Query 039645
Match_columns 188
No_of_seqs 335 out of 1506
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 11:44:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039645.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039645hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.4 6.9E-13 1.5E-17 87.9 8.1 58 63-121 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.4 6.3E-12 1.4E-16 86.2 9.1 66 59-125 1-70 (71)
3 KOG4656 Copper chaperone for s 99.3 2.8E-12 6.1E-17 103.6 4.5 95 59-154 6-101 (247)
4 KOG1603 Copper chaperone [Inor 99.3 4.2E-11 9.1E-16 82.5 9.0 67 59-126 4-71 (73)
5 PLN02957 copper, zinc superoxi 98.4 2E-06 4.3E-11 71.8 10.4 71 60-131 6-76 (238)
6 PRK10671 copA copper exporting 98.3 1.7E-06 3.7E-11 83.7 8.2 64 60-126 3-67 (834)
7 COG2217 ZntA Cation transport 98.1 1.1E-05 2.4E-10 76.8 7.9 63 60-124 2-69 (713)
8 TIGR00003 copper ion binding p 97.9 0.00019 4.2E-09 44.2 8.6 62 60-122 2-67 (68)
9 KOG0207 Cation transport ATPas 97.6 0.00014 3E-09 70.1 7.4 67 60-127 146-216 (951)
10 PRK10671 copA copper exporting 97.2 0.0012 2.5E-08 64.2 8.1 64 61-125 100-164 (834)
11 KOG0207 Cation transport ATPas 97.2 0.00085 1.8E-08 64.9 6.6 62 67-129 2-65 (951)
12 PRK11033 zntA zinc/cadmium/mer 96.9 0.0043 9.3E-08 59.7 8.2 66 59-125 52-119 (741)
13 TIGR02052 MerP mercuric transp 95.2 0.55 1.2E-05 31.3 10.9 63 61-124 24-90 (92)
14 COG1888 Uncharacterized protei 88.1 5.5 0.00012 28.6 7.9 66 60-126 6-80 (97)
15 cd00371 HMA Heavy-metal-associ 87.9 2.9 6.3E-05 22.6 7.2 54 65-119 3-59 (63)
16 PRK13748 putative mercuric red 87.3 3.8 8.3E-05 37.8 8.8 64 63-127 3-69 (561)
17 PF01206 TusA: Sulfurtransfera 82.6 5.5 0.00012 26.2 5.7 53 63-125 2-57 (70)
18 PF02680 DUF211: Uncharacteriz 78.6 6.3 0.00014 28.4 5.1 65 59-125 4-77 (95)
19 PF01883 DUF59: Domain of unkn 70.3 8.9 0.00019 25.3 4.0 33 60-92 34-72 (72)
20 cd03421 SirA_like_N SirA_like_ 63.3 29 0.00064 22.5 5.4 52 64-126 2-56 (67)
21 PRK14054 methionine sulfoxide 62.3 27 0.00058 27.8 5.9 45 71-115 10-76 (172)
22 PRK10553 assembly protein for 60.5 42 0.00091 23.7 6.0 45 71-115 16-61 (87)
23 PRK11018 hypothetical protein; 60.3 44 0.00096 22.7 6.0 55 61-125 8-65 (78)
24 PF02411 MerT: MerT mercuric t 59.0 9 0.00019 28.6 2.5 19 24-42 98-116 (116)
25 PF14437 MafB19-deam: MafB19-l 57.3 28 0.00061 27.1 5.0 40 60-100 100-141 (146)
26 cd03420 SirA_RHOD_Pry_redox Si 55.7 48 0.001 21.8 5.4 53 64-126 2-57 (69)
27 PF03927 NapD: NapD protein; 53.1 72 0.0016 21.9 6.2 42 73-115 16-58 (79)
28 PRK05528 methionine sulfoxide 44.8 80 0.0017 24.7 5.9 45 71-115 8-69 (156)
29 cd03423 SirA SirA (also known 44.3 89 0.0019 20.4 5.8 53 64-126 2-57 (69)
30 cd03422 YedF YedF is a bacteri 43.4 94 0.002 20.4 5.4 52 64-125 2-56 (69)
31 COG2177 FtsX Cell division pro 43.0 2.1E+02 0.0045 24.8 8.7 48 61-121 62-109 (297)
32 cd00291 SirA_YedF_YeeD SirA, Y 41.4 94 0.002 19.8 5.5 53 64-126 2-57 (69)
33 PRK00058 methionine sulfoxide 39.9 1E+02 0.0022 25.5 6.0 52 59-115 45-118 (213)
34 PRK13014 methionine sulfoxide 39.4 76 0.0016 25.6 5.1 45 71-115 15-81 (186)
35 PRK00299 sulfur transfer prote 36.8 1.4E+02 0.003 20.4 6.5 55 61-125 9-66 (81)
36 COG2151 PaaD Predicted metal-s 36.5 58 0.0013 24.1 3.7 32 62-93 51-88 (111)
37 PF09580 Spore_YhcN_YlaJ: Spor 36.4 1.1E+02 0.0024 23.7 5.6 34 70-103 73-106 (177)
38 TIGR03406 FeS_long_SufT probab 36.1 48 0.001 26.4 3.4 34 61-94 114-153 (174)
39 PF13732 DUF4162: Domain of un 34.6 1.4E+02 0.003 19.8 5.4 42 81-125 26-69 (84)
40 PF13106 DUF3961: Domain of un 34.4 45 0.00098 20.2 2.3 32 2-37 3-35 (40)
41 cd02410 archeal_CPSF_KH The ar 32.6 1.8E+02 0.004 22.6 6.0 60 70-129 51-116 (145)
42 PF08821 CGGC: CGGC domain; I 32.6 92 0.002 22.7 4.2 57 64-124 38-104 (107)
43 PHA01634 hypothetical protein 32.0 16 0.00034 28.3 0.1 16 64-79 93-109 (156)
44 PF04972 BON: BON domain; Int 30.8 40 0.00086 21.4 1.9 32 75-107 2-36 (64)
45 cd04888 ACT_PheB-BS C-terminal 29.8 1.5E+02 0.0033 18.9 5.0 33 60-92 41-74 (76)
46 PF11491 DUF3213: Protein of u 26.5 1E+02 0.0022 21.8 3.3 48 74-122 13-63 (88)
47 COG0425 SirA Predicted redox p 26.2 2.2E+02 0.0047 19.4 6.3 49 61-119 5-56 (78)
48 TIGR02945 SUF_assoc FeS assemb 25.8 77 0.0017 22.2 2.8 36 60-95 39-78 (99)
49 PRK11023 outer membrane lipopr 24.7 2.5E+02 0.0054 22.4 5.9 38 73-110 128-167 (191)
50 PF01625 PMSR: Peptide methion 24.7 2.5E+02 0.0053 21.9 5.6 27 71-97 7-33 (155)
51 TIGR03527 selenium_YedF seleni 23.8 2E+02 0.0043 23.2 5.1 49 67-125 5-55 (194)
52 PF08777 RRM_3: RNA binding mo 23.6 2.8E+02 0.0062 19.9 6.5 55 63-118 3-60 (105)
53 PF08002 DUF1697: Protein of u 23.3 3E+02 0.0064 20.7 5.8 49 75-124 22-74 (137)
54 PRK05550 bifunctional methioni 23.1 2.5E+02 0.0054 24.2 5.8 28 71-98 134-161 (283)
55 PRK09577 multidrug efflux prot 23.0 2.3E+02 0.0049 28.8 6.4 45 74-119 158-210 (1032)
56 PRK10555 aminoglycoside/multid 23.0 2.1E+02 0.0045 29.1 6.1 42 74-115 159-208 (1037)
57 PRK13751 putative mercuric tra 22.3 80 0.0017 23.6 2.3 19 24-42 98-116 (116)
58 PRK11023 outer membrane lipopr 21.5 2.1E+02 0.0046 22.8 4.9 47 69-115 46-95 (191)
59 PF13291 ACT_4: ACT domain; PD 21.2 2.5E+02 0.0054 18.3 4.7 34 58-91 46-79 (80)
60 PF10215 Ost4: Oligosaccaryltr 21.2 47 0.001 19.5 0.7 18 14-31 6-23 (35)
61 TIGR02898 spore_YhcN_YlaJ spor 20.8 3.6E+02 0.0079 21.1 5.9 32 72-103 54-85 (158)
62 PF08712 Nfu_N: Scaffold prote 20.6 2.3E+02 0.0049 19.7 4.3 50 62-115 26-77 (87)
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=99.44 E-value=6.9e-13 Score=87.87 Aligned_cols=58 Identities=31% Similarity=0.625 Sum_probs=54.2
Q ss_pred EEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee---CCHHHHHHHHHHhcCCc
Q 039645 63 EIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY---VDPDKVLERVRHRTGKK 121 (188)
Q Consensus 63 ~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~---v~~~~I~~~I~~~~G~~ 121 (188)
+|+| ||+|++|+.+|+++|.+++||.++.+|+.+++++|.++ +++++|.++|+ ++||+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~-~~Gy~ 62 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIE-KAGYE 62 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHH-HTTSE
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHH-HhCcC
Confidence 4889 99999999999999999999999999999999999986 45699999999 99985
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.36 E-value=6.3e-12 Score=86.20 Aligned_cols=66 Identities=30% Similarity=0.502 Sum_probs=58.9
Q ss_pred ceEEEEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee---CCHHHHHHHHHHhcCCceEEc
Q 039645 59 LQTVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY---VDPDKVLERVRHRTGKKAEFW 125 (188)
Q Consensus 59 ~~~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~---v~~~~I~~~I~~~~G~~a~l~ 125 (188)
|.+..|+| ||+|.+|+.+|+++|.+++||.++++|++.+.+.|..+ ++.+++.++|+ ++||.+..+
T Consensus 1 ~~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~-~aGy~~~~~ 70 (71)
T COG2608 1 MMKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIE-DAGYKVEEI 70 (71)
T ss_pred CceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHH-HcCCCeeec
Confidence 35678999 99999999999999999999999999999977777643 79999999999 999988754
No 3
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.29 E-value=2.8e-12 Score=103.56 Aligned_cols=95 Identities=28% Similarity=0.409 Sum_probs=79.9
Q ss_pred ceEEEEEEcCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEeeCCHHHHHHHHHHhcCCceEEcCCCCCCCCCCCCC
Q 039645 59 LQTVEIKIKMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGYVDPDKVLERVRHRTGKKAEFWPYVPYDVVPRPYA 138 (188)
Q Consensus 59 ~~~v~l~VgM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~v~~~~I~~~I~~~~G~~a~l~~~~p~~~~~~~~~ 138 (188)
.-+.+|.|.|+|++|+..|++.|..++||.+|++|++++.+.|.+...+.++..+|+ .+|.++.+.+.+...+++..-.
T Consensus 6 ~~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le-~tGr~Avl~G~G~psaval~at 84 (247)
T KOG4656|consen 6 TYEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLE-NTGRDAVLRGAGKPSAVALLAT 84 (247)
T ss_pred ceeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHH-hhChheEEecCCchhHHHHHHH
Confidence 356789999999999999999999999999999999999999999999999999999 9999999999876554433222
Q ss_pred CCCC-CCCCCCCCcccC
Q 039645 139 PEAY-DKKAPPGYVRNV 154 (188)
Q Consensus 139 ~~~~-~~~~~~g~~r~~ 154 (188)
-+.| ...+++|++|+.
T Consensus 85 ~a~~~~~~~v~GvvRf~ 101 (247)
T KOG4656|consen 85 VAKYTGPQAVQGVVRFV 101 (247)
T ss_pred HHHhcCCccceeEEEEE
Confidence 2223 334788998887
No 4
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.26 E-value=4.2e-11 Score=82.47 Aligned_cols=67 Identities=48% Similarity=0.945 Sum_probs=61.8
Q ss_pred ceEEEEEEcCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEeeCCHHHHHHHHHHhcC-CceEEcC
Q 039645 59 LQTVEIKIKMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGYVDPDKVLERVRHRTG-KKAEFWP 126 (188)
Q Consensus 59 ~~~v~l~VgM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~v~~~~I~~~I~~~~G-~~a~l~~ 126 (188)
+++.++++.|+|++|+.+|++.|+.++||.++.+|..+++++|.|.+++..|++.|+ +.| .++.+|.
T Consensus 4 ~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~-k~~~k~~~~~~ 71 (73)
T KOG1603|consen 4 IKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLK-KTGGKRAELWK 71 (73)
T ss_pred ccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHH-hcCCCceEEec
Confidence 467788889999999999999999999999999999999999999999999999999 676 7777774
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.44 E-value=2e-06 Score=71.84 Aligned_cols=71 Identities=30% Similarity=0.468 Sum_probs=63.6
Q ss_pred eEEEEEEcCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEeeCCHHHHHHHHHHhcCCceEEcCCCCCC
Q 039645 60 QTVEIKIKMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGYVDPDKVLERVRHRTGKKAEFWPYVPYD 131 (188)
Q Consensus 60 ~~v~l~VgM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~v~~~~I~~~I~~~~G~~a~l~~~~p~~ 131 (188)
++++|.++|+|+.|+.+|+++|++++||..+.+++..++++|.+.....++.+.++ +.||.+++++..+.+
T Consensus 6 ~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe-~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 6 LLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALE-QTGRKARLIGQGDPE 76 (238)
T ss_pred EEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHH-HcCCcEEEecCCCcc
Confidence 55678889999999999999999999999999999999999988778899999999 999999988765443
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.32 E-value=1.7e-06 Score=83.69 Aligned_cols=64 Identities=27% Similarity=0.507 Sum_probs=57.4
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEeeCCHHHHHHHHHHhcCCceEEcC
Q 039645 60 QTVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGYVDPDKVLERVRHRTGKKAEFWP 126 (188)
Q Consensus 60 ~~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~v~~~~I~~~I~~~~G~~a~l~~ 126 (188)
++.+++| ||+|++|+.+|+++|++++||.++++|+. +.+|++..+.+.+.+.++ +.||+++...
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~-~~Gy~~~~~~ 67 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIK-QAGYDASVSH 67 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHH-hcCCcccccc
Confidence 5788999 99999999999999999999999999994 556667788999999999 9999998753
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.08 E-value=1.1e-05 Score=76.82 Aligned_cols=63 Identities=24% Similarity=0.549 Sum_probs=56.8
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee---CC-HHHHHHHHHHhcCCceEE
Q 039645 60 QTVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY---VD-PDKVLERVRHRTGKKAEF 124 (188)
Q Consensus 60 ~~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~---v~-~~~I~~~I~~~~G~~a~l 124 (188)
.+.+|.| ||+|..|+.+|| +|++++||.++.+|+.++++.|..+ .+ .+++.+.++ +.||.+..
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~-~~gy~~~~ 69 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVE-KAGYSARL 69 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHH-hcCccccc
Confidence 4567999 999999999999 9999999999999999999999864 34 689999999 99998765
No 8
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.87 E-value=0.00019 Score=44.25 Aligned_cols=62 Identities=21% Similarity=0.390 Sum_probs=51.3
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee---CCHHHHHHHHHHhcCCce
Q 039645 60 QTVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY---VDPDKVLERVRHRTGKKA 122 (188)
Q Consensus 60 ~~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~---v~~~~I~~~I~~~~G~~a 122 (188)
.+..+.+ +++|..|...+++.++..+++....++.....+.+... .+...+...+. ..|+.+
T Consensus 2 ~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~ 67 (68)
T TIGR00003 2 QKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAIL-DAGYEV 67 (68)
T ss_pred cEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHH-HcCCCc
Confidence 3457899 99999999999999999999999999999999888753 46667777777 777643
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.65 E-value=0.00014 Score=70.15 Aligned_cols=67 Identities=22% Similarity=0.505 Sum_probs=62.3
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee---CCHHHHHHHHHHhcCCceEEcCC
Q 039645 60 QTVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY---VDPDKVLERVRHRTGKKAEFWPY 127 (188)
Q Consensus 60 ~~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~---v~~~~I~~~I~~~~G~~a~l~~~ 127 (188)
+++.|.| ||+|.+|+.+|++.|.+++||.+++++..++++.|.++ ..+.++.+.|+ .+|+++...+.
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie-~~~~~~~~~~~ 216 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIE-ETGFEASVRPY 216 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHH-hhcccceeeec
Confidence 6889999 99999999999999999999999999999999999865 78999999999 99999877664
No 10
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.22 E-value=0.0012 Score=64.19 Aligned_cols=64 Identities=27% Similarity=0.530 Sum_probs=57.0
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEeeCCHHHHHHHHHHhcCCceEEc
Q 039645 61 TVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGYVDPDKVLERVRHRTGKKAEFW 125 (188)
Q Consensus 61 ~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~v~~~~I~~~I~~~~G~~a~l~ 125 (188)
++.+.+ ||+|.+|..++++.+.+++||.++.+++..+++.+.+..+.+++.+.++ +.||.+.++
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~-~~Gy~a~~~ 164 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVE-KAGYGAEAI 164 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHH-hcCCCcccc
Confidence 567889 9999999999999999999999999999999988876677888888998 999987654
No 11
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.19 E-value=0.00085 Score=64.86 Aligned_cols=62 Identities=24% Similarity=0.436 Sum_probs=57.5
Q ss_pred cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee--CCHHHHHHHHHHhcCCceEEcCCCC
Q 039645 67 KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY--VDPDKVLERVRHRTGKKAEFWPYVP 129 (188)
Q Consensus 67 gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~--v~~~~I~~~I~~~~G~~a~l~~~~p 129 (188)
||+|..|.+.+++++...+||.+..+++.+++.+|.++ .+++.+.+.|+ ..|+.+++.....
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ie-d~gf~~~~~~~~~ 65 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIE-DMGFEASLLSDSE 65 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhh-cccceeeecccCc
Confidence 79999999999999999999999999999999999876 78999999999 9999999876543
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.85 E-value=0.0043 Score=59.70 Aligned_cols=66 Identities=29% Similarity=0.323 Sum_probs=54.3
Q ss_pred ceEEEEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEeeC-CHHHHHHHHHHhcCCceEEc
Q 039645 59 LQTVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGYV-DPDKVLERVRHRTGKKAEFW 125 (188)
Q Consensus 59 ~~~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~v-~~~~I~~~I~~~~G~~a~l~ 125 (188)
..+..+++ ||+|.+|..++++.+.+.+||.++.+++.++++.+..+. ..+++.+.++ +.||++...
T Consensus 52 ~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~-~~Gy~a~~~ 119 (741)
T PRK11033 52 GTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQ-KAGFSLRDE 119 (741)
T ss_pred CceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHH-hcccccccc
Confidence 35677889 999999999999999999999999999999998876531 2266777888 889876543
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=95.21 E-value=0.55 Score=31.32 Aligned_cols=63 Identities=22% Similarity=0.361 Sum_probs=47.2
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEe---eCCHHHHHHHHHHhcCCceEE
Q 039645 61 TVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIG---YVDPDKVLERVRHRTGKKAEF 124 (188)
Q Consensus 61 ~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~---~v~~~~I~~~I~~~~G~~a~l 124 (188)
++.+.+ ++.|..|...++..+...+|+....++.......+.. ..+...+...++ +.|+.+++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATT-DAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHH-hcCCCeEe
Confidence 345678 9999999999999999999988888888777765542 135555656666 77877654
No 14
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=88.06 E-value=5.5 Score=28.58 Aligned_cols=66 Identities=18% Similarity=0.249 Sum_probs=43.0
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhcCCCceEEEe-----ecCC--CEEEEEee-CCHHHHHHHHHHhcCCceEEcC
Q 039645 60 QTVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEV-----DPKQ--SKLTVIGY-VDPDKVLERVRHRTGKKAEFWP 126 (188)
Q Consensus 60 ~~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~v-----d~~~--~~v~V~~~-v~~~~I~~~I~~~~G~~a~l~~ 126 (188)
.++.+.+ .-+-.----.+-+.|.+++||+.|++ |.++ -+++|+|. ++-+++.+.|+ +.|..++.+.
T Consensus 6 RRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE-~~Gg~IHSiD 80 (97)
T COG1888 6 RRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIE-ELGGAIHSID 80 (97)
T ss_pred eeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHH-HcCCeeeehh
Confidence 4455555 33322223455667888888876665 3333 34566664 89999999999 9998776654
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=87.91 E-value=2.9 Score=22.61 Aligned_cols=54 Identities=37% Similarity=0.674 Sum_probs=36.3
Q ss_pred EE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee--CCHHHHHHHHHHhcC
Q 039645 65 KI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY--VDPDKVLERVRHRTG 119 (188)
Q Consensus 65 ~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~--v~~~~I~~~I~~~~G 119 (188)
.+ ++.|..|...++..+...+|+.....+.......+... .+...+...++ ..|
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 59 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIE-DAG 59 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHH-HcC
Confidence 35 78899999999999888889877777766666555432 24444433444 444
No 16
>PRK13748 putative mercuric reductase; Provisional
Probab=87.34 E-value=3.8 Score=37.79 Aligned_cols=64 Identities=25% Similarity=0.409 Sum_probs=50.2
Q ss_pred EEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee--CCHHHHHHHHHHhcCCceEEcCC
Q 039645 63 EIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY--VDPDKVLERVRHRTGKKAEFWPY 127 (188)
Q Consensus 63 ~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~--v~~~~I~~~I~~~~G~~a~l~~~ 127 (188)
.+.+ +|+|..|..+++..+...+++....++.......+... .+...+...++ ..|+..++...
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~-~~g~~~~~~~~ 69 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVA-GLGYRATLADA 69 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHH-HcCCeeeccCc
Confidence 3568 99999999999999999999998888888888766632 35566666777 88887766554
No 17
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=82.65 E-value=5.5 Score=26.21 Aligned_cols=53 Identities=11% Similarity=0.124 Sum_probs=38.5
Q ss_pred EEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee--CCHHHHHHHHHHhcCCceEEc
Q 039645 63 EIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY--VDPDKVLERVRHRTGKKAEFW 125 (188)
Q Consensus 63 ~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~--v~~~~I~~~I~~~~G~~a~l~ 125 (188)
++.+ |+.|+...-+++++|.+++.= +.+.|..+ ....+|...++ +.|++...+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~-~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCE-ENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHH-HHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHH-HCCCEEEEE
Confidence 5778 999999999999999997432 34444443 45578999998 999985544
No 18
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=78.63 E-value=6.3 Score=28.44 Aligned_cols=65 Identities=18% Similarity=0.325 Sum_probs=42.6
Q ss_pred ceEEEEEE-cCcChhHHHHHHHHHhcCCCceEEEe-----ecCCCE--EEEEee-CCHHHHHHHHHHhcCCceEEc
Q 039645 59 LQTVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEV-----DPKQSK--LTVIGY-VDPDKVLERVRHRTGKKAEFW 125 (188)
Q Consensus 59 ~~~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~v-----d~~~~~--v~V~~~-v~~~~I~~~I~~~~G~~a~l~ 125 (188)
..++.|.| --+-++= -.+-++|.+++||..|++ |..+.. ++|+|. ++.+++.++|+ +.|-.++.+
T Consensus 4 irRlVLDVlKP~~p~i-~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie-~~Gg~IHSI 77 (95)
T PF02680_consen 4 IRRLVLDVLKPHEPSI-VELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIE-ELGGVIHSI 77 (95)
T ss_dssp EEEEEEEEEEESSS-H-HHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHH-HTT-EEEEE
T ss_pred eeEEEEEeecCCCCCH-HHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHH-HcCCeEEee
Confidence 34566666 3344433 456778999999987765 444444 455675 89999999999 999766654
No 19
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=70.25 E-value=8.9 Score=25.35 Aligned_cols=33 Identities=18% Similarity=0.569 Sum_probs=22.1
Q ss_pred eEEEEEEcCcChhH------HHHHHHHHhcCCCceEEEe
Q 039645 60 QTVEIKIKMDCEGC------ERRVKKSVEGMKGVTQVEV 92 (188)
Q Consensus 60 ~~v~l~VgM~C~~C------~~kV~kaL~~l~GV~~v~v 92 (188)
.++.+.+.+..++| ...++++|..++||.+|+|
T Consensus 34 ~~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 34 GKVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp CEEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred CEEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 45566665555555 4778899999999998875
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=63.26 E-value=29 Score=22.50 Aligned_cols=52 Identities=15% Similarity=0.212 Sum_probs=36.7
Q ss_pred EEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee--CCHHHHHHHHHHhcCCceEEcC
Q 039645 64 IKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY--VDPDKVLERVRHRTGKKAEFWP 126 (188)
Q Consensus 64 l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~--v~~~~I~~~I~~~~G~~a~l~~ 126 (188)
+.+ |+.|+.-.-+++++| ++.. .+.+.|..+ ...+.|...++ +.|++.+...
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~~~s~~~i~~~~~-~~G~~~~~~~ 56 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEA---------GGEIEVLVDNEVAKENVSRFAE-SRGYEVSVEE 56 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCC---------CCEEEEEEcChhHHHHHHHHHH-HcCCEEEEEe
Confidence 456 899999999999999 5532 223444333 44578888888 9999886543
No 21
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=62.28 E-value=27 Score=27.84 Aligned_cols=45 Identities=18% Similarity=0.251 Sum_probs=34.3
Q ss_pred hhHHHHHHHHHhcCCCceEEEeecCCCE-------------------EEEEee---CCHHHHHHHHH
Q 039645 71 EGCERRVKKSVEGMKGVTQVEVDPKQSK-------------------LTVIGY---VDPDKVLERVR 115 (188)
Q Consensus 71 ~~C~~kV~kaL~~l~GV~~v~vd~~~~~-------------------v~V~~~---v~~~~I~~~I~ 115 (188)
.+|=..++..+.+++||.++.+-+.++. |.|.++ ++-++|++..-
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 6788888888999999999999877665 555554 66677776554
No 22
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=60.52 E-value=42 Score=23.67 Aligned_cols=45 Identities=13% Similarity=0.232 Sum_probs=32.7
Q ss_pred hhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee-CCHHHHHHHHH
Q 039645 71 EGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY-VDPDKVLERVR 115 (188)
Q Consensus 71 ~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~-v~~~~I~~~I~ 115 (188)
+.=...|.++|..++|++-...|.+++|+.|+-+ .+..++.+.+.
T Consensus 16 Pe~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 16 SERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred hHHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 3446789999999999987778888888777643 45555555554
No 23
>PRK11018 hypothetical protein; Provisional
Probab=60.35 E-value=44 Score=22.70 Aligned_cols=55 Identities=11% Similarity=0.051 Sum_probs=40.6
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEe--eCCHHHHHHHHHHhcCCceEEc
Q 039645 61 TVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIG--YVDPDKVLERVRHRTGKKAEFW 125 (188)
Q Consensus 61 ~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~--~v~~~~I~~~I~~~~G~~a~l~ 125 (188)
..++.+ |..|+.-.-+.+++|++++.- +.+.|.. ......|...++ +.|+++...
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~~G---------~~L~V~~d~~~a~~di~~~~~-~~G~~v~~~ 65 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLKKG---------EILEVVSDCPQSINNIPLDAR-NHGYTVLDI 65 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCCCC---------CEEEEEeCCccHHHHHHHHHH-HcCCEEEEE
Confidence 357888 999999999999999988532 2333333 245677888888 999987543
No 24
>PF02411 MerT: MerT mercuric transport protein; InterPro: IPR003457 MerT is an mercuric transport integral membrane protein and is responsible for transport of the Hg2+ iron from periplasmic MerP (also part of the transport system) to mercuric reductase (MerA).; GO: 0015097 mercury ion transmembrane transporter activity, 0015694 mercury ion transport, 0016020 membrane
Probab=58.96 E-value=9 Score=28.61 Aligned_cols=19 Identities=11% Similarity=0.251 Sum_probs=16.8
Q ss_pred hHHHHHHHHhHHHHHhhhc
Q 039645 24 YSLFAVIMGFLEYVSELCD 42 (188)
Q Consensus 24 ~~~~~~~m~~~~~~s~~~~ 42 (188)
.++++++|++|||++.+||
T Consensus 98 ~t~~vl~~l~~py~~p~fy 116 (116)
T PF02411_consen 98 VTVLVLLLLAFPYYAPLFY 116 (116)
T ss_pred HHHHHHHHHHHHHHHHHhC
Confidence 4588999999999999986
No 25
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=57.33 E-value=28 Score=27.08 Aligned_cols=40 Identities=13% Similarity=0.368 Sum_probs=31.9
Q ss_pred eEEEEEE-cCcChhHHHHHHHHHhcCCCceEEEeecC-CCEEE
Q 039645 60 QTVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPK-QSKLT 100 (188)
Q Consensus 60 ~~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~-~~~v~ 100 (188)
..+++.| .-.|..|..-|.....++ |+.++.|... ++++.
T Consensus 100 ~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~ 141 (146)
T PF14437_consen 100 RSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVY 141 (146)
T ss_pred CeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEE
Confidence 5678888 888999999998887775 9998888766 66443
No 26
>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=55.70 E-value=48 Score=21.81 Aligned_cols=53 Identities=15% Similarity=0.208 Sum_probs=38.6
Q ss_pred EEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEe--eCCHHHHHHHHHHhcCCceEEcC
Q 039645 64 IKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIG--YVDPDKVLERVRHRTGKKAEFWP 126 (188)
Q Consensus 64 l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~--~v~~~~I~~~I~~~~G~~a~l~~ 126 (188)
+.+ |+.|+.=.-+.+++|.+++. .+.+.|.. ....+.|....+ +.|++.....
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~---------G~~l~V~~d~~~a~~di~~~~~-~~G~~~~~~~ 57 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQD---------GEQLEVKASDPGFARDAQAWCK-STGNTLISLE 57 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHH-HcCCEEEEEE
Confidence 456 89999999999999998852 22334433 255678888888 9999876443
No 27
>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=53.07 E-value=72 Score=21.85 Aligned_cols=42 Identities=17% Similarity=0.223 Sum_probs=30.5
Q ss_pred HHHHHHHHHhcCCCceEEEeecCCCEEEEEee-CCHHHHHHHHH
Q 039645 73 CERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY-VDPDKVLERVR 115 (188)
Q Consensus 73 C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~-v~~~~I~~~I~ 115 (188)
=...+.++|.+++|++-...+.. +|+.|+-+ .+..++.+.+.
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~ 58 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLID 58 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHH
Confidence 35789999999999976666655 77766643 56666766666
No 28
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=44.82 E-value=80 Score=24.73 Aligned_cols=45 Identities=16% Similarity=0.202 Sum_probs=32.7
Q ss_pred hhHHHHHHHHHhcCCCceEEEeecCCCE--------------EEEEee---CCHHHHHHHHH
Q 039645 71 EGCERRVKKSVEGMKGVTQVEVDPKQSK--------------LTVIGY---VDPDKVLERVR 115 (188)
Q Consensus 71 ~~C~~kV~kaL~~l~GV~~v~vd~~~~~--------------v~V~~~---v~~~~I~~~I~ 115 (188)
.+|=.-++..+.+++||.++++-+.++. |.|.++ ++-++|++..-
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 5777778888999999999999776543 344443 56677777654
No 29
>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=44.32 E-value=89 Score=20.44 Aligned_cols=53 Identities=15% Similarity=0.118 Sum_probs=38.0
Q ss_pred EEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEe--eCCHHHHHHHHHHhcCCceEEcC
Q 039645 64 IKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIG--YVDPDKVLERVRHRTGKKAEFWP 126 (188)
Q Consensus 64 l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~--~v~~~~I~~~I~~~~G~~a~l~~ 126 (188)
+.+ |..|+.=.-+.+++|.+++- .+.+.|.. ....+.|.+.++ +.|+++....
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~~---------G~~l~V~~dd~~s~~di~~~~~-~~g~~~~~~~ 57 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMKP---------GDTLLVLATDPSTTRDIPKFCT-FLGHELLAQE 57 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCCC---------CCEEEEEeCCCchHHHHHHHHH-HcCCEEEEEE
Confidence 345 88999999999999998742 12333332 356778999998 9999876543
No 30
>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=43.38 E-value=94 Score=20.41 Aligned_cols=52 Identities=15% Similarity=0.103 Sum_probs=37.5
Q ss_pred EEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEe--eCCHHHHHHHHHHhcCCceEEc
Q 039645 64 IKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIG--YVDPDKVLERVRHRTGKKAEFW 125 (188)
Q Consensus 64 l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~--~v~~~~I~~~I~~~~G~~a~l~ 125 (188)
+.+ |..|+.=.-+.+++|++++.- +.+.|.. ....+.|.+.++ +.|+++...
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~~G---------~~l~V~~d~~~s~~ni~~~~~-~~g~~v~~~ 56 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLKPG---------EILEVISDCPQSINNIPIDAR-NHGYKVLAI 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCC---------CEEEEEecCchHHHHHHHHHH-HcCCEEEEE
Confidence 345 889999999999999988522 2333333 356677888888 999988643
No 31
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=43.04 E-value=2.1e+02 Score=24.77 Aligned_cols=48 Identities=25% Similarity=0.434 Sum_probs=36.7
Q ss_pred EEEEEEcCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEeeCCHHHHHHHHHHhcCCc
Q 039645 61 TVEIKIKMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGYVDPDKVLERVRHRTGKK 121 (188)
Q Consensus 61 ~v~l~VgM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~v~~~~I~~~I~~~~G~~ 121 (188)
++.++.+.+ ..|...+++.+.+.+||++++. .+.++-.+.+++..|+.
T Consensus 62 ~vyL~~~~~-~~~~~~v~~~i~~~~gV~~v~~------------~sre~~l~~L~~~lg~~ 109 (297)
T COG2177 62 TVYLQIDAD-QDDAALVREKIEGIPGVKSVRF------------ISREEALKELQPWLGFG 109 (297)
T ss_pred EEEEecCCC-hHHHHHHHHHHhcCCCcceEEE------------eCHHHHHHHHHHHcCch
Confidence 444555555 9999999999999999998876 36677777777678865
No 32
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=41.39 E-value=94 Score=19.84 Aligned_cols=53 Identities=17% Similarity=0.186 Sum_probs=37.9
Q ss_pred EEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee--CCHHHHHHHHHHhcCCceEEcC
Q 039645 64 IKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY--VDPDKVLERVRHRTGKKAEFWP 126 (188)
Q Consensus 64 l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~--v~~~~I~~~I~~~~G~~a~l~~ 126 (188)
+.+ |+.|+.=.-+++++|.+++. .+.+.|..+ .....|.+.++ +.|++.....
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~~---------g~~l~v~~d~~~~~~~i~~~~~-~~g~~~~~~~ 57 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLKS---------GEVLEVLLDDPGAVEDIPAWAK-ETGHEVLEVE 57 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCCC---------CCEEEEEecCCcHHHHHHHHHH-HcCCEEEEEE
Confidence 456 88999999999999988643 233344433 45788888898 9999865443
No 33
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=39.90 E-value=1e+02 Score=25.46 Aligned_cols=52 Identities=13% Similarity=0.168 Sum_probs=36.8
Q ss_pred ceEEEEEEcCcChhHHHHHHHHHhcCCCceEEEeecCCCE-------------------EEEEee---CCHHHHHHHHH
Q 039645 59 LQTVEIKIKMDCEGCERRVKKSVEGMKGVTQVEVDPKQSK-------------------LTVIGY---VDPDKVLERVR 115 (188)
Q Consensus 59 ~~~v~l~VgM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~-------------------v~V~~~---v~~~~I~~~I~ 115 (188)
++++.|. .||-.-++..+.+++||.++.+-+..+. |.|+++ ++-++|++..-
T Consensus 45 ~~~a~fa-----gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff 118 (213)
T PRK00058 45 MEQAIFG-----MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFW 118 (213)
T ss_pred ccEEEEE-----ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHH
Confidence 4455544 6777788888999999999999877542 445554 66777776654
No 34
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=39.37 E-value=76 Score=25.65 Aligned_cols=45 Identities=18% Similarity=0.197 Sum_probs=32.7
Q ss_pred hhHHHHHHHHHhcCCCceEEEeecCCCE-------------------EEEEee---CCHHHHHHHHH
Q 039645 71 EGCERRVKKSVEGMKGVTQVEVDPKQSK-------------------LTVIGY---VDPDKVLERVR 115 (188)
Q Consensus 71 ~~C~~kV~kaL~~l~GV~~v~vd~~~~~-------------------v~V~~~---v~~~~I~~~I~ 115 (188)
.+|=.-++..+.+++||.++++-+.++. |.|.++ ++-++|++..-
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 5677777788889999999999877664 445543 56677776554
No 35
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=36.82 E-value=1.4e+02 Score=20.39 Aligned_cols=55 Identities=15% Similarity=0.131 Sum_probs=39.5
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEe--eCCHHHHHHHHHHhcCCceEEc
Q 039645 61 TVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIG--YVDPDKVLERVRHRTGKKAEFW 125 (188)
Q Consensus 61 ~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~--~v~~~~I~~~I~~~~G~~a~l~ 125 (188)
..++.+ |..|+.=.-+++++|++++. .+.+.|.. ....+.|....+ ..|++....
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~~---------G~~l~V~~dd~~~~~di~~~~~-~~G~~~~~~ 66 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQP---------GETLLIIADDPATTRDIPSFCR-FMDHELLAQ 66 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCCC---------CCEEEEEeCCccHHHHHHHHHH-HcCCEEEEE
Confidence 356888 99999999999999998842 22333332 245677888888 999887543
No 36
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=36.47 E-value=58 Score=24.09 Aligned_cols=32 Identities=34% Similarity=0.739 Sum_probs=23.4
Q ss_pred EEEEEcCcChhH------HHHHHHHHhcCCCceEEEee
Q 039645 62 VEIKIKMDCEGC------ERRVKKSVEGMKGVTQVEVD 93 (188)
Q Consensus 62 v~l~VgM~C~~C------~~kV~kaL~~l~GV~~v~vd 93 (188)
+.+++.++-.+| ...++.++..++||++++++
T Consensus 51 v~v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~ 88 (111)
T COG2151 51 VKVKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVE 88 (111)
T ss_pred EEEEEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEE
Confidence 344444555666 67889999999999888775
No 37
>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=36.39 E-value=1.1e+02 Score=23.67 Aligned_cols=34 Identities=18% Similarity=0.171 Sum_probs=28.5
Q ss_pred ChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEe
Q 039645 70 CEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIG 103 (188)
Q Consensus 70 C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~ 103 (188)
-..=+.+|.+.+.+++||.++.+=.....+.|..
T Consensus 73 ~~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav 106 (177)
T PF09580_consen 73 RQQLADRIANRVKKVPGVEDATVVVTDDNAYVAV 106 (177)
T ss_pred HHHHHHHHHHHHhcCCCceEEEEEEECCEEEEEE
Confidence 3556789999999999999999988888887654
No 38
>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=36.09 E-value=48 Score=26.44 Aligned_cols=34 Identities=29% Similarity=0.564 Sum_probs=23.1
Q ss_pred EEEEEEcCcChhHH------HHHHHHHhcCCCceEEEeec
Q 039645 61 TVEIKIKMDCEGCE------RRVKKSVEGMKGVTQVEVDP 94 (188)
Q Consensus 61 ~v~l~VgM~C~~C~------~kV~kaL~~l~GV~~v~vd~ 94 (188)
++.+.+.++.++|. ..|+.+|.+++||.++++++
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 34455544555553 45889999999999887753
No 39
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=34.59 E-value=1.4e+02 Score=19.81 Aligned_cols=42 Identities=24% Similarity=0.359 Sum_probs=30.1
Q ss_pred HhcCCCceEEEeecCCCEE--EEEeeCCHHHHHHHHHHhcCCceEEc
Q 039645 81 VEGMKGVTQVEVDPKQSKL--TVIGYVDPDKVLERVRHRTGKKAEFW 125 (188)
Q Consensus 81 L~~l~GV~~v~vd~~~~~v--~V~~~v~~~~I~~~I~~~~G~~a~l~ 125 (188)
|..++||..+..+- .+.+ .+.......+|++.+. +.|. +.-.
T Consensus 26 l~~~~~v~~v~~~~-~~~~~i~l~~~~~~~~ll~~l~-~~g~-I~~f 69 (84)
T PF13732_consen 26 LEELPGVESVEQDG-DGKLRIKLEDEETANELLQELI-EKGI-IRSF 69 (84)
T ss_pred HhhCCCeEEEEEeC-CcEEEEEECCcccHHHHHHHHH-hCCC-eeEE
Confidence 77889999988643 4434 4445567889999998 8887 5543
No 40
>PF13106 DUF3961: Domain of unknown function (DUF3961)
Probab=34.45 E-value=45 Score=20.19 Aligned_cols=32 Identities=25% Similarity=0.523 Sum_probs=24.5
Q ss_pred hhhhHhhh-cccceeehhhhcchhHHHHHHHHhHHHH
Q 039645 2 INDVLALA-TKSSTIAFLRITSGYSLFAVIMGFLEYV 37 (188)
Q Consensus 2 ~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~m~~~~~~ 37 (188)
+||-..+- ++++||-|- |....++.|..+.|+
T Consensus 3 vn~~FGie~~~sdqIWFY----G~~~ls~~m~~~tyl 35 (40)
T PF13106_consen 3 VNEWFGIEECKSDQIWFY----GFFGLSIFMILFTYL 35 (40)
T ss_pred hhhhcCccccccccEEEe----eHHHHHHHHHHHHHH
Confidence 57777777 999999986 455667777777776
No 41
>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=32.60 E-value=1.8e+02 Score=22.55 Aligned_cols=60 Identities=15% Similarity=0.197 Sum_probs=41.0
Q ss_pred ChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee-----C-CHHHHHHHHHHhcCCceEEcCCCC
Q 039645 70 CEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY-----V-DPDKVLERVRHRTGKKAEFWPYVP 129 (188)
Q Consensus 70 C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~-----v-~~~~I~~~I~~~~G~~a~l~~~~p 129 (188)
=+.-...|++.+-.-.||.++..|..++.|.|... + .....+..|.+++|....+....|
T Consensus 51 ~e~A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 51 PEEAIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred HHHHHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 34555667776766679999999999999998743 1 223343444449998888765433
No 42
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=32.58 E-value=92 Score=22.75 Aligned_cols=57 Identities=16% Similarity=0.411 Sum_probs=30.0
Q ss_pred EEE-cC-cChhHH-HHHHHHHhc--CCCceEEEeecCCCEEEEEe----e-CCHHHHHHHHHHhcCCceEE
Q 039645 64 IKI-KM-DCEGCE-RRVKKSVEG--MKGVTQVEVDPKQSKLTVIG----Y-VDPDKVLERVRHRTGKKAEF 124 (188)
Q Consensus 64 l~V-gM-~C~~C~-~kV~kaL~~--l~GV~~v~vd~~~~~v~V~~----~-v~~~~I~~~I~~~~G~~a~l 124 (188)
.++ +| +|.+|- .++...+.+ ..|++.+-+. +- .+.+ . -..+++.+.|+++.|.++..
T Consensus 38 ~elvgf~~CgGCpg~~~~~~~~~l~~~~~d~IHls--sC--~~~~~~~~~CP~~~~~~~~I~~~~gi~VV~ 104 (107)
T PF08821_consen 38 VELVGFFTCGGCPGRKLVRRIKKLKKNGADVIHLS--SC--MVKGNPHGPCPHIDEIKKIIEEKFGIEVVE 104 (107)
T ss_pred eEEEEEeeCCCCChhHHHHHHHHHHHCCCCEEEEc--CC--EecCCCCCCCCCHHHHHHHHHHHhCCCEee
Confidence 555 66 899883 223222222 2455533332 11 1111 1 35788999999555876543
No 43
>PHA01634 hypothetical protein
Probab=31.96 E-value=16 Score=28.28 Aligned_cols=16 Identities=50% Similarity=1.159 Sum_probs=12.8
Q ss_pred EEE-cCcChhHHHHHHH
Q 039645 64 IKI-KMDCEGCERRVKK 79 (188)
Q Consensus 64 l~V-gM~C~~C~~kV~k 79 (188)
+.| -|+|++|++++.-
T Consensus 93 ~Di~~iDCeGCE~~l~v 109 (156)
T PHA01634 93 VDIFVMDCEGCEEKLNV 109 (156)
T ss_pred cceEEEEccchHHhcCH
Confidence 456 7999999998853
No 44
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=30.84 E-value=40 Score=21.37 Aligned_cols=32 Identities=16% Similarity=0.267 Sum_probs=14.9
Q ss_pred HHHHHHHhcC---CCceEEEeecCCCEEEEEeeCCH
Q 039645 75 RRVKKSVEGM---KGVTQVEVDPKQSKLTVIGYVDP 107 (188)
Q Consensus 75 ~kV~kaL~~l---~GV~~v~vd~~~~~v~V~~~v~~ 107 (188)
.+|+.+|... ++- .+.+...++.+.+.|.++.
T Consensus 2 ~~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v~s 36 (64)
T PF04972_consen 2 TKVRAALRADPWLPDS-NISVSVENGVVTLSGEVPS 36 (64)
T ss_dssp -----------CTT-T-TEEEEEECTEEEEEEEESS
T ss_pred cccccccccccccCCC-eEEEEEECCEEEEEeeCcH
Confidence 3566666653 333 5677777888888887533
No 45
>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=29.77 E-value=1.5e+02 Score=18.87 Aligned_cols=33 Identities=21% Similarity=0.304 Sum_probs=23.9
Q ss_pred eEEEEEEcCcChh-HHHHHHHHHhcCCCceEEEe
Q 039645 60 QTVEIKIKMDCEG-CERRVKKSVEGMKGVTQVEV 92 (188)
Q Consensus 60 ~~v~l~VgM~C~~-C~~kV~kaL~~l~GV~~v~v 92 (188)
..+.|.+...-.. --..+-+.|++++||.+|.+
T Consensus 41 ~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 41 ANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 4455655334443 77888999999999998875
No 46
>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=26.49 E-value=1e+02 Score=21.81 Aligned_cols=48 Identities=13% Similarity=0.039 Sum_probs=26.0
Q ss_pred HHHHHHHHhcCCCceEEEeecCCCEEEEEee---CCHHHHHHHHHHhcCCce
Q 039645 74 ERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY---VDPDKVLERVRHRTGKKA 122 (188)
Q Consensus 74 ~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~---v~~~~I~~~I~~~~G~~a 122 (188)
+..++-.|.+.++|-.+-+|.-.....|.++ ++.+++++.++ +.+..+
T Consensus 13 A~~~QYeLsk~~~vyRvFiNgYar~g~VifDe~kl~~e~lL~~le-~~kpEV 63 (88)
T PF11491_consen 13 AMVKQYELSKNEAVYRVFINGYARNGFVIFDESKLSKEELLEMLE-EFKPEV 63 (88)
T ss_dssp THHHHHTTTTTTTB------TTSS--EEE--B-S-SHHHH---HH-HTTT-S
T ss_pred HHHHHHHhhcccceeeeeecccccceEEEECcccCCHHHHHHHHH-hcChhh
Confidence 4556677899999999999987777777654 78999999999 777543
No 47
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=26.16 E-value=2.2e+02 Score=19.41 Aligned_cols=49 Identities=18% Similarity=0.323 Sum_probs=35.2
Q ss_pred EEEEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee--CCHHHHHHHHHHhcC
Q 039645 61 TVEIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY--VDPDKVLERVRHRTG 119 (188)
Q Consensus 61 ~v~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~--v~~~~I~~~I~~~~G 119 (188)
..++.+ |+.|+.=.-.++++|.+++- .+.+.|..+ ...++|....+ +.|
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~---------Ge~LeV~~ddp~~~~dIp~~~~-~~~ 56 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLKP---------GEILEVIADDPAAKEDIPAWAK-KEG 56 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCCC---------CCEEEEEecCcchHHHHHHHHH-HcC
Confidence 457889 99999999999999998843 233444433 45567777777 455
No 48
>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=25.78 E-value=77 Score=22.16 Aligned_cols=36 Identities=19% Similarity=0.385 Sum_probs=23.1
Q ss_pred eEEEEEE-cCcChhH---HHHHHHHHhcCCCceEEEeecC
Q 039645 60 QTVEIKI-KMDCEGC---ERRVKKSVEGMKGVTQVEVDPK 95 (188)
Q Consensus 60 ~~v~l~V-gM~C~~C---~~kV~kaL~~l~GV~~v~vd~~ 95 (188)
-.+.+.+ .-.|... ...++.+|.+++|+.++++++.
T Consensus 39 v~i~l~l~~p~~~~~~~l~~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 39 VDIQMTLTAPNCPVAGSMPGEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred EEEEEEECCCCCChHHHHHHHHHHHHHhCCCCceEEEEEE
Confidence 3444555 3444433 3457888999999998888653
No 49
>PRK11023 outer membrane lipoprotein; Provisional
Probab=24.68 E-value=2.5e+02 Score=22.37 Aligned_cols=38 Identities=16% Similarity=0.316 Sum_probs=22.7
Q ss_pred HHHHHHHHHhcCCCce--EEEeecCCCEEEEEeeCCHHHH
Q 039645 73 CERRVKKSVEGMKGVT--QVEVDPKQSKLTVIGYVDPDKV 110 (188)
Q Consensus 73 C~~kV~kaL~~l~GV~--~v~vd~~~~~v~V~~~v~~~~I 110 (188)
=..+|+.+|...+++. ++++...++.|++.|.++.++.
T Consensus 128 It~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~ 167 (191)
T PRK11023 128 ITTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREA 167 (191)
T ss_pred HHHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHH
Confidence 4556677776666554 3444455677777776655444
No 50
>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=24.67 E-value=2.5e+02 Score=21.87 Aligned_cols=27 Identities=22% Similarity=0.337 Sum_probs=22.7
Q ss_pred hhHHHHHHHHHhcCCCceEEEeecCCC
Q 039645 71 EGCERRVKKSVEGMKGVTQVEVDPKQS 97 (188)
Q Consensus 71 ~~C~~kV~kaL~~l~GV~~v~vd~~~~ 97 (188)
.||=..++..+.+++||.++.+-+..+
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 577788888999999999999977655
No 51
>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=23.84 E-value=2e+02 Score=23.21 Aligned_cols=49 Identities=20% Similarity=0.216 Sum_probs=36.2
Q ss_pred cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEE--eeCCHHHHHHHHHHhcCCceEEc
Q 039645 67 KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVI--GYVDPDKVLERVRHRTGKKAEFW 125 (188)
Q Consensus 67 gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~--~~v~~~~I~~~I~~~~G~~a~l~ 125 (188)
|+.|+.-.-+.+++|.+++. .+.++|. .....+.|.+.++ +.|+++...
T Consensus 5 Gl~CP~Pvi~tKkal~~l~~---------g~~L~VlvD~~~a~~nV~~~~~-~~G~~v~~~ 55 (194)
T TIGR03527 5 GLACPQPVILTKKALDELGE---------EGVLTVIVDNEAAKENVSKFAT-SLGYEVEVE 55 (194)
T ss_pred CCCCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHH-HcCCEEEEE
Confidence 88999999999999998852 1223333 2356678888888 999988754
No 52
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=23.56 E-value=2.8e+02 Score=19.86 Aligned_cols=55 Identities=15% Similarity=0.158 Sum_probs=33.9
Q ss_pred EEEE-cCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEee--CCHHHHHHHHHHhc
Q 039645 63 EIKI-KMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIGY--VDPDKVLERVRHRT 118 (188)
Q Consensus 63 ~l~V-gM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~--v~~~~I~~~I~~~~ 118 (188)
.+++ |+.-+-+...|+..+.....|.-|.+........|.+. -...++++++. ..
T Consensus 3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~-~~ 60 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLK-EA 60 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHH-HT
T ss_pred EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHH-hc
Confidence 3556 66666668999999999999999888888888888875 34677888877 44
No 53
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=23.32 E-value=3e+02 Score=20.74 Aligned_cols=49 Identities=16% Similarity=0.292 Sum_probs=31.8
Q ss_pred HHHHHHHhcCCCceEEEeecCCCEEEEEeeCCHHHHHH----HHHHhcCCceEE
Q 039645 75 RRVKKSVEGMKGVTQVEVDPKQSKLTVIGYVDPDKVLE----RVRHRTGKKAEF 124 (188)
Q Consensus 75 ~kV~kaL~~l~GV~~v~vd~~~~~v~V~~~v~~~~I~~----~I~~~~G~~a~l 124 (188)
..++..+.++ |..+|+.=+.++++..+...+++++.. .|++..|+.+.+
T Consensus 22 aeLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~fG~~v~v 74 (137)
T PF08002_consen 22 AELREALEDL-GFTNVRTYIQSGNVVFESDRDPAELAAKIEKALEERFGFDVPV 74 (137)
T ss_dssp HHHHHHHHHC-T-EEEEEETTTTEEEEEESS-HHHHHHHHHHHHHHH-TT---E
T ss_pred HHHHHHHHHc-CCCCceEEEeeCCEEEecCCChHHHHHHHHHHHHHhcCCCeEE
Confidence 4566677766 899999999999999996667666554 444467886554
No 54
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=23.10 E-value=2.5e+02 Score=24.22 Aligned_cols=28 Identities=25% Similarity=0.308 Sum_probs=22.9
Q ss_pred hhHHHHHHHHHhcCCCceEEEeecCCCE
Q 039645 71 EGCERRVKKSVEGMKGVTQVEVDPKQSK 98 (188)
Q Consensus 71 ~~C~~kV~kaL~~l~GV~~v~vd~~~~~ 98 (188)
.+|=..++..+.+++||.++.+-+.++.
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG~ 161 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGGD 161 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCCC
Confidence 6777788888999999999999776553
No 55
>PRK09577 multidrug efflux protein; Reviewed
Probab=23.00 E-value=2.3e+02 Score=28.78 Aligned_cols=45 Identities=13% Similarity=0.195 Sum_probs=34.8
Q ss_pred HHHHHHHHhcCCCceEEEeecCCCEEEEEe--------eCCHHHHHHHHHHhcC
Q 039645 74 ERRVKKSVEGMKGVTQVEVDPKQSKLTVIG--------YVDPDKVLERVRHRTG 119 (188)
Q Consensus 74 ~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~--------~v~~~~I~~~I~~~~G 119 (188)
+++++..|++++||.+|+++-....+.|.- .++..++.++|+ ..+
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~-~~n 210 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVR-AHN 210 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHH-HhC
Confidence 467999999999999999987555566642 277888999998 544
No 56
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=22.99 E-value=2.1e+02 Score=29.07 Aligned_cols=42 Identities=10% Similarity=0.236 Sum_probs=33.2
Q ss_pred HHHHHHHHhcCCCceEEEeecCCCEEEEEe--------eCCHHHHHHHHH
Q 039645 74 ERRVKKSVEGMKGVTQVEVDPKQSKLTVIG--------YVDPDKVLERVR 115 (188)
Q Consensus 74 ~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~--------~v~~~~I~~~I~ 115 (188)
++.++..|++++||.+|++.-....+.|.- .++..++.++|+
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~ 208 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIE 208 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 467899999999999999986555566653 277888888887
No 57
>PRK13751 putative mercuric transport protein; Provisional
Probab=22.34 E-value=80 Score=23.60 Aligned_cols=19 Identities=11% Similarity=0.085 Sum_probs=15.8
Q ss_pred hHHHHHHHHhHHHHHhhhc
Q 039645 24 YSLFAVIMGFLEYVSELCD 42 (188)
Q Consensus 24 ~~~~~~~m~~~~~~s~~~~ 42 (188)
.+++++++++|||+..+|+
T Consensus 98 ~~vlvl~~L~fPy~~p~fy 116 (116)
T PRK13751 98 VAALVLVALGFPYVMPFFY 116 (116)
T ss_pred HHHHHHHHHHhHHHHHHhC
Confidence 3488899999999998875
No 58
>PRK11023 outer membrane lipoprotein; Provisional
Probab=21.55 E-value=2.1e+02 Score=22.79 Aligned_cols=47 Identities=21% Similarity=0.290 Sum_probs=35.1
Q ss_pred cChhHHHHHHHHHhcCCCce---EEEeecCCCEEEEEeeCCHHHHHHHHH
Q 039645 69 DCEGCERRVKKSVEGMKGVT---QVEVDPKQSKLTVIGYVDPDKVLERVR 115 (188)
Q Consensus 69 ~C~~C~~kV~kaL~~l~GV~---~v~vd~~~~~v~V~~~v~~~~I~~~I~ 115 (188)
+...=+.+|+.+|..-+++. ++.+...++.|++.|.++.++......
T Consensus 46 dD~~i~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~V~~~~~k~~A~ 95 (191)
T PRK11023 46 DDGTLELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQSPNAELSERAK 95 (191)
T ss_pred hhHHHHHHHHHHHhhCcccCcCceEEEEEECCEEEEEEEeCCHHHHHHHH
Confidence 45666889999998877774 578888999999999876655444444
No 59
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=21.20 E-value=2.5e+02 Score=18.34 Aligned_cols=34 Identities=12% Similarity=0.237 Sum_probs=24.7
Q ss_pred CceEEEEEEcCcChhHHHHHHHHHhcCCCceEEE
Q 039645 58 QLQTVEIKIKMDCEGCERRVKKSVEGMKGVTQVE 91 (188)
Q Consensus 58 ~~~~v~l~VgM~C~~C~~kV~kaL~~l~GV~~v~ 91 (188)
....+.|.+...-..--..+-+.|++++||.+|+
T Consensus 46 ~~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 46 GTARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp TEEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred CEEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 3455666665555666678888899999998874
No 60
>PF10215 Ost4: Oligosaccaryltransferase ; InterPro: IPR018943 Ost4 is a very short, approximately 30 residues, enzyme found from fungi to vertebrates. It is a member of the ER oligosaccaryltansferase complex, 2.4.1.119 from EC, that catalyses the asparagine-linked glycosylation of proteins. It appears to be an integral membrane protein that mediates the en bloc transfer of a pre-assembled high-mannose oligosaccharide onto asparagine residues of nascent polypeptides as they enter the lumen of the rough endoplasmic reticulum. ; PDB: 1RKL_A 2LAT_A.
Probab=21.18 E-value=47 Score=19.50 Aligned_cols=18 Identities=17% Similarity=0.172 Sum_probs=10.7
Q ss_pred eeehhhhcchhHHHHHHH
Q 039645 14 TIAFLRITSGYSLFAVIM 31 (188)
Q Consensus 14 ~~~~l~~~~~~~~~~~~m 31 (188)
||..|-.+.|.+.|.++.
T Consensus 6 qL~~lan~lG~~~~~LIV 23 (35)
T PF10215_consen 6 QLYTLANFLGVAAMVLIV 23 (35)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 566666666666555544
No 61
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic 40-residue C-terminal domain that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=20.82 E-value=3.6e+02 Score=21.07 Aligned_cols=32 Identities=16% Similarity=0.068 Sum_probs=27.3
Q ss_pred hHHHHHHHHHhcCCCceEEEeecCCCEEEEEe
Q 039645 72 GCERRVKKSVEGMKGVTQVEVDPKQSKLTVIG 103 (188)
Q Consensus 72 ~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~ 103 (188)
.=+.+|.+.+.+++||.++.+=.....+.|-.
T Consensus 54 ~~A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vgv 85 (158)
T TIGR02898 54 DVADEIASEAAKVKGVKDATVVITGNYAYVGV 85 (158)
T ss_pred HHHHHHHHHHhcCCCCceEEEEEECCEEEEEE
Confidence 66889999999999999999888888877654
No 62
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=20.56 E-value=2.3e+02 Score=19.70 Aligned_cols=50 Identities=18% Similarity=0.242 Sum_probs=31.6
Q ss_pred EEEEEcCcChhHHHHHHHHHhcCCCceEEEeecCCCEEEEEe--eCCHHHHHHHHH
Q 039645 62 VEIKIKMDCEGCERRVKKSVEGMKGVTQVEVDPKQSKLTVIG--YVDPDKVLERVR 115 (188)
Q Consensus 62 v~l~VgM~C~~C~~kV~kaL~~l~GV~~v~vd~~~~~v~V~~--~v~~~~I~~~I~ 115 (188)
++|.-.-.|.. .-+-+.|-+++||.+|-+. .+=++|+- ++++++|...|.
T Consensus 26 ~~f~~~~~a~~--spLA~~Lf~i~gV~~Vf~~--~dfItVtK~~~~~W~~l~~~I~ 77 (87)
T PF08712_consen 26 FEFKSAEEASD--SPLAQALFAIPGVKSVFIG--DDFITVTKNPDADWEDLKPEIR 77 (87)
T ss_dssp -EEESSS-TTS---HHHHHHHTSTTEEEEEEE--TTEEEEEE-TTS-HHHHHHHHH
T ss_pred EEeCChHHccc--CHHHHHhcCCCCEeEEEEE--CCEEEEeeCCCCCHHHHHHHHH
Confidence 44443333333 4555667799999998875 55677763 489999988886
Done!