Query 043434
Match_columns 90
No_of_seqs 107 out of 519
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 05:01:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043434.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043434hhsearch_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 7.2E-16 1.6E-20 96.1 7.4 58 1-59 13-71 (73)
2 PF00403 HMA: Heavy-metal-asso 99.2 1.1E-10 2.3E-15 69.3 6.4 49 1-50 7-58 (62)
3 COG2608 CopZ Copper chaperone 98.3 2E-06 4.4E-11 53.2 6.0 51 1-52 11-64 (71)
4 KOG4656 Copper chaperone for s 97.9 3E-05 6.4E-10 58.4 6.2 61 1-62 15-75 (247)
5 PLN02957 copper, zinc superoxi 97.6 0.00052 1.1E-08 51.0 8.0 63 1-64 14-76 (238)
6 PRK10671 copA copper exporting 96.7 0.0039 8.4E-08 53.3 5.8 56 1-59 12-67 (834)
7 COG2217 ZntA Cation transport 94.4 0.12 2.6E-06 44.4 6.1 55 1-57 11-69 (713)
8 TIGR00003 copper ion binding p 93.2 0.29 6.2E-06 25.5 4.3 48 1-49 11-61 (68)
9 PRK10671 copA copper exporting 93.0 0.28 6.1E-06 42.1 6.0 51 1-53 108-158 (834)
10 KOG0207 Cation transport ATPas 86.4 1.9 4.1E-05 38.5 5.7 60 1-61 3-64 (951)
11 PF02680 DUF211: Uncharacteriz 85.9 1.7 3.7E-05 28.9 4.1 44 10-53 22-72 (95)
12 PRK11033 zntA zinc/cadmium/mer 81.8 2.8 6.2E-05 35.9 4.8 48 1-50 62-111 (741)
13 KOG0207 Cation transport ATPas 80.7 5.1 0.00011 35.9 6.0 58 1-59 155-215 (951)
14 COG1888 Uncharacterized protei 78.7 5.5 0.00012 26.6 4.4 43 11-53 25-74 (97)
15 PF13732 DUF4162: Domain of un 70.9 16 0.00035 21.9 4.9 40 13-52 25-64 (84)
16 COG1432 Uncharacterized conser 62.8 12 0.00025 26.7 3.5 31 32-62 114-144 (181)
17 cd06167 LabA_like LabA_like pr 61.3 14 0.0003 24.4 3.5 30 32-61 103-132 (149)
18 cd04888 ACT_PheB-BS C-terminal 60.1 12 0.00026 21.7 2.7 20 6-25 55-74 (76)
19 PF01883 DUF59: Domain of unkn 59.4 12 0.00025 22.2 2.6 20 6-25 53-72 (72)
20 PF05193 Peptidase_M16_C: Pept 59.3 11 0.00024 24.3 2.7 24 30-53 19-42 (184)
21 PF04972 BON: BON domain; Int 57.4 6.3 0.00014 22.7 1.1 35 9-45 3-40 (64)
22 PF01936 NYN: NYN domain; Int 55.4 18 0.00039 23.4 3.2 29 32-60 99-127 (146)
23 PF08712 Nfu_N: Scaffold prote 54.7 47 0.001 21.0 5.0 39 11-52 40-80 (87)
24 PF14492 EFG_II: Elongation Fa 54.0 46 0.00099 20.2 4.7 44 9-53 23-68 (75)
25 TIGR00288 conserved hypothetic 51.1 27 0.00058 25.0 3.7 30 32-61 109-138 (160)
26 PF02107 FlgH: Flagellar L-rin 48.9 13 0.00028 26.6 1.9 29 16-45 110-138 (179)
27 PF03927 NapD: NapD protein; 48.4 65 0.0014 20.0 6.2 42 7-50 17-59 (79)
28 cd03309 CmuC_like CmuC_like. P 48.0 17 0.00037 28.2 2.5 42 2-45 218-270 (321)
29 cd02643 R3H_NF-X1 R3H domain o 47.4 42 0.00092 20.6 3.8 30 7-36 44-73 (74)
30 PRK10553 assembly protein for 47.1 75 0.0016 20.4 6.0 52 7-59 19-76 (87)
31 smart00653 eIF2B_5 domain pres 46.7 36 0.00079 22.7 3.6 30 22-53 49-78 (110)
32 PRK10555 aminoglycoside/multid 46.4 46 0.00099 29.7 5.1 42 7-51 159-210 (1037)
33 PF09358 UBA_e1_C: Ubiquitin-a 45.9 41 0.00089 22.7 3.9 32 31-62 35-67 (125)
34 cd04910 ACT_AK-Ectoine_1 ACT d 45.3 73 0.0016 19.7 4.7 50 6-57 17-69 (71)
35 PHA00514 dsDNA binding protein 45.3 42 0.00092 22.2 3.7 34 31-64 32-67 (98)
36 PF01424 R3H: R3H domain; Int 44.4 48 0.001 19.0 3.6 30 7-36 32-61 (63)
37 KOG3411 40S ribosomal protein 44.4 19 0.00042 25.5 2.1 44 4-50 97-140 (143)
38 PRK09577 multidrug efflux prot 43.5 52 0.0011 29.4 5.1 45 7-52 158-210 (1032)
39 PF05922 Inhibitor_I9: Peptida 42.5 35 0.00075 20.0 2.8 19 9-27 59-77 (82)
40 PRK15127 multidrug efflux syst 42.1 57 0.0012 29.2 5.1 34 8-44 160-193 (1049)
41 cd04920 ACT_AKiii-DAPDC_2 ACT 41.1 72 0.0016 18.4 5.3 48 3-52 13-61 (63)
42 PF07683 CobW_C: Cobalamin syn 40.7 35 0.00076 20.7 2.7 22 29-50 70-92 (94)
43 COG0612 PqqL Predicted Zn-depe 40.7 42 0.00091 26.2 3.7 25 29-53 197-221 (438)
44 PRK11023 outer membrane lipopr 40.3 46 0.001 23.8 3.6 42 6-48 50-94 (191)
45 KOG3166 60S ribosomal protein 40.0 17 0.00037 27.2 1.4 32 17-48 111-144 (209)
46 TIGR00915 2A0602 The (Largely 39.8 63 0.0014 28.9 5.0 43 7-50 159-209 (1044)
47 PF07338 DUF1471: Protein of u 39.4 44 0.00096 19.6 2.8 32 31-62 6-43 (56)
48 cd04877 ACT_TyrR N-terminal AC 38.7 36 0.00078 20.1 2.5 18 8-25 52-69 (74)
49 PF06357 Omega-toxin: Omega-at 38.7 17 0.00037 20.1 0.9 11 78-88 9-19 (37)
50 PF05137 PilN: Fimbrial assemb 38.7 81 0.0018 18.3 4.4 41 21-64 17-63 (78)
51 PF12164 SporV_AA: Stage V spo 38.2 46 0.001 21.5 3.0 26 39-64 57-82 (93)
52 PF03958 Secretin_N: Bacterial 38.0 76 0.0016 18.7 3.9 20 22-42 47-66 (82)
53 PRK13748 putative mercuric red 37.3 1.4E+02 0.0031 24.0 6.4 49 1-50 9-59 (561)
54 PF08478 POTRA_1: POTRA domain 35.1 37 0.0008 19.5 2.1 28 8-35 37-64 (69)
55 PRK09579 multidrug efflux prot 35.0 86 0.0019 28.0 5.1 45 7-51 158-210 (1017)
56 cd00371 HMA Heavy-metal-associ 34.5 50 0.0011 14.7 6.1 47 1-48 7-55 (63)
57 PF15023 DUF4523: Protein of u 33.9 58 0.0012 23.6 3.2 44 8-52 105-149 (166)
58 COG3643 Glutamate formiminotra 33.7 83 0.0018 24.7 4.2 52 8-59 21-74 (302)
59 TIGR00489 aEF-1_beta translati 33.4 47 0.001 21.5 2.5 23 5-27 62-84 (88)
60 cd04879 ACT_3PGDH-like ACT_3PG 33.2 59 0.0013 17.7 2.7 18 8-25 53-70 (71)
61 cd00141 NT_POLXc Nucleotidyltr 33.1 75 0.0016 24.4 4.0 45 7-51 147-204 (307)
62 PRK12697 flgH flagellar basal 32.2 34 0.00073 25.8 1.9 28 17-45 157-184 (226)
63 cd07422 MPP_ApaH Escherichia c 31.9 1.3E+02 0.0028 22.6 5.0 44 5-55 9-57 (257)
64 cd06471 ACD_LpsHSP_like Group 31.8 26 0.00056 21.6 1.0 25 15-40 16-42 (93)
65 PRK12698 flgH flagellar basal 31.7 36 0.00077 25.5 1.9 28 17-45 154-181 (224)
66 PRK10503 multidrug efflux syst 31.5 1.1E+02 0.0023 27.5 5.1 35 8-44 169-203 (1040)
67 smart00833 CobW_C Cobalamin sy 31.1 67 0.0015 19.2 2.8 21 30-50 69-90 (92)
68 PRK00249 flgH flagellar basal 30.4 39 0.00085 25.2 2.0 28 17-45 153-180 (222)
69 PRK12788 flgH flagellar basal 30.1 39 0.00084 25.6 1.9 28 17-45 165-192 (234)
70 PRK12407 flgH flagellar basal 30.1 38 0.00083 25.3 1.9 28 17-45 151-178 (221)
71 PRK10614 multidrug efflux syst 29.5 1.2E+02 0.0026 27.1 5.1 36 7-44 159-194 (1025)
72 COG3062 NapD Uncharacterized p 29.2 1.8E+02 0.0038 19.3 5.4 41 7-49 20-61 (94)
73 cd04878 ACT_AHAS N-terminal AC 28.5 58 0.0013 17.8 2.1 17 8-24 56-72 (72)
74 COG4004 Uncharacterized protei 28.4 97 0.0021 20.6 3.3 24 13-37 35-58 (96)
75 PRK11198 LysM domain/BON super 28.3 1.5E+02 0.0032 20.3 4.4 47 6-56 27-77 (147)
76 PF00873 ACR_tran: AcrB/AcrD/A 28.0 85 0.0018 27.7 3.9 36 7-44 158-193 (1021)
77 cd04901 ACT_3PGDH C-terminal A 27.9 82 0.0018 17.6 2.7 17 9-25 52-68 (69)
78 PRK12701 flgH flagellar basal 27.3 46 0.001 25.0 1.9 28 17-45 160-187 (230)
79 PRK00166 apaH diadenosine tetr 27.0 1.5E+02 0.0033 22.5 4.7 40 5-51 11-55 (275)
80 PRK12700 flgH flagellar basal 26.6 49 0.0011 24.9 1.9 28 17-45 161-188 (230)
81 PF13363 BetaGal_dom3: Beta-ga 26.6 87 0.0019 19.9 2.8 19 20-41 26-44 (79)
82 TIGR02945 SUF_assoc FeS assemb 26.5 67 0.0015 20.1 2.3 21 7-27 57-77 (99)
83 PRK12696 flgH flagellar basal 26.0 49 0.0011 25.0 1.8 28 17-45 167-194 (236)
84 COG2177 FtsX Cell division pro 25.7 1.6E+02 0.0036 22.8 4.7 38 4-54 71-108 (297)
85 PRK12699 flgH flagellar basal 25.7 51 0.0011 25.1 1.9 28 17-45 178-205 (246)
86 cd06464 ACD_sHsps-like Alpha-c 25.6 37 0.0008 19.9 0.9 25 15-40 13-39 (88)
87 PRK00435 ef1B elongation facto 24.8 73 0.0016 20.6 2.2 23 5-27 62-84 (88)
88 KOG3167 Box H/ACA snoRNP compo 24.7 16 0.00034 26.2 -1.0 44 5-49 49-95 (153)
89 cd04903 ACT_LSD C-terminal ACT 24.5 95 0.0021 16.9 2.5 18 8-25 53-70 (71)
90 COG0841 AcrB Cation/multidrug 24.0 1.7E+02 0.0036 26.6 5.0 36 7-44 157-192 (1009)
91 PHA01634 hypothetical protein 23.6 25 0.00054 25.2 -0.1 11 1-11 98-108 (156)
92 PF01873 eIF-5_eIF-2B: Domain 23.1 56 0.0012 22.3 1.5 30 22-53 62-91 (125)
93 PF07744 SPOC: SPOC domain; I 23.0 1.1E+02 0.0023 19.4 2.8 23 30-52 38-60 (119)
94 TIGR00668 apaH bis(5'-nucleosy 22.9 2.2E+02 0.0047 22.0 4.9 44 5-55 11-59 (279)
95 PRK10568 periplasmic protein; 22.1 2.3E+02 0.0049 20.4 4.6 35 6-41 61-97 (203)
96 cd04887 ACT_MalLac-Enz ACT_Mal 21.7 1.3E+02 0.0027 17.2 2.7 19 7-25 54-72 (74)
97 PF11065 DUF2866: Protein of u 21.7 1.2E+02 0.0025 18.9 2.6 32 20-52 23-55 (65)
98 cd04876 ACT_RelA-SpoT ACT dom 21.7 1.2E+02 0.0026 15.7 2.5 18 7-24 53-70 (71)
99 KOG2768 Translation initiation 21.6 98 0.0021 23.6 2.7 37 21-59 149-186 (231)
100 cd06472 ACD_ScHsp26_like Alpha 21.6 73 0.0016 19.7 1.7 25 15-39 15-41 (92)
101 KOG2239 Transcription factor c 21.5 1.6E+02 0.0034 22.2 3.7 44 6-49 65-129 (209)
102 PRK13625 bis(5'-nucleosyl)-tet 21.0 1.9E+02 0.004 21.2 4.1 46 5-51 11-63 (245)
103 COG2092 EFB1 Translation elong 20.7 89 0.0019 20.5 2.0 20 7-26 64-83 (88)
104 PRK11439 pphA serine/threonine 20.6 1.4E+02 0.003 21.4 3.3 40 5-51 27-71 (218)
105 PF10105 DUF2344: Uncharacteri 20.5 1.9E+02 0.004 20.8 3.9 33 32-64 65-98 (187)
106 PRK10743 heat shock protein Ib 20.4 45 0.00098 22.9 0.6 24 15-39 51-76 (137)
107 PLN03175 hypothetical protein; 20.2 1.2E+02 0.0025 25.1 3.0 35 18-52 236-271 (415)
No 1
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.65 E-value=7.2e-16 Score=96.15 Aligned_cols=58 Identities=26% Similarity=0.414 Sum_probs=53.9
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccHHHHHHHHHhhc-CceEEEe
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKI-GYVEMMK 59 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~lv~~LrKk~-~~aeivs 59 (90)
|||+||++++.+.+..++||+++.+|. .+++|||+|++||..|+++|+|++ +++++|.
T Consensus 13 ~~C~gc~~kV~~~l~~~~GV~~v~id~-~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 13 MHCEGCARKVKRVLQKLKGVESVDIDI-KKQKVTVKGNVDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred cccccHHHHHHHHhhccCCeEEEEecC-CCCEEEEEEecCHHHHHHHHHhcCCCceEEec
Confidence 899999999999999999999999998 999999999999999999999977 4666654
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=1.1e-10 Score=69.31 Aligned_cols=49 Identities=18% Similarity=0.308 Sum_probs=45.9
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEec---cHHHHHHHHHh
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDI---DEVALANMLRR 50 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~v---Dp~~lv~~LrK 50 (90)
|+|++|++++.+++.+++||.++.+|. ..++++|.++. ++..|.+.|++
T Consensus 7 m~C~~C~~~v~~~l~~~~GV~~v~vd~-~~~~v~v~~~~~~~~~~~i~~~i~~ 58 (62)
T PF00403_consen 7 MTCEGCAKKVEKALSKLPGVKSVKVDL-ETKTVTVTYDPDKTSIEKIIEAIEK 58 (62)
T ss_dssp TTSHHHHHHHHHHHHTSTTEEEEEEET-TTTEEEEEESTTTSCHHHHHHHHHH
T ss_pred cccHHHHHHHHHHHhcCCCCcEEEEEC-CCCEEEEEEecCCCCHHHHHHHHHH
Confidence 899999999999999999999999998 89999999994 56999999986
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.34 E-value=2e-06 Score=53.22 Aligned_cols=51 Identities=14% Similarity=0.180 Sum_probs=44.3
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCC--CcEEEEEe-ccHHHHHHHHHhhc
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDL--RHMEVIGD-IDEVALANMLRRKI 52 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~--~kvtV~G~-vDp~~lv~~LrKk~ 52 (90)
|+|..|...+.++|.+++||.++.++. .+ ..|++.+. ++...+...+...+
T Consensus 11 MtC~~C~~~V~~al~~v~gv~~v~v~l-~~~~~~V~~d~~~~~~~~i~~ai~~aG 64 (71)
T COG2608 11 MTCGHCVKTVEKALEEVDGVASVDVDL-EKGTATVTFDSNKVDIEAIIEAIEDAG 64 (71)
T ss_pred cCcHHHHHHHHHHHhcCCCeeEEEEEc-ccCeEEEEEcCCcCCHHHHHHHHHHcC
Confidence 899999999999999999999999998 77 46666663 89999999998533
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=97.93 E-value=3e-05 Score=58.35 Aligned_cols=61 Identities=16% Similarity=0.197 Sum_probs=54.7
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccHHHHHHHHHhhcCceEEEecCC
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKIGYVEMMKLDI 62 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~lv~~LrKk~~~aeivsv~p 62 (90)
|||+.|...+++.+..++||++|++|. +++.|.|-+.+-|..+...|+.-.+.|.|.-.+.
T Consensus 15 M~cescvnavk~~L~~V~Gi~~vevdl-e~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G~ 75 (247)
T KOG4656|consen 15 MTCESCVNAVKACLKGVPGINSVEVDL-EQQIVSVETSVPPSEIQNTLENTGRDAVLRGAGK 75 (247)
T ss_pred chhHHHHHHHHHHhccCCCcceEEEEh-hhcEEEEEccCChHHHHHHHHhhChheEEecCCc
Confidence 899999999999999999999999998 8889999999999999999996556777765543
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=97.57 E-value=0.00052 Score=51.04 Aligned_cols=63 Identities=13% Similarity=0.158 Sum_probs=54.3
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccHHHHHHHHHhhcCceEEEecCCCC
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKIGYVEMMKLDILD 64 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~lv~~LrKk~~~aeivsv~p~k 64 (90)
|+|+.|..++.+.+..++||.++.++. ..++++|.+.+++..++..|++-...+++++.+...
T Consensus 14 MsC~~Ca~~Iek~L~~~~GV~~v~vn~-~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 14 MKCEGCVAAVKNKLETLEGVKAVEVDL-SNQVVRVLGSSPVKAMTAALEQTGRKARLIGQGDPE 76 (238)
T ss_pred ccCHHHHHHHHHHHhcCCCeEEEEEEc-CCCEEEEEecCCHHHHHHHHHHcCCcEEEecCCCcc
Confidence 789999999999999999999999998 888999999889999999998544467777765554
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.68 E-value=0.0039 Score=53.25 Aligned_cols=56 Identities=11% Similarity=0.137 Sum_probs=48.3
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccHHHHHHHHHhhcCceEEEe
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKIGYVEMMK 59 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~lv~~LrKk~~~aeivs 59 (90)
|+|..|.+++.+++.+++||.++.++. ++.+|.+..++..+...++.-+-.+++.+
T Consensus 12 mtC~~C~~~i~~al~~~~gv~~v~v~~---~~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 12 LSCGHCVKRVKESLEQRPDVEQADVSI---TEAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred cccHHHHHHHHHHHhcCCCcceEEEee---eEEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 899999999999999999999999997 35677788999999999986444677654
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=94.39 E-value=0.12 Score=44.41 Aligned_cols=55 Identities=13% Similarity=0.245 Sum_probs=46.5
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe---cc-HHHHHHHHHhhcCceEE
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD---ID-EVALANMLRRKIGYVEM 57 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~---vD-p~~lv~~LrKk~~~aei 57 (90)
|||..|.+++. .+.+++||++..++. ..++++|..+ .+ +..+...+++..-.+..
T Consensus 11 m~Ca~C~~~ie-~l~~~~gV~~~~vn~-~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 11 MTCAACASRIE-ALNKLPGVEEARVNL-ATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred cCcHHHHHHHH-HHhcCCCeeEEEeec-ccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 89999999999 999999999999997 8899999876 56 78888888864434443
No 8
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=93.23 E-value=0.29 Score=25.53 Aligned_cols=48 Identities=21% Similarity=0.310 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe---ccHHHHHHHHH
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD---IDEVALANMLR 49 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~---vDp~~lv~~Lr 49 (90)
|+|..|...+.+.+..+.|+.+..++. ..+.+.+..+ .+...+...+.
T Consensus 11 ~~~~~c~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 61 (68)
T TIGR00003 11 MTCQHCVDKIEKFVGELEGVSKVQVKL-EKASVKVEFDAPQATEICIAEAIL 61 (68)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEc-CCCEEEEEeCCCCCCHHHHHHHHH
Confidence 469999999999999999999999997 7778877642 56777766554
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=92.98 E-value=0.28 Score=42.08 Aligned_cols=51 Identities=18% Similarity=0.356 Sum_probs=44.7
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccHHHHHHHHHhhcC
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKIG 53 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~lv~~LrKk~~ 53 (90)
|||..|...+.+.+..++||.++.++. ..+++.|.+..++..+...++. .+
T Consensus 108 m~Ca~Ca~~Ie~~L~~~~GV~~a~vnl-~t~~~~V~~~~s~~~I~~~I~~-~G 158 (834)
T PRK10671 108 MSCASCVSRVQNALQSVPGVTQARVNL-AERTALVMGSASPQDLVQAVEK-AG 158 (834)
T ss_pred cCcHHHHHHHHHHHhcCCCceeeeeec-CCCeEEEEccCCHHHHHHHHHh-cC
Confidence 799999999999999999999999997 7778888877888888888874 44
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=86.42 E-value=1.9 Score=38.50 Aligned_cols=60 Identities=12% Similarity=0.159 Sum_probs=48.6
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe--ccHHHHHHHHHhhcCceEEEecC
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD--IDEVALANMLRRKIGYVEMMKLD 61 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~--vDp~~lv~~LrKk~~~aeivsv~ 61 (90)
|.|..|...+.+.+++.+||.++++.. ..++.+|.=+ +++..+.+.+.--+..+++++-.
T Consensus 3 mtc~ac~~si~~~~~~~~g~~~i~vsl-~~~~~~v~~~~~~~~~~i~~~ied~gf~~~~~~~~ 64 (951)
T KOG0207|consen 3 MTCSACSNSIEKAISRKPGVQKIEVSL-AQKRANVSYDNIVSPESIKETIEDMGFEASLLSDS 64 (951)
T ss_pred ccHHHHhhhHHHHHhcCCCceeEEEEe-ccccceEEEeeccCHHHHHHHhhcccceeeecccC
Confidence 789999999999999999999999997 5554444433 89999999998655577777643
No 11
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=85.88 E-value=1.7 Score=28.87 Aligned_cols=44 Identities=16% Similarity=0.247 Sum_probs=31.7
Q ss_pred HHHHHhCCCCeeEEEe-----CCCCCC-cEEEEEe-ccHHHHHHHHHhhcC
Q 043434 10 AFQIIAGFPGLLSVAM-----KGDDLR-HMEVIGD-IDEVALANMLRRKIG 53 (90)
Q Consensus 10 v~k~v~~~~GV~sv~i-----d~~~~~-kvtV~G~-vDp~~lv~~LrKk~~ 53 (90)
.-+.+++++||+.|.+ |.+-.+ ++||.|+ +|-..+.+.|.+-++
T Consensus 22 ~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg 72 (95)
T PF02680_consen 22 LAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGG 72 (95)
T ss_dssp HHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-
T ss_pred HHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCC
Confidence 3457889999998765 442223 8999999 999999999986544
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=81.75 E-value=2.8 Score=35.85 Aligned_cols=48 Identities=19% Similarity=0.322 Sum_probs=37.2
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe--ccHHHHHHHHHh
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD--IDEVALANMLRR 50 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~--vDp~~lv~~LrK 50 (90)
|+|..|..++.+.+.+++||.++.++. ..+++.+..+ .+ ..+...++.
T Consensus 62 m~C~sCa~~Ie~aL~~~~GV~~v~Vn~-at~k~~V~~d~~~~-~~I~~aI~~ 111 (741)
T PRK11033 62 MDCPSCARKVENAVRQLAGVNQVQVLF-ATEKLVVDADNDIR-AQVESAVQK 111 (741)
T ss_pred CCcHHHHHHHHHHHhcCCCeeeEEEEc-CCCeEEEEecccch-HHHHHHHHh
Confidence 789999999999999999999999996 6777776643 22 445455553
No 13
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=80.74 E-value=5.1 Score=35.91 Aligned_cols=58 Identities=14% Similarity=0.114 Sum_probs=46.4
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe---ccHHHHHHHHHhhcCceEEEe
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD---IDEVALANMLRRKIGYVEMMK 59 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~---vDp~~lv~~LrKk~~~aeivs 59 (90)
|.|+.|..++.+.+.+++||.+++++. ..+++.|.=+ .-|-++.+.|-...-.+.+..
T Consensus 155 ~~c~s~~~~ie~~l~~l~gV~~~sv~~-~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~ 215 (951)
T KOG0207|consen 155 MTCASCVSKIESILERLRGVKSFSVSL-ATDTAIVVYDPEITGPRDIIKAIEETGFEASVRP 215 (951)
T ss_pred ccccchhhhhHHHHhhccCeeEEEEec-cCCceEEEecccccChHHHHHHHHhhcccceeee
Confidence 679999999999999999999999998 8888888766 567777777765443444443
No 14
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=78.75 E-value=5.5 Score=26.55 Aligned_cols=43 Identities=12% Similarity=0.215 Sum_probs=31.5
Q ss_pred HHHHhCCCCeeEEEe-----CCCCCC-cEEEEEe-ccHHHHHHHHHhhcC
Q 043434 11 FQIIAGFPGLLSVAM-----KGDDLR-HMEVIGD-IDEVALANMLRRKIG 53 (90)
Q Consensus 11 ~k~v~~~~GV~sv~i-----d~~~~~-kvtV~G~-vDp~~lv~~LrKk~~ 53 (90)
-+.+++++||+.|.+ |.+-.+ ++||-|. +|=..+.+.|..-++
T Consensus 25 A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg 74 (97)
T COG1888 25 ALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGG 74 (97)
T ss_pred HHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCC
Confidence 355677888876644 443333 8999999 999999999986555
No 15
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=70.93 E-value=16 Score=21.93 Aligned_cols=40 Identities=23% Similarity=0.253 Sum_probs=31.2
Q ss_pred HHhCCCCeeEEEeCCCCCCcEEEEEeccHHHHHHHHHhhc
Q 043434 13 IIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKI 52 (90)
Q Consensus 13 ~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~lv~~LrKk~ 52 (90)
.+..++||.++..+.+..-.+.+....++..|++.|..+.
T Consensus 25 ~l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~~~g 64 (84)
T PF13732_consen 25 ELEELPGVESVEQDGDGKLRIKLEDEETANELLQELIEKG 64 (84)
T ss_pred HHhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHHhCC
Confidence 3677899999998652225788888889999999998654
No 16
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=62.82 E-value=12 Score=26.69 Aligned_cols=31 Identities=26% Similarity=0.205 Sum_probs=27.8
Q ss_pred cEEEEEeccHHHHHHHHHhhcCceEEEecCC
Q 043434 32 HMEVIGDIDEVALANMLRRKIGYVEMMKLDI 62 (90)
Q Consensus 32 kvtV~G~vDp~~lv~~LrKk~~~aeivsv~p 62 (90)
-+.++|+-|=.-+++.++.+++++++++.++
T Consensus 114 ivl~SgD~DF~p~v~~~~~~G~rv~v~~~~~ 144 (181)
T COG1432 114 IVLFSGDGDFIPLVEAARDKGKRVEVAGIEP 144 (181)
T ss_pred EEEEcCCccHHHHHHHHHHcCCEEEEEecCC
Confidence 4568899998999999999999999999887
No 17
>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=61.33 E-value=14 Score=24.37 Aligned_cols=30 Identities=30% Similarity=0.253 Sum_probs=26.6
Q ss_pred cEEEEEeccHHHHHHHHHhhcCceEEEecC
Q 043434 32 HMEVIGDIDEVALANMLRRKIGYVEMMKLD 61 (90)
Q Consensus 32 kvtV~G~vDp~~lv~~LrKk~~~aeivsv~ 61 (90)
=+.|+|+-|=.-++++||.++..+.+++..
T Consensus 103 ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~ 132 (149)
T cd06167 103 IVLVSGDSDFVPLVERLRELGKRVIVVGFE 132 (149)
T ss_pred EEEEECCccHHHHHHHHHHcCCEEEEEccC
Confidence 466899999999999999988899998876
No 18
>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=60.05 E-value=12 Score=21.70 Aligned_cols=20 Identities=10% Similarity=0.152 Sum_probs=17.2
Q ss_pred HHHHHHHHHhCCCCeeEEEe
Q 043434 6 CRTKAFQIIAGFPGLLSVAM 25 (90)
Q Consensus 6 C~~Kv~k~v~~~~GV~sv~i 25 (90)
--..+++.+.+++||.+|.+
T Consensus 55 ~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 55 DIDELLEELREIDGVEKVEL 74 (76)
T ss_pred HHHHHHHHHhcCCCeEEEEE
Confidence 34678999999999999986
No 19
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=59.44 E-value=12 Score=22.23 Aligned_cols=20 Identities=25% Similarity=0.448 Sum_probs=16.0
Q ss_pred HHHHHHHHHhCCCCeeEEEe
Q 043434 6 CRTKAFQIIAGFPGLLSVAM 25 (90)
Q Consensus 6 C~~Kv~k~v~~~~GV~sv~i 25 (90)
=+..+..++..++||.+|++
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 35788899999999999975
No 20
>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=59.31 E-value=11 Score=24.28 Aligned_cols=24 Identities=25% Similarity=0.524 Sum_probs=20.6
Q ss_pred CCcEEEEEeccHHHHHHHHHhhcC
Q 043434 30 LRHMEVIGDIDEVALANMLRRKIG 53 (90)
Q Consensus 30 ~~kvtV~G~vDp~~lv~~LrKk~~ 53 (90)
+-.+.++|++|+..+.+.+.+.++
T Consensus 19 n~~l~i~Gd~~~~~~~~~i~~~~~ 42 (184)
T PF05193_consen 19 NMTLVIVGDIDPDELEKLIEKYFG 42 (184)
T ss_dssp GEEEEEEESSGHHHHHHHHHHHHT
T ss_pred ceEEEEEcCccHHHHHHHHHhhhh
Confidence 347899999999999999998775
No 21
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=57.39 E-value=6.3 Score=22.67 Aligned_cols=35 Identities=9% Similarity=0.186 Sum_probs=17.5
Q ss_pred HHHHHHhC---CCCeeEEEeCCCCCCcEEEEEeccHHHHH
Q 043434 9 KAFQIIAG---FPGLLSVAMKGDDLRHMEVIGDIDEVALA 45 (90)
Q Consensus 9 Kv~k~v~~---~~GV~sv~id~~~~~kvtV~G~vDp~~lv 45 (90)
+++..+.. +++- +|.+.. ..+.|+++|.++.....
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v-~~g~v~L~G~v~s~~~~ 40 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSV-ENGVVTLSGEVPSQEQR 40 (64)
T ss_dssp ----------CTT-T-TEEEEE-ECTEEEEEEEESSCHHH
T ss_pred ccccccccccccCCC-eEEEEE-ECCEEEEEeeCcHHHHH
Confidence 44444444 4454 566665 67899999998444333
No 22
>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=55.39 E-value=18 Score=23.38 Aligned_cols=29 Identities=28% Similarity=0.208 Sum_probs=20.5
Q ss_pred cEEEEEeccHHHHHHHHHhhcCceEEEec
Q 043434 32 HMEVIGDIDEVALANMLRRKIGYVEMMKL 60 (90)
Q Consensus 32 kvtV~G~vDp~~lv~~LrKk~~~aeivsv 60 (90)
=+.|+|+-|=.-++++||.++.++.++..
T Consensus 99 ivLvSgD~Df~~~v~~l~~~g~~V~v~~~ 127 (146)
T PF01936_consen 99 IVLVSGDSDFAPLVRKLRERGKRVIVVGA 127 (146)
T ss_dssp EEEE---GGGHHHHHHHHHH--EEEEEE-
T ss_pred EEEEECcHHHHHHHHHHHHcCCEEEEEEe
Confidence 56799999999999999987778888884
No 23
>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=54.69 E-value=47 Score=21.03 Aligned_cols=39 Identities=26% Similarity=0.296 Sum_probs=29.4
Q ss_pred HHHHhCCCCeeEEEeCCCCCCcEEEEEe--ccHHHHHHHHHhhc
Q 043434 11 FQIIAGFPGLLSVAMKGDDLRHMEVIGD--IDEVALANMLRRKI 52 (90)
Q Consensus 11 ~k~v~~~~GV~sv~id~~~~~kvtV~G~--vDp~~lv~~LrKk~ 52 (90)
-+.|-.++||.+|-+.. |=|||+-+ +|=..|...++...
T Consensus 40 A~~Lf~i~gV~~Vf~~~---dfItVtK~~~~~W~~l~~~I~~~I 80 (87)
T PF08712_consen 40 AQALFAIPGVKSVFIGD---DFITVTKNPDADWEDLKPEIREVI 80 (87)
T ss_dssp HHHHHTSTTEEEEEEET---TEEEEEE-TTS-HHHHHHHHHHHT
T ss_pred HHHhcCCCCEeEEEEEC---CEEEEeeCCCCCHHHHHHHHHHHH
Confidence 34555899999999976 68888887 88888888887544
No 24
>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=53.99 E-value=46 Score=20.22 Aligned_cols=44 Identities=20% Similarity=0.252 Sum_probs=30.7
Q ss_pred HHHHHHhCCCCeeEEEeCCCCCCcEEEEEe--ccHHHHHHHHHhhcC
Q 043434 9 KAFQIIAGFPGLLSVAMKGDDLRHMEVIGD--IDEVALANMLRRKIG 53 (90)
Q Consensus 9 Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~--vDp~~lv~~LrKk~~ 53 (90)
.+++.+..-+=--.+..|. +.+++.|.|- +--..++++|+++++
T Consensus 23 ~aL~~l~~eDP~l~~~~d~-et~e~~l~g~Gelhlev~~~~L~~~~~ 68 (75)
T PF14492_consen 23 EALQKLSEEDPSLRVERDE-ETGELILSGMGELHLEVLLERLKRRFG 68 (75)
T ss_dssp HHHHHHHHH-TTSEEEEET-TTSEEEEEESSHHHHHHHHHHHHHTTC
T ss_pred HHHHHHHhcCCeEEEEEcc-hhceEEEEECCHHHHHHHHHHHHHHHC
Confidence 3444444444445677875 6777777765 888999999999886
No 25
>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=51.10 E-value=27 Score=24.99 Aligned_cols=30 Identities=13% Similarity=0.032 Sum_probs=26.2
Q ss_pred cEEEEEeccHHHHHHHHHhhcCceEEEecC
Q 043434 32 HMEVIGDIDEVALANMLRRKIGYVEMMKLD 61 (90)
Q Consensus 32 kvtV~G~vDp~~lv~~LrKk~~~aeivsv~ 61 (90)
=+.|+|+-|=.-|+.+||.++..+..++++
T Consensus 109 ~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~ 138 (160)
T TIGR00288 109 VALVTRDADFLPVINKAKENGKETIVIGAE 138 (160)
T ss_pred EEEEeccHhHHHHHHHHHHCCCEEEEEeCC
Confidence 567999999999999999987788888863
No 26
>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=48.93 E-value=13 Score=26.61 Aligned_cols=29 Identities=10% Similarity=0.210 Sum_probs=25.8
Q ss_pred CCCCeeEEEeCCCCCCcEEEEEeccHHHHH
Q 043434 16 GFPGLLSVAMKGDDLRHMEVIGDIDEVALA 45 (90)
Q Consensus 16 ~~~GV~sv~id~~~~~kvtV~G~vDp~~lv 45 (90)
.++|-..|.++. +...+++.|-|.|.++.
T Consensus 110 ~I~G~k~i~vn~-e~~~i~lsGiVRp~DI~ 138 (179)
T PF02107_consen 110 VIEGEKQIRVNG-EEQYIRLSGIVRPEDID 138 (179)
T ss_pred EEEEEEEEEECC-CEEEEEEEEEECHHHCC
Confidence 367889999997 88999999999999886
No 27
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=48.38 E-value=65 Score=20.00 Aligned_cols=42 Identities=14% Similarity=0.196 Sum_probs=31.3
Q ss_pred HHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe-ccHHHHHHHHHh
Q 043434 7 RTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD-IDEVALANMLRR 50 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~-vDp~~lv~~LrK 50 (90)
...+...+..++|++=-..+. + +|++|+=+ -+...+...+..
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 457889999999997666763 4 89998887 566666666653
No 28
>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=48.05 E-value=17 Score=28.16 Aligned_cols=42 Identities=26% Similarity=0.274 Sum_probs=29.7
Q ss_pred CChhHHHHHHHHHhCCCCeeEEEeCCCCC-----------CcEEEEEeccHHHHH
Q 043434 2 HSPKCRTKAFQIIAGFPGLLSVAMKGDDL-----------RHMEVIGDIDEVALA 45 (90)
Q Consensus 2 hCekC~~Kv~k~v~~~~GV~sv~id~~~~-----------~kvtV~G~vDp~~lv 45 (90)
|..|.....+..+..+ |++.+.+|. .. +++++-|++||..|.
T Consensus 218 H~cG~~~~~l~~~~e~-g~dvl~~d~-~~~dl~eak~~~g~k~~l~GNlDp~~L~ 270 (321)
T cd03309 218 HSCGAAASLVPSMAEM-GVDSWNVVM-TANNTAELRRLLGDKVVLAGAIDDVALD 270 (321)
T ss_pred EeCCCcHHHHHHHHHc-CCCEEEecC-CCCCHHHHHHHhCCCeEEEcCCChHHhc
Confidence 4445555566777666 888888876 43 479999999996553
No 29
>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=47.35 E-value=42 Score=20.64 Aligned_cols=30 Identities=17% Similarity=0.236 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCCCeeEEEeCCCCCCcEEEE
Q 043434 7 RTKAFQIIAGFPGLLSVAMKGDDLRHMEVI 36 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~ 36 (90)
.|++...++...||.|.+.+.+.+..|+|+
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 467777788999999999997444455553
No 30
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=47.12 E-value=75 Score=20.38 Aligned_cols=52 Identities=17% Similarity=0.206 Sum_probs=34.8
Q ss_pred HHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe-ccHHHHHH---HHHhhcC--ceEEEe
Q 043434 7 RTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD-IDEVALAN---MLRRKIG--YVEMMK 59 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~-vDp~~lv~---~LrKk~~--~aeivs 59 (90)
...+.+.+..++|++=-..|. ..+|++|+=+ -+...+++ .|+.-=| .|.++-
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~-~~GKiVVtiE~~~~~~~~~~i~~I~~l~GVlsa~lVY 76 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDA-PSGQLIVVVEAEDSETLLQTIESVRNVEGVLAVSLVY 76 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecC-CCCeEEEEEEeCChHHHHHHHHHHHcCCCceEEEEEE
Confidence 456788999999999888875 6788888766 44444444 4442113 555554
No 31
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=46.74 E-value=36 Score=22.73 Aligned_cols=30 Identities=27% Similarity=0.402 Sum_probs=24.6
Q ss_pred EEEeCCCCCCcEEEEEeccHHHHHHHHHhhcC
Q 043434 22 SVAMKGDDLRHMEVIGDIDEVALANMLRRKIG 53 (90)
Q Consensus 22 sv~id~~~~~kvtV~G~vDp~~lv~~LrKk~~ 53 (90)
+.++|+ + +++++.|..++..+-+.|++.+.
T Consensus 49 ~g~id~-~-~rlii~G~~~~~~i~~~l~~yI~ 78 (110)
T smart00653 49 QGSIDG-K-GRLIVNGRFTPKKLQDLLRRYIK 78 (110)
T ss_pred ceeECC-C-CeEEEEEeeCHHHHHHHHHHHHH
Confidence 345664 4 99999999999999999997664
No 32
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=46.39 E-value=46 Score=29.74 Aligned_cols=42 Identities=10% Similarity=0.209 Sum_probs=31.4
Q ss_pred HHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccH----------HHHHHHHHhh
Q 043434 7 RTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDE----------VALANMLRRK 51 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp----------~~lv~~LrKk 51 (90)
++.+...+.+++||.+|++.+ ...++.|. +|| .++...|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G-~~~ei~V~--vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYG-SQYSMRIW--LDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcC-CceEEEEE--ECHHHHHHcCCCHHHHHHHHHHh
Confidence 466888999999999999998 45556554 555 6667778754
No 33
>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=45.89 E-value=41 Score=22.73 Aligned_cols=32 Identities=28% Similarity=0.473 Sum_probs=25.8
Q ss_pred CcEEEEEeccHHHHHHHHHhhcC-ceEEEecCC
Q 043434 31 RHMEVIGDIDEVALANMLRRKIG-YVEMMKLDI 62 (90)
Q Consensus 31 ~kvtV~G~vDp~~lv~~LrKk~~-~aeivsv~p 62 (90)
+++.|.|++.-..++..|+++.+ .+.+++.+.
T Consensus 35 Dr~~v~~~~Tl~~li~~~~~~~~lev~ml~~g~ 67 (125)
T PF09358_consen 35 DRIEVNGDMTLQELIDYFKEKYGLEVTMLSQGV 67 (125)
T ss_dssp -EEEEES--BHHHHHHHHHHTTS-EEEEEEETT
T ss_pred eEEEEcCCCCHHHHHHHHHHHhCceEEEEEeCC
Confidence 68999999999999999999987 888888764
No 34
>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=45.34 E-value=73 Score=19.69 Aligned_cols=50 Identities=10% Similarity=0.145 Sum_probs=37.2
Q ss_pred HHHHHHHHHhCCCCeeEEEeCCCCCCcEE--EEEe-ccHHHHHHHHHhhcCceEE
Q 043434 6 CRTKAFQIIAGFPGLLSVAMKGDDLRHME--VIGD-IDEVALANMLRRKIGYVEM 57 (90)
Q Consensus 6 C~~Kv~k~v~~~~GV~sv~id~~~~~kvt--V~G~-vDp~~lv~~LrKk~~~aei 57 (90)
=..+++.++.+ .+|.=|.-+. ..|.+| +.|. -+...++..|.+.++.++|
T Consensus 17 ~d~~i~~~l~~-~~v~ii~K~~-nANtit~yl~~~~k~~~r~~~~Le~~~p~a~i 69 (71)
T cd04910 17 YDLEILELLQR-FKVSIIAKDT-NANTITHYLAGSLKTIKRLTEDLENRFPNAEI 69 (71)
T ss_pred HHHHHHHHHHH-cCCeEEEEec-CCCeEEEEEEcCHHHHHHHHHHHHHhCccCcc
Confidence 34567777764 5778788887 667766 5666 4778999999988987776
No 35
>PHA00514 dsDNA binding protein
Probab=45.29 E-value=42 Score=22.24 Aligned_cols=34 Identities=12% Similarity=0.261 Sum_probs=29.0
Q ss_pred CcEEEEEeccHHHHHHHHHhhc--CceEEEecCCCC
Q 043434 31 RHMEVIGDIDEVALANMLRRKI--GYVEMMKLDILD 64 (90)
Q Consensus 31 ~kvtV~G~vDp~~lv~~LrKk~--~~aeivsv~p~k 64 (90)
+..|..|+.....--..|.|+. +.+.++|++|.-
T Consensus 32 ~~~Tl~GNLtiEqAQ~e~~k~~k~~pvqVvsVEpnt 67 (98)
T PHA00514 32 NEQTLLGNLTIEQAQKELSKQYKHGPVQVVSVEPNT 67 (98)
T ss_pred CcceeecceeHHHHHHHHhhcccCCCeeEEEecCCC
Confidence 4678999998888899998885 589999999864
No 36
>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=44.41 E-value=48 Score=19.03 Aligned_cols=30 Identities=23% Similarity=0.194 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCCCeeEEEeCCCCCCcEEEE
Q 043434 7 RTKAFQIIAGFPGLLSVAMKGDDLRHMEVI 36 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~ 36 (90)
.+++...++..-|+.|.+.+.+.+..|+|.
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 467777778899999999986334456554
No 37
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=44.38 E-value=19 Score=25.49 Aligned_cols=44 Identities=18% Similarity=0.141 Sum_probs=32.0
Q ss_pred hhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccHHHHHHHHHh
Q 043434 4 PKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRR 50 (90)
Q Consensus 4 ekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~lv~~LrK 50 (90)
.+|.++++.++. ....|+.+.+.-.+||=.|.=|-..++.+++.
T Consensus 97 ~~i~rkvlQ~Le---~~~~ve~hp~gGR~lt~~GqrdldrIa~~i~~ 140 (143)
T KOG3411|consen 97 GGIARKVLQALE---KMGIVEKHPKGGRRLTEQGQRDLDRIAGQIRE 140 (143)
T ss_pred cHHHHHHHHHHH---hCCceeeCCCCcceeCcccchhHHHHHHHHHh
Confidence 356777766655 45566666544459999999999999998874
No 38
>PRK09577 multidrug efflux protein; Reviewed
Probab=43.51 E-value=52 Score=29.36 Aligned_cols=45 Identities=16% Similarity=0.190 Sum_probs=32.2
Q ss_pred HHHHHHHHhCCCCeeEEEeCCCCCCcEEEE-------Ee-ccHHHHHHHHHhhc
Q 043434 7 RTKAFQIIAGFPGLLSVAMKGDDLRHMEVI-------GD-IDEVALANMLRRKI 52 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~-------G~-vDp~~lv~~LrKk~ 52 (90)
+.++...+.+++||.+|++.+ ...++.|. .. +++.+|.+.|+...
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G-~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n 210 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWG-AEYAMRIWPDPVKLAALGLTASDIASAVRAHN 210 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecC-CceEEEEEeCHHHHHHcCCCHHHHHHHHHHhC
Confidence 467889999999999999998 55566662 11 44455677887643
No 39
>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=42.53 E-value=35 Score=20.04 Aligned_cols=19 Identities=21% Similarity=0.265 Sum_probs=16.1
Q ss_pred HHHHHHhCCCCeeEEEeCC
Q 043434 9 KAFQIIAGFPGLLSVAMKG 27 (90)
Q Consensus 9 Kv~k~v~~~~GV~sv~id~ 27 (90)
...+.|.+.+||.+|+.|.
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 4567889999999999985
No 40
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=42.11 E-value=57 Score=29.25 Aligned_cols=34 Identities=18% Similarity=0.199 Sum_probs=25.7
Q ss_pred HHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccHHHH
Q 043434 8 TKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVAL 44 (90)
Q Consensus 8 ~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~l 44 (90)
..++..+.+++||.+|++.+ ...++.|. +||.++
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G-~~~ei~V~--vDp~kl 193 (1049)
T PRK15127 160 ANMKDPISRTSGVGDVQLFG-SQYAMRIW--MNPNEL 193 (1049)
T ss_pred HHHHHHHhcCCCceEEEEcC-CceEEEEE--eCHHHH
Confidence 56888999999999999998 45556554 565544
No 41
>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=41.11 E-value=72 Score=18.42 Aligned_cols=48 Identities=10% Similarity=0.075 Sum_probs=36.5
Q ss_pred ChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEE-EEEeccHHHHHHHHHhhc
Q 043434 3 SPKCRTKAFQIIAGFPGLLSVAMKGDDLRHME-VIGDIDEVALANMLRRKI 52 (90)
Q Consensus 3 CekC~~Kv~k~v~~~~GV~sv~id~~~~~kvt-V~G~vDp~~lv~~LrKk~ 52 (90)
..+...++++++.. .||.-+.... ....++ |+-+-|-..+++.|.+.+
T Consensus 13 ~~gv~~~~~~~L~~-~~i~~i~~~~-s~~~is~vv~~~d~~~av~~LH~~f 61 (63)
T cd04920 13 LLHKLGPALEVFGK-KPVHLVSQAA-NDLNLTFVVDEDQADGLCARLHFQL 61 (63)
T ss_pred CccHHHHHHHHHhc-CCceEEEEeC-CCCeEEEEEeHHHHHHHHHHHHHHH
Confidence 45678899999976 5899999986 667774 555578888888887643
No 42
>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=40.75 E-value=35 Score=20.75 Aligned_cols=22 Identities=27% Similarity=0.366 Sum_probs=15.6
Q ss_pred CCCcEEEEEe-ccHHHHHHHHHh
Q 043434 29 DLRHMEVIGD-IDEVALANMLRR 50 (90)
Q Consensus 29 ~~~kvtV~G~-vDp~~lv~~LrK 50 (90)
..++|+++|. +|...|-+.|..
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 5579999999 999988888763
No 43
>COG0612 PqqL Predicted Zn-dependent peptidases [General function prediction only]
Probab=40.70 E-value=42 Score=26.19 Aligned_cols=25 Identities=24% Similarity=0.529 Sum_probs=21.9
Q ss_pred CCCcEEEEEeccHHHHHHHHHhhcC
Q 043434 29 DLRHMEVIGDIDEVALANMLRRKIG 53 (90)
Q Consensus 29 ~~~kvtV~G~vDp~~lv~~LrKk~~ 53 (90)
++=.|.|+|++|+..+...+.+.++
T Consensus 197 ~n~~l~vvGdi~~~~v~~~~~~~f~ 221 (438)
T COG0612 197 DNMVLVVVGDVDAEEVVELIEKYFG 221 (438)
T ss_pred CceEEEEecCCCHHHHHHHHHHHHc
Confidence 3457889999999999999999886
No 44
>PRK11023 outer membrane lipoprotein; Provisional
Probab=40.31 E-value=46 Score=23.81 Aligned_cols=42 Identities=5% Similarity=0.033 Sum_probs=29.8
Q ss_pred HHHHHHHHHhCCCCee---EEEeCCCCCCcEEEEEeccHHHHHHHH
Q 043434 6 CRTKAFQIIAGFPGLL---SVAMKGDDLRHMEVIGDIDEVALANML 48 (90)
Q Consensus 6 C~~Kv~k~v~~~~GV~---sv~id~~~~~kvtV~G~vDp~~lv~~L 48 (90)
=..++..++..-+++. .|.+.. .++.|+.+|.|+-...-.+.
T Consensus 50 i~~~V~~aL~~~~~l~~~~~I~V~v-~~G~V~L~G~V~~~~~k~~A 94 (191)
T PRK11023 50 LELRVNNALSKDEQIKKEARINVTA-YQGKVLLTGQSPNAELSERA 94 (191)
T ss_pred HHHHHHHHHhhCcccCcCceEEEEE-ECCEEEEEEEeCCHHHHHHH
Confidence 4567777777766664 577776 77899999998665544444
No 45
>KOG3166 consensus 60S ribosomal protein L7A [Translation, ribosomal structure and biogenesis]
Probab=40.03 E-value=17 Score=27.25 Aligned_cols=32 Identities=19% Similarity=0.269 Sum_probs=24.0
Q ss_pred CCCeeEEEeCC-CCCCcEEEEEe-ccHHHHHHHH
Q 043434 17 FPGLLSVAMKG-DDLRHMEVIGD-IDEVALANML 48 (90)
Q Consensus 17 ~~GV~sv~id~-~~~~kvtV~G~-vDp~~lv~~L 48 (90)
-.||+.|+.=. +.+.+++|+.. |||..|+-.|
T Consensus 111 ~~gvnTVttLVenKKAQLVV~ahDvDPIELVvFL 144 (209)
T KOG3166|consen 111 RAGVNTVTTLVENKKAQLVVTAHDVDPIELVVFL 144 (209)
T ss_pred ccCcceEeehhhccccceeEEecccCchhheeec
Confidence 46888887533 25568888887 9999998766
No 46
>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=39.77 E-value=63 Score=28.91 Aligned_cols=43 Identities=12% Similarity=0.164 Sum_probs=31.5
Q ss_pred HHHHHHHHhCCCCeeEEEeCCCCCCcEEEEE-------e-ccHHHHHHHHHh
Q 043434 7 RTKAFQIIAGFPGLLSVAMKGDDLRHMEVIG-------D-IDEVALANMLRR 50 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G-------~-vDp~~lv~~LrK 50 (90)
...+...+.+++||.+|++.+. ..++.|.= . +++.+|.+.|+.
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 3568889999999999999984 55666651 1 345666777875
No 47
>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=39.40 E-value=44 Score=19.56 Aligned_cols=32 Identities=19% Similarity=0.251 Sum_probs=24.1
Q ss_pred CcEEEEEe-ccHHHHHHHHHhhc---C--ceEEEecCC
Q 043434 31 RHMEVIGD-IDEVALANMLRRKI---G--YVEMMKLDI 62 (90)
Q Consensus 31 ~kvtV~G~-vDp~~lv~~LrKk~---~--~aeivsv~p 62 (90)
+.|+|+|. -.|..+.+.|.+|- | +-.|++...
T Consensus 6 G~Isvs~~~~s~~d~~~~la~kAd~~GA~~y~I~~~~~ 43 (56)
T PF07338_consen 6 GTISVSGNFGSPDDAEEALAKKADEKGAKYYRITSASE 43 (56)
T ss_dssp EEEEEEEECSSHHHHHHHHHHHHHHTT-SEEEEEEEEE
T ss_pred EEEEEccccCCHHHHHHHHHHHHHHcCCCEEEEEEEEc
Confidence 57899999 89999999998765 2 446666543
No 48
>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=38.71 E-value=36 Score=20.10 Aligned_cols=18 Identities=17% Similarity=0.165 Sum_probs=15.3
Q ss_pred HHHHHHHhCCCCeeEEEe
Q 043434 8 TKAFQIIAGFPGLLSVAM 25 (90)
Q Consensus 8 ~Kv~k~v~~~~GV~sv~i 25 (90)
..+++.+.+++||.+|.-
T Consensus 52 ~~li~~L~~i~gV~~V~R 69 (74)
T cd04877 52 QTLMPEIRRIDGVEDVKT 69 (74)
T ss_pred HHHHHHHhCCCCceEEEE
Confidence 578899999999999864
No 49
>PF06357 Omega-toxin: Omega-atracotoxin; InterPro: IPR009415 This family consists of several Hadronyche versuta (Blue mountains funnel-web spider) specific omega-atracotoxin proteins. Omega-Atracotoxin-Hv1a is an insect-specific neurotoxin whose phylogenetic specificity derives from its ability to antagonise insect, but not vertebrate, voltage-gated calcium channels. Two spatially proximal residues, Asn(27) and Arg(35), form a contiguous molecular surface that is essential for toxin activity. It has been proposed that this surface of the beta-hairpin is a key site for interaction of the toxin with insect calcium channels [].; GO: 0019855 calcium channel inhibitor activity, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1AXH_A 1HVW_A.
Probab=38.68 E-value=17 Score=20.13 Aligned_cols=11 Identities=55% Similarity=1.250 Sum_probs=9.0
Q ss_pred CCCCCCCCCcc
Q 043434 78 QPFPAETPCCS 88 (90)
Q Consensus 78 ~~~~~~~~~cs 88 (90)
+|-||..+|||
T Consensus 9 QPCPyne~CCs 19 (37)
T PF06357_consen 9 QPCPYNESCCS 19 (37)
T ss_dssp SB-SSCCCBSS
T ss_pred CcCCCCccccc
Confidence 77799999998
No 50
>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=38.67 E-value=81 Score=18.34 Aligned_cols=41 Identities=15% Similarity=0.175 Sum_probs=24.9
Q ss_pred eEEEeCCCCCCcEEEEEe-ccHHHHHHHHHh-----hcCceEEEecCCCC
Q 043434 21 LSVAMKGDDLRHMEVIGD-IDEVALANMLRR-----KIGYVEMMKLDILD 64 (90)
Q Consensus 21 ~sv~id~~~~~kvtV~G~-vDp~~lv~~LrK-----k~~~aeivsv~p~k 64 (90)
++++++ .++|++.|. -+...|...+++ .+..+.+.++....
T Consensus 17 ~~l~~~---~~~l~i~G~a~~~~~v~~f~~~L~~~~~f~~v~l~~~~~~~ 63 (78)
T PF05137_consen 17 TSLSIN---GNTLSISGYADSYQSVAAFLRNLEQSPFFSDVSLSSISRQE 63 (78)
T ss_pred EEEEEe---CCEEEEEEEECCHHHHHHHHHHHhhCCCccceEEEEEEeec
Confidence 455554 479999999 555555555442 12366666665544
No 51
>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=38.22 E-value=46 Score=21.47 Aligned_cols=26 Identities=8% Similarity=0.231 Sum_probs=20.6
Q ss_pred ccHHHHHHHHHhhcCceEEEecCCCC
Q 043434 39 IDEVALANMLRRKIGYVEMMKLDILD 64 (90)
Q Consensus 39 vDp~~lv~~LrKk~~~aeivsv~p~k 64 (90)
+|..++++.+++.++++++-.+|+..
T Consensus 57 isvm~II~~I~~~~p~l~I~~iGe~~ 82 (93)
T PF12164_consen 57 ISVMKIIEKIQEEYPNLDIQNIGETD 82 (93)
T ss_dssp EEHHHHHHHHHHH-SSEEEEE-S-SE
T ss_pred EEHHHHHHHHHHHCCCcEEEEcCCCc
Confidence 48999999999999999999998864
No 52
>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=38.00 E-value=76 Score=18.73 Aligned_cols=20 Identities=10% Similarity=0.215 Sum_probs=16.2
Q ss_pred EEEeCCCCCCcEEEEEeccHH
Q 043434 22 SVAMKGDDLRHMEVIGDIDEV 42 (90)
Q Consensus 22 sv~id~~~~~kvtV~G~vDp~ 42 (90)
+|..|. ..|.|.|.|.-+-.
T Consensus 47 ~i~~d~-~tNsliv~g~~~~~ 66 (82)
T PF03958_consen 47 RIVADE-RTNSLIVRGTPEDL 66 (82)
T ss_dssp EEEEEC-TTTEEEEEEEHHHH
T ss_pred EEEEEC-CCCEEEEEeCHHHH
Confidence 889996 89999999994333
No 53
>PRK13748 putative mercuric reductase; Provisional
Probab=37.34 E-value=1.4e+02 Score=24.02 Aligned_cols=49 Identities=14% Similarity=0.170 Sum_probs=36.8
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEE--eccHHHHHHHHHh
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIG--DIDEVALANMLRR 50 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G--~vDp~~lv~~LrK 50 (90)
|+|..|..++...+..++|+.+..++. ..+.+.+.. ..+...+...+..
T Consensus 9 ~~C~~c~~~ie~~l~~~~gv~~a~~~~-~~~~~~v~~~~~~~~~~i~~~i~~ 59 (561)
T PRK13748 9 MTCDSCAAHVKDALEKVPGVQSADVSY-PKGSAQLAIEVGTSPDALTAAVAG 59 (561)
T ss_pred eecHHHHHHHHHHHhcCCCeeEEEEEc-CCCEEEEEECCCCCHHHHHHHHHH
Confidence 579999999999999999999888886 666666653 2466666666543
No 54
>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=35.08 E-value=37 Score=19.49 Aligned_cols=28 Identities=21% Similarity=0.189 Sum_probs=21.7
Q ss_pred HHHHHHHhCCCCeeEEEeCCCCCCcEEE
Q 043434 8 TKAFQIIAGFPGLLSVAMKGDDLRHMEV 35 (90)
Q Consensus 8 ~Kv~k~v~~~~GV~sv~id~~~~~kvtV 35 (90)
.++.+.+.+++.|.++++....-++|.|
T Consensus 37 ~~~~~~l~~~p~V~~v~V~r~~P~~l~I 64 (69)
T PF08478_consen 37 KKIEQRLEKLPWVKSVSVSRRFPNTLEI 64 (69)
T ss_dssp HHHHHCCCCTTTEEEEEEEEETTTEEEE
T ss_pred HHHHHHHHcCCCEEEEEEEEeCCCEEEE
Confidence 4667788889999999998645566665
No 55
>PRK09579 multidrug efflux protein; Reviewed
Probab=35.02 E-value=86 Score=28.04 Aligned_cols=45 Identities=16% Similarity=0.253 Sum_probs=31.4
Q ss_pred HHHHHHHHhCCCCeeEEEeCCCCCCcEEEEE--------eccHHHHHHHHHhh
Q 043434 7 RTKAFQIIAGFPGLLSVAMKGDDLRHMEVIG--------DIDEVALANMLRRK 51 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G--------~vDp~~lv~~LrKk 51 (90)
.+.+...+.+++||..|.+.+....++.|.= .+.+.+|.+.|+..
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 3567889999999999999984434555530 04456677888754
No 56
>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=34.45 E-value=50 Score=14.72 Aligned_cols=47 Identities=21% Similarity=0.302 Sum_probs=31.0
Q ss_pred CCChhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe--ccHHHHHHHH
Q 043434 1 MHSPKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD--IDEVALANML 48 (90)
Q Consensus 1 mhCekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~--vDp~~lv~~L 48 (90)
++|..|...+........|+....... ....+.+... .+...+...+
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 55 (63)
T cd00371 7 MTCAGCVSKIEKALEKLPGVESVEVDL-ETGKATVEYDPEVSPEELLEAI 55 (63)
T ss_pred eEcHHHHHHHHHHHhcCCCEeEEEEEc-cCCEEEEEECCCCCHHHHHHHH
Confidence 468899999988888889987776664 4455555433 2555544444
No 57
>PF15023 DUF4523: Protein of unknown function (DUF4523)
Probab=33.87 E-value=58 Score=23.61 Aligned_cols=44 Identities=18% Similarity=0.258 Sum_probs=33.7
Q ss_pred HHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccHHH-HHHHHHhhc
Q 043434 8 TKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVA-LANMLRRKI 52 (90)
Q Consensus 8 ~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~-lv~~LrKk~ 52 (90)
+.+...++.|--|.||++.| .+.-++|-++++.++ -++.++.+.
T Consensus 105 ~sV~~~Ls~fGpI~SVT~cG-rqsavVvF~d~~SAC~Av~Af~s~~ 149 (166)
T PF15023_consen 105 KSVIQRLSVFGPIQSVTLCG-RQSAVVVFKDITSACKAVSAFQSRA 149 (166)
T ss_pred HHHHHHHHhcCCcceeeecC-CceEEEEehhhHHHHHHHHhhcCCC
Confidence 56778889999999999998 888888989866554 455555443
No 58
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=33.69 E-value=83 Score=24.70 Aligned_cols=52 Identities=17% Similarity=0.112 Sum_probs=34.0
Q ss_pred HHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe-ccHHHHHHHHHhhcC-ceEEEe
Q 043434 8 TKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD-IDEVALANMLRRKIG-YVEMMK 59 (90)
Q Consensus 8 ~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~-vDp~~lv~~LrKk~~-~aeivs 59 (90)
.++..++.+.++|.=+++++|.+..=+|+-- =||..+++..-.-.+ .++++-
T Consensus 21 e~i~a~~~~~~~v~ildve~danhNRsViT~vgdp~~~~~A~f~~ik~AaelID 74 (302)
T COG3643 21 EKIVAAAKSIPTVKILDVEMDANHNRSVITLVGDPSKVVNAAFALIKKAAELID 74 (302)
T ss_pred HHHHHHHhcCCceEEEEeccCCCCCceEEEEecChHHHHHHHHHHHHHHHHhhc
Confidence 4677888899999888887755544344333 388888887754443 444443
No 59
>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=33.44 E-value=47 Score=21.46 Aligned_cols=23 Identities=22% Similarity=0.271 Sum_probs=18.5
Q ss_pred hHHHHHHHHHhCCCCeeEEEeCC
Q 043434 5 KCRTKAFQIIAGFPGLLSVAMKG 27 (90)
Q Consensus 5 kC~~Kv~k~v~~~~GV~sv~id~ 27 (90)
+--..+..++++++||.|+++..
T Consensus 62 g~td~lee~i~~ve~V~svev~~ 84 (88)
T TIGR00489 62 GGTEAAEESLSGIEGVESVEVTD 84 (88)
T ss_pred cChHHHHHHHhcCCCccEEEEEE
Confidence 33467788999999999999863
No 60
>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=33.24 E-value=59 Score=17.71 Aligned_cols=18 Identities=17% Similarity=0.599 Sum_probs=14.4
Q ss_pred HHHHHHHhCCCCeeEEEe
Q 043434 8 TKAFQIIAGFPGLLSVAM 25 (90)
Q Consensus 8 ~Kv~k~v~~~~GV~sv~i 25 (90)
..+++.+..++||.++..
T Consensus 53 ~~l~~~l~~~~~V~~v~~ 70 (71)
T cd04879 53 EEVLEELKALPGIIRVRL 70 (71)
T ss_pred HHHHHHHHcCCCeEEEEE
Confidence 367888999999998863
No 61
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=33.05 E-value=75 Score=24.39 Aligned_cols=45 Identities=22% Similarity=0.254 Sum_probs=34.8
Q ss_pred HHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEecc-------------HHHHHHHHHhh
Q 043434 7 RTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDID-------------EVALANMLRRK 51 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vD-------------p~~lv~~LrKk 51 (90)
+..++..+..++++..|++-|.-+......|+|| +..|+..|++.
T Consensus 147 a~~i~~~l~~~~~~~~v~i~GS~RRg~et~gDiDilv~~~~~~~~~~~~~v~~~l~~~ 204 (307)
T cd00141 147 AEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDATSRGLLEKVVDALVEL 204 (307)
T ss_pred HHHHHHHHHhCCCceEEEEcccccCCCCccCCEEEEEecCCccccccHHHHHHHHHhC
Confidence 4567788888999999999884555666777776 77899999754
No 62
>PRK12697 flgH flagellar basal body L-ring protein; Reviewed
Probab=32.19 E-value=34 Score=25.80 Aligned_cols=28 Identities=7% Similarity=0.164 Sum_probs=24.6
Q ss_pred CCCeeEEEeCCCCCCcEEEEEeccHHHHH
Q 043434 17 FPGLLSVAMKGDDLRHMEVIGDIDEVALA 45 (90)
Q Consensus 17 ~~GV~sv~id~~~~~kvtV~G~vDp~~lv 45 (90)
++|=..|.++. +...+.|.|-|.|.++-
T Consensus 157 I~GeK~i~vN~-e~e~IrlsGvVRP~DI~ 184 (226)
T PRK12697 157 VSGEKQMLINQ-GNEFVRFSGVVNPNTIS 184 (226)
T ss_pred EEEEEEEEECC-CEEEEEEEEEECHHHCC
Confidence 57889999997 88999999999998874
No 63
>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=31.90 E-value=1.3e+02 Score=22.64 Aligned_cols=44 Identities=7% Similarity=0.218 Sum_probs=29.4
Q ss_pred hHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe-cc----HHHHHHHHHhhcCce
Q 043434 5 KCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD-ID----EVALANMLRRKIGYV 55 (90)
Q Consensus 5 kC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~-vD----p~~lv~~LrKk~~~a 55 (90)
||-....+.+..+ ..+. ..+++...|| || +..+++.|++-...+
T Consensus 9 G~~~~L~~LL~~i------~~~~-~~D~Li~lGDlVdRGp~s~evl~~l~~l~~~v 57 (257)
T cd07422 9 GCYDELQRLLEKI------NFDP-AKDRLWLVGDLVNRGPDSLETLRFVKSLGDSA 57 (257)
T ss_pred CCHHHHHHHHHhc------CCCC-CCCEEEEecCcCCCCcCHHHHHHHHHhcCCCe
Confidence 4555555555543 2333 5689999999 76 999999998643333
No 64
>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=31.84 E-value=26 Score=21.64 Aligned_cols=25 Identities=16% Similarity=0.282 Sum_probs=17.7
Q ss_pred hCCCCe--eEEEeCCCCCCcEEEEEecc
Q 043434 15 AGFPGL--LSVAMKGDDLRHMEVIGDID 40 (90)
Q Consensus 15 ~~~~GV--~sv~id~~~~~kvtV~G~vD 40 (90)
..++|| +.+++.. ..+.|+|.|+-.
T Consensus 16 ~~lPGv~~edi~v~~-~~~~L~I~g~~~ 42 (93)
T cd06471 16 ADLPGFKKEDIKLDY-KDGYLTISAKRD 42 (93)
T ss_pred EECCCCCHHHeEEEE-ECCEEEEEEEEc
Confidence 357788 4566665 568999999843
No 65
>PRK12698 flgH flagellar basal body L-ring protein; Reviewed
Probab=31.69 E-value=36 Score=25.49 Aligned_cols=28 Identities=7% Similarity=0.172 Sum_probs=24.5
Q ss_pred CCCeeEEEeCCCCCCcEEEEEeccHHHHH
Q 043434 17 FPGLLSVAMKGDDLRHMEVIGDIDEVALA 45 (90)
Q Consensus 17 ~~GV~sv~id~~~~~kvtV~G~vDp~~lv 45 (90)
++|-..|.++. +...+++.|-|.|.++-
T Consensus 154 I~GeK~i~vN~-~~e~I~lsGvVRP~DI~ 181 (224)
T PRK12698 154 IRGEKWISINN-GDEFIRLTGIVRSQDIT 181 (224)
T ss_pred EEEEEEEEECC-CEEEEEEEEEECHHHCC
Confidence 57889999997 88999999999998863
No 66
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=31.46 E-value=1.1e+02 Score=27.51 Aligned_cols=35 Identities=23% Similarity=0.313 Sum_probs=25.3
Q ss_pred HHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccHHHH
Q 043434 8 TKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVAL 44 (90)
Q Consensus 8 ~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~l 44 (90)
+.+...+.+++||.+|.+.+....++.|. +||.++
T Consensus 169 ~~l~~~L~~i~gV~~V~~~G~~~~ei~V~--vd~~kl 203 (1040)
T PRK10503 169 TRVAQKISQVSGVGLVTLSGGQRPAVRVK--LNAQAI 203 (1040)
T ss_pred HHHHHHhcCCCCceEEEecCCCceEEEEE--ECHHHH
Confidence 56888999999999999998433455553 555443
No 67
>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=31.07 E-value=67 Score=19.23 Aligned_cols=21 Identities=29% Similarity=0.404 Sum_probs=17.5
Q ss_pred CCcEEEEEe-ccHHHHHHHHHh
Q 043434 30 LRHMEVIGD-IDEVALANMLRR 50 (90)
Q Consensus 30 ~~kvtV~G~-vDp~~lv~~LrK 50 (90)
.++|+++|. +|...|-+.|..
T Consensus 69 ~~~lV~IG~~l~~~~l~~~l~~ 90 (92)
T smart00833 69 RTRLVFIGRDLDEEAIRAALDA 90 (92)
T ss_pred ceEEEEEeCCCCHHHHHHHHHH
Confidence 468999999 999988887763
No 68
>PRK00249 flgH flagellar basal body L-ring protein; Reviewed
Probab=30.42 E-value=39 Score=25.18 Aligned_cols=28 Identities=14% Similarity=0.213 Sum_probs=24.7
Q ss_pred CCCeeEEEeCCCCCCcEEEEEeccHHHHH
Q 043434 17 FPGLLSVAMKGDDLRHMEVIGDIDEVALA 45 (90)
Q Consensus 17 ~~GV~sv~id~~~~~kvtV~G~vDp~~lv 45 (90)
++|-..|.++. +...+.+.|-|.|.++-
T Consensus 153 I~G~K~i~vN~-e~~~i~lsGiVRP~DI~ 180 (222)
T PRK00249 153 IRGEKEVRVNQ-GTEFLRVSGVVRPRDIS 180 (222)
T ss_pred EEEEEEEEECC-CEEEEEEEEEECHHHCC
Confidence 57889999997 88999999999998874
No 69
>PRK12788 flgH flagellar basal body L-ring protein; Reviewed
Probab=30.05 E-value=39 Score=25.61 Aligned_cols=28 Identities=18% Similarity=0.317 Sum_probs=24.6
Q ss_pred CCCeeEEEeCCCCCCcEEEEEeccHHHHH
Q 043434 17 FPGLLSVAMKGDDLRHMEVIGDIDEVALA 45 (90)
Q Consensus 17 ~~GV~sv~id~~~~~kvtV~G~vDp~~lv 45 (90)
++|=..|.++. +...|.|.|-|.|.++-
T Consensus 165 I~G~kev~vN~-e~~~i~vsGvVRP~DI~ 192 (234)
T PRK12788 165 ISGSQEVRVNY-EMRVLNVGGIVRPLDIT 192 (234)
T ss_pred EEEEEEEEECC-CEEEEEEEEEECHHHCC
Confidence 57889999997 88999999999998874
No 70
>PRK12407 flgH flagellar basal body L-ring protein; Reviewed
Probab=30.05 E-value=38 Score=25.32 Aligned_cols=28 Identities=18% Similarity=0.153 Sum_probs=24.3
Q ss_pred CCCeeEEEeCCCCCCcEEEEEeccHHHHH
Q 043434 17 FPGLLSVAMKGDDLRHMEVIGDIDEVALA 45 (90)
Q Consensus 17 ~~GV~sv~id~~~~~kvtV~G~vDp~~lv 45 (90)
++|-..|.++. +...|.+.|-|.|.++-
T Consensus 151 I~GeK~i~vN~-e~e~i~~sGvVRP~DI~ 178 (221)
T PRK12407 151 IRGEKWLTLNQ-GDEYMRVTGLVRADDIA 178 (221)
T ss_pred EEEEEEEEECC-CEEEEEEEEEECHHHCC
Confidence 57889999997 88999999999998763
No 71
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=29.54 E-value=1.2e+02 Score=27.07 Aligned_cols=36 Identities=28% Similarity=0.369 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccHHHH
Q 043434 7 RTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVAL 44 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~l 44 (90)
+..+...+.+++||.+|.+.+....++.| ++||.++
T Consensus 159 ~~~l~~~L~~i~GV~~V~~~G~~~~ei~V--~vd~~kl 194 (1025)
T PRK10614 159 STQLAQTISQIDGVGDVDVGGSSLPAVRV--GLNPQAL 194 (1025)
T ss_pred HHHHHHHhcCCCCceEEEecCCCceEEEE--EeCHHHH
Confidence 35788999999999999998733334444 3555544
No 72
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=29.22 E-value=1.8e+02 Score=19.34 Aligned_cols=41 Identities=12% Similarity=0.168 Sum_probs=32.5
Q ss_pred HHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe-ccHHHHHHHHH
Q 043434 7 RTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD-IDEVALANMLR 49 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~-vDp~~lv~~Lr 49 (90)
...++.+++.++|++=..-|. . +|++|+=+ -|...|+..+.
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 356888999999998877774 4 89998888 67777877764
No 73
>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=28.54 E-value=58 Score=17.84 Aligned_cols=17 Identities=12% Similarity=0.245 Sum_probs=13.3
Q ss_pred HHHHHHHhCCCCeeEEE
Q 043434 8 TKAFQIIAGFPGLLSVA 24 (90)
Q Consensus 8 ~Kv~k~v~~~~GV~sv~ 24 (90)
..++..+.+++||.+|+
T Consensus 56 ~~l~~~l~~~~~v~~v~ 72 (72)
T cd04878 56 EQIVKQLNKLVDVLKVS 72 (72)
T ss_pred HHHHHHHhCCccEEEeC
Confidence 45678888899998874
No 74
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.42 E-value=97 Score=20.62 Aligned_cols=24 Identities=25% Similarity=0.439 Sum_probs=21.3
Q ss_pred HHhCCCCeeEEEeCCCCCCcEEEEE
Q 043434 13 IIAGFPGLLSVAMKGDDLRHMEVIG 37 (90)
Q Consensus 13 ~v~~~~GV~sv~id~~~~~kvtV~G 37 (90)
.++.++|+..|++.. ++.+|-|.+
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 467889999999998 889999988
No 75
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=28.28 E-value=1.5e+02 Score=20.34 Aligned_cols=47 Identities=17% Similarity=0.195 Sum_probs=31.4
Q ss_pred HHHHHHHHHhCCCCee----EEEeCCCCCCcEEEEEeccHHHHHHHHHhhcCceE
Q 043434 6 CRTKAFQIIAGFPGLL----SVAMKGDDLRHMEVIGDIDEVALANMLRRKIGYVE 56 (90)
Q Consensus 6 C~~Kv~k~v~~~~GV~----sv~id~~~~~kvtV~G~vDp~~lv~~LrKk~~~ae 56 (90)
-++.+++.+.+ .|.. +|++ ..+.|++.|.+....-..++....+.+.
T Consensus 27 ~~~~i~~~i~~-~~~~~~~i~V~v---~~G~v~l~G~v~s~~~~~~~~~aa~~v~ 77 (147)
T PRK11198 27 AADALKEHISK-QGLGDADVNVQV---EDGKATVSGDAASQEAKEKILLAVGNIQ 77 (147)
T ss_pred HHHHHHHHHHh-cCCCcCCceEEE---eCCEEEEEEEeCCHHHHHHHHHHhccCC
Confidence 45666777755 3333 4555 4589999999887777777776555543
No 76
>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=28.03 E-value=85 Score=27.73 Aligned_cols=36 Identities=19% Similarity=0.370 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccHHHH
Q 043434 7 RTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVAL 44 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~l 44 (90)
...++..+.+++||.+|.+.|....++.|. +||.+|
T Consensus 158 ~~~l~~~L~~i~gV~~v~~~G~~~~ei~i~--~d~~kl 193 (1021)
T PF00873_consen 158 EEQLKPRLERIPGVARVDISGGREREIQIE--LDPEKL 193 (1021)
T ss_dssp HHCTHHHHHTSTTEEEEEESSS--EEEEEE--E-HHHH
T ss_pred HHHHHHhccceeEEEEEEeccchhhhhhhe--echhhh
Confidence 456788999999999999998444466554 555443
No 77
>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=27.90 E-value=82 Score=17.62 Aligned_cols=17 Identities=18% Similarity=0.544 Sum_probs=13.4
Q ss_pred HHHHHHhCCCCeeEEEe
Q 043434 9 KAFQIIAGFPGLLSVAM 25 (90)
Q Consensus 9 Kv~k~v~~~~GV~sv~i 25 (90)
.+++.+.+++||.+|..
T Consensus 52 ~li~~l~~~~~V~~v~~ 68 (69)
T cd04901 52 ELLEALRAIPGTIRVRL 68 (69)
T ss_pred HHHHHHHcCCCeEEEEE
Confidence 56778888899988764
No 78
>PRK12701 flgH flagellar basal body L-ring protein; Reviewed
Probab=27.34 E-value=46 Score=25.03 Aligned_cols=28 Identities=11% Similarity=0.103 Sum_probs=24.3
Q ss_pred CCCeeEEEeCCCCCCcEEEEEeccHHHHH
Q 043434 17 FPGLLSVAMKGDDLRHMEVIGDIDEVALA 45 (90)
Q Consensus 17 ~~GV~sv~id~~~~~kvtV~G~vDp~~lv 45 (90)
+.|-..|.++. +...+.+.|-|.|.++-
T Consensus 160 I~GeK~v~vN~-e~e~i~lsGvVRP~DI~ 187 (230)
T PRK12701 160 VQGEKWVRINQ-GNEFVRLSGIVRPQDIK 187 (230)
T ss_pred EEEEEEEEECC-CeEEEEEEEEECHHHCC
Confidence 57889999997 88999999999888764
No 79
>PRK00166 apaH diadenosine tetraphosphatase; Reviewed
Probab=26.96 E-value=1.5e+02 Score=22.50 Aligned_cols=40 Identities=8% Similarity=0.309 Sum_probs=28.2
Q ss_pred hHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe-cc----HHHHHHHHHhh
Q 043434 5 KCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD-ID----EVALANMLRRK 51 (90)
Q Consensus 5 kC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~-vD----p~~lv~~LrKk 51 (90)
||-....+.+..+ ..+. ..+++.+.|| || +..+++.|++-
T Consensus 11 G~~~~l~~ll~~~------~~~~-~~D~li~lGDlVdrGp~s~~vl~~l~~l 55 (275)
T PRK00166 11 GCYDELQRLLEKI------DFDP-AKDTLWLVGDLVNRGPDSLEVLRFVKSL 55 (275)
T ss_pred CCHHHHHHHHHhc------CCCC-CCCEEEEeCCccCCCcCHHHHHHHHHhc
Confidence 5666666666653 2232 4579999999 75 99999999863
No 80
>PRK12700 flgH flagellar basal body L-ring protein; Reviewed
Probab=26.65 E-value=49 Score=24.90 Aligned_cols=28 Identities=14% Similarity=0.252 Sum_probs=24.4
Q ss_pred CCCeeEEEeCCCCCCcEEEEEeccHHHHH
Q 043434 17 FPGLLSVAMKGDDLRHMEVIGDIDEVALA 45 (90)
Q Consensus 17 ~~GV~sv~id~~~~~kvtV~G~vDp~~lv 45 (90)
+.|=..|.++. +...|.+.|-|.|.++-
T Consensus 161 I~GeK~i~vN~-~~e~irlsGiVRP~DI~ 188 (230)
T PRK12700 161 IAGEKQIAINR-GSEYVRFSGVVDPRSIT 188 (230)
T ss_pred EEEEEEEEECC-CEEEEEEEEEECHHHCC
Confidence 57888999997 88999999999998874
No 81
>PF13363 BetaGal_dom3: Beta-galactosidase, domain 3; PDB: 3OGS_A 3OGV_A 3OGR_A 3OG2_A 1TG7_A 1XC6_A.
Probab=26.61 E-value=87 Score=19.86 Aligned_cols=19 Identities=21% Similarity=0.518 Sum_probs=15.6
Q ss_pred eeEEEeCCCCCCcEEEEEeccH
Q 043434 20 LLSVAMKGDDLRHMEVIGDIDE 41 (90)
Q Consensus 20 V~sv~id~~~~~kvtV~G~vDp 41 (90)
|+|.++++ ++|.++||++-
T Consensus 26 VRsAsv~g---~tL~L~GD~n~ 44 (79)
T PF13363_consen 26 VRSASVSG---STLSLTGDFNA 44 (79)
T ss_dssp EEEEEEET---TEEEEEEEBSS
T ss_pred EEEEEEcC---CEEEEEeecCC
Confidence 78888875 79999999753
No 82
>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=26.55 E-value=67 Score=20.10 Aligned_cols=21 Identities=19% Similarity=0.233 Sum_probs=17.3
Q ss_pred HHHHHHHHhCCCCeeEEEeCC
Q 043434 7 RTKAFQIIAGFPGLLSVAMKG 27 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~ 27 (90)
+..+..++..++|+++|.+..
T Consensus 57 ~~~i~~al~~l~gv~~v~v~i 77 (99)
T TIGR02945 57 PGEVENAVRAVPGVGSVTVEL 77 (99)
T ss_pred HHHHHHHHHhCCCCceEEEEE
Confidence 456788889999999999864
No 83
>PRK12696 flgH flagellar basal body L-ring protein; Reviewed
Probab=26.01 E-value=49 Score=24.99 Aligned_cols=28 Identities=11% Similarity=0.165 Sum_probs=24.4
Q ss_pred CCCeeEEEeCCCCCCcEEEEEeccHHHHH
Q 043434 17 FPGLLSVAMKGDDLRHMEVIGDIDEVALA 45 (90)
Q Consensus 17 ~~GV~sv~id~~~~~kvtV~G~vDp~~lv 45 (90)
++|-..|.++. +...|.|.|-|.|.++-
T Consensus 167 I~G~k~v~vN~-e~~~i~lsGvVRP~DI~ 194 (236)
T PRK12696 167 VEGARETRVND-ETQYIVVSGLVRPRDIG 194 (236)
T ss_pred EEEEEEEEECC-CEEEEEEEEEECHHHCC
Confidence 57889999997 88999999999988864
No 84
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=25.74 E-value=1.6e+02 Score=22.79 Aligned_cols=38 Identities=24% Similarity=0.340 Sum_probs=31.0
Q ss_pred hhHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccHHHHHHHHHhhcCc
Q 043434 4 PKCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKIGY 54 (90)
Q Consensus 4 ekC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~lv~~LrKk~~~ 54 (90)
+.|+..+...+.+++||.|+.+ +|..+-.+.|++..|.
T Consensus 71 ~~~~~~v~~~i~~~~gV~~v~~-------------~sre~~l~~L~~~lg~ 108 (297)
T COG2177 71 QDDAALVREKIEGIPGVKSVRF-------------ISREEALKELQPWLGF 108 (297)
T ss_pred hHHHHHHHHHHhcCCCcceEEE-------------eCHHHHHHHHHHHcCc
Confidence 5678889999999999999988 4566777888877774
No 85
>PRK12699 flgH flagellar basal body L-ring protein; Reviewed
Probab=25.71 E-value=51 Score=25.14 Aligned_cols=28 Identities=11% Similarity=0.274 Sum_probs=24.8
Q ss_pred CCCeeEEEeCCCCCCcEEEEEeccHHHHH
Q 043434 17 FPGLLSVAMKGDDLRHMEVIGDIDEVALA 45 (90)
Q Consensus 17 ~~GV~sv~id~~~~~kvtV~G~vDp~~lv 45 (90)
++|=..|.++. +...+.+.|-|.|.++.
T Consensus 178 I~GeK~i~vN~-~~e~IrlsGvVRP~DI~ 205 (246)
T PRK12699 178 VSGEKQIGINQ-GHEFIRLSGVINPINVI 205 (246)
T ss_pred EEEEEEEEECC-CeEEEEEEEEEChhhcc
Confidence 57888999997 88999999999999984
No 86
>cd06464 ACD_sHsps-like Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps.
Probab=25.61 E-value=37 Score=19.88 Aligned_cols=25 Identities=16% Similarity=0.400 Sum_probs=17.8
Q ss_pred hCCCCe--eEEEeCCCCCCcEEEEEecc
Q 043434 15 AGFPGL--LSVAMKGDDLRHMEVIGDID 40 (90)
Q Consensus 15 ~~~~GV--~sv~id~~~~~kvtV~G~vD 40 (90)
..++|+ +++++.. ..+.|.|.|...
T Consensus 13 ~~lpg~~~~~i~V~v-~~~~l~I~g~~~ 39 (88)
T cd06464 13 ADLPGFKKEDIKVEV-EDGVLTISGERE 39 (88)
T ss_pred EECCCCCHHHeEEEE-ECCEEEEEEEEe
Confidence 357787 5666665 558999999844
No 87
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=24.77 E-value=73 Score=20.55 Aligned_cols=23 Identities=17% Similarity=0.143 Sum_probs=18.1
Q ss_pred hHHHHHHHHHhCCCCeeEEEeCC
Q 043434 5 KCRTKAFQIIAGFPGLLSVAMKG 27 (90)
Q Consensus 5 kC~~Kv~k~v~~~~GV~sv~id~ 27 (90)
+--..+...+++++||.|+++..
T Consensus 62 ~~td~lee~i~~~e~Vqsvei~~ 84 (88)
T PRK00435 62 GGTEPVEEAFANVEGVESVEVEE 84 (88)
T ss_pred cCcHHHHHHHhccCCCcEEEEEE
Confidence 34456778899999999999863
No 88
>KOG3167 consensus Box H/ACA snoRNP component, involved in ribosomal RNA pseudouridinylation [RNA processing and modification]
Probab=24.65 E-value=16 Score=26.19 Aligned_cols=44 Identities=23% Similarity=0.177 Sum_probs=29.3
Q ss_pred hHHHHHHHHHhCCCCeeEEE---eCCCCCCcEEEEEeccHHHHHHHHH
Q 043434 5 KCRTKAFQIIAGFPGLLSVA---MKGDDLRHMEVIGDIDEVALANMLR 49 (90)
Q Consensus 5 kC~~Kv~k~v~~~~GV~sv~---id~~~~~kvtV~G~vDp~~lv~~Lr 49 (90)
+|-+|+++.=.-..||..|. -.+ +++-++..|++-|.+|...|.
T Consensus 49 KlvkKa~k~k~lrrGvKevqK~vrkG-eKGl~VlAgd~sPiDvi~HlP 95 (153)
T KOG3167|consen 49 KLVKKAAKQKGLRRGVKEVQKRVRKG-EKGLCVLAGDTSPIDVITHLP 95 (153)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHhcC-CcceEEEecCCccHHHHhccc
Confidence 44445444433345555443 345 788999999999999998775
No 89
>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=24.55 E-value=95 Score=16.92 Aligned_cols=18 Identities=17% Similarity=0.357 Sum_probs=13.6
Q ss_pred HHHHHHHhCCCCeeEEEe
Q 043434 8 TKAFQIIAGFPGLLSVAM 25 (90)
Q Consensus 8 ~Kv~k~v~~~~GV~sv~i 25 (90)
..+++.+.+++||.+|..
T Consensus 53 ~~~i~~l~~~~~v~~v~~ 70 (71)
T cd04903 53 EEVIEEIKKIPNIHQVIL 70 (71)
T ss_pred HHHHHHHHcCCCceEEEE
Confidence 357788888888888753
No 90
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=24.03 E-value=1.7e+02 Score=26.64 Aligned_cols=36 Identities=22% Similarity=0.324 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEeccHHHH
Q 043434 7 RTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVAL 44 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~vDp~~l 44 (90)
.+.+...+.+++||-+|++-|.....+.|. +||.+|
T Consensus 157 ~~~l~~~L~~v~GV~~V~~~G~~~~~~rI~--ldp~kL 192 (1009)
T COG0841 157 ASNVRDELSRVPGVGSVQLFGAQEYAMRIW--LDPAKL 192 (1009)
T ss_pred HHHHHHHHhcCCCceEEEEcCCCceeEEEE--eCHHHH
Confidence 466888999999999999998434455553 555444
No 91
>PHA01634 hypothetical protein
Probab=23.64 E-value=25 Score=25.15 Aligned_cols=11 Identities=27% Similarity=0.422 Sum_probs=8.9
Q ss_pred CCChhHHHHHH
Q 043434 1 MHSPKCRTKAF 11 (90)
Q Consensus 1 mhCekC~~Kv~ 11 (90)
|.|+||.+++-
T Consensus 98 iDCeGCE~~l~ 108 (156)
T PHA01634 98 MDCEGCEEKLN 108 (156)
T ss_pred EEccchHHhcC
Confidence 67999998764
No 92
>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=23.11 E-value=56 Score=22.27 Aligned_cols=30 Identities=13% Similarity=0.310 Sum_probs=24.4
Q ss_pred EEEeCCCCCCcEEEEEeccHHHHHHHHHhhcC
Q 043434 22 SVAMKGDDLRHMEVIGDIDEVALANMLRRKIG 53 (90)
Q Consensus 22 sv~id~~~~~kvtV~G~vDp~~lv~~LrKk~~ 53 (90)
+.++|. + +++++.|..++..|-+.|++.+.
T Consensus 62 ~~~id~-~-~~lii~G~~~~~~i~~~L~~fI~ 91 (125)
T PF01873_consen 62 QGSIDG-K-GRLIINGRFSSKQIQDLLDKFIK 91 (125)
T ss_dssp EEEEET-T-TEEEEESSSSCCHHHHHHHHHHC
T ss_pred ceEECC-C-CEEEEEEecCHHHHHHHHHHHHH
Confidence 356775 4 99999999999999999987643
No 93
>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=23.04 E-value=1.1e+02 Score=19.36 Aligned_cols=23 Identities=17% Similarity=0.346 Sum_probs=17.1
Q ss_pred CCcEEEEEeccHHHHHHHHHhhc
Q 043434 30 LRHMEVIGDIDEVALANMLRRKI 52 (90)
Q Consensus 30 ~~kvtV~G~vDp~~lv~~LrKk~ 52 (90)
..++.|.|.+|+..+-+.|++-.
T Consensus 38 p~~i~i~gRl~~~~~~~yl~~i~ 60 (119)
T PF07744_consen 38 PKKIDIRGRLDPEKVWDYLRQIR 60 (119)
T ss_dssp -EEE-EEEE-SHHHHHHHHHHTS
T ss_pred CcEEEEEeecCHHHHHHHHHhcc
Confidence 46899999999999999997533
No 94
>TIGR00668 apaH bis(5'-nucleosyl)-tetraphosphatase (symmetrical). Alternate names include diadenosine-tetraphosphatase and Ap4A hydrolase.
Probab=22.90 E-value=2.2e+02 Score=22.03 Aligned_cols=44 Identities=9% Similarity=0.190 Sum_probs=30.1
Q ss_pred hHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe-c----cHHHHHHHHHhhcCce
Q 043434 5 KCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD-I----DEVALANMLRRKIGYV 55 (90)
Q Consensus 5 kC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~-v----Dp~~lv~~LrKk~~~a 55 (90)
||.....+.+..+ ..+. ..+++.+.|| | |+..++..|+.-...+
T Consensus 11 Gc~daL~~LL~~i------~f~~-~~D~l~~lGDlVdRGP~slevL~~l~~l~~~~ 59 (279)
T TIGR00668 11 GCYDELQALLERV------EFDP-GQDTLWLTGDLVARGPGSLEVLRYVKSLGDAV 59 (279)
T ss_pred CCHHHHHHHHHHh------CcCC-CCCEEEEeCCccCCCCCHHHHHHHHHhcCCCe
Confidence 5666666666554 2344 5689999999 6 5999999998633334
No 95
>PRK10568 periplasmic protein; Provisional
Probab=22.10 E-value=2.3e+02 Score=20.42 Aligned_cols=35 Identities=9% Similarity=0.184 Sum_probs=24.4
Q ss_pred HHHHHHHHHhCCCCee--EEEeCCCCCCcEEEEEeccH
Q 043434 6 CRTKAFQIIAGFPGLL--SVAMKGDDLRHMEVIGDIDE 41 (90)
Q Consensus 6 C~~Kv~k~v~~~~GV~--sv~id~~~~~kvtV~G~vDp 41 (90)
=..++...+..-+++. .|.+.- .++.|++.|.|+.
T Consensus 61 I~~~v~~~L~~~~~i~~~~I~V~v-~~G~V~L~G~V~s 97 (203)
T PRK10568 61 ITAKVKAALVDHDNIKSTDISVKT-HQKVVTLSGFVES 97 (203)
T ss_pred HHHHHHHHHHhCCCCCCCceEEEE-ECCEEEEEEEeCC
Confidence 4567777776666664 456665 6689999999863
No 96
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.73 E-value=1.3e+02 Score=17.19 Aligned_cols=19 Identities=5% Similarity=0.225 Sum_probs=15.5
Q ss_pred HHHHHHHHhCCCCeeEEEe
Q 043434 7 RTKAFQIIAGFPGLLSVAM 25 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~i 25 (90)
-..++..+..++||...++
T Consensus 54 l~~i~~~L~~i~gV~~~~~ 72 (74)
T cd04887 54 AETIVAAVRALPEVKVLSV 72 (74)
T ss_pred HHHHHHHHhcCCCeEEEEe
Confidence 3578899999999987765
No 97
>PF11065 DUF2866: Protein of unknown function (DUF2866); InterPro: IPR021294 This bacterial family of proteins have no known function.
Probab=21.68 E-value=1.2e+02 Score=18.88 Aligned_cols=32 Identities=19% Similarity=0.292 Sum_probs=26.2
Q ss_pred eeE-EEeCCCCCCcEEEEEeccHHHHHHHHHhhc
Q 043434 20 LLS-VAMKGDDLRHMEVIGDIDEVALANMLRRKI 52 (90)
Q Consensus 20 V~s-v~id~~~~~kvtV~G~vDp~~lv~~LrKk~ 52 (90)
|+. +..++ .-.+-+|-+++.+..+...++.-+
T Consensus 23 VEW~i~~~g-~~~RrvVpa~~T~~EIa~~ir~hv 55 (65)
T PF11065_consen 23 VEWTIDHDG-RISRRVVPADSTEAEIAEAIRSHV 55 (65)
T ss_pred EEEEecCCc-ceeEEeecccCChHHHHHHHHccC
Confidence 555 66676 667889999999999999998755
No 98
>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains. ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i
Probab=21.65 E-value=1.2e+02 Score=15.67 Aligned_cols=18 Identities=17% Similarity=0.475 Sum_probs=13.8
Q ss_pred HHHHHHHHhCCCCeeEEE
Q 043434 7 RTKAFQIIAGFPGLLSVA 24 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~ 24 (90)
...++..+..++||..+.
T Consensus 53 ~~~~~~~l~~~~~v~~v~ 70 (71)
T cd04876 53 LARIMRKLRQIPGVIDVR 70 (71)
T ss_pred HHHHHHHHhCCCCcEEEE
Confidence 456778888889988764
No 99
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=21.61 E-value=98 Score=23.61 Aligned_cols=37 Identities=27% Similarity=0.444 Sum_probs=28.9
Q ss_pred eEEEeCCCCCCcEEEEEeccHHHHHHHHHhhcC-ceEEEe
Q 043434 21 LSVAMKGDDLRHMEVIGDIDEVALANMLRRKIG-YVEMMK 59 (90)
Q Consensus 21 ~sv~id~~~~~kvtV~G~vDp~~lv~~LrKk~~-~aeivs 59 (90)
+|.++|+ +++|+|.|.+-+..+-+-||+-.. ++.=..
T Consensus 149 TsGSidg--~~rLviKGrfq~kq~e~VLRrYI~eyV~C~~ 186 (231)
T KOG2768|consen 149 TSGSIDG--QQRLVIKGRFQQKQFENVLRRYIKEYVTCKT 186 (231)
T ss_pred cccccCC--CceEEEeccccHHHHHHHHHHHHHHheEeee
Confidence 5778874 789999999999999999997664 544443
No 100
>cd06472 ACD_ScHsp26_like Alpha crystallin domain (ACD) found in Saccharomyces cerevisiae (Sc) small heat shock protein (Hsp)26 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. ScHsp26 is temperature-regulated, it switches from an inactive to a chaperone-active form upon elevation in temperature. It associates into large 24-mers storage forms which upon heat shock disassociate into dimers. These dimers initiate the interaction with non-native substrate proteins and re-assemble into large globular assemblies having one monomer of substrate bound per dimer. This group also contains Arabidopsis thaliana (Ath) Hsp15.7, a peroxisomal matrix protein which can complement the morphological phenotype of S. cerevisiae mutants deficient in Hsps26. AthHsp15.7 is minimally expressed under normal conditions and is strongly induced by heat and oxidative st
Probab=21.60 E-value=73 Score=19.65 Aligned_cols=25 Identities=28% Similarity=0.489 Sum_probs=16.1
Q ss_pred hCCCCee--EEEeCCCCCCcEEEEEec
Q 043434 15 AGFPGLL--SVAMKGDDLRHMEVIGDI 39 (90)
Q Consensus 15 ~~~~GV~--sv~id~~~~~kvtV~G~v 39 (90)
..++||. .++++.++.+.|+|.|+-
T Consensus 15 ~~lPGv~~edi~i~v~~~~~L~I~g~~ 41 (92)
T cd06472 15 ADVPGVKKEDVKVEVEDGRVLRISGER 41 (92)
T ss_pred EECCCCChHhEEEEEeCCCEEEEEEEe
Confidence 4578885 455554223589999984
No 101
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=21.45 E-value=1.6e+02 Score=22.20 Aligned_cols=44 Identities=14% Similarity=0.197 Sum_probs=28.5
Q ss_pred HHHHHHHHHhC-----CCCeeEEEeCC----------------CCCCcEEEEEeccHHHHHHHHH
Q 043434 6 CRTKAFQIIAG-----FPGLLSVAMKG----------------DDLRHMEVIGDIDEVALANMLR 49 (90)
Q Consensus 6 C~~Kv~k~v~~-----~~GV~sv~id~----------------~~~~kvtV~G~vDp~~lv~~Lr 49 (90)
..+|+++++.+ +.||..|++-. ...++.+|-|++-...|...+|
T Consensus 65 sekKark~m~KLGlk~v~gV~RVti~ksKNilfvI~kPdVyKsp~sdtYiiFGeakiedls~q~q 129 (209)
T KOG2239|consen 65 SEKKARKAMLKLGLKQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIIFGEAKIEDLSQQAQ 129 (209)
T ss_pred HHHHHHHHHHhcCCccccceeEEEEEecccEEEEecCCceeccCCCceEEEecccccchhHHHHH
Confidence 45667777665 48999988854 1334566777766666666555
No 102
>PRK13625 bis(5'-nucleosyl)-tetraphosphatase PrpE; Provisional
Probab=20.96 E-value=1.9e+02 Score=21.17 Aligned_cols=46 Identities=13% Similarity=0.264 Sum_probs=29.2
Q ss_pred hHHHHHHHHHhCCC--CeeEEEeCCCCCCcEEEEEe-cc----HHHHHHHHHhh
Q 043434 5 KCRTKAFQIIAGFP--GLLSVAMKGDDLRHMEVIGD-ID----EVALANMLRRK 51 (90)
Q Consensus 5 kC~~Kv~k~v~~~~--GV~sv~id~~~~~kvtV~G~-vD----p~~lv~~LrKk 51 (90)
||.....+.+..+. -...+.... .++++...|| || +..+++.|++.
T Consensus 11 G~~~~L~~lL~~~~~~~~~~~~~~~-~~d~li~lGDliDRGp~S~~vl~~~~~~ 63 (245)
T PRK13625 11 GCYQEFQALTEKLGYNWSSGLPVHP-DQRKLAFVGDLTDRGPHSLRMIEIVWEL 63 (245)
T ss_pred cCHHHHHHHHHHcCCCcccCcccCC-CCCEEEEECcccCCCcChHHHHHHHHHH
Confidence 67777666666542 111111222 4679999999 75 99999888754
No 103
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=20.71 E-value=89 Score=20.46 Aligned_cols=20 Identities=15% Similarity=0.182 Sum_probs=16.7
Q ss_pred HHHHHHHHhCCCCeeEEEeC
Q 043434 7 RTKAFQIIAGFPGLLSVAMK 26 (90)
Q Consensus 7 ~~Kv~k~v~~~~GV~sv~id 26 (90)
-..+-..+..++||.|+++.
T Consensus 64 td~~ee~l~~vegV~sveve 83 (88)
T COG2092 64 TDALEEALEEVEGVESVEVE 83 (88)
T ss_pred cHHHHHHHhhccCcceEEEE
Confidence 34677889999999999985
No 104
>PRK11439 pphA serine/threonine protein phosphatase 1; Provisional
Probab=20.65 E-value=1.4e+02 Score=21.37 Aligned_cols=40 Identities=13% Similarity=0.208 Sum_probs=27.2
Q ss_pred hHHHHHHHHHhCCCCeeEEEeCCCCCCcEEEEEe-c----cHHHHHHHHHhh
Q 043434 5 KCRTKAFQIIAGFPGLLSVAMKGDDLRHMEVIGD-I----DEVALANMLRRK 51 (90)
Q Consensus 5 kC~~Kv~k~v~~~~GV~sv~id~~~~~kvtV~G~-v----Dp~~lv~~LrKk 51 (90)
||....++.+..+ ..+. ..+++...|| | ||..+++.|++.
T Consensus 27 G~~~~L~~lL~~i------~~~~-~~D~li~lGDlvDrGp~s~~vl~~l~~~ 71 (218)
T PRK11439 27 GCFEQLMRKLRHC------RFDP-WRDLLISVGDLIDRGPQSLRCLQLLEEH 71 (218)
T ss_pred CCHHHHHHHHHhc------CCCc-ccCEEEEcCcccCCCcCHHHHHHHHHcC
Confidence 4555666666554 2222 4578999999 6 599999999763
No 105
>PF10105 DUF2344: Uncharacterized protein conserved in bacteria (DUF2344); InterPro: IPR018768 This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function.
Probab=20.48 E-value=1.9e+02 Score=20.79 Aligned_cols=33 Identities=15% Similarity=0.248 Sum_probs=27.1
Q ss_pred cEEEEEeccHHHHHHHHHhhcC-ceEEEecCCCC
Q 043434 32 HMEVIGDIDEVALANMLRRKIG-YVEMMKLDILD 64 (90)
Q Consensus 32 kvtV~G~vDp~~lv~~LrKk~~-~aeivsv~p~k 64 (90)
-+.+..++|+..+..+|.+..+ ..+|+.+.+..
T Consensus 65 di~l~~~~~~~~~~~rLn~~lP~Gl~i~~~~~i~ 98 (187)
T PF10105_consen 65 DIELEEDIDPEEVLERLNAVLPEGLRILEAEEIP 98 (187)
T ss_pred EEEEecCCCHHHHHHHHHHhCCCCCEEEEEEEcc
Confidence 4566778999999999998885 78888888654
No 106
>PRK10743 heat shock protein IbpA; Provisional
Probab=20.39 E-value=45 Score=22.89 Aligned_cols=24 Identities=13% Similarity=0.199 Sum_probs=15.7
Q ss_pred hCCCCee--EEEeCCCCCCcEEEEEec
Q 043434 15 AGFPGLL--SVAMKGDDLRHMEVIGDI 39 (90)
Q Consensus 15 ~~~~GV~--sv~id~~~~~kvtV~G~v 39 (90)
+.++||. .|+++. ..+.||+.|+-
T Consensus 51 aelPGv~kedi~V~v-~~~~LtI~ge~ 76 (137)
T PRK10743 51 IAVAGFAESELEITA-QDNLLVVKGAH 76 (137)
T ss_pred EECCCCCHHHeEEEE-ECCEEEEEEEE
Confidence 3567774 344444 45799999983
No 107
>PLN03175 hypothetical protein; Provisional
Probab=20.22 E-value=1.2e+02 Score=25.15 Aligned_cols=35 Identities=11% Similarity=0.077 Sum_probs=27.6
Q ss_pred CCeeEEEeCCCCCCcEEEEEe-ccHHHHHHHHHhhc
Q 043434 18 PGLLSVAMKGDDLRHMEVIGD-IDEVALANMLRRKI 52 (90)
Q Consensus 18 ~GV~sv~id~~~~~kvtV~G~-vDp~~lv~~LrKk~ 52 (90)
-|++.+++.+-..=+++-.|- +|+..++..|.-||
T Consensus 236 ~GvR~~eI~~~k~IKfyAiGVYle~~~v~~~L~~Kw 271 (415)
T PLN03175 236 TGSRTMKIIRIKSLKVYAFGFYVHPNSVCEKLGPKY 271 (415)
T ss_pred cccceeEEEeeceeEEEEEEEEeccchHHHHHhhhh
Confidence 489999997412338999999 99998999999555
Done!