Query 033568
Match_columns 116
No_of_seqs 146 out of 873
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 03:47:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033568.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033568hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1603 Copper chaperone [Inor 99.7 5.3E-17 1.1E-21 106.1 8.6 65 1-65 4-69 (73)
2 PF00403 HMA: Heavy-metal-asso 99.5 1.1E-13 2.3E-18 86.3 7.4 57 5-61 1-61 (62)
3 COG2608 CopZ Copper chaperone 99.3 5.2E-12 1.1E-16 82.2 7.6 61 1-61 1-65 (71)
4 KOG4656 Copper chaperone for s 98.8 3.2E-08 6.9E-13 77.4 8.3 66 3-68 8-74 (247)
5 PLN02957 copper, zinc superoxi 98.5 1.4E-06 3.1E-11 68.0 9.5 69 2-70 6-75 (238)
6 PRK10671 copA copper exporting 98.4 7.1E-07 1.5E-11 79.9 7.7 64 1-66 2-67 (834)
7 TIGR00003 copper ion binding p 97.8 0.00038 8.3E-09 39.2 8.1 60 1-60 1-64 (68)
8 COG2217 ZntA Cation transport 97.3 0.00072 1.6E-08 60.7 7.5 63 1-64 1-69 (713)
9 PRK10671 copA copper exporting 96.7 0.0053 1.1E-07 55.4 7.4 61 3-63 100-162 (834)
10 KOG0207 Cation transport ATPas 96.7 0.0058 1.3E-07 56.3 7.4 67 2-68 146-217 (951)
11 KOG0207 Cation transport ATPas 96.3 0.0077 1.7E-07 55.5 5.6 60 9-68 2-64 (951)
12 PRK11033 zntA zinc/cadmium/mer 95.3 0.067 1.5E-06 48.0 7.4 57 3-60 54-113 (741)
13 COG1888 Uncharacterized protei 93.5 0.26 5.7E-06 34.2 5.4 43 18-60 23-73 (97)
14 PF02680 DUF211: Uncharacteriz 93.1 0.32 7E-06 33.8 5.4 57 4-60 7-71 (95)
15 TIGR02052 MerP mercuric transp 82.8 8.4 0.00018 23.4 8.8 58 3-60 24-85 (92)
16 PF01883 DUF59: Domain of unkn 81.5 3.2 7E-05 26.0 4.0 32 3-34 35-72 (72)
17 PRK13748 putative mercuric red 81.1 9.4 0.0002 32.5 7.8 56 5-60 3-61 (561)
18 PF13732 DUF4162: Domain of un 80.3 9.4 0.0002 24.2 6.0 39 23-61 26-65 (84)
19 PF03927 NapD: NapD protein; 73.9 9.8 0.00021 24.9 4.7 32 3-34 40-71 (79)
20 cd04888 ACT_PheB-BS C-terminal 72.1 12 0.00027 22.8 4.7 31 4-34 43-74 (76)
21 PF04972 BON: BON domain; Int 69.3 4.4 9.6E-05 24.5 2.1 37 18-55 3-42 (64)
22 PF13291 ACT_4: ACT domain; PD 69.0 14 0.0003 23.2 4.5 31 3-33 49-79 (80)
23 PRK10553 assembly protein for 63.9 39 0.00086 22.7 6.1 52 16-67 19-77 (87)
24 PF14437 MafB19-deam: MafB19-l 63.5 20 0.00042 26.7 4.9 39 3-42 101-141 (146)
25 TIGR00489 aEF-1_beta translati 63.4 15 0.00033 24.9 4.0 32 4-35 51-83 (88)
26 cd00371 HMA Heavy-metal-associ 63.1 16 0.00035 17.5 6.7 50 9-58 6-57 (63)
27 PRK00435 ef1B elongation facto 62.6 15 0.00032 25.0 3.8 33 3-35 50-83 (88)
28 PF03927 NapD: NapD protein; 61.4 43 0.00093 21.8 6.8 44 15-59 16-60 (79)
29 KOG3411 40S ribosomal protein 61.2 7.3 0.00016 28.8 2.2 48 11-58 92-140 (143)
30 PRK10553 assembly protein for 58.8 27 0.00058 23.6 4.5 32 3-34 43-74 (87)
31 COG4004 Uncharacterized protei 56.4 16 0.00034 25.4 3.1 24 22-45 35-58 (96)
32 cd04877 ACT_TyrR N-terminal AC 52.4 37 0.00079 21.1 4.2 27 7-33 42-68 (74)
33 COG2092 EFB1 Translation elong 49.0 32 0.0007 23.5 3.7 33 3-35 50-83 (88)
34 cd04878 ACT_AHAS N-terminal AC 48.7 38 0.00082 19.6 3.7 19 14-32 53-71 (72)
35 PRK11198 LysM domain/BON super 47.2 42 0.00092 24.2 4.4 49 13-61 25-75 (147)
36 PRK11023 outer membrane lipopr 47.2 51 0.0011 24.8 5.0 47 11-57 46-95 (191)
37 smart00653 eIF2B_5 domain pres 46.3 36 0.00078 23.8 3.7 26 32-58 50-75 (110)
38 cd06471 ACD_LpsHSP_like Group 46.2 17 0.00036 23.7 1.9 24 24-47 16-41 (93)
39 PF15023 DUF4523: Protein of u 46.1 50 0.0011 25.0 4.6 58 1-58 86-147 (166)
40 cd06482 ACD_HspB10 Alpha cryst 45.9 19 0.00042 24.0 2.2 24 24-47 14-39 (87)
41 PF00736 EF1_GNE: EF-1 guanine 44.0 58 0.0013 21.9 4.4 33 3-35 50-84 (89)
42 PRK10555 aminoglycoside/multid 42.7 46 0.001 31.3 4.9 43 16-58 159-209 (1037)
43 PRK10743 heat shock protein Ib 42.3 20 0.00043 25.9 2.0 23 24-46 51-75 (137)
44 cd06475 ACD_HspB1_like Alpha c 42.3 26 0.00056 23.0 2.4 23 25-47 17-41 (86)
45 COG0071 IbpA Molecular chapero 41.9 15 0.00032 26.3 1.3 27 22-48 54-82 (146)
46 PRK04021 hypothetical protein; 41.8 86 0.0019 21.3 5.0 47 9-57 41-91 (92)
47 PRK15127 multidrug efflux syst 41.7 51 0.0011 31.1 5.0 43 16-58 159-209 (1049)
48 TIGR00288 conserved hypothetic 41.6 37 0.0008 25.5 3.4 29 40-68 109-138 (160)
49 cd06167 LabA_like LabA_like pr 41.6 39 0.00086 23.3 3.4 30 39-68 102-132 (149)
50 PF03958 Secretin_N: Bacterial 41.6 49 0.0011 20.6 3.6 27 31-57 47-74 (82)
51 PRK09577 multidrug efflux prot 40.9 51 0.0011 31.0 4.9 44 16-59 158-209 (1032)
52 COG1432 Uncharacterized conser 40.9 25 0.00054 26.3 2.4 35 36-70 110-145 (181)
53 cd06477 ACD_HspB3_Like Alpha c 40.7 27 0.00058 23.1 2.3 23 25-47 14-38 (83)
54 PRK11023 outer membrane lipopr 40.6 1.1E+02 0.0024 22.9 5.9 41 12-52 125-167 (191)
55 TIGR03406 FeS_long_SufT probab 40.6 45 0.00099 25.1 3.8 34 3-36 114-153 (174)
56 TIGR02945 SUF_assoc FeS assemb 40.1 50 0.0011 21.8 3.6 21 16-36 57-77 (99)
57 PRK11597 heat shock chaperone 39.7 22 0.00049 25.9 1.9 24 24-47 49-74 (142)
58 COG2177 FtsX Cell division pro 39.1 85 0.0018 25.6 5.4 43 5-60 64-107 (297)
59 cd06470 ACD_IbpA-B_like Alpha- 38.6 31 0.00068 22.6 2.4 23 25-47 18-42 (90)
60 cd00292 EF1B Elongation factor 38.4 63 0.0014 21.7 3.8 34 3-36 50-84 (88)
61 TIGR00915 2A0602 The (Largely 37.6 63 0.0014 30.4 4.9 44 15-58 158-209 (1044)
62 cd06476 ACD_HspB2_like Alpha c 36.6 34 0.00073 22.4 2.3 23 25-47 14-38 (83)
63 cd04887 ACT_MalLac-Enz ACT_Mal 36.4 97 0.0021 18.6 4.5 29 6-34 44-72 (74)
64 cd06497 ACD_alphaA-crystallin_ 36.2 36 0.00078 22.3 2.3 23 25-47 17-41 (86)
65 cd06478 ACD_HspB4-5-6 Alpha-cr 36.0 38 0.00082 22.0 2.4 22 25-46 14-37 (83)
66 cd06479 ACD_HspB7_like Alpha c 35.5 37 0.00081 22.2 2.3 22 25-46 15-38 (81)
67 PRK10568 periplasmic protein; 35.5 1E+02 0.0022 23.4 5.0 39 10-48 56-96 (203)
68 PF01873 eIF-5_eIF-2B: Domain 34.0 51 0.0011 23.6 3.0 29 28-58 60-88 (125)
69 PF05922 Inhibitor_I9: Peptida 33.6 52 0.0011 20.2 2.7 20 17-36 58-77 (82)
70 cd06481 ACD_HspB9_like Alpha c 33.5 42 0.00091 22.1 2.3 22 25-46 14-37 (87)
71 cd06464 ACD_sHsps-like Alpha-c 32.8 35 0.00076 21.0 1.8 25 24-48 13-39 (88)
72 PRK12342 hypothetical protein; 32.4 61 0.0013 25.8 3.5 43 27-70 11-62 (254)
73 PF02107 FlgH: Flagellar L-rin 31.8 26 0.00056 26.3 1.2 29 25-53 110-138 (179)
74 cd06498 ACD_alphaB-crystallin_ 31.8 47 0.001 21.7 2.4 22 25-46 14-37 (84)
75 COG3062 NapD Uncharacterized p 31.7 1.8E+02 0.0038 20.2 5.2 52 15-67 19-77 (94)
76 PF14492 EFG_II: Elongation Fa 31.4 1.4E+02 0.003 18.9 4.8 46 18-63 23-72 (75)
77 cd04879 ACT_3PGDH-like ACT_3PG 31.3 55 0.0012 18.8 2.4 19 16-34 52-70 (71)
78 PF01936 NYN: NYN domain; Int 31.1 49 0.0011 22.4 2.4 30 38-67 97-127 (146)
79 PF00013 KH_1: KH domain syndr 31.0 73 0.0016 18.8 3.0 36 19-57 21-58 (60)
80 cd03309 CmuC_like CmuC_like. P 29.7 79 0.0017 25.8 3.8 42 8-50 215-267 (321)
81 PF05193 Peptidase_M16_C: Pept 29.3 66 0.0014 21.7 2.9 21 40-60 21-42 (184)
82 PF02983 Pro_Al_protease: Alph 29.1 1.4E+02 0.003 18.5 4.1 22 25-46 21-42 (62)
83 smart00749 BON bacterial OsmY 28.8 1.2E+02 0.0025 17.1 4.5 41 17-57 2-45 (62)
84 PF10934 DUF2634: Protein of u 28.8 1E+02 0.0022 21.3 3.8 33 15-47 70-105 (112)
85 PF08712 Nfu_N: Scaffold prote 28.7 1.2E+02 0.0027 20.0 4.0 40 17-58 37-78 (87)
86 cd04910 ACT_AK-Ectoine_1 ACT d 28.7 1.7E+02 0.0036 18.9 5.9 51 13-64 15-69 (71)
87 PF08478 POTRA_1: POTRA domain 27.4 72 0.0016 19.1 2.5 28 16-43 36-64 (69)
88 cd06472 ACD_ScHsp26_like Alpha 27.4 69 0.0015 20.8 2.6 24 24-47 15-41 (92)
89 cd06526 metazoan_ACD Alpha-cry 27.2 57 0.0012 20.8 2.1 22 25-46 14-37 (83)
90 COG2151 PaaD Predicted metal-s 27.1 1.2E+02 0.0025 21.5 3.8 49 4-57 51-105 (111)
91 COG1908 FrhD Coenzyme F420-red 26.2 54 0.0012 24.0 2.0 46 9-58 5-52 (132)
92 PRK10503 multidrug efflux syst 26.1 1.3E+02 0.0029 28.4 5.0 42 17-58 169-219 (1040)
93 cd04881 ACT_HSDH-Hom ACT_HSDH_ 25.9 1.2E+02 0.0026 17.7 3.3 20 12-31 52-71 (79)
94 cd04903 ACT_LSD C-terminal ACT 25.9 79 0.0017 18.2 2.5 19 16-34 52-70 (71)
95 PF13241 NAD_binding_7: Putati 25.7 1.1E+02 0.0024 20.3 3.4 37 32-68 1-39 (103)
96 PHA00514 dsDNA binding protein 25.4 1.2E+02 0.0027 20.9 3.5 31 40-70 33-66 (98)
97 PF04468 PSP1: PSP1 C-terminal 25.3 2.1E+02 0.0045 18.9 5.6 37 28-64 43-83 (88)
98 cd00298 ACD_sHsps_p23-like Thi 24.9 60 0.0013 18.8 1.8 21 26-46 14-36 (80)
99 TIGR01676 GLDHase galactonolac 24.5 1.2E+02 0.0026 26.9 4.2 35 24-60 111-145 (541)
100 COG0841 AcrB Cation/multidrug 24.4 1.5E+02 0.0032 28.3 5.0 44 15-58 156-208 (1009)
101 PF08002 DUF1697: Protein of u 24.2 2.7E+02 0.0058 19.8 5.7 41 17-58 22-62 (137)
102 PF07683 CobW_C: Cobalamin syn 24.0 90 0.002 19.8 2.6 21 38-58 71-92 (94)
103 cd04876 ACT_RelA-SpoT ACT dom 24.0 1.4E+02 0.0029 16.3 4.6 17 16-32 53-69 (71)
104 cd04901 ACT_3PGDH C-terminal A 23.6 92 0.002 18.3 2.5 18 17-34 51-68 (69)
105 PRK09579 multidrug efflux prot 23.4 1.7E+02 0.0037 27.6 5.2 43 16-58 158-209 (1017)
106 PF10369 ALS_ss_C: Small subun 23.3 2.1E+02 0.0045 18.3 5.2 62 4-67 5-67 (75)
107 PRK11152 ilvM acetolactate syn 22.6 1.8E+02 0.0038 19.0 3.8 23 12-34 53-75 (76)
108 PRK03988 translation initiatio 22.4 1.5E+02 0.0032 21.6 3.7 22 37-58 76-97 (138)
109 PF13200 DUF4015: Putative gly 22.4 3.1E+02 0.0067 22.6 6.0 54 16-70 15-87 (316)
110 cd04920 ACT_AKiii-DAPDC_2 ACT 21.9 1.9E+02 0.0042 17.3 5.1 49 9-58 9-59 (63)
111 PF05309 TraE: TraE protein; 21.9 1E+02 0.0023 22.8 2.9 18 29-46 130-147 (187)
112 TIGR00311 aIF-2beta translatio 21.4 1.5E+02 0.0032 21.5 3.5 21 38-58 72-92 (133)
113 PRK10614 multidrug efflux syst 21.4 1.9E+02 0.0041 27.2 5.1 43 16-58 159-210 (1025)
114 COG4492 PheB ACT domain-contai 21.1 1.1E+02 0.0025 22.8 2.9 66 2-67 71-149 (150)
115 PRK08577 hypothetical protein; 21.0 2.2E+02 0.0049 19.8 4.4 19 16-34 113-131 (136)
116 PF05188 MutS_II: MutS domain 21.0 2.6E+02 0.0057 18.5 4.7 39 32-70 18-56 (137)
117 PF13192 Thioredoxin_3: Thiore 20.7 1.2E+02 0.0025 18.9 2.6 12 4-16 3-14 (76)
118 PF00352 TBP: Transcription fa 20.5 1.8E+02 0.004 18.8 3.6 22 37-58 56-77 (86)
119 PRK03359 putative electron tra 20.4 1.8E+02 0.0038 23.2 4.1 44 27-70 11-65 (256)
120 PRK15078 polysaccharide export 20.2 2.6E+02 0.0056 23.4 5.2 56 5-60 133-202 (379)
No 1
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.71 E-value=5.3e-17 Score=106.09 Aligned_cols=65 Identities=34% Similarity=0.488 Sum_probs=60.0
Q ss_pred CeEEEEEEeccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEeeCCHHHHHHHHHhcC-CeEEE
Q 033568 1 MKKAVFKVGVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGDIDLVSLVSKLKKLC-HAEIV 65 (116)
Q Consensus 1 M~kvvlKV~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g-~aeiv 65 (116)
|++.+++|+|||++|.++|++.++.+.||.++.+|.++++|||.|.+||..|+++|+|.+ +...+
T Consensus 4 ~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~ 69 (73)
T KOG1603|consen 4 IKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAEL 69 (73)
T ss_pred ccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEE
Confidence 578899999999999999999999999999999999999999999999999999999976 44333
No 2
>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=99.50 E-value=1.1e-13 Score=86.27 Aligned_cols=57 Identities=28% Similarity=0.397 Sum_probs=53.1
Q ss_pred EEEE-eccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEee---CCHHHHHHHHHhcCC
Q 033568 5 VFKV-GVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGD---IDLVSLVSKLKKLCH 61 (116)
Q Consensus 5 vlKV-~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~---vDp~~lv~~LrK~g~ 61 (116)
+|+| +|+|++|.++|.++|++++||.++.+|+.+++++|.++ +++.+|.++|++.|+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy 61 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGY 61 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTS
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCc
Confidence 6889 99999999999999999999999999999999999998 456999999999873
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.34 E-value=5.2e-12 Score=82.18 Aligned_cols=61 Identities=20% Similarity=0.315 Sum_probs=55.1
Q ss_pred CeEEEEEE-eccchhhHHHHHHHHhCCCCccEEEeeCCCC--eEEEEe-eCCHHHHHHHHHhcCC
Q 033568 1 MKKAVFKV-GVDDKKARTKVLKTMVGLAGVDTASMDEKEK--KLTVIG-DIDLVSLVSKLKKLCH 61 (116)
Q Consensus 1 M~kvvlKV-~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~--kvtV~G-~vDp~~lv~~LrK~g~ 61 (116)
|++..|+| +|+|++|..++.++|.+++||.+|.+|+..+ .+++.+ .++..+|.+++.+.|+
T Consensus 1 ~~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy 65 (71)
T COG2608 1 MMKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGY 65 (71)
T ss_pred CceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCC
Confidence 78899999 9999999999999999999999999999995 455556 3899999999999993
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.78 E-value=3.2e-08 Score=77.44 Aligned_cols=66 Identities=17% Similarity=0.280 Sum_probs=61.2
Q ss_pred EEEEEEeccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEeeCCHHHHHHHHHhcC-CeEEEeeC
Q 033568 3 KAVFKVGVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGDIDLVSLVSKLKKLC-HAEIVSVG 68 (116)
Q Consensus 3 kvvlKV~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g-~aeivsv~ 68 (116)
+++|-|+|||+.|...+++.|..++||++|++|++++.|.|.+.+-+..+...|+-.| .|-|.-.+
T Consensus 8 ~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G 74 (247)
T KOG4656|consen 8 EAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAG 74 (247)
T ss_pred eEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCC
Confidence 4678899999999999999999999999999999999999999999999999999999 77776544
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.47 E-value=1.4e-06 Score=68.04 Aligned_cols=69 Identities=17% Similarity=0.281 Sum_probs=62.9
Q ss_pred eEEEEEEeccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEeeCCHHHHHHHHHhcC-CeEEEeeCCC
Q 033568 2 KKAVFKVGVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGDIDLVSLVSKLKKLC-HAEIVSVGPA 70 (116)
Q Consensus 2 ~kvvlKV~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g-~aeivsv~p~ 70 (116)
+++.+.++|+|+.|..++.+.|.+++||.++.+|+..++++|.+..++..++.+|++.| .+++++.++.
T Consensus 6 ~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~~ 75 (238)
T PLN02957 6 LLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQGDP 75 (238)
T ss_pred EEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCCCc
Confidence 46788899999999999999999999999999999999999999889999999999999 7888877655
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.42 E-value=7.1e-07 Score=79.89 Aligned_cols=64 Identities=14% Similarity=0.215 Sum_probs=58.1
Q ss_pred CeEEEEEE-eccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEeeCCHHHHHHHHHhcC-CeEEEe
Q 033568 1 MKKAVFKV-GVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGDIDLVSLVSKLKKLC-HAEIVS 66 (116)
Q Consensus 1 M~kvvlKV-~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g-~aeivs 66 (116)
|++++|+| +|+|.+|.+++.++|.+++||.++.+|+ ++.+|.+..++..+..+++..| .+++.+
T Consensus 2 ~~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~--~~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 2 SQTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSI--TEAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred CeEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEee--eEEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 67899999 9999999999999999999999999999 4667778899999999999999 777764
No 7
>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=97.79 E-value=0.00038 Score=39.21 Aligned_cols=60 Identities=15% Similarity=0.147 Sum_probs=51.0
Q ss_pred CeEEEEEE-eccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEee---CCHHHHHHHHHhcC
Q 033568 1 MKKAVFKV-GVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGD---IDLVSLVSKLKKLC 60 (116)
Q Consensus 1 M~kvvlKV-~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~---vDp~~lv~~LrK~g 60 (116)
|++..+.+ +|+|..|...+.+.++.+.|+.+..++...+.+++..+ .+...+...+...|
T Consensus 1 ~~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g 64 (68)
T TIGR00003 1 KQKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAG 64 (68)
T ss_pred CcEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcC
Confidence 67788999 99999999999999999999999999999998888742 57777777666554
No 8
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.34 E-value=0.00072 Score=60.67 Aligned_cols=63 Identities=21% Similarity=0.392 Sum_probs=55.9
Q ss_pred CeEEEEEE-eccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEee---CC-HHHHHHHHHhcC-CeEE
Q 033568 1 MKKAVFKV-GVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGD---ID-LVSLVSKLKKLC-HAEI 64 (116)
Q Consensus 1 M~kvvlKV-~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~---vD-p~~lv~~LrK~g-~aei 64 (116)
+.+..|.+ +|||..|..++. +|.+++||.++.+++..++++|..+ .+ +..+..++++.| .+..
T Consensus 1 ~~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 1 LRETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred CceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 45678999 999999999999 9999999999999999999999865 56 789999999988 5554
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.74 E-value=0.0053 Score=55.35 Aligned_cols=61 Identities=21% Similarity=0.307 Sum_probs=54.0
Q ss_pred EEEEEE-eccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEeeCCHHHHHHHHHhcC-CeE
Q 033568 3 KAVFKV-GVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGDIDLVSLVSKLKKLC-HAE 63 (116)
Q Consensus 3 kvvlKV-~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g-~ae 63 (116)
.+.+.+ +|+|..|...+.+.+..++||.++.++...+++.+.+..++..+...++..| .+.
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~ 162 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAE 162 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCcc
Confidence 356778 9999999999999999999999999999998888887788989988888888 544
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.72 E-value=0.0058 Score=56.27 Aligned_cols=67 Identities=18% Similarity=0.248 Sum_probs=59.3
Q ss_pred eEEEEEE-eccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEee---CCHHHHHHHHHhcC-CeEEEeeC
Q 033568 2 KKAVFKV-GVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGD---IDLVSLVSKLKKLC-HAEIVSVG 68 (116)
Q Consensus 2 ~kvvlKV-~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~---vDp~~lv~~LrK~g-~aeivsv~ 68 (116)
++++|.| +|.|+.|..++.+.+.+++||.++++|...+++.|.-+ .-|-++.+.|...| .+.+....
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~~~ 217 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRPYG 217 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeeecc
Confidence 4789999 99999999999999999999999999999999999875 78999999999877 66665533
No 11
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.30 E-value=0.0077 Score=55.47 Aligned_cols=60 Identities=17% Similarity=0.238 Sum_probs=54.0
Q ss_pred eccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEee--CCHHHHHHHHHhcC-CeEEEeeC
Q 033568 9 GVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGD--IDLVSLVSKLKKLC-HAEIVSVG 68 (116)
Q Consensus 9 ~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~--vDp~~lv~~LrK~g-~aeivsv~ 68 (116)
+|+|.-|.+.+.+++++.+||.++.+++..+..+|.-+ +++..|.+.+...| .+.+++-.
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ied~gf~~~~~~~~ 64 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIEDMGFEASLLSDS 64 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhhcccceeeecccC
Confidence 79999999999999999999999999999988777665 99999999999988 78877543
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=95.32 E-value=0.067 Score=48.00 Aligned_cols=57 Identities=30% Similarity=0.333 Sum_probs=47.0
Q ss_pred EEEEEE-eccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEee--CCHHHHHHHHHhcC
Q 033568 3 KAVFKV-GVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGD--IDLVSLVSKLKKLC 60 (116)
Q Consensus 3 kvvlKV-~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~--vDp~~lv~~LrK~g 60 (116)
.+.+.+ +|+|..|..++.+.+..++||.++.++...+++.+..+ .+ ..+...++..|
T Consensus 54 r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~-~~I~~aI~~~G 113 (741)
T PRK11033 54 RYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIR-AQVESAVQKAG 113 (741)
T ss_pred eEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccch-HHHHHHHHhcc
Confidence 456788 99999999999999999999999999998888877643 23 55666666666
No 13
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=93.50 E-value=0.26 Score=34.19 Aligned_cols=43 Identities=21% Similarity=0.397 Sum_probs=34.2
Q ss_pred HHHHHHhCCCCccEEEe-----eCCC-C-eEEEEee-CCHHHHHHHHHhcC
Q 033568 18 KVLKTMVGLAGVDTASM-----DEKE-K-KLTVIGD-IDLVSLVSKLKKLC 60 (116)
Q Consensus 18 kv~k~ls~l~GV~sV~v-----D~~~-~-kvtV~G~-vDp~~lv~~LrK~g 60 (116)
-+-+.|++++||+.|.+ |.+. + ++||.|. +|-..|.+.|.+.|
T Consensus 23 e~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~G 73 (97)
T COG1888 23 ELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELG 73 (97)
T ss_pred HHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcC
Confidence 35577889999887654 4433 3 8999997 99999999999987
No 14
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=93.14 E-value=0.32 Score=33.79 Aligned_cols=57 Identities=26% Similarity=0.411 Sum_probs=38.9
Q ss_pred EEEEEeccchhhHHHHHHHHhCCCCccEEEe-----eCCCC--eEEEEee-CCHHHHHHHHHhcC
Q 033568 4 AVFKVGVDDKKARTKVLKTMVGLAGVDTASM-----DEKEK--KLTVIGD-IDLVSLVSKLKKLC 60 (116)
Q Consensus 4 vvlKV~m~C~~C~~kv~k~ls~l~GV~sV~v-----D~~~~--kvtV~G~-vDp~~lv~~LrK~g 60 (116)
++|-|--.-+=---.+-..|++++||+.|.+ |.+.. ++||.|+ +|...|.++|.+.|
T Consensus 7 lVLDVlKP~~p~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~G 71 (95)
T PF02680_consen 7 LVLDVLKPHEPSIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELG 71 (95)
T ss_dssp EEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT
T ss_pred EEEEeecCCCCCHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcC
Confidence 4444422222233456688999999998765 33442 7889998 99999999999987
No 15
>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=82.78 E-value=8.4 Score=23.39 Aligned_cols=58 Identities=17% Similarity=0.185 Sum_probs=42.1
Q ss_pred EEEEEE-eccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEE--e-eCCHHHHHHHHHhcC
Q 033568 3 KAVFKV-GVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVI--G-DIDLVSLVSKLKKLC 60 (116)
Q Consensus 3 kvvlKV-~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~--G-~vDp~~lv~~LrK~g 60 (116)
.+.+.+ +++|..|...+...+...+|+.+...+.......+. + ..+...+...++..|
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g 85 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAG 85 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcC
Confidence 445666 889999999999999999999888888777665443 2 246665555555555
No 16
>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=81.53 E-value=3.2 Score=25.97 Aligned_cols=32 Identities=16% Similarity=0.338 Sum_probs=21.2
Q ss_pred EEEEEEeccchhh------HHHHHHHHhCCCCccEEEe
Q 033568 3 KAVFKVGVDDKKA------RTKVLKTMVGLAGVDTASM 34 (116)
Q Consensus 3 kvvlKV~m~C~~C------~~kv~k~ls~l~GV~sV~v 34 (116)
++.|.+.+...+| ++.+..+|+.++||.+|++
T Consensus 35 ~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 35 KVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp EEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 3455554444333 5889999999999999975
No 17
>PRK13748 putative mercuric reductase; Provisional
Probab=81.05 E-value=9.4 Score=32.49 Aligned_cols=56 Identities=14% Similarity=0.191 Sum_probs=44.5
Q ss_pred EEEE-eccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEe--eCCHHHHHHHHHhcC
Q 033568 5 VFKV-GVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIG--DIDLVSLVSKLKKLC 60 (116)
Q Consensus 5 vlKV-~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G--~vDp~~lv~~LrK~g 60 (116)
.+.+ +|+|.+|...+...+..++|+....++...+.+.+.. ..+...+...+...+
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g 61 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLG 61 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcC
Confidence 4556 8999999999999999999999999998888776663 256666666666666
No 18
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=80.33 E-value=9.4 Score=24.17 Aligned_cols=39 Identities=15% Similarity=0.216 Sum_probs=31.9
Q ss_pred HhCCCCccEEEeeCCC-CeEEEEeeCCHHHHHHHHHhcCC
Q 033568 23 MVGLAGVDTASMDEKE-KKLTVIGDIDLVSLVSKLKKLCH 61 (116)
Q Consensus 23 ls~l~GV~sV~vD~~~-~kvtV~G~vDp~~lv~~LrK~g~ 61 (116)
|..++||.++..+... =.+.+.+..++..|+..|...|.
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~~~g~ 65 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDEETANELLQELIEKGI 65 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHHhCCC
Confidence 8888999999986555 36777777899999999988775
No 19
>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=73.89 E-value=9.8 Score=24.95 Aligned_cols=32 Identities=22% Similarity=0.413 Sum_probs=23.5
Q ss_pred EEEEEEeccchhhHHHHHHHHhCCCCccEEEe
Q 033568 3 KAVFKVGVDDKKARTKVLKTMVGLAGVDTASM 34 (116)
Q Consensus 3 kvvlKV~m~C~~C~~kv~k~ls~l~GV~sV~v 34 (116)
|+++-+.-...+-....++.|..++||-|+++
T Consensus 40 KiVVtiE~~~~~~~~~~~~~i~~l~GVlsa~l 71 (79)
T PF03927_consen 40 KIVVTIEAESSEEEVDLIDAINALPGVLSASL 71 (79)
T ss_dssp EEEEEEEESSHHHHHHHHHHHCCSTTEEEEEE
T ss_pred eEEEEEEeCChHHHHHHHHHHHcCCCceEEEE
Confidence 46666666667777777888888888887765
No 20
>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=72.11 E-value=12 Score=22.79 Aligned_cols=31 Identities=10% Similarity=0.304 Sum_probs=21.5
Q ss_pred EEEEEeccchh-hHHHHHHHHhCCCCccEEEe
Q 033568 4 AVFKVGVDDKK-ARTKVLKTMVGLAGVDTASM 34 (116)
Q Consensus 4 vvlKV~m~C~~-C~~kv~k~ls~l~GV~sV~v 34 (116)
+.|.+..+... --..+++.|.+++||.+|.+
T Consensus 43 i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 43 VTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 34444555554 66788888888888888864
No 21
>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=69.32 E-value=4.4 Score=24.51 Aligned_cols=37 Identities=16% Similarity=0.180 Sum_probs=20.0
Q ss_pred HHHHHHhC---CCCccEEEeeCCCCeEEEEeeCCHHHHHHH
Q 033568 18 KVLKTMVG---LAGVDTASMDEKEKKLTVIGDIDLVSLVSK 55 (116)
Q Consensus 18 kv~k~ls~---l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~ 55 (116)
+++.+|.. +++- +|.+...++.|+++|.++-.....+
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v~s~~~~~~ 42 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSVENGVVTLSGEVPSQEQRDA 42 (64)
T ss_dssp ----------CTT-T-TEEEEEECTEEEEEEEESSCHHHHH
T ss_pred ccccccccccccCCC-eEEEEEECCEEEEEeeCcHHHHHHh
Confidence 45556665 5555 6888889999999999744433333
No 22
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=68.96 E-value=14 Score=23.21 Aligned_cols=31 Identities=16% Similarity=0.355 Sum_probs=25.4
Q ss_pred EEEEEEeccchhhHHHHHHHHhCCCCccEEE
Q 033568 3 KAVFKVGVDDKKARTKVLKTMVGLAGVDTAS 33 (116)
Q Consensus 3 kvvlKV~m~C~~C~~kv~k~ls~l~GV~sV~ 33 (116)
.+.|.|....-.=-..++..|.+++||.+|.
T Consensus 49 ~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 49 RITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 3566677777777889999999999999884
No 23
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=63.88 E-value=39 Score=22.74 Aligned_cols=52 Identities=15% Similarity=0.228 Sum_probs=35.5
Q ss_pred HHHHHHHHhCCCCccEEEeeCCCCeEEEEee-CCHHHHHH---HHHh-cC--CeEEEee
Q 033568 16 RTKVLKTMVGLAGVDTASMDEKEKKLTVIGD-IDLVSLVS---KLKK-LC--HAEIVSV 67 (116)
Q Consensus 16 ~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~-vDp~~lv~---~LrK-~g--~aeivsv 67 (116)
...+.+.|..++|++=-..|...+|++|+=+ -+...+++ .|+. -| .|.++-.
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~~I~~l~GVlsa~lVYh 77 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIESVRNVEGVLAVSLVYH 77 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHHHHHcCCCceEEEEEEE
Confidence 5778999999999998888888777766543 44444444 4444 34 5666643
No 24
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=63.50 E-value=20 Score=26.71 Aligned_cols=39 Identities=13% Similarity=0.066 Sum_probs=30.3
Q ss_pred EEEEEE-eccchhhHHHHHHHHhCCCCccEEEeeCC-CCeEE
Q 033568 3 KAVFKV-GVDDKKARTKVLKTMVGLAGVDTASMDEK-EKKLT 42 (116)
Q Consensus 3 kvvlKV-~m~C~~C~~kv~k~ls~l~GV~sV~vD~~-~~kvt 42 (116)
.+++.| --.|+.|..-+...+.++ |+++++|-.. ++++.
T Consensus 101 ~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~ 141 (146)
T PF14437_consen 101 SMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVY 141 (146)
T ss_pred eEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEE
Confidence 467778 556999998887777777 9999999876 56443
No 25
>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=63.41 E-value=15 Score=24.88 Aligned_cols=32 Identities=16% Similarity=0.291 Sum_probs=24.4
Q ss_pred EEEEEeccch-hhHHHHHHHHhCCCCccEEEee
Q 033568 4 AVFKVGVDDK-KARTKVLKTMVGLAGVDTASMD 35 (116)
Q Consensus 4 vvlKV~m~C~-~C~~kv~k~ls~l~GV~sV~vD 35 (116)
+.+.+-|.++ +-...+..++++++||+|+++.
T Consensus 51 L~~~~vv~D~~g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 51 INVMVVMGDAEGGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred eEEEEEEecCCcChHHHHHHHhcCCCccEEEEE
Confidence 3444455454 5578999999999999999885
No 26
>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=63.09 E-value=16 Score=17.55 Aligned_cols=50 Identities=24% Similarity=0.325 Sum_probs=35.1
Q ss_pred eccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEee--CCHHHHHHHHHh
Q 033568 9 GVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGD--IDLVSLVSKLKK 58 (116)
Q Consensus 9 ~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~--vDp~~lv~~LrK 58 (116)
+++|..|...+...+....|+...........+.+... .+...+...++.
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 (63)
T cd00371 6 GMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIED 57 (63)
T ss_pred CeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHHH
Confidence 78899999999988999999887777766655555533 355554444443
No 27
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=62.61 E-value=15 Score=24.96 Aligned_cols=33 Identities=15% Similarity=0.263 Sum_probs=25.2
Q ss_pred EEEEEEeccch-hhHHHHHHHHhCCCCccEEEee
Q 033568 3 KAVFKVGVDDK-KARTKVLKTMVGLAGVDTASMD 35 (116)
Q Consensus 3 kvvlKV~m~C~-~C~~kv~k~ls~l~GV~sV~vD 35 (116)
++.+.+-|.++ +-...+..++++++||+|+++.
T Consensus 50 aL~i~~vv~D~~~~td~lee~i~~~e~Vqsvei~ 83 (88)
T PRK00435 50 ALKLYVIMPDEEGGTEPVEEAFANVEGVESVEVE 83 (88)
T ss_pred eEEEEEEEEcCCcCcHHHHHHHhccCCCcEEEEE
Confidence 44455555554 7778999999999999999885
No 28
>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=61.36 E-value=43 Score=21.85 Aligned_cols=44 Identities=18% Similarity=0.280 Sum_probs=31.2
Q ss_pred hHHHHHHHHhCCCCccEEEeeCCCCeEEEEee-CCHHHHHHHHHhc
Q 033568 15 ARTKVLKTMVGLAGVDTASMDEKEKKLTVIGD-IDLVSLVSKLKKL 59 (116)
Q Consensus 15 C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~-vDp~~lv~~LrK~ 59 (116)
=...+..+|..++|++=-..|.+ ++++|+=+ -+...+.+.++.+
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~i 60 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDAI 60 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHHH
Confidence 35788999999999955556655 77666644 6666777776654
No 29
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=61.19 E-value=7.3 Score=28.80 Aligned_cols=48 Identities=17% Similarity=0.168 Sum_probs=33.1
Q ss_pred cchhhHHHHHHHHhCCCCccEEEeeCCCC-eEEEEeeCCHHHHHHHHHh
Q 033568 11 DDKKARTKVLKTMVGLAGVDTASMDEKEK-KLTVIGDIDLVSLVSKLKK 58 (116)
Q Consensus 11 ~C~~C~~kv~k~ls~l~GV~sV~vD~~~~-kvtV~G~vDp~~lv~~LrK 58 (116)
+|+..-.-++++|+.|+.+.=|+.+++++ ++|=.|.-|-..|+..|+.
T Consensus 92 ~~~as~~i~rkvlQ~Le~~~~ve~hp~gGR~lt~~GqrdldrIa~~i~~ 140 (143)
T KOG3411|consen 92 FCDASGGIARKVLQALEKMGIVEKHPKGGRRLTEQGQRDLDRIAGQIRE 140 (143)
T ss_pred hhccccHHHHHHHHHHHhCCceeeCCCCcceeCcccchhHHHHHHHHHh
Confidence 35443344444555555556677777775 8999999999999998874
No 30
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=58.83 E-value=27 Score=23.58 Aligned_cols=32 Identities=16% Similarity=0.322 Sum_probs=27.2
Q ss_pred EEEEEEeccchhhHHHHHHHHhCCCCccEEEe
Q 033568 3 KAVFKVGVDDKKARTKVLKTMVGLAGVDTASM 34 (116)
Q Consensus 3 kvvlKV~m~C~~C~~kv~k~ls~l~GV~sV~v 34 (116)
|+++-+.-...+-.-...+.+..|+||-|+++
T Consensus 43 KiVVtiE~~~~~~~~~~i~~I~~l~GVlsa~l 74 (87)
T PRK10553 43 QLIVVVEAEDSETLLQTIESVRNVEGVLAVSL 74 (87)
T ss_pred eEEEEEEeCChHHHHHHHHHHHcCCCceEEEE
Confidence 67777777777778888999999999999876
No 31
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=56.40 E-value=16 Score=25.44 Aligned_cols=24 Identities=21% Similarity=0.311 Sum_probs=21.7
Q ss_pred HHhCCCCccEEEeeCCCCeEEEEe
Q 033568 22 TMVGLAGVDTASMDEKEKKLTVIG 45 (116)
Q Consensus 22 ~ls~l~GV~sV~vD~~~~kvtV~G 45 (116)
++..++|++.|++.+++++|-|.+
T Consensus 35 ivas~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 35 IVASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EEEecCCceEEEEecccceEEEec
Confidence 467889999999999999999987
No 32
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=52.39 E-value=37 Score=21.09 Aligned_cols=27 Identities=7% Similarity=0.155 Sum_probs=15.7
Q ss_pred EEeccchhhHHHHHHHHhCCCCccEEE
Q 033568 7 KVGVDDKKARTKVLKTMVGLAGVDTAS 33 (116)
Q Consensus 7 KV~m~C~~C~~kv~k~ls~l~GV~sV~ 33 (116)
.+....-.=-..+++.|.+++||.+|.
T Consensus 42 ~i~v~~~~~L~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 42 NFPTIEFEKLQTLMPEIRRIDGVEDVK 68 (74)
T ss_pred EeEecCHHHHHHHHHHHhCCCCceEEE
Confidence 333333333466677777777777664
No 33
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=48.99 E-value=32 Score=23.54 Aligned_cols=33 Identities=15% Similarity=0.295 Sum_probs=24.9
Q ss_pred EEEEEEeccc-hhhHHHHHHHHhCCCCccEEEee
Q 033568 3 KAVFKVGVDD-KKARTKVLKTMVGLAGVDTASMD 35 (116)
Q Consensus 3 kvvlKV~m~C-~~C~~kv~k~ls~l~GV~sV~vD 35 (116)
.+.|.+-|.+ ++--..+..+|+.++||+|+++-
T Consensus 50 al~l~vvv~D~Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 50 ALKLYVVVEDKEGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred eEEEEEEEcccccCcHHHHHHHhhccCcceEEEE
Confidence 3455555544 35578899999999999999875
No 34
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=48.65 E-value=38 Score=19.64 Aligned_cols=19 Identities=16% Similarity=0.195 Sum_probs=11.1
Q ss_pred hhHHHHHHHHhCCCCccEE
Q 033568 14 KARTKVLKTMVGLAGVDTA 32 (116)
Q Consensus 14 ~C~~kv~k~ls~l~GV~sV 32 (116)
.=-..++..|.+++||.+|
T Consensus 53 ~~~~~l~~~l~~~~~v~~v 71 (72)
T cd04878 53 DVIEQIVKQLNKLVDVLKV 71 (72)
T ss_pred HHHHHHHHHHhCCccEEEe
Confidence 3345556666666666655
No 35
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=47.19 E-value=42 Score=24.22 Aligned_cols=49 Identities=16% Similarity=0.164 Sum_probs=33.8
Q ss_pred hhhHHHHHHHHhCCC-CccEEEeeCCCCeEEEEeeCCHHHHHHHHHh-cCC
Q 033568 13 KKARTKVLKTMVGLA-GVDTASMDEKEKKLTVIGDIDLVSLVSKLKK-LCH 61 (116)
Q Consensus 13 ~~C~~kv~k~ls~l~-GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK-~g~ 61 (116)
+.-++++++.|++.. +...+.+...++.||+.|.+.-.....++.. .+.
T Consensus 25 ~~~~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~~~~~~aa~~ 75 (147)
T PRK11198 25 EDAADALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAKEKILLAVGN 75 (147)
T ss_pred HHHHHHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHHHHHHHHhcc
Confidence 344677777776632 3444666777999999999877777777764 443
No 36
>PRK11023 outer membrane lipoprotein; Provisional
Probab=47.16 E-value=51 Score=24.79 Aligned_cols=47 Identities=15% Similarity=0.181 Sum_probs=35.9
Q ss_pred cchhhHHHHHHHHhCCCCcc---EEEeeCCCCeEEEEeeCCHHHHHHHHH
Q 033568 11 DDKKARTKVLKTMVGLAGVD---TASMDEKEKKLTVIGDIDLVSLVSKLK 57 (116)
Q Consensus 11 ~C~~C~~kv~k~ls~l~GV~---sV~vD~~~~kvtV~G~vDp~~lv~~Lr 57 (116)
.+..=..+|..+|..-+++. .|.+...++.|+.+|.++-.....+..
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 34456788888888877774 588888999999999987766555544
No 37
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=46.27 E-value=36 Score=23.85 Aligned_cols=26 Identities=31% Similarity=0.406 Sum_probs=22.5
Q ss_pred EEeeCCCCeEEEEeeCCHHHHHHHHHh
Q 033568 32 ASMDEKEKKLTVIGDIDLVSLVSKLKK 58 (116)
Q Consensus 32 V~vD~~~~kvtV~G~vDp~~lv~~LrK 58 (116)
.++|.+ +++++.|.+++..|-+.|++
T Consensus 50 g~id~~-~rlii~G~~~~~~i~~~l~~ 75 (110)
T smart00653 50 GSIDGK-GRLIVNGRFTPKKLQDLLRR 75 (110)
T ss_pred eeECCC-CeEEEEEeeCHHHHHHHHHH
Confidence 455666 89999999999999999987
No 38
>cd06471 ACD_LpsHSP_like Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Transcription of the genes encoding Lp HSP 18.5, 18.55 and 19.3 is regulated by a variety of stresses including heat, cold and ethanol. Early growing L. plantarum cells contain elevated levels of these mRNAs which rapidly fall of as the cells enter stationary phase. Also belonging to this group is Bifidobacterium breve (Bb) HSP20 and Oenococcus oenis (syn. Leuconostoc oenos) (Oo) HSP18. Transcription of the gene encoding BbHSP20 is strongly induced following heat or osmotic shock, and that of the gene encoding OoHSP18 following heat, ethanol or acid shock. OoHSP18 is peripherally associated with the cytoplasmic me
Probab=46.24 E-value=17 Score=23.68 Aligned_cols=24 Identities=25% Similarity=0.347 Sum_probs=19.2
Q ss_pred hCCCCcc--EEEeeCCCCeEEEEeeC
Q 033568 24 VGLAGVD--TASMDEKEKKLTVIGDI 47 (116)
Q Consensus 24 s~l~GV~--sV~vD~~~~kvtV~G~v 47 (116)
..|+||. .|+++..++.|+|.|.-
T Consensus 16 ~~lPGv~~edi~v~~~~~~L~I~g~~ 41 (93)
T cd06471 16 ADLPGFKKEDIKLDYKDGYLTISAKR 41 (93)
T ss_pred EECCCCCHHHeEEEEECCEEEEEEEE
Confidence 3578884 58888888999999974
No 39
>PF15023 DUF4523: Protein of unknown function (DUF4523)
Probab=46.07 E-value=50 Score=25.01 Aligned_cols=58 Identities=14% Similarity=0.264 Sum_probs=43.2
Q ss_pred CeEEEEEE---eccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEeeCC-HHHHHHHHHh
Q 033568 1 MKKAVFKV---GVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGDID-LVSLVSKLKK 58 (116)
Q Consensus 1 M~kvvlKV---~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~vD-p~~lv~~LrK 58 (116)
|.+||++= +|.=..--+.|...|+.+--|+||+.-+...-++|-++++ +-.-+.++..
T Consensus 86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGrqsavVvF~d~~SAC~Av~Af~s 147 (166)
T PF15023_consen 86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGRQSAVVVFKDITSACKAVSAFQS 147 (166)
T ss_pred ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCCceEEEEehhhHHHHHHHHhhcC
Confidence 66777665 6766666799999999999999999998887666666644 3345666554
No 40
>cd06482 ACD_HspB10 Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB10, also known as sperm outer dense fiber protein (ODFP), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB10 occurs exclusively in the axoneme of sperm cells and may have a cytoskeletal role.
Probab=45.93 E-value=19 Score=24.04 Aligned_cols=24 Identities=21% Similarity=0.389 Sum_probs=19.8
Q ss_pred hCCCCccE--EEeeCCCCeEEEEeeC
Q 033568 24 VGLAGVDT--ASMDEKEKKLTVIGDI 47 (116)
Q Consensus 24 s~l~GV~s--V~vD~~~~kvtV~G~v 47 (116)
..|+|++. |++...++.|+|.|.-
T Consensus 14 adlPG~~kedI~V~v~~~~L~I~ger 39 (87)
T cd06482 14 VDVCGFEPDQVKVKVKDGKVQVSAER 39 (87)
T ss_pred EECCCCCHHHeEEEEECCEEEEEEEE
Confidence 46788875 8888889999999974
No 41
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=44.01 E-value=58 Score=21.86 Aligned_cols=33 Identities=12% Similarity=0.180 Sum_probs=25.2
Q ss_pred EEEEEEeccch-hhHHHHHHHH-hCCCCccEEEee
Q 033568 3 KAVFKVGVDDK-KARTKVLKTM-VGLAGVDTASMD 35 (116)
Q Consensus 3 kvvlKV~m~C~-~C~~kv~k~l-s~l~GV~sV~vD 35 (116)
++.+.+-|.++ +-...+..++ +.++||+|+++.
T Consensus 50 ~L~v~~vv~D~~~~~d~lee~i~~~~e~Vqsvei~ 84 (89)
T PF00736_consen 50 ALQVSCVVEDDEGSTDDLEEAIESFEEGVQSVEIE 84 (89)
T ss_dssp EEEEEEEECTTTCGHHHHHHHHTTCTTTEEEEEEE
T ss_pred EEEEEEEEEcCccChHHHHHHHHhcCCCccEEEEE
Confidence 44555566664 5688899999 999999999885
No 42
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=42.75 E-value=46 Score=31.31 Aligned_cols=43 Identities=5% Similarity=0.140 Sum_probs=33.6
Q ss_pred HHHHHHHHhCCCCccEEEeeCCCCeEEEEe--------eCCHHHHHHHHHh
Q 033568 16 RTKVLKTMVGLAGVDTASMDEKEKKLTVIG--------DIDLVSLVSKLKK 58 (116)
Q Consensus 16 ~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G--------~vDp~~lv~~LrK 58 (116)
.+.++..|.+++||.+|++......+.|.= .+++.+|..+|+.
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~ 209 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIES 209 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHH
Confidence 467889999999999999998655566651 1677888888885
No 43
>PRK10743 heat shock protein IbpA; Provisional
Probab=42.31 E-value=20 Score=25.90 Aligned_cols=23 Identities=22% Similarity=0.437 Sum_probs=18.2
Q ss_pred hCCCCccE--EEeeCCCCeEEEEee
Q 033568 24 VGLAGVDT--ASMDEKEKKLTVIGD 46 (116)
Q Consensus 24 s~l~GV~s--V~vD~~~~kvtV~G~ 46 (116)
..|+||.. |+++..++.|||.|+
T Consensus 51 aelPGv~kedi~V~v~~~~LtI~ge 75 (137)
T PRK10743 51 IAVAGFAESELEITAQDNLLVVKGA 75 (137)
T ss_pred EECCCCCHHHeEEEEECCEEEEEEE
Confidence 46788854 777788889999997
No 44
>cd06475 ACD_HspB1_like Alpha crystallin domain (ACD) found in mammalian small (s)heat shock protein (Hsp)-27 (also denoted HspB1 in human) and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Hsp27 shows enhanced synthesis in response to stress. It is a molecular chaperone which interacts with a large number of different proteins. It is found in many types of human cells including breast, uterus, cervix, platelets and cancer cells. Hsp27 has diverse cellular functions including, chaperoning, regulation of actin polymerization, keratinocyte differentiation, regulation of inflammatory pathways in keratinocytes, and protection from oxidative stress through modulating glutathione levels. It is also a subunit of AUF1-containing protein complexes. It has been linked to several transduction pathways regulating cellular functions including differentiat
Probab=42.27 E-value=26 Score=23.03 Aligned_cols=23 Identities=9% Similarity=0.177 Sum_probs=18.6
Q ss_pred CCCCccE--EEeeCCCCeEEEEeeC
Q 033568 25 GLAGVDT--ASMDEKEKKLTVIGDI 47 (116)
Q Consensus 25 ~l~GV~s--V~vD~~~~kvtV~G~v 47 (116)
.++|+.. +.++..++.|+|.|.-
T Consensus 17 dlPG~~~edi~V~v~~~~L~I~g~~ 41 (86)
T cd06475 17 DVNHFAPEELVVKTKDGVVEITGKH 41 (86)
T ss_pred ECCCCCHHHEEEEEECCEEEEEEEE
Confidence 5678764 8888888999999973
No 45
>COG0071 IbpA Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=41.87 E-value=15 Score=26.26 Aligned_cols=27 Identities=26% Similarity=0.437 Sum_probs=21.3
Q ss_pred HHhCCCCccE--EEeeCCCCeEEEEeeCC
Q 033568 22 TMVGLAGVDT--ASMDEKEKKLTVIGDID 48 (116)
Q Consensus 22 ~ls~l~GV~s--V~vD~~~~kvtV~G~vD 48 (116)
+...++||+. |++....+.|+|.|...
T Consensus 54 I~~elPG~~kedI~I~~~~~~l~I~g~~~ 82 (146)
T COG0071 54 ITAELPGVDKEDIEITVEGNTLTIRGERE 82 (146)
T ss_pred EEEEcCCCChHHeEEEEECCEEEEEEEec
Confidence 3457888875 88888999999999854
No 46
>PRK04021 hypothetical protein; Reviewed
Probab=41.78 E-value=86 Score=21.30 Aligned_cols=47 Identities=32% Similarity=0.364 Sum_probs=35.1
Q ss_pred eccchhhHHHHHHHHhCCCCccEEEeeC----CCCeEEEEeeCCHHHHHHHHH
Q 033568 9 GVDDKKARTKVLKTMVGLAGVDTASMDE----KEKKLTVIGDIDLVSLVSKLK 57 (116)
Q Consensus 9 ~m~C~~C~~kv~k~ls~l~GV~sV~vD~----~~~kvtV~G~vDp~~lv~~Lr 57 (116)
....+++-+.+.+.|++.=|+ +|++-. ..+.+.|.| +|++.+..+|+
T Consensus 41 pP~~GkAN~ali~~LAk~l~~-~I~I~~G~~sr~K~v~i~g-~~~e~l~~~L~ 91 (92)
T PRK04021 41 PPVKGKANKELVKFFSKLLGA-EVEIIRGETSREKDLLVKG-ISLEEVKKKLK 91 (92)
T ss_pred CCCCChHHHHHHHHHHHHhCC-CEEEEecCCcCceEEEEec-CCHHHHHHHhc
Confidence 556788889999999999898 677753 223566655 89999888774
No 47
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=41.66 E-value=51 Score=31.07 Aligned_cols=43 Identities=9% Similarity=0.196 Sum_probs=32.6
Q ss_pred HHHHHHHHhCCCCccEEEeeCCCCeEEEEe--------eCCHHHHHHHHHh
Q 033568 16 RTKVLKTMVGLAGVDTASMDEKEKKLTVIG--------DIDLVSLVSKLKK 58 (116)
Q Consensus 16 ~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G--------~vDp~~lv~~LrK 58 (116)
.+.++..|.+++||.+|++......+.|.= .+++.+|.++|+.
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~~ 209 (1049)
T PRK15127 159 AANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIKA 209 (1049)
T ss_pred HHHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHHH
Confidence 356889999999999999987755566651 1566777788884
No 48
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=41.63 E-value=37 Score=25.46 Aligned_cols=29 Identities=17% Similarity=0.252 Sum_probs=24.5
Q ss_pred eEEEEeeCCHHHHHHHHHhcC-CeEEEeeC
Q 033568 40 KLTVIGDIDLVSLVSKLKKLC-HAEIVSVG 68 (116)
Q Consensus 40 kvtV~G~vDp~~lv~~LrK~g-~aeivsv~ 68 (116)
-+.|+|+-|-.-|+.+||..| .+..++++
T Consensus 109 ~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~ 138 (160)
T TIGR00288 109 VALVTRDADFLPVINKAKENGKETIVIGAE 138 (160)
T ss_pred EEEEeccHhHHHHHHHHHHCCCEEEEEeCC
Confidence 577889999999999999888 78877653
No 49
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=41.62 E-value=39 Score=23.33 Aligned_cols=30 Identities=33% Similarity=0.495 Sum_probs=25.2
Q ss_pred CeEEEEeeCCHHHHHHHHHhcC-CeEEEeeC
Q 033568 39 KKLTVIGDIDLVSLVSKLKKLC-HAEIVSVG 68 (116)
Q Consensus 39 ~kvtV~G~vDp~~lv~~LrK~g-~aeivsv~ 68 (116)
.-+.|+|+-|-.-+++.||..| .+.+++..
T Consensus 102 ~ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~ 132 (149)
T cd06167 102 TIVLVSGDSDFVPLVERLRELGKRVIVVGFE 132 (149)
T ss_pred EEEEEECCccHHHHHHHHHHcCCEEEEEccC
Confidence 3566789999999999999988 88888765
No 50
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=41.60 E-value=49 Score=20.60 Aligned_cols=27 Identities=30% Similarity=0.363 Sum_probs=19.6
Q ss_pred EEEeeCCCCeEEEEee-CCHHHHHHHHH
Q 033568 31 TASMDEKEKKLTVIGD-IDLVSLVSKLK 57 (116)
Q Consensus 31 sV~vD~~~~kvtV~G~-vDp~~lv~~Lr 57 (116)
+|..|...|.|.|.|+ -+-..|..-|+
T Consensus 47 ~i~~d~~tNsliv~g~~~~~~~i~~li~ 74 (82)
T PF03958_consen 47 RIVADERTNSLIVRGTPEDLEQIRELIK 74 (82)
T ss_dssp EEEEECTTTEEEEEEEHHHHHHHHHHHH
T ss_pred EEEEECCCCEEEEEeCHHHHHHHHHHHH
Confidence 8999999999999998 33333333333
No 51
>PRK09577 multidrug efflux protein; Reviewed
Probab=40.93 E-value=51 Score=30.97 Aligned_cols=44 Identities=14% Similarity=0.204 Sum_probs=34.1
Q ss_pred HHHHHHHHhCCCCccEEEeeCCCCeEEEE--------eeCCHHHHHHHHHhc
Q 033568 16 RTKVLKTMVGLAGVDTASMDEKEKKLTVI--------GDIDLVSLVSKLKKL 59 (116)
Q Consensus 16 ~~kv~k~ls~l~GV~sV~vD~~~~kvtV~--------G~vDp~~lv~~LrK~ 59 (116)
.+.+...|.+++||.+|.++..+..+.|. -.+++.+|.++|+..
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~ 209 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAH 209 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 46789999999999999999866666663 126677788888864
No 52
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=40.89 E-value=25 Score=26.26 Aligned_cols=35 Identities=20% Similarity=0.362 Sum_probs=28.6
Q ss_pred CCCCeEEEEeeCCHHHHHHHHHhcC-CeEEEeeCCC
Q 033568 36 EKEKKLTVIGDIDLVSLVSKLKKLC-HAEIVSVGPA 70 (116)
Q Consensus 36 ~~~~kvtV~G~vDp~~lv~~LrK~g-~aeivsv~p~ 70 (116)
.-+.-+-++|+-|-.-++++++..| .+.++++++-
T Consensus 110 ~~D~ivl~SgD~DF~p~v~~~~~~G~rv~v~~~~~~ 145 (181)
T COG1432 110 NVDTIVLFSGDGDFIPLVEAARDKGKRVEVAGIEPM 145 (181)
T ss_pred CCCEEEEEcCCccHHHHHHHHHHcCCEEEEEecCCc
Confidence 3444677789999999999999877 9999998773
No 53
>cd06477 ACD_HspB3_Like Alpha crystallin domain (ACD) found in mammalian HspB3, also known as heat-shock protein 27-like protein (HSPL27, 17-kDa) and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB3 is expressed in adult skeletal muscle, smooth muscle, and heart, and in several other fetal tissues. In muscle cells HspB3 forms an oligomeric 150 kDa complex with myotonic dystrophy protein kinase-binding protein (MKBP/ HspB2), this complex may comprise one of two independent muscle-cell specific chaperone systems. The expression of HspB3 is induced during muscle differentiation controlled by the myogenic factor MyoD. HspB3 may also interact with Hsp22 (HspB8).
Probab=40.67 E-value=27 Score=23.11 Aligned_cols=23 Identities=13% Similarity=0.068 Sum_probs=19.1
Q ss_pred CCCCccE--EEeeCCCCeEEEEeeC
Q 033568 25 GLAGVDT--ASMDEKEKKLTVIGDI 47 (116)
Q Consensus 25 ~l~GV~s--V~vD~~~~kvtV~G~v 47 (116)
.++|+.. |.++..++.|+|.|.-
T Consensus 14 dlpG~~~edI~V~v~~~~L~I~ge~ 38 (83)
T cd06477 14 DVVQFRPEDIIIQVFEGWLLIKGQH 38 (83)
T ss_pred EcCCCCHHHeEEEEECCEEEEEEEE
Confidence 5677764 8899999999999974
No 54
>PRK11023 outer membrane lipoprotein; Provisional
Probab=40.61 E-value=1.1e+02 Score=22.94 Aligned_cols=41 Identities=15% Similarity=0.192 Sum_probs=28.6
Q ss_pred chhhHHHHHHHHhCCCCccE--EEeeCCCCeEEEEeeCCHHHH
Q 033568 12 DKKARTKVLKTMVGLAGVDT--ASMDEKEKKLTVIGDIDLVSL 52 (116)
Q Consensus 12 C~~C~~kv~k~ls~l~GV~s--V~vD~~~~kvtV~G~vDp~~l 52 (116)
+..-..+++.+|..-+++.+ |.+...++.|++.|.++....
T Consensus 125 D~~It~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~ 167 (191)
T PRK11023 125 DTWITTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREA 167 (191)
T ss_pred cHHHHHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHH
Confidence 34466777888877777665 455556788888888876554
No 55
>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=40.56 E-value=45 Score=25.13 Aligned_cols=34 Identities=9% Similarity=0.185 Sum_probs=24.6
Q ss_pred EEEEEEeccchhh------HHHHHHHHhCCCCccEEEeeC
Q 033568 3 KAVFKVGVDDKKA------RTKVLKTMVGLAGVDTASMDE 36 (116)
Q Consensus 3 kvvlKV~m~C~~C------~~kv~k~ls~l~GV~sV~vD~ 36 (116)
++.|.+.+.-..| +..+..+|..++||.+|.+++
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 4556665554444 366899999999999998853
No 56
>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=40.09 E-value=50 Score=21.78 Aligned_cols=21 Identities=14% Similarity=0.289 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCCccEEEeeC
Q 033568 16 RTKVLKTMVGLAGVDTASMDE 36 (116)
Q Consensus 16 ~~kv~k~ls~l~GV~sV~vD~ 36 (116)
++.+..+|+.++|+++|.+..
T Consensus 57 ~~~i~~al~~l~gv~~v~v~i 77 (99)
T TIGR02945 57 PGEVENAVRAVPGVGSVTVEL 77 (99)
T ss_pred HHHHHHHHHhCCCCceEEEEE
Confidence 356888999999999998864
No 57
>PRK11597 heat shock chaperone IbpB; Provisional
Probab=39.67 E-value=22 Score=25.90 Aligned_cols=24 Identities=29% Similarity=0.418 Sum_probs=19.7
Q ss_pred hCCCCccE--EEeeCCCCeEEEEeeC
Q 033568 24 VGLAGVDT--ASMDEKEKKLTVIGDI 47 (116)
Q Consensus 24 s~l~GV~s--V~vD~~~~kvtV~G~v 47 (116)
..++||.. |+++..++.|||.|+-
T Consensus 49 adlPGv~kedi~V~v~~~~LtI~ge~ 74 (142)
T PRK11597 49 LALAGFRQEDLDIQLEGTRLTVKGTP 74 (142)
T ss_pred EEeCCCCHHHeEEEEECCEEEEEEEE
Confidence 46788854 8888899999999973
No 58
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=39.07 E-value=85 Score=25.60 Aligned_cols=43 Identities=19% Similarity=0.356 Sum_probs=34.5
Q ss_pred EEEEeccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEeeCCHHHHHHHHHh-cC
Q 033568 5 VFKVGVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGDIDLVSLVSKLKK-LC 60 (116)
Q Consensus 5 vlKV~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK-~g 60 (116)
.|+.+.+ +.|.+.+.+.+.+++||.|+.+ +|.++-.+.|++ .|
T Consensus 64 yL~~~~~-~~~~~~v~~~i~~~~gV~~v~~------------~sre~~l~~L~~~lg 107 (297)
T COG2177 64 YLQIDAD-QDDAALVREKIEGIPGVKSVRF------------ISREEALKELQPWLG 107 (297)
T ss_pred EEecCCC-hHHHHHHHHHHhcCCCcceEEE------------eCHHHHHHHHHHHcC
Confidence 3444554 8899999999999999999988 677788888875 55
No 59
>cd06470 ACD_IbpA-B_like Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. IbpA and IbpB are produced during high-level production of various heterologous proteins, specifically human prorenin, renin and bovine insulin-like growth factor 2 (bIGF-2), and are strongly associated with inclusion bodies containing these heterologous proteins. IbpA and IbpB work as an integrated system to stabilize thermally aggregated proteins in a disaggregation competent state. The chaperone activity of IbpB is also significantly elevated as the temperature increases from normal to heat shock. The high temperature results in the disassociation of 2-3-MDa IbpB oligomers into smaller approximately 6
Probab=38.59 E-value=31 Score=22.55 Aligned_cols=23 Identities=26% Similarity=0.476 Sum_probs=18.5
Q ss_pred CCCCccE--EEeeCCCCeEEEEeeC
Q 033568 25 GLAGVDT--ASMDEKEKKLTVIGDI 47 (116)
Q Consensus 25 ~l~GV~s--V~vD~~~~kvtV~G~v 47 (116)
.++|+.. |++...++.|+|.|.-
T Consensus 18 ~lPG~~kedi~v~~~~~~L~I~g~~ 42 (90)
T cd06470 18 AVAGFSEDDLEIEVENNQLTVTGKK 42 (90)
T ss_pred ECCCCCHHHeEEEEECCEEEEEEEE
Confidence 5788765 7778888999999974
No 60
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=38.40 E-value=63 Score=21.74 Aligned_cols=34 Identities=12% Similarity=0.197 Sum_probs=24.5
Q ss_pred EEEEEEeccch-hhHHHHHHHHhCCCCccEEEeeC
Q 033568 3 KAVFKVGVDDK-KARTKVLKTMVGLAGVDTASMDE 36 (116)
Q Consensus 3 kvvlKV~m~C~-~C~~kv~k~ls~l~GV~sV~vD~ 36 (116)
++.+.+-+.++ +-...+..++++++||+|+++..
T Consensus 50 ~L~i~~vv~D~~~~td~lee~i~~~d~VqsveI~~ 84 (88)
T cd00292 50 ALQIYCVVEDDEGGTDELEEAISEEDGVQSVDVEA 84 (88)
T ss_pred EEEEEEEEEeCCcCcHHHHHHHhccCCceEEEEEE
Confidence 34444555554 44688889999999999998853
No 61
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=37.56 E-value=63 Score=30.44 Aligned_cols=44 Identities=9% Similarity=0.219 Sum_probs=34.5
Q ss_pred hHHHHHHHHhCCCCccEEEeeCCCCeEEEEe--------eCCHHHHHHHHHh
Q 033568 15 ARTKVLKTMVGLAGVDTASMDEKEKKLTVIG--------DIDLVSLVSKLKK 58 (116)
Q Consensus 15 C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G--------~vDp~~lv~~LrK 58 (116)
-...+...|.+++||.+|++...+..+.|.= .+++.+|..+|+.
T Consensus 158 ~~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~~ 209 (1044)
T TIGR00915 158 IASNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQA 209 (1044)
T ss_pred HHHHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHHH
Confidence 3467899999999999999998855666652 2677788888886
No 62
>cd06476 ACD_HspB2_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB2/heat shock 27kDa protein 2 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB2 is preferentially and constitutively expressed in skeletal muscle and heart. HspB2 shows homooligomeric activity and forms aggregates in muscle cytosol. Although its expression is not induced by heat shock, it redistributes to the insoluble fraction in response to heat shock. In the mouse heart, HspB2 plays a role in maintaining energetic balance, by protecting cardiac energetics during ischemia/reperfusion, and allowing for increased work during acute inotropic challenge. hHspB2 [previously also known as myotonic dystrophy protein kinase (DMPK) binding protein (MKBP)] is selectively up-regulated in skeletal muscles from myotonic dystrophy patients.
Probab=36.60 E-value=34 Score=22.44 Aligned_cols=23 Identities=9% Similarity=0.094 Sum_probs=18.4
Q ss_pred CCCCccE--EEeeCCCCeEEEEeeC
Q 033568 25 GLAGVDT--ASMDEKEKKLTVIGDI 47 (116)
Q Consensus 25 ~l~GV~s--V~vD~~~~kvtV~G~v 47 (116)
.++|+.. |+++..++.|+|.|.-
T Consensus 14 dlpG~~~edi~V~v~~~~L~I~g~~ 38 (83)
T cd06476 14 DVCHFTPDEITVRTVDNLLEVSARH 38 (83)
T ss_pred EcCCCCHHHeEEEEECCEEEEEEEE
Confidence 4677754 8888889999999974
No 63
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=36.43 E-value=97 Score=18.60 Aligned_cols=29 Identities=14% Similarity=0.240 Sum_probs=16.9
Q ss_pred EEEeccchhhHHHHHHHHhCCCCccEEEe
Q 033568 6 FKVGVDDKKARTKVLKTMVGLAGVDTASM 34 (116)
Q Consensus 6 lKV~m~C~~C~~kv~k~ls~l~GV~sV~v 34 (116)
|.+......=-+.++..|.+++||...++
T Consensus 44 ~~vev~~~~~l~~i~~~L~~i~gV~~~~~ 72 (74)
T cd04887 44 ITVDAPSEEHAETIVAAVRALPEVKVLSV 72 (74)
T ss_pred EEEEcCCHHHHHHHHHHHhcCCCeEEEEe
Confidence 33444444445667777777777665544
No 64
>cd06497 ACD_alphaA-crystallin_HspB4 Alpha-crystallin domain found in the small heat shock protein (sHsp) alphaA-crystallin (HspB4, 20kDa). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. Only trace amounts of HspB4 are found in tissues other than the lens. HspB5 does not belong to this group. Mutations inHspB4 have been associated with Autosomal Dominant Congenital Cataract (ADCC). The chaperone-like functions of HspB4 are considered important for maintaining lens transparency and preventing cataract.
Probab=36.24 E-value=36 Score=22.34 Aligned_cols=23 Identities=4% Similarity=0.115 Sum_probs=18.3
Q ss_pred CCCCccE--EEeeCCCCeEEEEeeC
Q 033568 25 GLAGVDT--ASMDEKEKKLTVIGDI 47 (116)
Q Consensus 25 ~l~GV~s--V~vD~~~~kvtV~G~v 47 (116)
.++|+.. |.++..++.|+|.|.-
T Consensus 17 dlpG~~~edi~V~v~~~~L~I~g~~ 41 (86)
T cd06497 17 DVKHFSPEDLTVKVLDDYVEIHGKH 41 (86)
T ss_pred ECCCCCHHHeEEEEECCEEEEEEEE
Confidence 4677754 8888889999999973
No 65
>cd06478 ACD_HspB4-5-6 Alpha-crystallin domain found in alphaA-crystallin (HspB4), alphaB-crystallin (HspB5), and the small heat shock protein (sHsp) HspB6, also known as Hsp20. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. Only trace amounts of HspB4 are found in tissues other than the lens. HspB5 on the other hand is also expressed constitutively in other tissues including brain, heart, and type I and type IIa skeletal muscle fibers, and in several cancers including gliomas, renal cell carcinomas, basal-like and metaplastic breast carcinomas, and head and neck cancer. HspB5's functions include effects on the apoptotic pathway and on metastasis. Phosphorylation of HspB5 reduces its ol
Probab=36.03 E-value=38 Score=22.00 Aligned_cols=22 Identities=9% Similarity=0.093 Sum_probs=17.7
Q ss_pred CCCCccE--EEeeCCCCeEEEEee
Q 033568 25 GLAGVDT--ASMDEKEKKLTVIGD 46 (116)
Q Consensus 25 ~l~GV~s--V~vD~~~~kvtV~G~ 46 (116)
.++|+.. |.++..++.|+|.|.
T Consensus 14 dlpG~~~edI~V~v~~~~L~I~g~ 37 (83)
T cd06478 14 DVKHFSPEELSVKVLGDFVEIHGK 37 (83)
T ss_pred ECCCCCHHHeEEEEECCEEEEEEE
Confidence 4677754 888888899999996
No 66
>cd06479 ACD_HspB7_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB7, also known as cardiovascular small heat shock protein (cvHsp), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB7 is a 25-kDa protein, preferentially expressed in heart and skeletal muscle. It binds the cytoskeleton protein alpha-filamin (also known as actin-binding protein 280). The expression of HspB7 is increased during rat muscle aging. Its expression is also modulated in obesity implicating this protein in this and related metabolic disorders. As the human gene encoding HspB7 is mapped to chromosome 1p36.23-p34.3 it is a positional candidate for several dystrophies and myopathies.
Probab=35.53 E-value=37 Score=22.25 Aligned_cols=22 Identities=5% Similarity=0.200 Sum_probs=18.1
Q ss_pred CCCCccE--EEeeCCCCeEEEEee
Q 033568 25 GLAGVDT--ASMDEKEKKLTVIGD 46 (116)
Q Consensus 25 ~l~GV~s--V~vD~~~~kvtV~G~ 46 (116)
.++|+.. |++...++.|+|.|+
T Consensus 15 dlpG~~pedi~V~v~~~~L~I~ge 38 (81)
T cd06479 15 DVSDFSPEDIIVTTSNNQIEVHAE 38 (81)
T ss_pred ECCCCCHHHeEEEEECCEEEEEEE
Confidence 5677764 888888999999997
No 67
>PRK10568 periplasmic protein; Provisional
Probab=35.53 E-value=1e+02 Score=23.39 Aligned_cols=39 Identities=23% Similarity=0.365 Sum_probs=30.9
Q ss_pred ccchhhHHHHHHHHhCCCCcc--EEEeeCCCCeEEEEeeCC
Q 033568 10 VDDKKARTKVLKTMVGLAGVD--TASMDEKEKKLTVIGDID 48 (116)
Q Consensus 10 m~C~~C~~kv~k~ls~l~GV~--sV~vD~~~~kvtV~G~vD 48 (116)
+.+..-..++..+|..-+++. .|.+...++.|++.|.++
T Consensus 56 ~~D~~I~~~v~~~L~~~~~i~~~~I~V~v~~G~V~L~G~V~ 96 (203)
T PRK10568 56 MDDSAITAKVKAALVDHDNIKSTDISVKTHQKVVTLSGFVE 96 (203)
T ss_pred ccHHHHHHHHHHHHHhCCCCCCCceEEEEECCEEEEEEEeC
Confidence 445566788888888777775 577888899999999986
No 68
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=34.02 E-value=51 Score=23.58 Aligned_cols=29 Identities=28% Similarity=0.423 Sum_probs=24.4
Q ss_pred CccEEEeeCCCCeEEEEeeCCHHHHHHHHHh
Q 033568 28 GVDTASMDEKEKKLTVIGDIDLVSLVSKLKK 58 (116)
Q Consensus 28 GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK 58 (116)
|.. .++|.+ ++++|.|.+++..|-+.|++
T Consensus 60 gt~-~~id~~-~~lii~G~~~~~~i~~~L~~ 88 (125)
T PF01873_consen 60 GTQ-GSIDGK-GRLIINGRFSSKQIQDLLDK 88 (125)
T ss_dssp SSE-EEEETT-TEEEEESSSSCCHHHHHHHH
T ss_pred CCc-eEECCC-CEEEEEEecCHHHHHHHHHH
Confidence 544 567877 89999999999999999986
No 69
>PF05922 Inhibitor_I9: Peptidase inhibitor I9; InterPro: IPR010259 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes []. The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route []. The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus. Proteinase propeptide inhibitors (sometimes refered to as activation peptides) are responsible for the modulation of folding and activity of the pro-enzyme or zymogen. The pro-segment docks into the enzyme moiety shielding the substrate binding site, thereby promoting inhibition of the enzyme. Several such propeptides share a similar topology [], despite often low sequence identities []. The propeptide region has an open-sandwich antiparallel-alpha/antiparallel-beta fold, with two alpha-helices and four beta-strands with a (beta/alpha/beta)x2 topology. This group of sequences contain the propeptide domain at the N terminus of peptidases belonging to MEROPS family S8A, subtilisins. A number of the members of this group of sequences belong to MEROPS inhibitor family I9, clan I-. The propeptide is removed by proteolytic cleavage; removal activating the enzyme.; GO: 0004252 serine-type endopeptidase activity, 0042802 identical protein binding, 0043086 negative regulation of catalytic activity; PDB: 3CNQ_P 1SPB_P 3CO0_P 1ITP_A 1V5I_B 1SCJ_B 3P5B_P 2XTJ_P 2W2M_P 2P4E_P ....
Probab=33.58 E-value=52 Score=20.22 Aligned_cols=20 Identities=15% Similarity=0.262 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCCccEEEeeC
Q 033568 17 TKVLKTMVGLAGVDTASMDE 36 (116)
Q Consensus 17 ~kv~k~ls~l~GV~sV~vD~ 36 (116)
....+.|.+.+||.+|+-|.
T Consensus 58 ~~~i~~L~~~p~V~~Ve~D~ 77 (82)
T PF05922_consen 58 EEEIEKLRKDPGVKSVEPDQ 77 (82)
T ss_dssp HHHHHHHHTSTTEEEEEEEC
T ss_pred HHHHHHHHcCCCeEEEEeCc
Confidence 34568899999999999884
No 70
>cd06481 ACD_HspB9_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB9 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB9 is expressed exclusively in the normal testis and in various tumor samples and is a cancer/testis antigen. hHspB9 interacts with TCTEL1 (T-complex testis expressed protein -1), a subunit of dynein. hHspB9 and TCTEL1 are co-expressed in similar cells within the testis and in tumor cells. Included in this group is Xenopus Hsp30, a developmentally-regulated heat-inducible molecular chaperone.
Probab=33.49 E-value=42 Score=22.06 Aligned_cols=22 Identities=27% Similarity=0.431 Sum_probs=17.9
Q ss_pred CCCCcc--EEEeeCCCCeEEEEee
Q 033568 25 GLAGVD--TASMDEKEKKLTVIGD 46 (116)
Q Consensus 25 ~l~GV~--sV~vD~~~~kvtV~G~ 46 (116)
.++|+. .|+++..++.|+|.|.
T Consensus 14 dlpG~~~edI~V~v~~~~L~I~g~ 37 (87)
T cd06481 14 DVRGFSPEDLSVRVDGRKLVVTGK 37 (87)
T ss_pred ECCCCChHHeEEEEECCEEEEEEE
Confidence 567875 4888888999999996
No 71
>cd06464 ACD_sHsps-like Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps.
Probab=32.79 E-value=35 Score=21.03 Aligned_cols=25 Identities=20% Similarity=0.456 Sum_probs=19.3
Q ss_pred hCCCCc--cEEEeeCCCCeEEEEeeCC
Q 033568 24 VGLAGV--DTASMDEKEKKLTVIGDID 48 (116)
Q Consensus 24 s~l~GV--~sV~vD~~~~kvtV~G~vD 48 (116)
..++|+ ++|.+...++.|.|.|...
T Consensus 13 ~~lpg~~~~~i~V~v~~~~l~I~g~~~ 39 (88)
T cd06464 13 ADLPGFKKEDIKVEVEDGVLTISGERE 39 (88)
T ss_pred EECCCCCHHHeEEEEECCEEEEEEEEe
Confidence 357888 5688888889999999743
No 72
>PRK12342 hypothetical protein; Provisional
Probab=32.40 E-value=61 Score=25.81 Aligned_cols=43 Identities=16% Similarity=0.212 Sum_probs=31.0
Q ss_pred CCccEEEeeCCCCeEE------EEeeCCHHHHHHHHH-h-cC-CeEEEeeCCC
Q 033568 27 AGVDTASMDEKEKKLT------VIGDIDLVSLVSKLK-K-LC-HAEIVSVGPA 70 (116)
Q Consensus 27 ~GV~sV~vD~~~~kvt------V~G~vDp~~lv~~Lr-K-~g-~aeivsv~p~ 70 (116)
+....+.+|. ++++. +.+.+|...|-.+|| | .| .+..+|+||+
T Consensus 11 PD~~~v~~~~-~~~l~r~~~~~~iNp~D~~AlE~AlrLk~~g~~Vtvls~Gp~ 62 (254)
T PRK12342 11 PEEQDIVVTP-ERTLNFDNAEAKISQFDLNAIEAASQLATDGDEIAALTVGGS 62 (254)
T ss_pred cCCCceEECC-CCCEEcCCCCccCChhhHHHHHHHHHHhhcCCEEEEEEeCCC
Confidence 4455777875 44444 344578888888888 5 55 8999999997
No 73
>PF02107 FlgH: Flagellar L-ring protein; InterPro: IPR000527 The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body []. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament []. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have an extensive beta-sheet structure, in keeping with other outer membrane proteins [].; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0009427 bacterial-type flagellum basal body, distal rod, L ring
Probab=31.82 E-value=26 Score=26.34 Aligned_cols=29 Identities=10% Similarity=0.178 Sum_probs=25.7
Q ss_pred CCCCccEEEeeCCCCeEEEEeeCCHHHHH
Q 033568 25 GLAGVDTASMDEKEKKLTVIGDIDLVSLV 53 (116)
Q Consensus 25 ~l~GV~sV~vD~~~~kvtV~G~vDp~~lv 53 (116)
-++|-..|.++.+.+.+++.|-|.|.+|-
T Consensus 110 ~I~G~k~i~vn~e~~~i~lsGiVRp~DI~ 138 (179)
T PF02107_consen 110 VIEGEKQIRVNGEEQYIRLSGIVRPEDID 138 (179)
T ss_pred EEEEEEEEEECCCEEEEEEEEEECHHHCC
Confidence 46788899999999999999999998876
No 74
>cd06498 ACD_alphaB-crystallin_HspB5 Alpha-crystallin domain found in the small heat shock protein (sHsp) alphaB-crystallin (HspB5, 20kDa). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. HspB4 does not belong to this group. HspB5 shows increased synthesis in response to stress. HspB5 is also expressed constitutively in other tissues including brain, heart, and type I and type IIa skeletal muscle fibers, and in several cancers including gliomas, renal cell carcinomas, basal-like and metaplastic breast carcinomas, and head and neck cancer. Its functions include effects on the apoptotic pathway and on metastasis. Phosphorylation of HspB5 reduces its oligomerization and anti-apoptotic activ
Probab=31.78 E-value=47 Score=21.71 Aligned_cols=22 Identities=5% Similarity=0.074 Sum_probs=17.7
Q ss_pred CCCCcc--EEEeeCCCCeEEEEee
Q 033568 25 GLAGVD--TASMDEKEKKLTVIGD 46 (116)
Q Consensus 25 ~l~GV~--sV~vD~~~~kvtV~G~ 46 (116)
.++|+. .|.++..++.|+|.|.
T Consensus 14 dlpG~~~edi~V~v~~~~L~I~g~ 37 (84)
T cd06498 14 DVKHFSPEELKVKVLGDFIEIHGK 37 (84)
T ss_pred ECCCCCHHHeEEEEECCEEEEEEE
Confidence 567775 4788888899999996
No 75
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=31.71 E-value=1.8e+02 Score=20.20 Aligned_cols=52 Identities=19% Similarity=0.288 Sum_probs=36.1
Q ss_pred hHHHHHHHHhCCCCccEEEeeCCCCeEEE-EeeCCHHHHHHHHHhc----C--CeEEEee
Q 033568 15 ARTKVLKTMVGLAGVDTASMDEKEKKLTV-IGDIDLVSLVSKLKKL----C--HAEIVSV 67 (116)
Q Consensus 15 C~~kv~k~ls~l~GV~sV~vD~~~~kvtV-~G~vDp~~lv~~LrK~----g--~aeivsv 67 (116)
=...++.+|+.|+|++=-.-|.+ ++++| .-.-|...|.+.|.-+ | .|.+|-.
T Consensus 19 ~l~av~~~L~~ip~~EV~~~d~~-GKlVVVie~~~~~~l~~tie~i~nl~gVlav~lVyh 77 (94)
T COG3062 19 RLSAVKTALLAIPGCEVYGEDAE-GKLVVVIEAEDSETLLETIESIRNLPGVLAVSLVYH 77 (94)
T ss_pred HHHHHHHHHhcCCCcEeeccCCC-ceEEEEEEcCchHHHHHHHHHHhcCCceeEEEEEEE
Confidence 35678999999999987777777 55554 4446777787777542 4 5555543
No 76
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=31.39 E-value=1.4e+02 Score=18.89 Aligned_cols=46 Identities=22% Similarity=0.333 Sum_probs=30.9
Q ss_pred HHHHHHhCCCCccEEEeeCCCCeEEEEe--eCCHHHHHHHHHh-cC-CeE
Q 033568 18 KVLKTMVGLAGVDTASMDEKEKKLTVIG--DIDLVSLVSKLKK-LC-HAE 63 (116)
Q Consensus 18 kv~k~ls~l~GV~sV~vD~~~~kvtV~G--~vDp~~lv~~LrK-~g-~ae 63 (116)
.++..|+.-+=--.+..|.+++.+.|.| ++--.-++++|+. +| .++
T Consensus 23 ~aL~~l~~eDP~l~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~ 72 (75)
T PF14492_consen 23 EALQKLSEEDPSLRVERDEETGELILSGMGELHLEVLLERLKRRFGVEVE 72 (75)
T ss_dssp HHHHHHHHH-TTSEEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEE
T ss_pred HHHHHHHhcCCeEEEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeE
Confidence 3344444444445788899999888875 5888889999986 55 443
No 77
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=31.27 E-value=55 Score=18.77 Aligned_cols=19 Identities=21% Similarity=0.405 Sum_probs=16.3
Q ss_pred HHHHHHHHhCCCCccEEEe
Q 033568 16 RTKVLKTMVGLAGVDTASM 34 (116)
Q Consensus 16 ~~kv~k~ls~l~GV~sV~v 34 (116)
-..+++.|.+++||.+|..
T Consensus 52 ~~~l~~~l~~~~~V~~v~~ 70 (71)
T cd04879 52 PEEVLEELKALPGIIRVRL 70 (71)
T ss_pred CHHHHHHHHcCCCeEEEEE
Confidence 4589999999999999863
No 78
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=31.11 E-value=49 Score=22.42 Aligned_cols=30 Identities=30% Similarity=0.430 Sum_probs=20.9
Q ss_pred CCeEEEEeeCCHHHHHHHHHhcC-CeEEEee
Q 033568 38 EKKLTVIGDIDLVSLVSKLKKLC-HAEIVSV 67 (116)
Q Consensus 38 ~~kvtV~G~vDp~~lv~~LrK~g-~aeivsv 67 (116)
+.-+.|+|+-|-.-++..||..| .+.++..
T Consensus 97 d~ivLvSgD~Df~~~v~~l~~~g~~V~v~~~ 127 (146)
T PF01936_consen 97 DTIVLVSGDSDFAPLVRKLRERGKRVIVVGA 127 (146)
T ss_dssp SEEEEE---GGGHHHHHHHHHH--EEEEEE-
T ss_pred CEEEEEECcHHHHHHHHHHHHcCCEEEEEEe
Confidence 34577889999999999999888 7888874
No 79
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=31.01 E-value=73 Score=18.75 Aligned_cols=36 Identities=17% Similarity=0.228 Sum_probs=23.1
Q ss_pred HHHHHhCCCCccEEEeeCC--CCeEEEEeeCCHHHHHHHHH
Q 033568 19 VLKTMVGLAGVDTASMDEK--EKKLTVIGDIDLVSLVSKLK 57 (116)
Q Consensus 19 v~k~ls~l~GV~sV~vD~~--~~kvtV~G~vDp~~lv~~Lr 57 (116)
..+.|....|+. |.++.. ...++|.| ++..+..+++
T Consensus 21 ~i~~I~~~t~~~-I~i~~~~~~~~v~I~G--~~~~v~~A~~ 58 (60)
T PF00013_consen 21 NIKEIEEETGVK-IQIPDDDERDIVTISG--SPEQVEKAKK 58 (60)
T ss_dssp HHHHHHHHHTSE-EEEESTTEEEEEEEEE--SHHHHHHHHH
T ss_pred cHHHhhhhcCeE-EEEcCCCCcEEEEEEe--CHHHHHHHHh
Confidence 344455555777 777654 34899999 6666666654
No 80
>cd03309 CmuC_like CmuC_like. Proteins similar to the putative corrinoid methyltransferase CmuC. Its function has been inferred from sequence similarity to the methyltransferases CmuA and MtaA. Mutants of Methylobacterium sp. disrupted in cmuC and purU appear deficient in some step of chloromethane metabolism.
Probab=29.74 E-value=79 Score=25.76 Aligned_cols=42 Identities=24% Similarity=0.314 Sum_probs=29.6
Q ss_pred EeccchhhHHHHHHHHhCCCCccEEEeeCCC-----------CeEEEEeeCCHH
Q 033568 8 VGVDDKKARTKVLKTMVGLAGVDTASMDEKE-----------KKLTVIGDIDLV 50 (116)
Q Consensus 8 V~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~-----------~kvtV~G~vDp~ 50 (116)
+-+|..+....+...+..+ |++.+++|... +++++.|.+||.
T Consensus 215 iilH~cG~~~~~l~~~~e~-g~dvl~~d~~~~dl~eak~~~g~k~~l~GNlDp~ 267 (321)
T cd03309 215 IVHHSCGAAASLVPSMAEM-GVDSWNVVMTANNTAELRRLLGDKVVLAGAIDDV 267 (321)
T ss_pred eEEEeCCCcHHHHHHHHHc-CCCEEEecCCCCCHHHHHHHhCCCeEEEcCCChH
Confidence 4456555556677778777 99999888754 357777877764
No 81
>PF05193 Peptidase_M16_C: Peptidase M16 inactive domain; InterPro: IPR007863 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. The peptidases in this group of sequences include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The mitochondrial processing peptidase consists of two structurally related domains. One is the active peptidase whereas the other, the C-terminal region, is inactive. The two domains hold the substrate like a clamp [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B 1SQX_B 1NU1_B 1L0L_B 2FYU_B ....
Probab=29.31 E-value=66 Score=21.70 Aligned_cols=21 Identities=33% Similarity=0.518 Sum_probs=18.3
Q ss_pred eEEEEeeCCHHHHHHHHHh-cC
Q 033568 40 KLTVIGDIDLVSLVSKLKK-LC 60 (116)
Q Consensus 40 kvtV~G~vDp~~lv~~LrK-~g 60 (116)
.+.|.|++|+..+...+++ ++
T Consensus 21 ~l~i~Gd~~~~~~~~~i~~~~~ 42 (184)
T PF05193_consen 21 TLVIVGDIDPDELEKLIEKYFG 42 (184)
T ss_dssp EEEEEESSGHHHHHHHHHHHHT
T ss_pred EEEEEcCccHHHHHHHHHhhhh
Confidence 6889999999999999987 44
No 82
>PF02983 Pro_Al_protease: Alpha-lytic protease prodomain; InterPro: IPR004236 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. The alpha-lytic protease prodomain is associated with serine peptidases, specifically the alpha-lytic endopeptidases and streptogrisin A, B, C, D and E, which are bacterial enzymes and which belong to MEROPS peptidase subfamily S1A (IPR001316 from INTERPRO). The protease precursor in Gram-negative bacterial proteases may be a general property of extracellular bacterial proteases []. The proteases are encoded with a large (166 amino acid) N-terminal pro region that is required transiently both in vivo and in vitro for the correct folding of the protease domain [, ]. The pro region also acts as a potent inhibitor of the mature enzyme []. ; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis, 0005576 extracellular region; PDB: 3PRO_C 2PRO_B 4PRO_C.
Probab=29.08 E-value=1.4e+02 Score=18.51 Aligned_cols=22 Identities=23% Similarity=0.311 Sum_probs=18.6
Q ss_pred CCCCccEEEeeCCCCeEEEEee
Q 033568 25 GLAGVDTASMDEKEKKLTVIGD 46 (116)
Q Consensus 25 ~l~GV~sV~vD~~~~kvtV~G~ 46 (116)
.-.++.+=.+|..+|+|+|+-+
T Consensus 21 ~~~~~~~WyvD~~tn~VVV~a~ 42 (62)
T PF02983_consen 21 APVAVTSWYVDPRTNKVVVTAD 42 (62)
T ss_dssp GGGCEEEEEEECCCTEEEEEEE
T ss_pred CCCCcceEEEeCCCCeEEEEEC
Confidence 3448999999999999999864
No 83
>smart00749 BON bacterial OsmY and nodulation domain.
Probab=28.76 E-value=1.2e+02 Score=17.14 Aligned_cols=41 Identities=10% Similarity=0.053 Sum_probs=27.0
Q ss_pred HHHHHHHhCCCCccE--EEeeCCCCeEEEEeeCCHHH-HHHHHH
Q 033568 17 TKVLKTMVGLAGVDT--ASMDEKEKKLTVIGDIDLVS-LVSKLK 57 (116)
Q Consensus 17 ~kv~k~ls~l~GV~s--V~vD~~~~kvtV~G~vDp~~-lv~~Lr 57 (116)
.++...|...+++.+ +.+....+.+++.|.+.+.. ...+..
T Consensus 2 ~~v~~~l~~~~~~~~~~~~v~~~~~~vvL~g~~~~~~~~~~~~~ 45 (62)
T smart00749 2 EKVKKALAKDGLIKADSIVVVTDGGVVVLLGGVVDNAEAAAAAA 45 (62)
T ss_pred hhHHHHHhhCCCCCcCceEEEEECCEEEEeeecCCHHHHHHHHH
Confidence 456777777776665 67777788888888754444 443333
No 84
>PF10934 DUF2634: Protein of unknown function (DUF2634); InterPro: IPR020288 This entry is represented by the Bacteriophage EJ-1, Orf60. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Bacteriophage EJ-1, Orf60 function has not been characterised. It has been shown to be simialr to XkdS (P54331 from SWISSPROT), which is encoded on a phage-like element (prophage) of PSBX found in Bacillus subtilis.
Probab=28.75 E-value=1e+02 Score=21.34 Aligned_cols=33 Identities=12% Similarity=0.160 Sum_probs=25.2
Q ss_pred hHHHHHHHH---hCCCCccEEEeeCCCCeEEEEeeC
Q 033568 15 ARTKVLKTM---VGLAGVDTASMDEKEKKLTVIGDI 47 (116)
Q Consensus 15 C~~kv~k~l---s~l~GV~sV~vD~~~~kvtV~G~v 47 (116)
-.+.|+.+| .++.+|+++++...++++.|.-+|
T Consensus 70 i~r~I~EaL~~d~rI~~V~~f~f~~~~~~l~v~f~V 105 (112)
T PF10934_consen 70 IEREIEEALLQDPRITSVENFSFEWEGDSLYVSFTV 105 (112)
T ss_pred HHHHHHHHHhcCCCcceEEEEEEEEECCEEEEEEEE
Confidence 356777777 567788889999888888877553
No 85
>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=28.72 E-value=1.2e+02 Score=19.99 Aligned_cols=40 Identities=18% Similarity=0.385 Sum_probs=28.9
Q ss_pred HHHHHHHhCCCCccEEEeeCCCCeEEEEe--eCCHHHHHHHHHh
Q 033568 17 TKVLKTMVGLAGVDTASMDEKEKKLTVIG--DIDLVSLVSKLKK 58 (116)
Q Consensus 17 ~kv~k~ls~l~GV~sV~vD~~~~kvtV~G--~vDp~~lv~~LrK 58 (116)
.-+-+.|-.++||.+|-+.. +=+||+- ++|-..|...++.
T Consensus 37 spLA~~Lf~i~gV~~Vf~~~--dfItVtK~~~~~W~~l~~~I~~ 78 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFIGD--DFITVTKNPDADWEDLKPEIRE 78 (87)
T ss_dssp -HHHHHHHTSTTEEEEEEET--TEEEEEE-TTS-HHHHHHHHHH
T ss_pred CHHHHHhcCCCCEeEEEEEC--CEEEEeeCCCCCHHHHHHHHHH
Confidence 34456677999999998864 4677765 4898888888875
No 86
>cd04910 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase
Probab=28.66 E-value=1.7e+02 Score=18.91 Aligned_cols=51 Identities=20% Similarity=0.255 Sum_probs=38.1
Q ss_pred hhhHHHHHHHHhCCCCccEEEeeCCCCeEEEE--ee-CCHHHHHHHHHhcC-CeEE
Q 033568 13 KKARTKVLKTMVGLAGVDTASMDEKEKKLTVI--GD-IDLVSLVSKLKKLC-HAEI 64 (116)
Q Consensus 13 ~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~--G~-vDp~~lv~~LrK~g-~aei 64 (116)
.+--..++++|.+. +|.=|..|...|++|.- |. -+..+++..|++.. .++|
T Consensus 15 ~g~d~~i~~~l~~~-~v~ii~K~~nANtit~yl~~~~k~~~r~~~~Le~~~p~a~i 69 (71)
T cd04910 15 VGYDLEILELLQRF-KVSIIAKDTNANTITHYLAGSLKTIKRLTEDLENRFPNAEI 69 (71)
T ss_pred hhHHHHHHHHHHHc-CCeEEEEecCCCeEEEEEEcCHHHHHHHHHHHHHhCccCcc
Confidence 45678899999998 89999999999988874 44 35567888887644 4444
No 87
>PF08478 POTRA_1: POTRA domain, FtsQ-type; InterPro: IPR013685 FtsQ/DivIB bacterial division proteins (IPR005548 from INTERPRO) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts []. ; PDB: 2ALJ_A 2VH1_B 3J00_Z 2VH2_B.
Probab=27.40 E-value=72 Score=19.14 Aligned_cols=28 Identities=18% Similarity=0.236 Sum_probs=21.1
Q ss_pred HHHHHHHHhCCCCccEEEeeCCC-CeEEE
Q 033568 16 RTKVLKTMVGLAGVDTASMDEKE-KKLTV 43 (116)
Q Consensus 16 ~~kv~k~ls~l~GV~sV~vD~~~-~kvtV 43 (116)
...+.+.|.+++.|.++++...- +++.|
T Consensus 36 ~~~~~~~l~~~p~V~~v~V~r~~P~~l~I 64 (69)
T PF08478_consen 36 LKKIEQRLEKLPWVKSVSVSRRFPNTLEI 64 (69)
T ss_dssp HHHHHHCCCCTTTEEEEEEEEETTTEEEE
T ss_pred HHHHHHHHHcCCCEEEEEEEEeCCCEEEE
Confidence 35677889999999999997533 56555
No 88
>cd06472 ACD_ScHsp26_like Alpha crystallin domain (ACD) found in Saccharomyces cerevisiae (Sc) small heat shock protein (Hsp)26 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. ScHsp26 is temperature-regulated, it switches from an inactive to a chaperone-active form upon elevation in temperature. It associates into large 24-mers storage forms which upon heat shock disassociate into dimers. These dimers initiate the interaction with non-native substrate proteins and re-assemble into large globular assemblies having one monomer of substrate bound per dimer. This group also contains Arabidopsis thaliana (Ath) Hsp15.7, a peroxisomal matrix protein which can complement the morphological phenotype of S. cerevisiae mutants deficient in Hsps26. AthHsp15.7 is minimally expressed under normal conditions and is strongly induced by heat and oxidative st
Probab=27.37 E-value=69 Score=20.78 Aligned_cols=24 Identities=17% Similarity=0.450 Sum_probs=17.6
Q ss_pred hCCCCcc--EEEeeCCC-CeEEEEeeC
Q 033568 24 VGLAGVD--TASMDEKE-KKLTVIGDI 47 (116)
Q Consensus 24 s~l~GV~--sV~vD~~~-~kvtV~G~v 47 (116)
..|+||. .+.++..+ +.|+|.|.-
T Consensus 15 ~~lPGv~~edi~i~v~~~~~L~I~g~~ 41 (92)
T cd06472 15 ADVPGVKKEDVKVEVEDGRVLRISGER 41 (92)
T ss_pred EECCCCChHhEEEEEeCCCEEEEEEEe
Confidence 3578886 47777765 589999974
No 89
>cd06526 metazoan_ACD Alpha-crystallin domain (ACD) of metazoan alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps.
Probab=27.17 E-value=57 Score=20.82 Aligned_cols=22 Identities=23% Similarity=0.403 Sum_probs=16.8
Q ss_pred CCCCccE--EEeeCCCCeEEEEee
Q 033568 25 GLAGVDT--ASMDEKEKKLTVIGD 46 (116)
Q Consensus 25 ~l~GV~s--V~vD~~~~kvtV~G~ 46 (116)
.++|+.. |.+...++.|+|.|.
T Consensus 14 dlpG~~~edI~v~v~~~~L~I~g~ 37 (83)
T cd06526 14 DVKGFKPEELKVKVSDNKLVVEGK 37 (83)
T ss_pred ECCCCCHHHcEEEEECCEEEEEEE
Confidence 4667654 777777899999997
No 90
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=27.15 E-value=1.2e+02 Score=21.46 Aligned_cols=49 Identities=12% Similarity=0.187 Sum_probs=30.8
Q ss_pred EEEEEeccchhh------HHHHHHHHhCCCCccEEEeeCCCCeEEEEeeCCHHHHHHHHH
Q 033568 4 AVFKVGVDDKKA------RTKVLKTMVGLAGVDTASMDEKEKKLTVIGDIDLVSLVSKLK 57 (116)
Q Consensus 4 vvlKV~m~C~~C------~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~Lr 57 (116)
+.+++.++-.+| ...++.++.+++||+++.++ ++....-.+..+..-.|
T Consensus 51 v~v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~-----l~~~p~Wt~~~ms~ear 105 (111)
T COG2151 51 VKVKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVE-----LTLSPPWTPDRMSEEAR 105 (111)
T ss_pred EEEEEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEE-----EEEcCCCchhhcCHHHH
Confidence 344555555555 57899999999999999883 44433344444444333
No 91
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=26.21 E-value=54 Score=24.02 Aligned_cols=46 Identities=15% Similarity=0.182 Sum_probs=31.8
Q ss_pred eccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEE--EeeCCHHHHHHHHHh
Q 033568 9 GVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTV--IGDIDLVSLVSKLKK 58 (116)
Q Consensus 9 ~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV--~G~vDp~~lv~~LrK 58 (116)
...|.-|.=-+ +.+.|...+..-..-.-+.| +|.|||+-++++|++
T Consensus 5 ~F~C~wcsyga----aDlag~~rmqyp~~vRiIrv~CsGrvn~~fvl~Al~~ 52 (132)
T COG1908 5 AFACNWCSYGA----ADLAGTSRMQYPPNVRIIRVMCSGRVNPEFVLKALRK 52 (132)
T ss_pred EEEcccccccc----hhhhccccccCCCceEEEEeeccCccCHHHHHHHHHc
Confidence 44566654222 35667777777666664444 689999999999998
No 92
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=26.10 E-value=1.3e+02 Score=28.36 Aligned_cols=42 Identities=12% Similarity=0.212 Sum_probs=32.0
Q ss_pred HHHHHHHhCCCCccEEEeeCCC-CeEEEEe--------eCCHHHHHHHHHh
Q 033568 17 TKVLKTMVGLAGVDTASMDEKE-KKLTVIG--------DIDLVSLVSKLKK 58 (116)
Q Consensus 17 ~kv~k~ls~l~GV~sV~vD~~~-~kvtV~G--------~vDp~~lv~~LrK 58 (116)
+.++..|.+++||.+|.+.+.. ..+.|.= .+++.+|..+|+.
T Consensus 169 ~~l~~~L~~i~gV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~~v~~ai~~ 219 (1040)
T PRK10503 169 TRVAQKISQVSGVGLVTLSGGQRPAVRVKLNAQAIAALGLTSETVRTAITG 219 (1040)
T ss_pred HHHHHHhcCCCCceEEEecCCCceEEEEEECHHHHHHcCCCHHHHHHHHHH
Confidence 5688999999999999998764 4566641 1667778888874
No 93
>cd04881 ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains. The ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) encoded by the hom gene of Bacillus subtilis and other related sequences. HSDH reduces aspartate semi-aldehyde to the amino acid homoserine, one that is required for the biosynthesis of Met, Thr, and Ile from Asp. Neither the enzyme nor the aspartate pathway is found in the animal kingdom. This mostly bacterial HSDH group has a C-terminal ACT domain and is believed to be involved in enzyme regulation. A C-terminal deletion in the Corynebacterium glutamicum HSDH abolished allosteric inhibition by L-threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=25.88 E-value=1.2e+02 Score=17.73 Aligned_cols=20 Identities=20% Similarity=0.230 Sum_probs=10.1
Q ss_pred chhhHHHHHHHHhCCCCccE
Q 033568 12 DKKARTKVLKTMVGLAGVDT 31 (116)
Q Consensus 12 C~~C~~kv~k~ls~l~GV~s 31 (116)
...--+.+...|.+++||.+
T Consensus 52 ~~~~l~~~i~~L~~~~~V~~ 71 (79)
T cd04881 52 SEAALNAALAEIEALDAVQG 71 (79)
T ss_pred CHHHHHHHHHHHHcCccccC
Confidence 34444455555555555544
No 94
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=25.86 E-value=79 Score=18.19 Aligned_cols=19 Identities=5% Similarity=0.281 Sum_probs=15.7
Q ss_pred HHHHHHHHhCCCCccEEEe
Q 033568 16 RTKVLKTMVGLAGVDTASM 34 (116)
Q Consensus 16 ~~kv~k~ls~l~GV~sV~v 34 (116)
-..+.+.|.+++||.+|..
T Consensus 52 ~~~~i~~l~~~~~v~~v~~ 70 (71)
T cd04903 52 DEEVIEEIKKIPNIHQVIL 70 (71)
T ss_pred CHHHHHHHHcCCCceEEEE
Confidence 4578899999999998864
No 95
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=25.67 E-value=1.1e+02 Score=20.28 Aligned_cols=37 Identities=19% Similarity=0.163 Sum_probs=20.5
Q ss_pred EEeeCCCCeEEEEee-CCHHHHHHHHHhcC-CeEEEeeC
Q 033568 32 ASMDEKEKKLTVIGD-IDLVSLVSKLKKLC-HAEIVSVG 68 (116)
Q Consensus 32 V~vD~~~~kvtV~G~-vDp~~lv~~LrK~g-~aeivsv~ 68 (116)
+.+|+++.++.|+|. --...-+..|.+.| +..++|..
T Consensus 1 l~l~l~~~~vlVvGgG~va~~k~~~Ll~~gA~v~vis~~ 39 (103)
T PF13241_consen 1 LFLDLKGKRVLVVGGGPVAARKARLLLEAGAKVTVISPE 39 (103)
T ss_dssp EEE--TT-EEEEEEESHHHHHHHHHHCCCTBEEEEEESS
T ss_pred CEEEcCCCEEEEECCCHHHHHHHHHHHhCCCEEEEECCc
Confidence 457889999999997 22223333444566 66666655
No 96
>PHA00514 dsDNA binding protein
Probab=25.37 E-value=1.2e+02 Score=20.93 Aligned_cols=31 Identities=26% Similarity=0.449 Sum_probs=24.9
Q ss_pred eEEEEeeCCHHHHHHHHHhc--C-CeEEEeeCCC
Q 033568 40 KLTVIGDIDLVSLVSKLKKL--C-HAEIVSVGPA 70 (116)
Q Consensus 40 kvtV~G~vDp~~lv~~LrK~--g-~aeivsv~p~ 70 (116)
..|..|....+.--..|.|. + .++++||+|-
T Consensus 33 ~~Tl~GNLtiEqAQ~e~~k~~k~~pvqVvsVEpn 66 (98)
T PHA00514 33 EQTLLGNLTIEQAQKELSKQYKHGPVQVVSVEPN 66 (98)
T ss_pred cceeecceeHHHHHHHHhhcccCCCeeEEEecCC
Confidence 34778998888888888763 4 9999999986
No 97
>PF04468 PSP1: PSP1 C-terminal conserved region; InterPro: IPR007557 The yeast polymerase suppressor 1 (PSP1) protein partially suppresses mutations in DNA polymerases alpha and delta []. The C-terminal half of PSP1 contains a domain, which is also found in several hypothetical proteins from both eukaryotic and prokaryotic sources: Crithidia fasciculata RBP45 and RBP33, subunits of the cycling sequence binding protein (CSBP) II. RBP45 and RBP33 proteins bind specifically to the cycling sequences present in several mRNAs that accumulate periodically during the cell cycle. RBP45 and RBP33 are phosphoproteins, which are phosphorylated differentially during progression through the cell cycle. Hypothetical proteins with high sequence similarity have been identified in other kinetoplastid organisms []. Bacillus subtilis yaaT protein, which plays a significant role in phosphorelay during initiation of sporulation. It is possible that the yaaT protein is also related to DNA replication. The sequence of the yaaT protein is widely conserved in prokaryotes (bacteria and archaea), but the functions of the protein are unknown []. The actual biological significance of the PSP1 C-terminal domain has not yet been clearly established.
Probab=25.32 E-value=2.1e+02 Score=18.87 Aligned_cols=37 Identities=22% Similarity=0.254 Sum_probs=27.0
Q ss_pred CccEEEeeCCCCeEEEE--e--eCCHHHHHHHHHhcCCeEE
Q 033568 28 GVDTASMDEKEKKLTVI--G--DIDLVSLVSKLKKLCHAEI 64 (116)
Q Consensus 28 GV~sV~vD~~~~kvtV~--G--~vDp~~lv~~LrK~g~aei 64 (116)
-+-.++...+.+++|+- + .+|--.|+.-|.+.-++.|
T Consensus 43 ~lvd~e~~~D~~k~~fyy~a~~rvDFR~Lvr~L~~~f~~RI 83 (88)
T PF04468_consen 43 KLVDVEYQFDGSKLTFYYTAESRVDFRELVRDLAREFKTRI 83 (88)
T ss_pred EEEEEEEEcCCCEEEEEEEeCCcCcHHHHHHHHHHHhCceE
Confidence 35567777888999984 3 3999999999987433333
No 98
>cd00298 ACD_sHsps_p23-like This domain family includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this family is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind
Probab=24.92 E-value=60 Score=18.82 Aligned_cols=21 Identities=29% Similarity=0.582 Sum_probs=16.2
Q ss_pred CCCc--cEEEeeCCCCeEEEEee
Q 033568 26 LAGV--DTASMDEKEKKLTVIGD 46 (116)
Q Consensus 26 l~GV--~sV~vD~~~~kvtV~G~ 46 (116)
++|+ +.+.++...+.|+|.|.
T Consensus 14 ~~~~~~~~i~v~~~~~~l~v~~~ 36 (80)
T cd00298 14 LPGVKKEDIKVEVEDNVLTISGK 36 (80)
T ss_pred CCCCCHHHeEEEEECCEEEEEEE
Confidence 4565 67888888889999886
No 99
>TIGR01676 GLDHase galactonolactone dehydrogenase. This model represents L-Galactono-gamma-lactone dehydrogenase (EC 1.3.2.3). This enzyme catalyzes the final step in ascorbic acid biosynthesis in higher plants. This protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD.
Probab=24.49 E-value=1.2e+02 Score=26.89 Aligned_cols=35 Identities=26% Similarity=0.366 Sum_probs=28.2
Q ss_pred hCCCCccEEEeeCCCCeEEEEeeCCHHHHHHHHHhcC
Q 033568 24 VGLAGVDTASMDEKEKKLTVIGDIDLVSLVSKLKKLC 60 (116)
Q Consensus 24 s~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g 60 (116)
+.+.|| +++|..++++||.+-+--.+|...|...|
T Consensus 111 ~~ln~V--l~vD~~~~tVtV~AG~~l~~L~~~L~~~G 145 (541)
T TIGR01676 111 ALMDKV--LEVDEEKKRVRVQAGIRVQQLVDAIKEYG 145 (541)
T ss_pred hhCCCC--EEEcCCCCEEEEcCCCCHHHHHHHHHHcC
Confidence 344444 36788899999999899999999999876
No 100
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=24.35 E-value=1.5e+02 Score=28.30 Aligned_cols=44 Identities=11% Similarity=0.181 Sum_probs=34.4
Q ss_pred hHHHHHHHHhCCCCccEEEeeCCC-CeEEEEe--------eCCHHHHHHHHHh
Q 033568 15 ARTKVLKTMVGLAGVDTASMDEKE-KKLTVIG--------DIDLVSLVSKLKK 58 (116)
Q Consensus 15 C~~kv~k~ls~l~GV~sV~vD~~~-~kvtV~G--------~vDp~~lv~~LrK 58 (116)
-.+.++..|++++||-+|++-+.. ..+.|.= .+.+.+|..+|+.
T Consensus 156 ~~~~l~~~L~~v~GV~~V~~~G~~~~~~rI~ldp~kLa~~gLt~~dV~~ai~~ 208 (1009)
T COG0841 156 AASNVRDELSRVPGVGSVQLFGAQEYAMRIWLDPAKLAAYGLTPSDVQSAIRA 208 (1009)
T ss_pred HHHHHHHHHhcCCCceEEEEcCCCceeEEEEeCHHHHHHcCCCHHHHHHHHHH
Confidence 456789999999999999998875 4666652 1667788888875
No 101
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=24.24 E-value=2.7e+02 Score=19.80 Aligned_cols=41 Identities=17% Similarity=0.252 Sum_probs=32.2
Q ss_pred HHHHHHHhCCCCccEEEeeCCCCeEEEEeeCCHHHHHHHHHh
Q 033568 17 TKVLKTMVGLAGVDTASMDEKEKKLTVIGDIDLVSLVSKLKK 58 (116)
Q Consensus 17 ~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK 58 (116)
...+..+.++ |-..|..=..++.|....+.|+..|..+|.+
T Consensus 22 aeLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~ 62 (137)
T PF08002_consen 22 AELREALEDL-GFTNVRTYIQSGNVVFESDRDPAELAAKIEK 62 (137)
T ss_dssp HHHHHHHHHC-T-EEEEEETTTTEEEEEESS-HHHHHHHHHH
T ss_pred HHHHHHHHHc-CCCCceEEEeeCCEEEecCCChHHHHHHHHH
Confidence 4566667777 9999999999999999987999988877753
No 102
>PF07683 CobW_C: Cobalamin synthesis protein cobW C-terminal domain; InterPro: IPR011629 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [].; PDB: 1NIJ_A.
Probab=24.03 E-value=90 Score=19.81 Aligned_cols=21 Identities=29% Similarity=0.496 Sum_probs=15.3
Q ss_pred CCeEEEEee-CCHHHHHHHHHh
Q 033568 38 EKKLTVIGD-IDLVSLVSKLKK 58 (116)
Q Consensus 38 ~~kvtV~G~-vDp~~lv~~LrK 58 (116)
.++++++|. +|...|.+.|..
T Consensus 71 ~~~lV~IG~~ld~~~l~~~l~~ 92 (94)
T PF07683_consen 71 DSRLVFIGKNLDKEALREALDA 92 (94)
T ss_dssp -EEEEEEEES--HHHHHHHHHT
T ss_pred CeEEEEEECCCCHHHHHHHHHc
Confidence 358999998 999999888864
No 103
>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains. ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i
Probab=23.97 E-value=1.4e+02 Score=16.28 Aligned_cols=17 Identities=12% Similarity=0.374 Sum_probs=9.2
Q ss_pred HHHHHHHHhCCCCccEE
Q 033568 16 RTKVLKTMVGLAGVDTA 32 (116)
Q Consensus 16 ~~kv~k~ls~l~GV~sV 32 (116)
-..+...|..++||..|
T Consensus 53 ~~~~~~~l~~~~~v~~v 69 (71)
T cd04876 53 LARIMRKLRQIPGVIDV 69 (71)
T ss_pred HHHHHHHHhCCCCcEEE
Confidence 45555555555555544
No 104
>cd04901 ACT_3PGDH C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-
Probab=23.64 E-value=92 Score=18.32 Aligned_cols=18 Identities=11% Similarity=0.342 Sum_probs=15.0
Q ss_pred HHHHHHHhCCCCccEEEe
Q 033568 17 TKVLKTMVGLAGVDTASM 34 (116)
Q Consensus 17 ~kv~k~ls~l~GV~sV~v 34 (116)
..+++.|.+++||.+|.+
T Consensus 51 ~~li~~l~~~~~V~~v~~ 68 (69)
T cd04901 51 EELLEALRAIPGTIRVRL 68 (69)
T ss_pred HHHHHHHHcCCCeEEEEE
Confidence 478889999999998864
No 105
>PRK09579 multidrug efflux protein; Reviewed
Probab=23.44 E-value=1.7e+02 Score=27.60 Aligned_cols=43 Identities=7% Similarity=0.156 Sum_probs=32.4
Q ss_pred HHHHHHHHhCCCCccEEEeeCCCC-eEEEEe--------eCCHHHHHHHHHh
Q 033568 16 RTKVLKTMVGLAGVDTASMDEKEK-KLTVIG--------DIDLVSLVSKLKK 58 (116)
Q Consensus 16 ~~kv~k~ls~l~GV~sV~vD~~~~-kvtV~G--------~vDp~~lv~~LrK 58 (116)
.+.++..|.+++||.+|.+..... .+.|.= .+.+.+|..+|+.
T Consensus 158 ~~~i~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~ 209 (1017)
T PRK09579 158 SRVIQPKLATLPGMAEAEILGNQVFAMRLWLDPVKLAGFGLSAGDVTQAVRR 209 (1017)
T ss_pred HHHHHHHhhcCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHH
Confidence 456889999999999999887653 555541 1667788888875
No 106
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=23.34 E-value=2.1e+02 Score=18.25 Aligned_cols=62 Identities=16% Similarity=0.225 Sum_probs=39.1
Q ss_pred EEEEEeccchhhHHHHHHHHhCCCCccEEEeeCCCCeEEEEee-CCHHHHHHHHHhcCCeEEEee
Q 033568 4 AVFKVGVDDKKARTKVLKTMVGLAGVDTASMDEKEKKLTVIGD-IDLVSLVSKLKKLCHAEIVSV 67 (116)
Q Consensus 4 vvlKV~m~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV~G~-vDp~~lv~~LrK~g~aeivsv 67 (116)
+-+||.. -..-+..+.+.+..+.| .=|.++.+.=.+-++|+ -.-..+++.|++.|-.+++--
T Consensus 5 ~LiKV~~-~~~~r~ei~~l~~~f~a-~ivd~~~~~~iie~tG~~~kid~fi~~l~~~gi~Ei~Rt 67 (75)
T PF10369_consen 5 ALIKVKA-TPENRSEILQLAEIFRA-RIVDVSPDSIIIELTGTPEKIDAFIKLLKPFGILEIART 67 (75)
T ss_dssp EEEEEE--SCHHHHHHHHHHHHTT--EEEEEETTEEEEEEEE-HHHHHHHHHHSTGGGEEEEEEE
T ss_pred EEEEEEC-CccCHHHHHHHHHHhCC-EEEEECCCEEEEEEcCCHHHHHHHHHHhhhcCCEEEEcc
Confidence 4567765 45677788888888755 55555555545666787 455567788888777776643
No 107
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=22.57 E-value=1.8e+02 Score=18.97 Aligned_cols=23 Identities=9% Similarity=0.137 Sum_probs=14.5
Q ss_pred chhhHHHHHHHHhCCCCccEEEe
Q 033568 12 DKKARTKVLKTMVGLAGVDTASM 34 (116)
Q Consensus 12 C~~C~~kv~k~ls~l~GV~sV~v 34 (116)
.++.-..+.+.|.++..|..|++
T Consensus 53 ~~~~i~ql~kQL~KL~dV~~V~~ 75 (76)
T PRK11152 53 SERPIDLLSSQLNKLVDVAHVEI 75 (76)
T ss_pred CCchHHHHHHHHhcCcCeEEEEE
Confidence 46666666666666666666654
No 108
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=22.43 E-value=1.5e+02 Score=21.58 Aligned_cols=22 Identities=14% Similarity=0.283 Sum_probs=19.9
Q ss_pred CCCeEEEEeeCCHHHHHHHHHh
Q 033568 37 KEKKLTVIGDIDLVSLVSKLKK 58 (116)
Q Consensus 37 ~~~kvtV~G~vDp~~lv~~LrK 58 (116)
+++++++.|.+++..|-+.|++
T Consensus 76 ~~~~lii~G~~~~~~i~~~L~~ 97 (138)
T PRK03988 76 EGGRLILQGKFSPRVINEKIDR 97 (138)
T ss_pred cCCEEEEEEeeCHHHHHHHHHH
Confidence 3589999999999999999987
No 109
>PF13200 DUF4015: Putative glycosyl hydrolase domain
Probab=22.36 E-value=3.1e+02 Score=22.62 Aligned_cols=54 Identities=30% Similarity=0.306 Sum_probs=40.1
Q ss_pred HHHHHHHHhCCCCccEEEeeCCC--CeEEEE---------e----e-CCHHHHHHHHHhcC---CeEEEeeCCC
Q 033568 16 RTKVLKTMVGLAGVDTASMDEKE--KKLTVI---------G----D-IDLVSLVSKLKKLC---HAEIVSVGPA 70 (116)
Q Consensus 16 ~~kv~k~ls~l~GV~sV~vD~~~--~kvtV~---------G----~-vDp~~lv~~LrK~g---~aeivsv~p~ 70 (116)
..++.+.+.+. |+.+|.+|+++ +.|+-. | . .|+..|++.|++-| .|.|+...+.
T Consensus 15 ~~~~~~~i~~t-~lNavVIDvKdd~G~i~y~s~~~~~~~~ga~~~~i~D~~~l~~~l~e~gIY~IARIv~FkD~ 87 (316)
T PF13200_consen 15 LDKLLDLIKRT-ELNAVVIDVKDDDGNITYDSQVPLAREIGAVKPYIKDLKALVKKLKEHGIYPIARIVVFKDP 87 (316)
T ss_pred HHHHHHHHHhc-CCceEEEEEecCCceEEecCCCchhhhcccccccccCHHHHHHHHHHCCCEEEEEEEEecCh
Confidence 34455555444 99999999976 577762 2 2 59999999999877 8999988654
No 110
>cd04920 ACT_AKiii-DAPDC_2 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC). This CD includes the second of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.94 E-value=1.9e+02 Score=17.34 Aligned_cols=49 Identities=16% Similarity=0.138 Sum_probs=35.5
Q ss_pred ec-cchhhHHHHHHHHhCCCCccEEEeeCCCCeEEE-EeeCCHHHHHHHHHh
Q 033568 9 GV-DDKKARTKVLKTMVGLAGVDTASMDEKEKKLTV-IGDIDLVSLVSKLKK 58 (116)
Q Consensus 9 ~m-~C~~C~~kv~k~ls~l~GV~sV~vD~~~~kvtV-~G~vDp~~lv~~LrK 58 (116)
+| ...+...++.++|++. ||.-+.....+..+++ +-+-|...++.+|.+
T Consensus 9 g~~~~~gv~~~~~~~L~~~-~i~~i~~~~s~~~is~vv~~~d~~~av~~LH~ 59 (63)
T cd04920 9 GIRSLLHKLGPALEVFGKK-PVHLVSQAANDLNLTFVVDEDQADGLCARLHF 59 (63)
T ss_pred CcccCccHHHHHHHHHhcC-CceEEEEeCCCCeEEEEEeHHHHHHHHHHHHH
Confidence 45 4567889999999885 8999988888777754 344566666666643
No 111
>PF05309 TraE: TraE protein; InterPro: IPR007973 This family consists of several bacterial sex pilus assembly and synthesis proteins (TraE). Conjugal transfer of plasmids from donor to recipient cells is a complex process in which a cell-to-cell contact plays a key role. Many genes encoded by self-transmissible plasmids are required for various processes of conjugation, including pilus formation, stabilisation of mating pairs, conjugative DNA metabolism, surface exclusion and regulation of transfer gene expression []. The exact function of the TraE protein is unknown.; GO: 0000746 conjugation
Probab=21.89 E-value=1e+02 Score=22.80 Aligned_cols=18 Identities=17% Similarity=0.252 Sum_probs=16.0
Q ss_pred ccEEEeeCCCCeEEEEee
Q 033568 29 VDTASMDEKEKKLTVIGD 46 (116)
Q Consensus 29 V~sV~vD~~~~kvtV~G~ 46 (116)
++++.+|+.++++.|.|+
T Consensus 130 ~~~i~~d~~~~~V~V~G~ 147 (187)
T PF05309_consen 130 PKSIEVDPETLTVFVTGT 147 (187)
T ss_pred EeEEEEecCCCEEEEEEE
Confidence 567899999999999996
No 112
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=21.44 E-value=1.5e+02 Score=21.46 Aligned_cols=21 Identities=14% Similarity=0.279 Sum_probs=19.3
Q ss_pred CCeEEEEeeCCHHHHHHHHHh
Q 033568 38 EKKLTVIGDIDLVSLVSKLKK 58 (116)
Q Consensus 38 ~~kvtV~G~vDp~~lv~~LrK 58 (116)
++++++.|.+++..|-+.|++
T Consensus 72 ~~rlii~G~~~~~~i~~~L~~ 92 (133)
T TIGR00311 72 GGRLILQGKFTHFLLNERIED 92 (133)
T ss_pred CCEEEEEeecCHHHHHHHHHH
Confidence 579999999999999999987
No 113
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=21.38 E-value=1.9e+02 Score=27.23 Aligned_cols=43 Identities=14% Similarity=0.200 Sum_probs=31.5
Q ss_pred HHHHHHHHhCCCCccEEEeeCCCC-eEEEEe--------eCCHHHHHHHHHh
Q 033568 16 RTKVLKTMVGLAGVDTASMDEKEK-KLTVIG--------DIDLVSLVSKLKK 58 (116)
Q Consensus 16 ~~kv~k~ls~l~GV~sV~vD~~~~-kvtV~G--------~vDp~~lv~~LrK 58 (116)
...++..|.+++||.+|.+..... .+.|.= .+.+.+|..+|+.
T Consensus 159 ~~~l~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~ 210 (1025)
T PRK10614 159 STQLAQTISQIDGVGDVDVGGSSLPAVRVGLNPQALFNQGVSLDDVRQAISN 210 (1025)
T ss_pred HHHHHHHhcCCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHH
Confidence 457899999999999999987543 555541 1566677777774
No 114
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=21.10 E-value=1.1e+02 Score=22.75 Aligned_cols=66 Identities=20% Similarity=0.343 Sum_probs=36.4
Q ss_pred eEEEEEEeccch-hhHHHHHHHHhCCC-CccEE----EeeCCCC-eEEEE--e-eCCHHHHHHHHHhcC---CeEEEee
Q 033568 2 KKAVFKVGVDDK-KARTKVLKTMVGLA-GVDTA----SMDEKEK-KLTVI--G-DIDLVSLVSKLKKLC---HAEIVSV 67 (116)
Q Consensus 2 ~kvvlKV~m~C~-~C~~kv~k~ls~l~-GV~sV----~vD~~~~-kvtV~--G-~vDp~~lv~~LrK~g---~aeivsv 67 (116)
+.++|.+.+.+- |--..++.++++.. .|-+| -++...+ ++++. | +-|...|+++||++- .++|++.
T Consensus 71 ri~TL~l~ledr~G~LS~vLd~iA~~~~nvLTI~Q~ipl~g~Anvtlsi~~ssm~~~V~~ii~kl~k~e~V~kVeivgs 149 (150)
T COG4492 71 RIITLSLSLEDRVGILSDVLDVIAREEINVLTIHQTIPLQGRANVTLSIDTSSMEKDVDKIIEKLRKVEGVEKVEIVGS 149 (150)
T ss_pred eEEEEEEEEhhhhhhHHHHHHHHHHhCCcEEEEecccccCceeeEEEEEEchhhhhhHHHHHHHHhcccceeEEEEeec
Confidence 345666666553 45567777777653 22222 2222221 22221 1 258889999999954 6777653
No 115
>PRK08577 hypothetical protein; Provisional
Probab=21.00 E-value=2.2e+02 Score=19.82 Aligned_cols=19 Identities=11% Similarity=0.157 Sum_probs=10.2
Q ss_pred HHHHHHHHhCCCCccEEEe
Q 033568 16 RTKVLKTMVGLAGVDTASM 34 (116)
Q Consensus 16 ~~kv~k~ls~l~GV~sV~v 34 (116)
-..+++.|.+++||.+|.+
T Consensus 113 l~~l~~~L~~l~~V~~V~~ 131 (136)
T PRK08577 113 LEELEEELKKLEEVKEVEI 131 (136)
T ss_pred HHHHHHHHHcCCCEEEEEE
Confidence 3455555555555555543
No 116
>PF05188 MutS_II: MutS domain II; InterPro: IPR007860 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the connector domain (domain 2) found in proteins of the MutS family. The structure of the MutS connector domain consists of a parallel beta-sheet surrounded by four alpha helices, which is similar to the structure of the Holliday junction resolvase ruvC.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2O8F_A 3THW_A 3THX_A 2O8C_A 3THY_A 2O8E_A 2O8B_A 3THZ_A 2O8D_A 2WTU_A ....
Probab=20.99 E-value=2.6e+02 Score=18.46 Aligned_cols=39 Identities=26% Similarity=0.178 Sum_probs=31.3
Q ss_pred EEeeCCCCeEEEEeeCCHHHHHHHHHhcCCeEEEeeCCC
Q 033568 32 ASMDEKEKKLTVIGDIDLVSLVSKLKKLCHAEIVSVGPA 70 (116)
Q Consensus 32 V~vD~~~~kvtV~G~vDp~~lv~~LrK~g~aeivsv~p~ 70 (116)
+-+|...+.+.+.---|...|...|.+....||+-....
T Consensus 18 a~~D~sTGe~~~~~~~d~~~L~~~L~~~~P~EIi~~~~~ 56 (137)
T PF05188_consen 18 AYIDLSTGEFYVTEFEDYSELKSELARLSPREIIIPEGF 56 (137)
T ss_dssp EEEETTTTEEEEEEEECHHHHHHHHHHH-ESEEEEETTC
T ss_pred EEEECCCCEEEEEEeCCHHHHHHHHHhcCCeEEEEcCCC
Confidence 556889999998776678999999999999999966544
No 117
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=20.66 E-value=1.2e+02 Score=18.92 Aligned_cols=12 Identities=0% Similarity=-0.272 Sum_probs=9.3
Q ss_pred EEEEEeccchhhH
Q 033568 4 AVFKVGVDDKKAR 16 (116)
Q Consensus 4 vvlKV~m~C~~C~ 16 (116)
|.+ ++..|..|.
T Consensus 3 I~v-~~~~C~~C~ 14 (76)
T PF13192_consen 3 IKV-FSPGCPYCP 14 (76)
T ss_dssp EEE-ECSSCTTHH
T ss_pred EEE-eCCCCCCcH
Confidence 455 688899997
No 118
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=20.52 E-value=1.8e+02 Score=18.76 Aligned_cols=22 Identities=14% Similarity=0.182 Sum_probs=17.7
Q ss_pred CCCeEEEEeeCCHHHHHHHHHh
Q 033568 37 KEKKLTVIGDIDLVSLVSKLKK 58 (116)
Q Consensus 37 ~~~kvtV~G~vDp~~lv~~LrK 58 (116)
.+++++++|.-++..+..++++
T Consensus 56 ~sGki~itGaks~~~~~~a~~~ 77 (86)
T PF00352_consen 56 SSGKIVITGAKSEEEAKKAIEK 77 (86)
T ss_dssp TTSEEEEEEESSHHHHHHHHHH
T ss_pred cCCEEEEEecCCHHHHHHHHHH
Confidence 5689999998788877777765
No 119
>PRK03359 putative electron transfer flavoprotein FixA; Reviewed
Probab=20.41 E-value=1.8e+02 Score=23.17 Aligned_cols=44 Identities=18% Similarity=0.280 Sum_probs=32.0
Q ss_pred CCccEEEeeCCCCeEE------EEeeCCHHHHHHHHH-h--c--CCeEEEeeCCC
Q 033568 27 AGVDTASMDEKEKKLT------VIGDIDLVSLVSKLK-K--L--CHAEIVSVGPA 70 (116)
Q Consensus 27 ~GV~sV~vD~~~~kvt------V~G~vDp~~lv~~Lr-K--~--g~aeivsv~p~ 70 (116)
+-..++.+|..++++. +....|...|-.+|| | . |.+..+|+||+
T Consensus 11 PD~~~~~~~~~~~~l~r~~~~~~iN~~D~~AlE~Alrlke~~~g~~Vtvvs~Gp~ 65 (256)
T PRK03359 11 PDEQDIAVNNADGSLDFSKADAKISQYDLNAIEAACQLKQQAAEAQVTALSVGGK 65 (256)
T ss_pred cCCcceEEeCCCCeEEcCCCccccChhhHHHHHHHHHHhhhcCCCEEEEEEECCc
Confidence 3345677776666655 445678888999988 4 3 38999999998
No 120
>PRK15078 polysaccharide export protein Wza; Provisional
Probab=20.20 E-value=2.6e+02 Score=23.39 Aligned_cols=56 Identities=11% Similarity=0.239 Sum_probs=40.2
Q ss_pred EEEE-eccchhhHHHHHHHHhCCCCccEEEeeC---CCCeEEEEeeC---------C-HHHHHHHHHhcC
Q 033568 5 VFKV-GVDDKKARTKVLKTMVGLAGVDTASMDE---KEKKLTVIGDI---------D-LVSLVSKLKKLC 60 (116)
Q Consensus 5 vlKV-~m~C~~C~~kv~k~ls~l~GV~sV~vD~---~~~kvtV~G~v---------D-p~~lv~~LrK~g 60 (116)
.++| +++-+.-++.+.+.|++.--=-.|.+.. .+++++|.|+| + +..|+++|...|
T Consensus 133 ~V~vaG~T~~e~~~~I~~~L~~~~~~PqV~V~v~~~~s~~V~V~GeV~~PG~~~l~~~~~tlldaIa~AG 202 (379)
T PRK15078 133 KVHVAGKTVTEIRSDITGRLAKYIESPQVDVNIAAFRSQKAYVTGEVNKSGQQAITNVPLTILDAINAAG 202 (379)
T ss_pred eEEECCCCHHHHHHHHHHHHHHhccCCeEEEEEccCCceEEEEEceecCCeEEEecCCCccHHHHHHHcc
Confidence 3677 8888889999999998753222344444 34689999964 2 578999998865
Done!