Query 030348
Match_columns 179
No_of_seqs 302 out of 1501
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 12:22:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030348.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030348hhsearch_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 5.4E-13 1.2E-17 86.1 8.5 58 50-107 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.4 6.8E-12 1.5E-16 83.6 9.2 65 47-111 2-70 (71)
3 KOG1603 Copper chaperone [Inor 99.3 1.2E-11 2.6E-16 82.8 9.1 68 46-113 4-72 (73)
4 KOG4656 Copper chaperone for s 99.0 3.5E-09 7.7E-14 83.0 8.2 71 47-117 7-77 (247)
5 PLN02957 copper, zinc superoxi 98.4 2.4E-06 5.3E-11 69.4 10.7 72 46-117 5-76 (238)
6 PRK10671 copA copper exporting 98.3 2.2E-06 4.7E-11 80.9 8.2 64 47-112 3-67 (834)
7 COG2217 ZntA Cation transport 98.1 1.1E-05 2.3E-10 74.8 7.9 63 47-110 2-69 (713)
8 TIGR00003 copper ion binding p 97.9 0.00024 5.2E-09 43.0 8.6 60 48-107 3-66 (68)
9 KOG0207 Cation transport ATPas 97.7 0.00011 2.4E-09 68.7 7.5 70 47-116 146-219 (951)
10 KOG0207 Cation transport ATPas 97.3 0.00044 9.5E-09 64.9 6.4 63 54-116 2-66 (951)
11 PRK10671 copA copper exporting 97.2 0.0013 2.8E-08 62.3 8.1 64 48-111 100-164 (834)
12 PRK11033 zntA zinc/cadmium/mer 97.1 0.003 6.6E-08 59.2 9.5 67 45-111 51-119 (741)
13 TIGR02052 MerP mercuric transp 94.9 0.63 1.4E-05 30.3 10.1 63 48-110 24-90 (92)
14 cd00371 HMA Heavy-metal-associ 88.4 2.5 5.5E-05 22.5 7.1 54 52-105 3-59 (63)
15 PRK13748 putative mercuric red 87.9 4 8.7E-05 36.8 9.1 65 50-114 3-70 (561)
16 COG1888 Uncharacterized protei 84.7 11 0.00024 26.2 7.7 67 46-112 5-80 (97)
17 PF01206 TusA: Sulfurtransfera 83.6 5.8 0.00013 25.3 5.9 53 50-111 2-57 (70)
18 PF02680 DUF211: Uncharacteriz 83.4 6.5 0.00014 27.5 6.2 65 46-111 4-77 (95)
19 PF01883 DUF59: Domain of unkn 69.6 11 0.00023 24.2 4.2 32 48-79 35-72 (72)
20 PRK14054 methionine sulfoxide 68.3 18 0.00039 28.0 5.8 44 58-101 10-75 (172)
21 PF13732 DUF4162: Domain of un 65.7 23 0.0005 23.2 5.3 49 68-117 26-75 (84)
22 cd03421 SirA_like_N SirA_like_ 63.1 31 0.00068 21.7 5.4 51 51-111 2-55 (67)
23 PRK11018 hypothetical protein; 62.5 42 0.00091 22.1 6.1 55 48-111 8-65 (78)
24 cd03420 SirA_RHOD_Pry_redox Si 56.2 51 0.0011 21.1 5.6 53 51-112 2-57 (69)
25 PRK00058 methionine sulfoxide 53.3 73 0.0016 25.6 6.9 44 58-101 52-117 (213)
26 PF14437 MafB19-deam: MafB19-l 52.9 42 0.0009 25.4 5.1 40 47-87 100-141 (146)
27 PRK10553 assembly protein for 49.0 80 0.0017 21.6 5.7 44 59-102 17-61 (87)
28 PRK13014 methionine sulfoxide 41.7 83 0.0018 24.7 5.5 44 58-101 15-80 (186)
29 cd00291 SirA_YedF_YeeD SirA, Y 41.0 88 0.0019 19.4 5.6 53 51-112 2-57 (69)
30 PF02672 CP12: CP12 domain; I 40.2 7.1 0.00015 25.8 -0.6 14 165-178 53-68 (71)
31 cd03422 YedF YedF is a bacteri 40.2 98 0.0021 19.7 5.3 52 51-111 2-56 (69)
32 COG2151 PaaD Predicted metal-s 39.3 54 0.0012 23.5 3.8 21 61-81 69-89 (111)
33 PRK05528 methionine sulfoxide 39.1 81 0.0018 24.0 5.0 44 58-101 8-68 (156)
34 cd03423 SirA SirA (also known 37.3 1.1E+02 0.0024 19.4 5.7 53 51-112 2-57 (69)
35 PF08712 Nfu_N: Scaffold prote 37.2 1.3E+02 0.0028 20.3 5.4 52 49-104 26-79 (87)
36 COG2177 FtsX Cell division pro 35.9 2.4E+02 0.0053 23.7 7.8 47 48-107 62-109 (297)
37 TIGR03406 FeS_long_SufT probab 35.9 51 0.0011 25.5 3.5 21 61-81 133-153 (174)
38 PF03927 NapD: NapD protein; 35.3 1.3E+02 0.0029 19.8 6.2 43 60-103 16-59 (79)
39 PF09580 Spore_YhcN_YlaJ: Spor 35.1 1.1E+02 0.0025 23.0 5.4 33 57-89 73-105 (177)
40 PF08821 CGGC: CGGC domain; I 34.9 62 0.0014 22.9 3.6 58 51-110 38-104 (107)
41 cd04888 ACT_PheB-BS C-terminal 33.3 1.2E+02 0.0027 18.8 4.9 33 47-79 41-74 (76)
42 PRK11152 ilvM acetolactate syn 32.5 1.3E+02 0.0027 20.0 4.5 35 43-79 41-75 (76)
43 PF08777 RRM_3: RNA binding mo 31.0 1.9E+02 0.0041 20.2 6.5 55 50-104 3-60 (105)
44 PRK09577 multidrug efflux prot 30.5 1.4E+02 0.0031 29.5 6.3 46 61-106 158-211 (1032)
45 PRK10555 aminoglycoside/multid 29.6 1.5E+02 0.0032 29.4 6.2 44 61-104 159-210 (1037)
46 PF13740 ACT_6: ACT domain; PD 29.3 1.6E+02 0.0035 18.9 5.2 56 48-103 2-64 (76)
47 COG0425 SirA Predicted redox p 28.7 1E+02 0.0022 20.4 3.6 49 48-105 5-56 (78)
48 KOG4730 D-arabinono-1, 4-lacto 28.6 72 0.0016 28.7 3.5 52 54-110 87-138 (518)
49 PF01625 PMSR: Peptide methion 28.5 2E+02 0.0043 21.7 5.6 27 58-84 7-33 (155)
50 PRK00299 sulfur transfer prote 28.3 1.8E+02 0.0039 19.2 6.3 55 48-111 9-66 (81)
51 PHA01634 hypothetical protein 27.8 21 0.00044 26.8 0.1 17 51-67 93-110 (156)
52 TIGR02945 SUF_assoc FeS assemb 27.7 77 0.0017 21.6 3.0 35 48-82 40-78 (99)
53 TIGR03527 selenium_YedF seleni 27.4 1.8E+02 0.0038 22.8 5.3 49 54-111 5-55 (194)
54 cd02410 archeal_CPSF_KH The ar 27.4 2.6E+02 0.0057 21.1 5.9 58 58-115 52-116 (145)
55 PRK07334 threonine dehydratase 26.2 3E+02 0.0066 23.8 7.1 64 48-111 326-402 (403)
56 PF04972 BON: BON domain; Int 25.6 42 0.00091 20.6 1.2 29 63-92 3-34 (64)
57 TIGR00489 aEF-1_beta translati 25.0 1.3E+02 0.0028 20.6 3.7 22 59-80 62-83 (88)
58 COG2092 EFB1 Translation elong 24.2 1.4E+02 0.003 20.6 3.6 35 46-80 48-83 (88)
59 PRK15127 multidrug efflux syst 24.0 2.1E+02 0.0045 28.4 6.2 44 61-104 159-210 (1049)
60 TIGR01676 GLDHase galactonolac 23.5 1.3E+02 0.0029 27.6 4.4 39 68-108 110-148 (541)
61 PLN00204 CP12 gene family prot 23.0 24 0.00052 25.8 -0.3 14 165-178 108-123 (126)
62 TIGR00915 2A0602 The (Largely 22.2 2.3E+02 0.0051 28.0 6.1 43 61-103 159-209 (1044)
63 TIGR03027 pepcterm_export puta 22.1 2.4E+02 0.0051 21.1 5.0 57 50-106 38-110 (165)
64 PF13291 ACT_4: ACT domain; PD 21.9 2.2E+02 0.0049 18.1 4.6 33 46-78 47-79 (80)
65 KOG3411 40S ribosomal protein 21.6 89 0.0019 23.2 2.4 43 58-103 97-140 (143)
66 COG4004 Uncharacterized protei 20.9 1.4E+02 0.0031 20.7 3.1 22 69-90 37-58 (96)
67 PF09158 MotCF: Bacteriophage 20.6 3.2E+02 0.007 19.4 5.1 40 70-110 39-78 (103)
68 PRK11023 outer membrane lipopr 20.2 2.3E+02 0.0049 22.0 4.7 45 56-100 46-93 (191)
69 PRK05550 bifunctional methioni 20.1 2E+02 0.0043 24.1 4.5 27 58-84 134-160 (283)
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=99.46 E-value=5.4e-13 Score=86.10 Aligned_cols=58 Identities=40% Similarity=0.645 Sum_probs=54.3
Q ss_pred EEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec---CCHHHHHHHHHhcCcc
Q 030348 50 ELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY---VDRNKVLKAVRRAGKR 107 (179)
Q Consensus 50 ~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~---~~~~~i~~~i~~~G~~ 107 (179)
+|+| ||+|++|+++|+++|.+++||.++.+|+.+++++|.++ +++++|.++|+++||+
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 4889 99999999999999999999999999999999999976 4679999999999985
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.36 E-value=6.8e-12 Score=83.58 Aligned_cols=65 Identities=34% Similarity=0.517 Sum_probs=57.9
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEE--e-cCCHHHHHHHHHhcCcceEEc
Q 030348 47 QTVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAV--G-YVDRNKVLKAVRRAGKRAEFW 111 (179)
Q Consensus 47 ~~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~--g-~~~~~~i~~~i~~~G~~a~~~ 111 (179)
.+..|+| ||+|++|+.+|+++|.+++||.++++|+..+++.|. + .++.++|.++|+++||.+..+
T Consensus 2 ~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~~ 70 (71)
T COG2608 2 MKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEEI 70 (71)
T ss_pred ceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeeec
Confidence 3568999 999999999999999999999999999999766665 4 379999999999999988754
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.33 E-value=1.2e-11 Score=82.78 Aligned_cols=68 Identities=49% Similarity=0.859 Sum_probs=62.6
Q ss_pred ceEEEEEEcCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEecCCHHHHHHHHHhcC-cceEEccC
Q 030348 46 LQTVELKVRMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAG-KRAEFWPY 113 (179)
Q Consensus 46 ~~~v~l~Vgm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~i~~~G-~~a~~~~~ 113 (179)
.++.++++.|+|++|..+|++.|..++||.++.+|...++++|.|.+++..|++.|++.| .++++|..
T Consensus 4 ~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~~~ 72 (73)
T KOG1603|consen 4 IKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELWKV 72 (73)
T ss_pred ccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEecC
Confidence 456778889999999999999999999999999999999999999999999999999888 78887743
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.95 E-value=3.5e-09 Score=83.00 Aligned_cols=71 Identities=27% Similarity=0.458 Sum_probs=67.1
Q ss_pred eEEEEEEcCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEecCCHHHHHHHHHhcCcceEEccCCCCC
Q 030348 47 QTVELKVRMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRAEFWPYPNPP 117 (179)
Q Consensus 47 ~~v~l~Vgm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~i~~~G~~a~~~~~~~~~ 117 (179)
-+.+|.|.|+|++|++.|++.|..++||.+|+||+.++.|.|.+...+.+|.+.|+.+|.+|.+...+.+.
T Consensus 7 ~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G~ps 77 (247)
T KOG4656|consen 7 YEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAGKPS 77 (247)
T ss_pred eeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCCchh
Confidence 46789999999999999999999999999999999999999999999999999999999999999887764
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.44 E-value=2.4e-06 Score=69.41 Aligned_cols=72 Identities=31% Similarity=0.479 Sum_probs=64.2
Q ss_pred ceEEEEEEcCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEecCCHHHHHHHHHhcCcceEEccCCCCC
Q 030348 46 LQTVELKVRMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRAEFWPYPNPP 117 (179)
Q Consensus 46 ~~~v~l~Vgm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~i~~~G~~a~~~~~~~~~ 117 (179)
.+++++.++|.|+.|+.+|++.|.+++||..+.+++..++++|.+......+.+.+++.||.++++....+.
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 345678889999999999999999999999999999999999987778889999999999999988775554
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.30 E-value=2.2e-06 Score=80.85 Aligned_cols=64 Identities=20% Similarity=0.447 Sum_probs=57.1
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEecCCHHHHHHHHHhcCcceEEcc
Q 030348 47 QTVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRAEFWP 112 (179)
Q Consensus 47 ~~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~i~~~G~~a~~~~ 112 (179)
++++++| ||+|.+|+.+|+++|++++||.++++++. +.+|.+..+.+.+.+++++.||+++...
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 4678999 99999999999999999999999999994 5566666789999999999999998753
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.09 E-value=1.1e-05 Score=74.84 Aligned_cols=63 Identities=35% Similarity=0.564 Sum_probs=56.9
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec---CC-HHHHHHHHHhcCcceEE
Q 030348 47 QTVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY---VD-RNKVLKAVRRAGKRAEF 110 (179)
Q Consensus 47 ~~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~---~~-~~~i~~~i~~~G~~a~~ 110 (179)
.+..+.| ||+|..|+.+|| +|++++||.++.+|+.++++.|..+ .+ .+.+..++++.||.+..
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 3567999 999999999999 9999999999999999999999854 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=97.85 E-value=0.00024 Score=43.00 Aligned_cols=60 Identities=25% Similarity=0.354 Sum_probs=50.5
Q ss_pred EEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec---CCHHHHHHHHHhcCcc
Q 030348 48 TVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY---VDRNKVLKAVRRAGKR 107 (179)
Q Consensus 48 ~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~---~~~~~i~~~i~~~G~~ 107 (179)
+..+.+ |+.|..|...+++.+...+++....+++...++.+... .+...+...+...|+.
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 66 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYE 66 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCC
Confidence 456899 99999999999999999999999999999998888742 4667777777777764
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.70 E-value=0.00011 Score=68.72 Aligned_cols=70 Identities=29% Similarity=0.502 Sum_probs=64.1
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec---CCHHHHHHHHHhcCcceEEccCCCC
Q 030348 47 QTVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY---VDRNKVLKAVRRAGKRAEFWPYPNP 116 (179)
Q Consensus 47 ~~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~---~~~~~i~~~i~~~G~~a~~~~~~~~ 116 (179)
+++.|.| ||.|.+|+.+|++.+.+++||.+++++..++++.|..+ ..+.++.+.|+.+|+++.+.+....
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~~~~~ 219 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRPYGDT 219 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeeecccc
Confidence 6889999 99999999999999999999999999999999999865 7899999999999999888775543
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.35 E-value=0.00044 Score=64.89 Aligned_cols=63 Identities=21% Similarity=0.373 Sum_probs=58.7
Q ss_pred cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec--CCHHHHHHHHHhcCcceEEccCCCC
Q 030348 54 RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY--VDRNKVLKAVRRAGKRAEFWPYPNP 116 (179)
Q Consensus 54 gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~i~~~G~~a~~~~~~~~ 116 (179)
||+|..|.+.|++++.+.+||.+..+++.++..+|..+ ++++.+.+.+++.|+++++......
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ied~gf~~~~~~~~~~ 66 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIEDMGFEASLLSDSEI 66 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhhcccceeeecccCcc
Confidence 89999999999999999999999999999999998865 8999999999999999999877664
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.20 E-value=0.0013 Score=62.28 Aligned_cols=64 Identities=28% Similarity=0.452 Sum_probs=56.9
Q ss_pred EEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEecCCHHHHHHHHHhcCcceEEc
Q 030348 48 TVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRAEFW 111 (179)
Q Consensus 48 ~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~i~~~G~~a~~~ 111 (179)
++.+.+ ||+|..|...+++.+.+++||.++.+++..+++.+.+..+.+++.+.+++.|+.+.++
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 9999999999999999999999999999999888876667888888999999987654
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.12 E-value=0.003 Score=59.17 Aligned_cols=67 Identities=34% Similarity=0.371 Sum_probs=55.0
Q ss_pred cceEEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec-CCHHHHHHHHHhcCcceEEc
Q 030348 45 SLQTVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY-VDRNKVLKAVRRAGKRAEFW 111 (179)
Q Consensus 45 ~~~~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~-~~~~~i~~~i~~~G~~a~~~ 111 (179)
..++..+.+ ||+|..|..++++.+.+++||.++.+++..+++.+..+ ...+++.+.+++.|+++..+
T Consensus 51 ~~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~~~ 119 (741)
T PRK11033 51 SGTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLRDE 119 (741)
T ss_pred CCceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccccccc
Confidence 345677899 99999999999999999999999999999998887643 12267778888899887544
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=94.89 E-value=0.63 Score=30.32 Aligned_cols=63 Identities=27% Similarity=0.404 Sum_probs=47.3
Q ss_pred EEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEe---cCCHHHHHHHHHhcCcceEE
Q 030348 48 TVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVG---YVDRNKVLKAVRRAGKRAEF 110 (179)
Q Consensus 48 ~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g---~~~~~~i~~~i~~~G~~a~~ 110 (179)
+..+.+ ++.|..|...++..+....++....++....+..+.. ..+...+...+++.|+.+++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 456778 9999999999999999999988888888777755542 13555665666777776544
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=88.39 E-value=2.5 Score=22.47 Aligned_cols=54 Identities=43% Similarity=0.642 Sum_probs=36.4
Q ss_pred EE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec--CCHHHHHHHHHhcC
Q 030348 52 KV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY--VDRNKVLKAVRRAG 105 (179)
Q Consensus 52 ~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~i~~~G 105 (179)
.+ ++.|..|...++..+....++.....+.......+... .+...+...+...+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIEDAG 59 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHHHcC
Confidence 35 78899999999998888888877777776666555432 24444434444443
No 15
>PRK13748 putative mercuric reductase; Provisional
Probab=87.90 E-value=4 Score=36.76 Aligned_cols=65 Identities=29% Similarity=0.393 Sum_probs=51.2
Q ss_pred EEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec--CCHHHHHHHHHhcCcceEEccCC
Q 030348 50 ELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY--VDRNKVLKAVRRAGKRAEFWPYP 114 (179)
Q Consensus 50 ~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~i~~~G~~a~~~~~~ 114 (179)
.+.+ ++.|..|..+++..+...+++....++.......+... .+...+...+.+.|+..+.+...
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~~~~ 70 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLADAP 70 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeeccCcc
Confidence 4668 99999999999999999999998899988887666532 45666666778888887666553
No 16
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=84.66 E-value=11 Score=26.17 Aligned_cols=67 Identities=19% Similarity=0.242 Sum_probs=44.7
Q ss_pred ceEEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeC-----C--ccEEEEEec-CCHHHHHHHHHhcCcceEEcc
Q 030348 46 LQTVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVEL-----E--LEKVTAVGY-VDRNKVLKAVRRAGKRAEFWP 112 (179)
Q Consensus 46 ~~~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~-----~--~~~v~V~g~-~~~~~i~~~i~~~G~~a~~~~ 112 (179)
.+++.+.+ .-+-+--.--+-+.|.+++||..|++.. + .-+++|.|. ++-++|.+.|++.|.-..-+.
T Consensus 5 iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHSiD 80 (97)
T COG1888 5 IRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHSID 80 (97)
T ss_pred ceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeeehh
Confidence 44556666 4333333445667788888887776433 2 345566776 999999999999998766543
No 17
>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=83.61 E-value=5.8 Score=25.34 Aligned_cols=53 Identities=13% Similarity=0.056 Sum_probs=38.8
Q ss_pred EEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec--CCHHHHHHHHHhcCcceEEc
Q 030348 50 ELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY--VDRNKVLKAVRRAGKRAEFW 111 (179)
Q Consensus 50 ~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~i~~~G~~a~~~ 111 (179)
++.+ |+.|+...-+++++|.+++.- +.+.|..+ ...+.|...++..|++...+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHCCCEEEEE
Confidence 5778 999999999999999997432 33444433 55678899999999986554
No 18
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=83.37 E-value=6.5 Score=27.46 Aligned_cols=65 Identities=23% Similarity=0.321 Sum_probs=43.0
Q ss_pred ceEEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEe-----CCccE--EEEEec-CCHHHHHHHHHhcCcceEEc
Q 030348 46 LQTVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVE-----LELEK--VTAVGY-VDRNKVLKAVRRAGKRAEFW 111 (179)
Q Consensus 46 ~~~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd-----~~~~~--v~V~g~-~~~~~i~~~i~~~G~~a~~~ 111 (179)
.+++.|.| .-+- --.-.+-+.|.+++||..|++. ..+.. ++|.|. ++.++|.++|++.|.-+.-+
T Consensus 4 irRlVLDVlKP~~-p~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHSI 77 (95)
T PF02680_consen 4 IRRLVLDVLKPHE-PSIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHSI 77 (95)
T ss_dssp EEEEEEEEEEESS-S-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEEE
T ss_pred eeEEEEEeecCCC-CCHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEee
Confidence 45666777 3333 3344667789999998877654 34443 455676 99999999999999866544
No 19
>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=69.58 E-value=11 Score=24.23 Aligned_cols=32 Identities=28% Similarity=0.534 Sum_probs=20.8
Q ss_pred EEEEEEcCcChhH------HHHHHHHHHcCCCeeEEEE
Q 030348 48 TVELKVRMCCTGC------ERVVKNAIYKLRGVDSVEV 79 (179)
Q Consensus 48 ~v~l~Vgm~C~~C------~~kI~~al~~~~GV~~v~v 79 (179)
++.+.+.+...+| ...|+++|..++||.+|+|
T Consensus 35 ~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 35 KVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp EEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 4555554444444 5778999999999998875
No 20
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=68.34 E-value=18 Score=27.99 Aligned_cols=44 Identities=18% Similarity=0.214 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHHcCCCeeEEEEeCCccE-------------------EEEEec---CCHHHHHHHH
Q 030348 58 TGCERVVKNAIYKLRGVDSVEVELELEK-------------------VTAVGY---VDRNKVLKAV 101 (179)
Q Consensus 58 ~~C~~kI~~al~~~~GV~~v~vd~~~~~-------------------v~V~g~---~~~~~i~~~i 101 (179)
.+|-.-++..+.+++||.++.+-...+. |.|..+ ++.++|++..
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 6788889999999999999998876654 455544 6777777754
No 21
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=65.74 E-value=23 Score=23.15 Aligned_cols=49 Identities=20% Similarity=0.261 Sum_probs=34.9
Q ss_pred HHcCCCeeEEEEeCCc-cEEEEEecCCHHHHHHHHHhcCcceEEccCCCCC
Q 030348 68 IYKLRGVDSVEVELEL-EKVTAVGYVDRNKVLKAVRRAGKRAEFWPYPNPP 117 (179)
Q Consensus 68 l~~~~GV~~v~vd~~~-~~v~V~g~~~~~~i~~~i~~~G~~a~~~~~~~~~ 117 (179)
|..++||..+..+-.. -++.+....+..+|+..+...|. +.-+....|+
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~f~~~~PS 75 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDEETANELLQELIEKGI-IRSFEEEEPS 75 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHHhCCC-eeEEEEcCCC
Confidence 7788999988765332 34445555788999999999998 7665555543
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=63.15 E-value=31 Score=21.72 Aligned_cols=51 Identities=14% Similarity=0.188 Sum_probs=35.9
Q ss_pred EEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEe--cCCHHHHHHHHHhcCcceEEc
Q 030348 51 LKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVG--YVDRNKVLKAVRRAGKRAEFW 111 (179)
Q Consensus 51 l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g--~~~~~~i~~~i~~~G~~a~~~ 111 (179)
+.+ |+.|+.-.-+++++| ++..- +.+.|.. ....+.|..-+++.|+..+..
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~g---------~~l~v~~d~~~s~~~i~~~~~~~G~~~~~~ 55 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEAG---------GEIEVLVDNEVAKENVSRFAESRGYEVSVE 55 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCCC---------CEEEEEEcChhHHHHHHHHHHHcCCEEEEE
Confidence 456 899999999999999 55322 2333332 245577888889999988544
No 23
>PRK11018 hypothetical protein; Provisional
Probab=62.54 E-value=42 Score=22.14 Aligned_cols=55 Identities=16% Similarity=0.047 Sum_probs=40.3
Q ss_pred EEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEE--ecCCHHHHHHHHHhcCcceEEc
Q 030348 48 TVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAV--GYVDRNKVLKAVRRAGKRAEFW 111 (179)
Q Consensus 48 ~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~--g~~~~~~i~~~i~~~G~~a~~~ 111 (179)
..++.+ |..|+.-.-+.+++|.+++.- +.+.|. .......|..-+++.|+++...
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~~G---------~~L~V~~d~~~a~~di~~~~~~~G~~v~~~ 65 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLKKG---------EILEVVSDCPQSINNIPLDARNHGYTVLDI 65 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCCCC---------CEEEEEeCCccHHHHHHHHHHHcCCEEEEE
Confidence 356889 999999999999999988532 223333 2255677888888999987543
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=56.23 E-value=51 Score=21.06 Aligned_cols=53 Identities=15% Similarity=0.095 Sum_probs=38.5
Q ss_pred EEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEe--cCCHHHHHHHHHhcCcceEEcc
Q 030348 51 LKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVG--YVDRNKVLKAVRRAGKRAEFWP 112 (179)
Q Consensus 51 l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g--~~~~~~i~~~i~~~G~~a~~~~ 112 (179)
+.+ |+.|+.=.-+.+++|.+++.- +.+.|.. ......|..-.+..|++.....
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~G---------~~l~V~~d~~~a~~di~~~~~~~G~~~~~~~ 57 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQDG---------EQLEVKASDPGFARDAQAWCKSTGNTLISLE 57 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCC---------CEEEEEECCccHHHHHHHHHHHcCCEEEEEE
Confidence 557 899999999999999988532 2334332 2566778888899999876443
No 25
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=53.32 E-value=73 Score=25.56 Aligned_cols=44 Identities=23% Similarity=0.271 Sum_probs=33.6
Q ss_pred hhHHHHHHHHHHcCCCeeEEEEeCCcc-------------------EEEEEec---CCHHHHHHHH
Q 030348 58 TGCERVVKNAIYKLRGVDSVEVELELE-------------------KVTAVGY---VDRNKVLKAV 101 (179)
Q Consensus 58 ~~C~~kI~~al~~~~GV~~v~vd~~~~-------------------~v~V~g~---~~~~~i~~~i 101 (179)
.+|-.-+|..+.+++||.++.+-...+ .|.|..+ ++.++|++..
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 678888899999999999999887743 2455544 6777877755
No 26
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=52.88 E-value=42 Score=25.35 Aligned_cols=40 Identities=25% Similarity=0.374 Sum_probs=31.1
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCC-ccEEE
Q 030348 47 QTVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELE-LEKVT 87 (179)
Q Consensus 47 ~~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~-~~~v~ 87 (179)
..+++.| .-.|..|..-|....+++ |+.++.|... ++++.
T Consensus 100 ~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~ 141 (146)
T PF14437_consen 100 RSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVY 141 (146)
T ss_pred CeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEE
Confidence 4677888 788999998888887765 8888888776 56544
No 27
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=49.04 E-value=80 Score=21.57 Aligned_cols=44 Identities=9% Similarity=0.120 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec-CCHHHHHHHHH
Q 030348 59 GCERVVKNAIYKLRGVDSVEVELELEKVTAVGY-VDRNKVLKAVR 102 (179)
Q Consensus 59 ~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~-~~~~~i~~~i~ 102 (179)
.=...+.+.|..++|+.-...|...+|+.|+-. .+...+.+.+.
T Consensus 17 e~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 17 ERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred HHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 336788999999999986666667788776632 34555555443
No 28
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=41.73 E-value=83 Score=24.67 Aligned_cols=44 Identities=23% Similarity=0.191 Sum_probs=32.8
Q ss_pred hhHHHHHHHHHHcCCCeeEEEEeCCccE-------------------EEEEec---CCHHHHHHHH
Q 030348 58 TGCERVVKNAIYKLRGVDSVEVELELEK-------------------VTAVGY---VDRNKVLKAV 101 (179)
Q Consensus 58 ~~C~~kI~~al~~~~GV~~v~vd~~~~~-------------------v~V~g~---~~~~~i~~~i 101 (179)
.+|-.-++..+.+++||.++.+-...+. |.|..+ ++.++|++..
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 5777888889999999999998876654 445443 6777777754
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=41.05 E-value=88 Score=19.42 Aligned_cols=53 Identities=15% Similarity=0.061 Sum_probs=37.8
Q ss_pred EEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec--CCHHHHHHHHHhcCcceEEcc
Q 030348 51 LKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY--VDRNKVLKAVRRAGKRAEFWP 112 (179)
Q Consensus 51 l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~i~~~G~~a~~~~ 112 (179)
+.+ |+.|+.=.-++.++|++++.- +.+.|..+ .....|..-++..|++...+.
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~~g---------~~l~v~~d~~~~~~~i~~~~~~~g~~~~~~~ 57 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLKSG---------EVLEVLLDDPGAVEDIPAWAKETGHEVLEVE 57 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCCCC---------CEEEEEecCCcHHHHHHHHHHHcCCEEEEEE
Confidence 456 899999999999999986532 23333332 457788888999999876543
No 30
>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=40.20 E-value=7.1 Score=25.75 Aligned_cols=14 Identities=29% Similarity=0.684 Sum_probs=11.1
Q ss_pred CCCcccCCCCc--ccc
Q 030348 165 SNMFNDDNVNA--CCL 178 (179)
Q Consensus 165 ~~~FsDeNPna--CsI 178 (179)
.-.|+|+||+| |-|
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 45899999997 754
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=40.15 E-value=98 Score=19.70 Aligned_cols=52 Identities=15% Similarity=0.071 Sum_probs=37.6
Q ss_pred EEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEE--ecCCHHHHHHHHHhcCcceEEc
Q 030348 51 LKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAV--GYVDRNKVLKAVRRAGKRAEFW 111 (179)
Q Consensus 51 l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~--g~~~~~~i~~~i~~~G~~a~~~ 111 (179)
+.+ |..|+.=.-+.+++|++++.- +.+.|. .....+.|..-++..|+++...
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~~G---------~~l~V~~d~~~s~~ni~~~~~~~g~~v~~~ 56 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLKPG---------EILEVISDCPQSINNIPIDARNHGYKVLAI 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCC---------CEEEEEecCchHHHHHHHHHHHcCCEEEEE
Confidence 346 889999999999999988532 223333 2356777888889999988644
No 32
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=39.30 E-value=54 Score=23.54 Aligned_cols=21 Identities=43% Similarity=0.624 Sum_probs=18.0
Q ss_pred HHHHHHHHHcCCCeeEEEEeC
Q 030348 61 ERVVKNAIYKLRGVDSVEVEL 81 (179)
Q Consensus 61 ~~kI~~al~~~~GV~~v~vd~ 81 (179)
...++.+|..++||.+++|++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 678899999999999887753
No 33
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=39.09 E-value=81 Score=23.98 Aligned_cols=44 Identities=20% Similarity=0.146 Sum_probs=32.1
Q ss_pred hhHHHHHHHHHHcCCCeeEEEEeCCccE--------------EEEEec---CCHHHHHHHH
Q 030348 58 TGCERVVKNAIYKLRGVDSVEVELELEK--------------VTAVGY---VDRNKVLKAV 101 (179)
Q Consensus 58 ~~C~~kI~~al~~~~GV~~v~vd~~~~~--------------v~V~g~---~~~~~i~~~i 101 (179)
.+|-.-+|..+.+++||.++.+-...+. |.|..+ ++.++|++..
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 5788888999999999999998775543 334433 5677777654
No 34
>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=37.27 E-value=1.1e+02 Score=19.41 Aligned_cols=53 Identities=9% Similarity=0.095 Sum_probs=38.1
Q ss_pred EEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEE--ecCCHHHHHHHHHhcCcceEEcc
Q 030348 51 LKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAV--GYVDRNKVLKAVRRAGKRAEFWP 112 (179)
Q Consensus 51 l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~--g~~~~~~i~~~i~~~G~~a~~~~ 112 (179)
+.+ |..|+.=.-+++++|.+++-- +.+.|. .....+.|..-+++.|++.....
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~~G---------~~l~V~~dd~~s~~di~~~~~~~g~~~~~~~ 57 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMKPG---------DTLLVLATDPSTTRDIPKFCTFLGHELLAQE 57 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCCCC---------CEEEEEeCCCchHHHHHHHHHHcCCEEEEEE
Confidence 456 889999999999999988421 223333 33567788888999999876543
No 35
>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=37.15 E-value=1.3e+02 Score=20.30 Aligned_cols=52 Identities=19% Similarity=0.255 Sum_probs=32.2
Q ss_pred EEEEEcCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEE--ecCCHHHHHHHHHhc
Q 030348 49 VELKVRMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAV--GYVDRNKVLKAVRRA 104 (179)
Q Consensus 49 v~l~Vgm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~--g~~~~~~i~~~i~~~ 104 (179)
.+++-.-.+.. .-+-+.|-.++||.+|-+. .+=++|+ ..++++.|...|...
T Consensus 26 ~~f~~~~~a~~--spLA~~Lf~i~gV~~Vf~~--~dfItVtK~~~~~W~~l~~~I~~~ 79 (87)
T PF08712_consen 26 FEFKSAEEASD--SPLAQALFAIPGVKSVFIG--DDFITVTKNPDADWEDLKPEIREV 79 (87)
T ss_dssp -EEESSS-TTS---HHHHHHHTSTTEEEEEEE--TTEEEEEE-TTS-HHHHHHHHHHH
T ss_pred EEeCChHHccc--CHHHHHhcCCCCEeEEEEE--CCEEEEeeCCCCCHHHHHHHHHHH
Confidence 44444333333 4555566699999987765 5566665 458999999888654
No 36
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=35.93 E-value=2.4e+02 Score=23.68 Aligned_cols=47 Identities=28% Similarity=0.326 Sum_probs=33.4
Q ss_pred EEEEEEcCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEecCCHHHHHHHHH-hcCcc
Q 030348 48 TVELKVRMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVR-RAGKR 107 (179)
Q Consensus 48 ~v~l~Vgm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~i~-~~G~~ 107 (179)
.+.++.+.+ +.|...+++.+.+++||.++++- +.++-.+.++ ..|+.
T Consensus 62 ~vyL~~~~~-~~~~~~v~~~i~~~~gV~~v~~~------------sre~~l~~L~~~lg~~ 109 (297)
T COG2177 62 TVYLQIDAD-QDDAALVREKIEGIPGVKSVRFI------------SREEALKELQPWLGFG 109 (297)
T ss_pred EEEEecCCC-hHHHHHHHHHHhcCCCcceEEEe------------CHHHHHHHHHHHcCch
Confidence 334444555 89999999999999999988764 4455555554 66765
No 37
>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=35.86 E-value=51 Score=25.53 Aligned_cols=21 Identities=38% Similarity=0.514 Sum_probs=16.8
Q ss_pred HHHHHHHHHcCCCeeEEEEeC
Q 030348 61 ERVVKNAIYKLRGVDSVEVEL 81 (179)
Q Consensus 61 ~~kI~~al~~~~GV~~v~vd~ 81 (179)
...|+.+|..++||.+++|++
T Consensus 133 ~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 133 VEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred HHHHHHHHHhCCCceeEEEEE
Confidence 355888999999999887764
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=35.28 E-value=1.3e+02 Score=19.85 Aligned_cols=43 Identities=14% Similarity=0.145 Sum_probs=28.9
Q ss_pred HHHHHHHHHHcCCCeeEEEEeCCccEEEEEe-cCCHHHHHHHHHh
Q 030348 60 CERVVKNAIYKLRGVDSVEVELELEKVTAVG-YVDRNKVLKAVRR 103 (179)
Q Consensus 60 C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g-~~~~~~i~~~i~~ 103 (179)
=...+.++|.+++|+.-...+.. +|+.|+- ..+...+.+.+..
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~ 59 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDA 59 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHH
Confidence 35678999999999975566655 7776653 2455666665543
No 39
>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=35.06 E-value=1.1e+02 Score=22.98 Aligned_cols=33 Identities=15% Similarity=0.187 Sum_probs=27.2
Q ss_pred ChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEE
Q 030348 57 CTGCERVVKNAIYKLRGVDSVEVELELEKVTAV 89 (179)
Q Consensus 57 C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~ 89 (179)
-..=+.+|.+.+.+++||.++.+-.....+.|-
T Consensus 73 ~~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 73 RQQLADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 345688999999999999999988877777664
No 40
>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=34.92 E-value=62 Score=22.93 Aligned_cols=58 Identities=22% Similarity=0.378 Sum_probs=30.6
Q ss_pred EEE-cC-cChhHH-HHHHHHHHcC--CCeeEEEEeCCccEEEEE--ec-CCHHHHHHHHHhc-CcceEE
Q 030348 51 LKV-RM-CCTGCE-RVVKNAIYKL--RGVDSVEVELELEKVTAV--GY-VDRNKVLKAVRRA-GKRAEF 110 (179)
Q Consensus 51 l~V-gm-~C~~C~-~kI~~al~~~--~GV~~v~vd~~~~~v~V~--g~-~~~~~i~~~i~~~-G~~a~~ 110 (179)
+.+ || +|.+|- .++...++++ .|+..+-+. +=...=. +. -..+++.+.|++. |.++..
T Consensus 38 ~elvgf~~CgGCpg~~~~~~~~~l~~~~~d~IHls--sC~~~~~~~~~CP~~~~~~~~I~~~~gi~VV~ 104 (107)
T PF08821_consen 38 VELVGFFTCGGCPGRKLVRRIKKLKKNGADVIHLS--SCMVKGNPHGPCPHIDEIKKIIEEKFGIEVVE 104 (107)
T ss_pred eEEEEEeeCCCCChhHHHHHHHHHHHCCCCEEEEc--CCEecCCCCCCCCCHHHHHHHHHHHhCCCEee
Confidence 455 75 899873 3333333333 455533322 1111100 11 4688899999876 876644
No 41
>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=33.31 E-value=1.2e+02 Score=18.83 Aligned_cols=33 Identities=15% Similarity=0.273 Sum_probs=23.7
Q ss_pred eEEEEEEcCcChh-HHHHHHHHHHcCCCeeEEEE
Q 030348 47 QTVELKVRMCCTG-CERVVKNAIYKLRGVDSVEV 79 (179)
Q Consensus 47 ~~v~l~Vgm~C~~-C~~kI~~al~~~~GV~~v~v 79 (179)
..+.|.+...-.. --..+-+.|++++||.+|.+
T Consensus 41 ~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 41 ANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 4455656334343 67889999999999998875
No 42
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=32.49 E-value=1.3e+02 Score=19.99 Aligned_cols=35 Identities=23% Similarity=0.235 Sum_probs=27.6
Q ss_pred CCcceEEEEEEcCcChhHHHHHHHHHHcCCCeeEEEE
Q 030348 43 PLSLQTVELKVRMCCTGCERVVKNAIYKLRGVDSVEV 79 (179)
Q Consensus 43 ~~~~~~v~l~Vgm~C~~C~~kI~~al~~~~GV~~v~v 79 (179)
.....++++.++ -+.....|.+.|+++.+|..|++
T Consensus 41 ~~~~sriti~v~--~~~~i~ql~kQL~KL~dV~~V~~ 75 (76)
T PRK11152 41 DAQNINIELTVA--SERPIDLLSSQLNKLVDVAHVEI 75 (76)
T ss_pred CCCEEEEEEEEC--CCchHHHHHHHHhcCcCeEEEEE
Confidence 445566677774 48888999999999999988876
No 43
>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=31.01 E-value=1.9e+02 Score=20.23 Aligned_cols=55 Identities=16% Similarity=0.059 Sum_probs=34.0
Q ss_pred EEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec--CCHHHHHHHHHhc
Q 030348 50 ELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY--VDRNKVLKAVRRA 104 (179)
Q Consensus 50 ~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~i~~~ 104 (179)
.+++ |+.-+.+...|+..++....|.-|++........|... .....+++.+...
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 4566 66666668999999999999999888888888888754 4577788877765
No 44
>PRK09577 multidrug efflux protein; Reviewed
Probab=30.51 E-value=1.4e+02 Score=29.46 Aligned_cols=46 Identities=17% Similarity=0.088 Sum_probs=35.4
Q ss_pred HHHHHHHHHcCCCeeEEEEeCCccEEEEE--------ecCCHHHHHHHHHhcCc
Q 030348 61 ERVVKNAIYKLRGVDSVEVELELEKVTAV--------GYVDRNKVLKAVRRAGK 106 (179)
Q Consensus 61 ~~kI~~al~~~~GV~~v~vd~~~~~v~V~--------g~~~~~~i~~~i~~~G~ 106 (179)
+..++..|++++||.+|+++.....+.|. ..++..+|.++|+..+.
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 46789999999999999998765556654 12788889999976543
No 45
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=29.57 E-value=1.5e+02 Score=29.38 Aligned_cols=44 Identities=9% Similarity=0.142 Sum_probs=34.2
Q ss_pred HHHHHHHHHcCCCeeEEEEeCCccEEEEEe--------cCCHHHHHHHHHhc
Q 030348 61 ERVVKNAIYKLRGVDSVEVELELEKVTAVG--------YVDRNKVLKAVRRA 104 (179)
Q Consensus 61 ~~kI~~al~~~~GV~~v~vd~~~~~v~V~g--------~~~~~~i~~~i~~~ 104 (179)
+..++..|++++||.+|++......+.|.- .++..+|.++|+..
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 467889999999999999987655566652 27888898998743
No 46
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=29.28 E-value=1.6e+02 Score=18.88 Aligned_cols=56 Identities=9% Similarity=-0.009 Sum_probs=35.3
Q ss_pred EEEEEE-cCcChhHHHHHHHHHHcCCC-eeEEEEeCCccEEEE----Eec-CCHHHHHHHHHh
Q 030348 48 TVELKV-RMCCTGCERVVKNAIYKLRG-VDSVEVELELEKVTA----VGY-VDRNKVLKAVRR 103 (179)
Q Consensus 48 ~v~l~V-gm~C~~C~~kI~~al~~~~G-V~~v~vd~~~~~v~V----~g~-~~~~~i~~~i~~ 103 (179)
.+.+.+ |.+.++-...|.+.|.+..+ +.+++.....+..+. ... .+.+++.+++++
T Consensus 2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~~~~~~~l~~~L~~ 64 (76)
T PF13740_consen 2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIPEDSLERLESALEE 64 (76)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEESHHHHHHHHHHHHH
T ss_pred EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeCcccHHHHHHHHHH
Confidence 567889 99999999999999999865 445555555555442 222 345556666644
No 47
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=28.70 E-value=1e+02 Score=20.41 Aligned_cols=49 Identities=18% Similarity=0.277 Sum_probs=34.8
Q ss_pred EEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec--CCHHHHHHHHHhcC
Q 030348 48 TVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY--VDRNKVLKAVRRAG 105 (179)
Q Consensus 48 ~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~--~~~~~i~~~i~~~G 105 (179)
..++.+ |+.|+.=.-.++++|++++-- +.+.|..+ .....|..-+++.|
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~G---------e~LeV~~ddp~~~~dIp~~~~~~~ 56 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLKPG---------EILEVIADDPAAKEDIPAWAKKEG 56 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCCCC---------CEEEEEecCcchHHHHHHHHHHcC
Confidence 457899 999999999999999998532 33444432 45566777777455
No 48
>KOG4730 consensus D-arabinono-1, 4-lactone oxidase [Defense mechanisms]
Probab=28.57 E-value=72 Score=28.74 Aligned_cols=52 Identities=23% Similarity=0.342 Sum_probs=37.4
Q ss_pred cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEecCCHHHHHHHHHhcCcceEE
Q 030348 54 RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRAEF 110 (179)
Q Consensus 54 gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~i~~~G~~a~~ 110 (179)
+|.|..- .--.+..++-| +++|.+..+|||+.-+...+|++.+++.|+....
T Consensus 87 ~l~ctdg---~lisl~~lnkV--v~~dpe~~tvTV~aGirlrQLie~~~~~GlsL~~ 138 (518)
T KOG4730|consen 87 KLVCTDG---LLISLDKLNKV--VEFDPELKTVTVQAGIRLRQLIEELAKLGLSLPN 138 (518)
T ss_pred cceeccc---cEEEhhhhccc--eeeCchhceEEeccCcCHHHHHHHHHhcCccccC
Confidence 4556544 22234445555 5668888999999889999999999999987543
No 49
>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=28.46 E-value=2e+02 Score=21.72 Aligned_cols=27 Identities=33% Similarity=0.324 Sum_probs=23.0
Q ss_pred hhHHHHHHHHHHcCCCeeEEEEeCCcc
Q 030348 58 TGCERVVKNAIYKLRGVDSVEVELELE 84 (179)
Q Consensus 58 ~~C~~kI~~al~~~~GV~~v~vd~~~~ 84 (179)
.||-.-++..+.+++||.++.+-...+
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 578888999999999999999877554
No 50
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=28.28 E-value=1.8e+02 Score=19.18 Aligned_cols=55 Identities=9% Similarity=0.078 Sum_probs=39.3
Q ss_pred EEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEE--ecCCHHHHHHHHHhcCcceEEc
Q 030348 48 TVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAV--GYVDRNKVLKAVRRAGKRAEFW 111 (179)
Q Consensus 48 ~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~--g~~~~~~i~~~i~~~G~~a~~~ 111 (179)
..++.+ |+.|+.=.-+++++|++++.- +.+.|. .....+.|..-.+..|++....
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~~G---------~~l~V~~dd~~~~~di~~~~~~~G~~~~~~ 66 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQPG---------ETLLIIADDPATTRDIPSFCRFMDHELLAQ 66 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCCCC---------CEEEEEeCCccHHHHHHHHHHHcCCEEEEE
Confidence 356888 999999999999999988522 223333 2245667777778999887543
No 51
>PHA01634 hypothetical protein
Probab=27.79 E-value=21 Score=26.77 Aligned_cols=17 Identities=29% Similarity=0.741 Sum_probs=13.5
Q ss_pred EEE-cCcChhHHHHHHHH
Q 030348 51 LKV-RMCCTGCERVVKNA 67 (179)
Q Consensus 51 l~V-gm~C~~C~~kI~~a 67 (179)
+.| -|+|++|++++.-.
T Consensus 93 ~Di~~iDCeGCE~~l~v~ 110 (156)
T PHA01634 93 VDIFVMDCEGCEEKLNVS 110 (156)
T ss_pred cceEEEEccchHHhcCHH
Confidence 567 78999999988543
No 52
>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=27.75 E-value=77 Score=21.55 Aligned_cols=35 Identities=31% Similarity=0.452 Sum_probs=22.9
Q ss_pred EEEEEE-cCcChhH---HHHHHHHHHcCCCeeEEEEeCC
Q 030348 48 TVELKV-RMCCTGC---ERVVKNAIYKLRGVDSVEVELE 82 (179)
Q Consensus 48 ~v~l~V-gm~C~~C---~~kI~~al~~~~GV~~v~vd~~ 82 (179)
.+.+.+ .-.|... ...++.+|..++|+.++++++.
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 344555 3444433 3457888888999998888754
No 53
>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=27.39 E-value=1.8e+02 Score=22.85 Aligned_cols=49 Identities=18% Similarity=0.187 Sum_probs=36.0
Q ss_pred cCcChhHHHHHHHHHHcCCCeeEEEEeCCccEEEEE--ecCCHHHHHHHHHhcCcceEEc
Q 030348 54 RMCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAV--GYVDRNKVLKAVRRAGKRAEFW 111 (179)
Q Consensus 54 gm~C~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~--g~~~~~~i~~~i~~~G~~a~~~ 111 (179)
|+.|+.-.-+.+++|.+++.- +.++|. .....+.|.+-++..|+++...
T Consensus 5 Gl~CP~Pvi~tKkal~~l~~g---------~~L~VlvD~~~a~~nV~~~~~~~G~~v~~~ 55 (194)
T TIGR03527 5 GLACPQPVILTKKALDELGEE---------GVLTVIVDNEAAKENVSKFATSLGYEVEVE 55 (194)
T ss_pred CCCCCHHHHHHHHHHHcCCCC---------CEEEEEECCccHHHHHHHHHHHcCCEEEEE
Confidence 889999999999999988521 123332 3356677888888999988654
No 54
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=27.37 E-value=2.6e+02 Score=21.05 Aligned_cols=58 Identities=9% Similarity=0.118 Sum_probs=39.4
Q ss_pred hhHHHHHHHHHHcCCCeeEEEEeCCccEEEEEec-------CCHHHHHHHHHhcCcceEEccCCC
Q 030348 58 TGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY-------VDRNKVLKAVRRAGKRAEFWPYPN 115 (179)
Q Consensus 58 ~~C~~kI~~al~~~~GV~~v~vd~~~~~v~V~g~-------~~~~~i~~~i~~~G~~a~~~~~~~ 115 (179)
+.-...|++.+-.-.|+.++.+|..++.|.|... -....+.+...++|+...+...++
T Consensus 52 e~A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 52 EEAIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred HHHHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 4445566666655569999999999999998732 122333445568999888775554
No 55
>PRK07334 threonine dehydratase; Provisional
Probab=26.23 E-value=3e+02 Score=23.81 Aligned_cols=64 Identities=19% Similarity=0.067 Sum_probs=42.8
Q ss_pred EEEEEE-cCcChhHHHHHHHHHHcCC-CeeEEEEeCC-----ccEEEEE--e----cCCHHHHHHHHHhcCcceEEc
Q 030348 48 TVELKV-RMCCTGCERVVKNAIYKLR-GVDSVEVELE-----LEKVTAV--G----YVDRNKVLKAVRRAGKRAEFW 111 (179)
Q Consensus 48 ~v~l~V-gm~C~~C~~kI~~al~~~~-GV~~v~vd~~-----~~~v~V~--g----~~~~~~i~~~i~~~G~~a~~~ 111 (179)
.+.|.| ..+-.+=-..|-+.|+..+ .|.+++.... .+...+. - ....+.|++.|++.|+.++++
T Consensus 326 ~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~~~L~~vi~~Lr~~g~~~~~~ 402 (403)
T PRK07334 326 LARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDAAHLQEVIAALRAAGFEARLV 402 (403)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCHHHHHHHHHHHHHcCCeeEeC
Confidence 467788 6777777888888887663 3455554422 3443332 1 135668999999999999875
No 56
>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=25.64 E-value=42 Score=20.65 Aligned_cols=29 Identities=28% Similarity=0.232 Sum_probs=12.8
Q ss_pred HHHHHHHcC---CCeeEEEEeCCccEEEEEecC
Q 030348 63 VVKNAIYKL---RGVDSVEVELELEKVTAVGYV 92 (179)
Q Consensus 63 kI~~al~~~---~GV~~v~vd~~~~~v~V~g~~ 92 (179)
+|+.+|... ++. .+.+....+.+++.|.+
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v 34 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSVENGVVTLSGEV 34 (64)
T ss_dssp ----------CTT-T-TEEEEEECTEEEEEEEE
T ss_pred ccccccccccccCCC-eEEEEEECCEEEEEeeC
Confidence 455555553 333 46666678888888764
No 57
>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=25.00 E-value=1.3e+02 Score=20.58 Aligned_cols=22 Identities=32% Similarity=0.554 Sum_probs=19.2
Q ss_pred hHHHHHHHHHHcCCCeeEEEEe
Q 030348 59 GCERVVKNAIYKLRGVDSVEVE 80 (179)
Q Consensus 59 ~C~~kI~~al~~~~GV~~v~vd 80 (179)
+-...++.++++++||+++++-
T Consensus 62 g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 62 GGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred cChHHHHHHHhcCCCccEEEEE
Confidence 5568999999999999999875
No 58
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=24.24 E-value=1.4e+02 Score=20.61 Aligned_cols=35 Identities=34% Similarity=0.452 Sum_probs=25.4
Q ss_pred ceEEEEEE-cCcChhHHHHHHHHHHcCCCeeEEEEe
Q 030348 46 LQTVELKV-RMCCTGCERVVKNAIYKLRGVDSVEVE 80 (179)
Q Consensus 46 ~~~v~l~V-gm~C~~C~~kI~~al~~~~GV~~v~vd 80 (179)
+..+.+.+ --+-++-...++++|+.++||.++++-
T Consensus 48 Lkal~l~vvv~D~Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 48 LKALKLYVVVEDKEGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred eeeEEEEEEEcccccCcHHHHHHHhhccCcceEEEE
Confidence 34445555 334456678999999999999998874
No 59
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=23.99 E-value=2.1e+02 Score=28.39 Aligned_cols=44 Identities=16% Similarity=0.145 Sum_probs=34.0
Q ss_pred HHHHHHHHHcCCCeeEEEEeCCccEEEEEe--------cCCHHHHHHHHHhc
Q 030348 61 ERVVKNAIYKLRGVDSVEVELELEKVTAVG--------YVDRNKVLKAVRRA 104 (179)
Q Consensus 61 ~~kI~~al~~~~GV~~v~vd~~~~~v~V~g--------~~~~~~i~~~i~~~ 104 (179)
++.++..|++++||.++++......+.|.- .++..+|.++|+..
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 356889999999999999987655566652 27888888888744
No 60
>TIGR01676 GLDHase galactonolactone dehydrogenase. This model represents L-Galactono-gamma-lactone dehydrogenase (EC 1.3.2.3). This enzyme catalyzes the final step in ascorbic acid biosynthesis in higher plants. This protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD.
Probab=23.50 E-value=1.3e+02 Score=27.55 Aligned_cols=39 Identities=18% Similarity=0.278 Sum_probs=30.8
Q ss_pred HHcCCCeeEEEEeCCccEEEEEecCCHHHHHHHHHhcCcce
Q 030348 68 IYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRA 108 (179)
Q Consensus 68 l~~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~i~~~G~~a 108 (179)
|.++++| +++|..+++|+|.+-+...+|.+.+...|+..
T Consensus 110 L~~ln~V--l~vD~~~~tVtV~AG~~l~~L~~~L~~~Glal 148 (541)
T TIGR01676 110 LALMDKV--LEVDEEKKRVRVQAGIRVQQLVDAIKEYGITL 148 (541)
T ss_pred hhhCCCC--EEEcCCCCEEEEcCCCCHHHHHHHHHHcCCEe
Confidence 3445555 46788889999998889999999999999654
No 61
>PLN00204 CP12 gene family protein; Provisional
Probab=22.96 E-value=24 Score=25.84 Aligned_cols=14 Identities=21% Similarity=0.401 Sum_probs=10.7
Q ss_pred CCCcccCCCCc--ccc
Q 030348 165 SNMFNDDNVNA--CCL 178 (179)
Q Consensus 165 ~~~FsDeNPna--CsI 178 (179)
--.|+||||.| |-|
T Consensus 108 lE~YCdeNPeA~ECRv 123 (126)
T PLN00204 108 LEEYCKDNPETDECRT 123 (126)
T ss_pred HHHHHHHCCCchhhhc
Confidence 45899999997 643
No 62
>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=22.18 E-value=2.3e+02 Score=28.03 Aligned_cols=43 Identities=16% Similarity=0.154 Sum_probs=34.1
Q ss_pred HHHHHHHHHcCCCeeEEEEeCCccEEEEEe--------cCCHHHHHHHHHh
Q 030348 61 ERVVKNAIYKLRGVDSVEVELELEKVTAVG--------YVDRNKVLKAVRR 103 (179)
Q Consensus 61 ~~kI~~al~~~~GV~~v~vd~~~~~v~V~g--------~~~~~~i~~~i~~ 103 (179)
...++..|++++||.+|++......+.|.- .++..+|.++|+.
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~~ 209 (1044)
T TIGR00915 159 ASNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQA 209 (1044)
T ss_pred HHHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHHH
Confidence 356889999999999999988855566652 2788889999976
No 63
>TIGR03027 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by Pfam model pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system.
Probab=22.12 E-value=2.4e+02 Score=21.13 Aligned_cols=57 Identities=23% Similarity=0.191 Sum_probs=38.6
Q ss_pred EEEE-cCcChhHHHHHHHHHHcC-C-CeeEEEEeC----CccEEEEEec---------CCHHHHHHHHHhcCc
Q 030348 50 ELKV-RMCCTGCERVVKNAIYKL-R-GVDSVEVEL----ELEKVTAVGY---------VDRNKVLKAVRRAGK 106 (179)
Q Consensus 50 ~l~V-gm~C~~C~~kI~~al~~~-~-GV~~v~vd~----~~~~v~V~g~---------~~~~~i~~~i~~~G~ 106 (179)
.+++ |++-+.=+..|++.|++. . -...+.+.. ...++.|.|. .....+.++|..+|.
T Consensus 38 ~v~v~G~T~~e~~~~I~~~l~~~~~~p~v~V~v~~~~~~~~~~V~V~GeV~~PG~y~~~~~~tl~~ai~~AGG 110 (165)
T TIGR03027 38 DLVASGKTPTQLARDIEEKLAKYVRNPVVTVIVTGFIGPFSEQIRVVGAAANPQALPYREGMTLLDVMIAVGG 110 (165)
T ss_pred eEEECCCCHHHHHHHHHHHHHHhccCCeEEEEEeecccCCCcEEEEEEEeCCCceeeeCCCCcHHHHHHHcCC
Confidence 5889 999999999999999874 1 222333332 2467888754 234568888887763
No 64
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=21.94 E-value=2.2e+02 Score=18.06 Aligned_cols=33 Identities=21% Similarity=0.185 Sum_probs=23.3
Q ss_pred ceEEEEEEcCcChhHHHHHHHHHHcCCCeeEEE
Q 030348 46 LQTVELKVRMCCTGCERVVKNAIYKLRGVDSVE 78 (179)
Q Consensus 46 ~~~v~l~Vgm~C~~C~~kI~~al~~~~GV~~v~ 78 (179)
...+.|.+...-..=-..+-+.|++++||.+|+
T Consensus 47 ~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 47 TARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 345555555555566678888899999998774
No 65
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=21.64 E-value=89 Score=23.23 Aligned_cols=43 Identities=26% Similarity=0.313 Sum_probs=27.7
Q ss_pred hhHHHHHHHHHHcCCCeeEEEEeCCcc-EEEEEecCCHHHHHHHHHh
Q 030348 58 TGCERVVKNAIYKLRGVDSVEVELELE-KVTAVGYVDRNKVLKAVRR 103 (179)
Q Consensus 58 ~~C~~kI~~al~~~~GV~~v~vd~~~~-~v~V~g~~~~~~i~~~i~~ 103 (179)
++|.+++-++|+++ .-|+.+...+ +++-.|.-+.++|...|..
T Consensus 97 ~~i~rkvlQ~Le~~---~~ve~hp~gGR~lt~~GqrdldrIa~~i~~ 140 (143)
T KOG3411|consen 97 GGIARKVLQALEKM---GIVEKHPKGGRRLTEQGQRDLDRIAGQIRE 140 (143)
T ss_pred cHHHHHHHHHHHhC---CceeeCCCCcceeCcccchhHHHHHHHHHh
Confidence 45666665555554 4456666543 5556687888888888764
No 66
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.91 E-value=1.4e+02 Score=20.74 Aligned_cols=22 Identities=18% Similarity=0.243 Sum_probs=19.0
Q ss_pred HcCCCeeEEEEeCCccEEEEEe
Q 030348 69 YKLRGVDSVEVELELEKVTAVG 90 (179)
Q Consensus 69 ~~~~GV~~v~vd~~~~~v~V~g 90 (179)
...+|++.+++..+++++.|.+
T Consensus 37 as~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 37 ASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EecCCceEEEEecccceEEEec
Confidence 3568899999999999999985
No 67
>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=20.62 E-value=3.2e+02 Score=19.36 Aligned_cols=40 Identities=15% Similarity=0.355 Sum_probs=30.5
Q ss_pred cCCCeeEEEEeCCccEEEEEecCCHHHHHHHHHhcCcceEE
Q 030348 70 KLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRAEF 110 (179)
Q Consensus 70 ~~~GV~~v~vd~~~~~v~V~g~~~~~~i~~~i~~~G~~a~~ 110 (179)
+..|+...++. ..+...|.|.--.+++++.+++.|..+..
T Consensus 39 Rt~GirqfEi~-n~G~~RI~gYk~se~~~~~f~slG~~~K~ 78 (103)
T PF09158_consen 39 RTKGIRQFEIR-NKGEFRIFGYKMSEEIIKKFTSLGMEVKQ 78 (103)
T ss_dssp EETTEEEEEEE-TTSEEEEEEES--HHHHHHHHHTT-EEEE
T ss_pred ccCceeEEEEe-cCCcEEEEEEcCCHHHHHHHHhcCcEEEE
Confidence 45788888885 67788888887888999999999988766
No 68
>PRK11023 outer membrane lipoprotein; Provisional
Probab=20.24 E-value=2.3e+02 Score=21.98 Aligned_cols=45 Identities=20% Similarity=0.094 Sum_probs=32.4
Q ss_pred cChhHHHHHHHHHHcCCCee---EEEEeCCccEEEEEecCCHHHHHHH
Q 030348 56 CCTGCERVVKNAIYKLRGVD---SVEVELELEKVTAVGYVDRNKVLKA 100 (179)
Q Consensus 56 ~C~~C~~kI~~al~~~~GV~---~v~vd~~~~~v~V~g~~~~~~i~~~ 100 (179)
+-..=..+|+.+|..-+++. .+++.-..+.|++.|.++.+.....
T Consensus 46 dD~~i~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~V~~~~~k~~ 93 (191)
T PRK11023 46 DDGTLELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQSPNAELSER 93 (191)
T ss_pred hhHHHHHHHHHHHhhCcccCcCceEEEEEECCEEEEEEEeCCHHHHHH
Confidence 34556789999998776663 5777778999999998655443333
No 69
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=20.14 E-value=2e+02 Score=24.14 Aligned_cols=27 Identities=37% Similarity=0.279 Sum_probs=22.9
Q ss_pred hhHHHHHHHHHHcCCCeeEEEEeCCcc
Q 030348 58 TGCERVVKNAIYKLRGVDSVEVELELE 84 (179)
Q Consensus 58 ~~C~~kI~~al~~~~GV~~v~vd~~~~ 84 (179)
.+|-.-++..+.+++||.++.+-...+
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG 160 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGG 160 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCC
Confidence 678888899999999999999877654
Done!