Query psy13021
Match_columns 287
No_of_seqs 302 out of 3010
Neff 9.3
Searched_HMMs 46136
Date Fri Aug 16 17:21:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13021.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13021hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0207|consensus 99.9 5.4E-26 1.2E-30 213.8 20.6 213 60-273 1-218 (951)
2 KOG0207|consensus 99.6 1.9E-15 4.1E-20 143.2 13.0 142 132-274 1-142 (951)
3 PRK10671 copA copper exporting 99.4 7.7E-12 1.7E-16 124.1 16.1 134 51-192 1-163 (834)
4 PF00403 HMA: Heavy-metal-asso 99.4 2.7E-12 5.9E-17 85.5 7.6 62 128-189 1-62 (62)
5 PF00403 HMA: Heavy-metal-asso 99.4 6.1E-12 1.3E-16 83.8 8.9 62 204-265 1-62 (62)
6 COG2608 CopZ Copper chaperone 99.3 1.5E-11 3.3E-16 83.9 8.8 67 53-119 2-68 (71)
7 PRK10671 copA copper exporting 99.3 7.1E-11 1.5E-15 117.3 15.3 136 126-269 4-164 (834)
8 COG2608 CopZ Copper chaperone 99.2 1.2E-10 2.7E-15 79.4 9.0 67 202-268 3-69 (71)
9 COG2217 ZntA Cation transport 98.4 8.9E-07 1.9E-11 85.5 7.3 66 126-192 3-69 (713)
10 COG2217 ZntA Cation transport 98.1 5.9E-06 1.3E-10 79.9 7.4 66 202-268 3-69 (713)
11 TIGR00003 copper ion binding p 97.9 0.00011 2.4E-09 47.4 7.8 64 127-190 4-67 (68)
12 TIGR00003 copper ion binding p 97.8 0.00022 4.8E-09 45.9 8.7 65 54-118 3-67 (68)
13 PLN02957 copper, zinc superoxi 97.8 0.00016 3.4E-09 61.4 9.4 72 200-275 5-76 (238)
14 KOG4656|consensus 97.7 0.00014 3.1E-09 58.4 7.2 61 54-118 8-68 (247)
15 PLN02957 copper, zinc superoxi 97.6 0.00053 1.2E-08 58.1 9.4 66 126-195 7-72 (238)
16 KOG4656|consensus 97.3 0.00064 1.4E-08 54.7 6.4 68 203-274 9-76 (247)
17 KOG1603|consensus 97.3 0.002 4.4E-08 43.9 7.6 54 59-115 10-63 (73)
18 KOG1603|consensus 97.1 0.0014 3E-08 44.8 5.6 55 130-187 9-63 (73)
19 PRK11033 zntA zinc/cadmium/mer 96.9 0.0029 6.2E-08 62.5 7.3 66 126-193 54-119 (741)
20 PRK11033 zntA zinc/cadmium/mer 96.7 0.0073 1.6E-07 59.7 8.9 66 52-119 52-117 (741)
21 TIGR02052 MerP mercuric transp 94.3 0.45 9.7E-06 32.8 8.2 66 126-191 24-89 (92)
22 TIGR02052 MerP mercuric transp 93.8 0.82 1.8E-05 31.4 8.8 66 202-267 24-89 (92)
23 PRK13748 putative mercuric red 89.1 2.3 4.9E-05 40.8 8.8 69 204-273 3-71 (561)
24 cd00371 HMA Heavy-metal-associ 88.9 2.9 6.4E-05 23.8 7.1 41 130-170 3-43 (63)
25 PRK13748 putative mercuric red 87.1 2.9 6.3E-05 40.1 8.1 67 128-195 3-69 (561)
26 PRK14054 methionine sulfoxide 86.5 1.5 3.2E-05 35.2 4.8 49 138-186 11-78 (172)
27 PF01206 TusA: Sulfurtransfera 84.7 4.2 9.1E-05 27.0 5.8 56 204-269 2-57 (70)
28 cd00371 HMA Heavy-metal-associ 84.4 5.6 0.00012 22.5 7.4 58 206-264 3-60 (63)
29 PF01206 TusA: Sulfurtransfera 82.0 7 0.00015 25.9 6.0 53 56-118 2-54 (70)
30 PRK14054 methionine sulfoxide 81.7 4.1 9E-05 32.6 5.5 48 215-262 12-78 (172)
31 PRK11018 hypothetical protein; 80.3 13 0.00028 25.4 7.0 58 202-269 8-65 (78)
32 PRK05528 methionine sulfoxide 80.2 4 8.6E-05 32.2 4.8 48 138-185 9-70 (156)
33 PRK13014 methionine sulfoxide 78.9 3 6.5E-05 33.8 3.9 48 138-185 16-82 (186)
34 PRK00058 methionine sulfoxide 78.3 4.1 8.8E-05 33.8 4.5 49 138-186 53-120 (213)
35 cd03422 YedF YedF is a bacteri 77.4 15 0.00032 24.4 6.4 56 205-270 2-57 (69)
36 cd03423 SirA SirA (also known 77.4 17 0.00037 24.1 6.7 56 205-270 2-57 (69)
37 cd00291 SirA_YedF_YeeD SirA, Y 76.3 17 0.00036 23.8 6.5 56 205-270 2-57 (69)
38 cd03420 SirA_RHOD_Pry_redox Si 75.3 20 0.00044 23.7 6.6 56 205-270 2-57 (69)
39 cd03421 SirA_like_N SirA_like_ 74.1 21 0.00046 23.3 6.5 54 205-269 2-55 (67)
40 PF01625 PMSR: Peptide methion 72.9 9.7 0.00021 30.0 5.2 49 138-186 8-75 (155)
41 PRK05528 methionine sulfoxide 71.8 13 0.00028 29.3 5.6 47 215-261 10-70 (156)
42 COG0425 SirA Predicted redox p 71.4 27 0.00058 24.0 6.5 60 202-271 5-65 (78)
43 PRK13014 methionine sulfoxide 70.1 9 0.0002 31.1 4.6 53 206-261 11-82 (186)
44 PRK11018 hypothetical protein; 70.1 24 0.00051 24.1 6.1 56 54-119 8-63 (78)
45 PRK00058 methionine sulfoxide 69.1 11 0.00023 31.3 4.9 53 206-261 48-119 (213)
46 PF01625 PMSR: Peptide methion 68.7 21 0.00046 28.1 6.3 49 214-262 8-75 (155)
47 TIGR00401 msrA methionine-S-su 68.1 9.8 0.00021 29.7 4.3 48 138-185 8-74 (149)
48 TIGR00401 msrA methionine-S-su 67.5 18 0.0004 28.2 5.7 47 215-261 9-74 (149)
49 PRK00299 sulfur transfer prote 63.2 46 0.001 22.8 7.2 58 202-269 9-66 (81)
50 COG0225 MsrA Peptide methionin 63.0 22 0.00047 28.5 5.3 54 206-262 9-81 (174)
51 PRK05550 bifunctional methioni 62.9 13 0.00028 32.4 4.4 48 138-185 135-201 (283)
52 cd03420 SirA_RHOD_Pry_redox Si 62.3 27 0.00058 23.1 5.1 53 57-119 2-54 (69)
53 COG0225 MsrA Peptide methionin 62.0 13 0.00027 29.8 3.8 49 138-186 14-81 (174)
54 cd03421 SirA_like_N SirA_like_ 61.3 42 0.00092 21.8 5.9 52 57-119 2-53 (67)
55 cd03423 SirA SirA (also known 58.9 41 0.00089 22.2 5.5 52 58-119 3-54 (69)
56 PF02680 DUF211: Uncharacteriz 58.7 30 0.00066 24.6 4.9 52 216-267 19-75 (95)
57 COG1888 Uncharacterized protei 58.5 63 0.0014 22.8 6.6 51 217-267 22-77 (97)
58 PRK00299 sulfur transfer prote 58.0 57 0.0012 22.4 6.2 55 55-119 10-64 (81)
59 PF02680 DUF211: Uncharacteriz 54.9 76 0.0016 22.7 6.3 64 53-117 5-73 (95)
60 COG2177 FtsX Cell division pro 54.0 1E+02 0.0023 27.0 8.6 88 128-233 62-150 (297)
61 KOG1635|consensus 53.5 49 0.0011 26.4 5.7 57 203-262 24-99 (191)
62 PRK05550 bifunctional methioni 53.1 32 0.0007 29.9 5.2 52 207-261 131-201 (283)
63 COG1888 Uncharacterized protei 52.3 82 0.0018 22.3 6.9 66 53-118 6-76 (97)
64 cd03422 YedF YedF is a bacteri 51.0 53 0.0012 21.7 5.0 52 58-119 3-54 (69)
65 PF11491 DUF3213: Protein of u 49.7 29 0.00062 24.0 3.5 52 215-266 12-63 (88)
66 PF11491 DUF3213: Protein of u 47.6 24 0.00052 24.4 2.8 53 139-191 12-64 (88)
67 cd00291 SirA_YedF_YeeD SirA, Y 46.5 79 0.0017 20.4 5.5 53 57-119 2-54 (69)
68 COG0425 SirA Predicted redox p 43.8 1E+02 0.0022 21.0 6.1 55 54-118 5-60 (78)
69 cd04888 ACT_PheB-BS C-terminal 43.2 93 0.002 20.3 7.4 60 175-234 13-74 (76)
70 KOG1635|consensus 42.6 46 0.001 26.6 4.1 49 138-186 32-99 (191)
71 TIGR03527 selenium_YedF seleni 41.7 1.1E+02 0.0024 25.0 6.5 53 206-268 2-54 (194)
72 PRK10555 aminoglycoside/multid 37.1 4.8E+02 0.01 27.4 11.7 122 140-262 62-210 (1037)
73 PRK14018 trifunctional thiored 36.2 59 0.0013 31.0 4.6 48 138-185 206-271 (521)
74 PF09580 Spore_YhcN_YlaJ: Spor 35.9 1.4E+02 0.003 23.7 6.2 48 213-260 74-123 (177)
75 COG2177 FtsX Cell division pro 32.8 3.2E+02 0.0069 24.1 8.3 78 65-159 71-152 (297)
76 PF09580 Spore_YhcN_YlaJ: Spor 30.8 1.3E+02 0.0028 23.8 5.3 36 137-172 74-109 (177)
77 PRK14018 trifunctional thiored 28.4 1.3E+02 0.0028 28.8 5.5 87 172-261 158-271 (521)
78 PF14437 MafB19-deam: MafB19-l 26.6 2E+02 0.0043 22.4 5.2 38 53-91 100-138 (146)
79 PF14424 Toxin-deaminase: The 25.8 1E+02 0.0022 23.5 3.6 30 125-154 97-126 (133)
80 PF02682 AHS1: Allophanate hyd 23.4 2.6E+02 0.0057 23.0 5.8 46 215-262 26-73 (202)
81 PHA02119 hypothetical protein 23.2 1.1E+02 0.0023 20.4 2.7 19 249-267 53-71 (87)
82 PF12156 ATPase-cat_bd: Putati 22.7 84 0.0018 22.0 2.4 22 60-83 25-46 (88)
83 PF01883 DUF59: Domain of unkn 21.3 1.7E+02 0.0036 19.2 3.6 33 54-86 37-72 (72)
84 PRK04435 hypothetical protein; 20.7 4E+02 0.0087 20.5 6.8 60 175-234 82-143 (147)
No 1
>KOG0207|consensus
Probab=99.94 E-value=5.4e-26 Score=213.78 Aligned_cols=213 Identities=43% Similarity=0.749 Sum_probs=195.2
Q ss_pred eCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhccccccCCCCC----ceeEEEECCCC
Q psy13021 60 DGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDARLPSTN----DEATFTVDGMK 135 (287)
Q Consensus 60 ~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~~~~~~----~~~~~~v~gm~ 135 (287)
.||+|..|.+.++.++...+|+.++.+++..+.+.+.|+ ...+.+.+++.++++||++...+.. ....+++.||+
T Consensus 1 ~gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~-~~~~~~~i~~~ied~gf~~~~~~~~~~~~~~~~l~v~Gmt 79 (951)
T KOG0207|consen 1 KGMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYD-NIVSPESIKETIEDMGFEASLLSDSEITASKCYLSVNGMT 79 (951)
T ss_pred CCccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEe-eccCHHHHHHHhhcccceeeecccCccccceeEEEecCce
Confidence 389999999999999999999999999999999999999 7778999999999999998765421 14589999999
Q ss_pred ChhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCChHHHHHHhhhcCCCceeeccCCCCC-ccceeeeccCCchh
Q psy13021 136 CQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLISPTEIAASISELGFPATVIDEAGSGE-GELELKISGMSCAS 214 (287)
Q Consensus 136 C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~~~~~~~~~~-~~~~~~v~gm~c~~ 214 (287)
|++|+..+++.|+..+|+.++.+.+..+.+.+.|+|..++.+.+.+.++++||.+..++..+... .+..|.+.||.|..
T Consensus 80 C~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~~~~~~~~~i~L~v~g~~c~s 159 (951)
T KOG0207|consen 80 CASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIESVNGNSNQKIYLDVLGMTCAS 159 (951)
T ss_pred eHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhcccCCCCCcEEEEeecccccc
Confidence 99999999999999999999999999999999999999999999999999999998876654332 67889999999999
Q ss_pred hHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEEeCCCC
Q psy13021 215 CVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTALLNSKD 273 (287)
Q Consensus 215 C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~~~~~~ 273 (287)
|+.+|+..|.+++||.++++++.+.++.+.|+|..++++++.+.|+..||.+......+
T Consensus 160 ~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~~~~ 218 (951)
T KOG0207|consen 160 CVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRPYGD 218 (951)
T ss_pred hhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeeeccc
Confidence 99999999999999999999999999999999999999999999999999877655433
No 2
>KOG0207|consensus
Probab=99.64 E-value=1.9e-15 Score=143.23 Aligned_cols=142 Identities=37% Similarity=0.744 Sum_probs=130.6
Q ss_pred CCCCChhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCChHHHHHHhhhcCCCceeeccCCCCCccceeeeccCC
Q psy13021 132 DGMKCQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLISPTEIAASISELGFPATVIDEAGSGEGELELKISGMS 211 (287)
Q Consensus 132 ~gm~C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~~~~~~~~~~~~~~~~v~gm~ 211 (287)
.||+|.+|++.++.++.+.+|+.++.+++..+.+.+.|+ ...+++.+.+.|+++||++...........+-.+.+.||+
T Consensus 1 ~gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~-~~~~~~~i~~~ied~gf~~~~~~~~~~~~~~~~l~v~Gmt 79 (951)
T KOG0207|consen 1 KGMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYD-NIVSPESIKETIEDMGFEASLLSDSEITASKCYLSVNGMT 79 (951)
T ss_pred CCccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEe-eccCHHHHHHHhhcccceeeecccCccccceeEEEecCce
Confidence 489999999999999999999999999999999999999 8889999999999999999887654433446679999999
Q ss_pred chhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEEeCCCCc
Q psy13021 212 CASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTALLNSKDK 274 (287)
Q Consensus 212 c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~~~~~~~ 274 (287)
|.+|+..+++.|+...|+.++.+.+......+.|+|..++...+.+.|+++||.+..+.....
T Consensus 80 C~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~~~~ 142 (951)
T KOG0207|consen 80 CASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIESVNG 142 (951)
T ss_pred eHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhcccC
Confidence 999999999999999999999999999999999999999999999999999999987766443
No 3
>PRK10671 copA copper exporting ATPase; Provisional
Probab=99.39 E-value=7.7e-12 Score=124.09 Aligned_cols=134 Identities=25% Similarity=0.559 Sum_probs=110.3
Q ss_pred CceEEEEEeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhccccccCCCC-------
Q psy13021 51 MASTVLISIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDARLPST------- 123 (287)
Q Consensus 51 ~~~~~~~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~~~~~------- 123 (287)
|++++++.|.||+|++|+.+++++|++++||..+.+++. +..+... .+.+.+.+.++++||.+.....
T Consensus 1 ~~~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~---~~~~~i~~~i~~~Gy~~~~~~~~~~~~~~ 75 (834)
T PRK10671 1 MSQTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGT---ASAEALIETIKQAGYDASVSHPKAKPLTE 75 (834)
T ss_pred CCeEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEec---CCHHHHHHHHHhcCCcccccccccccccc
Confidence 456789999999999999999999999999999999994 4444443 2678899999999999874210
Q ss_pred ----------------------CceeEEEECCCCChhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCChHHHHH
Q psy13021 124 ----------------------NDEATFTVDGMKCQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLISPTEIAA 181 (287)
Q Consensus 124 ----------------------~~~~~~~v~gm~C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~~~~i~~ 181 (287)
..+..+.+.||+|+.|++.+++.+...+|+..+.+++.+++..+.. ..+..++.+
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~---~~s~~~I~~ 152 (834)
T PRK10671 76 SSIPSEALTAASEELPAATADDDDSQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMG---SASPQDLVQ 152 (834)
T ss_pred cccCchhhhhhhhhccccccCcCceEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEc---cCCHHHHHH
Confidence 0134688999999999999999999999999999999998877763 245677888
Q ss_pred HhhhcCCCcee
Q psy13021 182 SISELGFPATV 192 (287)
Q Consensus 182 ~i~~~G~~~~~ 192 (287)
.+++.||.+.+
T Consensus 153 ~I~~~Gy~a~~ 163 (834)
T PRK10671 153 AVEKAGYGAEA 163 (834)
T ss_pred HHHhcCCCccc
Confidence 88999998754
No 4
>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=99.37 E-value=2.7e-12 Score=85.48 Aligned_cols=62 Identities=35% Similarity=0.663 Sum_probs=59.1
Q ss_pred EEEECCCCChhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCChHHHHHHhhhcCCC
Q psy13021 128 TFTVDGMKCQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLISPTEIAASISELGFP 189 (287)
Q Consensus 128 ~~~v~gm~C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~ 189 (287)
+|.|.||+|++|+.+|+++|.+++||.++.+|+.++++.|.|++...++++|.+.|+++||+
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 58899999999999999999999999999999999999999998878889999999999995
No 5
>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=99.36 E-value=6.1e-12 Score=83.78 Aligned_cols=62 Identities=37% Similarity=0.700 Sum_probs=59.3
Q ss_pred eeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCe
Q psy13021 204 ELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFT 265 (287)
Q Consensus 204 ~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~ 265 (287)
+|.|.||.|++|+.+|+++|.+++||.++.+++.++.+.|.|++....+++|.+.|+++||+
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 47899999999999999999999999999999999999999999888899999999999995
No 6
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.31 E-value=1.5e-11 Score=83.90 Aligned_cols=67 Identities=28% Similarity=0.572 Sum_probs=62.4
Q ss_pred eEEEEEeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhcccccc
Q psy13021 53 STVLISIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDAR 119 (287)
Q Consensus 53 ~~~~~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~ 119 (287)
++..+.++||+|.+|+.+++++|+.++||..+.+++..+.+.+.++....+.+.+.++++++||.+.
T Consensus 2 ~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~ 68 (71)
T COG2608 2 MKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVE 68 (71)
T ss_pred ceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCee
Confidence 4678999999999999999999999999999999999999999999866689999999999999864
No 7
>PRK10671 copA copper exporting ATPase; Provisional
Probab=99.28 E-value=7.1e-11 Score=117.26 Aligned_cols=136 Identities=25% Similarity=0.556 Sum_probs=110.6
Q ss_pred eeEEEECCCCChhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCChHHHHHHhhhcCCCceeeccCC--------
Q psy13021 126 EATFTVDGMKCQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLISPTEIAASISELGFPATVIDEAG-------- 197 (287)
Q Consensus 126 ~~~~~v~gm~C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~~~~~~~-------- 197 (287)
...+.|+||+|++|+.+++++|++++||..+.+++.+ ..+.. ..+.+.+.+.++++||++.......
T Consensus 4 ~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~~--~~v~~---~~~~~~i~~~i~~~Gy~~~~~~~~~~~~~~~~~ 78 (834)
T PRK10671 4 TIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSITE--AHVTG---TASAEALIETIKQAGYDASVSHPKAKPLTESSI 78 (834)
T ss_pred EEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeeeE--EEEEe---cCCHHHHHHHHHhcCCccccccccccccccccc
Confidence 4689999999999999999999999999999999954 44443 2467899999999999987642100
Q ss_pred -----------------CCCccceeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHH
Q psy13021 198 -----------------SGEGELELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIE 260 (287)
Q Consensus 198 -----------------~~~~~~~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~ 260 (287)
....+..+.+.||.|..|...+++.+...+|+..+.+++.+....+.+ ....+++.+.++
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~---~~s~~~I~~~I~ 155 (834)
T PRK10671 79 PSEALTAASEELPAATADDDDSQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMG---SASPQDLVQAVE 155 (834)
T ss_pred CchhhhhhhhhccccccCcCceEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEc---cCCHHHHHHHHH
Confidence 001245688999999999999999999999999999999998877763 345788888999
Q ss_pred hcCCeeEEe
Q psy13021 261 KLGFTTALL 269 (287)
Q Consensus 261 ~~G~~~~~~ 269 (287)
.+||.+.+.
T Consensus 156 ~~Gy~a~~~ 164 (834)
T PRK10671 156 KAGYGAEAI 164 (834)
T ss_pred hcCCCcccc
Confidence 999987643
No 8
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.21 E-value=1.2e-10 Score=79.38 Aligned_cols=67 Identities=25% Similarity=0.544 Sum_probs=63.3
Q ss_pred cceeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEE
Q psy13021 202 ELELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTAL 268 (287)
Q Consensus 202 ~~~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~ 268 (287)
+..|.++||+|.+|+..++++|.+++|+..+.+++..+...+.|++.....++|.++|+.+||.+..
T Consensus 3 ~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~ 69 (71)
T COG2608 3 KTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEE 69 (71)
T ss_pred eEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeee
Confidence 4679999999999999999999999999999999999999999998889999999999999998764
No 9
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.36 E-value=8.9e-07 Score=85.47 Aligned_cols=66 Identities=29% Similarity=0.715 Sum_probs=60.7
Q ss_pred eeEEEECCCCChhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCC-hHHHHHHhhhcCCCcee
Q psy13021 126 EATFTVDGMKCQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLIS-PTEIAASISELGFPATV 192 (287)
Q Consensus 126 ~~~~~v~gm~C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~-~~~i~~~i~~~G~~~~~ 192 (287)
+..|.++||+|++|++++| +|++++||.++++|+.++++.+.|++.... .+++...++..||.+..
T Consensus 3 ~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 3 ETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred eeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 4679999999999999999 999999999999999999999999987666 78999999999998754
No 10
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.13 E-value=5.9e-06 Score=79.88 Aligned_cols=66 Identities=39% Similarity=0.772 Sum_probs=61.1
Q ss_pred cceeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCC-HHHHHHHHHhcCCeeEE
Q psy13021 202 ELELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTG-PRDVMECIEKLGFTTAL 268 (287)
Q Consensus 202 ~~~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~-~~~i~~~I~~~G~~~~~ 268 (287)
+..|.+.||+|+.|+.+|| +|++++||..+.+|+.++.+.+.|++.... ..++...++..||.+..
T Consensus 3 ~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 3 ETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred eeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 5679999999999999999 999999999999999999999999987666 79999999999998764
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=0.00011 Score=47.37 Aligned_cols=64 Identities=33% Similarity=0.517 Sum_probs=54.9
Q ss_pred eEEEECCCCChhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCChHHHHHHhhhcCCCc
Q psy13021 127 ATFTVDGMKCQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLISPTEIAASISELGFPA 190 (287)
Q Consensus 127 ~~~~v~gm~C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~ 190 (287)
..+.+.|+.|..|.+.+++.+...+++....+++....+.+.+++.......+...+...||.+
T Consensus 4 ~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 4 FTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYEV 67 (68)
T ss_pred EEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCCc
Confidence 4688999999999999999999999999999999999999998766556677767778888864
No 12
>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=97.83 E-value=0.00022 Score=45.91 Aligned_cols=65 Identities=26% Similarity=0.510 Sum_probs=53.8
Q ss_pred EEEEEeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhccccc
Q psy13021 54 TVLISIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDA 118 (287)
Q Consensus 54 ~~~~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~ 118 (287)
+..+.+.|++|..|...++..+...+++....+++......+.+++.......+...+...||.+
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYEV 67 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCCc
Confidence 46799999999999999999999999999999999999999988754435556666677778753
No 13
>PLN02957 copper, zinc superoxide dismutase
Probab=97.80 E-value=0.00016 Score=61.38 Aligned_cols=72 Identities=22% Similarity=0.399 Sum_probs=62.0
Q ss_pred CccceeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEEeCCCCcc
Q psy13021 200 EGELELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTALLNSKDKD 275 (287)
Q Consensus 200 ~~~~~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~~~~~~~~ 275 (287)
++++.+.+ +|.|..|+..+++.|.+++|+..+.+++....+.+.|. ...+++...|+++||.+.+....+.+
T Consensus 5 ~~~~~~~V-gMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~---~~~~~I~~aIe~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 5 ELLTEFMV-DMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGS---SPVKAMTAALEQTGRKARLIGQGDPE 76 (238)
T ss_pred cEEEEEEE-CccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEec---CCHHHHHHHHHHcCCcEEEecCCCcc
Confidence 45667888 79999999999999999999999999999999999873 46888999999999998877665444
No 14
>KOG4656|consensus
Probab=97.72 E-value=0.00014 Score=58.40 Aligned_cols=61 Identities=28% Similarity=0.577 Sum_probs=52.9
Q ss_pred EEEEEeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhccccc
Q psy13021 54 TVLISIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDA 118 (287)
Q Consensus 54 ~~~~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~ 118 (287)
.++|.|. |+|.+|++.++..|+.++||.++.+++..+.+.+.... .+..+.+.++.+|-.+
T Consensus 8 ~~efaV~-M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~---p~s~i~~~le~tGr~A 68 (247)
T KOG4656|consen 8 EAEFAVQ-MTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSV---PPSEIQNTLENTGRDA 68 (247)
T ss_pred eEEEEEe-chhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccC---ChHHHHHHHHhhChhe
Confidence 4678886 99999999999999999999999999999888887643 5788999999999543
No 15
>PLN02957 copper, zinc superoxide dismutase
Probab=97.58 E-value=0.00053 Score=58.14 Aligned_cols=66 Identities=24% Similarity=0.407 Sum_probs=57.6
Q ss_pred eeEEEECCCCChhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCChHHHHHHhhhcCCCceeecc
Q psy13021 126 EATFTVDGMKCQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLISPTEIAASISELGFPATVIDE 195 (287)
Q Consensus 126 ~~~~~v~gm~C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~~~~~ 195 (287)
...+.+ +|.|.+|+.++++.|.+++||..+.+++..+++.+.+. .....+...+++.||.+.+...
T Consensus 7 ~~~~~V-gMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~---~~~~~I~~aIe~~Gy~a~~~~~ 72 (238)
T PLN02957 7 LTEFMV-DMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGS---SPVKAMTAALEQTGRKARLIGQ 72 (238)
T ss_pred EEEEEE-CccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEec---CCHHHHHHHHHHcCCcEEEecC
Confidence 456888 79999999999999999999999999999999998873 4677888999999999876654
No 16
>KOG4656|consensus
Probab=97.34 E-value=0.00064 Score=54.72 Aligned_cols=68 Identities=26% Similarity=0.458 Sum_probs=57.3
Q ss_pred ceeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEEeCCCCc
Q psy13021 203 LELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTALLNSKDK 274 (287)
Q Consensus 203 ~~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~~~~~~~ 274 (287)
..|.| .|+|.+|+..+...|..++||.++.+++..+.+.|. ......+|.+.|+..|-++.......+
T Consensus 9 ~efaV-~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~---ts~p~s~i~~~le~tGr~Avl~G~G~p 76 (247)
T KOG4656|consen 9 AEFAV-QMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVE---TSVPPSEIQNTLENTGRDAVLRGAGKP 76 (247)
T ss_pred EEEEE-echhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEE---ccCChHHHHHHHHhhChheEEecCCch
Confidence 34554 689999999999999999999999999999998887 345689999999999988876554433
No 17
>KOG1603|consensus
Probab=97.28 E-value=0.002 Score=43.94 Aligned_cols=54 Identities=15% Similarity=0.399 Sum_probs=47.3
Q ss_pred eeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhcc
Q psy13021 59 IDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMG 115 (287)
Q Consensus 59 v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G 115 (287)
.-+|+|.+|...+++.+..+.||.++.++...+.+++.... ++..+.+.+...|
T Consensus 10 kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~---~p~~vl~~l~k~~ 63 (73)
T KOG1603|consen 10 KVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNV---DPVKLLKKLKKTG 63 (73)
T ss_pred EECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEec---CHHHHHHHHHhcC
Confidence 34799999999999999999999999999999999998762 6777888887755
No 18
>KOG1603|consensus
Probab=97.13 E-value=0.0014 Score=44.79 Aligned_cols=55 Identities=18% Similarity=0.454 Sum_probs=48.6
Q ss_pred EECCCCChhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCChHHHHHHhhhcC
Q psy13021 130 TVDGMKCQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLISPTEIAASISELG 187 (287)
Q Consensus 130 ~v~gm~C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G 187 (287)
..-.|+|..|..++.+.|+.+.||.++.++...+++.+.- ..++..+.+.+.+.|
T Consensus 9 ~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g---~~~p~~vl~~l~k~~ 63 (73)
T KOG1603|consen 9 LKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKG---NVDPVKLLKKLKKTG 63 (73)
T ss_pred EEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEE---ecCHHHHHHHHHhcC
Confidence 3348999999999999999999999999999999999884 367889999998876
No 19
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.87 E-value=0.0029 Score=62.54 Aligned_cols=66 Identities=24% Similarity=0.531 Sum_probs=57.1
Q ss_pred eeEEEECCCCChhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCChHHHHHHhhhcCCCceee
Q psy13021 126 EATFTVDGMKCQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLISPTEIAASISELGFPATVI 193 (287)
Q Consensus 126 ~~~~~v~gm~C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~~~ 193 (287)
+..+.+.||+|++|++.+++.+.+.+||..+.+++.+++..+.|++.. . ..+.+.+++.||.+...
T Consensus 54 r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~-~-~~I~~aI~~~Gy~a~~~ 119 (741)
T PRK11033 54 RYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDI-R-AQVESAVQKAGFSLRDE 119 (741)
T ss_pred eEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccc-h-HHHHHHHHhcccccccc
Confidence 567899999999999999999999999999999999999999887652 3 67778888999987543
No 20
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.73 E-value=0.0073 Score=59.74 Aligned_cols=66 Identities=20% Similarity=0.449 Sum_probs=56.2
Q ss_pred ceEEEEEeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhcccccc
Q psy13021 52 ASTVLISIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDAR 119 (287)
Q Consensus 52 ~~~~~~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~ 119 (287)
..+..+.+.||+|++|...++..+...+||..+.+++.+.+..+.+++.. . ..+.+.+++.||.+.
T Consensus 52 ~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~-~-~~I~~aI~~~Gy~a~ 117 (741)
T PRK11033 52 GTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDI-R-AQVESAVQKAGFSLR 117 (741)
T ss_pred CceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccc-h-HHHHHHHHhcccccc
Confidence 34567899999999999999999999999999999999999888887653 3 567777888999764
No 21
>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=94.26 E-value=0.45 Score=32.81 Aligned_cols=66 Identities=18% Similarity=0.470 Sum_probs=49.0
Q ss_pred eeEEEECCCCChhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCChHHHHHHhhhcCCCce
Q psy13021 126 EATFTVDGMKCQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLISPTEIAASISELGFPAT 191 (287)
Q Consensus 126 ~~~~~v~gm~C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~ 191 (287)
...+.+.|+.|..|...++..+...+++.....++......+.++........+...+...||..+
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 89 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSS 89 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeE
Confidence 346778999999999999999999999888888877777666654433345555555667777654
No 22
>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=93.79 E-value=0.82 Score=31.43 Aligned_cols=66 Identities=26% Similarity=0.542 Sum_probs=50.9
Q ss_pred cceeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeE
Q psy13021 202 ELELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTA 267 (287)
Q Consensus 202 ~~~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~ 267 (287)
...+.+.++.|..|...++..+...+++.....++......+.+.+.......+...+...||..+
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 89 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSS 89 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeE
Confidence 345778999999999999999999999887888877777666665543456666667778888754
No 23
>PRK13748 putative mercuric reductase; Provisional
Probab=89.10 E-value=2.3 Score=40.82 Aligned_cols=69 Identities=26% Similarity=0.577 Sum_probs=54.9
Q ss_pred eeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEEeCCCC
Q psy13021 204 ELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTALLNSKD 273 (287)
Q Consensus 204 ~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~~~~~~ 273 (287)
.+.+.++.|..|...++..+...+++.....++......+.+.+ ......+...++..||...+...++
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~-~~~~~~i~~~i~~~g~~~~~~~~~~ 71 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEV-GTSPDALTAAVAGLGYRATLADAPP 71 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECC-CCCHHHHHHHHHHcCCeeeccCccc
Confidence 35688999999999999999999998888888888887777654 3466777777888999876655543
No 24
>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=88.88 E-value=2.9 Score=23.84 Aligned_cols=41 Identities=44% Similarity=0.822 Sum_probs=31.2
Q ss_pred EECCCCChhHHHHHHHHhccCCCeeEEEEeeecceeeeecc
Q psy13021 130 TVDGMKCQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYS 170 (287)
Q Consensus 130 ~v~gm~C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~ 170 (287)
.+.++.|..|...+...+...+++.....++......+.+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 43 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYD 43 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEEC
Confidence 46788999999999988888888777777766655555543
No 25
>PRK13748 putative mercuric reductase; Provisional
Probab=87.05 E-value=2.9 Score=40.08 Aligned_cols=67 Identities=28% Similarity=0.593 Sum_probs=51.8
Q ss_pred EEEECCCCChhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCChHHHHHHhhhcCCCceeecc
Q psy13021 128 TFTVDGMKCQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLISPTEIAASISELGFPATVIDE 195 (287)
Q Consensus 128 ~~~v~gm~C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~~~~~ 195 (287)
.+.+.||.|++|..+++..+...+++....+++......+.+.+. .....+...+...||...+...
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~-~~~~~i~~~i~~~g~~~~~~~~ 69 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVG-TSPDALTAAVAGLGYRATLADA 69 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCC-CCHHHHHHHHHHcCCeeeccCc
Confidence 366899999999999999999999998888888888877776532 4556666667788887655443
No 26
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=86.51 E-value=1.5 Score=35.18 Aligned_cols=49 Identities=24% Similarity=0.353 Sum_probs=42.1
Q ss_pred hHHHHHHHHhccCCCeeEEEEeeecce-------------------eeeeccCCCCChHHHHHHhhhc
Q psy13021 138 SCVKKIEATIGEKPGINSVLVALLAAK-------------------AEIRYSKDLISPTEIAASISEL 186 (287)
Q Consensus 138 ~C~~~ie~~l~~~~gV~~~~v~~~~~~-------------------~~v~~~~~~~~~~~i~~~i~~~ 186 (287)
.|=|-++..+.+++||.++.+-++.+. +.|.|||..++.++|++.....
T Consensus 11 GCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~~~ 78 (172)
T PRK14054 11 GCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFFQI 78 (172)
T ss_pred CChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHHHh
Confidence 578999999999999999998877775 6799999999999998877644
No 27
>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=84.68 E-value=4.2 Score=26.99 Aligned_cols=56 Identities=20% Similarity=0.272 Sum_probs=41.3
Q ss_pred eeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEEe
Q psy13021 204 ELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTALL 269 (287)
Q Consensus 204 ~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~~ 269 (287)
++.+.|..|+.....+.++|..++. ...+.|..+. ....++|...++..||....+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~---------G~~l~v~~d~-~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPP---------GEVLEVLVDD-PAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGT---------T-EEEEEESS-TTHHHHHHHHHHHHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCC---------CCEEEEEECC-ccHHHHHHHHHHHCCCEEEEE
Confidence 4678899999999999999999742 2344555543 345789999999999986544
No 28
>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=84.35 E-value=5.6 Score=22.52 Aligned_cols=58 Identities=41% Similarity=0.828 Sum_probs=39.7
Q ss_pred eeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCC
Q psy13021 206 KISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGF 264 (287)
Q Consensus 206 ~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~ 264 (287)
.+.++.|..|...+...+...+++.....++......+.+... .....+...+...|+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ 60 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPE-VSPEELLEAIEDAGY 60 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCC-CCHHHHHHHHHHcCC
Confidence 3568889999999998888888877777777666666666443 344444444455554
No 29
>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=81.99 E-value=7 Score=25.86 Aligned_cols=53 Identities=11% Similarity=0.256 Sum_probs=39.3
Q ss_pred EEEeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhccccc
Q psy13021 56 LISIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDA 118 (287)
Q Consensus 56 ~~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~ 118 (287)
++.+.|+.|+...-.+.++|..++.- ..+.+..+... ....+...++..||..
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~-~~~di~~~~~~~g~~~ 54 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPA-AVEDIPRWCEENGYEV 54 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTT-HHHHHHHHHHHHTEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCcc-HHHHHHHHHHHCCCEE
Confidence 46788999999999999999997532 33445555443 4678999999999974
No 30
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=81.70 E-value=4.1 Score=32.63 Aligned_cols=48 Identities=23% Similarity=0.394 Sum_probs=38.3
Q ss_pred hHHHHHHHhhcCCCeeEEEEEccCCe-------------------EEEEEcCCCCCHHHHHHHHHhc
Q psy13021 215 CVNKIETSVKKLAGIKSAVVALTTQR-------------------GKFRYDLEVTGPRDVMECIEKL 262 (287)
Q Consensus 215 C~~~ie~~l~~~~gv~~~~v~~~~~~-------------------~~v~~~~~~~~~~~i~~~I~~~ 262 (287)
|-..++..+.+++||.+..+-.+.+. +.|.|||..++.++|++..-..
T Consensus 12 CFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~~~ 78 (172)
T PRK14054 12 CFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFFQI 78 (172)
T ss_pred ChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHHHh
Confidence 45556777888999999988777764 7799999999999998865443
No 31
>PRK11018 hypothetical protein; Provisional
Probab=80.25 E-value=13 Score=25.41 Aligned_cols=58 Identities=12% Similarity=0.119 Sum_probs=44.1
Q ss_pred cceeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEEe
Q psy13021 202 ELELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTALL 269 (287)
Q Consensus 202 ~~~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~~ 269 (287)
...+.+.|..|+....+..++|.+++ ....+.|..+. ....+.+...++..||.+...
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~---------~G~~L~V~~d~-~~a~~di~~~~~~~G~~v~~~ 65 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLK---------KGEILEVVSDC-PQSINNIPLDARNHGYTVLDI 65 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCC---------CCCEEEEEeCC-ccHHHHHHHHHHHcCCEEEEE
Confidence 35688999999999999999999875 23334455443 345788999999999998643
No 32
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=80.16 E-value=4 Score=32.18 Aligned_cols=48 Identities=15% Similarity=0.310 Sum_probs=40.0
Q ss_pred hHHHHHHHHhccCCCeeEEEEeeecce--------------eeeeccCCCCChHHHHHHhhh
Q psy13021 138 SCVKKIEATIGEKPGINSVLVALLAAK--------------AEIRYSKDLISPTEIAASISE 185 (287)
Q Consensus 138 ~C~~~ie~~l~~~~gV~~~~v~~~~~~--------------~~v~~~~~~~~~~~i~~~i~~ 185 (287)
.|=|-+|..+.+++||.+..+-++.+. +.|.|||..++.++|++....
T Consensus 9 GCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~~ 70 (156)
T PRK05528 9 GCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLFE 70 (156)
T ss_pred CCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHHH
Confidence 578999999999999999888766543 568999999999999887654
No 33
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=78.89 E-value=3 Score=33.84 Aligned_cols=48 Identities=19% Similarity=0.335 Sum_probs=40.7
Q ss_pred hHHHHHHHHhccCCCeeEEEEeeecce-------------------eeeeccCCCCChHHHHHHhhh
Q psy13021 138 SCVKKIEATIGEKPGINSVLVALLAAK-------------------AEIRYSKDLISPTEIAASISE 185 (287)
Q Consensus 138 ~C~~~ie~~l~~~~gV~~~~v~~~~~~-------------------~~v~~~~~~~~~~~i~~~i~~ 185 (287)
.|=|-++..+.+++||.+..+-++.+. +.|.|||..++.++|++....
T Consensus 16 GCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff~ 82 (186)
T PRK13014 16 GCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFFS 82 (186)
T ss_pred CCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHHH
Confidence 567888999999999999998877764 578999999999999887764
No 34
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=78.34 E-value=4.1 Score=33.80 Aligned_cols=49 Identities=20% Similarity=0.260 Sum_probs=41.0
Q ss_pred hHHHHHHHHhccCCCeeEEEEeeecc-------------------eeeeeccCCCCChHHHHHHhhhc
Q psy13021 138 SCVKKIEATIGEKPGINSVLVALLAA-------------------KAEIRYSKDLISPTEIAASISEL 186 (287)
Q Consensus 138 ~C~~~ie~~l~~~~gV~~~~v~~~~~-------------------~~~v~~~~~~~~~~~i~~~i~~~ 186 (287)
.|=|-+|..+.+++||.+..+-++.+ .+.|.|||..++.++|++.....
T Consensus 53 GCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff~~ 120 (213)
T PRK00058 53 GCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFWEN 120 (213)
T ss_pred cCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHHHh
Confidence 57789999999999999999988744 26789999999999998877543
No 35
>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=77.37 E-value=15 Score=24.41 Aligned_cols=56 Identities=11% Similarity=0.105 Sum_probs=41.8
Q ss_pred eeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEEeC
Q psy13021 205 LKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTALLN 270 (287)
Q Consensus 205 ~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~~~ 270 (287)
+...|..|+.-..+..++|++++ ....+.|..+. ......|....+..||.+....
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~---------~G~~l~V~~d~-~~s~~ni~~~~~~~g~~v~~~~ 57 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLK---------PGEILEVISDC-PQSINNIPIDARNHGYKVLAIE 57 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCC---------CCCEEEEEecC-chHHHHHHHHHHHcCCEEEEEE
Confidence 45679999999999999999875 23334454443 3468889999999999986543
No 36
>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=77.35 E-value=17 Score=24.08 Aligned_cols=56 Identities=18% Similarity=0.194 Sum_probs=41.8
Q ss_pred eeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEEeC
Q psy13021 205 LKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTALLN 270 (287)
Q Consensus 205 ~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~~~ 270 (287)
+...|..|+.-.....++|.+++ ....+.|..+. ....+++...++..||......
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~---------~G~~l~V~~dd-~~s~~di~~~~~~~g~~~~~~~ 57 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMK---------PGDTLLVLATD-PSTTRDIPKFCTFLGHELLAQE 57 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCC---------CCCEEEEEeCC-CchHHHHHHHHHHcCCEEEEEE
Confidence 45679999999999999998874 22334555443 3468889999999999987543
No 37
>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=76.31 E-value=17 Score=23.81 Aligned_cols=56 Identities=18% Similarity=0.241 Sum_probs=41.1
Q ss_pred eeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEEeC
Q psy13021 205 LKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTALLN 270 (287)
Q Consensus 205 ~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~~~ 270 (287)
+...|+.|+.-...+.++|.+++ ....+.+..+. .....++...++..||......
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~---------~g~~l~v~~d~-~~~~~~i~~~~~~~g~~~~~~~ 57 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLK---------SGEVLEVLLDD-PGAVEDIPAWAKETGHEVLEVE 57 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCC---------CCCEEEEEecC-CcHHHHHHHHHHHcCCEEEEEE
Confidence 45679999999999999998865 23344455443 2368889999999999875443
No 38
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=75.28 E-value=20 Score=23.71 Aligned_cols=56 Identities=18% Similarity=0.239 Sum_probs=41.7
Q ss_pred eeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEEeC
Q psy13021 205 LKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTALLN 270 (287)
Q Consensus 205 ~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~~~ 270 (287)
+.+.|+.|+.-.....++|.++. ....+.|..+. .....++....+..||......
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~---------~G~~l~V~~d~-~~a~~di~~~~~~~G~~~~~~~ 57 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQ---------DGEQLEVKASD-PGFARDAQAWCKSTGNTLISLE 57 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCC---------CCCEEEEEECC-ccHHHHHHHHHHHcCCEEEEEE
Confidence 56789999999999999999875 22334444443 3457889999999999887543
No 39
>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=74.09 E-value=21 Score=23.30 Aligned_cols=54 Identities=17% Similarity=0.266 Sum_probs=38.3
Q ss_pred eeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEEe
Q psy13021 205 LKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTALL 269 (287)
Q Consensus 205 ~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~~ 269 (287)
+.+.|+.|+.......++| .+.. .+.+.|..+. ....+.|....+..||.....
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~-~~s~~~i~~~~~~~G~~~~~~ 55 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEA---------GGEIEVLVDN-EVAKENVSRFAESRGYEVSVE 55 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCC---------CCEEEEEEcC-hhHHHHHHHHHHHcCCEEEEE
Confidence 5578999999999999999 5532 2233444332 345678999999999998543
No 40
>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=72.87 E-value=9.7 Score=29.99 Aligned_cols=49 Identities=22% Similarity=0.378 Sum_probs=40.1
Q ss_pred hHHHHHHHHhccCCCeeEEEEeeecce-------------------eeeeccCCCCChHHHHHHhhhc
Q psy13021 138 SCVKKIEATIGEKPGINSVLVALLAAK-------------------AEIRYSKDLISPTEIAASISEL 186 (287)
Q Consensus 138 ~C~~~ie~~l~~~~gV~~~~v~~~~~~-------------------~~v~~~~~~~~~~~i~~~i~~~ 186 (287)
.|=|.++..+.+++||.+..+-++.+. +.|.|||..++.++|++.....
T Consensus 8 GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~is~~~Ll~~f~~~ 75 (155)
T PF01625_consen 8 GCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVISYEELLDVFFRI 75 (155)
T ss_dssp SSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS-HHHHHHHHHHH
T ss_pred CCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcccHHHHHHHHHHh
Confidence 578999999999999999999887763 4588999999999888877544
No 41
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=71.80 E-value=13 Score=29.34 Aligned_cols=47 Identities=17% Similarity=0.259 Sum_probs=36.3
Q ss_pred hHHHHHHHhhcCCCeeEEEEEccCC--------------eEEEEEcCCCCCHHHHHHHHHh
Q psy13021 215 CVNKIETSVKKLAGIKSAVVALTTQ--------------RGKFRYDLEVTGPRDVMECIEK 261 (287)
Q Consensus 215 C~~~ie~~l~~~~gv~~~~v~~~~~--------------~~~v~~~~~~~~~~~i~~~I~~ 261 (287)
|-.-+|..+.+++||.+..+-.+.+ .+.|.|||..++.++|++..-.
T Consensus 10 CFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~~ 70 (156)
T PRK05528 10 CLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLFE 70 (156)
T ss_pred CchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHHH
Confidence 4455667788889999887776653 2679999999999999886554
No 42
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=71.37 E-value=27 Score=23.96 Aligned_cols=60 Identities=17% Similarity=0.210 Sum_probs=43.5
Q ss_pred cceeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcC-CeeEEeCC
Q psy13021 202 ELELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLG-FTTALLNS 271 (287)
Q Consensus 202 ~~~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G-~~~~~~~~ 271 (287)
...+.+.|..|+.-.....++|.+++ ....+.|..+.. ...++|....+..| |.......
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~---------~Ge~LeV~~ddp-~~~~dIp~~~~~~~~~~ll~~e~ 65 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLK---------PGEILEVIADDP-AAKEDIPAWAKKEGGHELLEVEQ 65 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCC---------CCCEEEEEecCc-chHHHHHHHHHHcCCcEEEEEEe
Confidence 34688999999999999999999985 344455555433 34688999999665 77654443
No 43
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=70.08 E-value=9 Score=31.10 Aligned_cols=53 Identities=13% Similarity=0.196 Sum_probs=40.2
Q ss_pred eeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCe-------------------EEEEEcCCCCCHHHHHHHHHh
Q psy13021 206 KISGMSCASCVNKIETSVKKLAGIKSAVVALTTQR-------------------GKFRYDLEVTGPRDVMECIEK 261 (287)
Q Consensus 206 ~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~-------------------~~v~~~~~~~~~~~i~~~I~~ 261 (287)
.+-++.|-.| ++..+.+++||.+..+-++.+. +.|.|||..++.++|++..-.
T Consensus 11 a~~agGCFWg---~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff~ 82 (186)
T PRK13014 11 ATFAGGCFWG---VEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFFS 82 (186)
T ss_pred EEEecCCcee---eHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHHH
Confidence 3445566555 4566778899999888777663 679999999999999886554
No 44
>PRK11018 hypothetical protein; Provisional
Probab=70.06 E-value=24 Score=24.12 Aligned_cols=56 Identities=5% Similarity=0.037 Sum_probs=42.2
Q ss_pred EEEEEeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhcccccc
Q psy13021 54 TVLISIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDAR 119 (287)
Q Consensus 54 ~~~~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~ 119 (287)
...+.+.|..|+...-..+++|+++..-+ .+.+..+... ....+...++..||.+.
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~~G~---------~L~V~~d~~~-a~~di~~~~~~~G~~v~ 63 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLKKGE---------ILEVVSDCPQ-SINNIPLDARNHGYTVL 63 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCCCCC---------EEEEEeCCcc-HHHHHHHHHHHcCCEEE
Confidence 35688999999999999999999986322 3445555433 56778888999999874
No 45
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=69.11 E-value=11 Score=31.35 Aligned_cols=53 Identities=23% Similarity=0.273 Sum_probs=39.7
Q ss_pred eeccCCchhhHHHHHHHhhcCCCeeEEEEEccCC-------------------eEEEEEcCCCCCHHHHHHHHHh
Q psy13021 206 KISGMSCASCVNKIETSVKKLAGIKSAVVALTTQ-------------------RGKFRYDLEVTGPRDVMECIEK 261 (287)
Q Consensus 206 ~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~-------------------~~~v~~~~~~~~~~~i~~~I~~ 261 (287)
.+-|+.|-.| +|..+.+++||.+..+-++.+ .+.|.|||..++.++|++..-+
T Consensus 48 a~fagGCFWg---~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff~ 119 (213)
T PRK00058 48 AIFGMGCFWG---AERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFWE 119 (213)
T ss_pred EEEEccCcch---hHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHHH
Confidence 3344456544 566688889999998887744 3779999999999999887654
No 46
>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=68.72 E-value=21 Score=28.07 Aligned_cols=49 Identities=18% Similarity=0.399 Sum_probs=38.5
Q ss_pred hhHHHHHHHhhcCCCeeEEEEEccCC-------------------eEEEEEcCCCCCHHHHHHHHHhc
Q psy13021 214 SCVNKIETSVKKLAGIKSAVVALTTQ-------------------RGKFRYDLEVTGPRDVMECIEKL 262 (287)
Q Consensus 214 ~C~~~ie~~l~~~~gv~~~~v~~~~~-------------------~~~v~~~~~~~~~~~i~~~I~~~ 262 (287)
.|-...+..+.+++||.+..+-++.+ .+.|.|||..++.++|++..-..
T Consensus 8 GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~is~~~Ll~~f~~~ 75 (155)
T PF01625_consen 8 GCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVISYEELLDVFFRI 75 (155)
T ss_dssp SSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS-HHHHHHHHHHH
T ss_pred CCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcccHHHHHHHHHHh
Confidence 34666777888999999998888776 36789999999999998876554
No 47
>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=68.14 E-value=9.8 Score=29.74 Aligned_cols=48 Identities=23% Similarity=0.315 Sum_probs=38.9
Q ss_pred hHHHHHHHHhccCCCeeEEEEeeecce-------------------eeeeccCCCCChHHHHHHhhh
Q psy13021 138 SCVKKIEATIGEKPGINSVLVALLAAK-------------------AEIRYSKDLISPTEIAASISE 185 (287)
Q Consensus 138 ~C~~~ie~~l~~~~gV~~~~v~~~~~~-------------------~~v~~~~~~~~~~~i~~~i~~ 185 (287)
.|=|-++..+.+++||.+..+-++.+. +.|.|||..++.++|++....
T Consensus 8 GCFWg~E~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~g~tgh~E~V~V~yDp~~is~~~Ll~~f~~ 74 (149)
T TIGR00401 8 GCFWGVEKYFWLIPGVYSTAVGYTGGYTPNPTYEEVCSGDTGHAEAVQVTYDPKVISYEELLDVFWE 74 (149)
T ss_pred CCchhhHHHHhcCCCEEEEEEeeCCCCCCCCChhhcccCCCCceEEEEEEECCCcCcHHHHHHHHHH
Confidence 578889999999999999888765553 458899999999998886654
No 48
>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=67.52 E-value=18 Score=28.21 Aligned_cols=47 Identities=19% Similarity=0.296 Sum_probs=35.5
Q ss_pred hHHHHHHHhhcCCCeeEEEEEccCC-------------------eEEEEEcCCCCCHHHHHHHHHh
Q psy13021 215 CVNKIETSVKKLAGIKSAVVALTTQ-------------------RGKFRYDLEVTGPRDVMECIEK 261 (287)
Q Consensus 215 C~~~ie~~l~~~~gv~~~~v~~~~~-------------------~~~v~~~~~~~~~~~i~~~I~~ 261 (287)
|-..++..+.+++||.+..+-++.+ .+.|.|||..++.++|++..-+
T Consensus 9 CFWg~E~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~g~tgh~E~V~V~yDp~~is~~~Ll~~f~~ 74 (149)
T TIGR00401 9 CFWGVEKYFWLIPGVYSTAVGYTGGYTPNPTYEEVCSGDTGHAEAVQVTYDPKVISYEELLDVFWE 74 (149)
T ss_pred CchhhHHHHhcCCCEEEEEEeeCCCCCCCCChhhcccCCCCceEEEEEEECCCcCcHHHHHHHHHH
Confidence 4444566777889998887766655 3568999999999999886544
No 49
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=63.20 E-value=46 Score=22.84 Aligned_cols=58 Identities=14% Similarity=0.155 Sum_probs=43.2
Q ss_pred cceeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEEe
Q psy13021 202 ELELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTALL 269 (287)
Q Consensus 202 ~~~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~~ 269 (287)
...+...|..|+.-.....++|.+++ ....+.|..+. ....++|....+..|+.....
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~---------~G~~l~V~~dd-~~~~~di~~~~~~~G~~~~~~ 66 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQ---------PGETLLIIADD-PATTRDIPSFCRFMDHELLAQ 66 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCC---------CCCEEEEEeCC-ccHHHHHHHHHHHcCCEEEEE
Confidence 45688999999999999999999875 22334444432 235788888999999988643
No 50
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=63.03 E-value=22 Score=28.47 Aligned_cols=54 Identities=17% Similarity=0.258 Sum_probs=40.4
Q ss_pred eeccCCchhhHHHHHHHhhcCCCeeEEEEEccCC-------------------eEEEEEcCCCCCHHHHHHHHHhc
Q psy13021 206 KISGMSCASCVNKIETSVKKLAGIKSAVVALTTQ-------------------RGKFRYDLEVTGPRDVMECIEKL 262 (287)
Q Consensus 206 ~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~-------------------~~~v~~~~~~~~~~~i~~~I~~~ 262 (287)
.+-++.|-.| +++.+..++||.+..+-.+.+ .+.|.|||..++.++|++..-+.
T Consensus 9 a~fagGCFWg---~E~~f~~i~GV~~t~~GYagG~~~nptY~~Vcsg~TgHaE~V~V~yDp~~isy~~LL~~ff~i 81 (174)
T COG0225 9 AYFAGGCFWG---VEAYFEQIPGVLSTVSGYAGGHTPNPTYEEVCSGTTGHAEAVEVTYDPKVISYEELLEVFFEI 81 (174)
T ss_pred EEEeccCccc---hHHHHhhCCCeEEEeeeEcCCCCCCCChhhccCCCCCceEEEEEEeCCccccHHHHHHHHhee
Confidence 3345556655 566777899999887776665 35689999999999999887654
No 51
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=62.87 E-value=13 Score=32.37 Aligned_cols=48 Identities=19% Similarity=0.261 Sum_probs=39.8
Q ss_pred hHHHHHHHHhccCCCeeEEEEeeecce-------------------eeeeccCCCCChHHHHHHhhh
Q psy13021 138 SCVKKIEATIGEKPGINSVLVALLAAK-------------------AEIRYSKDLISPTEIAASISE 185 (287)
Q Consensus 138 ~C~~~ie~~l~~~~gV~~~~v~~~~~~-------------------~~v~~~~~~~~~~~i~~~i~~ 185 (287)
.|=|-++..+.+++||.+..+-++.+. +.|.|||..++.++|++....
T Consensus 135 GCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~VcsG~tgH~EaV~V~yDp~~isy~~LL~~F~~ 201 (283)
T PRK05550 135 GCFWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEFDPAKISYETLLKVFFE 201 (283)
T ss_pred CCchhhhhhHhhCcCEEEEEEeeCCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHHh
Confidence 577899999999999999888776653 568999999999998887654
No 52
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=62.27 E-value=27 Score=23.10 Aligned_cols=53 Identities=8% Similarity=0.068 Sum_probs=39.5
Q ss_pred EEeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhcccccc
Q psy13021 57 ISIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDAR 119 (287)
Q Consensus 57 ~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~ 119 (287)
+.+.|+.|+.-.-..+++|.++..- ..+.+..+... ....+...++..||...
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~G---------~~l~V~~d~~~-a~~di~~~~~~~G~~~~ 54 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQDG---------EQLEVKASDPG-FARDAQAWCKSTGNTLI 54 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCC---------CEEEEEECCcc-HHHHHHHHHHHcCCEEE
Confidence 3467999999999999999998632 23445555433 56788889999999864
No 53
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=62.04 E-value=13 Score=29.78 Aligned_cols=49 Identities=24% Similarity=0.416 Sum_probs=40.6
Q ss_pred hHHHHHHHHhccCCCeeEEEEeeecce-------------------eeeeccCCCCChHHHHHHhhhc
Q psy13021 138 SCVKKIEATIGEKPGINSVLVALLAAK-------------------AEIRYSKDLISPTEIAASISEL 186 (287)
Q Consensus 138 ~C~~~ie~~l~~~~gV~~~~v~~~~~~-------------------~~v~~~~~~~~~~~i~~~i~~~ 186 (287)
.|=|-+++.+.+++||.++.+-.+.+. +.|.|||..++.++|++...+.
T Consensus 14 GCFWg~E~~f~~i~GV~~t~~GYagG~~~nptY~~Vcsg~TgHaE~V~V~yDp~~isy~~LL~~ff~i 81 (174)
T COG0225 14 GCFWGVEAYFEQIPGVLSTVSGYAGGHTPNPTYEEVCSGTTGHAEAVEVTYDPKVISYEELLEVFFEI 81 (174)
T ss_pred cCccchHHHHhhCCCeEEEeeeEcCCCCCCCChhhccCCCCCceEEEEEEeCCccccHHHHHHHHhee
Confidence 577888999999999999888766654 4588999999999999887655
No 54
>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=61.28 E-value=42 Score=21.83 Aligned_cols=52 Identities=13% Similarity=0.234 Sum_probs=36.2
Q ss_pred EEeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhcccccc
Q psy13021 57 ISIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDAR 119 (287)
Q Consensus 57 ~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~ 119 (287)
+-+.|+.|+.-.-...+++ ++..-. .+.+..+... +...+...++..||...
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~g~---------~l~v~~d~~~-s~~~i~~~~~~~G~~~~ 53 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEAGG---------EIEVLVDNEV-AKENVSRFAESRGYEVS 53 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCCCC---------EEEEEEcChh-HHHHHHHHHHHcCCEEE
Confidence 3467999999999999999 654322 2334444332 45678888999999874
No 55
>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=58.93 E-value=41 Score=22.19 Aligned_cols=52 Identities=10% Similarity=0.085 Sum_probs=38.9
Q ss_pred EeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhcccccc
Q psy13021 58 SIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDAR 119 (287)
Q Consensus 58 ~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~ 119 (287)
...|..|+.-.-..+++|++++.- ..+.+..+... +...+...++..||.+.
T Consensus 3 D~~G~~CP~P~i~~k~~l~~l~~G---------~~l~V~~dd~~-s~~di~~~~~~~g~~~~ 54 (69)
T cd03423 3 DTRGLRCPEPVMMLHKKVRKMKPG---------DTLLVLATDPS-TTRDIPKFCTFLGHELL 54 (69)
T ss_pred cccCCcCCHHHHHHHHHHHcCCCC---------CEEEEEeCCCc-hHHHHHHHHHHcCCEEE
Confidence 457899999999999999998522 23445555433 56788899999999875
No 56
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=58.73 E-value=30 Score=24.64 Aligned_cols=52 Identities=17% Similarity=0.292 Sum_probs=37.2
Q ss_pred HHHHHHHhhcCCCeeEEEEE-----ccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeE
Q psy13021 216 VNKIETSVKKLAGIKSAVVA-----LTTQRGKFRYDLEVTGPRDVMECIEKLGFTTA 267 (287)
Q Consensus 216 ~~~ie~~l~~~~gv~~~~v~-----~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~ 267 (287)
.-.+-.+|..++||..+++. ..+..+.++.....+..+++.++|+.+|-.+.
T Consensus 19 i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IH 75 (95)
T PF02680_consen 19 IVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIH 75 (95)
T ss_dssp HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEE
T ss_pred HHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEE
Confidence 34456678889998877554 44556677777777899999999999995443
No 57
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=58.47 E-value=63 Score=22.83 Aligned_cols=51 Identities=20% Similarity=0.257 Sum_probs=37.1
Q ss_pred HHHHHHhhcCCCeeEEEE-----EccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeE
Q psy13021 217 NKIETSVKKLAGIKSAVV-----ALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTA 267 (287)
Q Consensus 217 ~~ie~~l~~~~gv~~~~v-----~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~ 267 (287)
.-+-..|.+++||..+++ +..+..+.++.....++-.+|.+.|++.|--++
T Consensus 22 ve~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IH 77 (97)
T COG1888 22 VELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIH 77 (97)
T ss_pred HHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeee
Confidence 345556777888776644 445566777777777899999999999996544
No 58
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=58.01 E-value=57 Score=22.38 Aligned_cols=55 Identities=13% Similarity=0.042 Sum_probs=40.6
Q ss_pred EEEEeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhcccccc
Q psy13021 55 VLISIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDAR 119 (287)
Q Consensus 55 ~~~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~ 119 (287)
.++...|+.|+.-.-..+++|++++.-+ .+.+..+... ....+...++..|+...
T Consensus 10 ~~lD~~Gl~CP~Pll~~kk~l~~l~~G~---------~l~V~~dd~~-~~~di~~~~~~~G~~~~ 64 (81)
T PRK00299 10 HTLDALGLRCPEPVMMVRKTVRNMQPGE---------TLLIIADDPA-TTRDIPSFCRFMDHELL 64 (81)
T ss_pred eEEecCCCCCCHHHHHHHHHHHcCCCCC---------EEEEEeCCcc-HHHHHHHHHHHcCCEEE
Confidence 5688899999999999999999986322 3344444332 56778888888998764
No 59
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=54.88 E-value=76 Score=22.68 Aligned_cols=64 Identities=13% Similarity=0.236 Sum_probs=39.0
Q ss_pred eEEEEEeeCCCChhhHHHHHHHHhcCCCeeEEEE-----eccCCeEEEEeCCCCCCHHHHHHHhhhcccc
Q psy13021 53 STVLISIDGMTCQSCVNTITDTIRAKPGVFNIKV-----SLEQKNANIRFNPIITNEETLRISIEDMGFD 117 (287)
Q Consensus 53 ~~~~~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v-----~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~ 117 (287)
+++.+-+--.+ ..-..-+...|.+++||..+.+ +..+....+......++.+.+.+++++.|-.
T Consensus 5 rRlVLDVlKP~-~p~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~ 73 (95)
T PF02680_consen 5 RRLVLDVLKPH-EPSIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGV 73 (95)
T ss_dssp EEEEEEEEEES-SS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-E
T ss_pred eEEEEEeecCC-CCCHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCe
Confidence 34444444442 2334467788999999988775 3444555555555555788888999888844
No 60
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=54.01 E-value=1e+02 Score=27.04 Aligned_cols=88 Identities=16% Similarity=0.164 Sum_probs=56.3
Q ss_pred EEEECCCCChhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCChHHHHHHhhhcCCCceeecc-CCCCCccceee
Q psy13021 128 TFTVDGMKCQSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLISPTEIAASISELGFPATVIDE-AGSGEGELELK 206 (287)
Q Consensus 128 ~~~v~gm~C~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~~~~~-~~~~~~~~~~~ 206 (287)
...+.--.-..|...+++.++..+||.++++- + ..+...+..+..|+. ..... .+.-.+.+.++
T Consensus 62 ~vyL~~~~~~~~~~~v~~~i~~~~gV~~v~~~--s------------re~~l~~L~~~lg~~-~~~~l~~nPLP~~~vV~ 126 (297)
T COG2177 62 TVYLQIDADQDDAALVREKIEGIPGVKSVRFI--S------------REEALKELQPWLGFG-ALLMLDENPLPDVFVVT 126 (297)
T ss_pred EEEEecCCChHHHHHHHHHHhcCCCcceEEEe--C------------HHHHHHHHHHHcCch-hhhcCCCCCCCceEEEE
Confidence 33333333478999999999999999987753 1 123344455577775 22211 12233455556
Q ss_pred eccCCchhhHHHHHHHhhcCCCeeEEE
Q psy13021 207 ISGMSCASCVNKIETSVKKLAGIKSAV 233 (287)
Q Consensus 207 v~gm~c~~C~~~ie~~l~~~~gv~~~~ 233 (287)
+.. +.-...+.++++.++||..+.
T Consensus 127 ~~~---p~~~~~i~~~l~~l~gV~~V~ 150 (297)
T COG2177 127 PDD---PPQVKAIAAALRDLPGVAEVD 150 (297)
T ss_pred eCC---CccHHHHHHHHHcCccceehh
Confidence 554 666888999999999998655
No 61
>KOG1635|consensus
Probab=53.47 E-value=49 Score=26.45 Aligned_cols=57 Identities=18% Similarity=0.321 Sum_probs=44.6
Q ss_pred ceeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCC-------------------eEEEEEcCCCCCHHHHHHHHHhc
Q psy13021 203 LELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQ-------------------RGKFRYDLEVTGPRDVMECIEKL 262 (287)
Q Consensus 203 ~~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~-------------------~~~v~~~~~~~~~~~i~~~I~~~ 262 (287)
.++.+-|+. |-..+|.+...++||..-.+.++.+ .+.|.|+|..++-++|++...+.
T Consensus 24 ~q~a~fg~G---CFWg~E~a~~~l~gV~~T~vGYagG~~~nPtYk~vc~~tT~HaEvvrV~ydpk~~sy~~Lld~Fw~~ 99 (191)
T KOG1635|consen 24 LQFATFGAG---CFWGVELAYQRLPGVVRTEVGYAGGITDNPTYKDVCSGTTNHAEVVRVQYDPKVISYEELLDFFWSR 99 (191)
T ss_pred cceeeeecc---chhhHHHHHhhcCCeEEEeecccCCccCCcchhhhccCCCCcceEEEEEeCcccccHHHHHHHHHHc
Confidence 455565655 4788899999999998888777665 35789999999999999876654
No 62
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=53.11 E-value=32 Score=29.93 Aligned_cols=52 Identities=19% Similarity=0.216 Sum_probs=38.5
Q ss_pred eccCCchhhHHHHHHHhhcCCCeeEEEEEccCC-------------------eEEEEEcCCCCCHHHHHHHHHh
Q psy13021 207 ISGMSCASCVNKIETSVKKLAGIKSAVVALTTQ-------------------RGKFRYDLEVTGPRDVMECIEK 261 (287)
Q Consensus 207 v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~-------------------~~~v~~~~~~~~~~~i~~~I~~ 261 (287)
+-++.| -..++..+.+++||....+-++.+ .+.|.|+|..++.++|++..-+
T Consensus 131 ~fagGC---FWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~VcsG~tgH~EaV~V~yDp~~isy~~LL~~F~~ 201 (283)
T PRK05550 131 IFAGGC---FWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEFDPAKISYETLLKVFFE 201 (283)
T ss_pred EEecCC---chhhhhhHhhCcCEEEEEEeeCCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHHh
Confidence 334455 455566778889999888776665 3679999999999999886543
No 63
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=52.29 E-value=82 Score=22.28 Aligned_cols=66 Identities=12% Similarity=0.187 Sum_probs=42.4
Q ss_pred eEEEEEeeCCCChhhHHHHHHHHhcCCCeeEEEE-----eccCCeEEEEeCCCCCCHHHHHHHhhhccccc
Q psy13021 53 STVLISIDGMTCQSCVNTITDTIRAKPGVFNIKV-----SLEQKNANIRFNPIITNEETLRISIEDMGFDA 118 (287)
Q Consensus 53 ~~~~~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v-----~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~ 118 (287)
+++.+-+--.+-..-..-+...|.+++||..+++ +..+....+......++.+.+.+.+++.|-.+
T Consensus 6 RRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~I 76 (97)
T COG1888 6 RRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAI 76 (97)
T ss_pred eeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCee
Confidence 3444554444444445566677888999887664 44555555555555567888999999888443
No 64
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=50.95 E-value=53 Score=21.67 Aligned_cols=52 Identities=8% Similarity=0.071 Sum_probs=38.6
Q ss_pred EeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhcccccc
Q psy13021 58 SIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDAR 119 (287)
Q Consensus 58 ~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~ 119 (287)
...|..|+.-.-..+++|++++.-+ .+.+..+... +...+...++..||.+.
T Consensus 3 D~rG~~CP~Pvi~~kkal~~l~~G~---------~l~V~~d~~~-s~~ni~~~~~~~g~~v~ 54 (69)
T cd03422 3 DLRGEPCPYPAIATLEALPSLKPGE---------ILEVISDCPQ-SINNIPIDARNHGYKVL 54 (69)
T ss_pred ccCCCcCCHHHHHHHHHHHcCCCCC---------EEEEEecCch-HHHHHHHHHHHcCCEEE
Confidence 3568999999999999999986322 3444554433 56778888999999874
No 65
>PF11491 DUF3213: Protein of unknown function (DUF3213) ; InterPro: IPR021583 The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold []. ; PDB: 2F40_A.
Probab=49.71 E-value=29 Score=24.02 Aligned_cols=52 Identities=10% Similarity=0.089 Sum_probs=29.6
Q ss_pred hHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCee
Q psy13021 215 CVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTT 266 (287)
Q Consensus 215 C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~ 266 (287)
-+..++=.|...++|-.+.+|--.....|.+|+..+..+++.+.++.+.+.+
T Consensus 12 eA~~~QYeLsk~~~vyRvFiNgYar~g~VifDe~kl~~e~lL~~le~~kpEV 63 (88)
T PF11491_consen 12 EAMVKQYELSKNEAVYRVFINGYARNGFVIFDESKLSKEELLEMLEEFKPEV 63 (88)
T ss_dssp TTHHHHHTTTTTTTB------TTSS--EEE--B-S-SHHHH---HHHTTT-S
T ss_pred HHHHHHHHhhcccceeeeeecccccceEEEECcccCCHHHHHHHHHhcChhh
Confidence 3455566678888999999999999999999999999999999999998754
No 66
>PF11491 DUF3213: Protein of unknown function (DUF3213) ; InterPro: IPR021583 The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold []. ; PDB: 2F40_A.
Probab=47.64 E-value=24 Score=24.41 Aligned_cols=53 Identities=9% Similarity=0.113 Sum_probs=30.4
Q ss_pred HHHHHHHHhccCCCeeEEEEeeecceeeeeccCCCCChHHHHHHhhhcCCCce
Q psy13021 139 CVKKIEATIGEKPGINSVLVALLAAKAEIRYSKDLISPTEIAASISELGFPAT 191 (287)
Q Consensus 139 C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~ 191 (287)
-+..++=.|...++|-.+-+|-......|.||+...+.+++.+.++...+.+.
T Consensus 12 eA~~~QYeLsk~~~vyRvFiNgYar~g~VifDe~kl~~e~lL~~le~~kpEVi 64 (88)
T PF11491_consen 12 EAMVKQYELSKNEAVYRVFINGYARNGFVIFDESKLSKEELLEMLEEFKPEVI 64 (88)
T ss_dssp TTHHHHHTTTTTTTB------TTSS--EEE--B-S-SHHHH---HHHTTT-SS
T ss_pred HHHHHHHHhhcccceeeeeecccccceEEEECcccCCHHHHHHHHHhcChhhe
Confidence 34556667888899999999999999999999999999999999999888764
No 67
>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=46.47 E-value=79 Score=20.43 Aligned_cols=53 Identities=9% Similarity=0.124 Sum_probs=38.4
Q ss_pred EEeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhcccccc
Q psy13021 57 ISIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFDAR 119 (287)
Q Consensus 57 ~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~~~ 119 (287)
+-..|+.|+.-.-.+.++|.+++.-. ...+..+... ....+...+...||...
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~~g~---------~l~v~~d~~~-~~~~i~~~~~~~g~~~~ 54 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLKSGE---------VLEVLLDDPG-AVEDIPAWAKETGHEVL 54 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCCCCC---------EEEEEecCCc-HHHHHHHHHHHcCCEEE
Confidence 34678999999999999999976322 3444454433 56778888999999854
No 68
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=43.75 E-value=1e+02 Score=21.01 Aligned_cols=55 Identities=9% Similarity=0.158 Sum_probs=39.3
Q ss_pred EEEEEeeCCCChhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhcc-ccc
Q psy13021 54 TVLISIDGMTCQSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMG-FDA 118 (287)
Q Consensus 54 ~~~~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G-~~~ 118 (287)
..++.+.|+.|+.-.-.+.++|++++- ...+.|..+... +...|...++..| |..
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~---------Ge~LeV~~ddp~-~~~dIp~~~~~~~~~~l 60 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLKP---------GEILEVIADDPA-AKEDIPAWAKKEGGHEL 60 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCCC---------CCEEEEEecCcc-hHHHHHHHHHHcCCcEE
Confidence 357889999999999999999999864 234455555433 4567777777444 654
No 69
>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=43.25 E-value=93 Score=20.31 Aligned_cols=60 Identities=8% Similarity=0.250 Sum_probs=39.2
Q ss_pred ChHHHHHHhhhcCCCceeeccCCC--CCccceeeeccCCchhhHHHHHHHhhcCCCeeEEEE
Q psy13021 175 SPTEIAASISELGFPATVIDEAGS--GEGELELKISGMSCASCVNKIETSVKKLAGIKSAVV 234 (287)
Q Consensus 175 ~~~~i~~~i~~~G~~~~~~~~~~~--~~~~~~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v 234 (287)
.+.++...+.+.|..+..+..... ....+.|.+.--.-......+.++|++++||.++.+
T Consensus 13 ~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 13 VLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred hHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 467888899988888766544221 223344545432222367888899999999987653
No 70
>KOG1635|consensus
Probab=42.55 E-value=46 Score=26.60 Aligned_cols=49 Identities=18% Similarity=0.272 Sum_probs=39.4
Q ss_pred hHHHHHHHHhccCCCeeEEEEeeecce-------------------eeeeccCCCCChHHHHHHhhhc
Q psy13021 138 SCVKKIEATIGEKPGINSVLVALLAAK-------------------AEIRYSKDLISPTEIAASISEL 186 (287)
Q Consensus 138 ~C~~~ie~~l~~~~gV~~~~v~~~~~~-------------------~~v~~~~~~~~~~~i~~~i~~~ 186 (287)
.|-|.+|.+..+++||..-+|-++.+. +.|.|||..++-+++++.....
T Consensus 32 GCFWg~E~a~~~l~gV~~T~vGYagG~~~nPtYk~vc~~tT~HaEvvrV~ydpk~~sy~~Lld~Fw~~ 99 (191)
T KOG1635|consen 32 GCFWGVELAYQRLPGVVRTEVGYAGGITDNPTYKDVCSGTTNHAEVVRVQYDPKVISYEELLDFFWSR 99 (191)
T ss_pred cchhhHHHHHhhcCCeEEEeecccCCccCCcchhhhccCCCCcceEEEEEeCcccccHHHHHHHHHHc
Confidence 568999999999999998888766553 4588888888888888877644
No 71
>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=41.68 E-value=1.1e+02 Score=24.96 Aligned_cols=53 Identities=15% Similarity=0.238 Sum_probs=38.8
Q ss_pred eeccCCchhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhcCCeeEE
Q psy13021 206 KISGMSCASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKLGFTTAL 268 (287)
Q Consensus 206 ~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~G~~~~~ 268 (287)
...|..||.......++|.+++. ...+.|..+. ....+.+....+..||....
T Consensus 2 D~rGl~CP~Pvi~tKkal~~l~~---------g~~L~VlvD~-~~a~~nV~~~~~~~G~~v~~ 54 (194)
T TIGR03527 2 DARGLACPQPVILTKKALDELGE---------EGVLTVIVDN-EAAKENVSKFATSLGYEVEV 54 (194)
T ss_pred CCCCCCCCHHHHHHHHHHHcCCC---------CCEEEEEECC-ccHHHHHHHHHHHcCCEEEE
Confidence 45799999999999999998752 2233444433 34577899999999998764
No 72
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=37.09 E-value=4.8e+02 Score=27.41 Aligned_cols=122 Identities=13% Similarity=0.186 Sum_probs=72.1
Q ss_pred HHHHHHHhccCCCeeEEEEee---ecceeeeeccCCCCCh----HHHHHHhhhc--CCCcee--ecc---CCCCCcccee
Q psy13021 140 VKKIEATIGEKPGINSVLVAL---LAAKAEIRYSKDLISP----TEIAASISEL--GFPATV--IDE---AGSGEGELEL 205 (287)
Q Consensus 140 ~~~ie~~l~~~~gV~~~~v~~---~~~~~~v~~~~~~~~~----~~i~~~i~~~--G~~~~~--~~~---~~~~~~~~~~ 205 (287)
...+|+.|+.++|+.+.+-.- ......+.|+.+. +. .++.+.+..+ .+.... ... ......-+.+
T Consensus 62 t~plE~~l~~v~gv~~i~S~S~~~G~s~i~v~f~~g~-d~~~a~~~V~~~v~~~~~~LP~~v~~~~~~~~~~~~~~v~~~ 140 (1037)
T PRK10555 62 TQVIEQNMTGLDNLMYMSSQSSGTGQASVTLSFKAGT-DPDEAVQQVQNQLQSAMRKLPQAVQNQGVTVRKTGDTNILTI 140 (1037)
T ss_pred hHHHHHHhcCCCCceEEEEEecCCCeEEEEEEEECCC-CHHHHHHHHHHHHHHHHHhCCCccccCCceEeCCCCCceEEE
Confidence 357899999999999887632 2345667777653 33 3455555432 222110 000 0111112333
Q ss_pred eec---c-CCc----hhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCC-----CCCHHHHHHHHHhc
Q psy13021 206 KIS---G-MSC----ASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLE-----VTGPRDVMECIEKL 262 (287)
Q Consensus 206 ~v~---g-m~c----~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~-----~~~~~~i~~~I~~~ 262 (287)
.+. + +.- ..-...++..|.+++||.++.++-....+.|.+||. .++..++.++|+..
T Consensus 141 ~~~~~~~~~~~~~l~~~~~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 141 AFVSTDGSMDKQDIADYVASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred EEEcCCCCCCHHHHHHHHHHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 332 2 211 112356888999999999998875445567888774 36889999999874
No 73
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=36.19 E-value=59 Score=31.04 Aligned_cols=48 Identities=17% Similarity=0.252 Sum_probs=40.0
Q ss_pred hHHHHHHHHhccCCCeeEEEEeeecce------------------eeeeccCCCCChHHHHHHhhh
Q psy13021 138 SCVKKIEATIGEKPGINSVLVALLAAK------------------AEIRYSKDLISPTEIAASISE 185 (287)
Q Consensus 138 ~C~~~ie~~l~~~~gV~~~~v~~~~~~------------------~~v~~~~~~~~~~~i~~~i~~ 185 (287)
.|=|-+|..+.+++||.+..+-++.+. +.|.|||..++.++|++....
T Consensus 206 GCFWg~e~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~gtgH~E~V~V~yDp~~is~~~Ll~~f~~ 271 (521)
T PRK14018 206 GCFWGLEAYFQRIDGVVDAVSGYANGNTKNPSYEDVYRHSGHAETVKVTYDADKLSLDTILQYYFR 271 (521)
T ss_pred CCchhhHHHHccCCCEEEEEEeeCCCCCCCCChhhccCCCCcEEEEEEEECCCcCcHHHHHHHHHH
Confidence 578999999999999999888766653 568899999999999887654
No 74
>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=35.86 E-value=1.4e+02 Score=23.71 Aligned_cols=48 Identities=23% Similarity=0.397 Sum_probs=35.7
Q ss_pred hhhHHHHHHHhhcCCCeeEEEEEccCCeEEEEEcCC--CCCHHHHHHHHH
Q psy13021 213 ASCVNKIETSVKKLAGIKSAVVALTTQRGKFRYDLE--VTGPRDVMECIE 260 (287)
Q Consensus 213 ~~C~~~ie~~l~~~~gv~~~~v~~~~~~~~v~~~~~--~~~~~~i~~~I~ 260 (287)
..-+..|...+.+++||..+.+=.....+.|.+... .....+|.+.|+
T Consensus 74 ~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~~~~~~~~~~~i~~~V~ 123 (177)
T PF09580_consen 74 QQLADRIANRVKKVPGVEDATVVVTDDNAYVAVDLDFNRFNTKKIKKKVE 123 (177)
T ss_pred HHHHHHHHHHHhcCCCceEEEEEEECCEEEEEEEecccccchhHHHHHHH
Confidence 345788999999999999999888888888888765 344444444433
No 75
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=32.78 E-value=3.2e+02 Score=24.06 Aligned_cols=78 Identities=27% Similarity=0.342 Sum_probs=52.2
Q ss_pred hhhHHHHHHHHhcCCCeeEEEEeccCCeEEEEeCCCCCCHHHHHHHhhhcccc-ccCCCCC---ceeEEEECCCCChhHH
Q psy13021 65 QSCVNTITDTIRAKPGVFNIKVSLEQKNANIRFNPIITNEETLRISIEDMGFD-ARLPSTN---DEATFTVDGMKCQSCV 140 (287)
Q Consensus 65 ~~C~~~i~~~l~~~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~G~~-~~~~~~~---~~~~~~v~gm~C~~C~ 140 (287)
..|...++..+++++||.++..- . ..+.+.+..+..|+. ....+.+ ....+.+.. +.-.
T Consensus 71 ~~~~~~v~~~i~~~~gV~~v~~~-----------s---re~~l~~L~~~lg~~~~~~l~~nPLP~~~vV~~~~---p~~~ 133 (297)
T COG2177 71 QDDAALVREKIEGIPGVKSVRFI-----------S---REEALKELQPWLGFGALLMLDENPLPDVFVVTPDD---PPQV 133 (297)
T ss_pred hHHHHHHHHHHhcCCCcceEEEe-----------C---HHHHHHHHHHHcCchhhhcCCCCCCCceEEEEeCC---CccH
Confidence 88999999999999999986642 1 245566666677764 1111111 133444443 5566
Q ss_pred HHHHHHhccCCCeeEEEEe
Q psy13021 141 KKIEATIGEKPGINSVLVA 159 (287)
Q Consensus 141 ~~ie~~l~~~~gV~~~~v~ 159 (287)
..+.++++.++||.+++.+
T Consensus 134 ~~i~~~l~~l~gV~~V~~~ 152 (297)
T COG2177 134 KAIAAALRDLPGVAEVDDD 152 (297)
T ss_pred HHHHHHHHcCccceehhcc
Confidence 7889999999999876643
No 76
>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=30.76 E-value=1.3e+02 Score=23.83 Aligned_cols=36 Identities=19% Similarity=0.331 Sum_probs=29.7
Q ss_pred hhHHHHHHHHhccCCCeeEEEEeeecceeeeeccCC
Q psy13021 137 QSCVKKIEATIGEKPGINSVLVALLAAKAEIRYSKD 172 (287)
Q Consensus 137 ~~C~~~ie~~l~~~~gV~~~~v~~~~~~~~v~~~~~ 172 (287)
..-+..|.+.+.+++||.++.+-.....+.|.+...
T Consensus 74 ~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~~~ 109 (177)
T PF09580_consen 74 QQLADRIANRVKKVPGVEDATVVVTDDNAYVAVDLD 109 (177)
T ss_pred HHHHHHHHHHHhcCCCceEEEEEEECCEEEEEEEec
Confidence 346788999999999999999988888888776544
No 77
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=28.38 E-value=1.3e+02 Score=28.77 Aligned_cols=87 Identities=16% Similarity=0.156 Sum_probs=53.7
Q ss_pred CCCChHHHHHHhhhcCCCceeec-----cCC----CCCccceeeeccCCchhhHHHHHHHhhcCCCeeEEEEEccCC---
Q psy13021 172 DLISPTEIAASISELGFPATVID-----EAG----SGEGELELKISGMSCASCVNKIETSVKKLAGIKSAVVALTTQ--- 239 (287)
Q Consensus 172 ~~~~~~~i~~~i~~~G~~~~~~~-----~~~----~~~~~~~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v~~~~~--- 239 (287)
+..+.+++.+.|+...++...+. ..+ .........+-++.|-. -+|..+.+++||.+..+-++.+
T Consensus 158 G~~~~eeL~a~Ie~~~~~~~~~~~~~~~~~~q~~d~~~~~~~~~~~agGCFW---g~e~~f~~~~GV~~t~~GYagG~~~ 234 (521)
T PRK14018 158 GSISEAQALALIRNPNADLGSLKHSYYKPDGQKKDSKIMNTRTIYLAGGCFW---GLEAYFQRIDGVVDAVSGYANGNTK 234 (521)
T ss_pred CCCCHHHHHHHHHHhhhhhHHhhhhhccccCCccccCCCCccEEEEecCCch---hhHHHHccCCCEEEEEEeeCCCCCC
Confidence 44667788777774444332111 111 01112223334445554 4566788899999988777665
Q ss_pred ---------------eEEEEEcCCCCCHHHHHHHHHh
Q psy13021 240 ---------------RGKFRYDLEVTGPRDVMECIEK 261 (287)
Q Consensus 240 ---------------~~~v~~~~~~~~~~~i~~~I~~ 261 (287)
.+.|.|+|..++.++|++..-+
T Consensus 235 ~PtY~~Vc~gtgH~E~V~V~yDp~~is~~~Ll~~f~~ 271 (521)
T PRK14018 235 NPSYEDVYRHSGHAETVKVTYDADKLSLDTILQYYFR 271 (521)
T ss_pred CCChhhccCCCCcEEEEEEEECCCcCcHHHHHHHHHH
Confidence 2678999999999999887654
No 78
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=26.58 E-value=2e+02 Score=22.42 Aligned_cols=38 Identities=13% Similarity=0.281 Sum_probs=30.3
Q ss_pred eEEEEEeeCCCChhhHHHHHHHHhcCCCeeEEEEecc-CC
Q psy13021 53 STVLISIDGMTCQSCVNTITDTIRAKPGVFNIKVSLE-QK 91 (287)
Q Consensus 53 ~~~~~~v~gm~C~~C~~~i~~~l~~~~gv~~~~v~~~-~~ 91 (287)
+.+++.|+--.|..|..-|....+++ |+.++.+... ++
T Consensus 100 ~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG 138 (146)
T PF14437_consen 100 RSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSG 138 (146)
T ss_pred CeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCC
Confidence 46778888889999999988888876 8888777655 44
No 79
>PF14424 Toxin-deaminase: The BURPS668_1122 family of deaminases
Probab=25.81 E-value=1e+02 Score=23.53 Aligned_cols=30 Identities=23% Similarity=0.373 Sum_probs=26.5
Q ss_pred ceeEEEECCCCChhHHHHHHHHhccCCCee
Q psy13021 125 DEATFTVDGMKCQSCVKKIEATIGEKPGIN 154 (287)
Q Consensus 125 ~~~~~~v~gm~C~~C~~~ie~~l~~~~gV~ 154 (287)
+++.+..+--.|.+|...|++-....|.+.
T Consensus 97 G~i~l~te~~pC~SC~~vi~qF~~~~pni~ 126 (133)
T PF14424_consen 97 GTIDLFTELPPCESCSNVIEQFKKDFPNIK 126 (133)
T ss_pred ceEEEEecCCcChhHHHHHHHHHHHCCCcE
Confidence 477888888899999999999999998875
No 80
>PF02682 AHS1: Allophanate hydrolase subunit 1; InterPro: IPR003833 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 1 of allophanate hydrolase (AHS1), which is found in urea carboxylase.; PDB: 3VA7_A 3MML_H 3OEP_A 3OPF_C 3ORE_A 2ZP2_A 2KWA_A 2PHC_B.
Probab=23.40 E-value=2.6e+02 Score=22.95 Aligned_cols=46 Identities=20% Similarity=0.228 Sum_probs=33.9
Q ss_pred hHHHHHHHhhc--CCCeeEEEEEccCCeEEEEEcCCCCCHHHHHHHHHhc
Q psy13021 215 CVNKIETSVKK--LAGIKSAVVALTTQRGKFRYDLEVTGPRDVMECIEKL 262 (287)
Q Consensus 215 C~~~ie~~l~~--~~gv~~~~v~~~~~~~~v~~~~~~~~~~~i~~~I~~~ 262 (287)
....+.+.|.+ .+||.++...+ .++.|.|+|..++..++.+.|+.+
T Consensus 26 ~v~al~~~l~~~~~~gi~e~vp~~--~sllV~fdp~~~~~~~l~~~l~~~ 73 (202)
T PF02682_consen 26 RVLALARALRAAPLPGIVEVVPAY--RSLLVHFDPLRIDRAALRAALEEL 73 (202)
T ss_dssp HHHHHHHHHHHHT-TTEEEEEEES--SEEEEEESTTTSHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCCCeEEeeccc--cEEEEEEcCCcCCHHHHHHHHHHh
Confidence 45566667776 78888776554 478899999888888888888775
No 81
>PHA02119 hypothetical protein
Probab=23.16 E-value=1.1e+02 Score=20.42 Aligned_cols=19 Identities=21% Similarity=0.651 Sum_probs=16.2
Q ss_pred CCCHHHHHHHHHhcCCeeE
Q psy13021 249 VTGPRDVMECIEKLGFTTA 267 (287)
Q Consensus 249 ~~~~~~i~~~I~~~G~~~~ 267 (287)
.+-+++|.+.++.+||.+.
T Consensus 53 ~i~~~divdylr~lgy~~~ 71 (87)
T PHA02119 53 AIMPKDIVDYLRSLGYDAK 71 (87)
T ss_pred ccccHHHHHHHHHccchhc
Confidence 3568999999999999875
No 82
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=22.68 E-value=84 Score=22.00 Aligned_cols=22 Identities=14% Similarity=0.283 Sum_probs=16.3
Q ss_pred eCCCChhhHHHHHHHHhcCCCeeE
Q psy13021 60 DGMTCQSCVNTITDTIRAKPGVFN 83 (287)
Q Consensus 60 ~gm~C~~C~~~i~~~l~~~~gv~~ 83 (287)
.-|+|.+|....+...+. |..+
T Consensus 25 ~~FCC~GC~~V~~~i~~~--gL~~ 46 (88)
T PF12156_consen 25 RPFCCPGCQAVYQLIHEN--GLES 46 (88)
T ss_pred cccccHHHHHHHHHHHHc--chHH
Confidence 469999999887777665 4443
No 83
>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=21.30 E-value=1.7e+02 Score=19.18 Aligned_cols=33 Identities=27% Similarity=0.524 Sum_probs=20.0
Q ss_pred EEEEEeeCCCCh---hhHHHHHHHHhcCCCeeEEEE
Q psy13021 54 TVLISIDGMTCQ---SCVNTITDTIRAKPGVFNIKV 86 (287)
Q Consensus 54 ~~~~~v~gm~C~---~C~~~i~~~l~~~~gv~~~~v 86 (287)
++.+.+....|+ .=...++.+|.+++|+.++.+
T Consensus 37 ~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 37 SVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp EEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred EEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 344555555665 234567778889999988764
No 84
>PRK04435 hypothetical protein; Provisional
Probab=20.67 E-value=4e+02 Score=20.52 Aligned_cols=60 Identities=15% Similarity=0.297 Sum_probs=38.6
Q ss_pred ChHHHHHHhhhcCCCceeeccCC--CCCccceeeeccCCchhhHHHHHHHhhcCCCeeEEEE
Q psy13021 175 SPTEIAASISELGFPATVIDEAG--SGEGELELKISGMSCASCVNKIETSVKKLAGIKSAVV 234 (287)
Q Consensus 175 ~~~~i~~~i~~~G~~~~~~~~~~--~~~~~~~~~v~gm~c~~C~~~ie~~l~~~~gv~~~~v 234 (287)
.+.+|...+.+.|-.+..+.... .+...+.|.++--........+-..|..++||..+.+
T Consensus 82 lLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs~~~~~L~~Li~~L~~i~gV~~V~i 143 (147)
T PRK04435 82 TLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTSSMEGDIDELLEKLRNLDGVEKVEL 143 (147)
T ss_pred HHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeCChHHHHHHHHHHHHcCCCcEEEEE
Confidence 36778888888888776554321 1222344444443333468888899999999987764
Done!