Query 045104
Match_columns 151
No_of_seqs 231 out of 1162
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 09:53:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045104.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045104hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.5 3.5E-13 7.5E-18 86.0 8.5 58 3-60 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.3 1.2E-11 2.6E-16 81.8 9.2 62 2-63 4-69 (71)
3 KOG1603 Copper chaperone [Inor 99.1 9.2E-10 2E-14 73.0 8.5 63 2-64 7-70 (73)
4 KOG4656 Copper chaperone for s 98.8 1.3E-08 2.7E-13 79.8 8.0 66 2-67 9-74 (247)
5 PLN02957 copper, zinc superoxi 98.4 2.7E-06 6E-11 68.1 9.7 66 2-67 8-73 (238)
6 PRK10671 copA copper exporting 98.3 1.4E-06 3E-11 80.6 7.9 62 2-65 5-67 (834)
7 COG2217 ZntA Cation transport 98.3 1.6E-06 3.6E-11 79.0 7.8 61 2-63 4-69 (713)
8 KOG0207 Cation transport ATPas 98.0 8E-06 1.7E-10 75.4 5.9 64 2-65 148-215 (951)
9 TIGR00003 copper ion binding p 97.9 0.0002 4.4E-09 42.3 8.4 59 2-60 4-66 (68)
10 KOG0207 Cation transport ATPas 97.7 0.00012 2.6E-09 67.9 7.0 65 2-66 71-139 (951)
11 PRK10671 copA copper exporting 97.5 0.00038 8.2E-09 64.6 7.8 64 2-65 101-165 (834)
12 PRK11033 zntA zinc/cadmium/mer 97.2 0.0016 3.4E-08 60.0 8.2 63 2-64 55-119 (741)
13 TIGR02052 MerP mercuric transp 94.6 0.7 1.5E-05 29.5 9.0 60 3-62 26-89 (92)
14 PRK13748 putative mercuric red 92.3 0.96 2.1E-05 39.9 8.7 65 3-67 3-70 (561)
15 cd00371 HMA Heavy-metal-associ 87.9 2.5 5.4E-05 21.9 7.3 39 4-42 2-41 (63)
16 PF01206 TusA: Sulfurtransfera 76.3 12 0.00025 23.6 5.5 53 3-64 2-57 (70)
17 PF02680 DUF211: Uncharacteriz 72.2 18 0.00039 25.2 5.8 49 16-64 21-77 (95)
18 PF01883 DUF59: Domain of unkn 69.3 7.5 0.00016 24.7 3.3 19 14-32 54-72 (72)
19 PRK11018 hypothetical protein; 67.5 32 0.00069 22.5 6.1 53 2-63 9-64 (78)
20 cd03421 SirA_like_N SirA_like_ 65.4 23 0.0005 22.1 5.0 50 4-63 2-54 (67)
21 PRK14054 methionine sulfoxide 63.7 18 0.0004 27.7 4.9 45 11-55 10-76 (172)
22 PRK10553 assembly protein for 60.6 46 0.001 22.6 6.0 45 11-55 16-61 (87)
23 COG1888 Uncharacterized protei 59.8 47 0.001 23.1 5.8 49 17-65 24-80 (97)
24 cd03420 SirA_RHOD_Pry_redox Si 53.6 49 0.0011 20.9 5.0 51 4-63 2-55 (69)
25 cd03422 YedF YedF is a bacteri 49.1 66 0.0014 20.3 5.1 52 4-64 2-56 (69)
26 PRK05528 methionine sulfoxide 49.0 52 0.0011 24.8 5.2 45 11-55 8-69 (156)
27 PRK00058 methionine sulfoxide 48.0 41 0.00089 26.7 4.7 45 11-55 52-118 (213)
28 cd03423 SirA SirA (also known 44.2 80 0.0017 19.9 5.5 52 4-64 2-56 (69)
29 PRK13014 methionine sulfoxide 42.6 44 0.00095 26.0 4.0 45 11-55 15-81 (186)
30 cd00291 SirA_YedF_YeeD SirA, Y 42.3 81 0.0018 19.4 5.5 51 4-63 2-55 (69)
31 PF03927 NapD: NapD protein; 40.6 1.1E+02 0.0023 20.2 6.7 43 13-56 16-59 (79)
32 PF13732 DUF4162: Domain of un 38.8 1E+02 0.0022 19.7 4.9 42 21-64 26-69 (84)
33 TIGR03406 FeS_long_SufT probab 37.6 41 0.00088 25.8 3.2 20 15-34 134-153 (174)
34 PF09580 Spore_YhcN_YlaJ: Spor 37.4 1.2E+02 0.0026 22.5 5.8 30 13-42 76-105 (177)
35 COG2151 PaaD Predicted metal-s 35.5 62 0.0013 23.0 3.6 21 14-34 69-89 (111)
36 PRK00299 sulfur transfer prote 31.7 1.5E+02 0.0033 19.4 6.3 53 2-63 10-65 (81)
37 cd02410 archeal_CPSF_KH The ar 30.9 2.1E+02 0.0046 21.4 5.9 56 13-68 54-116 (145)
38 cd04888 ACT_PheB-BS C-terminal 30.5 1.3E+02 0.0029 18.4 4.4 20 13-32 55-74 (76)
39 TIGR02945 SUF_assoc FeS assemb 28.7 1E+02 0.0022 20.6 3.8 21 15-35 58-78 (99)
40 PRK09577 multidrug efflux prot 27.9 1.7E+02 0.0037 28.4 6.2 46 14-59 158-211 (1032)
41 PF01625 PMSR: Peptide methion 27.6 62 0.0013 24.3 2.7 27 11-37 7-33 (155)
42 PRK10555 aminoglycoside/multid 26.8 1.8E+02 0.0038 28.3 6.1 44 14-57 159-210 (1037)
43 PRK05550 bifunctional methioni 26.7 1.4E+02 0.003 24.8 4.8 27 11-37 134-160 (283)
44 COG0425 SirA Predicted redox p 26.4 1.2E+02 0.0026 19.9 3.6 51 2-61 6-60 (78)
45 TIGR03527 selenium_YedF seleni 26.1 2.3E+02 0.005 21.9 5.7 48 7-63 5-54 (194)
46 TIGR00401 msrA methionine-S-su 24.5 61 0.0013 24.2 2.1 27 11-37 7-33 (149)
47 PF13192 Thioredoxin_3: Thiore 24.0 88 0.0019 19.8 2.6 13 3-15 2-15 (76)
48 PRK11200 grxA glutaredoxin 1; 22.3 1.4E+02 0.0031 19.1 3.4 28 7-35 8-39 (85)
49 PF15643 Tox-PL-2: Papain fold 21.6 96 0.0021 21.8 2.5 21 7-28 18-38 (100)
50 PF13291 ACT_4: ACT domain; PD 21.2 1.9E+02 0.0042 18.1 3.8 21 11-31 59-79 (80)
51 PRK15127 multidrug efflux syst 20.8 2.7E+02 0.0058 27.2 6.1 43 15-57 160-210 (1049)
52 TIGR00489 aEF-1_beta translati 20.6 1.1E+02 0.0023 20.9 2.5 21 13-33 63-83 (88)
53 PRK10509 bacterioferritin-asso 20.5 55 0.0012 20.8 1.0 20 5-24 34-53 (64)
54 TIGR00915 2A0602 The (Largely 20.5 2.7E+02 0.0058 27.1 6.0 44 14-57 159-210 (1044)
No 1
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.47 E-value=3.5e-13 Score=85.97 Aligned_cols=58 Identities=33% Similarity=0.606 Sum_probs=54.2
Q ss_pred EEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEee---CCHHHHHHHHHhCCCc
Q 045104 3 VLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVN---VDSAILIKKLVRSGKY 60 (151)
Q Consensus 3 ~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~---~~~~~I~~~I~k~Gy~ 60 (151)
+|+| ||+|++|+.+|+++|.+++||.++.+|+.+++++|.++ +++++|.++|+++||+
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 4899 99999999999999999999999999999999999976 4569999999999995
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.34 E-value=1.2e-11 Score=81.75 Aligned_cols=62 Identities=32% Similarity=0.531 Sum_probs=56.2
Q ss_pred EEEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEe---eCCHHHHHHHHHhCCCcEEE
Q 045104 2 HVLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSV---NVDSAILIKKLVRSGKYVEL 63 (151)
Q Consensus 2 ~~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~---~~~~~~I~~~I~k~Gy~a~l 63 (151)
..|+| ||+|.+|+.+|+++|.+++||.++.+++..+++.|.. .++.++|..+|+++||.+..
T Consensus 4 ~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~ 69 (71)
T COG2608 4 TTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEE 69 (71)
T ss_pred EEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeee
Confidence 57899 9999999999999999999999999999997777764 36899999999999998764
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.09 E-value=9.2e-10 Score=72.97 Aligned_cols=63 Identities=51% Similarity=0.804 Sum_probs=57.5
Q ss_pred EEEEEcCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEeeCCHHHHHHHHHhCC-CcEEEc
Q 045104 2 HVLKVHIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVNVDSAILIKKLVRSG-KYVELL 64 (151)
Q Consensus 2 ~~l~Vgm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~~~~~~I~~~I~k~G-y~a~l~ 64 (151)
.++++.|+|.+|..+|++.|..++||.++.++...++++|.+.++|..|++.|.+.| .++.++
T Consensus 7 ~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~ 70 (73)
T KOG1603|consen 7 VVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELW 70 (73)
T ss_pred EEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEe
Confidence 456779999999999999999999999999999999999999999999999999987 665554
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.85 E-value=1.3e-08 Score=79.78 Aligned_cols=66 Identities=26% Similarity=0.470 Sum_probs=62.2
Q ss_pred EEEEEcCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEeeCCHHHHHHHHHhCCCcEEEcCCC
Q 045104 2 HVLKVHIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVNVDSAILIKKLVRSGKYVELLSPS 67 (151)
Q Consensus 2 ~~l~Vgm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~~~~~~I~~~I~k~Gy~a~l~~~~ 67 (151)
.+|.|.|+|.+|+..|++.|..++||.+++|+++.+.|.|.+...+++|...|+.+|.+|.+....
T Consensus 9 ~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G 74 (247)
T KOG4656|consen 9 AEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAG 74 (247)
T ss_pred EEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCC
Confidence 578889999999999999999999999999999999999999999999999999999999987654
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.39 E-value=2.7e-06 Score=68.13 Aligned_cols=66 Identities=29% Similarity=0.487 Sum_probs=59.2
Q ss_pred EEEEEcCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEeeCCHHHHHHHHHhCCCcEEEcCCC
Q 045104 2 HVLKVHIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVNVDSAILIKKLVRSGKYVELLSPS 67 (151)
Q Consensus 2 ~~l~Vgm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~~~~~~I~~~I~k~Gy~a~l~~~~ 67 (151)
+.+.++|+|..|+.+|++.|.+++||..+.+++..+++.|.+...+..+...|++.||.++++...
T Consensus 8 ~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~ 73 (238)
T PLN02957 8 TEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQG 73 (238)
T ss_pred EEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCC
Confidence 456669999999999999999999999999999999999987778889999999999999887653
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.35 E-value=1.4e-06 Score=80.59 Aligned_cols=62 Identities=18% Similarity=0.273 Sum_probs=54.9
Q ss_pred EEEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEeeCCHHHHHHHHHhCCCcEEEcC
Q 045104 2 HVLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVNVDSAILIKKLVRSGKYVELLS 65 (151)
Q Consensus 2 ~~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~~~~~~I~~~I~k~Gy~a~l~~ 65 (151)
.+++| ||+|++|+.+|+++|.+++||..+.+++. +.++.+..+++.+.+.+++.||++....
T Consensus 5 ~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 5 IDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred EEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 57899 99999999999999999999999999994 4556666788999999999999998653
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.33 E-value=1.6e-06 Score=79.01 Aligned_cols=61 Identities=23% Similarity=0.455 Sum_probs=55.3
Q ss_pred EEEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEee---CC-HHHHHHHHHhCCCcEEE
Q 045104 2 HVLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVN---VD-SAILIKKLVRSGKYVEL 63 (151)
Q Consensus 2 ~~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~---~~-~~~I~~~I~k~Gy~a~l 63 (151)
..|.| ||+|..|+++|| +|++++||..+.+|+.++++.|..+ .+ ++++..++++.||.+..
T Consensus 4 ~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 4 TSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred eEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 57899 999999999999 9999999999999999999999854 34 78999999999998865
No 8
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.04 E-value=8e-06 Score=75.41 Aligned_cols=64 Identities=22% Similarity=0.421 Sum_probs=59.1
Q ss_pred EEEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEee---CCHHHHHHHHHhCCCcEEEcC
Q 045104 2 HVLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVN---VDSAILIKKLVRSGKYVELLS 65 (151)
Q Consensus 2 ~~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~---~~~~~I~~~I~k~Gy~a~l~~ 65 (151)
..|.| ||.|.+|..+|++.|.+++||.++.++..++++.|.++ +.+.++++.|+..|+.+....
T Consensus 148 i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~ 215 (951)
T KOG0207|consen 148 IYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRP 215 (951)
T ss_pred EEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeee
Confidence 57899 99999999999999999999999999999999999754 789999999999999987655
No 9
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.88 E-value=0.0002 Score=42.25 Aligned_cols=59 Identities=22% Similarity=0.486 Sum_probs=49.3
Q ss_pred EEEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEee---CCHHHHHHHHHhCCCc
Q 045104 2 HVLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVN---VDSAILIKKLVRSGKY 60 (151)
Q Consensus 2 ~~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~---~~~~~I~~~I~k~Gy~ 60 (151)
..+.+ |++|..|...+++.+...+++....+++....+.+... .+...+...+...||.
T Consensus 4 ~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 66 (68)
T TIGR00003 4 FTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYE 66 (68)
T ss_pred EEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCC
Confidence 46789 99999999999999999999999999999998888742 4566776677777774
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.66 E-value=0.00012 Score=67.85 Aligned_cols=65 Identities=25% Similarity=0.363 Sum_probs=59.2
Q ss_pred EEEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEee---CCHHHHHHHHHhCCCcEEEcCC
Q 045104 2 HVLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVN---VDSAILIKKLVRSGKYVELLSP 66 (151)
Q Consensus 2 ~~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~---~~~~~I~~~I~k~Gy~a~l~~~ 66 (151)
..|++ ||+|.+|.+.|++.|++++||.++.+.+...+..+..+ +.++.+.+.+++.|+.+.+...
T Consensus 71 ~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~ 139 (951)
T KOG0207|consen 71 CYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIES 139 (951)
T ss_pred eEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhc
Confidence 46899 99999999999999999999999999999999999754 6889999999999999987654
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.49 E-value=0.00038 Score=64.64 Aligned_cols=64 Identities=17% Similarity=0.383 Sum_probs=56.0
Q ss_pred EEEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEeeCCHHHHHHHHHhCCCcEEEcC
Q 045104 2 HVLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVNVDSAILIKKLVRSGKYVELLS 65 (151)
Q Consensus 2 ~~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~~~~~~I~~~I~k~Gy~a~l~~ 65 (151)
+.+.+ ||+|..|...|++.+.+++||..+.+++.++++.+.+..+++++.+.+++.||.+.+..
T Consensus 101 ~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~~~ 165 (834)
T PRK10671 101 QQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEAIE 165 (834)
T ss_pred EEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCccccc
Confidence 35789 99999999999999999999999999999998888755678888889999999876543
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.18 E-value=0.0016 Score=59.98 Aligned_cols=63 Identities=19% Similarity=0.325 Sum_probs=52.2
Q ss_pred EEEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEeeC-CHHHHHHHHHhCCCcEEEc
Q 045104 2 HVLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVNV-DSAILIKKLVRSGKYVELL 64 (151)
Q Consensus 2 ~~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~~-~~~~I~~~I~k~Gy~a~l~ 64 (151)
..+++ ||+|.+|..++++.+.+.+||..+.+++.++++.+..+. ..+++...+++.||.+...
T Consensus 55 ~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~~~ 119 (741)
T PRK11033 55 YSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLRDE 119 (741)
T ss_pred EEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccccccc
Confidence 46789 999999999999999999999999999999998876431 2266777888999987543
No 13
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=94.56 E-value=0.7 Score=29.48 Aligned_cols=60 Identities=20% Similarity=0.412 Sum_probs=44.5
Q ss_pred EEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEe---eCCHHHHHHHHHhCCCcEE
Q 045104 3 VLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSV---NVDSAILIKKLVRSGKYVE 62 (151)
Q Consensus 3 ~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~---~~~~~~I~~~I~k~Gy~a~ 62 (151)
.+.+ ++.|..|...++..+...+++....++....+..+.. ......+...+...|+.++
T Consensus 26 ~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 89 (92)
T TIGR02052 26 TLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSS 89 (92)
T ss_pred EEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeE
Confidence 4567 8999999999999999999988888888777765542 1345555556667777644
No 14
>PRK13748 putative mercuric reductase; Provisional
Probab=92.26 E-value=0.96 Score=39.92 Aligned_cols=65 Identities=22% Similarity=0.381 Sum_probs=51.4
Q ss_pred EEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEee--CCHHHHHHHHHhCCCcEEEcCCC
Q 045104 3 VLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVN--VDSAILIKKLVRSGKYVELLSPS 67 (151)
Q Consensus 3 ~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~--~~~~~I~~~I~k~Gy~a~l~~~~ 67 (151)
.+.+ +++|..|..+++..+...+++....++.......+... .+...+...+...|+..++...+
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~~~~ 70 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLADAP 70 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeeccCcc
Confidence 4678 99999999999999999999988889988887666532 35566666778889887766553
No 15
>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=87.89 E-value=2.5 Score=21.86 Aligned_cols=39 Identities=38% Similarity=0.672 Sum_probs=30.4
Q ss_pred EEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEE
Q 045104 4 LKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVS 42 (151)
Q Consensus 4 l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~ 42 (151)
+.+ ++.|..|...++..+...+++.....++......+.
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (63)
T cd00371 2 LSVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVE 41 (63)
T ss_pred eeECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEE
Confidence 346 889999999999988888888777777766655554
No 16
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=76.32 E-value=12 Score=23.60 Aligned_cols=53 Identities=21% Similarity=0.181 Sum_probs=37.5
Q ss_pred EEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEee--CCHHHHHHHHHhCCCcEEEc
Q 045104 3 VLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVN--VDSAILIKKLVRSGKYVELL 64 (151)
Q Consensus 3 ~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~--~~~~~I~~~I~k~Gy~a~l~ 64 (151)
++.+ |..|+...-++.++|.+++.= +.+.|..+ ....+|...+++.|+....+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHCCCEEEEE
Confidence 5778 999999999999999997432 33344332 34578999999999975433
No 17
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=72.22 E-value=18 Score=25.20 Aligned_cols=49 Identities=18% Similarity=0.325 Sum_probs=33.8
Q ss_pred HHHHHHhccCCeeEEEEec-----cCCEEE--EEee-CCHHHHHHHHHhCCCcEEEc
Q 045104 16 KVKKLLRKIEGVYSLHIDA-----ENQVVI--VSVN-VDSAILIKKLVRSGKYVELL 64 (151)
Q Consensus 16 kIek~L~~~~GV~~v~Vn~-----~~~~v~--V~~~-~~~~~I~~~I~k~Gy~a~l~ 64 (151)
.+-+.|.+++||..+.+.. .+..+. |.|. ++.++|.++|++.|-..+.+
T Consensus 21 e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHSI 77 (95)
T PF02680_consen 21 ELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHSI 77 (95)
T ss_dssp HHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEEE
T ss_pred HHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEee
Confidence 4567788999988775443 444444 4454 89999999999999776654
No 18
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=69.26 E-value=7.5 Score=24.72 Aligned_cols=19 Identities=21% Similarity=0.604 Sum_probs=14.9
Q ss_pred HHHHHHHHhccCCeeEEEE
Q 045104 14 QQKVKKLLRKIEGVYSLHI 32 (151)
Q Consensus 14 ~~kIek~L~~~~GV~~v~V 32 (151)
...|+.+|..++||.+|+|
T Consensus 54 ~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 54 REEIREALKALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHHTSTT-SEEEE
T ss_pred HHHHHHHHHhCCCCceEeC
Confidence 4678888999999998875
No 19
>PRK11018 hypothetical protein; Provisional
Probab=67.53 E-value=32 Score=22.53 Aligned_cols=53 Identities=11% Similarity=-0.034 Sum_probs=38.0
Q ss_pred EEEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEe--eCCHHHHHHHHHhCCCcEEE
Q 045104 2 HVLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSV--NVDSAILIKKLVRSGKYVEL 63 (151)
Q Consensus 2 ~~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~--~~~~~~I~~~I~k~Gy~a~l 63 (151)
.++.+ |..|+.-.-+.+++|.+++.- +.+.|.. ......|...+++.|+....
T Consensus 9 ~~lD~rG~~CP~Pvl~~kk~l~~l~~G---------~~L~V~~d~~~a~~di~~~~~~~G~~v~~ 64 (78)
T PRK11018 9 YRLDMVGEPCPYPAVATLEALPQLKKG---------EILEVVSDCPQSINNIPLDARNHGYTVLD 64 (78)
T ss_pred eeEECCCCcCCHHHHHHHHHHHhCCCC---------CEEEEEeCCccHHHHHHHHHHHcCCEEEE
Confidence 35777 999999999999999988522 2223322 24456788888999998753
No 20
>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=65.40 E-value=23 Score=22.11 Aligned_cols=50 Identities=22% Similarity=0.237 Sum_probs=34.6
Q ss_pred EEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEe--eCCHHHHHHHHHhCCCcEEE
Q 045104 4 LKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSV--NVDSAILIKKLVRSGKYVEL 63 (151)
Q Consensus 4 l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~--~~~~~~I~~~I~k~Gy~a~l 63 (151)
+.+ |+.|+.-.-+++++| ++.. .+.+.|.. ......|....++.||....
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~~~s~~~i~~~~~~~G~~~~~ 54 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEA---------GGEIEVLVDNEVAKENVSRFAESRGYEVSV 54 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCC---------CCEEEEEEcChhHHHHHHHHHHHcCCEEEE
Confidence 456 999999999999999 5532 12233332 23456888888999998854
No 21
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=63.65 E-value=18 Score=27.69 Aligned_cols=45 Identities=16% Similarity=0.308 Sum_probs=34.8
Q ss_pred HhHHHHHHHHHhccCCeeEEEEeccCCE-------------------EEEEee---CCHHHHHHHHH
Q 045104 11 QGCQQKVKKLLRKIEGVYSLHIDAENQV-------------------VIVSVN---VDSAILIKKLV 55 (151)
Q Consensus 11 ~~C~~kIek~L~~~~GV~~v~Vn~~~~~-------------------v~V~~~---~~~~~I~~~I~ 55 (151)
.+|-+-+|..+.+++||.++.+-...+. |.|..+ ++.++|++..-
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~ 76 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFF 76 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHH
Confidence 5788999999999999999998876654 555543 67777877654
No 22
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=60.62 E-value=46 Score=22.60 Aligned_cols=45 Identities=22% Similarity=0.224 Sum_probs=31.7
Q ss_pred HhHHHHHHHHHhccCCeeEEEEeccCCEEEEEe-eCCHHHHHHHHH
Q 045104 11 QGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSV-NVDSAILIKKLV 55 (151)
Q Consensus 11 ~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~-~~~~~~I~~~I~ 55 (151)
+.=...|.+.|..+||++-...+...+|+.|+- ..+...+.+.|.
T Consensus 16 Pe~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 16 SERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred hHHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 344678899999999998777777788888763 344555555444
No 23
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=59.82 E-value=47 Score=23.08 Aligned_cols=49 Identities=22% Similarity=0.307 Sum_probs=33.5
Q ss_pred HHHHHhccCCeeEEEE-----eccC--CEEEEEe-eCCHHHHHHHHHhCCCcEEEcC
Q 045104 17 VKKLLRKIEGVYSLHI-----DAEN--QVVIVSV-NVDSAILIKKLVRSGKYVELLS 65 (151)
Q Consensus 17 Iek~L~~~~GV~~v~V-----n~~~--~~v~V~~-~~~~~~I~~~I~k~Gy~a~l~~ 65 (151)
+-+.|.+++||+.|.+ |.++ -+++|.| +++-++|.+.|++.|-..+.+.
T Consensus 24 ~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHSiD 80 (97)
T COG1888 24 LALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHSID 80 (97)
T ss_pred HHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeeehh
Confidence 4456778888776644 3334 3444555 4889999999999998766543
No 24
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=53.59 E-value=49 Score=20.93 Aligned_cols=51 Identities=16% Similarity=0.109 Sum_probs=36.9
Q ss_pred EEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEe--eCCHHHHHHHHHhCCCcEEE
Q 045104 4 LKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSV--NVDSAILIKKLVRSGKYVEL 63 (151)
Q Consensus 4 l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~--~~~~~~I~~~I~k~Gy~a~l 63 (151)
+.+ |+.|+.=.-+.+++|.+++.- +.+.|.. .....+|....++.|+....
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~G---------~~l~V~~d~~~a~~di~~~~~~~G~~~~~ 55 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQDG---------EQLEVKASDPGFARDAQAWCKSTGNTLIS 55 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCC---------CEEEEEECCccHHHHHHHHHHHcCCEEEE
Confidence 456 999999999999999987521 2233332 24557888888999998764
No 25
>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=49.09 E-value=66 Score=20.34 Aligned_cols=52 Identities=12% Similarity=0.014 Sum_probs=36.9
Q ss_pred EEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEE--eeCCHHHHHHHHHhCCCcEEEc
Q 045104 4 LKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVS--VNVDSAILIKKLVRSGKYVELL 64 (151)
Q Consensus 4 l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~--~~~~~~~I~~~I~k~Gy~a~l~ 64 (151)
+.+ |..|+.=.-+.+++|.+++.- +.+.|. .......|....++.|+.....
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~~G---------~~l~V~~d~~~s~~ni~~~~~~~g~~v~~~ 56 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLKPG---------EILEVISDCPQSINNIPIDARNHGYKVLAI 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCC---------CEEEEEecCchHHHHHHHHHHHcCCEEEEE
Confidence 345 899999999999999988522 222332 2245677888889999988543
No 26
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=48.95 E-value=52 Score=24.79 Aligned_cols=45 Identities=22% Similarity=0.318 Sum_probs=33.2
Q ss_pred HhHHHHHHHHHhccCCeeEEEEeccCCE--------------EEEEee---CCHHHHHHHHH
Q 045104 11 QGCQQKVKKLLRKIEGVYSLHIDAENQV--------------VIVSVN---VDSAILIKKLV 55 (151)
Q Consensus 11 ~~C~~kIek~L~~~~GV~~v~Vn~~~~~--------------v~V~~~---~~~~~I~~~I~ 55 (151)
++|-+-+|..+.+++||.++.+-...+. |.|..+ ++-++|+....
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~ 69 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLF 69 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHH
Confidence 5788999999999999999988765532 344443 56777777654
No 27
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=47.97 E-value=41 Score=26.73 Aligned_cols=45 Identities=24% Similarity=0.408 Sum_probs=34.1
Q ss_pred HhHHHHHHHHHhccCCeeEEEEeccCC-------------------EEEEEee---CCHHHHHHHHH
Q 045104 11 QGCQQKVKKLLRKIEGVYSLHIDAENQ-------------------VVIVSVN---VDSAILIKKLV 55 (151)
Q Consensus 11 ~~C~~kIek~L~~~~GV~~v~Vn~~~~-------------------~v~V~~~---~~~~~I~~~I~ 55 (151)
++|-+-+|..+.+++||.++.+-...+ .|.|..+ ++-++|+....
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff 118 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFW 118 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHH
Confidence 578999999999999999999987743 2445543 57777777654
No 28
>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=44.23 E-value=80 Score=19.87 Aligned_cols=52 Identities=15% Similarity=0.123 Sum_probs=36.8
Q ss_pred EEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEE--eeCCHHHHHHHHHhCCCcEEEc
Q 045104 4 LKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVS--VNVDSAILIKKLVRSGKYVELL 64 (151)
Q Consensus 4 l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~--~~~~~~~I~~~I~k~Gy~a~l~ 64 (151)
+.+ |..|+.=.-+.+++|.+++- .+.+.|. .......|....++.||.....
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~~---------G~~l~V~~dd~~s~~di~~~~~~~g~~~~~~ 56 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMKP---------GDTLLVLATDPSTTRDIPKFCTFLGHELLAQ 56 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCCC---------CCEEEEEeCCCchHHHHHHHHHHcCCEEEEE
Confidence 456 89999999999999998742 1222332 2245678888999999987543
No 29
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=42.59 E-value=44 Score=25.99 Aligned_cols=45 Identities=20% Similarity=0.313 Sum_probs=33.9
Q ss_pred HhHHHHHHHHHhccCCeeEEEEeccCCE-------------------EEEEee---CCHHHHHHHHH
Q 045104 11 QGCQQKVKKLLRKIEGVYSLHIDAENQV-------------------VIVSVN---VDSAILIKKLV 55 (151)
Q Consensus 11 ~~C~~kIek~L~~~~GV~~v~Vn~~~~~-------------------v~V~~~---~~~~~I~~~I~ 55 (151)
.+|-+-+|..+.+++||.++++-...+. |.|..+ ++.++|+....
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff 81 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFF 81 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHH
Confidence 5788888999999999999998776654 445443 57777777654
No 30
>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=42.31 E-value=81 Score=19.35 Aligned_cols=51 Identities=22% Similarity=0.177 Sum_probs=36.3
Q ss_pred EEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEee--CCHHHHHHHHHhCCCcEEE
Q 045104 4 LKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVN--VDSAILIKKLVRSGKYVEL 63 (151)
Q Consensus 4 l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~--~~~~~I~~~I~k~Gy~a~l 63 (151)
+.+ |+.|+.=.-++.++|.+++. .+.+.|..+ .....|...++..||....
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~~---------g~~l~v~~d~~~~~~~i~~~~~~~g~~~~~ 55 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLKS---------GEVLEVLLDDPGAVEDIPAWAKETGHEVLE 55 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCCC---------CCEEEEEecCCcHHHHHHHHHHHcCCEEEE
Confidence 456 89999999999999988642 223333322 3467888889999998654
No 31
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=40.56 E-value=1.1e+02 Score=20.19 Aligned_cols=43 Identities=19% Similarity=0.196 Sum_probs=30.3
Q ss_pred HHHHHHHHHhccCCeeEEEEeccCCEEEEE-eeCCHHHHHHHHHh
Q 045104 13 CQQKVKKLLRKIEGVYSLHIDAENQVVIVS-VNVDSAILIKKLVR 56 (151)
Q Consensus 13 C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~-~~~~~~~I~~~I~k 56 (151)
=...+.++|..+||++-...+.. +++.|+ ...+...+.+.+..
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~ 59 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDA 59 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHH
Confidence 35678999999999976666655 777765 33556666666654
No 32
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=38.79 E-value=1e+02 Score=19.70 Aligned_cols=42 Identities=19% Similarity=0.353 Sum_probs=29.5
Q ss_pred HhccCCeeEEEEeccCCEEEE--EeeCCHHHHHHHHHhCCCcEEEc
Q 045104 21 LRKIEGVYSLHIDAENQVVIV--SVNVDSAILIKKLVRSGKYVELL 64 (151)
Q Consensus 21 L~~~~GV~~v~Vn~~~~~v~V--~~~~~~~~I~~~I~k~Gy~a~l~ 64 (151)
|..++||..+...- .+.+.+ .......+|+..+...|. ..-+
T Consensus 26 l~~~~~v~~v~~~~-~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~f 69 (84)
T PF13732_consen 26 LEELPGVESVEQDG-DGKLRIKLEDEETANELLQELIEKGI-IRSF 69 (84)
T ss_pred HhhCCCeEEEEEeC-CcEEEEEECCcccHHHHHHHHHhCCC-eeEE
Confidence 77789999887643 443444 444677889999999998 6443
No 33
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=37.61 E-value=41 Score=25.78 Aligned_cols=20 Identities=10% Similarity=0.252 Sum_probs=16.2
Q ss_pred HHHHHHHhccCCeeEEEEec
Q 045104 15 QKVKKLLRKIEGVYSLHIDA 34 (151)
Q Consensus 15 ~kIek~L~~~~GV~~v~Vn~ 34 (151)
..|+.+|..++||.++.|++
T Consensus 134 ~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 134 EDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred HHHHHHHHhCCCceeEEEEE
Confidence 45888888899999888764
No 34
>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=37.45 E-value=1.2e+02 Score=22.46 Aligned_cols=30 Identities=13% Similarity=0.277 Sum_probs=26.1
Q ss_pred HHHHHHHHHhccCCeeEEEEeccCCEEEEE
Q 045104 13 CQQKVKKLLRKIEGVYSLHIDAENQVVIVS 42 (151)
Q Consensus 13 C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~ 42 (151)
=+..|.+.+.+++||..+.|-.....+.|-
T Consensus 76 ~a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 76 LADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 367889999999999999998888888875
No 35
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=35.47 E-value=62 Score=23.05 Aligned_cols=21 Identities=24% Similarity=0.460 Sum_probs=17.8
Q ss_pred HHHHHHHHhccCCeeEEEEec
Q 045104 14 QQKVKKLLRKIEGVYSLHIDA 34 (151)
Q Consensus 14 ~~kIek~L~~~~GV~~v~Vn~ 34 (151)
...++.++..++||..++|++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 677899999999999888764
No 36
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=31.71 E-value=1.5e+02 Score=19.37 Aligned_cols=53 Identities=11% Similarity=0.124 Sum_probs=37.2
Q ss_pred EEEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEe--eCCHHHHHHHHHhCCCcEEE
Q 045104 2 HVLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSV--NVDSAILIKKLVRSGKYVEL 63 (151)
Q Consensus 2 ~~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~--~~~~~~I~~~I~k~Gy~a~l 63 (151)
.++.+ |..|+.=.-+++++|.+++.- +.+.|.. .....+|....+..|++...
T Consensus 10 ~~lD~~Gl~CP~Pll~~kk~l~~l~~G---------~~l~V~~dd~~~~~di~~~~~~~G~~~~~ 65 (81)
T PRK00299 10 HTLDALGLRCPEPVMMVRKTVRNMQPG---------ETLLIIADDPATTRDIPSFCRFMDHELLA 65 (81)
T ss_pred eEEecCCCCCCHHHHHHHHHHHcCCCC---------CEEEEEeCCccHHHHHHHHHHHcCCEEEE
Confidence 35677 999999999999999988421 2223322 23456788888899998753
No 37
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=30.91 E-value=2.1e+02 Score=21.39 Aligned_cols=56 Identities=11% Similarity=0.171 Sum_probs=38.2
Q ss_pred HHHHHHHHHhccCCeeEEEEeccCCEEEEEee-------CCHHHHHHHHHhCCCcEEEcCCCc
Q 045104 13 CQQKVKKLLRKIEGVYSLHIDAENQVVIVSVN-------VDSAILIKKLVRSGKYVELLSPSY 68 (151)
Q Consensus 13 C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~-------~~~~~I~~~I~k~Gy~a~l~~~~~ 68 (151)
-...|++.+-.-.||..+.++..++.|.|... -.-..+.+...++|+...+....+
T Consensus 54 A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 54 AIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred HHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 34456666655579999999999999998632 122334455568999988764443
No 38
>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=30.55 E-value=1.3e+02 Score=18.39 Aligned_cols=20 Identities=25% Similarity=0.403 Sum_probs=14.4
Q ss_pred HHHHHHHHHhccCCeeEEEE
Q 045104 13 CQQKVKKLLRKIEGVYSLHI 32 (151)
Q Consensus 13 C~~kIek~L~~~~GV~~v~V 32 (151)
-...+-+.|++++||.+|.+
T Consensus 55 ~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 55 DIDELLEELREIDGVEKVEL 74 (76)
T ss_pred HHHHHHHHHhcCCCeEEEEE
Confidence 55677777788888877654
No 39
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=28.68 E-value=1e+02 Score=20.61 Aligned_cols=21 Identities=24% Similarity=0.406 Sum_probs=16.2
Q ss_pred HHHHHHHhccCCeeEEEEecc
Q 045104 15 QKVKKLLRKIEGVYSLHIDAE 35 (151)
Q Consensus 15 ~kIek~L~~~~GV~~v~Vn~~ 35 (151)
..++.+|..++|+.++.+++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 457778888899988888754
No 40
>PRK09577 multidrug efflux protein; Reviewed
Probab=27.95 E-value=1.7e+02 Score=28.42 Aligned_cols=46 Identities=13% Similarity=0.200 Sum_probs=35.5
Q ss_pred HHHHHHHHhccCCeeEEEEeccCCEEEEE--------eeCCHHHHHHHHHhCCC
Q 045104 14 QQKVKKLLRKIEGVYSLHIDAENQVVIVS--------VNVDSAILIKKLVRSGK 59 (151)
Q Consensus 14 ~~kIek~L~~~~GV~~v~Vn~~~~~v~V~--------~~~~~~~I~~~I~k~Gy 59 (151)
...++..|.+++||.+|++......+.|. ..+++.+|.++|+..+.
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n~ 211 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAHNA 211 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhCC
Confidence 46789999999999999998765556664 22678889999987543
No 41
>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=27.64 E-value=62 Score=24.26 Aligned_cols=27 Identities=26% Similarity=0.453 Sum_probs=23.3
Q ss_pred HhHHHHHHHHHhccCCeeEEEEeccCC
Q 045104 11 QGCQQKVKKLLRKIEGVYSLHIDAENQ 37 (151)
Q Consensus 11 ~~C~~kIek~L~~~~GV~~v~Vn~~~~ 37 (151)
.+|-+-++..+.+++||.++.+-...+
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG 33 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGG 33 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESS
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCC
Confidence 478899999999999999999877654
No 42
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=26.84 E-value=1.8e+02 Score=28.30 Aligned_cols=44 Identities=7% Similarity=0.165 Sum_probs=34.2
Q ss_pred HHHHHHHHhccCCeeEEEEeccCCEEEEEe--------eCCHHHHHHHHHhC
Q 045104 14 QQKVKKLLRKIEGVYSLHIDAENQVVIVSV--------NVDSAILIKKLVRS 57 (151)
Q Consensus 14 ~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~--------~~~~~~I~~~I~k~ 57 (151)
...++..|++++||.+|++......+.|.- .+++.++..+|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 467889999999999999987655566652 26888899999753
No 43
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=26.74 E-value=1.4e+02 Score=24.78 Aligned_cols=27 Identities=26% Similarity=0.411 Sum_probs=23.3
Q ss_pred HhHHHHHHHHHhccCCeeEEEEeccCC
Q 045104 11 QGCQQKVKKLLRKIEGVYSLHIDAENQ 37 (151)
Q Consensus 11 ~~C~~kIek~L~~~~GV~~v~Vn~~~~ 37 (151)
.+|-+-+|..+.+++||.++.+-...+
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG 160 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGG 160 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCC
Confidence 678899999999999999998877654
No 44
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=26.40 E-value=1.2e+02 Score=19.95 Aligned_cols=51 Identities=20% Similarity=0.305 Sum_probs=34.1
Q ss_pred EEEEE-cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEEee--CCHHHHHHHHHhCC-CcE
Q 045104 2 HVLKV-HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVSVN--VDSAILIKKLVRSG-KYV 61 (151)
Q Consensus 2 ~~l~V-gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~~--~~~~~I~~~I~k~G-y~a 61 (151)
.+|.+ |+.|+.=.-.+.++|.+++- .+.+.|..+ ....+|....++.| +..
T Consensus 6 ~~LD~rG~~CP~Pv~~~kk~l~~m~~---------Ge~LeV~~ddp~~~~dIp~~~~~~~~~~l 60 (78)
T COG0425 6 KVLDLRGLRCPGPVVETKKALAKLKP---------GEILEVIADDPAAKEDIPAWAKKEGGHEL 60 (78)
T ss_pred eEEeccCCcCCccHHHHHHHHHcCCC---------CCEEEEEecCcchHHHHHHHHHHcCCcEE
Confidence 36788 99999999999999998842 223333322 33456777777455 543
No 45
>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=26.07 E-value=2.3e+02 Score=21.91 Aligned_cols=48 Identities=21% Similarity=0.139 Sum_probs=34.4
Q ss_pred cCcCHhHHHHHHHHHhccCCeeEEEEeccCCEEEEE--eeCCHHHHHHHHHhCCCcEEE
Q 045104 7 HIHCQGCQQKVKKLLRKIEGVYSLHIDAENQVVIVS--VNVDSAILIKKLVRSGKYVEL 63 (151)
Q Consensus 7 gm~C~~C~~kIek~L~~~~GV~~v~Vn~~~~~v~V~--~~~~~~~I~~~I~k~Gy~a~l 63 (151)
|+.|+.-.-+.+++|.+++.- +.++|. .....+.|....++.||+...
T Consensus 5 Gl~CP~Pvi~tKkal~~l~~g---------~~L~VlvD~~~a~~nV~~~~~~~G~~v~~ 54 (194)
T TIGR03527 5 GLACPQPVILTKKALDELGEE---------GVLTVIVDNEAAKENVSKFATSLGYEVEV 54 (194)
T ss_pred CCCCCHHHHHHHHHHHcCCCC---------CEEEEEECCccHHHHHHHHHHHcCCEEEE
Confidence 889999999999999988521 122222 224556788888899998754
No 46
>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=24.51 E-value=61 Score=24.20 Aligned_cols=27 Identities=33% Similarity=0.476 Sum_probs=22.8
Q ss_pred HhHHHHHHHHHhccCCeeEEEEeccCC
Q 045104 11 QGCQQKVKKLLRKIEGVYSLHIDAENQ 37 (151)
Q Consensus 11 ~~C~~kIek~L~~~~GV~~v~Vn~~~~ 37 (151)
.+|-+-++..+.+++||.++.+-...+
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG 33 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGG 33 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCC
Confidence 578889999999999999998866544
No 47
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=23.98 E-value=88 Score=19.85 Aligned_cols=13 Identities=31% Similarity=0.611 Sum_probs=9.4
Q ss_pred EEEE-cCcCHhHHH
Q 045104 3 VLKV-HIHCQGCQQ 15 (151)
Q Consensus 3 ~l~V-gm~C~~C~~ 15 (151)
.+++ +..|+.|..
T Consensus 2 ~I~v~~~~C~~C~~ 15 (76)
T PF13192_consen 2 KIKVFSPGCPYCPE 15 (76)
T ss_dssp EEEEECSSCTTHHH
T ss_pred EEEEeCCCCCCcHH
Confidence 3455 778999973
No 48
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=22.27 E-value=1.4e+02 Score=19.09 Aligned_cols=28 Identities=21% Similarity=0.376 Sum_probs=17.7
Q ss_pred cCcCHhHHHHHHHHHhcc----CCeeEEEEecc
Q 045104 7 HIHCQGCQQKVKKLLRKI----EGVYSLHIDAE 35 (151)
Q Consensus 7 gm~C~~C~~kIek~L~~~----~GV~~v~Vn~~ 35 (151)
--+|+.|. ++.+.|..+ .|+.-..+|..
T Consensus 8 ~~~C~~C~-~a~~~L~~l~~~~~~i~~~~idi~ 39 (85)
T PRK11200 8 RPGCPYCV-RAKELAEKLSEERDDFDYRYVDIH 39 (85)
T ss_pred CCCChhHH-HHHHHHHhhcccccCCcEEEEECC
Confidence 45699998 566666664 46655555543
No 49
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=21.64 E-value=96 Score=21.78 Aligned_cols=21 Identities=24% Similarity=0.679 Sum_probs=16.7
Q ss_pred cCcCHhHHHHHHHHHhccCCee
Q 045104 7 HIHCQGCQQKVKKLLRKIEGVY 28 (151)
Q Consensus 7 gm~C~~C~~kIek~L~~~~GV~ 28 (151)
-..|..|+..+++.|... ||.
T Consensus 18 ~~qC~~cA~Al~~~L~~~-gI~ 38 (100)
T PF15643_consen 18 IFQCVECASALKQFLKQA-GIP 38 (100)
T ss_pred ceehHHHHHHHHHHHHHC-CCC
Confidence 467999999999999863 443
No 50
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=21.23 E-value=1.9e+02 Score=18.15 Aligned_cols=21 Identities=29% Similarity=0.412 Sum_probs=14.0
Q ss_pred HhHHHHHHHHHhccCCeeEEE
Q 045104 11 QGCQQKVKKLLRKIEGVYSLH 31 (151)
Q Consensus 11 ~~C~~kIek~L~~~~GV~~v~ 31 (151)
..=-..|-..|++++||.+|.
T Consensus 59 ~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 59 LEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp HHHHHHHHHHHCTSTTEEEEE
T ss_pred HHHHHHHHHHHHCCCCeeEEE
Confidence 344456677778888887653
No 51
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=20.77 E-value=2.7e+02 Score=27.15 Aligned_cols=43 Identities=9% Similarity=0.179 Sum_probs=33.6
Q ss_pred HHHHHHHhccCCeeEEEEeccCCEEEEEe--------eCCHHHHHHHHHhC
Q 045104 15 QKVKKLLRKIEGVYSLHIDAENQVVIVSV--------NVDSAILIKKLVRS 57 (151)
Q Consensus 15 ~kIek~L~~~~GV~~v~Vn~~~~~v~V~~--------~~~~~~I~~~I~k~ 57 (151)
..++..|.+++||.++++.-....+.|.- .+++.+|..+|+..
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~~~ 210 (1049)
T PRK15127 160 ANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIKAQ 210 (1049)
T ss_pred HHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 56889999999999999876655566652 26888889998854
No 52
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=20.58 E-value=1.1e+02 Score=20.88 Aligned_cols=21 Identities=29% Similarity=0.395 Sum_probs=18.2
Q ss_pred HHHHHHHHHhccCCeeEEEEe
Q 045104 13 CQQKVKKLLRKIEGVYSLHID 33 (151)
Q Consensus 13 C~~kIek~L~~~~GV~~v~Vn 33 (151)
-...++.++++++||+++.+.
T Consensus 63 ~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 63 GTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred ChHHHHHHHhcCCCccEEEEE
Confidence 358899999999999998875
No 53
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=20.53 E-value=55 Score=20.77 Aligned_cols=20 Identities=15% Similarity=0.464 Sum_probs=15.9
Q ss_pred EEcCcCHhHHHHHHHHHhcc
Q 045104 5 KVHIHCQGCQQKVKKLLRKI 24 (151)
Q Consensus 5 ~Vgm~C~~C~~kIek~L~~~ 24 (151)
.+|-.|++|...+++.|...
T Consensus 34 ~~g~~CG~C~~~i~~il~~~ 53 (64)
T PRK10509 34 PVGNQCGKCIRAAREVMQDE 53 (64)
T ss_pred CCCCCccchHHHHHHHHHHH
Confidence 44678999999999888654
No 54
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=20.49 E-value=2.7e+02 Score=27.12 Aligned_cols=44 Identities=11% Similarity=0.206 Sum_probs=34.4
Q ss_pred HHHHHHHHhccCCeeEEEEeccCCEEEEEe--------eCCHHHHHHHHHhC
Q 045104 14 QQKVKKLLRKIEGVYSLHIDAENQVVIVSV--------NVDSAILIKKLVRS 57 (151)
Q Consensus 14 ~~kIek~L~~~~GV~~v~Vn~~~~~v~V~~--------~~~~~~I~~~I~k~ 57 (151)
...++..|.+++||.+|++......+.|.- .+++.++..+|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~~~ 210 (1044)
T TIGR00915 159 ASNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQAQ 210 (1044)
T ss_pred HHHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 356889999999999999987755566652 26888899999863
Done!