Query 032895
Match_columns 131
No_of_seqs 218 out of 1380
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 07:16:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032895.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032895hhsearch_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 5.6E-14 1.2E-18 85.7 8.5 58 71-128 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.4 1.1E-12 2.4E-17 82.7 8.7 63 68-130 2-68 (71)
3 KOG1603 Copper chaperone [Inor 98.7 1.2E-07 2.6E-12 59.9 8.1 59 68-126 5-63 (73)
4 COG2217 ZntA Cation transport 98.6 2.1E-07 4.6E-12 80.6 8.2 62 68-130 2-68 (713)
5 KOG4656 Copper chaperone for s 98.6 2.7E-07 5.9E-12 68.8 7.4 62 68-129 7-68 (247)
6 PRK10671 copA copper exporting 98.5 5.6E-07 1.2E-11 79.2 8.3 61 68-130 3-64 (834)
7 PLN02957 copper, zinc superoxi 98.4 1.7E-06 3.6E-11 66.1 9.1 63 67-129 5-67 (238)
8 KOG0207 Cation transport ATPas 98.3 1.7E-06 3.7E-11 75.9 6.8 62 68-129 146-211 (951)
9 TIGR00003 copper ion binding p 98.3 2.1E-05 4.6E-10 44.9 9.0 61 69-129 3-67 (68)
10 KOG0207 Cation transport ATPas 98.2 3E-06 6.6E-11 74.4 7.1 82 49-130 42-135 (951)
11 PRK10671 copA copper exporting 98.2 7.2E-06 1.6E-10 72.3 7.9 61 69-129 100-161 (834)
12 PRK11033 zntA zinc/cadmium/mer 97.6 0.00033 7.1E-09 61.4 8.8 62 68-129 53-116 (741)
13 TIGR02052 MerP mercuric transp 94.8 0.53 1.1E-05 28.8 8.8 61 69-129 24-88 (92)
14 cd00371 HMA Heavy-metal-associ 92.0 0.89 1.9E-05 22.8 8.0 57 73-129 3-62 (63)
15 PRK13748 putative mercuric red 90.7 1.8 3.9E-05 36.4 8.4 58 71-128 3-63 (561)
16 PF01206 TusA: Sulfurtransfera 90.1 1.1 2.3E-05 27.3 4.9 49 71-128 2-53 (70)
17 PRK14054 methionine sulfoxide 88.6 1.1 2.4E-05 32.8 4.8 44 79-122 10-75 (172)
18 PRK11018 hypothetical protein; 85.1 4.8 0.0001 25.3 5.8 52 69-129 8-62 (78)
19 PRK05528 methionine sulfoxide 83.7 3.3 7.1E-05 29.8 5.1 44 79-122 8-68 (156)
20 PRK13014 methionine sulfoxide 83.7 3.7 8E-05 30.4 5.5 44 79-122 15-80 (186)
21 PRK00058 methionine sulfoxide 79.7 4.2 9E-05 30.8 4.6 44 79-122 52-117 (213)
22 PF01625 PMSR: Peptide methion 77.0 8.3 0.00018 27.6 5.3 44 79-122 7-72 (155)
23 cd03421 SirA_like_N SirA_like_ 76.7 7.8 0.00017 23.2 4.5 48 72-129 2-52 (67)
24 cd03420 SirA_RHOD_Pry_redox Si 75.5 11 0.00023 23.0 4.9 49 72-129 2-53 (69)
25 cd03423 SirA SirA (also known 72.7 17 0.00036 22.0 5.3 49 72-129 2-53 (69)
26 COG0225 MsrA Peptide methionin 72.4 17 0.00038 26.6 6.0 45 79-123 13-79 (174)
27 cd00291 SirA_YedF_YeeD SirA, Y 71.9 15 0.00033 21.7 5.0 49 72-129 2-53 (69)
28 PF01883 DUF59: Domain of unkn 70.7 10 0.00022 23.0 4.0 33 68-100 34-72 (72)
29 cd03422 YedF YedF is a bacteri 70.6 16 0.00034 22.2 4.8 49 72-129 2-53 (69)
30 PRK05550 bifunctional methioni 69.5 10 0.00022 29.9 4.6 44 79-122 134-199 (283)
31 PRK00299 sulfur transfer prote 66.6 29 0.00064 21.8 6.1 52 69-129 9-63 (81)
32 PF11491 DUF3213: Protein of u 65.5 13 0.00029 24.1 3.7 50 81-130 12-64 (88)
33 PRK10553 assembly protein for 64.2 36 0.00079 22.0 5.9 42 81-122 18-60 (87)
34 PF02680 DUF211: Uncharacteriz 61.2 35 0.00076 22.6 5.2 60 68-128 5-73 (95)
35 COG0425 SirA Predicted redox p 59.3 42 0.00091 21.1 5.9 51 69-128 5-59 (78)
36 PF13732 DUF4162: Domain of un 52.2 40 0.00087 20.6 4.4 38 89-127 26-65 (84)
37 TIGR00401 msrA methionine-S-su 52.0 13 0.00027 26.5 2.2 27 79-105 7-33 (149)
38 PF03927 NapD: NapD protein; 51.0 60 0.0013 20.4 6.1 41 82-123 17-58 (79)
39 PRK14018 trifunctional thiored 48.2 36 0.00079 29.2 4.7 44 79-122 205-269 (521)
40 TIGR03527 selenium_YedF seleni 46.3 50 0.0011 24.4 4.7 46 75-129 5-52 (194)
41 COG1888 Uncharacterized protei 46.2 85 0.0018 20.7 6.5 61 69-129 7-76 (97)
42 PF09580 Spore_YhcN_YlaJ: Spor 46.0 80 0.0017 22.4 5.7 34 79-112 74-107 (177)
43 TIGR03406 FeS_long_SufT probab 41.5 40 0.00087 24.6 3.5 34 69-102 114-153 (174)
44 TIGR02898 spore_YhcN_YlaJ spor 40.3 1.2E+02 0.0027 21.8 5.8 33 80-112 54-86 (158)
45 PRK09577 multidrug efflux prot 39.8 1E+02 0.0022 28.5 6.5 46 82-127 158-211 (1032)
46 PRK10555 aminoglycoside/multid 36.4 1.1E+02 0.0024 28.3 6.2 44 82-125 159-210 (1037)
47 PF14026 DUF4242: Protein of u 34.2 1.2E+02 0.0026 18.9 6.8 46 86-131 25-73 (77)
48 TIGR02945 SUF_assoc FeS assemb 32.8 56 0.0012 21.0 2.8 35 69-103 40-78 (99)
49 COG2151 PaaD Predicted metal-s 30.0 1E+02 0.0022 20.9 3.8 20 82-101 69-88 (111)
50 TIGR00915 2A0602 The (Largely 29.6 1.6E+02 0.0035 27.3 6.1 44 82-125 159-210 (1044)
51 PRK15127 multidrug efflux syst 29.4 1.7E+02 0.0036 27.3 6.2 44 82-125 159-210 (1049)
52 PF14056 DUF4250: Domain of un 27.4 55 0.0012 19.4 1.9 19 112-130 31-49 (55)
53 PF14437 MafB19-deam: MafB19-l 26.7 2.1E+02 0.0046 20.4 5.1 40 67-107 99-140 (146)
54 KOG1635 Peptide methionine sul 26.3 63 0.0014 23.9 2.4 27 79-105 31-57 (191)
55 cd04886 ACT_ThrD-II-like C-ter 25.5 50 0.0011 18.8 1.5 17 115-131 57-73 (73)
56 PF08821 CGGC: CGGC domain; I 25.5 67 0.0014 21.5 2.2 56 72-129 38-102 (107)
57 PF01514 YscJ_FliF: Secretory 25.4 91 0.002 23.2 3.2 22 81-102 116-137 (206)
58 PF08777 RRM_3: RNA binding mo 25.4 2.1E+02 0.0045 18.9 6.6 55 71-125 3-60 (105)
59 PF13193 AMP-binding_C: AMP-bi 25.0 91 0.002 18.5 2.6 17 85-101 2-18 (73)
60 PRK10614 multidrug efflux syst 24.3 2.3E+02 0.0049 26.3 6.0 44 82-125 159-211 (1025)
61 PHA02119 hypothetical protein 24.2 86 0.0019 19.7 2.4 18 113-130 54-71 (87)
62 COG3062 NapD Uncharacterized p 23.6 2.3E+02 0.0049 18.7 5.0 28 82-110 20-47 (94)
63 COG4844 Uncharacterized protei 21.3 20 0.00043 22.4 -0.9 23 8-30 30-52 (78)
64 PRK10503 multidrug efflux syst 21.1 2.8E+02 0.0061 25.8 6.0 43 83-125 169-220 (1040)
65 PF09158 MotCF: Bacteriophage 20.9 2.2E+02 0.0047 19.2 3.9 39 91-130 39-77 (103)
66 PF05046 Img2: Mitochondrial l 20.7 2.4E+02 0.0052 17.9 5.5 57 69-127 29-87 (87)
67 TIGR02159 PA_CoA_Oxy4 phenylac 20.7 1.5E+02 0.0033 20.9 3.4 42 83-128 46-89 (146)
68 PRK09579 multidrug efflux prot 20.5 3.4E+02 0.0074 25.2 6.4 44 82-125 158-210 (1017)
69 TIGR02544 III_secr_YscJ type I 20.3 1.1E+02 0.0024 22.6 2.7 22 81-102 108-129 (193)
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=99.54 E-value=5.6e-14 Score=85.72 Aligned_cols=58 Identities=47% Similarity=0.652 Sum_probs=54.4
Q ss_pred EEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecC---CHHHHHHHHHhCCCC
Q 032895 71 VLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDI---IPFEVLESVSKAHLF 128 (131)
Q Consensus 71 ~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~~---~~~~I~~~I~~~Gy~ 128 (131)
+|.| ||+|++|+.+|+++|.+++||.++.+|+.+++++|.++. ++++|.++|+++||+
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 999999999999999999999999999999999999984 459999999999994
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.44 E-value=1.1e-12 Score=82.68 Aligned_cols=63 Identities=29% Similarity=0.444 Sum_probs=58.0
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec---CCHHHHHHHHHhCCCCcC
Q 032895 68 KMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD---IIPFEVLESVSKAHLFYK 130 (131)
Q Consensus 68 ~~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~---~~~~~I~~~I~~~Gy~~~ 130 (131)
.+..|.| ||+|.+|+..|+++|.+++||.++.+|+..+.+.|.++ .+.++|.++|.++||.+.
T Consensus 2 ~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~ 68 (71)
T COG2608 2 MKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVE 68 (71)
T ss_pred ceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCee
Confidence 4578999 99999999999999999999999999999999888887 478999999999999864
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.72 E-value=1.2e-07 Score=59.86 Aligned_cols=59 Identities=44% Similarity=0.803 Sum_probs=55.2
Q ss_pred eEEEEEEcCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecCCHHHHHHHHHhCC
Q 032895 68 KMVVLRVSMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDIIPFEVLESVSKAH 126 (131)
Q Consensus 68 ~~~~l~VGm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~~~~~~I~~~I~~~G 126 (131)
+...+.+.|+|.+|...|++.+..+.||.++.+|...++++|.++.++..+++.+.+.|
T Consensus 5 ~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~ 63 (73)
T KOG1603|consen 5 KTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTG 63 (73)
T ss_pred cEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcC
Confidence 45677779999999999999999999999999999999999999999999999999876
No 4
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.58 E-value=2.1e-07 Score=80.63 Aligned_cols=62 Identities=32% Similarity=0.531 Sum_probs=56.2
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecC---C-HHHHHHHHHhCCCCcC
Q 032895 68 KMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDI---I-PFEVLESVSKAHLFYK 130 (131)
Q Consensus 68 ~~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~~---~-~~~I~~~I~~~Gy~~~ 130 (131)
.+..|.| ||+|++|+++|| +|++++||.++.+|+.++++.|.++. . .+++...+++.||.+.
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~ 68 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSAR 68 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCcccc
Confidence 3578999 999999999999 99999999999999999999999873 3 6789999999999754
No 5
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.57 E-value=2.7e-07 Score=68.84 Aligned_cols=62 Identities=23% Similarity=0.375 Sum_probs=57.5
Q ss_pred eEEEEEEcCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecCCHHHHHHHHHhCCCCc
Q 032895 68 KMVVLRVSMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDIIPFEVLESVSKAHLFY 129 (131)
Q Consensus 68 ~~~~l~VGm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~~~~~~I~~~I~~~Gy~~ 129 (131)
-+.+|.|.|+|.+|+..|++.|+.++|+.++++++..+.+.|.....+++|...|+..|-++
T Consensus 7 ~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~A 68 (247)
T KOG4656|consen 7 YEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDA 68 (247)
T ss_pred eeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChhe
Confidence 46789999999999999999999999999999999999999999999999999999888653
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.48 E-value=5.6e-07 Score=79.25 Aligned_cols=61 Identities=16% Similarity=0.334 Sum_probs=54.4
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecCCHHHHHHHHHhCCCCcC
Q 032895 68 KMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDIIPFEVLESVSKAHLFYK 130 (131)
Q Consensus 68 ~~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~~~~~~I~~~I~~~Gy~~~ 130 (131)
++.++.| ||+|++|+.+|+++|++++||.++.+++. +.++....+.+.+.+.+++.||.++
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~ 64 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDAS 64 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCccc
Confidence 4688999 99999999999999999999999999994 5566666788999999999999864
No 7
>PLN02957 copper, zinc superoxide dismutase
Probab=98.44 E-value=1.7e-06 Score=66.13 Aligned_cols=63 Identities=25% Similarity=0.439 Sum_probs=57.5
Q ss_pred ceEEEEEEcCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecCCHHHHHHHHHhCCCCc
Q 032895 67 PKMVVLRVSMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDIIPFEVLESVSKAHLFY 129 (131)
Q Consensus 67 ~~~~~l~VGm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~~~~~~I~~~I~~~Gy~~ 129 (131)
.+++.+.++|+|.+|+..|++.|.+++||..+.+++..+++.|.++.....+.+.+++.||.+
T Consensus 5 ~~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a 67 (238)
T PLN02957 5 ELLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKA 67 (238)
T ss_pred cEEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcE
Confidence 456778889999999999999999999999999999999999998778889999999999974
No 8
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.29 E-value=1.7e-06 Score=75.86 Aligned_cols=62 Identities=27% Similarity=0.554 Sum_probs=58.1
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec---CCHHHHHHHHHhCCCCc
Q 032895 68 KMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD---IIPFEVLESVSKAHLFY 129 (131)
Q Consensus 68 ~~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~---~~~~~I~~~I~~~Gy~~ 129 (131)
.++.|.| ||.|.+|+.+|++.+.+++||.++++++.++++.|.++ ..+.++.+.|++.||..
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~ 211 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEA 211 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccc
Confidence 5789999 99999999999999999999999999999999999998 47899999999999863
No 9
>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=98.26 E-value=2.1e-05 Score=44.88 Aligned_cols=61 Identities=33% Similarity=0.436 Sum_probs=52.6
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec---CCHHHHHHHHHhCCCCc
Q 032895 69 MVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD---IIPFEVLESVSKAHLFY 129 (131)
Q Consensus 69 ~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~---~~~~~I~~~I~~~Gy~~ 129 (131)
+..+.+ |++|..|.+.+++.+...+++....+++....+.+.++ .....+...+...||.+
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYEV 67 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCCc
Confidence 456889 99999999999999999999999999999999998875 35566777788889875
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.24 E-value=3e-06 Score=74.36 Aligned_cols=82 Identities=24% Similarity=0.391 Sum_probs=67.6
Q ss_pred cchhhhhhhhhhcccccC--------ceEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec---CCHH
Q 032895 49 LRLKDVVSGNQTLAFQLK--------PKMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD---IIPF 116 (131)
Q Consensus 49 ~~~~~~~~~~~~~~~~~~--------~~~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~---~~~~ 116 (131)
++...+.+.++..|++.. ..+-.+.+ ||+|.+|+..|++.+++.+|+.++.+.+...++.+.++ .+++
T Consensus 42 ~~~~~i~~~ied~gf~~~~~~~~~~~~~~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~ 121 (951)
T KOG0207|consen 42 VSPESIKETIEDMGFEASLLSDSEITASKCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPD 121 (951)
T ss_pred cCHHHHHHHhhcccceeeecccCccccceeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCch
Confidence 444455556666665432 12567999 99999999999999999999999999999999999998 4779
Q ss_pred HHHHHHHhCCCCcC
Q 032895 117 EVLESVSKAHLFYK 130 (131)
Q Consensus 117 ~I~~~I~~~Gy~~~ 130 (131)
.+.+.+++.||.+.
T Consensus 122 ~~~e~ie~~gf~a~ 135 (951)
T KOG0207|consen 122 SIAESIEDLGFSAE 135 (951)
T ss_pred hHHHHHHhcCccce
Confidence 99999999999864
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.16 E-value=7.2e-06 Score=72.33 Aligned_cols=61 Identities=28% Similarity=0.505 Sum_probs=54.3
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecCCHHHHHHHHHhCCCCc
Q 032895 69 MVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDIIPFEVLESVSKAHLFY 129 (131)
Q Consensus 69 ~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~~~~~~I~~~I~~~Gy~~ 129 (131)
++.+.+ ||+|.+|++.+++.+.+++||..+.+++.+++..+....+.+++.+.+++.||.+
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a 161 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGA 161 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCc
Confidence 467889 9999999999999999999999999999999988875567788888899999964
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.62 E-value=0.00033 Score=61.38 Aligned_cols=62 Identities=37% Similarity=0.485 Sum_probs=53.6
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecC-CHHHHHHHHHhCCCCc
Q 032895 68 KMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDI-IPFEVLESVSKAHLFY 129 (131)
Q Consensus 68 ~~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~~-~~~~I~~~I~~~Gy~~ 129 (131)
.++.+.+ ||+|++|++.+++.+.+.+||.++.+++.++++.+.++. ..+++.+.+++.||.+
T Consensus 53 ~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a 116 (741)
T PRK11033 53 TRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSL 116 (741)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhccccc
Confidence 4677889 999999999999999999999999999999998888763 2366778888999975
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=94.76 E-value=0.53 Score=28.80 Aligned_cols=61 Identities=30% Similarity=0.401 Sum_probs=47.0
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec---CCHHHHHHHHHhCCCCc
Q 032895 69 MVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD---IIPFEVLESVSKAHLFY 129 (131)
Q Consensus 69 ~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~---~~~~~I~~~I~~~Gy~~ 129 (131)
...+.+ ++.|..|...++..+...+++....++.......+.++ .....+...+.+.||..
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 88 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPS 88 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCe
Confidence 456778 99999999999999999999888888888887666543 24455556667778753
No 14
>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=91.95 E-value=0.89 Score=22.84 Aligned_cols=57 Identities=40% Similarity=0.558 Sum_probs=40.0
Q ss_pred EE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecC--CHHHHHHHHHhCCCCc
Q 032895 73 RV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDI--IPFEVLESVSKAHLFY 129 (131)
Q Consensus 73 ~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~~--~~~~I~~~I~~~Gy~~ 129 (131)
.+ ++.|..|...++..+...+++.....++......+.++. ....+...+...|+..
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIEDAGYKA 62 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHHHcCCCC
Confidence 35 788999999999999888998877777777766665542 3444444455555543
No 15
>PRK13748 putative mercuric reductase; Provisional
Probab=90.72 E-value=1.8 Score=36.45 Aligned_cols=58 Identities=22% Similarity=0.363 Sum_probs=46.2
Q ss_pred EEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec--CCHHHHHHHHHhCCCC
Q 032895 71 VLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKAHLF 128 (131)
Q Consensus 71 ~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--~~~~~I~~~I~~~Gy~ 128 (131)
.+.+ +++|.+|...++..+...+++....+++..+...+.++ .....+...+.+.||.
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~ 63 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYR 63 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCe
Confidence 3568 99999999999999999999999999998888777653 2445565666777775
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=90.10 E-value=1.1 Score=27.28 Aligned_cols=49 Identities=14% Similarity=0.156 Sum_probs=36.7
Q ss_pred EEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec--CCHHHHHHHHHhCCCC
Q 032895 71 VLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKAHLF 128 (131)
Q Consensus 71 ~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--~~~~~I~~~I~~~Gy~ 128 (131)
++.+ |+.|+.....+.++|.+++ ....+.|..+ ....+|...++..||.
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~---------~G~~l~v~~d~~~~~~di~~~~~~~g~~ 53 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELP---------PGEVLEVLVDDPAAVEDIPRWCEENGYE 53 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSG---------TT-EEEEEESSTTHHHHHHHHHHHHTEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcC---------CCCEEEEEECCccHHHHHHHHHHHCCCE
Confidence 5778 9999999999999999874 2345555555 3457899999999986
No 17
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=88.61 E-value=1.1 Score=32.76 Aligned_cols=44 Identities=30% Similarity=0.377 Sum_probs=36.4
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCCE-------------------EEEEec---CCHHHHHHHH
Q 032895 79 NGCARKVEKHVSKLEGVTSYKVDLASKM-------------------VVVIGD---IIPFEVLESV 122 (131)
Q Consensus 79 ~~C~~~Ie~~L~~l~GV~~v~vnl~~~~-------------------~~V~~~---~~~~~I~~~I 122 (131)
++|=|-+|..+.+++||.++.+-+..+. +.|.+| ++.++|++..
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f 75 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELF 75 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHH
Confidence 6899999999999999999999888775 667787 3567777655
No 18
>PRK11018 hypothetical protein; Provisional
Probab=85.10 E-value=4.8 Score=25.26 Aligned_cols=52 Identities=12% Similarity=0.047 Sum_probs=39.4
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec--CCHHHHHHHHHhCCCCc
Q 032895 69 MVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKAHLFY 129 (131)
Q Consensus 69 ~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--~~~~~I~~~I~~~Gy~~ 129 (131)
.+++.+ |..|+.-..+..++|++++ ....+.|..+ .+...|...+++.||.+
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~---------~G~~L~V~~d~~~a~~di~~~~~~~G~~v 62 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLK---------KGEILEVVSDCPQSINNIPLDARNHGYTV 62 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCC---------CCCEEEEEeCCccHHHHHHHHHHHcCCEE
Confidence 467888 9999999999999999874 2334455544 35577888888999875
No 19
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=83.72 E-value=3.3 Score=29.83 Aligned_cols=44 Identities=20% Similarity=0.243 Sum_probs=34.8
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCCE--------------EEEEec---CCHHHHHHHH
Q 032895 79 NGCARKVEKHVSKLEGVTSYKVDLASKM--------------VVVIGD---IIPFEVLESV 122 (131)
Q Consensus 79 ~~C~~~Ie~~L~~l~GV~~v~vnl~~~~--------------~~V~~~---~~~~~I~~~I 122 (131)
++|=|-+|..+.+++||.++.+-+..+. +.|.+| ++.++|++..
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 6899999999999999999998876643 456777 3557777655
No 20
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=83.70 E-value=3.7 Score=30.42 Aligned_cols=44 Identities=23% Similarity=0.254 Sum_probs=35.9
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCCE-------------------EEEEec---CCHHHHHHHH
Q 032895 79 NGCARKVEKHVSKLEGVTSYKVDLASKM-------------------VVVIGD---IIPFEVLESV 122 (131)
Q Consensus 79 ~~C~~~Ie~~L~~l~GV~~v~vnl~~~~-------------------~~V~~~---~~~~~I~~~I 122 (131)
++|=|-+|..+.+++||.++.+-+..+. +.|.+| ++.++|++..
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~F 80 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIF 80 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHH
Confidence 7899999999999999999999888774 567777 3567777655
No 21
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=79.67 E-value=4.2 Score=30.81 Aligned_cols=44 Identities=32% Similarity=0.335 Sum_probs=35.5
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCC-------------------EEEEEec---CCHHHHHHHH
Q 032895 79 NGCARKVEKHVSKLEGVTSYKVDLASK-------------------MVVVIGD---IIPFEVLESV 122 (131)
Q Consensus 79 ~~C~~~Ie~~L~~l~GV~~v~vnl~~~-------------------~~~V~~~---~~~~~I~~~I 122 (131)
++|-|-+|..+.+++||.++.+-+..+ .+.|.|| ++.++|++..
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~F 117 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVF 117 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHH
Confidence 789999999999999999999998854 2567787 3567777655
No 22
>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=77.00 E-value=8.3 Score=27.65 Aligned_cols=44 Identities=36% Similarity=0.407 Sum_probs=34.0
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCC-------------------EEEEEec---CCHHHHHHHH
Q 032895 79 NGCARKVEKHVSKLEGVTSYKVDLASK-------------------MVVVIGD---IIPFEVLESV 122 (131)
Q Consensus 79 ~~C~~~Ie~~L~~l~GV~~v~vnl~~~-------------------~~~V~~~---~~~~~I~~~I 122 (131)
.+|-|-+|..+.+++||.++.+.+..+ .+.|.+| ++.++|++..
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~is~~~Ll~~f 72 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVISYEELLDVF 72 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS-HHHHHHHH
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcccHHHHHHHH
Confidence 579999999999999999999987766 2456776 3556666654
No 23
>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=76.69 E-value=7.8 Score=23.19 Aligned_cols=48 Identities=19% Similarity=0.183 Sum_probs=34.2
Q ss_pred EEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec--CCHHHHHHHHHhCCCCc
Q 032895 72 LRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKAHLFY 129 (131)
Q Consensus 72 l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--~~~~~I~~~I~~~Gy~~ 129 (131)
+.+ |+.|+.-.....++| ++. ..+.+.|..+ .+...|....++.||.+
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~---------~g~~l~v~~d~~~s~~~i~~~~~~~G~~~ 52 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELE---------AGGEIEVLVDNEVAKENVSRFAESRGYEV 52 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcC---------CCCEEEEEEcChhHHHHHHHHHHHcCCEE
Confidence 456 899999999999999 543 2334444444 34578888889999875
No 24
>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=75.48 E-value=11 Score=22.95 Aligned_cols=49 Identities=14% Similarity=0.190 Sum_probs=36.5
Q ss_pred EEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec--CCHHHHHHHHHhCCCCc
Q 032895 72 LRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKAHLFY 129 (131)
Q Consensus 72 l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--~~~~~I~~~I~~~Gy~~ 129 (131)
+.+ |+.|+.=.....++|.+++ ..+.+.|..+ .....|..-.+..||..
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~---------~G~~l~V~~d~~~a~~di~~~~~~~G~~~ 53 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQ---------DGEQLEVKASDPGFARDAQAWCKSTGNTL 53 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCC---------CCCEEEEEECCccHHHHHHHHHHHcCCEE
Confidence 456 8999999999999999874 2334455544 35578888889999864
No 25
>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=72.66 E-value=17 Score=22.01 Aligned_cols=49 Identities=12% Similarity=0.170 Sum_probs=35.9
Q ss_pred EEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec--CCHHHHHHHHHhCCCCc
Q 032895 72 LRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKAHLFY 129 (131)
Q Consensus 72 l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--~~~~~I~~~I~~~Gy~~ 129 (131)
+.. |..|+.=.-...++|.+++ ..+.+.|..+ .....|....++.||.+
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~---------~G~~l~V~~dd~~s~~di~~~~~~~g~~~ 53 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMK---------PGDTLLVLATDPSTTRDIPKFCTFLGHEL 53 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCC---------CCCEEEEEeCCCchHHHHHHHHHHcCCEE
Confidence 345 8899999999999999874 2334455444 45678888899999875
No 26
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=72.43 E-value=17 Score=26.65 Aligned_cols=45 Identities=33% Similarity=0.285 Sum_probs=34.7
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCCE-------------------EEEEec---CCHHHHHHHHH
Q 032895 79 NGCARKVEKHVSKLEGVTSYKVDLASKM-------------------VVVIGD---IIPFEVLESVS 123 (131)
Q Consensus 79 ~~C~~~Ie~~L~~l~GV~~v~vnl~~~~-------------------~~V~~~---~~~~~I~~~I~ 123 (131)
.+|=|=+|+.+.++|||.++.+-.+.+. +.|.+| ++.++|++..-
T Consensus 13 gGCFWg~E~~f~~i~GV~~t~~GYagG~~~nptY~~Vcsg~TgHaE~V~V~yDp~~isy~~LL~~ff 79 (174)
T COG0225 13 GGCFWGVEAYFEQIPGVLSTVSGYAGGHTPNPTYEEVCSGTTGHAEAVEVTYDPKVISYEELLEVFF 79 (174)
T ss_pred ccCccchHHHHhhCCCeEEEeeeEcCCCCCCCChhhccCCCCCceEEEEEEeCCccccHHHHHHHHh
Confidence 7899999999999999999998877664 345666 35577776653
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=71.90 E-value=15 Score=21.71 Aligned_cols=49 Identities=16% Similarity=0.134 Sum_probs=36.0
Q ss_pred EEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec--CCHHHHHHHHHhCCCCc
Q 032895 72 LRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKAHLFY 129 (131)
Q Consensus 72 l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--~~~~~I~~~I~~~Gy~~ 129 (131)
+.+ |+.|+.=...+.++|.+++ ....+.|..+ .....|...+++.||.+
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~---------~g~~l~v~~d~~~~~~~i~~~~~~~g~~~ 53 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLK---------SGEVLEVLLDDPGAVEDIPAWAKETGHEV 53 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCC---------CCCEEEEEecCCcHHHHHHHHHHHcCCEE
Confidence 445 8899998889999998864 2344455555 34678888899999874
No 28
>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=70.66 E-value=10 Score=22.95 Aligned_cols=33 Identities=24% Similarity=0.440 Sum_probs=20.9
Q ss_pred eEEEEEEcCcChhH------HHHHHHHHhCCCCeeEEEE
Q 032895 68 KMVVLRVSMHCNGC------ARKVEKHVSKLEGVTSYKV 100 (131)
Q Consensus 68 ~~~~l~VGm~C~~C------~~~Ie~~L~~l~GV~~v~v 100 (131)
.++.+.+.+..++| ...|+++|..++||.+++|
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 44555553334443 5778899999999998875
No 29
>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=70.57 E-value=16 Score=22.22 Aligned_cols=49 Identities=14% Similarity=0.084 Sum_probs=36.0
Q ss_pred EEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec--CCHHHHHHHHHhCCCCc
Q 032895 72 LRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKAHLFY 129 (131)
Q Consensus 72 l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--~~~~~I~~~I~~~Gy~~ 129 (131)
+.. |..|+.=..+..++|++++ ....+.|..+ .+...|....+..||.+
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~---------~G~~l~V~~d~~~s~~ni~~~~~~~g~~v 53 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLK---------PGEILEVISDCPQSINNIPIDARNHGYKV 53 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCC---------CCCEEEEEecCchHHHHHHHHHHHcCCEE
Confidence 345 8899999999999999874 2333455444 35677888888999875
No 30
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=69.52 E-value=10 Score=29.93 Aligned_cols=44 Identities=32% Similarity=0.251 Sum_probs=34.9
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCCE-------------------EEEEec---CCHHHHHHHH
Q 032895 79 NGCARKVEKHVSKLEGVTSYKVDLASKM-------------------VVVIGD---IIPFEVLESV 122 (131)
Q Consensus 79 ~~C~~~Ie~~L~~l~GV~~v~vnl~~~~-------------------~~V~~~---~~~~~I~~~I 122 (131)
.+|=|-+|..+.+++||.++.+-+..+. +.|++| ++.++|++..
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~VcsG~tgH~EaV~V~yDp~~isy~~LL~~F 199 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEFDPAKISYETLLKVF 199 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHH
Confidence 7899999999999999999999877663 566777 3556776654
No 31
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=66.64 E-value=29 Score=21.77 Aligned_cols=52 Identities=13% Similarity=0.165 Sum_probs=37.4
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec--CCHHHHHHHHHhCCCCc
Q 032895 69 MVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKAHLFY 129 (131)
Q Consensus 69 ~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--~~~~~I~~~I~~~Gy~~ 129 (131)
.+++.. |+.|+.=.....++|++++ ..+.+.|..+ .....|..-.+..|+..
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~---------~G~~l~V~~dd~~~~~di~~~~~~~G~~~ 63 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQ---------PGETLLIIADDPATTRDIPSFCRFMDHEL 63 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCC---------CCCEEEEEeCCccHHHHHHHHHHHcCCEE
Confidence 456888 9999999999999999874 2233444443 34567777778888764
No 32
>PF11491 DUF3213: Protein of unknown function (DUF3213) ; InterPro: IPR021583 The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold []. ; PDB: 2F40_A.
Probab=65.55 E-value=13 Score=24.06 Aligned_cols=50 Identities=22% Similarity=0.027 Sum_probs=28.2
Q ss_pred HHHHHHHHHhCCCCeeEEEEecCCCEEEEEec---CCHHHHHHHHHhCCCCcC
Q 032895 81 CARKVEKHVSKLEGVTSYKVDLASKMVVVIGD---IIPFEVLESVSKAHLFYK 130 (131)
Q Consensus 81 C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~---~~~~~I~~~I~~~Gy~~~ 130 (131)
-+..++=.|...++|-.+-+|.......|.+| .+.+++++.+++.++.+.
T Consensus 12 eA~~~QYeLsk~~~vyRvFiNgYar~g~VifDe~kl~~e~lL~~le~~kpEVi 64 (88)
T PF11491_consen 12 EAMVKQYELSKNEAVYRVFINGYARNGFVIFDESKLSKEELLEMLEEFKPEVI 64 (88)
T ss_dssp TTHHHHHTTTTTTTB------TTSS--EEE--B-S-SHHHH---HHHTTT-SS
T ss_pred HHHHHHHHhhcccceeeeeecccccceEEEECcccCCHHHHHHHHHhcChhhe
Confidence 34556667888899999999999999999998 467999999999888754
No 33
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=64.21 E-value=36 Score=21.99 Aligned_cols=42 Identities=12% Similarity=0.184 Sum_probs=27.3
Q ss_pred HHHHHHHHHhCCCCeeEEEEecCCCEEEEEec-CCHHHHHHHH
Q 032895 81 CARKVEKHVSKLEGVTSYKVDLASKMVVVIGD-IIPFEVLESV 122 (131)
Q Consensus 81 C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~-~~~~~I~~~I 122 (131)
=...+.+.|..+||+.-...+...+++.|+.. .+...+.+.+
T Consensus 18 ~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i 60 (87)
T PRK10553 18 RISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTI 60 (87)
T ss_pred HHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHH
Confidence 35677788888888877777767777776654 3444444433
No 34
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=61.24 E-value=35 Score=22.59 Aligned_cols=60 Identities=25% Similarity=0.315 Sum_probs=36.9
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEe-----cCCCEE--EEEec-CCHHHHHHHHHhCCCC
Q 032895 68 KMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVD-----LASKMV--VVIGD-IIPFEVLESVSKAHLF 128 (131)
Q Consensus 68 ~~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vn-----l~~~~~--~V~~~-~~~~~I~~~I~~~Gy~ 128 (131)
+++.|.+ --+-+ -...+-+.|.+++||..+++. ..+..+ +|.++ ++.++|.++|++.|-.
T Consensus 5 rRlVLDVlKP~~p-~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~ 73 (95)
T PF02680_consen 5 RRLVLDVLKPHEP-SIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGV 73 (95)
T ss_dssp EEEEEEEEEESSS--HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-E
T ss_pred eEEEEEeecCCCC-CHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCe
Confidence 3455555 22322 234566778999999877754 344444 44454 7889999999999864
No 35
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=59.31 E-value=42 Score=21.08 Aligned_cols=51 Identities=22% Similarity=0.286 Sum_probs=36.4
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec--CCHHHHHHHHHhCC-CC
Q 032895 69 MVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKAH-LF 128 (131)
Q Consensus 69 ~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--~~~~~I~~~I~~~G-y~ 128 (131)
..+|.+ |+.|+.=...+.++|.+++ ....+.|..+ ....+|....++.| |.
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~---------~Ge~LeV~~ddp~~~~dIp~~~~~~~~~~ 59 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLK---------PGEILEVIADDPAAKEDIPAWAKKEGGHE 59 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCC---------CCCEEEEEecCcchHHHHHHHHHHcCCcE
Confidence 467888 9999999999999999884 3445555554 34466777776454 54
No 36
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=52.22 E-value=40 Score=20.64 Aligned_cols=38 Identities=18% Similarity=0.239 Sum_probs=27.4
Q ss_pred HhCCCCeeEEEEecCCCEEEEEec--CCHHHHHHHHHhCCC
Q 032895 89 VSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKAHL 127 (131)
Q Consensus 89 L~~l~GV~~v~vnl~~~~~~V~~~--~~~~~I~~~I~~~Gy 127 (131)
|..++||..+... ..+.+.+..+ ....+|++.+.+.|+
T Consensus 26 l~~~~~v~~v~~~-~~~~~~i~l~~~~~~~~ll~~l~~~g~ 65 (84)
T PF13732_consen 26 LEELPGVESVEQD-GDGKLRIKLEDEETANELLQELIEKGI 65 (84)
T ss_pred HhhCCCeEEEEEe-CCcEEEEEECCcccHHHHHHHHHhCCC
Confidence 7788999988764 3443555443 566889999988887
No 37
>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=51.96 E-value=13 Score=26.55 Aligned_cols=27 Identities=33% Similarity=0.370 Sum_probs=23.9
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCC
Q 032895 79 NGCARKVEKHVSKLEGVTSYKVDLASK 105 (131)
Q Consensus 79 ~~C~~~Ie~~L~~l~GV~~v~vnl~~~ 105 (131)
++|=|-+|..+.+++||.++.+-+..+
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG 33 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGG 33 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCC
Confidence 679999999999999999999876655
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=51.03 E-value=60 Score=20.36 Aligned_cols=41 Identities=20% Similarity=0.205 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCCCeeEEEEecCCCEEEEEec-CCHHHHHHHHH
Q 032895 82 ARKVEKHVSKLEGVTSYKVDLASKMVVVIGD-IIPFEVLESVS 123 (131)
Q Consensus 82 ~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~-~~~~~I~~~I~ 123 (131)
...+.++|..+||+.-...+.. +++.|+.. .+..++.+.+.
T Consensus 17 ~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~ 58 (79)
T PF03927_consen 17 LEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLID 58 (79)
T ss_dssp HHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHH
T ss_pred HHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHH
Confidence 3567777888888866666655 66666654 34455544444
No 39
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=48.17 E-value=36 Score=29.17 Aligned_cols=44 Identities=23% Similarity=0.271 Sum_probs=34.7
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCCE------------------EEEEec---CCHHHHHHHH
Q 032895 79 NGCARKVEKHVSKLEGVTSYKVDLASKM------------------VVVIGD---IIPFEVLESV 122 (131)
Q Consensus 79 ~~C~~~Ie~~L~~l~GV~~v~vnl~~~~------------------~~V~~~---~~~~~I~~~I 122 (131)
++|=|-+|..+.+++||.++.+-++.+. +.|.|| ++.++|++..
T Consensus 205 gGCFWg~e~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~gtgH~E~V~V~yDp~~is~~~Ll~~f 269 (521)
T PRK14018 205 GGCFWGLEAYFQRIDGVVDAVSGYANGNTKNPSYEDVYRHSGHAETVKVTYDADKLSLDTILQYY 269 (521)
T ss_pred cCCchhhHHHHccCCCEEEEEEeeCCCCCCCCChhhccCCCCcEEEEEEEECCCcCcHHHHHHHH
Confidence 6899999999999999999999877663 456676 3556766655
No 40
>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=46.31 E-value=50 Score=24.44 Aligned_cols=46 Identities=15% Similarity=0.103 Sum_probs=33.4
Q ss_pred cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec--CCHHHHHHHHHhCCCCc
Q 032895 75 SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKAHLFY 129 (131)
Q Consensus 75 Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--~~~~~I~~~I~~~Gy~~ 129 (131)
|+.||.=.....++|.+++. .+.++|..| ...+.|.+..+..||.+
T Consensus 5 Gl~CP~Pvi~tKkal~~l~~---------g~~L~VlvD~~~a~~nV~~~~~~~G~~v 52 (194)
T TIGR03527 5 GLACPQPVILTKKALDELGE---------EGVLTVIVDNEAAKENVSKFATSLGYEV 52 (194)
T ss_pred CCCCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHHHcCCEE
Confidence 88999999999999998752 223444443 35567888888888865
No 41
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=46.17 E-value=85 Score=20.72 Aligned_cols=61 Identities=21% Similarity=0.233 Sum_probs=36.9
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEe-----cCCC--EEEEEec-CCHHHHHHHHHhCCCCc
Q 032895 69 MVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVD-----LASK--MVVVIGD-IIPFEVLESVSKAHLFY 129 (131)
Q Consensus 69 ~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vn-----l~~~--~~~V~~~-~~~~~I~~~I~~~Gy~~ 129 (131)
++.+.+ --+-..-...+-+.|.+++||..+++. ..+. +++|.++ .+-++|.+.|++.|-.+
T Consensus 7 RlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~I 76 (97)
T COG1888 7 RLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAI 76 (97)
T ss_pred eeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCee
Confidence 445555 222222233455667888888766643 3333 3445553 78899999999998653
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=45.99 E-value=80 Score=22.39 Aligned_cols=34 Identities=24% Similarity=0.281 Sum_probs=29.3
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec
Q 032895 79 NGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD 112 (131)
Q Consensus 79 ~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~ 112 (131)
..=+..|.+.+.+++||.++.+-.....+.|-.+
T Consensus 74 ~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~ 107 (177)
T PF09580_consen 74 QQLADRIANRVKKVPGVEDATVVVTDDNAYVAVD 107 (177)
T ss_pred HHHHHHHHHHHhcCCCceEEEEEEECCEEEEEEE
Confidence 4567899999999999999999999998877654
No 43
>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=41.50 E-value=40 Score=24.60 Aligned_cols=34 Identities=26% Similarity=0.499 Sum_probs=22.3
Q ss_pred EEEEEEcCcChhH------HHHHHHHHhCCCCeeEEEEec
Q 032895 69 MVVLRVSMHCNGC------ARKVEKHVSKLEGVTSYKVDL 102 (131)
Q Consensus 69 ~~~l~VGm~C~~C------~~~Ie~~L~~l~GV~~v~vnl 102 (131)
++.+.+-+..++| ...++.+|..++||.+++|++
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 3444443344444 345888999999999888753
No 44
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ 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 that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=40.35 E-value=1.2e+02 Score=21.76 Aligned_cols=33 Identities=21% Similarity=0.275 Sum_probs=28.3
Q ss_pred hHHHHHHHHHhCCCCeeEEEEecCCCEEEEEec
Q 032895 80 GCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD 112 (131)
Q Consensus 80 ~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~ 112 (131)
.=+.+|.+.+.++|||.++.+=.....+.|-.+
T Consensus 54 ~~A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vgv~ 86 (158)
T TIGR02898 54 DVADEIASEAAKVKGVKDATVVITGNYAYVGVD 86 (158)
T ss_pred HHHHHHHHHHhcCCCCceEEEEEECCEEEEEEE
Confidence 456789999999999999999888888887765
No 45
>PRK09577 multidrug efflux protein; Reviewed
Probab=39.78 E-value=1e+02 Score=28.53 Aligned_cols=46 Identities=15% Similarity=0.173 Sum_probs=34.4
Q ss_pred HHHHHHHHhCCCCeeEEEEecCCCEEEEEec--------CCHHHHHHHHHhCCC
Q 032895 82 ARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--------IIPFEVLESVSKAHL 127 (131)
Q Consensus 82 ~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--------~~~~~I~~~I~~~Gy 127 (131)
...++..|+++|||.++.++-....+.|..| .+..+|.++|+....
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 4678999999999999998865445555544 467888888877543
No 46
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=36.42 E-value=1.1e+02 Score=28.29 Aligned_cols=44 Identities=14% Similarity=0.215 Sum_probs=33.9
Q ss_pred HHHHHHHHhCCCCeeEEEEecCCCEEEEEec--------CCHHHHHHHHHhC
Q 032895 82 ARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--------IIPFEVLESVSKA 125 (131)
Q Consensus 82 ~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--------~~~~~I~~~I~~~ 125 (131)
++.++..|++++||.++.++-....+.|..| .+..+|.++|+..
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 4678899999999999998755455667665 4668888888753
No 47
>PF14026 DUF4242: Protein of unknown function (DUF4242)
Probab=34.19 E-value=1.2e+02 Score=18.91 Aligned_cols=46 Identities=15% Similarity=0.071 Sum_probs=32.7
Q ss_pred HHHHhCCCCeeEEEEecC--CCEEEEEec-CCHHHHHHHHHhCCCCcCC
Q 032895 86 EKHVSKLEGVTSYKVDLA--SKMVVVIGD-IIPFEVLESVSKAHLFYKR 131 (131)
Q Consensus 86 e~~L~~l~GV~~v~vnl~--~~~~~V~~~-~~~~~I~~~I~~~Gy~~~~ 131 (131)
...+.+++||..+..-.. .++..=.+. ++.+.|.+.-++.|+.+.+
T Consensus 25 ~~~~~~~~~V~w~~s~v~~d~~k~~Cly~Ap~~eaV~~~~~~aG~p~d~ 73 (77)
T PF14026_consen 25 CAVQAEMPGVQWLRSYVSEDDGKIFCLYEAPDEEAVREHARRAGLPADR 73 (77)
T ss_pred HHHHhhcCCeEEEEEEEecCCCeEEEEEECCCHHHHHHHHHHcCCCcce
Confidence 334455589988876655 666554455 6888999999999998753
No 48
>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=32.84 E-value=56 Score=20.95 Aligned_cols=35 Identities=26% Similarity=0.407 Sum_probs=23.3
Q ss_pred EEEEEE-cCcChhH---HHHHHHHHhCCCCeeEEEEecC
Q 032895 69 MVVLRV-SMHCNGC---ARKVEKHVSKLEGVTSYKVDLA 103 (131)
Q Consensus 69 ~~~l~V-Gm~C~~C---~~~Ie~~L~~l~GV~~v~vnl~ 103 (131)
.+.+.+ .-.|+.. ...++.+|..++|+.++++++.
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 445555 3444443 3457788889999998888764
No 49
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=30.01 E-value=1e+02 Score=20.88 Aligned_cols=20 Identities=30% Similarity=0.526 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCCeeEEEEe
Q 032895 82 ARKVEKHVSKLEGVTSYKVD 101 (131)
Q Consensus 82 ~~~Ie~~L~~l~GV~~v~vn 101 (131)
...++.++...+||.+++|+
T Consensus 69 ~~~v~~al~~~~~v~~v~V~ 88 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVE 88 (111)
T ss_pred HHHHHHHHHhcCCcceEEEE
Confidence 67889999999999988875
No 50
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=29.57 E-value=1.6e+02 Score=27.30 Aligned_cols=44 Identities=20% Similarity=0.308 Sum_probs=34.4
Q ss_pred HHHHHHHHhCCCCeeEEEEecCCCEEEEEec--------CCHHHHHHHHHhC
Q 032895 82 ARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--------IIPFEVLESVSKA 125 (131)
Q Consensus 82 ~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--------~~~~~I~~~I~~~ 125 (131)
.+.++..|++++||.++++.-....+.|..| .++.+|.++|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~~~ 210 (1044)
T TIGR00915 159 ASNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQAQ 210 (1044)
T ss_pred HHHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 3568899999999999999866555667665 4678888888763
No 51
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=29.44 E-value=1.7e+02 Score=27.27 Aligned_cols=44 Identities=14% Similarity=0.274 Sum_probs=33.5
Q ss_pred HHHHHHHHhCCCCeeEEEEecCCCEEEEEec--------CCHHHHHHHHHhC
Q 032895 82 ARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--------IIPFEVLESVSKA 125 (131)
Q Consensus 82 ~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~--------~~~~~I~~~I~~~ 125 (131)
.+.++..|++++||.++.+.-....+.|..| .++.+|.++|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~~~ 210 (1049)
T PRK15127 159 AANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIKAQ 210 (1049)
T ss_pred HHHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 3568899999999999998755455667665 4668888888754
No 52
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=27.37 E-value=55 Score=19.40 Aligned_cols=19 Identities=26% Similarity=0.211 Sum_probs=15.9
Q ss_pred cCCHHHHHHHHHhCCCCcC
Q 032895 112 DIIPFEVLESVSKAHLFYK 130 (131)
Q Consensus 112 ~~~~~~I~~~I~~~Gy~~~ 130 (131)
+++.++|.+.+..+||.+.
T Consensus 31 ~id~~~l~~kL~~~Gy~Y~ 49 (55)
T PF14056_consen 31 DIDKEELEEKLASIGYEYD 49 (55)
T ss_pred CCCHHHHHHHHHHcCCeEc
Confidence 4678899999999999764
No 53
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=26.74 E-value=2.1e+02 Score=20.38 Aligned_cols=40 Identities=23% Similarity=0.365 Sum_probs=31.2
Q ss_pred ceEEEEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecC-CCEE
Q 032895 67 PKMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLA-SKMV 107 (131)
Q Consensus 67 ~~~~~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~-~~~~ 107 (131)
....++.| --.|..|..-|.....++ |+.++.|... +++.
T Consensus 99 g~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~ 140 (146)
T PF14437_consen 99 GRSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKV 140 (146)
T ss_pred CCeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcE
Confidence 35788888 788999998888777765 8888888766 5543
No 54
>KOG1635 consensus Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=26.26 E-value=63 Score=23.91 Aligned_cols=27 Identities=33% Similarity=0.452 Sum_probs=24.3
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEecCCC
Q 032895 79 NGCARKVEKHVSKLEGVTSYKVDLASK 105 (131)
Q Consensus 79 ~~C~~~Ie~~L~~l~GV~~v~vnl~~~ 105 (131)
.+|-|-+|.+..+++||...+|.++.+
T Consensus 31 ~GCFWg~E~a~~~l~gV~~T~vGYagG 57 (191)
T KOG1635|consen 31 AGCFWGVELAYQRLPGVVRTEVGYAGG 57 (191)
T ss_pred ccchhhHHHHHhhcCCeEEEeecccCC
Confidence 678999999999999999999988766
No 55
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=25.51 E-value=50 Score=18.82 Aligned_cols=17 Identities=18% Similarity=0.192 Sum_probs=14.1
Q ss_pred HHHHHHHHHhCCCCcCC
Q 032895 115 PFEVLESVSKAHLFYKR 131 (131)
Q Consensus 115 ~~~I~~~I~~~Gy~~~~ 131 (131)
.+.+.+.|++.||.+.|
T Consensus 57 l~~l~~~l~~~g~~~~~ 73 (73)
T cd04886 57 IEEIIAALREAGYDVRR 73 (73)
T ss_pred HHHHHHHHHHcCCEEeC
Confidence 35899999999998764
No 56
>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=25.49 E-value=67 Score=21.50 Aligned_cols=56 Identities=23% Similarity=0.351 Sum_probs=29.3
Q ss_pred EEE-cC-cChhHH-HHHHHHHhCC--CCeeEEEEecCCCEEEEEe--c-CCHHHHHHHHHhC-CCCc
Q 032895 72 LRV-SM-HCNGCA-RKVEKHVSKL--EGVTSYKVDLASKMVVVIG--D-IIPFEVLESVSKA-HLFY 129 (131)
Q Consensus 72 l~V-Gm-~C~~C~-~~Ie~~L~~l--~GV~~v~vnl~~~~~~V~~--~-~~~~~I~~~I~~~-Gy~~ 129 (131)
..+ || +|++|. ..+...++++ .|+.-+. +++-...=.. . +..+.+.+.|++. |+++
T Consensus 38 ~elvgf~~CgGCpg~~~~~~~~~l~~~~~d~IH--lssC~~~~~~~~~CP~~~~~~~~I~~~~gi~V 102 (107)
T PF08821_consen 38 VELVGFFTCGGCPGRKLVRRIKKLKKNGADVIH--LSSCMVKGNPHGPCPHIDEIKKIIEEKFGIEV 102 (107)
T ss_pred eEEEEEeeCCCCChhHHHHHHHHHHHCCCCEEE--EcCCEecCCCCCCCCCHHHHHHHHHHHhCCCE
Confidence 445 75 899873 2333333332 4555333 2232221111 1 4568999999988 8864
No 57
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=25.45 E-value=91 Score=23.16 Aligned_cols=22 Identities=27% Similarity=0.543 Sum_probs=18.6
Q ss_pred HHHHHHHHHhCCCCeeEEEEec
Q 032895 81 CARKVEKHVSKLEGVTSYKVDL 102 (131)
Q Consensus 81 C~~~Ie~~L~~l~GV~~v~vnl 102 (131)
=...+++.|+.++||.+++|.+
T Consensus 116 le~eL~~tI~~i~gV~~A~V~l 137 (206)
T PF01514_consen 116 LEGELERTIESIDGVESARVHL 137 (206)
T ss_dssp HHHHHHHHHTTSTTEEEEEEEE
T ss_pred HHHHHHHHHHcCCCeeEEEEEE
Confidence 3567899999999999999873
No 58
>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=25.39 E-value=2.1e+02 Score=18.87 Aligned_cols=55 Identities=13% Similarity=0.109 Sum_probs=32.9
Q ss_pred EEEE-cCcChhHHHHHHHHHhCCCCeeEEEEecCCCEEEEEecC--CHHHHHHHHHhC
Q 032895 71 VLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDI--IPFEVLESVSKA 125 (131)
Q Consensus 71 ~l~V-Gm~C~~C~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~~--~~~~I~~~I~~~ 125 (131)
.+.+ |+.-+.+...|...+.....|..+.+..-.....|.|.. ....+++.+...
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 3555 655556688889999998889988888888888999873 355666666655
No 59
>PF13193 AMP-binding_C: AMP-binding enzyme C-terminal domain; PDB: 3L8C_B 2VSQ_A 3R44_A 3RG2_B 3A9U_A 3A9V_A 3NI2_A 1V26_B 1ULT_B 1V25_B ....
Probab=25.01 E-value=91 Score=18.48 Aligned_cols=17 Identities=24% Similarity=0.280 Sum_probs=14.3
Q ss_pred HHHHHhCCCCeeEEEEe
Q 032895 85 VEKHVSKLEGVTSYKVD 101 (131)
Q Consensus 85 Ie~~L~~l~GV~~v~vn 101 (131)
||.+|.+.+||.++.+-
T Consensus 2 IE~~l~~~~~V~~~~V~ 18 (73)
T PF13193_consen 2 IESVLRQHPGVAEAAVV 18 (73)
T ss_dssp HHHHHHTSTTEEEEEEE
T ss_pred HHHHHhcCCCccEEEEE
Confidence 78999999999877653
No 60
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=24.32 E-value=2.3e+02 Score=26.31 Aligned_cols=44 Identities=23% Similarity=0.270 Sum_probs=32.4
Q ss_pred HHHHHHHHhCCCCeeEEEEecCC-CEEEEEec--------CCHHHHHHHHHhC
Q 032895 82 ARKVEKHVSKLEGVTSYKVDLAS-KMVVVIGD--------IIPFEVLESVSKA 125 (131)
Q Consensus 82 ~~~Ie~~L~~l~GV~~v~vnl~~-~~~~V~~~--------~~~~~I~~~I~~~ 125 (131)
.+.++..|+++|||.++.+.-.. ..+.|..| .++++|.++|+..
T Consensus 159 ~~~l~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~~ 211 (1025)
T PRK10614 159 STQLAQTISQIDGVGDVDVGGSSLPAVRVGLNPQALFNQGVSLDDVRQAISNA 211 (1025)
T ss_pred HHHHHHHhcCCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 36789999999999999987433 24566655 4667888888754
No 61
>PHA02119 hypothetical protein
Probab=24.16 E-value=86 Score=19.68 Aligned_cols=18 Identities=17% Similarity=0.276 Sum_probs=15.3
Q ss_pred CCHHHHHHHHHhCCCCcC
Q 032895 113 IIPFEVLESVSKAHLFYK 130 (131)
Q Consensus 113 ~~~~~I~~~I~~~Gy~~~ 130 (131)
+.+.+|+.-++.+||+++
T Consensus 54 i~~~divdylr~lgy~~~ 71 (87)
T PHA02119 54 IMPKDIVDYLRSLGYDAK 71 (87)
T ss_pred cccHHHHHHHHHccchhc
Confidence 457899999999999864
No 62
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=23.60 E-value=2.3e+02 Score=18.73 Aligned_cols=28 Identities=21% Similarity=0.319 Sum_probs=15.0
Q ss_pred HHHHHHHHhCCCCeeEEEEecCCCEEEEE
Q 032895 82 ARKVEKHVSKLEGVTSYKVDLASKMVVVI 110 (131)
Q Consensus 82 ~~~Ie~~L~~l~GV~~v~vnl~~~~~~V~ 110 (131)
-..|..+|..+||+.-..-+.. +++.|.
T Consensus 20 l~av~~~L~~ip~~EV~~~d~~-GKlVVV 47 (94)
T COG3062 20 LSAVKTALLAIPGCEVYGEDAE-GKLVVV 47 (94)
T ss_pred HHHHHHHHhcCCCcEeeccCCC-ceEEEE
Confidence 3455566666666655555444 444444
No 63
>COG4844 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.26 E-value=20 Score=22.39 Aligned_cols=23 Identities=17% Similarity=0.478 Sum_probs=16.3
Q ss_pred cchheeccCCCCCcccccccccc
Q 032895 8 KILDCLCISSPGSCSCFCLNTFE 30 (131)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~ 30 (131)
-+|.+.|++.|+.|+..---..+
T Consensus 30 DvlEYgCLt~Cg~Ca~~lfALVn 52 (78)
T COG4844 30 DVLEYGCLTHCGICAASLFALVN 52 (78)
T ss_pred cchhhhhHhhhhhHHHhHHHHhc
Confidence 36788899999987765544333
No 64
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=21.14 E-value=2.8e+02 Score=25.79 Aligned_cols=43 Identities=19% Similarity=0.209 Sum_probs=31.8
Q ss_pred HHHHHHHhCCCCeeEEEEecC-CCEEEEEec--------CCHHHHHHHHHhC
Q 032895 83 RKVEKHVSKLEGVTSYKVDLA-SKMVVVIGD--------IIPFEVLESVSKA 125 (131)
Q Consensus 83 ~~Ie~~L~~l~GV~~v~vnl~-~~~~~V~~~--------~~~~~I~~~I~~~ 125 (131)
+.++..|+++|||.++.+.-. ...+.|..| .++.+|.++|+..
T Consensus 169 ~~l~~~L~~i~gV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~~v~~ai~~~ 220 (1040)
T PRK10503 169 TRVAQKISQVSGVGLVTLSGGQRPAVRVKLNAQAIAALGLTSETVRTAITGA 220 (1040)
T ss_pred HHHHHHhcCCCCceEEEecCCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 578999999999999887633 245666665 4667888888654
No 65
>PF09158 MotCF: Bacteriophage T4 MotA, C-terminal; InterPro: IPR015241 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the C-terminal domain of MotA factors, which adopts a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. It contains a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [].; PDB: 1KAF_B.
Probab=20.92 E-value=2.2e+02 Score=19.15 Aligned_cols=39 Identities=10% Similarity=0.274 Sum_probs=26.3
Q ss_pred CCCCeeEEEEecCCCEEEEEecCCHHHHHHHHHhCCCCcC
Q 032895 91 KLEGVTSYKVDLASKMVVVIGDIIPFEVLESVSKAHLFYK 130 (131)
Q Consensus 91 ~l~GV~~v~vnl~~~~~~V~~~~~~~~I~~~I~~~Gy~~~ 130 (131)
+..|+....+. ..+...|.+--..+++++.+.++|..++
T Consensus 39 Rt~GirqfEi~-n~G~~RI~gYk~se~~~~~f~slG~~~K 77 (103)
T PF09158_consen 39 RTKGIRQFEIR-NKGEFRIFGYKMSEEIIKKFTSLGMEVK 77 (103)
T ss_dssp EETTEEEEEEE-TTSEEEEEEES--HHHHHHHHHTT-EEE
T ss_pred ccCceeEEEEe-cCCcEEEEEEcCCHHHHHHHHhcCcEEE
Confidence 44678888874 5666776655566888999999998654
No 66
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=20.75 E-value=2.4e+02 Score=17.94 Aligned_cols=57 Identities=12% Similarity=0.113 Sum_probs=38.0
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhCCCC-eeEEEEecCCCEEEEEecCCHHHHHHHHHhCCC
Q 032895 69 MVVLRV-SMHCNGCARKVEKHVSKLEG-VTSYKVDLASKMVVVIGDIIPFEVLESVSKAHL 127 (131)
Q Consensus 69 ~~~l~V-Gm~C~~C~~~Ie~~L~~l~G-V~~v~vnl~~~~~~V~~~~~~~~I~~~I~~~Gy 127 (131)
++.=+| |- =..+...+.+.|....+ -..+.|+..++.+.|.++ ...+|.+-+.+.||
T Consensus 29 T~IrkI~GD-~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~-~~~~Vk~wL~~~GF 87 (87)
T PF05046_consen 29 TVIRKIEGD-IWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGD-HVEEVKKWLLEKGF 87 (87)
T ss_pred EEEEeecCC-HHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCc-cHHHHHHHHHHCcC
Confidence 344455 42 24555556666654433 246788899999999987 46778888888887
No 67
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=20.65 E-value=1.5e+02 Score=20.91 Aligned_cols=42 Identities=17% Similarity=0.142 Sum_probs=24.1
Q ss_pred HHHHHHHhCCCCeeEEEEecCCCEEEEEecC--CHHHHHHHHHhCCCC
Q 032895 83 RKVEKHVSKLEGVTSYKVDLASKMVVVIGDI--IPFEVLESVSKAHLF 128 (131)
Q Consensus 83 ~~Ie~~L~~l~GV~~v~vnl~~~~~~V~~~~--~~~~I~~~I~~~Gy~ 128 (131)
..|+++|... |+.+++|++.-.. .|.. -.++-.+.+++.|..
T Consensus 46 ~~I~~aL~~~-Gv~~V~V~i~~~p---~Wt~d~it~~gr~~l~~~gia 89 (146)
T TIGR02159 46 QDIRDAVRAL-GVEVVEVSTSLDP---PWTTDWITEDAREKLREYGIA 89 (146)
T ss_pred HHHHHHHHhc-CCCeEEEeEeeCC---CCChHHCCHHHHHHHHhcCcc
Confidence 4577888876 8877777532111 1221 124557777777764
No 68
>PRK09579 multidrug efflux protein; Reviewed
Probab=20.52 E-value=3.4e+02 Score=25.19 Aligned_cols=44 Identities=14% Similarity=0.163 Sum_probs=31.4
Q ss_pred HHHHHHHHhCCCCeeEEEEecCC-CEEEEEec--------CCHHHHHHHHHhC
Q 032895 82 ARKVEKHVSKLEGVTSYKVDLAS-KMVVVIGD--------IIPFEVLESVSKA 125 (131)
Q Consensus 82 ~~~Ie~~L~~l~GV~~v~vnl~~-~~~~V~~~--------~~~~~I~~~I~~~ 125 (131)
...++..|++++||.++.+.=.. ..+.|..| .+.++|.++|+..
T Consensus 158 ~~~i~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~~ 210 (1017)
T PRK09579 158 SRVIQPKLATLPGMAEAEILGNQVFAMRLWLDPVKLAGFGLSAGDVTQAVRRY 210 (1017)
T ss_pred HHHHHHHhhcCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 45688999999999999875322 23455544 4678888888764
No 69
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=20.28 E-value=1.1e+02 Score=22.57 Aligned_cols=22 Identities=27% Similarity=0.582 Sum_probs=18.1
Q ss_pred HHHHHHHHHhCCCCeeEEEEec
Q 032895 81 CARKVEKHVSKLEGVTSYKVDL 102 (131)
Q Consensus 81 C~~~Ie~~L~~l~GV~~v~vnl 102 (131)
=...+++.|..++||.+++|++
T Consensus 108 le~EL~rtI~~i~~V~~ArVhl 129 (193)
T TIGR02544 108 IEQRLEQTLSQIDGVISARVHV 129 (193)
T ss_pred HHHHHHHHHHhcCCeeeeEEEE
Confidence 3567888899999999888864
Done!