Query 034955
Match_columns 78
No_of_seqs 122 out of 1489
Neff 11.1
Searched_HMMs 46136
Date Fri Mar 29 08:00:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034955.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034955hhsearch_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 5.4E-12 1.2E-16 56.2 7.6 53 1-53 7-62 (62)
2 COG2608 CopZ Copper chaperone 99.2 2.5E-10 5.4E-15 52.2 7.6 56 1-56 11-69 (71)
3 KOG1603 Copper chaperone [Inor 98.7 3.2E-07 7E-12 42.1 7.0 51 1-51 13-63 (73)
4 KOG4656 Copper chaperone for s 98.7 2.6E-07 5.5E-12 49.7 6.6 57 1-57 15-71 (247)
5 PLN02957 copper, zinc superoxi 98.3 1.8E-05 3.9E-10 43.9 8.6 59 1-59 14-72 (238)
6 PRK10671 copA copper exporting 98.2 1.5E-05 3.3E-10 50.8 7.7 56 1-58 12-67 (834)
7 COG2217 ZntA Cation transport 98.1 1.6E-05 3.5E-10 50.0 6.5 55 1-56 11-69 (713)
8 TIGR00003 copper ion binding p 97.4 0.0021 4.5E-08 27.2 7.1 53 1-53 11-66 (68)
9 KOG0207 Cation transport ATPas 97.3 0.0017 3.7E-08 42.1 6.5 62 1-62 3-66 (951)
10 KOG0207 Cation transport ATPas 97.2 0.0017 3.6E-08 42.1 5.7 57 1-57 155-214 (951)
11 PRK10671 copA copper exporting 97.0 0.0054 1.2E-07 39.7 6.7 56 1-56 108-163 (834)
12 PRK11033 zntA zinc/cadmium/mer 96.9 0.008 1.7E-07 38.6 6.7 55 1-55 62-117 (741)
13 TIGR02052 MerP mercuric transp 89.2 1.3 2.7E-05 20.1 7.7 55 1-55 32-89 (92)
14 PRK13748 putative mercuric red 87.6 5.2 0.00011 25.2 7.7 57 1-57 9-67 (561)
15 PRK05528 methionine sulfoxide 70.0 6.6 0.00014 20.9 2.4 28 4-31 8-35 (156)
16 PRK14054 methionine sulfoxide 66.0 8.5 0.00018 20.8 2.4 28 4-31 10-37 (172)
17 PF01625 PMSR: Peptide methion 64.2 15 0.00031 19.6 3.0 27 4-30 7-33 (155)
18 TIGR00401 msrA methionine-S-su 64.2 8.6 0.00019 20.3 2.1 28 4-31 7-34 (149)
19 PRK00058 methionine sulfoxide 58.1 13 0.00027 21.0 2.2 27 4-30 52-78 (213)
20 PF15643 Tox-PL-2: Papain fold 56.9 17 0.00036 17.9 2.3 25 1-26 19-43 (100)
21 PRK13014 methionine sulfoxide 51.5 12 0.00026 20.5 1.5 28 4-31 15-42 (186)
22 cd00371 HMA Heavy-metal-associ 50.6 15 0.00032 13.2 6.9 34 2-35 8-41 (63)
23 PF01883 DUF59: Domain of unkn 47.1 28 0.00061 15.4 2.7 19 7-25 54-72 (72)
24 COG1888 Uncharacterized protei 45.7 38 0.00082 16.5 5.8 47 10-56 24-78 (97)
25 COG0225 MsrA Peptide methionin 44.6 27 0.00058 19.1 2.1 28 4-31 13-40 (174)
26 PF14437 MafB19-deam: MafB19-l 43.7 52 0.0011 17.5 3.5 26 2-28 110-135 (146)
27 PF01514 YscJ_FliF: Secretory 42.4 56 0.0012 18.2 3.2 22 7-28 117-138 (206)
28 PF01206 TusA: Sulfurtransfera 39.6 38 0.00083 14.8 4.5 48 1-57 8-57 (70)
29 PHA03005 sulfhydryl oxidase; P 39.2 26 0.00056 17.1 1.4 20 2-21 42-61 (96)
30 TIGR02544 III_secr_YscJ type I 39.1 54 0.0012 18.1 2.8 22 7-28 109-130 (193)
31 PF04805 Pox_E10: E10-like pro 37.4 33 0.00071 15.7 1.5 22 1-22 16-37 (70)
32 PF02680 DUF211: Uncharacteriz 36.9 57 0.0012 16.0 5.2 47 10-56 22-76 (95)
33 COG4669 EscJ Type III secretor 36.6 65 0.0014 18.7 2.8 22 7-28 111-132 (246)
34 PRK05550 bifunctional methioni 35.7 42 0.00092 19.8 2.1 28 4-31 134-161 (283)
35 PF14424 Toxin-deaminase: The 35.6 68 0.0015 16.6 2.7 21 2-22 107-127 (133)
36 PRK15348 type III secretion sy 34.2 73 0.0016 18.5 2.9 22 7-28 109-130 (249)
37 PRK10509 bacterioferritin-asso 33.8 35 0.00076 15.2 1.3 15 2-16 38-52 (64)
38 TIGR02945 SUF_assoc FeS assemb 33.6 61 0.0013 15.4 2.7 21 8-28 58-78 (99)
39 COG2331 Uncharacterized protei 32.7 28 0.00061 16.3 0.9 16 2-17 35-50 (82)
40 KOG3411 40S ribosomal protein 30.5 64 0.0014 16.9 2.0 41 5-48 98-139 (143)
41 PF08394 Arc_trans_TRASH: Arch 29.6 37 0.0008 13.5 0.9 12 2-13 25-36 (37)
42 PRK15324 type III secretion sy 29.1 88 0.0019 18.2 2.6 23 7-29 110-132 (252)
43 PRK14018 trifunctional thiored 29.0 63 0.0014 20.9 2.2 28 4-31 205-232 (521)
44 COG2151 PaaD Predicted metal-s 28.8 88 0.0019 15.8 2.6 21 7-27 69-89 (111)
45 TIGR00489 aEF-1_beta translati 26.6 88 0.0019 15.0 2.5 20 7-26 64-83 (88)
46 smart00834 CxxC_CXXC_SSSS Puta 26.2 4.5 9.7E-05 15.8 -2.1 9 2-10 28-36 (41)
47 PF12156 ATPase-cat_bd: Putati 26.1 77 0.0017 15.0 1.8 14 1-14 27-40 (88)
48 PF14149 YhfH: YhfH-like prote 25.9 60 0.0013 12.9 1.3 13 2-14 15-27 (37)
49 COG1856 Uncharacterized homolo 25.9 52 0.0011 19.1 1.4 13 1-13 23-35 (275)
50 PF13732 DUF4162: Domain of un 25.6 80 0.0017 14.2 5.3 43 14-58 26-70 (84)
51 PF07582 AP_endonuc_2_N: AP en 25.2 75 0.0016 13.8 1.9 14 40-53 2-15 (55)
52 COG1251 NirB NAD(P)H-nitrite r 23.9 1.3E+02 0.0028 20.8 3.0 20 2-21 449-468 (793)
53 PRK10553 assembly protein for 23.6 1E+02 0.0022 14.7 5.9 40 7-46 19-59 (87)
54 KOG3476 Microtubule-associated 23.1 56 0.0012 15.8 1.0 15 1-15 1-15 (100)
55 TIGR02830 spore_III_AG stage I 22.7 1.1E+02 0.0025 16.9 2.3 26 7-32 63-90 (186)
56 cd04888 ACT_PheB-BS C-terminal 22.6 87 0.0019 13.6 2.7 19 7-25 56-74 (76)
57 PHA01634 hypothetical protein 22.6 28 0.0006 18.3 -0.1 11 1-11 98-108 (156)
58 COG4545 Glutaredoxin-related p 22.4 55 0.0012 15.4 0.9 13 1-13 10-22 (85)
59 PF09580 Spore_YhcN_YlaJ: Spor 22.4 1.4E+02 0.003 15.9 5.8 29 7-35 77-105 (177)
60 TIGR03406 FeS_long_SufT probab 21.8 1.5E+02 0.0033 16.2 2.8 21 8-28 134-154 (174)
61 PF13193 AMP-binding_C: AMP-bi 21.2 96 0.0021 13.6 2.5 17 10-26 2-18 (73)
62 PF12292 DUF3624: Protein of u 20.5 71 0.0015 15.0 1.0 9 1-9 1-9 (77)
63 PF03698 UPF0180: Uncharacteri 20.4 1.2E+02 0.0026 14.3 2.5 21 38-58 8-28 (80)
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=99.41 E-value=5.4e-12 Score=56.19 Aligned_cols=53 Identities=32% Similarity=0.690 Sum_probs=48.3
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEee---CCCHHHHHHHHHhCCCc
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKG---NVQPDAVLQTVSKTGKK 53 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~~---~~~~~~~~~~i~~~g~~ 53 (78)
|+|.+|..++++.|..++||..+.+++..+++.+.. ...++.+...|.+.||+
T Consensus 7 m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 7 MTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGYE 62 (62)
T ss_dssp TTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTSE
T ss_pred cccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCcC
Confidence 789999999999999999999999999999999882 24679999999999984
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.23 E-value=2.5e-10 Score=52.17 Aligned_cols=56 Identities=32% Similarity=0.641 Sum_probs=49.9
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEe--e-CCCHHHHHHHHHhCCCceee
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--G-NVQPDAVLQTVSKTGKKTAF 56 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~--~-~~~~~~~~~~i~~~g~~~~~ 56 (78)
|+|.+|+..+++.|..++|+..+.+++..+...+. + ..+.+.+...+...||....
T Consensus 11 MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~ 69 (71)
T COG2608 11 MTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEE 69 (71)
T ss_pred cCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeee
Confidence 79999999999999999999999999999666666 3 57899999999999998654
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.70 E-value=3.2e-07 Score=42.08 Aligned_cols=51 Identities=63% Similarity=1.012 Sum_probs=47.9
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEeeCCCHHHHHHHHHhCC
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPDAVLQTVSKTG 51 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~~~~~~~~~~~~i~~~g 51 (78)
|+|.+|...+.+.+..+.||....++...+++++.+..++..+...+.+.+
T Consensus 13 ~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~ 63 (73)
T KOG1603|consen 13 MHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTG 63 (73)
T ss_pred cccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcC
Confidence 789999999999999999999999999999999997789999999998876
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.66 E-value=2.6e-07 Score=49.72 Aligned_cols=57 Identities=35% Similarity=0.698 Sum_probs=53.2
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEeeCCCHHHHHHHHHhCCCceeec
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPDAVLQTVSKTGKKTAFW 57 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~~~~~~~~~~~~i~~~g~~~~~~ 57 (78)
|+|.+|++.++..|...+||..+++++..+.+.+.....+..+...++..|-++.+.
T Consensus 15 M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~ 71 (247)
T KOG4656|consen 15 MTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLR 71 (247)
T ss_pred chhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEe
Confidence 889999999999999999999999999999999988788999999999999887765
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.32 E-value=1.8e-05 Score=43.86 Aligned_cols=59 Identities=37% Similarity=0.670 Sum_probs=51.0
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEeeCCCHHHHHHHHHhCCCceeeccC
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPDAVLQTVSKTGKKTAFWEE 59 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~~~~~~~~~~~~i~~~g~~~~~~~~ 59 (78)
|.|..|...+++.|+.++|+....+++...++.+........+...+.+.||.+.+...
T Consensus 14 MsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~ 72 (238)
T PLN02957 14 MKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQ 72 (238)
T ss_pred ccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecC
Confidence 68999999999999999999999999999988877545777888899999999776544
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.21 E-value=1.5e-05 Score=50.81 Aligned_cols=56 Identities=27% Similarity=0.519 Sum_probs=47.3
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEeeCCCHHHHHHHHHhCCCceeecc
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPDAVLQTVSKTGKKTAFWE 58 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~~~~~~~~~~~~i~~~g~~~~~~~ 58 (78)
|+|.+|..++++.+.+++|+..+.+++. +..+....+.+.+...+...||.+....
T Consensus 12 mtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 12 LSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred cccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 7999999999999999999999999984 3345444577889999999999887643
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.13 E-value=1.6e-05 Score=49.95 Aligned_cols=55 Identities=29% Similarity=0.627 Sum_probs=48.3
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEe-e--CCC-HHHHHHHHHhCCCceee
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK-G--NVQ-PDAVLQTVSKTGKKTAF 56 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~-~--~~~-~~~~~~~i~~~g~~~~~ 56 (78)
|+|..|.++++ .+++++||....+|+..+++.+. . ... .+.+...+...||....
T Consensus 11 m~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 11 MTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred cCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 79999999999 99999999999999999999887 2 234 67889999999998664
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=97.35 E-value=0.0021 Score=27.15 Aligned_cols=53 Identities=21% Similarity=0.551 Sum_probs=40.2
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEee---CCCHHHHHHHHHhCCCc
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKG---NVQPDAVLQTVSKTGKK 53 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~~---~~~~~~~~~~i~~~g~~ 53 (78)
+.|..|...++..++...++....+++....+.+.. ......+...+...||.
T Consensus 11 ~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 66 (68)
T TIGR00003 11 MTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYE 66 (68)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCC
Confidence 469999999999999999999889998888877661 23555555556666764
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.31 E-value=0.0017 Score=42.06 Aligned_cols=62 Identities=18% Similarity=0.559 Sum_probs=54.4
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEe--eCCCHHHHHHHHHhCCCceeeccCCCC
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTGKKTAFWEEEKP 62 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g~~~~~~~~~~~ 62 (78)
|+|..|.+.+++.+...+|+....+++..+...+. ....++.+...+...||+.........
T Consensus 3 mtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ied~gf~~~~~~~~~~ 66 (951)
T KOG0207|consen 3 MTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIEDMGFEASLLSDSEI 66 (951)
T ss_pred ccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhhcccceeeecccCcc
Confidence 78999999999999999999999999999998887 456788899999999999887765543
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.21 E-value=0.0017 Score=42.12 Aligned_cols=57 Identities=23% Similarity=0.584 Sum_probs=50.6
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEe---eCCCHHHHHHHHHhCCCceeec
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK---GNVQPDAVLQTVSKTGKKTAFW 57 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~---~~~~~~~~~~~i~~~g~~~~~~ 57 (78)
|.|..|..++++.+..+.||...++++.+.++.+. ....+.++.+.+...|+.....
T Consensus 155 ~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~ 214 (951)
T KOG0207|consen 155 MTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVR 214 (951)
T ss_pred ccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceee
Confidence 68999999999999999999999999999998877 4578899999999999875544
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.02 E-value=0.0054 Score=39.72 Aligned_cols=56 Identities=32% Similarity=0.576 Sum_probs=46.3
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEeeCCCHHHHHHHHHhCCCceee
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPDAVLQTVSKTGKKTAF 56 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~~~~~~~~~~~~i~~~g~~~~~ 56 (78)
|+|..|...+++.+...+|+....+++...+..+....+...+...+...||...+
T Consensus 108 m~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~ 163 (834)
T PRK10671 108 MSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEA 163 (834)
T ss_pred cCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCccc
Confidence 68999999999999999999999999988886665444667777778888987543
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.91 E-value=0.008 Score=38.57 Aligned_cols=55 Identities=24% Similarity=0.409 Sum_probs=43.3
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEe-eCCCHHHHHHHHHhCCCcee
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK-GNVQPDAVLQTVSKTGKKTA 55 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~-~~~~~~~~~~~i~~~g~~~~ 55 (78)
|+|.+|...+++.+...+|+....+++...+..+. .......+...+...||...
T Consensus 62 m~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~ 117 (741)
T PRK11033 62 MDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLR 117 (741)
T ss_pred CCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccccc
Confidence 68999999999999999999999999988887665 22222555666778888754
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=89.21 E-value=1.3 Score=20.06 Aligned_cols=55 Identities=24% Similarity=0.457 Sum_probs=36.3
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEe-e--CCCHHHHHHHHHhCCCcee
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK-G--NVQPDAVLQTVSKTGKKTA 55 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~-~--~~~~~~~~~~i~~~g~~~~ 55 (78)
+.|..|...++..+....++.....++......+. . ......+...+...|+..+
T Consensus 32 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 89 (92)
T TIGR02052 32 MTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSS 89 (92)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeE
Confidence 35889999999888888887777777666664443 1 2344444455566666543
No 14
>PRK13748 putative mercuric reductase; Provisional
Probab=87.62 E-value=5.2 Score=25.19 Aligned_cols=57 Identities=26% Similarity=0.513 Sum_probs=40.5
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEe--eCCCHHHHHHHHHhCCCceeec
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTGKKTAFW 57 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g~~~~~~ 57 (78)
+.|..|...++..+...+++.....++......+. .......+...+...++.....
T Consensus 9 ~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~ 67 (561)
T PRK13748 9 MTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLA 67 (561)
T ss_pred eecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeecc
Confidence 46999999999999988888888888777775554 2234455555666777765443
No 15
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=70.03 E-value=6.6 Score=20.89 Aligned_cols=28 Identities=18% Similarity=0.357 Sum_probs=23.9
Q ss_pred HhHHHHHHHHhhCCCCeeEEEEEccCCE
Q 034955 4 EGCVGAVKRVLGKMDGVETFDIDLKEQK 31 (78)
Q Consensus 4 ~~c~~~i~~~l~~~~gv~~~~~~~~~~~ 31 (78)
.+|-+-++..+..++||....+-...+.
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~ 35 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGR 35 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCC
Confidence 5799999999999999999988777643
No 16
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=65.99 E-value=8.5 Score=20.82 Aligned_cols=28 Identities=14% Similarity=0.354 Sum_probs=24.5
Q ss_pred HhHHHHHHHHhhCCCCeeEEEEEccCCE
Q 034955 4 EGCVGAVKRVLGKMDGVETFDIDLKEQK 31 (78)
Q Consensus 4 ~~c~~~i~~~l~~~~gv~~~~~~~~~~~ 31 (78)
.+|-+.++..+..++||....+-...+.
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~ 37 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGH 37 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCC
Confidence 5799999999999999999988877664
No 17
>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=64.21 E-value=15 Score=19.55 Aligned_cols=27 Identities=19% Similarity=0.385 Sum_probs=23.8
Q ss_pred HhHHHHHHHHhhCCCCeeEEEEEccCC
Q 034955 4 EGCVGAVKRVLGKMDGVETFDIDLKEQ 30 (78)
Q Consensus 4 ~~c~~~i~~~l~~~~gv~~~~~~~~~~ 30 (78)
.+|-+.++..+..++||....+-+..+
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 479999999999999999999887765
No 18
>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=64.15 E-value=8.6 Score=20.28 Aligned_cols=28 Identities=18% Similarity=0.281 Sum_probs=23.7
Q ss_pred HhHHHHHHHHhhCCCCeeEEEEEccCCE
Q 034955 4 EGCVGAVKRVLGKMDGVETFDIDLKEQK 31 (78)
Q Consensus 4 ~~c~~~i~~~l~~~~gv~~~~~~~~~~~ 31 (78)
.+|-+.++..+..++||....+-+..+.
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG~ 34 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGGY 34 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCCC
Confidence 4799999999999999999888776553
No 19
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=58.14 E-value=13 Score=20.98 Aligned_cols=27 Identities=19% Similarity=0.364 Sum_probs=23.7
Q ss_pred HhHHHHHHHHhhCCCCeeEEEEEccCC
Q 034955 4 EGCVGAVKRVLGKMDGVETFDIDLKEQ 30 (78)
Q Consensus 4 ~~c~~~i~~~l~~~~gv~~~~~~~~~~ 30 (78)
.+|-+.++..+..++||....+-+..+
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG 78 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGG 78 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCC
Confidence 579999999999999999999888754
No 20
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=56.90 E-value=17 Score=17.95 Aligned_cols=25 Identities=28% Similarity=0.534 Sum_probs=17.7
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEE
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDID 26 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~ 26 (78)
+.|..|+..+.+-|... |+...-+.
T Consensus 19 ~qC~~cA~Al~~~L~~~-gI~Gk~i~ 43 (100)
T PF15643_consen 19 FQCVECASALKQFLKQA-GIPGKIIR 43 (100)
T ss_pred eehHHHHHHHHHHHHHC-CCCceEEE
Confidence 36999999999988764 44443333
No 21
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=51.47 E-value=12 Score=20.55 Aligned_cols=28 Identities=21% Similarity=0.328 Sum_probs=24.0
Q ss_pred HhHHHHHHHHhhCCCCeeEEEEEccCCE
Q 034955 4 EGCVGAVKRVLGKMDGVETFDIDLKEQK 31 (78)
Q Consensus 4 ~~c~~~i~~~l~~~~gv~~~~~~~~~~~ 31 (78)
.+|-+-++..+..++||....+-...+.
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~ 42 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGH 42 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCC
Confidence 4788999999999999999988877654
No 22
>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=50.62 E-value=15 Score=13.24 Aligned_cols=34 Identities=41% Similarity=0.885 Sum_probs=23.6
Q ss_pred ccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEe
Q 034955 2 SCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK 35 (78)
Q Consensus 2 ~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~ 35 (78)
.|..|...++..+....++.....++......+.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (63)
T cd00371 8 TCAGCVSKIEKALEKLPGVESVEVDLETGKATVE 41 (63)
T ss_pred EcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEE
Confidence 5788888888877777787666666655553333
No 23
>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=47.06 E-value=28 Score=15.42 Aligned_cols=19 Identities=16% Similarity=0.431 Sum_probs=13.3
Q ss_pred HHHHHHHhhCCCCeeEEEE
Q 034955 7 VGAVKRVLGKMDGVETFDI 25 (78)
Q Consensus 7 ~~~i~~~l~~~~gv~~~~~ 25 (78)
...++..|..++|+.++++
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 3457788889999887653
No 24
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=45.66 E-value=38 Score=16.51 Aligned_cols=47 Identities=19% Similarity=0.376 Sum_probs=32.5
Q ss_pred HHHHhhCCCCeeEEEEEcc-----CCEEEE--e-eCCCHHHHHHHHHhCCCceee
Q 034955 10 VKRVLGKMDGVETFDIDLK-----EQKVTV--K-GNVQPDAVLQTVSKTGKKTAF 56 (78)
Q Consensus 10 i~~~l~~~~gv~~~~~~~~-----~~~~~v--~-~~~~~~~~~~~i~~~g~~~~~ 56 (78)
+-..|+++.||..+++.+. ...+.+ . ...+.+++...+...|...+.
T Consensus 24 ~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHS 78 (97)
T COG1888 24 LALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHS 78 (97)
T ss_pred HHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeee
Confidence 4456788888887776544 222233 3 467889999999999887654
No 25
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=44.59 E-value=27 Score=19.10 Aligned_cols=28 Identities=18% Similarity=0.259 Sum_probs=23.4
Q ss_pred HhHHHHHHHHhhCCCCeeEEEEEccCCE
Q 034955 4 EGCVGAVKRVLGKMDGVETFDIDLKEQK 31 (78)
Q Consensus 4 ~~c~~~i~~~l~~~~gv~~~~~~~~~~~ 31 (78)
.+|-|-+++.+..++||....+-...+.
T Consensus 13 gGCFWg~E~~f~~i~GV~~t~~GYagG~ 40 (174)
T COG0225 13 GGCFWGVEAYFEQIPGVLSTVSGYAGGH 40 (174)
T ss_pred ccCccchHHHHhhCCCeEEEeeeEcCCC
Confidence 4799999999999999999887766554
No 26
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=43.69 E-value=52 Score=17.50 Aligned_cols=26 Identities=23% Similarity=0.542 Sum_probs=18.6
Q ss_pred ccHhHHHHHHHHhhCCCCeeEEEEEcc
Q 034955 2 SCEGCVGAVKRVLGKMDGVETFDIDLK 28 (78)
Q Consensus 2 ~c~~c~~~i~~~l~~~~gv~~~~~~~~ 28 (78)
-|..|...|.....++ |+....+...
T Consensus 110 vC~~C~~~i~~~a~~l-Gl~~L~I~~~ 135 (146)
T PF14437_consen 110 VCGYCGGDIPSMAEKL-GLKSLTIHEP 135 (146)
T ss_pred cchHHHHHHHHHHHHc-CCCeEEEEec
Confidence 4889988887776664 7777666654
No 27
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=42.41 E-value=56 Score=18.16 Aligned_cols=22 Identities=32% Similarity=0.607 Sum_probs=18.1
Q ss_pred HHHHHHHhhCCCCeeEEEEEcc
Q 034955 7 VGAVKRVLGKMDGVETFDIDLK 28 (78)
Q Consensus 7 ~~~i~~~l~~~~gv~~~~~~~~ 28 (78)
...+++.++.++||..+++++.
T Consensus 117 e~eL~~tI~~i~gV~~A~V~l~ 138 (206)
T PF01514_consen 117 EGELERTIESIDGVESARVHLV 138 (206)
T ss_dssp HHHHHHHHTTSTTEEEEEEEEE
T ss_pred HHHHHHHHHcCCCeeEEEEEEe
Confidence 3467889999999999998854
No 28
>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=39.58 E-value=38 Score=14.84 Aligned_cols=48 Identities=13% Similarity=0.117 Sum_probs=31.6
Q ss_pred CccHhHHHHHHHHhhCCCCeeEEEEEccCCEEEEe--eCCCHHHHHHHHHhCCCceeec
Q 034955 1 MSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTGKKTAFW 57 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g~~~~~~ 57 (78)
+.|+.....+.+.+..++.- ..+.+. .......+..-....||.+...
T Consensus 8 ~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 8 LSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp -STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred CCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHCCCEEEEE
Confidence 36888899999999987332 233333 3345567888888889875543
No 29
>PHA03005 sulfhydryl oxidase; Provisional
Probab=39.23 E-value=26 Score=17.10 Aligned_cols=20 Identities=20% Similarity=0.433 Sum_probs=14.5
Q ss_pred ccHhHHHHHHHHhhCCCCee
Q 034955 2 SCEGCVGAVKRVLGKMDGVE 21 (78)
Q Consensus 2 ~c~~c~~~i~~~l~~~~gv~ 21 (78)
=|+.|..+..+.+....=++
T Consensus 42 PC~~Cr~HA~~ai~knnimS 61 (96)
T PHA03005 42 PCPACRRHAKEAIEKNNIMS 61 (96)
T ss_pred CCHHHHHHHHHHHhhcCccc
Confidence 48999999888887643333
No 30
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=39.14 E-value=54 Score=18.09 Aligned_cols=22 Identities=18% Similarity=0.363 Sum_probs=17.5
Q ss_pred HHHHHHHhhCCCCeeEEEEEcc
Q 034955 7 VGAVKRVLGKMDGVETFDIDLK 28 (78)
Q Consensus 7 ~~~i~~~l~~~~gv~~~~~~~~ 28 (78)
...+.+.++.++||.++++++.
T Consensus 109 e~EL~rtI~~i~~V~~ArVhl~ 130 (193)
T TIGR02544 109 EQRLEQTLSQIDGVISARVHVV 130 (193)
T ss_pred HHHHHHHHHhcCCeeeeEEEEE
Confidence 3457888999999998888763
No 31
>PF04805 Pox_E10: E10-like protein conserved region; InterPro: IPR006890 This entry represents a family of probable FAD-linked sulphydryl oxidases found in poxviruses.; GO: 0016972 thiol oxidase activity, 0055114 oxidation-reduction process
Probab=37.42 E-value=33 Score=15.68 Aligned_cols=22 Identities=18% Similarity=0.383 Sum_probs=15.5
Q ss_pred CccHhHHHHHHHHhhCCCCeeE
Q 034955 1 MSCEGCVGAVKRVLGKMDGVET 22 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~~~~gv~~ 22 (78)
+-|+.|..+..+++.+..=++.
T Consensus 16 LPC~~Cr~HA~~ai~kNNiMSs 37 (70)
T PF04805_consen 16 LPCPECRIHAKEAIQKNNIMSS 37 (70)
T ss_pred CCCHHHHHHHHHHHHhcCcccc
Confidence 3489999988888776544443
No 32
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=36.90 E-value=57 Score=16.01 Aligned_cols=47 Identities=13% Similarity=0.385 Sum_probs=32.0
Q ss_pred HHHHhhCCCCeeEEEEEcc-----CCEEEEe---eCCCHHHHHHHHHhCCCceee
Q 034955 10 VKRVLGKMDGVETFDIDLK-----EQKVTVK---GNVQPDAVLQTVSKTGKKTAF 56 (78)
Q Consensus 10 i~~~l~~~~gv~~~~~~~~-----~~~~~v~---~~~~~~~~~~~i~~~g~~~~~ 56 (78)
+-..|..++|+..+++.+. ...+.+. ...+.+.+...+...|...+.
T Consensus 22 ~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHS 76 (95)
T PF02680_consen 22 LAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHS 76 (95)
T ss_dssp HHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEE
T ss_pred HHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEe
Confidence 4567888999988877654 2233333 457899999999999987664
No 33
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=36.60 E-value=65 Score=18.70 Aligned_cols=22 Identities=27% Similarity=0.465 Sum_probs=18.2
Q ss_pred HHHHHHHhhCCCCeeEEEEEcc
Q 034955 7 VGAVKRVLGKMDGVETFDIDLK 28 (78)
Q Consensus 7 ~~~i~~~l~~~~gv~~~~~~~~ 28 (78)
.+.++..|+.++||..+++...
T Consensus 111 eQ~le~tLs~mDGVi~ArV~I~ 132 (246)
T COG4669 111 EQQLEQTLSKMDGVISARVHIS 132 (246)
T ss_pred HHHHHHHHHhcCceEEEEEEEE
Confidence 5678999999999998877655
No 34
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=35.65 E-value=42 Score=19.84 Aligned_cols=28 Identities=21% Similarity=0.363 Sum_probs=23.9
Q ss_pred HhHHHHHHHHhhCCCCeeEEEEEccCCE
Q 034955 4 EGCVGAVKRVLGKMDGVETFDIDLKEQK 31 (78)
Q Consensus 4 ~~c~~~i~~~l~~~~gv~~~~~~~~~~~ 31 (78)
.+|-+.++..+..++||....+-+..+.
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG~ 161 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGGD 161 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCCC
Confidence 5799999999999999999988777653
No 35
>PF14424 Toxin-deaminase: The BURPS668_1122 family of deaminases
Probab=35.61 E-value=68 Score=16.59 Aligned_cols=21 Identities=14% Similarity=0.567 Sum_probs=15.8
Q ss_pred ccHhHHHHHHHHhhCCCCeeE
Q 034955 2 SCEGCVGAVKRVLGKMDGVET 22 (78)
Q Consensus 2 ~c~~c~~~i~~~l~~~~gv~~ 22 (78)
-|.+|...+++-...-|++.-
T Consensus 107 pC~SC~~vi~qF~~~~pni~~ 127 (133)
T PF14424_consen 107 PCESCSNVIEQFKKDFPNIKV 127 (133)
T ss_pred cChhHHHHHHHHHHHCCCcEE
Confidence 499999988887776666653
No 36
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=34.16 E-value=73 Score=18.50 Aligned_cols=22 Identities=18% Similarity=0.392 Sum_probs=18.1
Q ss_pred HHHHHHHhhCCCCeeEEEEEcc
Q 034955 7 VGAVKRVLGKMDGVETFDIDLK 28 (78)
Q Consensus 7 ~~~i~~~l~~~~gv~~~~~~~~ 28 (78)
...+++.++.++||..+++++.
T Consensus 109 egELarTI~~idgV~~ArVhL~ 130 (249)
T PRK15348 109 EQRIEGMLSQMEGVINAKVTIA 130 (249)
T ss_pred HHHHHHHHHhCCCeeEeEEEEE
Confidence 3457888999999999988765
No 37
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=33.82 E-value=35 Score=15.17 Aligned_cols=15 Identities=27% Similarity=0.771 Sum_probs=11.2
Q ss_pred ccHhHHHHHHHHhhC
Q 034955 2 SCEGCVGAVKRVLGK 16 (78)
Q Consensus 2 ~c~~c~~~i~~~l~~ 16 (78)
.|+.|...+++.|..
T Consensus 38 ~CG~C~~~i~~il~~ 52 (64)
T PRK10509 38 QCGKCIRAAREVMQD 52 (64)
T ss_pred CccchHHHHHHHHHH
Confidence 488888888877654
No 38
>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=33.57 E-value=61 Score=15.40 Aligned_cols=21 Identities=24% Similarity=0.506 Sum_probs=16.1
Q ss_pred HHHHHHhhCCCCeeEEEEEcc
Q 034955 8 GAVKRVLGKMDGVETFDIDLK 28 (78)
Q Consensus 8 ~~i~~~l~~~~gv~~~~~~~~ 28 (78)
..++..+..++|+.++.+++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 346777888899998888764
No 39
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.65 E-value=28 Score=16.34 Aligned_cols=16 Identities=31% Similarity=0.812 Sum_probs=13.1
Q ss_pred ccHhHHHHHHHHhhCC
Q 034955 2 SCEGCVGAVKRVLGKM 17 (78)
Q Consensus 2 ~c~~c~~~i~~~l~~~ 17 (78)
.|..|...+++.|+..
T Consensus 35 ~ce~c~a~~kk~l~~v 50 (82)
T COG2331 35 TCEECGARLKKLLNAV 50 (82)
T ss_pred cChhhChHHHHhhccc
Confidence 5889999999988763
No 40
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=30.52 E-value=64 Score=16.90 Aligned_cols=41 Identities=17% Similarity=0.229 Sum_probs=19.8
Q ss_pred hHHHHHHHHhhCCCCeeEEEEEccCCE-EEEeeCCCHHHHHHHHH
Q 034955 5 GCVGAVKRVLGKMDGVETFDIDLKEQK-VTVKGNVQPDAVLQTVS 48 (78)
Q Consensus 5 ~c~~~i~~~l~~~~gv~~~~~~~~~~~-~~v~~~~~~~~~~~~i~ 48 (78)
+|..++-..|+ .+.-++.+...++ ++-.+..+++++...+.
T Consensus 98 ~i~rkvlQ~Le---~~~~ve~hp~gGR~lt~~GqrdldrIa~~i~ 139 (143)
T KOG3411|consen 98 GIARKVLQALE---KMGIVEKHPKGGRRLTEQGQRDLDRIAGQIR 139 (143)
T ss_pred HHHHHHHHHHH---hCCceeeCCCCcceeCcccchhHHHHHHHHH
Confidence 34444444444 4444444444433 22225667777766654
No 41
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=29.61 E-value=37 Score=13.51 Aligned_cols=12 Identities=25% Similarity=0.772 Sum_probs=8.2
Q ss_pred ccHhHHHHHHHH
Q 034955 2 SCEGCVGAVKRV 13 (78)
Q Consensus 2 ~c~~c~~~i~~~ 13 (78)
.|..|.....+.
T Consensus 25 CC~tC~~~fk~k 36 (37)
T PF08394_consen 25 CCPTCLSQFKKK 36 (37)
T ss_pred ECHHHHHHHHhh
Confidence 477887776654
No 42
>PRK15324 type III secretion system lipoprotein PrgK; Provisional
Probab=29.06 E-value=88 Score=18.21 Aligned_cols=23 Identities=17% Similarity=0.290 Sum_probs=18.3
Q ss_pred HHHHHHHhhCCCCeeEEEEEccC
Q 034955 7 VGAVKRVLGKMDGVETFDIDLKE 29 (78)
Q Consensus 7 ~~~i~~~l~~~~gv~~~~~~~~~ 29 (78)
...+.+.|+.++||..+++++.-
T Consensus 110 e~ELarTI~~IdgV~~ARVHl~l 132 (252)
T PRK15324 110 EQRLEQSLQTMEGVLSARVHISY 132 (252)
T ss_pred HHHHHHHHHhcCCcceEEEEEEC
Confidence 35678889999999998887653
No 43
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=29.01 E-value=63 Score=20.92 Aligned_cols=28 Identities=18% Similarity=0.330 Sum_probs=24.1
Q ss_pred HhHHHHHHHHhhCCCCeeEEEEEccCCE
Q 034955 4 EGCVGAVKRVLGKMDGVETFDIDLKEQK 31 (78)
Q Consensus 4 ~~c~~~i~~~l~~~~gv~~~~~~~~~~~ 31 (78)
.+|-+-++..+..++||....+-+..+.
T Consensus 205 gGCFWg~e~~f~~~~GV~~t~~GYagG~ 232 (521)
T PRK14018 205 GGCFWGLEAYFQRIDGVVDAVSGYANGN 232 (521)
T ss_pred cCCchhhHHHHccCCCEEEEEEeeCCCC
Confidence 5799999999999999999988877653
No 44
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=28.80 E-value=88 Score=15.76 Aligned_cols=21 Identities=29% Similarity=0.580 Sum_probs=16.9
Q ss_pred HHHHHHHhhCCCCeeEEEEEc
Q 034955 7 VGAVKRVLGKMDGVETFDIDL 27 (78)
Q Consensus 7 ~~~i~~~l~~~~gv~~~~~~~ 27 (78)
...++.++..++|+.++++++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 456788999999999888774
No 45
>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=26.63 E-value=88 Score=15.03 Aligned_cols=20 Identities=25% Similarity=0.531 Sum_probs=16.0
Q ss_pred HHHHHHHhhCCCCeeEEEEE
Q 034955 7 VGAVKRVLGKMDGVETFDID 26 (78)
Q Consensus 7 ~~~i~~~l~~~~gv~~~~~~ 26 (78)
...++..++++.||+.+.+-
T Consensus 64 td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 64 TEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred hHHHHHHHhcCCCccEEEEE
Confidence 35688999999999887764
No 46
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=26.20 E-value=4.5 Score=15.81 Aligned_cols=9 Identities=44% Similarity=1.095 Sum_probs=4.6
Q ss_pred ccHhHHHHH
Q 034955 2 SCEGCVGAV 10 (78)
Q Consensus 2 ~c~~c~~~i 10 (78)
.|+.|...+
T Consensus 28 ~CP~Cg~~~ 36 (41)
T smart00834 28 TCPECGGDV 36 (41)
T ss_pred CCCCCCCcc
Confidence 356665433
No 47
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=26.11 E-value=77 Score=15.04 Aligned_cols=14 Identities=21% Similarity=0.698 Sum_probs=9.2
Q ss_pred CccHhHHHHHHHHh
Q 034955 1 MSCEGCVGAVKRVL 14 (78)
Q Consensus 1 ~~c~~c~~~i~~~l 14 (78)
|+|.+|....+-+.
T Consensus 27 FCC~GC~~V~~~i~ 40 (88)
T PF12156_consen 27 FCCPGCQAVYQLIH 40 (88)
T ss_pred cccHHHHHHHHHHH
Confidence 57888876655543
No 48
>PF14149 YhfH: YhfH-like protein
Probab=25.95 E-value=60 Score=12.93 Aligned_cols=13 Identities=15% Similarity=0.509 Sum_probs=9.6
Q ss_pred ccHhHHHHHHHHh
Q 034955 2 SCEGCVGAVKRVL 14 (78)
Q Consensus 2 ~c~~c~~~i~~~l 14 (78)
.|..|...|+..-
T Consensus 15 ~C~~CG~~i~EQ~ 27 (37)
T PF14149_consen 15 KCTECGKEIEEQA 27 (37)
T ss_pred ccHHHHHHHHHHH
Confidence 4888888887653
No 49
>COG1856 Uncharacterized homolog of biotin synthetase [Function unknown]
Probab=25.89 E-value=52 Score=19.10 Aligned_cols=13 Identities=15% Similarity=0.383 Sum_probs=8.9
Q ss_pred CccHhHHHHHHHH
Q 034955 1 MSCEGCVGAVKRV 13 (78)
Q Consensus 1 ~~c~~c~~~i~~~ 13 (78)
+.|++|..++-..
T Consensus 23 lnC~HCg~~~L~~ 35 (275)
T COG1856 23 LNCPHCGRHYLEH 35 (275)
T ss_pred ecChHHHHHHHHH
Confidence 4688888876443
No 50
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=25.60 E-value=80 Score=14.24 Aligned_cols=43 Identities=26% Similarity=0.450 Sum_probs=29.2
Q ss_pred hhCCCCeeEEEEEccCCEEEEe--eCCCHHHHHHHHHhCCCceeecc
Q 034955 14 LGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTGKKTAFWE 58 (78)
Q Consensus 14 l~~~~gv~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g~~~~~~~ 58 (78)
|..++++..+... ....+.+. .......+...+...|. +..+.
T Consensus 26 l~~~~~v~~v~~~-~~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~f~ 70 (84)
T PF13732_consen 26 LEELPGVESVEQD-GDGKLRIKLEDEETANELLQELIEKGI-IRSFE 70 (84)
T ss_pred HhhCCCeEEEEEe-CCcEEEEEECCcccHHHHHHHHHhCCC-eeEEE
Confidence 6677898887754 34434444 44567888899988888 66543
No 51
>PF07582 AP_endonuc_2_N: AP endonuclease family 2 C terminus; InterPro: IPR011418 DNA damaging agents such as the anti-tumour drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3' termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3' terminus of DNA strand breaks. AP endonucleases can be classified into two families based on sequence similarity []. This entry represents a highly-conserved sequence found at the C terminus of several apurinic/apyrimidinic (AP) endonucleases in a range of Gram-positive and Gram-negative bacteria. ; PDB: 3LMZ_A 2ZDS_D.
Probab=25.20 E-value=75 Score=13.78 Aligned_cols=14 Identities=7% Similarity=0.192 Sum_probs=9.9
Q ss_pred HHHHHHHHHhCCCc
Q 034955 40 PDAVLQTVSKTGKK 53 (78)
Q Consensus 40 ~~~~~~~i~~~g~~ 53 (78)
...+...++..||+
T Consensus 2 w~~i~~~L~~~GYd 15 (55)
T PF07582_consen 2 WKRIFSALREIGYD 15 (55)
T ss_dssp HHHHHHHHHHTT--
T ss_pred HHHHHHHHHHcCCC
Confidence 46788889999997
No 52
>COG1251 NirB NAD(P)H-nitrite reductase [Energy production and conversion]
Probab=23.88 E-value=1.3e+02 Score=20.77 Aligned_cols=20 Identities=30% Similarity=0.552 Sum_probs=15.9
Q ss_pred ccHhHHHHHHHHhhCCCCee
Q 034955 2 SCEGCVGAVKRVLGKMDGVE 21 (78)
Q Consensus 2 ~c~~c~~~i~~~l~~~~gv~ 21 (78)
+|.+|...+++.|...-+..
T Consensus 449 sCGsC~plveqlL~~~~~~~ 468 (793)
T COG1251 449 SCGSCKPLVEQLLAATLGDQ 468 (793)
T ss_pred CCcCcHHHHHHHHHhhcccc
Confidence 69999999999988754433
No 53
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=23.59 E-value=1e+02 Score=14.74 Aligned_cols=40 Identities=20% Similarity=0.268 Sum_probs=26.4
Q ss_pred HHHHHHHhhCCCCeeEEEEEccCCEEEEe-eCCCHHHHHHH
Q 034955 7 VGAVKRVLGKMDGVETFDIDLKEQKVTVK-GNVQPDAVLQT 46 (78)
Q Consensus 7 ~~~i~~~l~~~~gv~~~~~~~~~~~~~v~-~~~~~~~~~~~ 46 (78)
...+.+.|..++|+.-...+-..+++.++ .......+.+.
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~ 59 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQT 59 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHH
Confidence 45677889999999876665556787777 33444444443
No 54
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=23.09 E-value=56 Score=15.76 Aligned_cols=15 Identities=40% Similarity=0.950 Sum_probs=10.9
Q ss_pred CccHhHHHHHHHHhh
Q 034955 1 MSCEGCVGAVKRVLG 15 (78)
Q Consensus 1 ~~c~~c~~~i~~~l~ 15 (78)
|-|..|..++.+++-
T Consensus 1 MVC~kCEkKLskvi~ 15 (100)
T KOG3476|consen 1 MVCEKCEKKLSKVIG 15 (100)
T ss_pred CchhHHHHHhccccc
Confidence 678889887766643
No 55
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=22.72 E-value=1.1e+02 Score=16.93 Aligned_cols=26 Identities=23% Similarity=0.480 Sum_probs=17.5
Q ss_pred HHHHHHHhhCCCCeeEEEE--EccCCEE
Q 034955 7 VGAVKRVLGKMDGVETFDI--DLKEQKV 32 (78)
Q Consensus 7 ~~~i~~~l~~~~gv~~~~~--~~~~~~~ 32 (78)
..+++..|+.+.|+..+.+ .+.+..-
T Consensus 63 E~~L~~iL~~I~GvG~V~VmItl~s~~e 90 (186)
T TIGR02830 63 ENELKEILEKIEGVGDVTVMVNLDSSEE 90 (186)
T ss_pred HHHHHHHHHhccCcceeEEEEEECCCce
Confidence 4568888999999877554 4444443
No 56
>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=22.62 E-value=87 Score=13.59 Aligned_cols=19 Identities=26% Similarity=0.564 Sum_probs=13.8
Q ss_pred HHHHHHHhhCCCCeeEEEE
Q 034955 7 VGAVKRVLGKMDGVETFDI 25 (78)
Q Consensus 7 ~~~i~~~l~~~~gv~~~~~ 25 (78)
...+-+.|.+++||..+.+
T Consensus 56 l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 56 IDELLEELREIDGVEKVEL 74 (76)
T ss_pred HHHHHHHHhcCCCeEEEEE
Confidence 3456677888899987754
No 57
>PHA01634 hypothetical protein
Probab=22.55 E-value=28 Score=18.33 Aligned_cols=11 Identities=45% Similarity=1.135 Sum_probs=8.1
Q ss_pred CccHhHHHHHH
Q 034955 1 MSCEGCVGAVK 11 (78)
Q Consensus 1 ~~c~~c~~~i~ 11 (78)
|+|.+|..++.
T Consensus 98 iDCeGCE~~l~ 108 (156)
T PHA01634 98 MDCEGCEEKLN 108 (156)
T ss_pred EEccchHHhcC
Confidence 57888987753
No 58
>COG4545 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=22.45 E-value=55 Score=15.44 Aligned_cols=13 Identities=31% Similarity=0.611 Sum_probs=9.8
Q ss_pred CccHhHHHHHHHH
Q 034955 1 MSCEGCVGAVKRV 13 (78)
Q Consensus 1 ~~c~~c~~~i~~~ 13 (78)
+.|+.|+..++..
T Consensus 10 n~Cpdca~a~eyl 22 (85)
T COG4545 10 NLCPDCAPAVEYL 22 (85)
T ss_pred ccCcchHHHHHHH
Confidence 4699998877664
No 59
>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=22.37 E-value=1.4e+02 Score=15.85 Aligned_cols=29 Identities=17% Similarity=0.282 Sum_probs=24.6
Q ss_pred HHHHHHHhhCCCCeeEEEEEccCCEEEEe
Q 034955 7 VGAVKRVLGKMDGVETFDIDLKEQKVTVK 35 (78)
Q Consensus 7 ~~~i~~~l~~~~gv~~~~~~~~~~~~~v~ 35 (78)
+..+...+..++||..+.+-.....+.|.
T Consensus 77 a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 77 ADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 46688889999999999998888887766
No 60
>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=21.85 E-value=1.5e+02 Score=16.15 Aligned_cols=21 Identities=14% Similarity=0.267 Sum_probs=16.2
Q ss_pred HHHHHHhhCCCCeeEEEEEcc
Q 034955 8 GAVKRVLGKMDGVETFDIDLK 28 (78)
Q Consensus 8 ~~i~~~l~~~~gv~~~~~~~~ 28 (78)
..++..+..++|+..+++++.
T Consensus 134 ~dV~~aL~~l~gV~~V~V~l~ 154 (174)
T TIGR03406 134 EDVEDKVLAVPNVDEVEVELV 154 (174)
T ss_pred HHHHHHHHhCCCceeEEEEEE
Confidence 447788888999998887743
No 61
>PF13193 AMP-binding_C: AMP-binding enzyme C-terminal domain; PDB: 3L8C_B 2VSQ_A 3R44_A 3RG2_B 3A9U_A 3A9V_A 3NI2_A 1V26_B 1ULT_B 1V25_B ....
Probab=21.22 E-value=96 Score=13.56 Aligned_cols=17 Identities=24% Similarity=0.344 Sum_probs=13.0
Q ss_pred HHHHhhCCCCeeEEEEE
Q 034955 10 VKRVLGKMDGVETFDID 26 (78)
Q Consensus 10 i~~~l~~~~gv~~~~~~ 26 (78)
|+..+.++++|.+.-+-
T Consensus 2 IE~~l~~~~~V~~~~V~ 18 (73)
T PF13193_consen 2 IESVLRQHPGVAEAAVV 18 (73)
T ss_dssp HHHHHHTSTTEEEEEEE
T ss_pred HHHHHhcCCCccEEEEE
Confidence 67888899998876543
No 62
>PF12292 DUF3624: Protein of unknown function (DUF3624); InterPro: IPR022072 This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved GRC sequence motif.
Probab=20.50 E-value=71 Score=15.03 Aligned_cols=9 Identities=33% Similarity=1.043 Sum_probs=5.1
Q ss_pred CccHhHHHH
Q 034955 1 MSCEGCVGA 9 (78)
Q Consensus 1 ~~c~~c~~~ 9 (78)
|.|..|...
T Consensus 1 M~C~~C~~~ 9 (77)
T PF12292_consen 1 MACNDCQES 9 (77)
T ss_pred CChhhHHHH
Confidence 566666444
No 63
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=20.38 E-value=1.2e+02 Score=14.33 Aligned_cols=21 Identities=14% Similarity=0.093 Sum_probs=16.4
Q ss_pred CCHHHHHHHHHhCCCceeecc
Q 034955 38 VQPDAVLQTVSKTGKKTAFWE 58 (78)
Q Consensus 38 ~~~~~~~~~i~~~g~~~~~~~ 58 (78)
..+..+.+.|++.||.+....
T Consensus 8 ~~Ls~v~~~L~~~GyeVv~l~ 28 (80)
T PF03698_consen 8 EGLSNVKEALREKGYEVVDLE 28 (80)
T ss_pred CCchHHHHHHHHCCCEEEecC
Confidence 356678899999999887654
Done!