C~~kv~k~l~~~~GV~~v~vd~~~~ 61 (146)
.+|-|-++..+.+++||.++.+-...+
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 579999999999999999999975544
No 46
>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=32.56 E-value=2e+02 Score=21.13 Aligned_cols=50 Identities=18% Similarity=0.147 Sum_probs=36.4
Q ss_pred cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEe--eCCHHHHHHHHHhcCCceEEec
Q 032167 31 KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTG--HVDPNKVLKKVRSTGKRAEFWP 89 (146)
Q Consensus 31 ~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g--~~~~~~i~~~l~~~G~~a~~~~ 89 (146)
|+.|+.-.-+.+++|.+++. .+.++|.. ....+.|.+-++..|+......
T Consensus 5 Gl~CP~Pvi~tKkal~~l~~---------g~~L~VlvD~~~a~~nV~~~~~~~G~~v~~~e 56 (194)
T TIGR03527 5 GLACPQPVILTKKALDELGE---------EGVLTVIVDNEAAKENVSKFATSLGYEVEVEE 56 (194)
T ss_pred CCCCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHHHcCCEEEEEE
Confidence 78899999999999998742 22334433 2566678888889999887543
No 47
>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=32.38 E-value=66 Score=20.54 Aligned_cols=36 Identities=22% Similarity=0.355 Sum_probs=23.3
Q ss_pred eEEEEEE-cCcChhh---HHHHHHHHhCCCCceEEEEecc
Q 032167 24 QTVEIKV-KMDCDGC---ERRVRHAVSSMKGAKSVEVNRK 59 (146)
Q Consensus 24 ~~~~l~V-~m~C~~C---~~kv~k~l~~~~GV~~v~vd~~ 59 (146)
-.+.+.+ .-.|... ...++.+|..++|+.++++++.
T Consensus 39 v~i~l~l~~p~~~~~~~l~~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 39 VDIQMTLTAPNCPVAGSMPGEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred EEEEEEECCCCCChHHHHHHHHHHHHHhCCCCceEEEEEE
Confidence 4455555 3344433 2456778888899998888754
No 48
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=31.63 E-value=1.5e+02 Score=19.40 Aligned_cols=54 Identities=17% Similarity=0.204 Sum_probs=36.6
Q ss_pred CchhhhhhhccccCccc--------cCCCCceEEEEEEcCcChhhHHHHHHHHhCCCCceEEEE
Q 032167 1 MGVLDHLFDLFEITPRR--------KRRKPWQTVEIKVKMDCDGCERRVRHAVSSMKGAKSVEV 56 (146)
Q Consensus 1 ~~~~~~~~~~~~~~~~~--------~~~~~~~~~~l~V~m~C~~C~~kv~k~l~~~~GV~~v~v 56 (146)
.|++-.+++|+.+-..+ -......++++-+. . +.-..++.+.|.++..|..+..
T Consensus 19 pGVL~RIaglFsRRgyNIeSLtvg~te~~~iSRmtivv~-~-~~~i~Qi~kQL~KLidVikV~~ 80 (96)
T PRK08178 19 PGVMSHVCGLFARRAFNVEGILCLPIQDGDKSRIWLLVN-D-DQRLEQMISQIEKLEDVLKVRR 80 (96)
T ss_pred cCHHHHHHHHHhcCCcCeeeEEEeecCCCCceEEEEEEc-C-chHHHHHHHHHhCCcCEEEEEE
Confidence 38888999998663211 12344577777664 2 5678888889999988876543
No 49
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=31.28 E-value=1.3e+02 Score=18.62 Aligned_cols=50 Identities=12% Similarity=0.234 Sum_probs=35.4
Q ss_pred EEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHhcCC
Q 032167 25 TVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH--VDPNKVLKKVRSTGK 83 (146)
Q Consensus 25 ~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~l~~~G~ 83 (146)
..+|.+ |+.|+.=.-.++++|.+++- .+.+.|..+ ....+|..-+++.|.
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~---------Ge~LeV~~ddp~~~~dIp~~~~~~~~ 57 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLKP---------GEILEVIADDPAAKEDIPAWAKKEGG 57 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCCC---------CCEEEEEecCcchHHHHHHHHHHcCC
Confidence 457899 99999999999999998732 334555543 444566666675663
No 50
>PRK04435 hypothetical protein; Provisional
Probab=30.47 E-value=1.9e+02 Score=20.15 Aligned_cols=33 Identities=18% Similarity=0.365 Sum_probs=18.2
Q ss_pred eEEEEEEcCc-ChhhHHHHHHHHhCCCCceEEEE
Q 032167 24 QTVEIKVKMD-CDGCERRVRHAVSSMKGAKSVEV 56 (146)
Q Consensus 24 ~~~~l~V~m~-C~~C~~kv~k~l~~~~GV~~v~v 56 (146)
..+.|.+... -......+...|.+++||.++.+
T Consensus 110 a~vs~tVevs~~~~~L~~Li~~L~~i~gV~~V~i 143 (147)
T PRK04435 110 ANVTISIDTSSMEGDIDELLEKLRNLDGVEKVEL 143 (147)
T ss_pred EEEEEEEEeCChHHHHHHHHHHHHcCCCcEEEEE
Confidence 3344444222 23356666677777777776654
No 51
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=29.86 E-value=2.2e+02 Score=22.46 Aligned_cols=27 Identities=26% Similarity=0.304 Sum_probs=23.0
Q ss_pred hhhHHHHHHHHhCCCCceEEEEeccCC
Q 032167 35 DGCERRVRHAVSSMKGAKSVEVNRKQS 61 (146)
Q Consensus 35 ~~C~~kv~k~l~~~~GV~~v~vd~~~~ 61 (146)
.+|-|-++..+.+++||.++.+-...+
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG 160 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGG 160 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCC
Confidence 789999999999999999999875443
No 52
>PF08256 Antimicrobial20: Aurein-like antibiotic peptide; InterPro: IPR013157 This family of antibacterial peptides are secreted from the granular dorsal glands of Litoria aurea (Green and golden bell frog), Litoria raniformis (Southern bell frog), Litoria citropa (Australian blue mountains tree frog) and frogs from genus Uperoleia. They are a part of the FSAP peptide family. Amongst the more active of these are aurein 1.2, aurein 2.2 and aurein 3.1; caerin 1.1, maculatin 1.1, uperin 3.6 []; citropin 1.1, citropin 1.2, citropin 1.3 and a minor peptide are wide-spectrum antibacterial peptides [].; GO: 0006952 defense response
Probab=26.96 E-value=28 Score=14.29 Aligned_cols=8 Identities=25% Similarity=0.372 Sum_probs=4.6
Q ss_pred chhhhhhh
Q 032167 2 GVLDHLFD 9 (146)
Q Consensus 2 ~~~~~~~~ 9 (146)
|++|++.-
T Consensus 1 Gl~Di~Kk 8 (13)
T PF08256_consen 1 GLFDIAKK 8 (13)
T ss_pred CHHHHHHH
Confidence 56666553
No 53
>PRK09577 multidrug efflux protein; Reviewed
Probab=26.20 E-value=2.2e+02 Score=26.51 Aligned_cols=45 Identities=13% Similarity=0.198 Sum_probs=34.2
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEEe--------eCCHHHHHHHHHhcC
Q 032167 38 ERRVRHAVSSMKGAKSVEVNRKQSRVTVTG--------HVDPNKVLKKVRSTG 82 (146)
Q Consensus 38 ~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g--------~~~~~~i~~~l~~~G 82 (146)
.+.++..|.+++||.+++++.....+.|.- .++..+|.+.|+...
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n 210 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAHN 210 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhC
Confidence 467889999999999999987555555541 177888888887654
No 54
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=25.53 E-value=1.2e+02 Score=22.23 Aligned_cols=35 Identities=14% Similarity=0.132 Sum_probs=26.8
Q ss_pred CceEEEEEEcCcChhhHHHHHHHHhCCCCceEEEEeccCC
Q 032167 22 PWQTVEIKVKMDCDGCERRVRHAVSSMKGAKSVEVNRKQS 61 (146)
Q Consensus 22 ~~~~~~l~V~m~C~~C~~kv~k~l~~~~GV~~v~vd~~~~ 61 (146)
.+.++.|. .+|-|=+++...+++||.++.+-...+
T Consensus 5 ~~~~a~fa-----gGCFWg~E~~f~~i~GV~~t~~GYagG 39 (174)
T COG0225 5 GMEKAYFA-----GGCFWGVEAYFEQIPGVLSTVSGYAGG 39 (174)
T ss_pred CcEEEEEe-----ccCccchHHHHhhCCCeEEEeeeEcCC
Confidence 34556665 678888999999999999998864443
No 55
>PRK11023 outer membrane lipoprotein; Provisional
Probab=25.23 E-value=2.3e+02 Score=20.64 Aligned_cols=47 Identities=26% Similarity=0.326 Sum_probs=34.1
Q ss_pred cChhhHHHHHHHHhCCCCce---EEEEeccCCEEEEEeeCCHHHHHHHHH
Q 032167 33 DCDGCERRVRHAVSSMKGAK---SVEVNRKQSRVTVTGHVDPNKVLKKVR 79 (146)
Q Consensus 33 ~C~~C~~kv~k~l~~~~GV~---~v~vd~~~~~v~V~g~~~~~~i~~~l~ 79 (146)
....=..+|+.+|...+++. .+++.-.++.|++.|.++.........
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 44566788889988777664 577778899999999866555444443
No 56
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=24.94 E-value=2.2e+02 Score=26.51 Aligned_cols=43 Identities=12% Similarity=0.233 Sum_probs=32.9
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEEee--------CCHHHHHHHHHh
Q 032167 38 ERRVRHAVSSMKGAKSVEVNRKQSRVTVTGH--------VDPNKVLKKVRS 80 (146)
Q Consensus 38 ~~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~--------~~~~~i~~~l~~ 80 (146)
.+.++..|..++||.++++......+.|.-+ ++..+|...|+.
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~ 209 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIES 209 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHH
Confidence 4668889999999999999876544555521 778888888874
No 57
>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=24.03 E-value=74 Score=22.51 Aligned_cols=27 Identities=22% Similarity=0.234 Sum_probs=22.6
Q ss_pred hhhHHHHHHHHhCCCCceEEEEeccCC
Q 032167 35 DGCERRVRHAVSSMKGAKSVEVNRKQS 61 (146)
Q Consensus 35 ~~C~~kv~k~l~~~~GV~~v~vd~~~~ 61 (146)
.+|-|-++....+++||.++.+-...+
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG 33 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGG 33 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCC
Confidence 678899999999999999998865443
No 58
>PF04805 Pox_E10: E10-like protein conserved region; InterPro: IPR006890 This entry represents a family of probable FAD-linked sulphydryl oxidases found in poxviruses.; GO: 0016972 thiol oxidase activity, 0055114 oxidation-reduction process
Probab=23.79 E-value=66 Score=19.72 Aligned_cols=21 Identities=14% Similarity=0.393 Sum_probs=16.8
Q ss_pred cCcChhhHHHHHHHHhCCCCc
Q 032167 31 KMDCDGCERRVRHAVSSMKGA 51 (146)
Q Consensus 31 ~m~C~~C~~kv~k~l~~~~GV 51 (146)
.+-|..|...+.+++++-.=.
T Consensus 15 tLPC~~Cr~HA~~ai~kNNiM 35 (70)
T PF04805_consen 15 TLPCPECRIHAKEAIQKNNIM 35 (70)
T ss_pred cCCCHHHHHHHHHHHHhcCcc
Confidence 578999999999998865333
No 59
>PRK07334 threonine dehydratase; Provisional
Probab=23.47 E-value=4.1e+02 Score=21.65 Aligned_cols=63 Identities=17% Similarity=0.201 Sum_probs=41.1
Q ss_pred EEEEE-cCcChhhHHHHHHHHhCCC-CceEEEEecc-----CCEEEEE--ee----CCHHHHHHHHHhcCCceEEe
Q 032167 26 VEIKV-KMDCDGCERRVRHAVSSMK-GAKSVEVNRK-----QSRVTVT--GH----VDPNKVLKKVRSTGKRAEFW 88 (146)
Q Consensus 26 ~~l~V-~m~C~~C~~kv~k~l~~~~-GV~~v~vd~~-----~~~v~V~--g~----~~~~~i~~~l~~~G~~a~~~ 88 (146)
+.|.| ..+-.+=-..|...|+... .|.+++.... .+...+. -. ...+.|+++|++.|+.++++
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 6666777888888887552 2455555432 3443333 21 35568899999999998875
No 60
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=23.27 E-value=1.5e+02 Score=20.07 Aligned_cols=29 Identities=28% Similarity=0.403 Sum_probs=24.5
Q ss_pred EEEEeeCCHHHHHHHHHhcCCceEEeccC
Q 032167 63 VTVTGHVDPNKVLKKVRSTGKRAEFWPYV 91 (146)
Q Consensus 63 v~V~g~~~~~~i~~~l~~~G~~a~~~~~~ 91 (146)
+.++|+-|-..+++.+++.|+++.+++..
T Consensus 104 vLvSgD~Df~~~i~~lr~~G~~V~v~~~~ 132 (149)
T cd06167 104 VLVSGDSDFVPLVERLRELGKRVIVVGFE 132 (149)
T ss_pred EEEECCccHHHHHHHHHHcCCEEEEEccC
Confidence 34568889999999999999999999864
No 61
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=23.27 E-value=1.6e+02 Score=18.98 Aligned_cols=34 Identities=26% Similarity=0.443 Sum_probs=24.1
Q ss_pred eEEEEEE-cCcChhhHHHHHHHHhCCCCceEEEEe
Q 032167 24 QTVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEVN 57 (146)
Q Consensus 24 ~~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~vd 57 (146)
..+.+.+ --+-.+-...++.+|+.++||.++++-
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 3344444 233455678999999999999988764
No 62
>PF02672 CP12: CP12 domain; InterPro: IPR003823 This entry represents an uncharacterised domain in proteins of unknown function. This domain is found associated with CBS domains in some proteins IPR000644 from INTERPRO.; PDB: 3B1K_I 3B1J_D 3RVD_N 3QV1_I 2LJ9_A.
Probab=22.93 E-value=21 Score=22.06 Aligned_cols=14 Identities=50% Similarity=1.156 Sum_probs=10.8
Q ss_pred cccCccCCCCC--ccc
Q 032167 132 VSLFSDENPNA--CSI 145 (146)
Q Consensus 132 ~~~fsddnp~a--CsI 145 (146)
...|+++||.+ |-|
T Consensus 53 lE~yC~~nPea~Ecrv 68 (71)
T PF02672_consen 53 LELYCDENPEADECRV 68 (71)
T ss_dssp HHHHHHHSTTSTTTTT
T ss_pred HHHHHHHCCCcHHhhh
Confidence 44789999997 754
No 63
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=21.80 E-value=1.7e+02 Score=16.72 Aligned_cols=31 Identities=16% Similarity=0.123 Sum_probs=20.1
Q ss_pred CceEEEEEE-cCcChhhHHHHHHHHhCCCCceEEEE
Q 032167 22 PWQTVEIKV-KMDCDGCERRVRHAVSSMKGAKSVEV 56 (146)
Q Consensus 22 ~~~~~~l~V-~m~C~~C~~kv~k~l~~~~GV~~v~v 56 (146)
....+.+++ +.. ...+.+.|..++||..+.+
T Consensus 39 ~~~~~~i~v~~~~----~~~~~~~l~~~~~v~~v~~ 70 (73)
T cd04902 39 GEALMVLSVDEPV----PDEVLEELRALPGILSAKV 70 (73)
T ss_pred CEEEEEEEeCCCC----CHHHHHHHHcCCCccEEEE
Confidence 345566777 422 2367777888899877654
No 64
>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=21.08 E-value=2.1e+02 Score=18.36 Aligned_cols=22 Identities=32% Similarity=0.537 Sum_probs=19.1
Q ss_pred hhHHHHHHHHhCCCCceEEEEe
Q 032167 36 GCERRVRHAVSSMKGAKSVEVN 57 (146)
Q Consensus 36 ~C~~kv~k~l~~~~GV~~v~vd 57 (146)
+-...++.++++++||+++++-
T Consensus 62 g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 62 GGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred cChHHHHHHHhcCCCccEEEEE
Confidence 5568999999999999998875
No 65
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=20.62 E-value=3.1e+02 Score=25.67 Aligned_cols=43 Identities=14% Similarity=0.299 Sum_probs=32.6
Q ss_pred HHHHHHHhCCCCceEEEEeccCCEEEEEee--------CCHHHHHHHHHhc
Q 032167 39 RRVRHAVSSMKGAKSVEVNRKQSRVTVTGH--------VDPNKVLKKVRST 81 (146)
Q Consensus 39 ~kv~k~l~~~~GV~~v~vd~~~~~v~V~g~--------~~~~~i~~~l~~~ 81 (146)
+.++..|.+++||.++++......+.|.-+ +++.+|...|+..
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~~~ 210 (1049)
T PRK15127 160 ANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIKAQ 210 (1049)
T ss_pred HHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 568899999999999999866544666521 7778888888743
No 66
>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=20.13 E-value=1.5e+02 Score=17.76 Aligned_cols=11 Identities=18% Similarity=0.422 Sum_probs=8.3
Q ss_pred EcCcChhhHHH
Q 032167 30 VKMDCDGCERR 40 (146)
Q Consensus 30 V~m~C~~C~~k 40 (146)
++..|..|...
T Consensus 6 ~~~~C~~C~~~ 16 (76)
T PF13192_consen 6 FSPGCPYCPEL 16 (76)
T ss_dssp ECSSCTTHHHH
T ss_pred eCCCCCCcHHH
Confidence 47789999843
Done!