Query 032648
Match_columns 136
No_of_seqs 240 out of 1392
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 04:09:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032648.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032648hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.4 7.8E-13 1.7E-17 81.3 8.5 57 71-127 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.3 1.1E-11 2.3E-16 78.9 8.8 63 68-130 2-69 (71)
3 KOG1603 Copper chaperone [Inor 99.0 3.7E-09 8.1E-14 67.4 8.5 67 67-133 4-72 (73)
4 KOG4656 Copper chaperone for s 98.7 1.1E-07 2.5E-12 71.5 7.6 65 67-131 6-71 (247)
5 PLN02957 copper, zinc superoxi 98.4 4.1E-06 8.9E-11 64.6 9.8 66 67-132 5-71 (238)
6 COG2217 ZntA Cation transport 98.3 1.8E-06 4E-11 75.7 7.9 61 68-129 2-68 (713)
7 PRK11033 zntA zinc/cadmium/mer 98.3 5.8E-06 1.3E-10 72.9 10.6 64 67-130 52-118 (741)
8 PRK10671 copA copper exporting 98.3 2.8E-06 6.2E-11 75.6 8.1 62 68-131 3-66 (834)
9 KOG0207 Cation transport ATPas 98.2 5.2E-06 1.1E-10 73.7 8.5 87 45-131 114-214 (951)
10 KOG0207 Cation transport ATPas 97.9 6.1E-05 1.3E-09 67.1 8.4 87 47-133 40-139 (951)
11 TIGR00003 copper ion binding p 97.9 0.00027 5.9E-09 40.4 8.6 57 69-125 3-63 (68)
12 PRK10671 copA copper exporting 97.7 0.00032 7E-09 62.6 9.8 62 69-130 100-163 (834)
13 TIGR02052 MerP mercuric transp 92.7 1.5 3.2E-05 27.0 9.3 63 68-130 23-90 (92)
14 PRK13748 putative mercuric red 90.0 2.5 5.3E-05 36.0 8.7 61 71-131 3-67 (561)
15 PRK14054 methionine sulfoxide 82.0 3.3 7.2E-05 30.5 4.7 46 79-124 10-77 (172)
16 cd00371 HMA Heavy-metal-associ 79.7 5.9 0.00013 19.6 7.4 39 73-111 3-42 (63)
17 PF01206 TusA: Sulfurtransfera 77.8 11 0.00024 22.8 5.5 48 71-127 2-53 (70)
18 PRK05528 methionine sulfoxide 74.7 8.7 0.00019 27.9 5.0 46 79-124 8-70 (156)
19 PRK13014 methionine sulfoxide 74.1 10 0.00023 28.3 5.4 46 79-124 15-82 (186)
20 PRK00058 methionine sulfoxide 72.8 7.9 0.00017 29.6 4.5 46 79-124 52-119 (213)
21 PF01883 DUF59: Domain of unkn 72.5 8.4 0.00018 23.5 4.0 33 68-100 34-72 (72)
22 PRK10553 assembly protein for 67.5 31 0.00067 22.5 5.9 46 79-124 16-62 (87)
23 PF09580 Spore_YhcN_YlaJ: Spor 65.9 15 0.00034 26.4 4.8 47 79-125 74-125 (177)
24 PF01625 PMSR: Peptide methion 62.3 27 0.00058 25.2 5.4 46 79-124 7-74 (155)
25 TIGR02898 spore_YhcN_YlaJ spor 61.6 23 0.0005 25.7 4.9 33 80-112 54-86 (158)
26 PF03927 NapD: NapD protein; 55.6 51 0.0011 20.9 6.3 44 81-125 16-60 (79)
27 PRK05550 bifunctional methioni 54.8 26 0.00055 28.0 4.5 45 79-123 134-200 (283)
28 PF02680 DUF211: Uncharacteriz 48.9 62 0.0013 21.6 4.9 57 68-125 5-70 (95)
29 COG3062 NapD Uncharacterized p 43.8 91 0.002 20.8 5.1 46 79-125 17-63 (94)
30 COG0225 MsrA Peptide methionin 41.7 59 0.0013 24.1 4.4 28 79-106 13-40 (174)
31 COG1888 Uncharacterized protei 40.8 1.1E+02 0.0024 20.4 5.1 57 68-125 6-72 (97)
32 PRK11018 hypothetical protein; 38.2 1E+02 0.0022 19.3 5.5 51 69-128 8-62 (78)
33 TIGR03406 FeS_long_SufT probab 37.8 46 0.00099 24.5 3.3 34 69-102 114-153 (174)
34 PRK10555 aminoglycoside/multid 35.9 1.1E+02 0.0024 28.7 6.1 44 82-125 159-210 (1037)
35 TIGR00401 msrA methionine-S-su 35.1 30 0.00065 24.9 1.9 27 79-105 7-33 (149)
36 PF04468 PSP1: PSP1 C-terminal 33.6 1.3E+02 0.0029 19.3 5.0 52 79-131 29-84 (88)
37 cd03421 SirA_like_N SirA_like_ 32.0 1.1E+02 0.0025 18.1 4.8 48 72-129 2-53 (67)
38 PRK09577 multidrug efflux prot 31.9 1.4E+02 0.003 28.0 6.1 44 82-125 158-209 (1032)
39 PRK14018 trifunctional thiored 31.6 88 0.0019 27.1 4.5 45 79-123 205-270 (521)
40 TIGR02945 SUF_assoc FeS assemb 30.4 47 0.001 21.5 2.2 35 69-103 40-78 (99)
41 TIGR00915 2A0602 The (Largely 28.9 1.7E+02 0.0036 27.5 6.1 44 82-125 159-210 (1044)
42 TIGR00489 aEF-1_beta translati 27.8 63 0.0014 21.1 2.4 22 80-101 62-83 (88)
43 COG2151 PaaD Predicted metal-s 27.5 1.1E+02 0.0024 20.9 3.6 21 82-102 69-89 (111)
44 PRK10509 bacterioferritin-asso 26.4 27 0.00058 21.3 0.4 21 72-92 33-53 (64)
45 PRK15127 multidrug efflux syst 26.3 2E+02 0.0043 27.0 6.1 43 83-125 160-210 (1049)
46 TIGR02159 PA_CoA_Oxy4 phenylac 26.0 70 0.0015 22.8 2.5 19 83-102 46-64 (146)
47 COG0435 ECM4 Predicted glutath 24.0 1.8E+02 0.0038 23.6 4.6 42 60-101 42-84 (324)
48 PF01514 YscJ_FliF: Secretory 22.4 89 0.0019 23.4 2.6 22 81-102 116-137 (206)
49 cd04888 ACT_PheB-BS C-terminal 21.9 1.8E+02 0.004 17.0 4.8 31 70-100 43-74 (76)
50 COG0425 SirA Predicted redox p 20.9 1.8E+02 0.004 18.3 3.5 47 69-124 5-54 (78)
51 PRK10614 multidrug efflux syst 20.9 2.8E+02 0.0062 25.9 6.0 44 82-125 159-211 (1025)
52 PRK00435 ef1B elongation facto 20.2 1.1E+02 0.0023 20.1 2.3 23 79-101 61-83 (88)
53 cd08623 PI-PLCc_beta1 Catalyti 20.2 1.5E+02 0.0033 23.4 3.6 47 48-94 71-119 (258)
54 COG4669 EscJ Type III secretor 20.2 1E+02 0.0023 24.1 2.6 23 80-102 109-131 (246)
No 1
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.45 E-value=7.8e-13 Score=81.33 Aligned_cols=57 Identities=46% Similarity=0.686 Sum_probs=52.8
Q ss_pred EEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec---CCHHHHHHHHHhc-cC
Q 032648 71 VLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD---IIPFEVLESVSKV-KN 127 (136)
Q Consensus 71 ~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~---~~~~~I~~~I~~~-~~ 127 (136)
+|+| ||+|++|+++|+++|.+++||.++.+|+.+++++|.++ +++++|.++|+++ |+
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 99999999999999999999999999999999999997 4669999999988 63
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.34 E-value=1.1e-11 Score=78.86 Aligned_cols=63 Identities=29% Similarity=0.454 Sum_probs=57.0
Q ss_pred eEEEEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec---CCHHHHHHHHHhc-cCcee
Q 032648 68 KMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD---IIPFEVLESVSKV-KNAEL 130 (136)
Q Consensus 68 ~~~~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~---~~~~~I~~~I~~~-~~a~~ 130 (136)
.+..|.| ||+|.+|+..|+++|.+++||.++++++..+.+.|.++ ++.++|+++|+++ |.+..
T Consensus 2 ~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~ 69 (71)
T COG2608 2 MKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEE 69 (71)
T ss_pred ceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeee
Confidence 3578999 99999999999999999999999999999988888775 6899999999999 87754
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.00 E-value=3.7e-09 Score=67.41 Aligned_cols=67 Identities=46% Similarity=0.837 Sum_probs=59.1
Q ss_pred ceEEEEEEcCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHhc--cCceecCC
Q 032648 67 PKMVVLRVSMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDIIPFEVLESVSKV--KNAELWSA 133 (136)
Q Consensus 67 ~~~~~l~Vgm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~~~~~~I~~~I~~~--~~a~~~~~ 133 (136)
.+...+.++|+|.+|..+|++.+..++||.++.++...++++|.+..++..+++.+.+. ..+.+|..
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 34567788999999999999999999999999999999999999999999999999887 45555544
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.66 E-value=1.1e-07 Score=71.46 Aligned_cols=65 Identities=25% Similarity=0.448 Sum_probs=59.9
Q ss_pred ceEEEEEEcCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHhc-cCceec
Q 032648 67 PKMVVLRVSMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDIIPFEVLESVSKV-KNAELW 131 (136)
Q Consensus 67 ~~~~~l~Vgm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~~~~~~I~~~I~~~-~~a~~~ 131 (136)
.-+.+|.|.|+|.+|++.|++.|..++||.++.|++..+.+.|.....+.+|++.|+.. .+|.+.
T Consensus 6 ~~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~ 71 (247)
T KOG4656|consen 6 TYEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLR 71 (247)
T ss_pred ceeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEe
Confidence 34678999999999999999999999999999999999999999988999999999998 888764
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.37 E-value=4.1e-06 Score=64.59 Aligned_cols=66 Identities=27% Similarity=0.507 Sum_probs=59.3
Q ss_pred ceEEEEEEcCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHhc-cCceecC
Q 032648 67 PKMVVLRVSMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDIIPFEVLESVSKV-KNAELWS 132 (136)
Q Consensus 67 ~~~~~l~Vgm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~~~~~~I~~~I~~~-~~a~~~~ 132 (136)
.+++.+.++|.|.+|+.+|++.|.+++||..+.+++..+++.|.+......+.+.+++. |.++++.
T Consensus 5 ~~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~ 71 (238)
T PLN02957 5 ELLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIG 71 (238)
T ss_pred cEEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEec
Confidence 45677888999999999999999999999999999999999998877888999999999 9887763
No 6
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.33 E-value=1.8e-06 Score=75.65 Aligned_cols=61 Identities=33% Similarity=0.587 Sum_probs=54.6
Q ss_pred eEEEEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec---CC-HHHHHHHHHhc-cCce
Q 032648 68 KMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD---II-PFEVLESVSKV-KNAE 129 (136)
Q Consensus 68 ~~~~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~---~~-~~~I~~~I~~~-~~a~ 129 (136)
.+..|.| ||+|++|+.+|| +|++++||..+.||+.++++.|.++ .+ .+++...+++. |.+.
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 3567999 999999999999 9999999999999999999999986 34 68899999998 8664
No 7
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=98.31 E-value=5.8e-06 Score=72.93 Aligned_cols=64 Identities=34% Similarity=0.424 Sum_probs=52.7
Q ss_pred ceEEEEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEecC-CHHHHHHHHHhc-cCcee
Q 032648 67 PKMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDI-IPFEVLESVSKV-KNAEL 130 (136)
Q Consensus 67 ~~~~~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~~-~~~~I~~~I~~~-~~a~~ 130 (136)
..+..+.+ ||+|++|+.++++.+.+++||..+.+++.++++.+.++. ..+.+.+.+++. |.+..
T Consensus 52 ~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~~ 118 (741)
T PRK11033 52 GTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLRD 118 (741)
T ss_pred CceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhccccccc
Confidence 44677899 999999999999999999999999999999998887652 225666777777 76544
No 8
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.28 E-value=2.8e-06 Score=75.61 Aligned_cols=62 Identities=16% Similarity=0.366 Sum_probs=54.6
Q ss_pred eEEEEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHhc-cCceec
Q 032648 68 KMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDIIPFEVLESVSKV-KNAELW 131 (136)
Q Consensus 68 ~~~~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~~~~~~I~~~I~~~-~~a~~~ 131 (136)
++.++.| ||+|++|+.+|++++.+++||.++++++. +..|.+..+++.+.+++++. |.+...
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~ 66 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVS 66 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCccccc
Confidence 4688999 99999999999999999999999999994 45566667899999999999 988753
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.24 E-value=5.2e-06 Score=73.66 Aligned_cols=87 Identities=23% Similarity=0.462 Sum_probs=75.4
Q ss_pred CCCcccHHHHHhhhhhcccccC--------c-eEEEEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec--
Q 032648 45 GGQLLRLKDVVSGNQTLAFQLK--------P-KMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD-- 112 (136)
Q Consensus 45 ~~~~~~~~~i~~~~~~~g~~~~--------~-~~~~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~-- 112 (136)
++..++...+.+.++..||... . .+..|.| ||.|.+|+.+|++.+.+++||.++.+++.++++.|.++
T Consensus 114 dp~v~s~~~~~e~ie~~gf~a~~i~~~~~~~~~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~ 193 (951)
T KOG0207|consen 114 DPAVTSPDSIAESIEDLGFSAELIESVNGNSNQKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPE 193 (951)
T ss_pred CCcccCchhHHHHHHhcCccceehhcccCCCCCcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEeccc
Confidence 4456778888888888888643 1 5788999 99999999999999999999999999999999999987
Q ss_pred -CCHHHHHHHHHhc-cCceec
Q 032648 113 -IIPFEVLESVSKV-KNAELW 131 (136)
Q Consensus 113 -~~~~~I~~~I~~~-~~a~~~ 131 (136)
+.+.++.+.|++. +.+...
T Consensus 194 ~~~pr~i~k~ie~~~~~~~~~ 214 (951)
T KOG0207|consen 194 ITGPRDIIKAIEETGFEASVR 214 (951)
T ss_pred ccChHHHHHHHHhhcccceee
Confidence 7999999999998 876554
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.88 E-value=6.1e-05 Score=67.06 Aligned_cols=87 Identities=26% Similarity=0.432 Sum_probs=74.4
Q ss_pred CcccHHHHHhhhhhcccccC--------ceEEEEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec---CC
Q 032648 47 QLLRLKDVVSGNQTLAFQLK--------PKMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD---II 114 (136)
Q Consensus 47 ~~~~~~~i~~~~~~~g~~~~--------~~~~~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~---~~ 114 (136)
..+....+.+.++..|++.. ..+-.+.+ ||+|.+|+..|++.+++++||.++.|.+...+..+.++ .+
T Consensus 40 ~~~~~~~i~~~ied~gf~~~~~~~~~~~~~~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s 119 (951)
T KOG0207|consen 40 NIVSPESIKETIEDMGFEASLLSDSEITASKCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTS 119 (951)
T ss_pred eccCHHHHHHHhhcccceeeecccCccccceeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccC
Confidence 56677778888888888543 12456899 99999999999999999999999999999999999987 78
Q ss_pred HHHHHHHHHhc-cCceecCC
Q 032648 115 PFEVLESVSKV-KNAELWSA 133 (136)
Q Consensus 115 ~~~I~~~I~~~-~~a~~~~~ 133 (136)
++.+.+.+++. +.+.++..
T Consensus 120 ~~~~~e~ie~~gf~a~~i~~ 139 (951)
T KOG0207|consen 120 PDSIAESIEDLGFSAELIES 139 (951)
T ss_pred chhHHHHHHhcCccceehhc
Confidence 99999999999 98887643
No 11
>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=97.87 E-value=0.00027 Score=40.42 Aligned_cols=57 Identities=33% Similarity=0.490 Sum_probs=47.5
Q ss_pred EEEEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec---CCHHHHHHHHHhc
Q 032648 69 MVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD---IIPFEVLESVSKV 125 (136)
Q Consensus 69 ~~~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~---~~~~~I~~~I~~~ 125 (136)
+..+.| |++|..|+..+++.++..+++....+++...++.+.++ .....+...+...
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDA 63 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHc
Confidence 456899 99999999999999999999999999999999988874 3556666666554
No 12
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.68 E-value=0.00032 Score=62.64 Aligned_cols=62 Identities=29% Similarity=0.548 Sum_probs=53.8
Q ss_pred EEEEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHhc-cCcee
Q 032648 69 MVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDIIPFEVLESVSKV-KNAEL 130 (136)
Q Consensus 69 ~~~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~~~~~~I~~~I~~~-~~a~~ 130 (136)
+..+.+ ||+|.+|+..+++.+.+++||.++.+++.+++..+.+..++.++.+.+++. |.+.+
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~ 163 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEA 163 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCccc
Confidence 456889 999999999999999999999999999999998887556778888888888 77654
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=92.67 E-value=1.5 Score=26.97 Aligned_cols=63 Identities=29% Similarity=0.434 Sum_probs=46.0
Q ss_pred eEEEEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec---CCHHHHHHHHHhc-cCcee
Q 032648 68 KMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD---IIPFEVLESVSKV-KNAEL 130 (136)
Q Consensus 68 ~~~~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~---~~~~~I~~~I~~~-~~a~~ 130 (136)
.+..+.+ ++.|..|...++..+...+++....+++......+... .....+...+.+. +..++
T Consensus 23 ~~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 23 QTVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred eEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 3556778 99999999999999999999888888888887666542 3445554555555 55433
No 14
>PRK13748 putative mercuric reductase; Provisional
Probab=89.99 E-value=2.5 Score=36.02 Aligned_cols=61 Identities=25% Similarity=0.392 Sum_probs=46.2
Q ss_pred EEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec--CCHHHHHHHHHhc-cCceec
Q 032648 71 VLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKV-KNAELW 131 (136)
Q Consensus 71 ~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~--~~~~~I~~~I~~~-~~a~~~ 131 (136)
.+.+ +|+|.+|..+++..+...+++....+++......+.+. .+...+...++.. +...+.
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~ 67 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLA 67 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeecc
Confidence 3568 89999999999999999999999999998888777643 3455555556555 554443
No 15
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=81.96 E-value=3.3 Score=30.54 Aligned_cols=46 Identities=28% Similarity=0.351 Sum_probs=36.8
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeCCCcE-------------------EEEEec---CCHHHHHHHHHh
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVDLASKM-------------------VVVIGD---IIPFEVLESVSK 124 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~-------------------v~V~~~---~~~~~I~~~I~~ 124 (136)
.+|-+-+|..+.+++||.++.+-+.++. |.|.+| ++.++|++..-+
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~~ 77 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFFQ 77 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHHH
Confidence 6788999999999999999999888775 567776 577777765543
No 16
>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=79.73 E-value=5.9 Score=19.64 Aligned_cols=39 Identities=44% Similarity=0.666 Sum_probs=31.3
Q ss_pred EE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEe
Q 032648 73 RV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIG 111 (136)
Q Consensus 73 ~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~ 111 (136)
.+ ++.|..|...++..+...+++.....++......+.+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 42 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEY 42 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEE
Confidence 35 7889999999999998889987777777777666654
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=77.75 E-value=11 Score=22.77 Aligned_cols=48 Identities=15% Similarity=0.136 Sum_probs=33.9
Q ss_pred EEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec--CCHHHHHHHHHhc-cC
Q 032648 71 VLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKV-KN 127 (136)
Q Consensus 71 ~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~--~~~~~I~~~I~~~-~~ 127 (136)
++.+ |+.||....++.++|.+++.- +.+.|..+ ....+|....++. +.
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~g~~ 53 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEENGYE 53 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHCCCE
Confidence 5778 999999999999999998542 34444443 4457788888776 64
No 18
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=74.74 E-value=8.7 Score=27.91 Aligned_cols=46 Identities=20% Similarity=0.221 Sum_probs=35.0
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeCCCcE--------------EEEEec---CCHHHHHHHHHh
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVDLASKM--------------VVVIGD---IIPFEVLESVSK 124 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~--------------v~V~~~---~~~~~I~~~I~~ 124 (136)
.+|-+-+|..+.+++||.++.+-+.++. |.|.+| ++.++|++..-+
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~~ 70 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLFE 70 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHHH
Confidence 6788899999999999999999876643 456666 566777665543
No 19
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=74.11 E-value=10 Score=28.31 Aligned_cols=46 Identities=22% Similarity=0.224 Sum_probs=35.7
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeCCCcE-------------------EEEEec---CCHHHHHHHHHh
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVDLASKM-------------------VVVIGD---IIPFEVLESVSK 124 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~-------------------v~V~~~---~~~~~I~~~I~~ 124 (136)
.+|-+-+|..+.+++||.++.+-+.++. |.|.+| ++.++|++..-+
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff~ 82 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFFS 82 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHHH
Confidence 6788888999999999999999887774 556676 566777665543
No 20
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=72.79 E-value=7.9 Score=29.61 Aligned_cols=46 Identities=30% Similarity=0.306 Sum_probs=36.0
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeCCCc-------------------EEEEEec---CCHHHHHHHHHh
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVDLASK-------------------MVVVIGD---IIPFEVLESVSK 124 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~~~~~-------------------~v~V~~~---~~~~~I~~~I~~ 124 (136)
.+|-+-+|..+.+++||.++.+-+.++ .|.|.+| ++.++|++..-+
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff~ 119 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFWE 119 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHHH
Confidence 678889999999999999999998844 3566776 577777766543
No 21
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=72.51 E-value=8.4 Score=23.55 Aligned_cols=33 Identities=24% Similarity=0.440 Sum_probs=21.2
Q ss_pred eEEEEEEcCcCHhH------HHHHHHHHhcCCCceEEEE
Q 032648 68 KMVVLRVSMHCNGC------ARKVEKHVSKLEGVTSYKV 100 (136)
Q Consensus 68 ~~~~l~Vgm~C~~C------a~~Ie~~L~~l~GV~~v~v 100 (136)
.++.+.+.+..++| ...|+++|..++||.+++|
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 45555553344444 5778899999999998875
No 22
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=67.53 E-value=31 Score=22.52 Aligned_cols=46 Identities=11% Similarity=0.172 Sum_probs=32.8
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec-CCHHHHHHHHHh
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD-IIPFEVLESVSK 124 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~-~~~~~I~~~I~~ 124 (136)
|.=...+.+.|..++|++-...+-..+|+.|+-. .+...+.+.+..
T Consensus 16 Pe~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~~ 62 (87)
T PRK10553 16 SERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIES 62 (87)
T ss_pred hHHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHHH
Confidence 4446788999999999987777777788887754 455555555544
No 23
>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=65.88 E-value=15 Score=26.40 Aligned_cols=47 Identities=21% Similarity=0.255 Sum_probs=35.5
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEecC-----CHHHHHHHHHhc
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGDI-----IPFEVLESVSKV 125 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~~-----~~~~I~~~I~~~ 125 (136)
..=+..|.+.+.+++||.++.|-.....+.|...+ ...+|.+.|++.
T Consensus 74 ~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~~~~~~~~~~~i~~~V~~~ 125 (177)
T PF09580_consen 74 QQLADRIANRVKKVPGVEDATVVVTDDNAYVAVDLDFNRFNTKKIKKKVEKA 125 (177)
T ss_pred HHHHHHHHHHHhcCCCceEEEEEEECCEEEEEEEecccccchhHHHHHHHHH
Confidence 56688999999999999999999999998876542 334455555443
No 24
>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=62.27 E-value=27 Score=25.23 Aligned_cols=46 Identities=35% Similarity=0.389 Sum_probs=34.1
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeCCCc-------------------EEEEEec---CCHHHHHHHHHh
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVDLASK-------------------MVVVIGD---IIPFEVLESVSK 124 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~~~~~-------------------~v~V~~~---~~~~~I~~~I~~ 124 (136)
.+|-+.+|..+.+++||.++.+-+.++ .|.|.+| ++.++|++..-+
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~is~~~Ll~~f~~ 74 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVISYEELLDVFFR 74 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS-HHHHHHHHHH
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcccHHHHHHHHHH
Confidence 578889999999999999999987665 3456665 566776665543
No 25
>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=61.59 E-value=23 Score=25.74 Aligned_cols=33 Identities=21% Similarity=0.275 Sum_probs=29.0
Q ss_pred hHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec
Q 032648 80 GCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD 112 (136)
Q Consensus 80 ~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~ 112 (136)
.=+.+|.+.+.+++||.++.+-.....+.|-.+
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 567899999999999999999998888887764
No 26
>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=55.60 E-value=51 Score=20.89 Aligned_cols=44 Identities=18% Similarity=0.195 Sum_probs=31.0
Q ss_pred HHHHHHHHHhcCCCceEEEEeCCCcEEEEEec-CCHHHHHHHHHhc
Q 032648 81 CARKVEKHVSKLEGVTSYKVDLASKMVVVIGD-IIPFEVLESVSKV 125 (136)
Q Consensus 81 Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~-~~~~~I~~~I~~~ 125 (136)
=...+.++|..++|++-...+-. +|+.|+.. .+..++.+.+...
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~i 60 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDAI 60 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHHH
Confidence 34678899999999976666655 88877654 4566666666543
No 27
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=54.82 E-value=26 Score=27.99 Aligned_cols=45 Identities=31% Similarity=0.225 Sum_probs=34.4
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeCCCcE-------------------EEEEec---CCHHHHHHHHH
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVDLASKM-------------------VVVIGD---IIPFEVLESVS 123 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~-------------------v~V~~~---~~~~~I~~~I~ 123 (136)
.+|-+-+|..+.+++||.++.+-+.++. |.|.+| ++.++|++..-
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~VcsG~tgH~EaV~V~yDp~~isy~~LL~~F~ 200 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEFDPAKISYETLLKVFF 200 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHH
Confidence 6788889999999999999999877653 456666 56666666553
No 28
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=48.88 E-value=62 Score=21.63 Aligned_cols=57 Identities=26% Similarity=0.382 Sum_probs=37.0
Q ss_pred eEEEEEE-cCcCHhHHHHHHHHHhcCCCceEEEEe-----CCCcEE--EEEec-CCHHHHHHHHHhc
Q 032648 68 KMVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVD-----LASKMV--VVIGD-IIPFEVLESVSKV 125 (136)
Q Consensus 68 ~~~~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~-----~~~~~v--~V~~~-~~~~~I~~~I~~~ 125 (136)
.++.|.| --+-++= -.+-+.|.+++||..+++. ..+..+ +|.++ ++.++|.++|++.
T Consensus 5 rRlVLDVlKP~~p~i-~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~ 70 (95)
T PF02680_consen 5 RRLVLDVLKPHEPSI-VELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEEL 70 (95)
T ss_dssp EEEEEEEEEESSS-H-HHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHT
T ss_pred eEEEEEeecCCCCCH-HHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHc
Confidence 4566666 3344443 3567788999998877643 444444 44564 8999999999986
No 29
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=43.84 E-value=91 Score=20.77 Aligned_cols=46 Identities=17% Similarity=0.207 Sum_probs=31.9
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec-CCHHHHHHHHHhc
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD-IIPFEVLESVSKV 125 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~-~~~~~I~~~I~~~ 125 (136)
+.=-..|.++|..+||++-..-+.. +|+.|..+ .+...+.+.++..
T Consensus 17 pe~l~av~~~L~~ip~~EV~~~d~~-GKlVVVie~~~~~~l~~tie~i 63 (94)
T COG3062 17 PERLSAVKTALLAIPGCEVYGEDAE-GKLVVVIEAEDSETLLETIESI 63 (94)
T ss_pred HHHHHHHHHHHhcCCCcEeeccCCC-ceEEEEEEcCchHHHHHHHHHH
Confidence 4556788999999999876666655 77776654 4556666666554
No 30
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=41.70 E-value=59 Score=24.13 Aligned_cols=28 Identities=29% Similarity=0.344 Sum_probs=23.8
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeCCCcE
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVDLASKM 106 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~ 106 (136)
.+|-+=+|+.+.+++||.++.+-.+++.
T Consensus 13 gGCFWg~E~~f~~i~GV~~t~~GYagG~ 40 (174)
T COG0225 13 GGCFWGVEAYFEQIPGVLSTVSGYAGGH 40 (174)
T ss_pred ccCccchHHHHhhCCCeEEEeeeEcCCC
Confidence 6788888999999999999998877664
No 31
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=40.75 E-value=1.1e+02 Score=20.40 Aligned_cols=57 Identities=21% Similarity=0.309 Sum_probs=35.0
Q ss_pred eEEEEEE--cCcCHhHHHHHHHHHhcCCCceEEEEe-----CCCc--EEEEEec-CCHHHHHHHHHhc
Q 032648 68 KMVVLRV--SMHCNGCARKVEKHVSKLEGVTSYKVD-----LASK--MVVVIGD-IIPFEVLESVSKV 125 (136)
Q Consensus 68 ~~~~l~V--gm~C~~Ca~~Ie~~L~~l~GV~~v~v~-----~~~~--~v~V~~~-~~~~~I~~~I~~~ 125 (136)
.++.+.+ ++.-+.= .-+-+.|.+++||..+++. ..+. +++|.+. .+.++|.+.|++.
T Consensus 6 RRlVLDvlKP~~~p~i-ve~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~ 72 (97)
T COG1888 6 RRLVLDVLKPHRGPTI-VELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEEL 72 (97)
T ss_pred eeeeeeecCCcCCCcH-HHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHc
Confidence 3455555 3323332 3455667888888766533 3333 4455554 8999999999987
No 32
>PRK11018 hypothetical protein; Provisional
Probab=38.22 E-value=1e+02 Score=19.29 Aligned_cols=51 Identities=12% Similarity=0.056 Sum_probs=35.3
Q ss_pred EEEEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec--CCHHHHHHHHHhc-cCc
Q 032648 69 MVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKV-KNA 128 (136)
Q Consensus 69 ~~~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~--~~~~~I~~~I~~~-~~a 128 (136)
.+++.+ |..||.=.-+.+++|.+++. ++.+.|..+ .....|....++. +..
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~~---------G~~L~V~~d~~~a~~di~~~~~~~G~~v 62 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLKK---------GEILEVVSDCPQSINNIPLDARNHGYTV 62 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCCC---------CCEEEEEeCCccHHHHHHHHHHHcCCEE
Confidence 366888 99999999999999998853 233344333 3456677777666 543
No 33
>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=37.84 E-value=46 Score=24.54 Aligned_cols=34 Identities=26% Similarity=0.499 Sum_probs=22.8
Q ss_pred EEEEEEcCcCHhH------HHHHHHHHhcCCCceEEEEeC
Q 032648 69 MVVLRVSMHCNGC------ARKVEKHVSKLEGVTSYKVDL 102 (136)
Q Consensus 69 ~~~l~Vgm~C~~C------a~~Ie~~L~~l~GV~~v~v~~ 102 (136)
++.+.+-+.-++| ...++.+|..++||.+++|++
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 3444443444444 345889999999999888764
No 34
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=35.86 E-value=1.1e+02 Score=28.65 Aligned_cols=44 Identities=14% Similarity=0.206 Sum_probs=34.4
Q ss_pred HHHHHHHHhcCCCceEEEEeCCCcEEEEEec--------CCHHHHHHHHHhc
Q 032648 82 ARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--------IIPFEVLESVSKV 125 (136)
Q Consensus 82 a~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~--------~~~~~I~~~I~~~ 125 (136)
+..++..|.+++||.++++.-....+.|..| +++.++.++|...
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 4678899999999999998755455666654 6888899999864
No 35
>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=35.12 E-value=30 Score=24.86 Aligned_cols=27 Identities=33% Similarity=0.370 Sum_probs=23.2
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeCCCc
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVDLASK 105 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~~~~~ 105 (136)
.+|-+-+|..+.+++||.++.+-+.++
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG 33 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGG 33 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCC
Confidence 578888999999999999999876654
No 36
>PF04468 PSP1: PSP1 C-terminal conserved region; InterPro: IPR007557 The yeast polymerase suppressor 1 (PSP1) protein partially suppresses mutations in DNA polymerases alpha and delta []. The C-terminal half of PSP1 contains a domain, which is also found in several hypothetical proteins from both eukaryotic and prokaryotic sources: Crithidia fasciculata RBP45 and RBP33, subunits of the cycling sequence binding protein (CSBP) II. RBP45 and RBP33 proteins bind specifically to the cycling sequences present in several mRNAs that accumulate periodically during the cell cycle. RBP45 and RBP33 are phosphoproteins, which are phosphorylated differentially during progression through the cell cycle. Hypothetical proteins with high sequence similarity have been identified in other kinetoplastid organisms []. Bacillus subtilis yaaT protein, which plays a significant role in phosphorelay during initiation of sporulation. It is possible that the yaaT protein is also related to DNA replication. The sequence of the yaaT protein is widely conserved in prokaryotes (bacteria and archaea), but the functions of the protein are unknown []. The actual biological significance of the PSP1 C-terminal domain has not yet been clearly established.
Probab=33.60 E-value=1.3e+02 Score=19.30 Aligned_cols=52 Identities=6% Similarity=0.039 Sum_probs=36.7
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec----CCHHHHHHHHHhccCceec
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD----IIPFEVLESVSKVKNAELW 131 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~----~~~~~I~~~I~~~~~a~~~ 131 (136)
..|...+...-..+ -+.++...+..+++++-+. ++..+++..+.+.|++.+|
T Consensus 29 ~~c~~~~~~~~L~m-~lvd~e~~~D~~k~~fyy~a~~rvDFR~Lvr~L~~~f~~RIe 84 (88)
T PF04468_consen 29 KFCRELVKELGLPM-KLVDVEYQFDGSKLTFYYTAESRVDFRELVRDLAREFKTRIE 84 (88)
T ss_pred HHHHHHHHHcCCCe-EEEEEEEEcCCCEEEEEEEeCCcCcHHHHHHHHHHHhCceEE
Confidence 45666665543222 2557888889999998874 7888898888776777665
No 37
>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=31.96 E-value=1.1e+02 Score=18.07 Aligned_cols=48 Identities=17% Similarity=0.198 Sum_probs=31.2
Q ss_pred EEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec--CCHHHHHHHHHhc-cCce
Q 032648 72 LRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSKV-KNAE 129 (136)
Q Consensus 72 l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~--~~~~~I~~~I~~~-~~a~ 129 (136)
+.+ |+.||.=..+..+++ ++.. ++.+.|..+ .....|....++. +...
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~~~s~~~i~~~~~~~G~~~~ 53 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEA---------GGEIEVLVDNEVAKENVSRFAESRGYEVS 53 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCC---------CCEEEEEEcChhHHHHHHHHHHHcCCEEE
Confidence 456 889999999999999 5532 223444333 3456777777776 6553
No 38
>PRK09577 multidrug efflux protein; Reviewed
Probab=31.91 E-value=1.4e+02 Score=27.98 Aligned_cols=44 Identities=16% Similarity=0.172 Sum_probs=33.8
Q ss_pred HHHHHHHHhcCCCceEEEEeCCCcEEEEEec--------CCHHHHHHHHHhc
Q 032648 82 ARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--------IIPFEVLESVSKV 125 (136)
Q Consensus 82 a~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~--------~~~~~I~~~I~~~ 125 (136)
...++..|.+++||.++++.-....+.|..| .+..+|.++|+..
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~ 209 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAH 209 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 4678999999999999998765444555433 6888899998765
No 39
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=31.62 E-value=88 Score=27.13 Aligned_cols=45 Identities=22% Similarity=0.245 Sum_probs=34.2
Q ss_pred HhHHHHHHHHHhcCCCceEEEEeCCCcE------------------EEEEec---CCHHHHHHHHH
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVDLASKM------------------VVVIGD---IIPFEVLESVS 123 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~------------------v~V~~~---~~~~~I~~~I~ 123 (136)
.+|-+-+|..+.+++||.++.+-++++. |.|.+| ++.++|++..-
T Consensus 205 gGCFWg~e~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~gtgH~E~V~V~yDp~~is~~~Ll~~f~ 270 (521)
T PRK14018 205 GGCFWGLEAYFQRIDGVVDAVSGYANGNTKNPSYEDVYRHSGHAETVKVTYDADKLSLDTILQYYF 270 (521)
T ss_pred cCCchhhHHHHccCCCEEEEEEeeCCCCCCCCChhhccCCCCcEEEEEEEECCCcCcHHHHHHHHH
Confidence 6788889999999999999999887663 445665 56666666553
No 40
>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=30.42 E-value=47 Score=21.52 Aligned_cols=35 Identities=26% Similarity=0.411 Sum_probs=22.9
Q ss_pred EEEEEEc-CcCHhH---HHHHHHHHhcCCCceEEEEeCC
Q 032648 69 MVVLRVS-MHCNGC---ARKVEKHVSKLEGVTSYKVDLA 103 (136)
Q Consensus 69 ~~~l~Vg-m~C~~C---a~~Ie~~L~~l~GV~~v~v~~~ 103 (136)
.+.+.++ -.|+.. ...++.+|..++|+.++++++.
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 3444442 344433 3457888999999999888764
No 41
>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=28.89 E-value=1.7e+02 Score=27.51 Aligned_cols=44 Identities=20% Similarity=0.298 Sum_probs=34.4
Q ss_pred HHHHHHHHhcCCCceEEEEeCCCcEEEEEec--------CCHHHHHHHHHhc
Q 032648 82 ARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--------IIPFEVLESVSKV 125 (136)
Q Consensus 82 a~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~--------~~~~~I~~~I~~~ 125 (136)
...++..|.+++||.++++.-....+.|..| +++.++.++|+..
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 3568899999999999998766455666654 6888899998863
No 42
>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=27.80 E-value=63 Score=21.14 Aligned_cols=22 Identities=36% Similarity=0.528 Sum_probs=19.0
Q ss_pred hHHHHHHHHHhcCCCceEEEEe
Q 032648 80 GCARKVEKHVSKLEGVTSYKVD 101 (136)
Q Consensus 80 ~Ca~~Ie~~L~~l~GV~~v~v~ 101 (136)
.-...++.++++++||.++.+.
T Consensus 62 g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 62 GGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred cChHHHHHHHhcCCCccEEEEE
Confidence 4458999999999999999875
No 43
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=27.54 E-value=1.1e+02 Score=20.90 Aligned_cols=21 Identities=33% Similarity=0.564 Sum_probs=18.1
Q ss_pred HHHHHHHHhcCCCceEEEEeC
Q 032648 82 ARKVEKHVSKLEGVTSYKVDL 102 (136)
Q Consensus 82 a~~Ie~~L~~l~GV~~v~v~~ 102 (136)
...++.++..++||.++.|++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 678899999999999888864
No 44
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=26.36 E-value=27 Score=21.34 Aligned_cols=21 Identities=19% Similarity=0.457 Sum_probs=16.7
Q ss_pred EEEcCcCHhHHHHHHHHHhcC
Q 032648 72 LRVSMHCNGCARKVEKHVSKL 92 (136)
Q Consensus 72 l~Vgm~C~~Ca~~Ie~~L~~l 92 (136)
+.+|-.|.+|...+++.|...
T Consensus 33 ~~~g~~CG~C~~~i~~il~~~ 53 (64)
T PRK10509 33 VPVGNQCGKCIRAAREVMQDE 53 (64)
T ss_pred cCCCCCccchHHHHHHHHHHH
Confidence 455788999999998887643
No 45
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=26.29 E-value=2e+02 Score=27.04 Aligned_cols=43 Identities=12% Similarity=0.251 Sum_probs=33.3
Q ss_pred HHHHHHHhcCCCceEEEEeCCCcEEEEEec--------CCHHHHHHHHHhc
Q 032648 83 RKVEKHVSKLEGVTSYKVDLASKMVVVIGD--------IIPFEVLESVSKV 125 (136)
Q Consensus 83 ~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~--------~~~~~I~~~I~~~ 125 (136)
+.++..|.+++||.++++.-....+.|..| +++.++.++|+..
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~~~ 210 (1049)
T PRK15127 160 ANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIKAQ 210 (1049)
T ss_pred HHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 568899999999999998755455666654 6888888888754
No 46
>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=26.00 E-value=70 Score=22.85 Aligned_cols=19 Identities=26% Similarity=0.415 Sum_probs=13.8
Q ss_pred HHHHHHHhcCCCceEEEEeC
Q 032648 83 RKVEKHVSKLEGVTSYKVDL 102 (136)
Q Consensus 83 ~~Ie~~L~~l~GV~~v~v~~ 102 (136)
..|+.+|... |+.+++|++
T Consensus 46 ~~I~~aL~~~-Gv~~V~V~i 64 (146)
T TIGR02159 46 QDIRDAVRAL-GVEVVEVST 64 (146)
T ss_pred HHHHHHHHhc-CCCeEEEeE
Confidence 4578888876 888777753
No 47
>COG0435 ECM4 Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]
Probab=24.02 E-value=1.8e+02 Score=23.58 Aligned_cols=42 Identities=26% Similarity=0.216 Sum_probs=34.1
Q ss_pred hcccccCceEEEEEEcCcCHhH-HHHHHHHHhcCCCceEEEEe
Q 032648 60 TLAFQLKPKMVVLRVSMHCNGC-ARKVEKHVSKLEGVTSYKVD 101 (136)
Q Consensus 60 ~~g~~~~~~~~~l~Vgm~C~~C-a~~Ie~~L~~l~GV~~v~v~ 101 (136)
+.||..+.-++.+.|++.|+=- ...|-++|++|+++.++.|-
T Consensus 42 ~~~f~~e~GRYhLYvslaCPWAHRTLI~R~LkgLE~~Isvsvv 84 (324)
T COG0435 42 TGGFKAEKGRYHLYVSLACPWAHRTLIFRALKGLEPVISVSVV 84 (324)
T ss_pred cCCcCCCCCeEEEEEEecCchHHHHHHHHHHhcccccceEEEe
Confidence 3568888889999999999855 45678999999999888764
No 48
>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=22.38 E-value=89 Score=23.43 Aligned_cols=22 Identities=27% Similarity=0.543 Sum_probs=18.5
Q ss_pred HHHHHHHHHhcCCCceEEEEeC
Q 032648 81 CARKVEKHVSKLEGVTSYKVDL 102 (136)
Q Consensus 81 Ca~~Ie~~L~~l~GV~~v~v~~ 102 (136)
=...+++.|..++||.+++|.+
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 3567889999999999999874
No 49
>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=21.87 E-value=1.8e+02 Score=17.04 Aligned_cols=31 Identities=10% Similarity=0.262 Sum_probs=21.8
Q ss_pred EEEEEcCcCHh-HHHHHHHHHhcCCCceEEEE
Q 032648 70 VVLRVSMHCNG-CARKVEKHVSKLEGVTSYKV 100 (136)
Q Consensus 70 ~~l~Vgm~C~~-Ca~~Ie~~L~~l~GV~~v~v 100 (136)
+.|.+...-.. --..+-+.|++++||.++.+
T Consensus 43 i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 43 VTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 44444333343 66888899999999998875
No 50
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=20.93 E-value=1.8e+02 Score=18.26 Aligned_cols=47 Identities=23% Similarity=0.347 Sum_probs=32.9
Q ss_pred EEEEEE-cCcCHhHHHHHHHHHhcCCCceEEEEeCCCcEEEEEec--CCHHHHHHHHHh
Q 032648 69 MVVLRV-SMHCNGCARKVEKHVSKLEGVTSYKVDLASKMVVVIGD--IIPFEVLESVSK 124 (136)
Q Consensus 69 ~~~l~V-gm~C~~Ca~~Ie~~L~~l~GV~~v~v~~~~~~v~V~~~--~~~~~I~~~I~~ 124 (136)
..++.+ |+.|+.=...+.++|.+++- ++.+.|..+ ....+|....++
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~---------Ge~LeV~~ddp~~~~dIp~~~~~ 54 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLKP---------GEILEVIADDPAAKEDIPAWAKK 54 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCCC---------CCEEEEEecCcchHHHHHHHHHH
Confidence 457888 99999999999999998853 344555443 344566666653
No 51
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=20.86 E-value=2.8e+02 Score=25.93 Aligned_cols=44 Identities=18% Similarity=0.237 Sum_probs=0.0
Q ss_pred HHHHHHHHhcCCCceEEEEe-CCCcEEEEEec--------CCHHHHHHHHHhc
Q 032648 82 ARKVEKHVSKLEGVTSYKVD-LASKMVVVIGD--------IIPFEVLESVSKV 125 (136)
Q Consensus 82 a~~Ie~~L~~l~GV~~v~v~-~~~~~v~V~~~--------~~~~~I~~~I~~~ 125 (136)
...++..|.+++||.++.+. .....+.|..| +++.++.++|...
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
No 52
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=20.22 E-value=1.1e+02 Score=20.07 Aligned_cols=23 Identities=35% Similarity=0.566 Sum_probs=19.7
Q ss_pred HhHHHHHHHHHhcCCCceEEEEe
Q 032648 79 NGCARKVEKHVSKLEGVTSYKVD 101 (136)
Q Consensus 79 ~~Ca~~Ie~~L~~l~GV~~v~v~ 101 (136)
..-...++.++++++||.++++.
T Consensus 61 ~~~td~lee~i~~~e~Vqsvei~ 83 (88)
T PRK00435 61 EGGTEPVEEAFANVEGVESVEVE 83 (88)
T ss_pred CcCcHHHHHHHhccCCCcEEEEE
Confidence 45568999999999999999875
No 53
>cd08623 PI-PLCc_beta1 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-beta1. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-beta isozyme 1. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PLC-beta represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and a unique C-terminal coiled-coil (CT) domain necessary for ho
Probab=20.16 E-value=1.5e+02 Score=23.35 Aligned_cols=47 Identities=19% Similarity=0.282 Sum_probs=36.1
Q ss_pred cccHHHHHhhhhhcccccCceEEEEEEcCcCH--hHHHHHHHHHhcCCC
Q 032648 48 LLRLKDVVSGNQTLAFQLKPKMVVLRVSMHCN--GCARKVEKHVSKLEG 94 (136)
Q Consensus 48 ~~~~~~i~~~~~~~g~~~~~~~~~l~Vgm~C~--~Ca~~Ie~~L~~l~G 94 (136)
.+++.+++.+|.+.+|....-.+.+.+.+||. ....++-+.+..+=|
T Consensus 71 ~i~f~dv~~~I~~~AF~~S~yPvIlSlE~Hc~s~~qQ~~ma~~l~~~lG 119 (258)
T cd08623 71 EISFKEVIEAIAECAFKTSPFPILLSFENHVDSPKQQAKMAEYCRLIFG 119 (258)
T ss_pred CcCHHHHHHHHHHHhccCCCCCEEEEehhcCCCHHHHHHHHHHHHHHHh
Confidence 68899999999999998877778888878883 566666555555433
No 54
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=20.16 E-value=1e+02 Score=24.07 Aligned_cols=23 Identities=30% Similarity=0.562 Sum_probs=18.2
Q ss_pred hHHHHHHHHHhcCCCceEEEEeC
Q 032648 80 GCARKVEKHVSKLEGVTSYKVDL 102 (136)
Q Consensus 80 ~Ca~~Ie~~L~~l~GV~~v~v~~ 102 (136)
.=.+.+++.|++++||.+++|..
T Consensus 109 ~~eQ~le~tLs~mDGVi~ArV~I 131 (246)
T COG4669 109 AKEQQLEQTLSKMDGVISARVHI 131 (246)
T ss_pred HHHHHHHHHHHhcCceEEEEEEE
Confidence 34678999999999998776543
Done!