Query 034639
Match_columns 88
No_of_seqs 103 out of 1078
Neff 11.3
Searched_HMMs 46136
Date Fri Mar 29 04:56:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034639.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034639hhsearch_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 99.3 3.8E-11 8.2E-16 54.3 8.3 58 6-63 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.3 1.5E-10 3.3E-15 53.7 8.8 62 4-65 3-68 (71)
3 KOG4656 Copper chaperone for s 98.5 2.2E-06 4.8E-11 46.9 7.9 64 4-67 8-71 (247)
4 PRK10671 copA copper exporting 98.5 1.7E-06 3.6E-11 56.2 8.2 65 1-67 1-66 (834)
5 KOG1603 Copper chaperone [Inor 98.4 1.4E-05 3E-10 37.2 7.9 58 4-61 6-63 (73)
6 COG2217 ZntA Cation transport 98.2 2.2E-05 4.8E-10 50.4 7.7 63 3-66 2-69 (713)
7 PLN02957 copper, zinc superoxi 98.1 0.00027 6E-09 40.0 10.3 65 4-68 7-71 (238)
8 KOG0207 Cation transport ATPas 97.6 0.00042 9.2E-09 45.5 6.8 64 4-67 147-214 (951)
9 TIGR00003 copper ion binding p 97.6 0.001 2.2E-08 28.7 8.5 59 5-63 4-66 (68)
10 KOG0207 Cation transport ATPas 97.2 0.0036 7.9E-08 41.5 7.0 62 6-67 72-137 (951)
11 PRK10671 copA copper exporting 97.0 0.0096 2.1E-07 39.5 7.9 61 5-65 101-162 (834)
12 PRK11033 zntA zinc/cadmium/mer 97.0 0.011 2.4E-07 38.8 8.0 62 4-65 54-117 (741)
13 PRK13748 putative mercuric red 68.1 30 0.00065 22.4 8.9 59 7-65 4-65 (561)
14 TIGR02052 MerP mercuric transp 62.2 15 0.00032 16.7 9.3 59 5-63 25-87 (92)
15 PRK14054 methionine sulfoxide 56.6 33 0.00071 19.0 3.8 28 14-41 10-37 (172)
16 COG0225 MsrA Peptide methionin 47.9 49 0.0011 18.4 3.6 27 14-40 13-39 (174)
17 PF01206 TusA: Sulfurtransfera 46.9 29 0.00062 15.5 4.9 55 6-67 2-57 (70)
18 PRK11018 hypothetical protein; 46.7 33 0.0007 16.0 6.1 55 5-66 9-64 (78)
19 cd00371 HMA Heavy-metal-associ 45.7 19 0.00042 13.2 5.3 34 8-41 3-37 (63)
20 PRK05528 methionine sulfoxide 43.7 55 0.0012 17.8 3.5 27 14-40 8-34 (156)
21 PF14599 zinc_ribbon_6: Zinc-r 43.6 9.8 0.00021 17.2 0.3 15 4-18 41-56 (61)
22 KOG3150 Uncharacterized conser 43.3 6.5 0.00014 21.4 -0.3 22 6-27 107-129 (182)
23 COG0425 SirA Predicted redox p 35.9 54 0.0012 15.4 3.5 54 4-64 5-60 (78)
24 PF01625 PMSR: Peptide methion 35.4 78 0.0017 17.2 3.0 27 14-40 7-33 (155)
25 TIGR00401 msrA methionine-S-su 30.4 79 0.0017 17.0 2.5 27 14-40 7-33 (149)
26 PRK00299 sulfur transfer prote 29.2 73 0.0016 15.0 6.2 55 4-65 9-64 (81)
27 COG4837 Uncharacterized protei 26.5 47 0.001 16.5 1.1 19 1-19 1-22 (106)
28 PRK00058 methionine sulfoxide 26.5 83 0.0018 18.2 2.2 27 14-40 52-78 (213)
29 PF15643 Tox-PL-2: Papain fold 25.7 64 0.0014 16.2 1.5 17 10-26 18-34 (100)
30 PRK10509 bacterioferritin-asso 21.3 78 0.0017 14.3 1.3 18 10-27 36-53 (64)
31 PRK13014 methionine sulfoxide 20.2 91 0.002 17.6 1.6 27 14-40 15-41 (186)
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=99.35 E-value=3.8e-11 Score=54.26 Aligned_cols=58 Identities=34% Similarity=0.705 Sum_probs=52.0
Q ss_pred EEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEEee---CCHHHHHHHHHhcCCc
Q 034639 6 VLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGN---VQPGAVLQTVSKTGKK 63 (88)
Q Consensus 6 ~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~---~~~~~i~~~i~~~g~~ 63 (88)
.|.+ ||.|.+|...+++.|.+++|+..+.+++..+++.+... ...+.+...+...||.
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 3788 99999999999999999999999999999999998832 4569999999999984
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.30 E-value=1.5e-10 Score=53.67 Aligned_cols=62 Identities=35% Similarity=0.675 Sum_probs=55.2
Q ss_pred EEEEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEE--e-eCCHHHHHHHHHhcCCcee
Q 034639 4 TVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--G-NVQPGAVLQTVSKTGKKTA 65 (88)
Q Consensus 4 ~~~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~--~-~~~~~~i~~~i~~~g~~~~ 65 (88)
+..|.+ ||+|.+|...+.+.|..+.|+..+.+++..+...+. . ....+.+...+..+||...
T Consensus 3 ~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~ 68 (71)
T COG2608 3 KTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVE 68 (71)
T ss_pred eEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCee
Confidence 467899 999999999999999999999999999999777666 3 5789999999999999764
No 3
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.52 E-value=2.2e-06 Score=46.90 Aligned_cols=64 Identities=33% Similarity=0.633 Sum_probs=57.0
Q ss_pred EEEEEecccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEEeeCCHHHHHHHHHhcCCceeee
Q 034639 4 TVVLKVGMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPGAVLQTVSKTGKKTAFW 67 (88)
Q Consensus 4 ~~~~~~g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~i~~~i~~~g~~~~~~ 67 (88)
+.+|.+.|.|..|.+.++..|..++|+..+++++..+.+.+.....+.++...++..|..+...
T Consensus 8 ~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~ 71 (247)
T KOG4656|consen 8 EAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLR 71 (247)
T ss_pred eEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEe
Confidence 3567779999999999999999999999999999999998887778899999999998877654
No 4
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.49 E-value=1.7e-06 Score=56.23 Aligned_cols=65 Identities=32% Similarity=0.552 Sum_probs=55.5
Q ss_pred CceEEEEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEEeeCCHHHHHHHHHhcCCceeee
Q 034639 1 MSQTVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPGAVLQTVSKTGKKTAFW 67 (88)
Q Consensus 1 ~~~~~~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~i~~~i~~~g~~~~~~ 67 (88)
|+++..+.+ ||+|.+|...+++.+.+++|+..+.+++. +..+....+.+.+...+...||.....
T Consensus 1 ~~~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~ 66 (834)
T PRK10671 1 MSQTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVS 66 (834)
T ss_pred CCeEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCccccc
Confidence 788899999 99999999999999999999999999984 344444457788999999999987653
No 5
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.38 E-value=1.4e-05 Score=37.21 Aligned_cols=58 Identities=66% Similarity=1.004 Sum_probs=51.4
Q ss_pred EEEEEecccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEEeeCCHHHHHHHHHhcC
Q 034639 4 TVVLKVGMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPGAVLQTVSKTG 61 (88)
Q Consensus 4 ~~~~~~g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~i~~~i~~~g 61 (88)
...+.+.|+|..|...+.+.+..+.|+....++...+.+.+.+..++..+...+.+.+
T Consensus 6 ~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~ 63 (73)
T KOG1603|consen 6 TVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTG 63 (73)
T ss_pred EEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcC
Confidence 3455568999999999999999999999999999999998887789999999988766
No 6
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.16 E-value=2.2e-05 Score=50.37 Aligned_cols=63 Identities=30% Similarity=0.628 Sum_probs=53.8
Q ss_pred eEEEEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEE-e--eCC-HHHHHHHHHhcCCceee
Q 034639 3 QTVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK-G--NVQ-PGAVLQTVSKTGKKTAF 66 (88)
Q Consensus 3 ~~~~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~-~--~~~-~~~i~~~i~~~g~~~~~ 66 (88)
.+..|.+ ||+|..|.+.++ .+++++|+....+++......+. . ... ...+...+...||....
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 3567899 999999999999 99999999999999999999877 2 233 67889999999997653
No 7
>PLN02957 copper, zinc superoxide dismutase
Probab=98.08 E-value=0.00027 Score=40.01 Aligned_cols=65 Identities=35% Similarity=0.596 Sum_probs=53.8
Q ss_pred EEEEEecccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEEeeCCHHHHHHHHHhcCCceeeec
Q 034639 4 TVVLKVGMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPGAVLQTVSKTGKKTAFWE 68 (88)
Q Consensus 4 ~~~~~~g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~i~~~i~~~g~~~~~~~ 68 (88)
++.+.++|.|..|...++..+..+.++....+++....+.+........+...+...||...+..
T Consensus 7 ~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~ 71 (238)
T PLN02957 7 LTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIG 71 (238)
T ss_pred EEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEec
Confidence 45555699999999999999999999999999999988777654567778888999999876543
No 8
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.63 E-value=0.00042 Score=45.52 Aligned_cols=64 Identities=25% Similarity=0.603 Sum_probs=56.9
Q ss_pred EEEEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEE---eeCCHHHHHHHHHhcCCceeee
Q 034639 4 TVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK---GNVQPGAVLQTVSKTGKKTAFW 67 (88)
Q Consensus 4 ~~~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~---~~~~~~~i~~~i~~~g~~~~~~ 67 (88)
+..|.+ ||.|..|...++..+.++.|+...++++...++.+. ....+.++.+.+...|+.....
T Consensus 147 ~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~ 214 (951)
T KOG0207|consen 147 KIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVR 214 (951)
T ss_pred cEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceee
Confidence 567889 999999999999999999999999999999998876 4588999999999999976543
No 9
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.57 E-value=0.001 Score=28.71 Aligned_cols=59 Identities=20% Similarity=0.532 Sum_probs=43.9
Q ss_pred EEEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEEe---eCCHHHHHHHHHhcCCc
Q 034639 5 VVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKG---NVQPGAVLQTVSKTGKK 63 (88)
Q Consensus 5 ~~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~---~~~~~~i~~~i~~~g~~ 63 (88)
..+.+ ++.|..|...++..+....++....+++......+.. ......+...+...|+.
T Consensus 4 ~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 66 (68)
T TIGR00003 4 FTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYE 66 (68)
T ss_pred EEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCC
Confidence 56889 9999999999999998888888888888887766652 23455555555555553
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.18 E-value=0.0036 Score=41.46 Aligned_cols=62 Identities=29% Similarity=0.568 Sum_probs=54.1
Q ss_pred EEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEE---eeCCHHHHHHHHHhcCCceeee
Q 034639 6 VLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK---GNVQPGAVLQTVSKTGKKTAFW 67 (88)
Q Consensus 6 ~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~---~~~~~~~i~~~i~~~g~~~~~~ 67 (88)
.+++ ||.|..|...+++.+++++|+....+.+....+.+. .....+.+...+.+.|+.....
T Consensus 72 ~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i 137 (951)
T KOG0207|consen 72 YLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELI 137 (951)
T ss_pred EEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceeh
Confidence 4788 999999999999999999999999999988888766 4578888888899999987654
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.01 E-value=0.0096 Score=39.49 Aligned_cols=61 Identities=33% Similarity=0.571 Sum_probs=49.3
Q ss_pred EEEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEEeeCCHHHHHHHHHhcCCcee
Q 034639 5 VVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPGAVLQTVSKTGKKTA 65 (88)
Q Consensus 5 ~~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~i~~~i~~~g~~~~ 65 (88)
..+.+ ||+|..|...+++.+...+|+....+++......+........+...+...||...
T Consensus 101 ~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~ 162 (834)
T PRK10671 101 QQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAE 162 (834)
T ss_pred EEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCcc
Confidence 45789 99999999999999999999999999988877666533456667777788888653
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.00 E-value=0.011 Score=38.76 Aligned_cols=62 Identities=26% Similarity=0.422 Sum_probs=47.7
Q ss_pred EEEEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEE-eeCCHHHHHHHHHhcCCcee
Q 034639 4 TVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK-GNVQPGAVLQTVSKTGKKTA 65 (88)
Q Consensus 4 ~~~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~-~~~~~~~i~~~i~~~g~~~~ 65 (88)
+..+.+ ||+|..|...++..+...+|+....+++...+..+. .......+...+...||...
T Consensus 54 r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~ 117 (741)
T PRK11033 54 RYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLR 117 (741)
T ss_pred eEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccccc
Confidence 456889 999999999999999999999999999888876665 22122555666777777643
No 13
>PRK13748 putative mercuric reductase; Provisional
Probab=68.07 E-value=30 Score=22.44 Aligned_cols=59 Identities=29% Similarity=0.567 Sum_probs=40.5
Q ss_pred EEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEEe--eCCHHHHHHHHHhcCCcee
Q 034639 7 LKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKG--NVQPGAVLQTVSKTGKKTA 65 (88)
Q Consensus 7 ~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~--~~~~~~i~~~i~~~g~~~~ 65 (88)
+.+ ++.|..|...++..+...+++.....++......+.. ......+...+...++...
T Consensus 4 i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~ 65 (561)
T PRK13748 4 LKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRAT 65 (561)
T ss_pred EEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeee
Confidence 557 9999999999999888888877777777776644441 1234445455566666543
No 14
>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=62.24 E-value=15 Score=16.73 Aligned_cols=59 Identities=29% Similarity=0.477 Sum_probs=37.0
Q ss_pred EEEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEEe---eCCHHHHHHHHHhcCCc
Q 034639 5 VVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKG---NVQPGAVLQTVSKTGKK 63 (88)
Q Consensus 5 ~~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~---~~~~~~i~~~i~~~g~~ 63 (88)
..+.+ ++.|..|...++..+....++.............+.. ......+...+...++.
T Consensus 25 ~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 87 (92)
T TIGR02052 25 VTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYP 87 (92)
T ss_pred EEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCC
Confidence 34567 8999999999988888887776666666655543331 12333343444455554
No 15
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=56.59 E-value=33 Score=18.99 Aligned_cols=28 Identities=14% Similarity=0.354 Sum_probs=23.5
Q ss_pred HhhHHHHHHHHhcCCCeeEEEEEcCCCE
Q 034639 14 EGCVGAVKRVLGKMDGVETFDIDLKEQK 41 (88)
Q Consensus 14 ~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (88)
..|-+.++..+.+++||....+-...+.
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~ 37 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGH 37 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCC
Confidence 6799999999999999998888766553
No 16
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=47.86 E-value=49 Score=18.44 Aligned_cols=27 Identities=19% Similarity=0.261 Sum_probs=22.2
Q ss_pred HhhHHHHHHHHhcCCCeeEEEEEcCCC
Q 034639 14 EGCVGAVKRVLGKMDGVETFDIDLKEQ 40 (88)
Q Consensus 14 ~~c~~~~~~~~~~~~~~~~~~~~~~~~ 40 (88)
..|-|.++..+.+++||.+..+-...+
T Consensus 13 gGCFWg~E~~f~~i~GV~~t~~GYagG 39 (174)
T COG0225 13 GGCFWGVEAYFEQIPGVLSTVSGYAGG 39 (174)
T ss_pred ccCccchHHHHhhCCCeEEEeeeEcCC
Confidence 678999999999999998887765444
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=46.94 E-value=29 Score=15.52 Aligned_cols=55 Identities=16% Similarity=0.209 Sum_probs=35.5
Q ss_pred EEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEEeeCCHHHHHHHHHhcCCceeee
Q 034639 6 VLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPGAVLQTVSKTGKKTAFW 67 (88)
Q Consensus 6 ~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~i~~~i~~~g~~~~~~ 67 (88)
.+.+ |..|+.....+.+.+..++......+- .........+.......|+.....
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G~~l~v~-------~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPGEVLEVL-------VDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT-EEEEE-------ESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCCCEEEEE-------ECCccHHHHHHHHHHHCCCEEEEE
Confidence 4567 899999999999999987543322221 113345567788888888875433
No 18
>PRK11018 hypothetical protein; Provisional
Probab=46.67 E-value=33 Score=16.05 Aligned_cols=55 Identities=13% Similarity=0.072 Sum_probs=37.3
Q ss_pred EEEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEEeeCCHHHHHHHHHhcCCceee
Q 034639 5 VVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPGAVLQTVSKTGKKTAF 66 (88)
Q Consensus 5 ~~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~i~~~i~~~g~~~~~ 66 (88)
..+.. |..|+.......+.+.++.......+- .........+.......|+....
T Consensus 9 ~~lD~rG~~CP~Pvl~~kk~l~~l~~G~~L~V~-------~d~~~a~~di~~~~~~~G~~v~~ 64 (78)
T PRK11018 9 YRLDMVGEPCPYPAVATLEALPQLKKGEILEVV-------SDCPQSINNIPLDARNHGYTVLD 64 (78)
T ss_pred eeEECCCCcCCHHHHHHHHHHHhCCCCCEEEEE-------eCCccHHHHHHHHHHHcCCEEEE
Confidence 56778 999999999999999887543333221 11333455677777888887643
No 19
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=45.70 E-value=19 Score=13.17 Aligned_cols=34 Identities=44% Similarity=0.955 Sum_probs=23.5
Q ss_pred Ee-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCE
Q 034639 8 KV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQK 41 (88)
Q Consensus 8 ~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (88)
.+ ++.|..|...+...+....++......+....
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGK 37 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCE
Confidence 35 77889999888877777777655555544444
No 20
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=43.73 E-value=55 Score=17.83 Aligned_cols=27 Identities=19% Similarity=0.337 Sum_probs=22.7
Q ss_pred HhhHHHHHHHHhcCCCeeEEEEEcCCC
Q 034639 14 EGCVGAVKRVLGKMDGVETFDIDLKEQ 40 (88)
Q Consensus 14 ~~c~~~~~~~~~~~~~~~~~~~~~~~~ 40 (88)
..|-+.++..+.+++||....+-...+
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG 34 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANG 34 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCC
Confidence 579999999999999999888876553
No 21
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=43.55 E-value=9.8 Score=17.18 Aligned_cols=15 Identities=27% Similarity=0.634 Sum_probs=5.7
Q ss_pred EEEEEe-cccCHhhHH
Q 034639 4 TVVLKV-GMSCEGCVG 18 (88)
Q Consensus 4 ~~~~~~-g~~c~~c~~ 18 (88)
.+.|++ |+.|.+|.+
T Consensus 41 ~v~fH~lg~KC~~C~S 56 (61)
T PF14599_consen 41 EVPFHFLGHKCSHCGS 56 (61)
T ss_dssp EEE--TT----TTTS-
T ss_pred ceeeeHhhhcCCCCCC
Confidence 356788 999998864
No 22
>KOG3150 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.30 E-value=6.5 Score=21.37 Aligned_cols=22 Identities=23% Similarity=0.572 Sum_probs=17.5
Q ss_pred EEEe-cccCHhhHHHHHHHHhcC
Q 034639 6 VLKV-GMSCEGCVGAVKRVLGKM 27 (88)
Q Consensus 6 ~~~~-g~~c~~c~~~~~~~~~~~ 27 (88)
.-++ .+.|..|+..+...|+++
T Consensus 107 ~hr~hNi~cdNCHShVA~aLn~m 129 (182)
T KOG3150|consen 107 KHRTHNIFCDNCHSHVANALNRM 129 (182)
T ss_pred hhcccceeeccHHHHHHHHHHHh
Confidence 3456 778999999999988765
No 23
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=35.88 E-value=54 Score=15.45 Aligned_cols=54 Identities=22% Similarity=0.350 Sum_probs=33.2
Q ss_pred EEEEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEEeeCCHHHHHHHHHhcC-Cce
Q 034639 4 TVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPGAVLQTVSKTG-KKT 64 (88)
Q Consensus 4 ~~~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~i~~~i~~~g-~~~ 64 (88)
...+.+ |..|+.......+.+..++......+- ........++-......| +..
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~Ge~LeV~-------~ddp~~~~dIp~~~~~~~~~~l 60 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLKPGEILEVI-------ADDPAAKEDIPAWAKKEGGHEL 60 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCCCCCEEEEE-------ecCcchHHHHHHHHHHcCCcEE
Confidence 356788 999999999999999887554333321 112234455555555344 543
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=35.41 E-value=78 Score=17.18 Aligned_cols=27 Identities=19% Similarity=0.385 Sum_probs=22.8
Q ss_pred HhhHHHHHHHHhcCCCeeEEEEEcCCC
Q 034639 14 EGCVGAVKRVLGKMDGVETFDIDLKEQ 40 (88)
Q Consensus 14 ~~c~~~~~~~~~~~~~~~~~~~~~~~~ 40 (88)
.+|-+.++..+.+++||....+-...+
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 578999999999999999888876554
No 25
>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=30.44 E-value=79 Score=17.04 Aligned_cols=27 Identities=19% Similarity=0.317 Sum_probs=22.1
Q ss_pred HhhHHHHHHHHhcCCCeeEEEEEcCCC
Q 034639 14 EGCVGAVKRVLGKMDGVETFDIDLKEQ 40 (88)
Q Consensus 14 ~~c~~~~~~~~~~~~~~~~~~~~~~~~ 40 (88)
..|-+.++..+.+++||....+-...+
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG 33 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGG 33 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCC
Confidence 578899999999999998888775544
No 26
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=29.21 E-value=73 Score=14.98 Aligned_cols=55 Identities=16% Similarity=0.159 Sum_probs=36.1
Q ss_pred EEEEEe-cccCHhhHHHHHHHHhcCCCeeEEEEEcCCCEEEEEeeCCHHHHHHHHHhcCCcee
Q 034639 4 TVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPGAVLQTVSKTGKKTA 65 (88)
Q Consensus 4 ~~~~~~-g~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~i~~~i~~~g~~~~ 65 (88)
...+.. |+.|+.......+.+.+++......+- .........+.......|+...
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~~G~~l~V~-------~dd~~~~~di~~~~~~~G~~~~ 64 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQPGETLLII-------ADDPATTRDIPSFCRFMDHELL 64 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCCCCCEEEEE-------eCCccHHHHHHHHHHHcCCEEE
Confidence 456778 999999999999999887543322221 1123345566666677787764
No 27
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.51 E-value=47 Score=16.54 Aligned_cols=19 Identities=42% Similarity=0.732 Sum_probs=12.5
Q ss_pred CceEEEEEe-cc--cCHhhHHH
Q 034639 1 MSQTVVLKV-GM--SCEGCVGA 19 (88)
Q Consensus 1 ~~~~~~~~~-g~--~c~~c~~~ 19 (88)
|++...+.+ |- -|.+|.+.
T Consensus 1 M~~~~~l~VyGae~iCASCV~a 22 (106)
T COG4837 1 MVNEAKLVVYGAEVICASCVNA 22 (106)
T ss_pred CCceeEEEEecchhhhHHhcCC
Confidence 666666666 64 48888754
No 28
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=26.47 E-value=83 Score=18.18 Aligned_cols=27 Identities=19% Similarity=0.364 Sum_probs=23.1
Q ss_pred HhhHHHHHHHHhcCCCeeEEEEEcCCC
Q 034639 14 EGCVGAVKRVLGKMDGVETFDIDLKEQ 40 (88)
Q Consensus 14 ~~c~~~~~~~~~~~~~~~~~~~~~~~~ 40 (88)
..|-|.++..+.+++||....+-...+
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG 78 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGG 78 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCC
Confidence 679999999999999999988886644
No 29
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=25.72 E-value=64 Score=16.23 Aligned_cols=17 Identities=29% Similarity=0.618 Sum_probs=14.3
Q ss_pred cccCHhhHHHHHHHHhc
Q 034639 10 GMSCEGCVGAVKRVLGK 26 (88)
Q Consensus 10 g~~c~~c~~~~~~~~~~ 26 (88)
-++|..|+..+.+.|..
T Consensus 18 ~~qC~~cA~Al~~~L~~ 34 (100)
T PF15643_consen 18 IFQCVECASALKQFLKQ 34 (100)
T ss_pred ceehHHHHHHHHHHHHH
Confidence 46799999999998764
No 30
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=21.32 E-value=78 Score=14.27 Aligned_cols=18 Identities=28% Similarity=0.687 Sum_probs=13.6
Q ss_pred cccCHhhHHHHHHHHhcC
Q 034639 10 GMSCEGCVGAVKRVLGKM 27 (88)
Q Consensus 10 g~~c~~c~~~~~~~~~~~ 27 (88)
|-.|..|...+.+.+.+.
T Consensus 36 g~~CG~C~~~i~~il~~~ 53 (64)
T PRK10509 36 GNQCGKCIRAAREVMQDE 53 (64)
T ss_pred CCCccchHHHHHHHHHHH
Confidence 557889998888876543
No 31
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=20.20 E-value=91 Score=17.58 Aligned_cols=27 Identities=22% Similarity=0.332 Sum_probs=22.4
Q ss_pred HhhHHHHHHHHhcCCCeeEEEEEcCCC
Q 034639 14 EGCVGAVKRVLGKMDGVETFDIDLKEQ 40 (88)
Q Consensus 14 ~~c~~~~~~~~~~~~~~~~~~~~~~~~ 40 (88)
..|-+.++..+.+++||....+-...+
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG 41 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGG 41 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCC
Confidence 578888999999999999888876554
Done!