Query 033712
Match_columns 113
No_of_seqs 147 out of 742
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 05:25:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033712.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033712hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1603 Copper chaperone [Inor 99.6 4.3E-15 9.4E-20 95.8 7.2 58 1-60 13-71 (73)
2 PF00403 HMA: Heavy-metal-asso 99.2 1.4E-10 3.1E-15 71.3 7.2 51 1-54 7-60 (62)
3 COG2608 CopZ Copper chaperone 98.5 3.8E-07 8.2E-12 58.5 6.5 52 1-54 11-64 (71)
4 KOG4656 Copper chaperone for s 98.2 5.1E-06 1.1E-10 64.1 6.2 59 1-62 15-74 (247)
5 PLN02957 copper, zinc superoxi 97.6 0.00038 8.2E-09 53.8 8.3 62 1-65 14-76 (238)
6 PRK10671 copA copper exporting 96.9 0.002 4.4E-08 57.3 6.1 55 1-60 12-67 (834)
7 TIGR00003 copper ion binding p 94.6 0.27 5.8E-06 26.8 6.2 49 1-50 11-61 (68)
8 COG2217 ZntA Cation transport 93.4 0.21 4.6E-06 44.5 6.1 55 1-58 11-69 (713)
9 PRK10671 copA copper exporting 92.4 0.38 8.2E-06 43.1 6.3 56 1-59 108-164 (834)
10 PF02680 DUF211: Uncharacteriz 91.0 0.65 1.4E-05 31.7 4.8 51 9-61 21-77 (95)
11 COG1888 Uncharacterized protei 89.8 1.1 2.4E-05 30.6 5.1 44 10-54 24-73 (97)
12 KOG0207 Cation transport ATPas 89.1 1.1 2.3E-05 41.3 6.0 59 1-61 3-63 (951)
13 PRK11033 zntA zinc/cadmium/mer 82.4 4.6 0.0001 36.0 6.5 51 1-54 62-113 (741)
14 KOG0207 Cation transport ATPas 82.0 3.1 6.8E-05 38.4 5.4 58 1-60 155-215 (951)
15 PRK10553 assembly protein for 72.3 23 0.00049 23.6 6.2 43 7-50 19-61 (87)
16 PF03927 NapD: NapD protein; 70.8 25 0.00055 22.6 6.4 43 7-51 17-59 (79)
17 cd04910 ACT_AK-Ectoine_1 ACT d 70.7 15 0.00032 23.5 4.8 52 6-58 17-69 (71)
18 PF13732 DUF4162: Domain of un 68.4 19 0.00041 22.5 5.0 39 13-52 25-63 (84)
19 PF08712 Nfu_N: Scaffold prote 62.9 37 0.00081 22.2 5.8 41 9-52 38-79 (87)
20 cd04888 ACT_PheB-BS C-terminal 62.7 9.5 0.00021 23.0 2.7 20 6-25 55-74 (76)
21 PF01883 DUF59: Domain of unkn 60.0 12 0.00025 23.1 2.8 20 6-25 53-72 (72)
22 PF04972 BON: BON domain; Int 59.6 5.9 0.00013 23.6 1.3 35 9-46 3-40 (64)
23 COG1432 Uncharacterized conser 54.2 18 0.0004 26.7 3.4 31 32-63 114-144 (181)
24 PHA00514 dsDNA binding protein 51.6 24 0.00053 23.9 3.3 33 31-64 32-66 (98)
25 PF14492 EFG_II: Elongation Fa 50.5 56 0.0012 20.5 4.9 48 9-57 23-72 (75)
26 cd06167 LabA_like LabA_like pr 49.3 26 0.00057 24.0 3.4 30 32-62 103-132 (149)
27 PF09358 UBA_e1_C: Ubiquitin-a 48.9 29 0.00062 24.3 3.6 32 31-63 35-67 (125)
28 TIGR00288 conserved hypothetic 48.0 27 0.00059 25.8 3.5 29 32-61 109-137 (160)
29 COG3062 NapD Uncharacterized p 47.7 79 0.0017 21.6 5.4 42 7-50 20-61 (94)
30 PF05137 PilN: Fimbrial assemb 47.1 61 0.0013 19.6 4.6 40 20-62 16-60 (78)
31 PF07683 CobW_C: Cobalamin syn 46.4 24 0.00052 22.4 2.7 23 29-51 70-92 (94)
32 PRK09577 multidrug efflux prot 46.1 41 0.0009 31.2 5.0 45 7-52 158-209 (1032)
33 PRK10555 aminoglycoside/multid 45.2 45 0.00098 31.0 5.2 45 7-52 159-210 (1037)
34 KOG3411 40S ribosomal protein 45.2 21 0.00045 26.0 2.4 43 5-51 98-140 (143)
35 PF05193 Peptidase_M16_C: Pept 45.1 26 0.00056 23.6 2.8 23 31-54 20-42 (184)
36 PF12164 SporV_AA: Stage V spo 42.9 53 0.0011 21.9 4.0 49 9-65 34-82 (93)
37 TIGR00915 2A0602 The (Largely 42.6 50 0.0011 30.7 5.0 44 7-51 159-209 (1044)
38 PRK11023 outer membrane lipopr 42.2 56 0.0012 24.3 4.5 43 5-49 49-94 (191)
39 smart00653 eIF2B_5 domain pres 42.1 48 0.001 22.9 3.8 28 23-53 50-77 (110)
40 COG3643 Glutamate formiminotra 41.9 51 0.0011 26.6 4.3 41 8-51 21-64 (302)
41 PRK15127 multidrug efflux syst 41.6 52 0.0011 30.7 4.9 44 7-51 159-209 (1049)
42 PF01253 SUI1: Translation ini 41.3 36 0.00077 21.8 2.9 30 30-59 17-51 (83)
43 PF01936 NYN: NYN domain; Int 40.9 35 0.00075 22.9 2.9 29 32-61 99-127 (146)
44 PRK11023 outer membrane lipopr 40.1 68 0.0015 23.8 4.6 44 5-54 89-137 (191)
45 cd04877 ACT_TyrR N-terminal AC 40.0 30 0.00066 21.2 2.4 17 8-24 52-68 (74)
46 PF07338 DUF1471: Protein of u 38.9 45 0.00098 20.1 2.9 23 31-53 6-28 (56)
47 PRK10503 multidrug efflux syst 38.4 64 0.0014 30.0 5.0 44 8-51 169-219 (1040)
48 cd00474 SUI1_eIF1 The SUI1/eIF 38.2 54 0.0012 21.1 3.4 28 31-58 13-45 (77)
49 PF00873 ACR_tran: AcrB/AcrD/A 36.2 46 0.001 30.6 3.7 46 7-52 158-210 (1021)
50 PRK04021 hypothetical protein; 36.1 98 0.0021 20.7 4.5 44 5-50 46-91 (92)
51 PRK10614 multidrug efflux syst 35.4 78 0.0017 29.4 5.1 46 7-52 159-211 (1025)
52 smart00833 CobW_C Cobalamin sy 35.2 57 0.0012 20.3 3.1 22 30-51 69-90 (92)
53 cd04879 ACT_3PGDH-like ACT_3PG 34.9 51 0.0011 18.7 2.7 18 8-25 53-70 (71)
54 PRK00378 nucleoid-associated p 34.2 47 0.001 26.5 3.1 29 21-53 303-331 (334)
55 PF08478 POTRA_1: POTRA domain 33.6 42 0.00092 20.0 2.2 29 8-36 37-65 (69)
56 PRK09579 multidrug efflux prot 33.5 1.2E+02 0.0025 28.3 5.9 46 7-52 158-210 (1017)
57 TIGR00489 aEF-1_beta translati 33.1 43 0.00094 22.3 2.3 22 6-27 63-84 (88)
58 COG0841 AcrB Cation/multidrug 32.9 88 0.0019 29.4 5.0 45 7-51 157-208 (1009)
59 PRK00939 translation initiatio 32.9 85 0.0018 21.2 3.8 41 18-58 23-69 (99)
60 cd00371 HMA Heavy-metal-associ 32.9 60 0.0013 15.1 6.5 49 1-50 7-56 (63)
61 PRK13748 putative mercuric red 32.3 2E+02 0.0044 24.1 6.8 59 1-61 9-69 (561)
62 TIGR02052 MerP mercuric transp 31.5 1.1E+02 0.0025 17.9 6.9 49 1-50 32-82 (92)
63 PF05922 Inhibitor_I9: Peptida 30.7 70 0.0015 19.4 2.9 19 9-27 59-77 (82)
64 PF01424 R3H: R3H domain; Int 30.3 1.2E+02 0.0026 17.9 4.1 30 7-36 32-61 (63)
65 cd04901 ACT_3PGDH C-terminal A 29.7 70 0.0015 18.6 2.7 18 8-25 51-68 (69)
66 PRK11198 LysM domain/BON super 29.6 1.8E+02 0.0039 20.6 5.3 50 5-57 26-77 (147)
67 PF02107 FlgH: Flagellar L-rin 29.2 41 0.0009 24.9 1.9 29 16-46 110-138 (179)
68 cd07422 MPP_ApaH Escherichia c 28.6 1.6E+02 0.0034 23.0 5.2 40 5-51 9-52 (257)
69 COG0612 PqqL Predicted Zn-depe 27.9 59 0.0013 26.4 2.8 24 30-54 198-221 (438)
70 TIGR01158 SUI1_rel translation 27.7 1.9E+02 0.0042 19.5 4.9 40 18-57 23-69 (101)
71 cd02643 R3H_NF-X1 R3H domain o 27.7 1.4E+02 0.003 18.9 4.0 30 7-36 44-73 (74)
72 PF13241 NAD_binding_7: Putati 27.6 1.1E+02 0.0024 20.0 3.6 38 24-63 2-40 (103)
73 PF03958 Secretin_N: Bacterial 27.3 1.1E+02 0.0025 18.6 3.5 26 22-48 47-72 (82)
74 PLN02625 uroporphyrin-III C-me 27.3 87 0.0019 24.1 3.5 33 29-61 13-46 (263)
75 PF14437 MafB19-deam: MafB19-l 27.1 1.1E+02 0.0023 22.5 3.7 32 2-34 110-141 (146)
76 cd04903 ACT_LSD C-terminal ACT 27.0 78 0.0017 18.0 2.6 18 8-25 53-70 (71)
77 PF15235 GRIN_C: G protein-reg 26.8 98 0.0021 22.5 3.4 32 18-51 42-74 (137)
78 PRK09019 translation initiatio 26.1 1.6E+02 0.0035 20.4 4.3 40 14-54 26-72 (108)
79 PRK10568 periplasmic protein; 26.0 2E+02 0.0044 21.5 5.2 36 5-42 60-97 (203)
80 TIGR02945 SUF_assoc FeS assemb 26.0 77 0.0017 20.6 2.6 21 7-27 57-77 (99)
81 PF02983 Pro_Al_protease: Alph 25.9 1.6E+02 0.0035 17.9 4.5 23 15-38 20-42 (62)
82 PRK00435 ef1B elongation facto 25.9 66 0.0014 21.4 2.3 23 5-27 62-84 (88)
83 PF01873 eIF-5_eIF-2B: Domain 25.8 77 0.0017 22.3 2.7 37 13-53 54-90 (125)
84 PF10262 Rdx: Rdx family; Int 25.6 1.3E+02 0.0029 18.7 3.6 12 40-51 64-75 (76)
85 COG4004 Uncharacterized protei 25.1 1.2E+02 0.0026 20.7 3.4 24 13-37 35-58 (96)
86 PF01849 NAC: NAC domain; Int 25.0 1E+02 0.0022 18.4 2.8 30 8-38 2-36 (58)
87 KOG3476 Microtubule-associated 25.0 34 0.00073 23.3 0.7 20 1-24 1-20 (100)
88 TIGR00914 2A0601 heavy metal e 24.2 1.4E+02 0.003 27.8 4.7 38 7-47 168-205 (1051)
89 cd03309 CmuC_like CmuC_like. P 24.0 80 0.0017 25.4 2.8 25 2-27 218-242 (321)
90 cd06471 ACD_LpsHSP_like Group 24.0 51 0.0011 21.0 1.4 22 16-38 17-40 (93)
91 PF07744 SPOC: SPOC domain; I 23.8 98 0.0021 20.3 2.9 21 30-51 38-58 (119)
92 cd04878 ACT_AHAS N-terminal AC 23.6 72 0.0016 18.2 2.0 17 8-24 56-72 (72)
93 COG2092 EFB1 Translation elong 23.6 73 0.0016 21.5 2.1 20 7-26 64-83 (88)
94 KOG3166 60S ribosomal protein 23.2 52 0.0011 25.5 1.5 32 18-49 112-144 (209)
95 PF14847 Ras_bdg_2: Ras-bindin 22.5 56 0.0012 22.4 1.5 26 29-55 11-36 (105)
96 PRK03988 translation initiatio 22.5 1.2E+02 0.0026 21.7 3.2 23 31-54 78-100 (138)
97 COG1992 Uncharacterized conser 22.4 2.3E+02 0.0049 21.5 4.8 39 10-50 133-175 (181)
98 PRK06136 uroporphyrin-III C-me 22.3 1.3E+02 0.0027 22.6 3.5 31 31-61 3-34 (249)
99 PRK00166 apaH diadenosine tetr 22.2 2.1E+02 0.0045 22.6 4.8 40 5-51 11-54 (275)
100 TIGR00668 apaH bis(5'-nucleosy 21.9 2.4E+02 0.0052 22.6 5.1 40 5-51 11-54 (279)
101 cd04920 ACT_AKiii-DAPDC_2 ACT 21.4 1.9E+02 0.0042 17.1 5.4 48 3-52 13-60 (63)
102 PRK15039 transcriptional repre 21.0 54 0.0012 21.9 1.1 18 2-19 3-20 (90)
103 PRK11439 pphA serine/threonine 20.9 1.3E+02 0.0029 22.3 3.4 41 5-52 27-71 (218)
104 PF00013 KH_1: KH domain syndr 20.8 1.8E+02 0.0039 16.8 3.3 36 11-50 22-58 (60)
105 PRK06719 precorrin-2 dehydroge 20.8 1.8E+02 0.0039 20.7 3.9 39 22-61 6-44 (157)
106 PRK13625 bis(5'-nucleosyl)-tet 20.7 1.8E+02 0.0038 22.2 4.0 46 5-51 11-62 (245)
107 smart00749 BON bacterial OsmY 20.7 1.7E+02 0.0037 16.2 4.3 40 8-49 2-43 (62)
108 PF12971 NAGLU_N: Alpha-N-acet 20.2 2.5E+02 0.0054 18.1 4.2 38 19-58 30-70 (86)
No 1
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.59 E-value=4.3e-15 Score=95.85 Aligned_cols=58 Identities=41% Similarity=0.606 Sum_probs=53.1
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHHHHHhhcC-ceeEEe
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQKKLG-FASLLS 60 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~LrKk~~-~aeivs 60 (113)
|||+||+++|++.+.+++||.++.+|. .+++|||.|. +||..|+++|+|.++ .+++|.
T Consensus 13 ~~C~gc~~kV~~~l~~~~GV~~v~id~-~~~kvtV~g~-~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 13 MHCEGCARKVKRVLQKLKGVESVDIDI-KKQKVTVKGN-VDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred cccccHHHHHHHHhhccCCeEEEEecC-CCCEEEEEEe-cCHHHHHHHHHhcCCCceEEec
Confidence 899999999999999999999999999 7799999999 999999999998664 566653
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=99.18 E-value=1.4e-10 Score=71.29 Aligned_cols=51 Identities=31% Similarity=0.453 Sum_probs=46.7
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeeccCH---HHHHHHHHhhcC
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEVDS---VKLTRKLQKKLG 54 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp---~~l~~~LrKk~~ 54 (113)
|+|++|+++|.++|.+++||.++.+|. .+++++|.++ .+. ..|.++|++ .|
T Consensus 7 m~C~~C~~~v~~~l~~~~GV~~v~vd~-~~~~v~v~~~-~~~~~~~~i~~~i~~-~G 60 (62)
T PF00403_consen 7 MTCEGCAKKVEKALSKLPGVKSVKVDL-ETKTVTVTYD-PDKTSIEKIIEAIEK-AG 60 (62)
T ss_dssp TTSHHHHHHHHHHHHTSTTEEEEEEET-TTTEEEEEES-TTTSCHHHHHHHHHH-TT
T ss_pred cccHHHHHHHHHHHhcCCCCcEEEEEC-CCCEEEEEEe-cCCCCHHHHHHHHHH-hC
Confidence 899999999999999999999999999 7899999999 554 999999986 55
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.54 E-value=3.8e-07 Score=58.45 Aligned_cols=52 Identities=29% Similarity=0.457 Sum_probs=45.0
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCC--eEEEEeeccCHHHHHHHHHhhcC
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKD--ELVVIGNEVDSVKLTRKLQKKLG 54 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~--kvtV~G~~vDp~~l~~~LrKk~~ 54 (113)
|+|++|..++.++|.+++||.+|.++. +++ .|++.+..++...|.+.+.. .|
T Consensus 11 MtC~~C~~~V~~al~~v~gv~~v~v~l-~~~~~~V~~d~~~~~~~~i~~ai~~-aG 64 (71)
T COG2608 11 MTCGHCVKTVEKALEEVDGVASVDVDL-EKGTATVTFDSNKVDIEAIIEAIED-AG 64 (71)
T ss_pred cCcHHHHHHHHHHHhcCCCeeEEEEEc-ccCeEEEEEcCCcCCHHHHHHHHHH-cC
Confidence 899999999999999999999999999 664 55555634899999999986 66
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.17 E-value=5.1e-06 Score=64.14 Aligned_cols=59 Identities=22% Similarity=0.295 Sum_probs=52.9
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHHHHHhhcC-ceeEEecC
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQKKLG-FASLLSVQ 62 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~LrKk~~-~aeivsv~ 62 (113)
|||+.|...+++.|..++||++|++|. +++.|.|.+. +-+..+...|+. +| .|.|.-.+
T Consensus 15 M~cescvnavk~~L~~V~Gi~~vevdl-e~q~v~v~ts-~p~s~i~~~le~-tGr~Avl~G~G 74 (247)
T KOG4656|consen 15 MTCESCVNAVKACLKGVPGINSVEVDL-EQQIVSVETS-VPPSEIQNTLEN-TGRDAVLRGAG 74 (247)
T ss_pred chhHHHHHHHHHHhccCCCcceEEEEh-hhcEEEEEcc-CChHHHHHHHHh-hChheEEecCC
Confidence 899999999999999999999999999 7788888888 999999999996 77 77766444
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=97.62 E-value=0.00038 Score=53.80 Aligned_cols=62 Identities=23% Similarity=0.362 Sum_probs=54.5
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHHHHHhhcC-ceeEEecCCCc
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQKKLG-FASLLSVQEEK 65 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~LrKk~~-~aeivsv~~~k 65 (113)
|+|+.|..++.+.|.+++||.++.++. ..++++|.+. +++..++..|.+ .+ .+++++.+...
T Consensus 14 MsC~~Ca~~Iek~L~~~~GV~~v~vn~-~~~~v~V~~~-~~~~~I~~aIe~-~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 14 MKCEGCVAAVKNKLETLEGVKAVEVDL-SNQVVRVLGS-SPVKAMTAALEQ-TGRKARLIGQGDPE 76 (238)
T ss_pred ccCHHHHHHHHHHHhcCCCeEEEEEEc-CCCEEEEEec-CCHHHHHHHHHH-cCCcEEEecCCCcc
Confidence 789999999999999999999999998 7789999997 899999999985 66 68888776554
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.92 E-value=0.002 Score=57.30 Aligned_cols=55 Identities=20% Similarity=0.329 Sum_probs=48.5
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHHHHHhhcC-ceeEEe
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQKKLG-FASLLS 60 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~LrKk~~-~aeivs 60 (113)
|+|..|.+++.+.|.+++||.++.++. ++.+|.+. .++..+...+.. .| .+++.+
T Consensus 12 mtC~~C~~~i~~al~~~~gv~~v~v~~---~~~~v~~~-~~~~~i~~~i~~-~Gy~~~~~~ 67 (834)
T PRK10671 12 LSCGHCVKRVKESLEQRPDVEQADVSI---TEAHVTGT-ASAEALIETIKQ-AGYDASVSH 67 (834)
T ss_pred cccHHHHHHHHHHHhcCCCcceEEEee---eEEEEEec-CCHHHHHHHHHh-cCCcccccc
Confidence 899999999999999999999999997 36677787 899999999985 67 787764
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=94.62 E-value=0.27 Score=26.83 Aligned_cols=49 Identities=27% Similarity=0.409 Sum_probs=38.6
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEee--ccCHHHHHHHHH
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGN--EVDSVKLTRKLQ 50 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~--~vDp~~l~~~Lr 50 (113)
|+|..|...+.+.+....|+.+..++. ....+++..+ ..+...+...+.
T Consensus 11 ~~~~~c~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 61 (68)
T TIGR00003 11 MTCQHCVDKIEKFVGELEGVSKVQVKL-EKASVKVEFDAPQATEICIAEAIL 61 (68)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEc-CCCEEEEEeCCCCCCHHHHHHHHH
Confidence 469999999999999999999999988 6677777642 246777766654
No 8
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=93.40 E-value=0.21 Score=44.53 Aligned_cols=55 Identities=27% Similarity=0.433 Sum_probs=46.7
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEee--ccC-HHHHHHHHHhhcC-ceeE
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGN--EVD-SVKLTRKLQKKLG-FASL 58 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~--~vD-p~~l~~~LrKk~~-~aei 58 (113)
|||..|..++. .|.+++||....++. ...+++|..+ ..+ +..+...+++ .| .+..
T Consensus 11 m~Ca~C~~~ie-~l~~~~gV~~~~vn~-~t~~~~v~~~~~~~~~~~~~~~~v~~-~gy~~~~ 69 (713)
T COG2217 11 MTCAACASRIE-ALNKLPGVEEARVNL-ATERATVVYDPEEVDLPADIVAAVEK-AGYSARL 69 (713)
T ss_pred cCcHHHHHHHH-HHhcCCCeeEEEeec-ccceEEEEecccccccHHHHHHHHHh-cCccccc
Confidence 89999999999 999999999999998 7789988875 256 7888999886 55 5544
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=92.38 E-value=0.38 Score=43.08 Aligned_cols=56 Identities=20% Similarity=0.404 Sum_probs=47.1
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHHHHHhhcC-ceeEE
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQKKLG-FASLL 59 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~LrKk~~-~aeiv 59 (113)
|+|..|...+.+.+.+++||.++.++. ..+++.+.+. .++..+.+.++. .| .+.++
T Consensus 108 m~Ca~Ca~~Ie~~L~~~~GV~~a~vnl-~t~~~~V~~~-~s~~~I~~~I~~-~Gy~a~~~ 164 (834)
T PRK10671 108 MSCASCVSRVQNALQSVPGVTQARVNL-AERTALVMGS-ASPQDLVQAVEK-AGYGAEAI 164 (834)
T ss_pred cCcHHHHHHHHHHHhcCCCceeeeeec-CCCeEEEEcc-CCHHHHHHHHHh-cCCCcccc
Confidence 799999999999999999999999998 6677888776 889998888875 66 55443
No 10
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=90.96 E-value=0.65 Score=31.74 Aligned_cols=51 Identities=22% Similarity=0.412 Sum_probs=35.8
Q ss_pred HHHHHHhcCCCeeEEEe-----cCCCCC-eEEEEeeccCHHHHHHHHHhhcCceeEEec
Q 033712 9 KAMKIAVKADGVIKVEI-----KGEGKD-ELVVIGNEVDSVKLTRKLQKKLGFASLLSV 61 (113)
Q Consensus 9 kv~k~l~~~~GV~sV~v-----d~~~k~-kvtV~G~~vDp~~l~~~LrKk~~~aeivsv 61 (113)
.+-+.|++++||..|.+ |.+-.+ ++||.|+.+|-..+.+.|.+ +| +.|=|+
T Consensus 21 e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~-~G-g~IHSI 77 (95)
T PF02680_consen 21 ELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEE-LG-GVIHSI 77 (95)
T ss_dssp HHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHH-TT--EEEEE
T ss_pred HHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHH-cC-CeEEee
Confidence 35678999999888765 432223 89999999999999999996 54 333344
No 11
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=89.75 E-value=1.1 Score=30.56 Aligned_cols=44 Identities=23% Similarity=0.353 Sum_probs=33.5
Q ss_pred HHHHHhcCCCeeEEEe-----cCCCCC-eEEEEeeccCHHHHHHHHHhhcC
Q 033712 10 AMKIAVKADGVIKVEI-----KGEGKD-ELVVIGNEVDSVKLTRKLQKKLG 54 (113)
Q Consensus 10 v~k~l~~~~GV~sV~v-----d~~~k~-kvtV~G~~vDp~~l~~~LrKk~~ 54 (113)
+-+.|++++||+.|-+ |.+-.+ ++||.|..+|-..|.+.|-+ +|
T Consensus 24 ~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~-~G 73 (97)
T COG1888 24 LALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEE-LG 73 (97)
T ss_pred HHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHH-cC
Confidence 4567888888776644 432233 99999999999999999986 54
No 12
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=89.14 E-value=1.1 Score=41.33 Aligned_cols=59 Identities=31% Similarity=0.422 Sum_probs=49.2
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCC-eEEEEeeccCHHHHHHHHHhhcC-ceeEEec
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKD-ELVVIGNEVDSVKLTRKLQKKLG-FASLLSV 61 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~-kvtV~G~~vDp~~l~~~LrKk~~-~aeivsv 61 (113)
|.|..|.+.+.+.+++.+||.++.+....+. +|.-. ..++++.+.+.+.- .| .+++++-
T Consensus 3 mtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~-~~~~~~~i~~~ied-~gf~~~~~~~ 63 (951)
T KOG0207|consen 3 MTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYD-NIVSPESIKETIED-MGFEASLLSD 63 (951)
T ss_pred ccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEe-eccCHHHHHHHhhc-ccceeeeccc
Confidence 7899999999999999999999999984333 67777 55899999999986 55 7887754
No 13
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=82.40 E-value=4.6 Score=36.01 Aligned_cols=51 Identities=25% Similarity=0.469 Sum_probs=38.4
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeec-cCHHHHHHHHHhhcC
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNE-VDSVKLTRKLQKKLG 54 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~-vDp~~l~~~LrKk~~ 54 (113)
|+|..|..++.+.+.+++||.++.++. ...++.+.-+. .+ ..+...++. .|
T Consensus 62 m~C~sCa~~Ie~aL~~~~GV~~v~Vn~-at~k~~V~~d~~~~-~~I~~aI~~-~G 113 (741)
T PRK11033 62 MDCPSCARKVENAVRQLAGVNQVQVLF-ATEKLVVDADNDIR-AQVESAVQK-AG 113 (741)
T ss_pred CCcHHHHHHHHHHHhcCCCeeeEEEEc-CCCeEEEEecccch-HHHHHHHHh-cc
Confidence 789999999999999999999999987 55677665431 22 455555553 55
No 14
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=82.03 E-value=3.1 Score=38.39 Aligned_cols=58 Identities=22% Similarity=0.355 Sum_probs=46.7
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEee--ccCHHHHHHHHHhhcC-ceeEEe
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGN--EVDSVKLTRKLQKKLG-FASLLS 60 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~--~vDp~~l~~~LrKk~~-~aeivs 60 (113)
|.|+.|..++.+.+.+++||.++.++. ..+++.|.=+ ..-|.++.+.|-. ++ .+.+..
T Consensus 155 ~~c~s~~~~ie~~l~~l~gV~~~sv~~-~t~~~~V~~~~~~~~pr~i~k~ie~-~~~~~~~~~ 215 (951)
T KOG0207|consen 155 MTCASCVSKIESILERLRGVKSFSVSL-ATDTAIVVYDPEITGPRDIIKAIEE-TGFEASVRP 215 (951)
T ss_pred ccccchhhhhHHHHhhccCeeEEEEec-cCCceEEEecccccChHHHHHHHHh-hcccceeee
Confidence 679999999999999999999999998 6788777655 3467888888875 45 555443
No 15
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=72.33 E-value=23 Score=23.56 Aligned_cols=43 Identities=14% Similarity=0.084 Sum_probs=32.9
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHHHHH
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQ 50 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~Lr 50 (113)
...+.+.|..++|++=-..|. +.+|++|+=++-+...+++.|.
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~-~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDA-PSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecC-CCCeEEEEEEeCChHHHHHHHH
Confidence 457889999999998887776 5688888877566666666655
No 16
>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=70.83 E-value=25 Score=22.62 Aligned_cols=43 Identities=12% Similarity=0.068 Sum_probs=33.9
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHHHHHh
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQK 51 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~LrK 51 (113)
...+.+.|..++||+=-..+. + +|++|+=+.-+...+++.|..
T Consensus 17 ~~~v~~~l~~~~gvEVh~~~~-~-GKiVVtiE~~~~~~~~~~~~~ 59 (79)
T PF03927_consen 17 LEEVAEALAAIPGVEVHAVDE-D-GKIVVTIEAESSEEEVDLIDA 59 (79)
T ss_dssp HHHHHHHHCCSTTEEEEEEET-T-TEEEEEEEESSHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCcEEEeeCC-C-CeEEEEEEeCChHHHHHHHHH
Confidence 357889999999997666664 3 899888886777888877764
No 17
>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=70.67 E-value=15 Score=23.53 Aligned_cols=52 Identities=12% Similarity=0.146 Sum_probs=36.8
Q ss_pred HHHHHHHHHhcCCCeeEEEecCCCCC-eEEEEeeccCHHHHHHHHHhhcCceeE
Q 033712 6 CRKKAMKIAVKADGVIKVEIKGEGKD-ELVVIGNEVDSVKLTRKLQKKLGFASL 58 (113)
Q Consensus 6 C~~kv~k~l~~~~GV~sV~vd~~~k~-kvtV~G~~vDp~~l~~~LrKk~~~aei 58 (113)
=..+++++|.+. +|.=|..+.+.+. +.-+.|..-+..+++..|.+.++.|+|
T Consensus 17 ~d~~i~~~l~~~-~v~ii~K~~nANtit~yl~~~~k~~~r~~~~Le~~~p~a~i 69 (71)
T cd04910 17 YDLEILELLQRF-KVSIIAKDTNANTITHYLAGSLKTIKRLTEDLENRFPNAEI 69 (71)
T ss_pred HHHHHHHHHHHc-CCeEEEEecCCCeEEEEEEcCHHHHHHHHHHHHHhCccCcc
Confidence 456788888877 6777777774433 555666633678899999888887775
No 18
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=68.40 E-value=19 Score=22.45 Aligned_cols=39 Identities=26% Similarity=0.286 Sum_probs=30.4
Q ss_pred HHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHHHHHhh
Q 033712 13 IAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQKK 52 (113)
Q Consensus 13 ~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~LrKk 52 (113)
.|..++||.++..+.+..-.+.+... .++..|++.|..+
T Consensus 25 ~l~~~~~v~~v~~~~~~~~~i~l~~~-~~~~~ll~~l~~~ 63 (84)
T PF13732_consen 25 ELEELPGVESVEQDGDGKLRIKLEDE-ETANELLQELIEK 63 (84)
T ss_pred HHhhCCCeEEEEEeCCcEEEEEECCc-ccHHHHHHHHHhC
Confidence 37788999999976522237888877 8999999999864
No 19
>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=62.91 E-value=37 Score=22.22 Aligned_cols=41 Identities=22% Similarity=0.212 Sum_probs=30.1
Q ss_pred HHHHHHhcCCCeeEEEecCCCCCeEEEEee-ccCHHHHHHHHHhh
Q 033712 9 KAMKIAVKADGVIKVEIKGEGKDELVVIGN-EVDSVKLTRKLQKK 52 (113)
Q Consensus 9 kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~-~vDp~~l~~~LrKk 52 (113)
-+-+.|-.++||.+|-+.. +=|||+-. .+|-..|...++.-
T Consensus 38 pLA~~Lf~i~gV~~Vf~~~---dfItVtK~~~~~W~~l~~~I~~~ 79 (87)
T PF08712_consen 38 PLAQALFAIPGVKSVFIGD---DFITVTKNPDADWEDLKPEIREV 79 (87)
T ss_dssp HHHHHHHTSTTEEEEEEET---TEEEEEE-TTS-HHHHHHHHHHH
T ss_pred HHHHHhcCCCCEeEEEEEC---CEEEEeeCCCCCHHHHHHHHHHH
Confidence 4456677999999999975 67777766 47888888887753
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=62.73 E-value=9.5 Score=23.03 Aligned_cols=20 Identities=30% Similarity=0.308 Sum_probs=17.2
Q ss_pred HHHHHHHHHhcCCCeeEEEe
Q 033712 6 CRKKAMKIAVKADGVIKVEI 25 (113)
Q Consensus 6 C~~kv~k~l~~~~GV~sV~v 25 (113)
--..+++.|.+++||.+|.+
T Consensus 55 ~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 55 DIDELLEELREIDGVEKVEL 74 (76)
T ss_pred HHHHHHHHHhcCCCeEEEEE
Confidence 34688999999999999975
No 21
>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=60.03 E-value=12 Score=23.07 Aligned_cols=20 Identities=20% Similarity=0.235 Sum_probs=16.3
Q ss_pred HHHHHHHHHhcCCCeeEEEe
Q 033712 6 CRKKAMKIAVKADGVIKVEI 25 (113)
Q Consensus 6 C~~kv~k~l~~~~GV~sV~v 25 (113)
=+..+.++|..++||.+|++
T Consensus 53 l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 53 LREEIREALKALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHHHTSTT-SEEEE
T ss_pred HHHHHHHHHHhCCCCceEeC
Confidence 46788999999999999975
No 22
>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=59.59 E-value=5.9 Score=23.62 Aligned_cols=35 Identities=11% Similarity=0.081 Sum_probs=17.0
Q ss_pred HHHHHHhc---CCCeeEEEecCCCCCeEEEEeeccCHHHHH
Q 033712 9 KAMKIAVK---ADGVIKVEIKGEGKDELVVIGNEVDSVKLT 46 (113)
Q Consensus 9 kv~k~l~~---~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~ 46 (113)
+++..|.. +++- +|.+.. ..+.|+++|. ++-....
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v-~~g~v~L~G~-v~s~~~~ 40 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSV-ENGVVTLSGE-VPSQEQR 40 (64)
T ss_dssp ----------CTT-T-TEEEEE-ECTEEEEEEE-ESSCHHH
T ss_pred ccccccccccccCCC-eEEEEE-ECCEEEEEee-CcHHHHH
Confidence 45556665 4444 566666 5689999999 7443333
No 23
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=54.24 E-value=18 Score=26.66 Aligned_cols=31 Identities=13% Similarity=0.153 Sum_probs=26.9
Q ss_pred eEEEEeeccCHHHHHHHHHhhcCceeEEecCC
Q 033712 32 ELVVIGNEVDSVKLTRKLQKKLGFASLLSVQE 63 (113)
Q Consensus 32 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~~ 63 (113)
-|.++|+ -|-.-+++.++.++++++++++++
T Consensus 114 ivl~SgD-~DF~p~v~~~~~~G~rv~v~~~~~ 144 (181)
T COG1432 114 IVLFSGD-GDFIPLVEAARDKGKRVEVAGIEP 144 (181)
T ss_pred EEEEcCC-ccHHHHHHHHHHcCCEEEEEecCC
Confidence 4566799 999999999998888999999976
No 24
>PHA00514 dsDNA binding protein
Probab=51.55 E-value=24 Score=23.95 Aligned_cols=33 Identities=24% Similarity=0.454 Sum_probs=27.7
Q ss_pred CeEEEEeeccCHHHHHHHHHhhc--CceeEEecCCC
Q 033712 31 DELVVIGNEVDSVKLTRKLQKKL--GFASLLSVQEE 64 (113)
Q Consensus 31 ~kvtV~G~~vDp~~l~~~LrKk~--~~aeivsv~~~ 64 (113)
+-.|..|+ +..+.-...|.|+. +.+.+|||+|-
T Consensus 32 ~~~Tl~GN-LtiEqAQ~e~~k~~k~~pvqVvsVEpn 66 (98)
T PHA00514 32 NEQTLLGN-LTIEQAQKELSKQYKHGPVQVVSVEPN 66 (98)
T ss_pred Ccceeecc-eeHHHHHHHHhhcccCCCeeEEEecCC
Confidence 45689999 99999999998874 47999999864
No 25
>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=50.48 E-value=56 Score=20.50 Aligned_cols=48 Identities=23% Similarity=0.369 Sum_probs=30.5
Q ss_pred HHHHHHhcCCCeeEEEecCCCCCeEEEEee-ccCHHHHHHHHHhhcC-cee
Q 033712 9 KAMKIAVKADGVIKVEIKGEGKDELVVIGN-EVDSVKLTRKLQKKLG-FAS 57 (113)
Q Consensus 9 kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~-~vDp~~l~~~LrKk~~-~ae 57 (113)
.+++.|..-+=--.+..|. +.+++.|.|- .+--+-++++|+.+++ .++
T Consensus 23 ~aL~~l~~eDP~l~~~~d~-et~e~~l~g~Gelhlev~~~~L~~~~~v~v~ 72 (75)
T PF14492_consen 23 EALQKLSEEDPSLRVERDE-ETGELILSGMGELHLEVLLERLKRRFGVEVE 72 (75)
T ss_dssp HHHHHHHHH-TTSEEEEET-TTSEEEEEESSHHHHHHHHHHHHHTTCEBEE
T ss_pred HHHHHHHhcCCeEEEEEcc-hhceEEEEECCHHHHHHHHHHHHHHHCCeeE
Confidence 3444444444445777776 5676666654 1677889999998887 544
No 26
>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=49.29 E-value=26 Score=23.97 Aligned_cols=30 Identities=20% Similarity=0.247 Sum_probs=24.6
Q ss_pred eEEEEeeccCHHHHHHHHHhhcCceeEEecC
Q 033712 32 ELVVIGNEVDSVKLTRKLQKKLGFASLLSVQ 62 (113)
Q Consensus 32 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~ 62 (113)
=|.|+|+ -|-.-+++.||.+...+.+++..
T Consensus 103 ivLvSgD-~Df~~~i~~lr~~G~~V~v~~~~ 132 (149)
T cd06167 103 IVLVSGD-SDFVPLVERLRELGKRVIVVGFE 132 (149)
T ss_pred EEEEECC-ccHHHHHHHHHHcCCEEEEEccC
Confidence 5678888 89999999999864488888765
No 27
>PF09358 UBA_e1_C: Ubiquitin-activating enzyme e1 C-terminal domain; InterPro: IPR018965 This presumed domain found at the C terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterised. ; PDB: 3CMM_A.
Probab=48.93 E-value=29 Score=24.33 Aligned_cols=32 Identities=25% Similarity=0.339 Sum_probs=26.5
Q ss_pred CeEEEEeeccCHHHHHHHHHhhcC-ceeEEecCC
Q 033712 31 DELVVIGNEVDSVKLTRKLQKKLG-FASLLSVQE 63 (113)
Q Consensus 31 ~kvtV~G~~vDp~~l~~~LrKk~~-~aeivsv~~ 63 (113)
+++.|.|+ +-...|+..|+++.| .+.+++.+.
T Consensus 35 Dr~~v~~~-~Tl~~li~~~~~~~~lev~ml~~g~ 67 (125)
T PF09358_consen 35 DRIEVNGD-MTLQELIDYFKEKYGLEVTMLSQGV 67 (125)
T ss_dssp -EEEEES---BHHHHHHHHHHTTS-EEEEEEETT
T ss_pred eEEEEcCC-CCHHHHHHHHHHHhCceEEEEEeCC
Confidence 68999997 999999999999988 888888874
No 28
>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=48.03 E-value=27 Score=25.76 Aligned_cols=29 Identities=10% Similarity=0.087 Sum_probs=24.0
Q ss_pred eEEEEeeccCHHHHHHHHHhhcCceeEEec
Q 033712 32 ELVVIGNEVDSVKLTRKLQKKLGFASLLSV 61 (113)
Q Consensus 32 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv 61 (113)
=+.|+|+ -|-..|+.+||.++..+..+++
T Consensus 109 ~vLvSgD-~DF~~Lv~~lre~G~~V~v~g~ 137 (160)
T TIGR00288 109 VALVTRD-ADFLPVINKAKENGKETIVIGA 137 (160)
T ss_pred EEEEecc-HhHHHHHHHHHHCCCEEEEEeC
Confidence 5678898 9999999999986447887765
No 29
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=47.68 E-value=79 Score=21.57 Aligned_cols=42 Identities=17% Similarity=0.117 Sum_probs=33.0
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHHHHH
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQ 50 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~Lr 50 (113)
...++..|+.++|++--.-|. + +|++|+=++-|...|+..|.
T Consensus 20 l~av~~~L~~ip~~EV~~~d~-~-GKlVVVie~~~~~~l~~tie 61 (94)
T COG3062 20 LSAVKTALLAIPGCEVYGEDA-E-GKLVVVIEAEDSETLLETIE 61 (94)
T ss_pred HHHHHHHHhcCCCcEeeccCC-C-ceEEEEEEcCchHHHHHHHH
Confidence 457899999999998777665 3 88888887678888877664
No 30
>PF05137 PilN: Fimbrial assembly protein (PilN); InterPro: IPR007813 PilN is a plasmid-encoded, lipoprotein which locates to the outer membrane of bacteria and are part of a thin pilus required only for liquid mating [].
Probab=47.06 E-value=61 Score=19.62 Aligned_cols=40 Identities=18% Similarity=0.145 Sum_probs=24.5
Q ss_pred eeEEEecCCCCCeEEEEeeccCHHHHHHHHHhh--cC---ceeEEecC
Q 033712 20 VIKVEIKGEGKDELVVIGNEVDSVKLTRKLQKK--LG---FASLLSVQ 62 (113)
Q Consensus 20 V~sV~vd~~~k~kvtV~G~~vDp~~l~~~LrKk--~~---~aeivsv~ 62 (113)
+++++++ .++|++.|...+...|...+++- .+ .+.+.++.
T Consensus 16 l~~l~~~---~~~l~i~G~a~~~~~v~~f~~~L~~~~~f~~v~l~~~~ 60 (78)
T PF05137_consen 16 LTSLSIN---GNTLSISGYADSYQSVAAFLRNLEQSPFFSDVSLSSIS 60 (78)
T ss_pred EEEEEEe---CCEEEEEEEECCHHHHHHHHHHHhhCCCccceEEEEEE
Confidence 3455544 47999999976776666665531 22 45555553
No 31
>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=46.35 E-value=24 Score=22.36 Aligned_cols=23 Identities=30% Similarity=0.476 Sum_probs=16.8
Q ss_pred CCCeEEEEeeccCHHHHHHHHHh
Q 033712 29 GKDELVVIGNEVDSVKLTRKLQK 51 (113)
Q Consensus 29 ~k~kvtV~G~~vDp~~l~~~LrK 51 (113)
..++++++|..+|...|.+.|..
T Consensus 70 ~~~~lV~IG~~ld~~~l~~~l~~ 92 (94)
T PF07683_consen 70 RDSRLVFIGKNLDKEALREALDA 92 (94)
T ss_dssp --EEEEEEEES--HHHHHHHHHT
T ss_pred CCeEEEEEECCCCHHHHHHHHHc
Confidence 34699999999999999988864
No 32
>PRK09577 multidrug efflux protein; Reviewed
Probab=46.08 E-value=41 Score=31.20 Aligned_cols=45 Identities=11% Similarity=0.227 Sum_probs=33.8
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEE-------eeccCHHHHHHHHHhh
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVI-------GNEVDSVKLTRKLQKK 52 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~-------G~~vDp~~l~~~LrKk 52 (113)
...++..|.+++||.+|.+.+ ...++.|. .-++++.+|.+.|+..
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G-~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~ 209 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWG-AEYAMRIWPDPVKLAALGLTASDIASAVRAH 209 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecC-CceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 467899999999999999988 54566663 1245667778888863
No 33
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=45.23 E-value=45 Score=30.98 Aligned_cols=45 Identities=9% Similarity=0.203 Sum_probs=33.4
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEEee-------ccCHHHHHHHHHhh
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVIGN-------EVDSVKLTRKLQKK 52 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~-------~vDp~~l~~~LrKk 52 (113)
+..++..|.+++||.+|++.+ ...++.|.=+ ++++.+|.+.|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G-~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYG-SQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcC-CceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 467889999999999999998 4455555422 45667778888853
No 34
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=45.16 E-value=21 Score=26.01 Aligned_cols=43 Identities=19% Similarity=0.233 Sum_probs=29.8
Q ss_pred hHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHHHHHh
Q 033712 5 KCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQK 51 (113)
Q Consensus 5 ~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~LrK 51 (113)
+|.++|...|.+ +.-|+.+.+.-.+||=.|. =|...++.+|+.
T Consensus 98 ~i~rkvlQ~Le~---~~~ve~hp~gGR~lt~~Gq-rdldrIa~~i~~ 140 (143)
T KOG3411|consen 98 GIARKVLQALEK---MGIVEKHPKGGRRLTEQGQ-RDLDRIAGQIRE 140 (143)
T ss_pred HHHHHHHHHHHh---CCceeeCCCCcceeCcccc-hhHHHHHHHHHh
Confidence 455555555554 4455666544349999999 899999988874
No 35
>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=45.07 E-value=26 Score=23.55 Aligned_cols=23 Identities=30% Similarity=0.645 Sum_probs=20.2
Q ss_pred CeEEEEeeccCHHHHHHHHHhhcC
Q 033712 31 DELVVIGNEVDSVKLTRKLQKKLG 54 (113)
Q Consensus 31 ~kvtV~G~~vDp~~l~~~LrKk~~ 54 (113)
-.|+|+|+ +|+..+.+.+.+.++
T Consensus 20 ~~l~i~Gd-~~~~~~~~~i~~~~~ 42 (184)
T PF05193_consen 20 MTLVIVGD-IDPDELEKLIEKYFG 42 (184)
T ss_dssp EEEEEEES-SGHHHHHHHHHHHHT
T ss_pred eEEEEEcC-ccHHHHHHHHHhhhh
Confidence 48999999 999999999987666
No 36
>PF12164 SporV_AA: Stage V sporulation protein AA; InterPro: IPR021997 This domain family is found in bacteria - primarily Firmicutes, and is approximately 90 amino acids in length. There is a single completely conserved residue G that may be functionally important. Most annotation associated with this domain suggests that it is involved in the fifth stage of sporulation, however there is little publication to back this up. ; PDB: 3G74_B.
Probab=42.94 E-value=53 Score=21.89 Aligned_cols=49 Identities=16% Similarity=0.196 Sum_probs=28.0
Q ss_pred HHHHHHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHHHHHhhcCceeEEecCCCc
Q 033712 9 KAMKIAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQKKLGFASLLSVQEEK 65 (113)
Q Consensus 9 kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~~~k 65 (113)
.+...|..+ -=..++..++++++ +|.-+|++++++.+++++|-.+|+..
T Consensus 34 ~~~~klk~l---~i~~~~~~d~~r~V-----isvm~II~~I~~~~p~l~I~~iGe~~ 82 (93)
T PF12164_consen 34 EIENKLKAL---PIYKIKKKDKNRYV-----ISVMKIIEKIQEEYPNLDIQNIGETD 82 (93)
T ss_dssp HHHHHHHTS---EEEE-BTTT--EEE-----EEHHHHHHHHHHH-SSEEEEE-S-SE
T ss_pred HHHHHhhcc---EeeeecCCCCCEEE-----EEHHHHHHHHHHHCCCcEEEEcCCCc
Confidence 344444444 33344553334443 35789999999989999999988764
No 37
>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=42.64 E-value=50 Score=30.73 Aligned_cols=44 Identities=11% Similarity=0.212 Sum_probs=33.6
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEEee-------ccCHHHHHHHHHh
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVIGN-------EVDSVKLTRKLQK 51 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~-------~vDp~~l~~~LrK 51 (113)
...++..|.+++||.+|++.+. ..++.|.=+ ++++.+|...|+.
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~-~~ei~V~vD~~kl~~~gls~~dV~~~i~~ 209 (1044)
T TIGR00915 159 ASNMVDPISRLEGVGDVQLFGS-QYAMRIWLDPAKLNSYQLTPADVISAIQA 209 (1044)
T ss_pred HHHHHHHHhCCCCceEEEecCC-ceEEEEEECHHHHHHcCCCHHHHHHHHHH
Confidence 3568999999999999999985 556666521 4566777888886
No 38
>PRK11023 outer membrane lipoprotein; Provisional
Probab=42.23 E-value=56 Score=24.26 Aligned_cols=43 Identities=7% Similarity=0.235 Sum_probs=29.7
Q ss_pred hHHHHHHHHHhcCCCee---EEEecCCCCCeEEEEeeccCHHHHHHHH
Q 033712 5 KCRKKAMKIAVKADGVI---KVEIKGEGKDELVVIGNEVDSVKLTRKL 49 (113)
Q Consensus 5 ~C~~kv~k~l~~~~GV~---sV~vd~~~k~kvtV~G~~vDp~~l~~~L 49 (113)
.-..+|+..|..-+++. .|.+.. .++.|+++|. ++-.....+.
T Consensus 49 ~i~~~V~~aL~~~~~l~~~~~I~V~v-~~G~V~L~G~-V~~~~~k~~A 94 (191)
T PRK11023 49 TLELRVNNALSKDEQIKKEARINVTA-YQGKVLLTGQ-SPNAELSERA 94 (191)
T ss_pred HHHHHHHHHHhhCcccCcCceEEEEE-ECCEEEEEEE-eCCHHHHHHH
Confidence 34677888888777664 477766 5689999998 7665444443
No 39
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=42.08 E-value=48 Score=22.90 Aligned_cols=28 Identities=32% Similarity=0.463 Sum_probs=22.8
Q ss_pred EEecCCCCCeEEEEeeccCHHHHHHHHHhhc
Q 033712 23 VEIKGEGKDELVVIGNEVDSVKLTRKLQKKL 53 (113)
Q Consensus 23 V~vd~~~k~kvtV~G~~vDp~~l~~~LrKk~ 53 (113)
.++|. ++++++.|. +++..|-+.|++-.
T Consensus 50 g~id~--~~rlii~G~-~~~~~i~~~l~~yI 77 (110)
T smart00653 50 GSIDG--KGRLIVNGR-FTPKKLQDLLRRYI 77 (110)
T ss_pred eeECC--CCeEEEEEe-eCHHHHHHHHHHHH
Confidence 34564 499999999 99999999998744
No 40
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=41.86 E-value=51 Score=26.58 Aligned_cols=41 Identities=12% Similarity=0.212 Sum_probs=29.6
Q ss_pred HHHHHHHhcCCCeeEEEecCCCCC---eEEEEeeccCHHHHHHHHHh
Q 033712 8 KKAMKIAVKADGVIKVEIKGEGKD---ELVVIGNEVDSVKLTRKLQK 51 (113)
Q Consensus 8 ~kv~k~l~~~~GV~sV~vd~~~k~---kvtV~G~~vDp~~l~~~LrK 51 (113)
.++...+..+++|.-+.+++|.+. -+|++|+ |.+++.++-.
T Consensus 21 e~i~a~~~~~~~v~ildve~danhNRsViT~vgd---p~~~~~A~f~ 64 (302)
T COG3643 21 EKIVAAAKSIPTVKILDVEMDANHNRSVITLVGD---PSKVVNAAFA 64 (302)
T ss_pred HHHHHHHhcCCceEEEEeccCCCCCceEEEEecC---hHHHHHHHHH
Confidence 467788888999988888775544 4555565 8888877654
No 41
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=41.61 E-value=52 Score=30.69 Aligned_cols=44 Identities=14% Similarity=0.221 Sum_probs=31.2
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEEee-------ccCHHHHHHHHHh
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVIGN-------EVDSVKLTRKLQK 51 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~-------~vDp~~l~~~LrK 51 (113)
...++..|.+++||.+|++.+. ..++.|.=+ ++++.+|...|+.
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~-~~ei~V~vDp~kl~~~gls~~~V~~~l~~ 209 (1049)
T PRK15127 159 AANMKDPISRTSGVGDVQLFGS-QYAMRIWMNPNELNKFQLTPVDVINAIKA 209 (1049)
T ss_pred HHHHHHHHhcCCCceEEEEcCC-ceEEEEEeCHHHHHHcCCCHHHHHHHHHH
Confidence 3568899999999999999884 445555422 3455666677874
No 42
>PF01253 SUI1: Translation initiation factor SUI1; InterPro: IPR001950 In Saccharomyces cerevisiae (Baker's yeast), SUI1 is a translation initiation factor that functions in concert with eIF-2 and the initiator tRNA-Met in directing the ribosome to the proper start site of translation []. SUI1 is a protein of 108 residues. Close homologs of SUI1 have been found [] in mammals, insects and plants. SUI1 is also evolutionary related to hypothetical proteins from Escherichia coli (yciH), Haemophilus influenzae (HI1225) and Methanococcus vannielii.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2OGH_A 1D1R_A 2IF1_A 2XZN_F 2XZM_F.
Probab=41.27 E-value=36 Score=21.85 Aligned_cols=30 Identities=20% Similarity=0.372 Sum_probs=22.4
Q ss_pred CCeEEEEee----ccCHHHHHHHHHhhcC-ceeEE
Q 033712 30 KDELVVIGN----EVDSVKLTRKLQKKLG-FASLL 59 (113)
Q Consensus 30 k~kvtV~G~----~vDp~~l~~~LrKk~~-~aeiv 59 (113)
+..||++.. ++|+..|++.|+++++ .+.+.
T Consensus 17 ~K~vT~V~gl~~~~~d~~~lak~lkk~~ac~~sv~ 51 (83)
T PF01253_consen 17 RKFVTIVSGLELFGIDLKELAKELKKKFACGGSVT 51 (83)
T ss_dssp SEEEEEEES--STTSHHHHHHHHHHHHHTS-EEEE
T ss_pred CeEEEEEECCcccccCHHHHHHHHHHhccCceEEe
Confidence 337777654 4689999999999998 77665
No 43
>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=40.88 E-value=35 Score=22.93 Aligned_cols=29 Identities=24% Similarity=0.308 Sum_probs=19.6
Q ss_pred eEEEEeeccCHHHHHHHHHhhcCceeEEec
Q 033712 32 ELVVIGNEVDSVKLTRKLQKKLGFASLLSV 61 (113)
Q Consensus 32 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv 61 (113)
=|.|+|+ -|-..++++||.+..++.++..
T Consensus 99 ivLvSgD-~Df~~~v~~l~~~g~~V~v~~~ 127 (146)
T PF01936_consen 99 IVLVSGD-SDFAPLVRKLRERGKRVIVVGA 127 (146)
T ss_dssp EEEE----GGGHHHHHHHHHH--EEEEEE-
T ss_pred EEEEECc-HHHHHHHHHHHHcCCEEEEEEe
Confidence 5678898 9999999999975447888864
No 44
>PRK11023 outer membrane lipoprotein; Provisional
Probab=40.11 E-value=68 Score=23.82 Aligned_cols=44 Identities=25% Similarity=0.317 Sum_probs=32.2
Q ss_pred hHHHHHHHHHhcCCCeeEEEecCCCCCeEEEE-----eeccCHHHHHHHHHhhcC
Q 033712 5 KCRKKAMKIAVKADGVIKVEIKGEGKDELVVI-----GNEVDSVKLTRKLQKKLG 54 (113)
Q Consensus 5 ~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~-----G~~vDp~~l~~~LrKk~~ 54 (113)
.=+..+.+++.+++||.+|. ++|+|. |..+|=..|..+++..+-
T Consensus 89 ~~k~~A~~ia~~v~GV~~V~------N~l~V~~~~~~~~~~~D~~It~kik~~L~ 137 (191)
T PRK11023 89 ELSERAKQIAMGVEGVNEVY------NEIRQGQPIGLGTASKDTWITTKVRSQLL 137 (191)
T ss_pred HHHHHHHHHHhcCCCceeec------ceeeeccccccccccCcHHHHHHHHHHHh
Confidence 34678899999999999994 566773 222444669999987764
No 45
>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=40.05 E-value=30 Score=21.17 Aligned_cols=17 Identities=29% Similarity=0.346 Sum_probs=15.1
Q ss_pred HHHHHHHhcCCCeeEEE
Q 033712 8 KKAMKIAVKADGVIKVE 24 (113)
Q Consensus 8 ~kv~k~l~~~~GV~sV~ 24 (113)
..+++.|.+++||.+|+
T Consensus 52 ~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 52 QTLMPEIRRIDGVEDVK 68 (74)
T ss_pred HHHHHHHhCCCCceEEE
Confidence 57889999999999986
No 46
>PF07338 DUF1471: Protein of unknown function (DUF1471); InterPro: IPR010854 This entry consists of several hypothetical Enterobacterial proteins of around 90 residues in length. Some of the proteins are annotated as ydgH precursors and contain two copies of this region, one at the N terminus and the other at the C terminus. The function of this family is unknown.; PDB: 2NOC_A 2JNA_B 4EVU_B.
Probab=38.92 E-value=45 Score=20.12 Aligned_cols=23 Identities=26% Similarity=0.188 Sum_probs=18.8
Q ss_pred CeEEEEeeccCHHHHHHHHHhhc
Q 033712 31 DELVVIGNEVDSVKLTRKLQKKL 53 (113)
Q Consensus 31 ~kvtV~G~~vDp~~l~~~LrKk~ 53 (113)
+.|+|.|..-.|.++.+.|.+|-
T Consensus 6 G~Isvs~~~~s~~d~~~~la~kA 28 (56)
T PF07338_consen 6 GTISVSGNFGSPDDAEEALAKKA 28 (56)
T ss_dssp EEEEEEEECSSHHHHHHHHHHHH
T ss_pred EEEEEccccCCHHHHHHHHHHHH
Confidence 57889997678999999998763
No 47
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=38.36 E-value=64 Score=30.04 Aligned_cols=44 Identities=16% Similarity=0.175 Sum_probs=31.8
Q ss_pred HHHHHHHhcCCCeeEEEecCCCCCeEEEEee-------ccCHHHHHHHHHh
Q 033712 8 KKAMKIAVKADGVIKVEIKGEGKDELVVIGN-------EVDSVKLTRKLQK 51 (113)
Q Consensus 8 ~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~-------~vDp~~l~~~LrK 51 (113)
..++..|.+++||.+|.+.+....++.|.=+ ++++.+|...|+.
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 5688999999999999999844445665422 3456666777764
No 48
>cd00474 SUI1_eIF1 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two antiparallel alpha helices packed against the same side of a five-strand beta sheet, is structurally similar to other RNA-binding domains suggesting that SUI1/eIF1 may bind RNA. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown.
Probab=38.23 E-value=54 Score=21.12 Aligned_cols=28 Identities=21% Similarity=0.290 Sum_probs=21.0
Q ss_pred CeEEEEee----ccCHHHHHHHHHhhcC-ceeE
Q 033712 31 DELVVIGN----EVDSVKLTRKLQKKLG-FASL 58 (113)
Q Consensus 31 ~kvtV~G~----~vDp~~l~~~LrKk~~-~aei 58 (113)
..||++.. .+|+.+|++.|+++++ ...+
T Consensus 13 K~VT~I~Gl~~~~~dlk~l~k~lKk~~~cggtv 45 (77)
T cd00474 13 KTVTTVQGLDLEYADLKKLAKELKKKCACGGTV 45 (77)
T ss_pred ccEEEEECCCCchHhHHHHHHHHHHHcCCCcEE
Confidence 37887765 2378999999999987 5554
No 49
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=36.22 E-value=46 Score=30.58 Aligned_cols=46 Identities=17% Similarity=0.263 Sum_probs=31.4
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEEee-------ccCHHHHHHHHHhh
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVIGN-------EVDSVKLTRKLQKK 52 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~-------~vDp~~l~~~LrKk 52 (113)
...++..|.+++||.+|.+.+....++.|.=+ ++++.+|...|+..
T Consensus 158 ~~~l~~~L~~i~gV~~v~~~G~~~~ei~i~~d~~kl~~~gls~~~v~~~l~~~ 210 (1021)
T PF00873_consen 158 EEQLKPRLERIPGVARVDISGGREREIQIELDPEKLAAYGLSLSDVAQALQAN 210 (1021)
T ss_dssp HHCTHHHHHTSTTEEEEEESSS--EEEEEEE-HHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHhccceeEEEEEEeccchhhhhhheechhhhhhhCCCHHHHHHHHHHh
Confidence 45688999999999999999844446666533 44566677788753
No 50
>PRK04021 hypothetical protein; Reviewed
Probab=36.07 E-value=98 Score=20.69 Aligned_cols=44 Identities=23% Similarity=0.303 Sum_probs=28.7
Q ss_pred hHHHHHHHHHhcCCCeeEEEecCCCCC--eEEEEeeccCHHHHHHHHH
Q 033712 5 KCRKKAMKIAVKADGVIKVEIKGEGKD--ELVVIGNEVDSVKLTRKLQ 50 (113)
Q Consensus 5 ~C~~kv~k~l~~~~GV~sV~vd~~~k~--kvtV~G~~vDp~~l~~~Lr 50 (113)
+.-+.+.+.|++.=|| +|++-...++ |+..+-. +|++.|..+|+
T Consensus 46 kAN~ali~~LAk~l~~-~I~I~~G~~sr~K~v~i~g-~~~e~l~~~L~ 91 (92)
T PRK04021 46 KANKELVKFFSKLLGA-EVEIIRGETSREKDLLVKG-ISLEEVKKKLK 91 (92)
T ss_pred hHHHHHHHHHHHHhCC-CEEEEecCCcCceEEEEec-CCHHHHHHHhc
Confidence 4556677788888887 6777432333 4444433 78999988874
No 51
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=35.43 E-value=78 Score=29.41 Aligned_cols=46 Identities=17% Similarity=0.185 Sum_probs=31.9
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEEee-------ccCHHHHHHHHHhh
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVIGN-------EVDSVKLTRKLQKK 52 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~-------~vDp~~l~~~LrKk 52 (113)
+..++..|.+++||.+|.+.+....++.|.=+ ++.+.+|...|+..
T Consensus 159 ~~~l~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~~ 211 (1025)
T PRK10614 159 STQLAQTISQIDGVGDVDVGGSSLPAVRVGLNPQALFNQGVSLDDVRQAISNA 211 (1025)
T ss_pred HHHHHHHhcCCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 35789999999999999998743335555422 34555666777753
No 52
>smart00833 CobW_C Cobalamin synthesis protein cobW C-terminal domain. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis PUBMED:12869542. 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, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression PUBMED:7765511.
Probab=35.16 E-value=57 Score=20.35 Aligned_cols=22 Identities=27% Similarity=0.527 Sum_probs=17.7
Q ss_pred CCeEEEEeeccCHHHHHHHHHh
Q 033712 30 KDELVVIGNEVDSVKLTRKLQK 51 (113)
Q Consensus 30 k~kvtV~G~~vDp~~l~~~LrK 51 (113)
..+|+++|..+|...|-+.|..
T Consensus 69 ~~~lV~IG~~l~~~~l~~~l~~ 90 (92)
T smart00833 69 RTRLVFIGRDLDEEAIRAALDA 90 (92)
T ss_pred ceEEEEEeCCCCHHHHHHHHHH
Confidence 4589999998998888887753
No 53
>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=34.91 E-value=51 Score=18.71 Aligned_cols=18 Identities=17% Similarity=0.401 Sum_probs=14.6
Q ss_pred HHHHHHHhcCCCeeEEEe
Q 033712 8 KKAMKIAVKADGVIKVEI 25 (113)
Q Consensus 8 ~kv~k~l~~~~GV~sV~v 25 (113)
..+++.|..++||.+|..
T Consensus 53 ~~l~~~l~~~~~V~~v~~ 70 (71)
T cd04879 53 EEVLEELKALPGIIRVRL 70 (71)
T ss_pred HHHHHHHHcCCCeEEEEE
Confidence 367888999999998863
No 54
>PRK00378 nucleoid-associated protein NdpA; Validated
Probab=34.20 E-value=47 Score=26.54 Aligned_cols=29 Identities=24% Similarity=0.406 Sum_probs=24.4
Q ss_pred eEEEecCCCCCeEEEEeeccCHHHHHHHHHhhc
Q 033712 21 IKVEIKGEGKDELVVIGNEVDSVKLTRKLQKKL 53 (113)
Q Consensus 21 ~sV~vd~~~k~kvtV~G~~vDp~~l~~~LrKk~ 53 (113)
+.|.+|. .+++||+.|- |..|.+.|++..
T Consensus 303 ~~i~yd~-~~~~ltI~~~---p~~l~~ql~r~~ 331 (334)
T PRK00378 303 ERIFYDP-ATDTLTIKGT---PPNLRDQLQRRL 331 (334)
T ss_pred CceEEcC-CCCEEEEeCC---CHHHHHHHHHHh
Confidence 3788887 7899999998 999999997654
No 55
>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=33.63 E-value=42 Score=19.96 Aligned_cols=29 Identities=21% Similarity=0.047 Sum_probs=22.3
Q ss_pred HHHHHHHhcCCCeeEEEecCCCCCeEEEE
Q 033712 8 KKAMKIAVKADGVIKVEIKGEGKDELVVI 36 (113)
Q Consensus 8 ~kv~k~l~~~~GV~sV~vd~~~k~kvtV~ 36 (113)
.++.+.|.+++.|.++++...--++|.|.
T Consensus 37 ~~~~~~l~~~p~V~~v~V~r~~P~~l~I~ 65 (69)
T PF08478_consen 37 KKIEQRLEKLPWVKSVSVSRRFPNTLEIK 65 (69)
T ss_dssp HHHHHCCCCTTTEEEEEEEEETTTEEEEE
T ss_pred HHHHHHHHcCCCEEEEEEEEeCCCEEEEE
Confidence 56778888999999999986445666653
No 56
>PRK09579 multidrug efflux protein; Reviewed
Probab=33.47 E-value=1.2e+02 Score=28.32 Aligned_cols=46 Identities=11% Similarity=0.115 Sum_probs=34.3
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEEee-------ccCHHHHHHHHHhh
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVIGN-------EVDSVKLTRKLQKK 52 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~-------~vDp~~l~~~LrKk 52 (113)
.+.++..|.+++||.+|.+.+....++.|.=+ ++.+.+|.+.|+..
T Consensus 158 ~~~i~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~~ 210 (1017)
T PRK09579 158 SRVIQPKLATLPGMAEAEILGNQVFAMRLWLDPVKLAGFGLSAGDVTQAVRRY 210 (1017)
T ss_pred HHHHHHHhhcCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 45688999999999999998844446666422 46677888888764
No 57
>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=33.11 E-value=43 Score=22.29 Aligned_cols=22 Identities=23% Similarity=0.225 Sum_probs=18.1
Q ss_pred HHHHHHHHHhcCCCeeEEEecC
Q 033712 6 CRKKAMKIAVKADGVIKVEIKG 27 (113)
Q Consensus 6 C~~kv~k~l~~~~GV~sV~vd~ 27 (113)
--..+..++++++||+|+++..
T Consensus 63 ~td~lee~i~~ve~V~svev~~ 84 (88)
T TIGR00489 63 GTEAAEESLSGIEGVESVEVTD 84 (88)
T ss_pred ChHHHHHHHhcCCCccEEEEEE
Confidence 3467888999999999999863
No 58
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=32.92 E-value=88 Score=29.39 Aligned_cols=45 Identities=9% Similarity=0.124 Sum_probs=32.7
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEEee-------ccCHHHHHHHHHh
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVIGN-------EVDSVKLTRKLQK 51 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~-------~vDp~~l~~~LrK 51 (113)
.+.++..|++++||-+|++-+.....+.|.=+ ++++.+|...|+.
T Consensus 157 ~~~l~~~L~~v~GV~~V~~~G~~~~~~rI~ldp~kLa~~gLt~~dV~~ai~~ 208 (1009)
T COG0841 157 ASNVRDELSRVPGVGSVQLFGAQEYAMRIWLDPAKLAAYGLTPSDVQSAIRA 208 (1009)
T ss_pred HHHHHHHHhcCCCceEEEEcCCCceeEEEEeCHHHHHHcCCCHHHHHHHHHH
Confidence 46789999999999999999843446665422 4556667777874
No 59
>PRK00939 translation initiation factor Sui1; Reviewed
Probab=32.90 E-value=85 Score=21.25 Aligned_cols=41 Identities=24% Similarity=0.409 Sum_probs=26.1
Q ss_pred CCeeEEEecCC-CCCeEEEEee----ccCHHHHHHHHHhhcC-ceeE
Q 033712 18 DGVIKVEIKGE-GKDELVVIGN----EVDSVKLTRKLQKKLG-FASL 58 (113)
Q Consensus 18 ~GV~sV~vd~~-~k~kvtV~G~----~vDp~~l~~~LrKk~~-~aei 58 (113)
.+.-.|.+... .+..||++.. .+|+..|++.|+++++ ...+
T Consensus 23 ~~~i~I~~ekr~~gK~VTiI~Gl~~~~~~lk~l~k~lKk~~gcGgsv 69 (99)
T PRK00939 23 QQRIKIKVDKRRYGKEVTIIEGIDPKDIDLKELAKKLKSKLACGGTV 69 (99)
T ss_pred CceEEEEEEecCCCceEEEEeCCCCcchhHHHHHHHHHHHhCCCceE
Confidence 34334444431 2338888876 1268999999999986 5543
No 60
>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=32.89 E-value=60 Score=15.13 Aligned_cols=49 Identities=29% Similarity=0.339 Sum_probs=31.6
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeec-cCHHHHHHHHH
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNE-VDSVKLTRKLQ 50 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~-vDp~~l~~~Lr 50 (113)
++|..|...+...+....|+....... ....+.+.... .+...+...++
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 56 (63)
T cd00371 7 MTCAGCVSKIEKALEKLPGVESVEVDL-ETGKATVEYDPEVSPEELLEAIE 56 (63)
T ss_pred eEcHHHHHHHHHHHhcCCCEeEEEEEc-cCCEEEEEECCCCCHHHHHHHHH
Confidence 468899999998888899987776665 33455554321 25555544443
No 61
>PRK13748 putative mercuric reductase; Provisional
Probab=32.26 E-value=2e+02 Score=24.15 Aligned_cols=59 Identities=24% Similarity=0.296 Sum_probs=41.1
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEee-ccCHHHHHHHHHhhcC-ceeEEec
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGN-EVDSVKLTRKLQKKLG-FASLLSV 61 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~-~vDp~~l~~~LrKk~~-~aeivsv 61 (113)
|+|..|..++...+...+|+....++. ....+.+... ..+...+...+.. .+ .+++.+.
T Consensus 9 ~~C~~c~~~ie~~l~~~~gv~~a~~~~-~~~~~~v~~~~~~~~~~i~~~i~~-~g~~~~~~~~ 69 (561)
T PRK13748 9 MTCDSCAAHVKDALEKVPGVQSADVSY-PKGSAQLAIEVGTSPDALTAAVAG-LGYRATLADA 69 (561)
T ss_pred eecHHHHHHHHHHHhcCCCeeEEEEEc-CCCEEEEEECCCCCHHHHHHHHHH-cCCeeeccCc
Confidence 579999999999999999999888877 5556555531 2466667666653 45 4444433
No 62
>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=31.52 E-value=1.1e+02 Score=17.91 Aligned_cols=49 Identities=29% Similarity=0.333 Sum_probs=32.6
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEE--eeccCHHHHHHHHH
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVI--GNEVDSVKLTRKLQ 50 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~--G~~vDp~~l~~~Lr 50 (113)
++|..|...+...+....|+....... ....+.+. +...+...+...+.
T Consensus 32 ~~c~~c~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 82 (92)
T TIGR02052 32 MTCVACPITVETALQKVDGVSKAEVTF-KTKLAVVTFDDEKTNVKALTEATT 82 (92)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEe-cCCEEEEEECCCCCCHHHHHHHHH
Confidence 469999999999999999988877765 43444333 21245555544444
No 63
>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=30.66 E-value=70 Score=19.40 Aligned_cols=19 Identities=26% Similarity=0.242 Sum_probs=15.7
Q ss_pred HHHHHHhcCCCeeEEEecC
Q 033712 9 KAMKIAVKADGVIKVEIKG 27 (113)
Q Consensus 9 kv~k~l~~~~GV~sV~vd~ 27 (113)
...+.|.+.+||.+|+-|.
T Consensus 59 ~~i~~L~~~p~V~~Ve~D~ 77 (82)
T PF05922_consen 59 EEIEKLRKDPGVKSVEPDQ 77 (82)
T ss_dssp HHHHHHHTSTTEEEEEEEC
T ss_pred HHHHHHHcCCCeEEEEeCc
Confidence 3457899999999999874
No 64
>PF01424 R3H: R3H domain; InterPro: IPR001374 The R3H motif: a domain that binds single-stranded nucleic acids. The most prominent feature of the R3H motif is the presence of an invariant arginine residue and a highly conserved histidine residue that are separated by three residues. The motif also displays a conserved pattern of hydrophobic residues, prolines and glycines. The R3H motif is present in proteins from a diverse range of organisms that includes Eubacteria, green plants, fungi and various groups of metazoans. Intriguingly, it has not yet been identified in Archaea and Escherichia coli. The sequences that contain the R3H domain, many of which are hypothetical proteins predicted from genome sequencing projects, can be grouped into eight families on the basis of similarities outside the R3H region. Three of the families contain ATPase domains either upstream (families II and VII) or downstream of the R3H domain (family VIII). The N-terminal part of members of family VII contains an SF1 helicase domain5. The C-terminal part of family VIII contains an SF2 DEAH helicase domain5. The ATPase domain in the members of family II is similar to the stage-III sporulation protein AA (S3AA_BACSU), the proteasome ATPase, bacterial transcription-termination factor r and the mitochondrial F1-ATPase b subunit (the F5 helicase family5). Family VI contains Cys-rich repeats6, as well as a ring-type zinc finger upstream of the R3H domain. JAG bacterial proteins (family I) contain a KH domain N-terminal to the R3H domain. The functions of other domains in R3H proteins support the notion that the R3H domain might be involved in interactions with single-stranded nucleic acids [].; GO: 0003676 nucleic acid binding; PDB: 1WHR_A 1MSZ_A 1UG8_A 3GKU_B 2CPM_A.
Probab=30.31 E-value=1.2e+02 Score=17.87 Aligned_cols=30 Identities=13% Similarity=0.071 Sum_probs=21.3
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEE
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVI 36 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~ 36 (113)
.+++...++..-|+.|.+.+.+.+..|+|.
T Consensus 32 ~R~~iH~~a~~~gL~s~S~g~~~~R~vvv~ 61 (63)
T PF01424_consen 32 ERKLIHELAEYYGLKSKSEGEGPNRRVVVS 61 (63)
T ss_dssp HHHHHHHHHHHCTEEEEEESSSSSSEEEEE
T ss_pred HHHHHHHHHHHCCCEEEEecCCCCeEEEEE
Confidence 456666677799999999986444466664
No 65
>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=29.67 E-value=70 Score=18.63 Aligned_cols=18 Identities=17% Similarity=0.357 Sum_probs=14.1
Q ss_pred HHHHHHHhcCCCeeEEEe
Q 033712 8 KKAMKIAVKADGVIKVEI 25 (113)
Q Consensus 8 ~kv~k~l~~~~GV~sV~v 25 (113)
..+++.|.+++||.+|.+
T Consensus 51 ~~li~~l~~~~~V~~v~~ 68 (69)
T cd04901 51 EELLEALRAIPGTIRVRL 68 (69)
T ss_pred HHHHHHHHcCCCeEEEEE
Confidence 357788888999988864
No 66
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=29.63 E-value=1.8e+02 Score=20.61 Aligned_cols=50 Identities=16% Similarity=0.175 Sum_probs=31.9
Q ss_pred hHHHHHHHHHhcCCCee--EEEecCCCCCeEEEEeeccCHHHHHHHHHhhcCcee
Q 033712 5 KCRKKAMKIAVKADGVI--KVEIKGEGKDELVVIGNEVDSVKLTRKLQKKLGFAS 57 (113)
Q Consensus 5 ~C~~kv~k~l~~~~GV~--sV~vd~~~k~kvtV~G~~vDp~~l~~~LrKk~~~ae 57 (113)
.-+.+|++.|.+. |.. .+.+.. ..+.||+.|. +.-.....++....+.+.
T Consensus 26 ~~~~~i~~~i~~~-~~~~~~i~V~v-~~G~v~l~G~-v~s~~~~~~~~~aa~~v~ 77 (147)
T PRK11198 26 DAADALKEHISKQ-GLGDADVNVQV-EDGKATVSGD-AASQEAKEKILLAVGNIQ 77 (147)
T ss_pred HHHHHHHHHHHhc-CCCcCCceEEE-eCCEEEEEEE-eCCHHHHHHHHHHhccCC
Confidence 3456777777653 332 233333 4589999999 877777777766555544
No 67
>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=29.23 E-value=41 Score=24.89 Aligned_cols=29 Identities=14% Similarity=0.305 Sum_probs=25.0
Q ss_pred cCCCeeEEEecCCCCCeEEEEeeccCHHHHH
Q 033712 16 KADGVIKVEIKGEGKDELVVIGNEVDSVKLT 46 (113)
Q Consensus 16 ~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~ 46 (113)
.++|-..|.++. +...+++.|- |.|.+|.
T Consensus 110 ~I~G~k~i~vn~-e~~~i~lsGi-VRp~DI~ 138 (179)
T PF02107_consen 110 VIEGEKQIRVNG-EEQYIRLSGI-VRPEDID 138 (179)
T ss_pred EEEEEEEEEECC-CEEEEEEEEE-ECHHHCC
Confidence 467888999997 7789999998 9999986
No 68
>cd07422 MPP_ApaH Escherichia coli ApaH and related proteins, metallophosphatase domain. ApaH (also known as symmetrically cleaving Ap4A hydrolase and bis(5'nucleosyl)-tetraphosphatase) is a bacterial member of the PPP (phosphoprotein phosphatase) family of serine/threonine phosphatases that hydrolyzes the nucleotide-signaling molecule diadenosine tetraphosphate (Ap(4)A) into two ADP and also hydrolyzes Ap(5)A, Gp(4)G, and other extending compounds. Null mutations in apaH result in high intracellular levels of Ap(4)A which correlate with multiple phenotypes, including a decreased expression of catabolite-repressible genes, a reduction in the expression of flagellar operons, and an increased sensitivity to UV and heat. Ap4A hydrolase is important in responding to heat shock and oxidative stress via regulating the concentration of Ap4A in bacteria. Ap4A hydrolase is also thought to play a role in siderophore production, but the mechanism by which ApaH interacts with siderophore pathwa
Probab=28.64 E-value=1.6e+02 Score=23.01 Aligned_cols=40 Identities=25% Similarity=0.431 Sum_probs=29.9
Q ss_pred hHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeecc----CHHHHHHHHHh
Q 033712 5 KCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEV----DSVKLTRKLQK 51 (113)
Q Consensus 5 ~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~v----Dp~~l~~~LrK 51 (113)
||.....+.|.++. .+. ..+++...|+-| |+..+++.|++
T Consensus 9 G~~~~L~~LL~~i~------~~~-~~D~Li~lGDlVdRGp~s~evl~~l~~ 52 (257)
T cd07422 9 GCYDELQRLLEKIN------FDP-AKDRLWLVGDLVNRGPDSLETLRFVKS 52 (257)
T ss_pred CCHHHHHHHHHhcC------CCC-CCCEEEEecCcCCCCcCHHHHHHHHHh
Confidence 67777778877752 232 457999999955 49999999986
No 69
>COG0612 PqqL Predicted Zn-dependent peptidases [General function prediction only]
Probab=27.90 E-value=59 Score=26.44 Aligned_cols=24 Identities=33% Similarity=0.576 Sum_probs=21.5
Q ss_pred CCeEEEEeeccCHHHHHHHHHhhcC
Q 033712 30 KDELVVIGNEVDSVKLTRKLQKKLG 54 (113)
Q Consensus 30 k~kvtV~G~~vDp~~l~~~LrKk~~ 54 (113)
+-.|.|+|+ +|+..+...+.+.++
T Consensus 198 n~~l~vvGd-i~~~~v~~~~~~~f~ 221 (438)
T COG0612 198 NMVLVVVGD-VDAEEVVELIEKYFG 221 (438)
T ss_pred ceEEEEecC-CCHHHHHHHHHHHHc
Confidence 348999999 999999999998877
No 70
>TIGR01158 SUI1_rel translation initation factor SUI1, putative, prokaryotic. This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met.
Probab=27.74 E-value=1.9e+02 Score=19.47 Aligned_cols=40 Identities=20% Similarity=0.409 Sum_probs=26.0
Q ss_pred CCeeEEEecCC--CCCeEEEEee----ccCHHHHHHHHHhhcC-cee
Q 033712 18 DGVIKVEIKGE--GKDELVVIGN----EVDSVKLTRKLQKKLG-FAS 57 (113)
Q Consensus 18 ~GV~sV~vd~~--~k~kvtV~G~----~vDp~~l~~~LrKk~~-~ae 57 (113)
++.-.|.++.. ....|||+.. ..|+..|++.|+++++ ...
T Consensus 23 ~~~i~i~~e~rgr~gK~VTvV~Gl~~~~~~l~~l~k~LKk~~gcGgt 69 (101)
T TIGR01158 23 DQVVRIQRETRGRKGKGVTIIEGLDLSDIDLKELAKELKSKCGCGGT 69 (101)
T ss_pred CceEEEEEEEecCCCCEEEEEeCCcCchhhHHHHHHHHHHHhcCCee
Confidence 44555555532 2348888876 2357889999999875 444
No 71
>cd02643 R3H_NF-X1 R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system and, the yeast homolog FAP1 encodes a dosage suppressor of rapamycin toxicity. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=27.73 E-value=1.4e+02 Score=18.87 Aligned_cols=30 Identities=17% Similarity=0.242 Sum_probs=21.3
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEE
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVI 36 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~ 36 (113)
.+++...|....||.|.+.+.+-+..|+|+
T Consensus 44 eR~iIH~la~~~~l~S~S~G~ep~R~VvI~ 73 (74)
T cd02643 44 KRRIVHELAEHFGIESVSYDQEPKRNVVAT 73 (74)
T ss_pred HHHHHHHHHhhCCCEEEecCCCCCceEEEe
Confidence 355666678889999999987444455553
No 72
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=27.61 E-value=1.1e+02 Score=19.99 Aligned_cols=38 Identities=16% Similarity=0.191 Sum_probs=22.3
Q ss_pred EecCCCCCeEEEEeeccCHHHHHHHHHhhcC-ceeEEecCC
Q 033712 24 EIKGEGKDELVVIGNEVDSVKLTRKLQKKLG-FASLLSVQE 63 (113)
Q Consensus 24 ~vd~~~k~kvtV~G~~vDp~~l~~~LrKk~~-~aeivsv~~ 63 (113)
-++. +..++.|+|.|--...-++.|.+ .| +..++|...
T Consensus 2 ~l~l-~~~~vlVvGgG~va~~k~~~Ll~-~gA~v~vis~~~ 40 (103)
T PF13241_consen 2 FLDL-KGKRVLVVGGGPVAARKARLLLE-AGAKVTVISPEI 40 (103)
T ss_dssp EE---TT-EEEEEEESHHHHHHHHHHCC-CTBEEEEEESSE
T ss_pred EEEc-CCCEEEEECCCHHHHHHHHHHHh-CCCEEEEECCch
Confidence 3455 55799999997555555555554 44 666776653
No 73
>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=27.33 E-value=1.1e+02 Score=18.61 Aligned_cols=26 Identities=15% Similarity=0.261 Sum_probs=17.8
Q ss_pred EEEecCCCCCeEEEEeeccCHHHHHHH
Q 033712 22 KVEIKGEGKDELVVIGNEVDSVKLTRK 48 (113)
Q Consensus 22 sV~vd~~~k~kvtV~G~~vDp~~l~~~ 48 (113)
+|..|. ..|.|.|.|..-+-..+.+.
T Consensus 47 ~i~~d~-~tNsliv~g~~~~~~~i~~l 72 (82)
T PF03958_consen 47 RIVADE-RTNSLIVRGTPEDLEQIREL 72 (82)
T ss_dssp EEEEEC-TTTEEEEEEEHHHHHHHHHH
T ss_pred EEEEEC-CCCEEEEEeCHHHHHHHHHH
Confidence 788887 78999999993333333333
No 74
>PLN02625 uroporphyrin-III C-methyltransferase
Probab=27.26 E-value=87 Score=24.12 Aligned_cols=33 Identities=24% Similarity=0.282 Sum_probs=27.5
Q ss_pred CCCeEEEEeecc-CHHHHHHHHHhhcCceeEEec
Q 033712 29 GKDELVVIGNEV-DSVKLTRKLQKKLGFASLLSV 61 (113)
Q Consensus 29 ~k~kvtV~G~~v-Dp~~l~~~LrKk~~~aeivsv 61 (113)
..++|+++|.+. ||.-|+-+..+...+|++|-.
T Consensus 13 ~~g~l~vVG~GpGdp~~LTl~a~~~l~~ADvI~~ 46 (263)
T PLN02625 13 GPGNVFLVGTGPGDPDLLTLKALRLLQTADVVLY 46 (263)
T ss_pred CCCEEEEEEeCCCChHHhHHHHHHHHhcCCEEEE
Confidence 357999999988 899998888877888887765
No 75
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=27.12 E-value=1.1e+02 Score=22.46 Aligned_cols=32 Identities=19% Similarity=0.352 Sum_probs=23.0
Q ss_pred CchhHHHHHHHHHhcCCCeeEEEecCCCCCeEE
Q 033712 2 TCKKCRKKAMKIAVKADGVIKVEIKGEGKDELV 34 (113)
Q Consensus 2 ~Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvt 34 (113)
-|.-|..-+.+.+.++ |+.+++|-....+++.
T Consensus 110 vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~ 141 (146)
T PF14437_consen 110 VCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVY 141 (146)
T ss_pred cchHHHHHHHHHHHHc-CCCeEEEEecCCCcEE
Confidence 4999997777777766 9999998752244443
No 76
>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=26.95 E-value=78 Score=17.99 Aligned_cols=18 Identities=11% Similarity=0.169 Sum_probs=13.8
Q ss_pred HHHHHHHhcCCCeeEEEe
Q 033712 8 KKAMKIAVKADGVIKVEI 25 (113)
Q Consensus 8 ~kv~k~l~~~~GV~sV~v 25 (113)
..+.+.|.+++||.+|..
T Consensus 53 ~~~i~~l~~~~~v~~v~~ 70 (71)
T cd04903 53 EEVIEEIKKIPNIHQVIL 70 (71)
T ss_pred HHHHHHHHcCCCceEEEE
Confidence 467788888888888763
No 77
>PF15235 GRIN_C: G protein-regulated inducer of neurite outgrowth C-terminus
Probab=26.77 E-value=98 Score=22.48 Aligned_cols=32 Identities=28% Similarity=0.256 Sum_probs=27.3
Q ss_pred CCeeEEEecCCCCC-eEEEEeeccCHHHHHHHHHh
Q 033712 18 DGVIKVEIKGEGKD-ELVVIGNEVDSVKLTRKLQK 51 (113)
Q Consensus 18 ~GV~sV~vd~~~k~-kvtV~G~~vDp~~l~~~LrK 51 (113)
+=|..|..| +++ +-.|=|-.+||+.|=-+|.|
T Consensus 42 spVrdV~WD--e~GMTWEVYGAs~DpEvLG~AIQk 74 (137)
T PF15235_consen 42 SPVRDVSWD--EQGMTWEVYGASVDPEVLGMAIQK 74 (137)
T ss_pred Cccccceec--CCCceEEEeccccCHHHHHHHHHH
Confidence 458889988 456 99999999999999988887
No 78
>PRK09019 translation initiation factor Sui1; Validated
Probab=26.06 E-value=1.6e+02 Score=20.36 Aligned_cols=40 Identities=28% Similarity=0.555 Sum_probs=27.2
Q ss_pred HhcCCCeeEEEecCCCCC--eEEEEeecc-----CHHHHHHHHHhhcC
Q 033712 14 AVKADGVIKVEIKGEGKD--ELVVIGNEV-----DSVKLTRKLQKKLG 54 (113)
Q Consensus 14 l~~~~GV~sV~vd~~~k~--kvtV~G~~v-----Dp~~l~~~LrKk~~ 54 (113)
+..-+|+-.|..+...+. .|||+.. + |...|++.|+++++
T Consensus 26 ~~~~~~~vri~~~r~gRkGK~VTiI~G-l~~~~~dlk~l~K~lKkk~g 72 (108)
T PRK09019 26 RPKGDGIVRIQRQTSGRKGKGVCLITG-LDLDDAELKKLAAELKKKCG 72 (108)
T ss_pred CCCcCceEEEEEecCCCCCCeEEEEeC-CcCCHHHHHHHHHHHHHHhc
Confidence 344567666766542222 7888875 4 56889999998876
No 79
>PRK10568 periplasmic protein; Provisional
Probab=26.00 E-value=2e+02 Score=21.46 Aligned_cols=36 Identities=19% Similarity=0.260 Sum_probs=26.0
Q ss_pred hHHHHHHHHHhcCCCee--EEEecCCCCCeEEEEeeccCH
Q 033712 5 KCRKKAMKIAVKADGVI--KVEIKGEGKDELVVIGNEVDS 42 (113)
Q Consensus 5 ~C~~kv~k~l~~~~GV~--sV~vd~~~k~kvtV~G~~vDp 42 (113)
.-..+|+..|..-+++. .|.+.. .++.|++.|. ++-
T Consensus 60 ~I~~~v~~~L~~~~~i~~~~I~V~v-~~G~V~L~G~-V~s 97 (203)
T PRK10568 60 AITAKVKAALVDHDNIKSTDISVKT-HQKVVTLSGF-VES 97 (203)
T ss_pred HHHHHHHHHHHhCCCCCCCceEEEE-ECCEEEEEEE-eCC
Confidence 34677888887776664 456666 5689999999 763
No 80
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=25.97 E-value=77 Score=20.55 Aligned_cols=21 Identities=14% Similarity=0.053 Sum_probs=17.6
Q ss_pred HHHHHHHHhcCCCeeEEEecC
Q 033712 7 RKKAMKIAVKADGVIKVEIKG 27 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~ 27 (113)
+..+..+|..++|+++|.+..
T Consensus 57 ~~~i~~al~~l~gv~~v~v~i 77 (99)
T TIGR02945 57 PGEVENAVRAVPGVGSVTVEL 77 (99)
T ss_pred HHHHHHHHHhCCCCceEEEEE
Confidence 466888899999999998865
No 81
>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=25.95 E-value=1.6e+02 Score=17.89 Aligned_cols=23 Identities=13% Similarity=0.153 Sum_probs=19.1
Q ss_pred hcCCCeeEEEecCCCCCeEEEEee
Q 033712 15 VKADGVIKVEIKGEGKDELVVIGN 38 (113)
Q Consensus 15 ~~~~GV~sV~vd~~~k~kvtV~G~ 38 (113)
..-.++.+..+|. ..|+|+|+-.
T Consensus 20 ~~~~~~~~WyvD~-~tn~VVV~a~ 42 (62)
T PF02983_consen 20 AAPVAVTSWYVDP-RTNKVVVTAD 42 (62)
T ss_dssp HGGGCEEEEEEEC-CCTEEEEEEE
T ss_pred cCCCCcceEEEeC-CCCeEEEEEC
Confidence 3456899999999 7899999876
No 82
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=25.86 E-value=66 Score=21.39 Aligned_cols=23 Identities=17% Similarity=0.221 Sum_probs=18.1
Q ss_pred hHHHHHHHHHhcCCCeeEEEecC
Q 033712 5 KCRKKAMKIAVKADGVIKVEIKG 27 (113)
Q Consensus 5 ~C~~kv~k~l~~~~GV~sV~vd~ 27 (113)
+--..+...++.++||+|+++..
T Consensus 62 ~~td~lee~i~~~e~Vqsvei~~ 84 (88)
T PRK00435 62 GGTEPVEEAFANVEGVESVEVEE 84 (88)
T ss_pred cCcHHHHHHHhccCCCcEEEEEE
Confidence 33456778899999999999853
No 83
>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=25.80 E-value=77 Score=22.31 Aligned_cols=37 Identities=27% Similarity=0.310 Sum_probs=26.7
Q ss_pred HHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHHHHHhhc
Q 033712 13 IAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQKKL 53 (113)
Q Consensus 13 ~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~LrKk~ 53 (113)
-+..-=|.. ..+|. ++++++.|. +++..|-+.|++-.
T Consensus 54 y~~~ELgt~-~~id~--~~~lii~G~-~~~~~i~~~L~~fI 90 (125)
T PF01873_consen 54 YFGKELGTQ-GSIDG--KGRLIINGR-FSSKQIQDLLDKFI 90 (125)
T ss_dssp HHHHHSSSE-EEEET--TTEEEEESS-SSCCHHHHHHHHHH
T ss_pred HHHHHHCCc-eEECC--CCEEEEEEe-cCHHHHHHHHHHHH
Confidence 333333544 45665 399999999 99999999998743
No 84
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=25.64 E-value=1.3e+02 Score=18.67 Aligned_cols=12 Identities=8% Similarity=0.241 Sum_probs=7.4
Q ss_pred cCHHHHHHHHHh
Q 033712 40 VDSVKLTRKLQK 51 (113)
Q Consensus 40 vDp~~l~~~LrK 51 (113)
.|+..|+++|++
T Consensus 64 P~~~~i~~~I~~ 75 (76)
T PF10262_consen 64 PDPDEIVQLIRD 75 (76)
T ss_dssp S-HHHHHHHHHH
T ss_pred CCHHHHHHHHhc
Confidence 377777777764
No 85
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.10 E-value=1.2e+02 Score=20.69 Aligned_cols=24 Identities=29% Similarity=0.482 Sum_probs=20.7
Q ss_pred HHhcCCCeeEEEecCCCCCeEEEEe
Q 033712 13 IAVKADGVIKVEIKGEGKDELVVIG 37 (113)
Q Consensus 13 ~l~~~~GV~sV~vd~~~k~kvtV~G 37 (113)
++..++|+..|++.. ++.+|-|.+
T Consensus 35 ivas~pgis~ieik~-E~kkL~v~t 58 (96)
T COG4004 35 IVASSPGISRIEIKP-ENKKLLVNT 58 (96)
T ss_pred EEEecCCceEEEEec-ccceEEEec
Confidence 456789999999999 788999988
No 86
>PF01849 NAC: NAC domain; InterPro: IPR002715 Nascent polypeptide-associated complex (NAC) is among the first ribosome-associated entities to bind the nascent polypeptide after peptide bond formation. The nascent polypeptide-associated complex (NAC) of yeast functions in the targeting process of ribosomes to the ER membrane []. NAC may prevent binding of ribosome nascent chains (RNCs) without a signal sequence to yeast membranes.; PDB: 3MCE_D 3MCB_A 3LKX_B 1TR8_B.
Probab=25.00 E-value=1e+02 Score=18.44 Aligned_cols=30 Identities=30% Similarity=0.411 Sum_probs=17.2
Q ss_pred HHHHHHHhc-----CCCeeEEEecCCCCCeEEEEee
Q 033712 8 KKAMKIAVK-----ADGVIKVEIKGEGKDELVVIGN 38 (113)
Q Consensus 8 ~kv~k~l~~-----~~GV~sV~vd~~~k~kvtV~G~ 38 (113)
+++++.|.+ ++||+.|.+-. ..+++.+.-.
T Consensus 2 kk~~~~l~klgl~~i~~i~eV~i~~-~dg~~~~~~~ 36 (58)
T PF01849_consen 2 KKLQKMLKKLGLKEIPGIEEVTIRK-DDGTVFVFNN 36 (58)
T ss_dssp ------GHHCT-EEETTEEEEEEEE-TTTEEEEEES
T ss_pred HHHHHHHHHcCCcccCCcEEEEEEE-CCceEEEEcC
Confidence 344555544 57999999987 5567776655
No 87
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=24.96 E-value=34 Score=23.29 Aligned_cols=20 Identities=40% Similarity=0.561 Sum_probs=13.5
Q ss_pred CCchhHHHHHHHHHhcCCCeeEEE
Q 033712 1 MTCKKCRKKAMKIAVKADGVIKVE 24 (113)
Q Consensus 1 m~Ce~C~~kv~k~l~~~~GV~sV~ 24 (113)
|-|++|.+|+- ++-|++-..
T Consensus 1 MVC~kCEkKLs----kvi~pd~wr 20 (100)
T KOG3476|consen 1 MVCEKCEKKLS----KVIGPDPWR 20 (100)
T ss_pred CchhHHHHHhc----cccccCccc
Confidence 78999998754 444555543
No 88
>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium). This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=24.25 E-value=1.4e+02 Score=27.80 Aligned_cols=38 Identities=21% Similarity=0.121 Sum_probs=0.0
Q ss_pred HHHHHHHHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHH
Q 033712 7 RKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTR 47 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~ 47 (113)
...++..|.+++||.+|.+.+....++.|. +|+.+|..
T Consensus 168 ~~~l~~~L~~i~GV~~V~~~G~~~~ei~V~---iD~~kl~~ 205 (1051)
T TIGR00914 168 DWIIRPQLRTVPGVAEVNSIGGYVKQFLVA---PDPEKLAA 205 (1051)
T ss_pred HHHHHHHHhcCCCceEeeecCCceEEEEEE---ECHHHHHH
No 89
>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=23.98 E-value=80 Score=25.42 Aligned_cols=25 Identities=8% Similarity=-0.052 Sum_probs=13.7
Q ss_pred CchhHHHHHHHHHhcCCCeeEEEecC
Q 033712 2 TCKKCRKKAMKIAVKADGVIKVEIKG 27 (113)
Q Consensus 2 ~Ce~C~~kv~k~l~~~~GV~sV~vd~ 27 (113)
|..|....+...+..+ |++.+.+|.
T Consensus 218 H~cG~~~~~l~~~~e~-g~dvl~~d~ 242 (321)
T cd03309 218 HSCGAAASLVPSMAEM-GVDSWNVVM 242 (321)
T ss_pred EeCCCcHHHHHHHHHc-CCCEEEecC
Confidence 3334444455555555 777777665
No 90
>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=23.95 E-value=51 Score=21.04 Aligned_cols=22 Identities=9% Similarity=0.155 Sum_probs=15.4
Q ss_pred cCCCe--eEEEecCCCCCeEEEEee
Q 033712 16 KADGV--IKVEIKGEGKDELVVIGN 38 (113)
Q Consensus 16 ~~~GV--~sV~vd~~~k~kvtV~G~ 38 (113)
.++|| +.+++.. ..+.|+|.|.
T Consensus 17 ~lPGv~~edi~v~~-~~~~L~I~g~ 40 (93)
T cd06471 17 DLPGFKKEDIKLDY-KDGYLTISAK 40 (93)
T ss_pred ECCCCCHHHeEEEE-ECCEEEEEEE
Confidence 46777 4566665 4579999998
No 91
>PF07744 SPOC: SPOC domain; InterPro: IPR012921 Spen (split end) proteins regulate the expression of key transcriptional effectors in diverse signalling pathways. They are large proteins characterised by N-terminal RNA-binding motifs and a highly conserved C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The function of the SPOC domain is unknown, but the SPOC domain of the SHARP Spen protein has been implicated in the interaction of SHARP with the SMRT/NcoR corepressor, where SHARP plays an essential role in the repressor complex []. The SPOC domain is folded into a single compact domain consisting of a beta-barrel with seven strands framed by six alpha helices. A number of deep grooves and clefts in the surface, plus two nonpolar loops, render the SPOC domain well suited to protein-protein interactions; most of the conserved residues occur on the protein surface rather than in the core. Other proteins containing a SPOC domain include drosophila Split ends, which promotes sclerite development in the head and restricts it in the thorax, and mouse MINT (homologue of SHARP), which is involved in skeletal and neuronal development via its repression of Msx2.; PDB: 1OW1_A.
Probab=23.76 E-value=98 Score=20.32 Aligned_cols=21 Identities=19% Similarity=0.314 Sum_probs=16.4
Q ss_pred CCeEEEEeeccCHHHHHHHHHh
Q 033712 30 KDELVVIGNEVDSVKLTRKLQK 51 (113)
Q Consensus 30 k~kvtV~G~~vDp~~l~~~LrK 51 (113)
..+|+|.|. +|+..+.+.|++
T Consensus 38 p~~i~i~gR-l~~~~~~~yl~~ 58 (119)
T PF07744_consen 38 PKKIDIRGR-LDPEKVWDYLRQ 58 (119)
T ss_dssp -EEE-EEEE--SHHHHHHHHHH
T ss_pred CcEEEEEee-cCHHHHHHHHHh
Confidence 368999999 999999999985
No 92
>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=23.62 E-value=72 Score=18.16 Aligned_cols=17 Identities=29% Similarity=0.268 Sum_probs=13.2
Q ss_pred HHHHHHHhcCCCeeEEE
Q 033712 8 KKAMKIAVKADGVIKVE 24 (113)
Q Consensus 8 ~kv~k~l~~~~GV~sV~ 24 (113)
..+++.|.+++||.+|+
T Consensus 56 ~~l~~~l~~~~~v~~v~ 72 (72)
T cd04878 56 EQIVKQLNKLVDVLKVS 72 (72)
T ss_pred HHHHHHHhCCccEEEeC
Confidence 45778888888888873
No 93
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=23.60 E-value=73 Score=21.46 Aligned_cols=20 Identities=20% Similarity=0.280 Sum_probs=17.0
Q ss_pred HHHHHHHHhcCCCeeEEEec
Q 033712 7 RKKAMKIAVKADGVIKVEIK 26 (113)
Q Consensus 7 ~~kv~k~l~~~~GV~sV~vd 26 (113)
-..+...|+.++||.|+++.
T Consensus 64 td~~ee~l~~vegV~sveve 83 (88)
T COG2092 64 TDALEEALEEVEGVESVEVE 83 (88)
T ss_pred cHHHHHHHhhccCcceEEEE
Confidence 45678899999999999875
No 94
>KOG3166 consensus 60S ribosomal protein L7A [Translation, ribosomal structure and biogenesis]
Probab=23.17 E-value=52 Score=25.52 Aligned_cols=32 Identities=38% Similarity=0.433 Sum_probs=23.2
Q ss_pred CCeeEEEecCC-CCCeEEEEeeccCHHHHHHHH
Q 033712 18 DGVIKVEIKGE-GKDELVVIGNEVDSVKLTRKL 49 (113)
Q Consensus 18 ~GV~sV~vd~~-~k~kvtV~G~~vDp~~l~~~L 49 (113)
.||..|+.=.+ .+.+++|+...+||-.|+-+|
T Consensus 112 ~gvnTVttLVenKKAQLVV~ahDvDPIELVvFL 144 (209)
T KOG3166|consen 112 AGVNTVTTLVENKKAQLVVTAHDVDPIELVVFL 144 (209)
T ss_pred cCcceEeehhhccccceeEEecccCchhheeec
Confidence 47777775332 344888888779999997766
No 95
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=22.54 E-value=56 Score=22.40 Aligned_cols=26 Identities=23% Similarity=0.482 Sum_probs=17.9
Q ss_pred CCCeEEEEeeccCHHHHHHHHHhhcCc
Q 033712 29 GKDELVVIGNEVDSVKLTRKLQKKLGF 55 (113)
Q Consensus 29 ~k~kvtV~G~~vDp~~l~~~LrKk~~~ 55 (113)
...+|-|.|- .+++.|+.++-||+|.
T Consensus 11 ~tk~VNV~~c-~~a~eI~~rvLKKfg~ 36 (105)
T PF14847_consen 11 STKTVNVSGC-FNAQEIKRRVLKKFGL 36 (105)
T ss_dssp EEEEEE--S---HHHHHHHHHHHHHTS
T ss_pred cEEEEEECCC-CCHHHHHHHHHHHcCC
Confidence 3447888887 9999999999888983
No 96
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=22.48 E-value=1.2e+02 Score=21.72 Aligned_cols=23 Identities=13% Similarity=0.351 Sum_probs=20.5
Q ss_pred CeEEEEeeccCHHHHHHHHHhhcC
Q 033712 31 DELVVIGNEVDSVKLTRKLQKKLG 54 (113)
Q Consensus 31 ~kvtV~G~~vDp~~l~~~LrKk~~ 54 (113)
+++++.|. +++..|-..|++-..
T Consensus 78 ~~lii~G~-~~~~~i~~~L~~yI~ 100 (138)
T PRK03988 78 GRLILQGK-FSPRVINEKIDRYVK 100 (138)
T ss_pred CEEEEEEe-eCHHHHHHHHHHHHH
Confidence 89999999 999999999987543
No 97
>COG1992 Uncharacterized conserved protein [Function unknown]
Probab=22.36 E-value=2.3e+02 Score=21.53 Aligned_cols=39 Identities=21% Similarity=0.240 Sum_probs=30.5
Q ss_pred HHHHHhcCCCeeEEEecCCCCC---eEEEEeeccCHHHHHHH-HH
Q 033712 10 AMKIAVKADGVIKVEIKGEGKD---ELVVIGNEVDSVKLTRK-LQ 50 (113)
Q Consensus 10 v~k~l~~~~GV~sV~vd~~~k~---kvtV~G~~vDp~~l~~~-Lr 50 (113)
+..++....|+-.|-+|...-+ .+.|-|. ||.+++++ |+
T Consensus 133 i~~a~~~~~~~PDVIyd~G~~GkEpmi~v~gr--~a~evv~k~l~ 175 (181)
T COG1992 133 IESAFRELGGAPDVIYDLGGVGKEPMIRVLGR--NAVEVVEKALR 175 (181)
T ss_pred HHHHHHhcCCCCCEEEeCCCCCcccEEEEeCC--CHHHHHHHHHH
Confidence 5667888888889999874444 7888886 79999998 54
No 98
>PRK06136 uroporphyrin-III C-methyltransferase; Reviewed
Probab=22.33 E-value=1.3e+02 Score=22.61 Aligned_cols=31 Identities=19% Similarity=0.170 Sum_probs=26.1
Q ss_pred CeEEEEeecc-CHHHHHHHHHhhcCceeEEec
Q 033712 31 DELVVIGNEV-DSVKLTRKLQKKLGFASLLSV 61 (113)
Q Consensus 31 ~kvtV~G~~v-Dp~~l~~~LrKk~~~aeivsv 61 (113)
++|.++|.+. ||.-|+-+.++....|++|-.
T Consensus 3 g~l~iVGvGpGdp~~lT~~A~~~L~~advI~~ 34 (249)
T PRK06136 3 GKVYLVGAGPGDPDLITLKGVRLLEQADVVLY 34 (249)
T ss_pred cEEEEEEECCCChHHHHHHHHHHHhcCCEEEE
Confidence 6899999988 899999888877788887765
No 99
>PRK00166 apaH diadenosine tetraphosphatase; Reviewed
Probab=22.22 E-value=2.1e+02 Score=22.56 Aligned_cols=40 Identities=28% Similarity=0.473 Sum_probs=29.4
Q ss_pred hHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeecc----CHHHHHHHHHh
Q 033712 5 KCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEV----DSVKLTRKLQK 51 (113)
Q Consensus 5 ~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~v----Dp~~l~~~LrK 51 (113)
||-...++.|.++. ++. ..+++.+.|+-+ ++..+++.|++
T Consensus 11 G~~~~l~~ll~~~~------~~~-~~D~li~lGDlVdrGp~s~~vl~~l~~ 54 (275)
T PRK00166 11 GCYDELQRLLEKID------FDP-AKDTLWLVGDLVNRGPDSLEVLRFVKS 54 (275)
T ss_pred CCHHHHHHHHHhcC------CCC-CCCEEEEeCCccCCCcCHHHHHHHHHh
Confidence 67778888887752 222 346899999955 59999999986
No 100
>TIGR00668 apaH bis(5'-nucleosyl)-tetraphosphatase (symmetrical). Alternate names include diadenosine-tetraphosphatase and Ap4A hydrolase.
Probab=21.93 E-value=2.4e+02 Score=22.56 Aligned_cols=40 Identities=20% Similarity=0.412 Sum_probs=30.6
Q ss_pred hHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeecc----CHHHHHHHHHh
Q 033712 5 KCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEV----DSVKLTRKLQK 51 (113)
Q Consensus 5 ~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~v----Dp~~l~~~LrK 51 (113)
||....++.|.++. ++. ..+++.+.|+-| |+..+++.|+.
T Consensus 11 Gc~daL~~LL~~i~------f~~-~~D~l~~lGDlVdRGP~slevL~~l~~ 54 (279)
T TIGR00668 11 GCYDELQALLERVE------FDP-GQDTLWLTGDLVARGPGSLEVLRYVKS 54 (279)
T ss_pred CCHHHHHHHHHHhC------cCC-CCCEEEEeCCccCCCCCHHHHHHHHHh
Confidence 68888888888763 333 457899999844 69999999986
No 101
>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=21.36 E-value=1.9e+02 Score=17.10 Aligned_cols=48 Identities=17% Similarity=0.057 Sum_probs=32.8
Q ss_pred chhHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeeccCHHHHHHHHHhh
Q 033712 3 CKKCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQKK 52 (113)
Q Consensus 3 Ce~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~LrKk 52 (113)
..+...++.++|... ||.-+.... ....+++.=+.-|..+++++|...
T Consensus 13 ~~gv~~~~~~~L~~~-~i~~i~~~~-s~~~is~vv~~~d~~~av~~LH~~ 60 (63)
T cd04920 13 LLHKLGPALEVFGKK-PVHLVSQAA-NDLNLTFVVDEDQADGLCARLHFQ 60 (63)
T ss_pred CccHHHHHHHHHhcC-CceEEEEeC-CCCeEEEEEeHHHHHHHHHHHHHH
Confidence 356778889999774 888888876 555664433325677777777643
No 102
>PRK15039 transcriptional repressor RcnR to maintain nickel and cobalt homeostasis; Provisional
Probab=21.01 E-value=54 Score=21.91 Aligned_cols=18 Identities=22% Similarity=0.185 Sum_probs=16.2
Q ss_pred CchhHHHHHHHHHhcCCC
Q 033712 2 TCKKCRKKAMKIAVKADG 19 (113)
Q Consensus 2 ~Ce~C~~kv~k~l~~~~G 19 (113)
|+...++++.++|.+++|
T Consensus 3 ~~~~~k~~ll~RL~RIeG 20 (90)
T PRK15039 3 HTIRDKQKLKARASKIQG 20 (90)
T ss_pred CcHHhHHHHHHHHHHHHH
Confidence 788889999999999988
No 103
>PRK11439 pphA serine/threonine protein phosphatase 1; Provisional
Probab=20.86 E-value=1.3e+02 Score=22.28 Aligned_cols=41 Identities=17% Similarity=0.340 Sum_probs=29.9
Q ss_pred hHHHHHHHHHhcCCCeeEEEecCCCCCeEEEEeecc----CHHHHHHHHHhh
Q 033712 5 KCRKKAMKIAVKADGVIKVEIKGEGKDELVVIGNEV----DSVKLTRKLQKK 52 (113)
Q Consensus 5 ~C~~kv~k~l~~~~GV~sV~vd~~~k~kvtV~G~~v----Dp~~l~~~LrKk 52 (113)
||....++.|.++. .+. ..++|...|+-+ |+..+++.|++.
T Consensus 27 G~~~~L~~lL~~i~------~~~-~~D~li~lGDlvDrGp~s~~vl~~l~~~ 71 (218)
T PRK11439 27 GCFEQLMRKLRHCR------FDP-WRDLLISVGDLIDRGPQSLRCLQLLEEH 71 (218)
T ss_pred CCHHHHHHHHHhcC------CCc-ccCEEEEcCcccCCCcCHHHHHHHHHcC
Confidence 57777888888762 222 347899899844 799999999863
No 104
>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=20.81 E-value=1.8e+02 Score=16.75 Aligned_cols=36 Identities=17% Similarity=0.364 Sum_probs=21.9
Q ss_pred HHHHhcCCCeeEEEecCCC-CCeEEEEeeccCHHHHHHHHH
Q 033712 11 MKIAVKADGVIKVEIKGEG-KDELVVIGNEVDSVKLTRKLQ 50 (113)
Q Consensus 11 ~k~l~~~~GV~sV~vd~~~-k~kvtV~G~~vDp~~l~~~Lr 50 (113)
.+.|....|+. |.++.++ ...++|.|. +..+..+++
T Consensus 22 i~~I~~~t~~~-I~i~~~~~~~~v~I~G~---~~~v~~A~~ 58 (60)
T PF00013_consen 22 IKEIEEETGVK-IQIPDDDERDIVTISGS---PEQVEKAKK 58 (60)
T ss_dssp HHHHHHHHTSE-EEEESTTEEEEEEEEES---HHHHHHHHH
T ss_pred HHHhhhhcCeE-EEEcCCCCcEEEEEEeC---HHHHHHHHh
Confidence 44455555776 7776411 348999996 666655543
No 105
>PRK06719 precorrin-2 dehydrogenase; Validated
Probab=20.81 E-value=1.8e+02 Score=20.74 Aligned_cols=39 Identities=15% Similarity=0.192 Sum_probs=26.5
Q ss_pred EEEecCCCCCeEEEEeeccCHHHHHHHHHhhcCceeEEec
Q 033712 22 KVEIKGEGKDELVVIGNEVDSVKLTRKLQKKLGFASLLSV 61 (113)
Q Consensus 22 sV~vd~~~k~kvtV~G~~vDp~~l~~~LrKk~~~aeivsv 61 (113)
-+-++. ...++.|+|.|-=....++.|.+....+.+|+.
T Consensus 6 P~~l~l-~~~~vlVvGGG~va~rka~~Ll~~ga~V~VIsp 44 (157)
T PRK06719 6 PLMFNL-HNKVVVIIGGGKIAYRKASGLKDTGAFVTVVSP 44 (157)
T ss_pred ceEEEc-CCCEEEEECCCHHHHHHHHHHHhCCCEEEEEcC
Confidence 355677 567999999875566667777753337777753
No 106
>PRK13625 bis(5'-nucleosyl)-tetraphosphatase PrpE; Provisional
Probab=20.70 E-value=1.8e+02 Score=22.15 Aligned_cols=46 Identities=11% Similarity=0.222 Sum_probs=30.8
Q ss_pred hHHHHHHHHHhcCCC--eeEEEecCCCCCeEEEEeecc----CHHHHHHHHHh
Q 033712 5 KCRKKAMKIAVKADG--VIKVEIKGEGKDELVVIGNEV----DSVKLTRKLQK 51 (113)
Q Consensus 5 ~C~~kv~k~l~~~~G--V~sV~vd~~~k~kvtV~G~~v----Dp~~l~~~LrK 51 (113)
||.....+.|.++.= ...+.... .++++...|+-+ |...+++.|++
T Consensus 11 G~~~~L~~lL~~~~~~~~~~~~~~~-~~d~li~lGDliDRGp~S~~vl~~~~~ 62 (245)
T PRK13625 11 GCYQEFQALTEKLGYNWSSGLPVHP-DQRKLAFVGDLTDRGPHSLRMIEIVWE 62 (245)
T ss_pred cCHHHHHHHHHHcCCCcccCcccCC-CCCEEEEECcccCCCcChHHHHHHHHH
Confidence 788888888887631 11122222 457999999955 48888888875
No 107
>smart00749 BON bacterial OsmY and nodulation domain.
Probab=20.68 E-value=1.7e+02 Score=16.19 Aligned_cols=40 Identities=15% Similarity=0.111 Sum_probs=24.1
Q ss_pred HHHHHHHhcCCCeeE--EEecCCCCCeEEEEeeccCHHHHHHHH
Q 033712 8 KKAMKIAVKADGVIK--VEIKGEGKDELVVIGNEVDSVKLTRKL 49 (113)
Q Consensus 8 ~kv~k~l~~~~GV~s--V~vd~~~k~kvtV~G~~vDp~~l~~~L 49 (113)
.++...|...+.+.+ +.+.. ..+.+++.|. +++..-....
T Consensus 2 ~~v~~~l~~~~~~~~~~~~v~~-~~~~vvL~g~-~~~~~~~~~~ 43 (62)
T smart00749 2 EKVKKALAKDGLIKADSIVVVT-DGGVVVLLGG-VVDNAEAAAA 43 (62)
T ss_pred hhHHHHHhhCCCCCcCceEEEE-ECCEEEEeee-cCCHHHHHHH
Confidence 456677766665554 44443 4578888888 6555444433
No 108
>PF12971 NAGLU_N: Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain; InterPro: IPR024240 Alpha-N-acetylglucosaminidase, is a lysosomal enzyme required for the stepwise degradation of heparan sulphate []. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations []. The structure shows that the enzyme is composed of three domains. This entry represents the N-terminal domain of Alpha-N-acetylglucosaminidase which has an alpha-beta fold [].; PDB: 4A4A_A 2VC9_A 2VCC_A 2VCB_A 2VCA_A.
Probab=20.24 E-value=2.5e+02 Score=18.09 Aligned_cols=38 Identities=24% Similarity=0.348 Sum_probs=22.7
Q ss_pred CeeEEEecCCCCCeEEEEeeccCHHHHHHHHH---hhcCceeE
Q 033712 19 GVIKVEIKGEGKDELVVIGNEVDSVKLTRKLQ---KKLGFASL 58 (113)
Q Consensus 19 GV~sV~vd~~~k~kvtV~G~~vDp~~l~~~Lr---Kk~~~aei 58 (113)
|-+..++.....++|+|.|. ++..|+.-|. |-.+++.|
T Consensus 30 ~~d~F~l~~~~~gki~I~G~--s~vala~Gl~~YLk~~c~~~i 70 (86)
T PF12971_consen 30 GKDVFELSSADNGKIVIRGN--SGVALASGLNWYLKYYCHVHI 70 (86)
T ss_dssp TBEEEEEEE-SSS-EEEEES--SHHHHHHHHHHHHHHHS--B-
T ss_pred CCCEEEEEeCCCCeEEEEeC--CHHHHHHHHHHHHHHHhCceE
Confidence 66677766435579999998 4788877664 23455554
Done!