Query 046486
Match_columns 202
No_of_seqs 156 out of 1197
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 12:37:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046486.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046486hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.5 3.6E-13 7.8E-18 92.5 8.9 57 2-59 1-60 (62)
2 KOG1603 Copper chaperone [Inor 99.5 2.1E-13 4.6E-18 98.5 7.6 63 2-68 8-70 (73)
3 COG2608 CopZ Copper chaperone 99.3 1.7E-11 3.7E-16 88.4 8.4 58 1-59 4-64 (71)
4 KOG4656 Copper chaperone for s 99.1 1.8E-10 3.8E-15 100.2 7.6 69 1-74 9-77 (247)
5 PLN02957 copper, zinc superoxi 98.3 5.1E-06 1.1E-10 72.2 9.3 67 1-72 8-74 (238)
6 PRK10671 copA copper exporting 98.1 7.6E-06 1.6E-10 81.7 8.1 62 1-69 5-67 (834)
7 TIGR00003 copper ion binding p 97.4 0.0017 3.8E-08 39.9 8.0 57 2-59 5-64 (68)
8 COG2217 ZntA Cation transport 97.1 0.0012 2.7E-08 66.1 7.2 56 2-59 5-64 (713)
9 KOG0207 Cation transport ATPas 96.4 0.0073 1.6E-07 62.0 6.7 64 6-73 2-66 (951)
10 PRK10671 copA copper exporting 96.4 0.0085 1.8E-07 60.2 7.2 56 2-59 102-158 (834)
11 KOG0207 Cation transport ATPas 96.0 0.016 3.5E-07 59.5 6.8 58 1-59 148-208 (951)
12 PRK11033 zntA zinc/cadmium/mer 95.5 0.041 9E-07 55.0 7.3 57 2-59 56-113 (741)
13 COG1888 Uncharacterized protei 95.5 0.038 8.3E-07 42.9 5.5 59 15-74 23-88 (97)
14 PF02680 DUF211: Uncharacteriz 95.4 0.035 7.5E-07 43.2 5.1 59 14-73 20-85 (95)
15 TIGR02052 MerP mercuric transp 89.4 4.7 0.0001 27.3 8.3 56 3-59 27-85 (92)
16 PF13732 DUF4162: Domain of un 84.5 4.8 0.0001 28.5 6.3 49 19-70 25-74 (84)
17 PF01206 TusA: Sulfurtransfera 83.9 4.3 9.4E-05 28.1 5.8 49 2-60 2-52 (70)
18 PF03927 NapD: NapD protein; 78.4 21 0.00045 26.3 7.9 54 13-68 17-72 (79)
19 PRK13748 putative mercuric red 78.3 14 0.0003 35.1 8.8 57 2-59 3-61 (561)
20 PRK10553 assembly protein for 75.5 13 0.00027 28.3 6.2 55 13-69 19-76 (87)
21 PF01883 DUF59: Domain of unkn 71.8 5.3 0.00011 27.9 3.2 29 3-31 38-72 (72)
22 cd00371 HMA Heavy-metal-associ 71.4 14 0.0003 19.8 7.7 52 4-55 3-56 (63)
23 PF14535 AMP-binding_C_2: AMP- 67.2 18 0.00038 26.9 5.4 59 14-73 7-82 (96)
24 PRK11018 hypothetical protein; 65.5 40 0.00087 24.4 6.9 54 2-65 10-65 (78)
25 PF09580 Spore_YhcN_YlaJ: Spor 64.0 31 0.00066 28.0 6.7 30 13-42 77-106 (177)
26 PF04972 BON: BON domain; Int 61.9 5.6 0.00012 26.9 1.7 31 14-46 2-35 (64)
27 PF14492 EFG_II: Elongation Fa 61.0 37 0.0008 24.3 5.9 54 11-67 16-73 (75)
28 PRK11198 LysM domain/BON super 59.9 14 0.00031 29.9 4.0 46 13-59 28-74 (147)
29 COG3062 NapD Uncharacterized p 56.8 33 0.00071 26.8 5.3 56 12-68 19-75 (94)
30 PF08777 RRM_3: RNA binding mo 56.3 82 0.0018 24.2 7.5 57 1-57 2-60 (105)
31 COG3643 Glutamate formiminotra 56.1 11 0.00025 34.4 3.0 54 13-70 20-75 (302)
32 COG0425 SirA Predicted redox p 55.7 79 0.0017 23.2 7.5 56 2-66 7-64 (78)
33 cd03421 SirA_like_N SirA_like_ 55.2 50 0.0011 22.6 5.6 49 3-62 2-52 (67)
34 cd03420 SirA_RHOD_Pry_redox Si 55.1 60 0.0013 22.7 6.1 53 3-65 2-56 (69)
35 cd00291 SirA_YedF_YeeD SirA, Y 53.5 68 0.0015 21.7 6.2 49 3-61 2-52 (69)
36 PF08260 Kinin: Insect kinin p 52.3 6.2 0.00013 18.0 0.4 7 151-157 2-8 (8)
37 PF07837 FTCD_N: Formiminotran 51.2 13 0.00029 31.8 2.5 53 13-69 18-72 (178)
38 cd04888 ACT_PheB-BS C-terminal 49.0 35 0.00076 23.1 4.0 8 48-55 57-64 (76)
39 cd03423 SirA SirA (also known 48.6 91 0.002 21.7 6.5 50 3-62 2-53 (69)
40 cd02410 archeal_CPSF_KH The ar 48.1 58 0.0013 27.2 5.8 55 13-70 55-114 (145)
41 PRK11023 outer membrane lipopr 48.1 56 0.0012 27.5 5.9 40 10-50 126-167 (191)
42 PF03958 Secretin_N: Bacterial 47.6 27 0.00059 24.4 3.4 28 28-55 47-74 (82)
43 smart00362 RRM_2 RNA recogniti 46.4 71 0.0015 19.9 8.0 53 3-57 2-59 (72)
44 PRK10555 aminoglycoside/multid 46.1 48 0.001 34.8 6.1 45 13-57 159-210 (1037)
45 PRK06418 transcription elongat 45.6 61 0.0013 27.4 5.7 64 4-70 11-98 (166)
46 cd03422 YedF YedF is a bacteri 44.8 1.1E+02 0.0023 21.5 6.1 51 3-63 2-54 (69)
47 PF02983 Pro_Al_protease: Alph 44.5 51 0.0011 23.1 4.3 29 15-43 8-42 (62)
48 PRK09577 multidrug efflux prot 43.4 56 0.0012 34.3 6.1 44 13-56 158-208 (1032)
49 cd04883 ACT_AcuB C-terminal AC 41.6 1.1E+02 0.0023 20.5 7.5 57 2-59 3-65 (72)
50 TIGR00915 2A0602 The (Largely 40.7 65 0.0014 33.9 6.1 44 13-56 159-209 (1044)
51 COG2177 FtsX Cell division pro 39.6 93 0.002 28.4 6.3 43 3-59 65-107 (297)
52 TIGR02945 SUF_assoc FeS assemb 39.5 25 0.00054 26.0 2.2 38 14-57 58-95 (99)
53 KOG0559 Dihydrolipoamide succi 39.4 50 0.0011 31.9 4.6 15 28-42 104-118 (457)
54 PRK15127 multidrug efflux syst 38.5 75 0.0016 33.5 6.2 42 14-55 160-208 (1049)
55 PRK11023 outer membrane lipopr 38.1 59 0.0013 27.4 4.5 44 11-55 49-95 (191)
56 COG2151 PaaD Predicted metal-s 38.0 42 0.0009 26.6 3.3 30 4-33 54-89 (111)
57 PF01849 NAC: NAC domain; Int 37.1 28 0.00061 23.9 2.0 29 14-42 2-35 (58)
58 PF08478 POTRA_1: POTRA domain 36.3 37 0.00081 22.9 2.5 30 13-42 36-66 (69)
59 TIGR02024 FtcD glutamate formi 35.0 27 0.00058 32.3 2.1 55 13-71 20-76 (298)
60 PF08712 Nfu_N: Scaffold prote 34.9 92 0.002 23.2 4.7 41 14-56 37-78 (87)
61 COG1094 Predicted RNA-binding 34.9 86 0.0019 27.4 5.0 38 14-52 27-66 (194)
62 TIGR02898 spore_YhcN_YlaJ spor 34.4 2E+02 0.0043 24.1 7.0 32 11-42 54-85 (158)
63 PF13291 ACT_4: ACT domain; PD 33.6 68 0.0015 22.3 3.6 24 7-30 56-79 (80)
64 PRK03195 hypothetical protein; 32.9 94 0.002 26.7 4.9 43 31-73 116-167 (186)
65 PRK04021 hypothetical protein; 32.0 1.3E+02 0.0029 22.9 5.2 46 7-55 42-91 (92)
66 TIGR00914 2A0601 heavy metal e 30.6 66 0.0014 33.8 4.3 47 12-58 699-754 (1051)
67 PF12685 SpoIIIAH: SpoIIIAH-li 30.6 1.8E+02 0.0039 24.5 6.3 53 14-67 138-195 (196)
68 PF08002 DUF1697: Protein of u 30.2 2E+02 0.0042 23.1 6.1 44 14-59 22-69 (137)
69 PF04312 DUF460: Protein of un 29.4 2E+02 0.0044 23.8 6.1 40 28-71 45-85 (138)
70 PRK09579 multidrug efflux prot 29.1 1.3E+02 0.0027 31.8 6.0 44 13-56 158-209 (1017)
71 TIGR00489 aEF-1_beta translati 28.8 61 0.0013 24.6 2.8 23 11-33 62-84 (88)
72 COG0217 Uncharacterized conser 28.4 1.1E+02 0.0023 27.7 4.6 50 14-67 150-199 (241)
73 PRK10568 periplasmic protein; 28.0 1.2E+02 0.0026 25.8 4.8 38 8-46 57-96 (203)
74 PRK06719 precorrin-2 dehydroge 27.8 1.2E+02 0.0026 24.6 4.6 39 29-71 7-45 (157)
75 TIGR02515 IV_pilus_PilQ type I 27.6 1.7E+02 0.0036 27.3 6.1 57 13-70 109-177 (418)
76 PF01709 Transcrip_reg: Transc 27.1 1.7E+02 0.0037 25.7 5.7 48 17-69 150-197 (234)
77 PF00013 KH_1: KH domain syndr 27.0 1E+02 0.0022 20.4 3.4 34 18-55 23-58 (60)
78 PF14605 Nup35_RRM_2: Nup53/35 26.9 2E+02 0.0044 19.3 4.9 33 10-42 11-43 (53)
79 TIGR01676 GLDHase galactonolac 26.9 95 0.0021 30.8 4.5 35 21-59 111-145 (541)
80 COG4892 Predicted heme/steroid 26.9 24 0.00052 26.6 0.3 16 145-161 20-41 (81)
81 PRK10614 multidrug efflux syst 26.8 1.5E+02 0.0032 31.2 6.1 45 13-57 159-211 (1025)
82 PRK00299 sulfur transfer prote 26.7 2.5E+02 0.0055 20.3 7.1 51 2-62 11-63 (81)
83 TIGR00334 5S_RNA_mat_M5 ribonu 26.5 89 0.0019 26.8 3.7 44 10-55 57-106 (174)
84 PRK13568 hofQ putative outer m 26.2 1.9E+02 0.0041 26.8 6.1 58 13-71 94-160 (381)
85 PRK13763 putative RNA-processi 26.2 1.4E+02 0.003 25.0 4.8 38 15-53 23-61 (180)
86 COG4492 PheB ACT domain-contai 26.1 92 0.002 26.1 3.6 24 45-70 126-149 (150)
87 PF10934 DUF2634: Protein of u 25.6 1.1E+02 0.0025 23.7 3.9 31 12-42 70-103 (112)
88 PRK11670 antiporter inner memb 25.5 1.4E+02 0.0029 27.8 5.0 55 13-71 67-145 (369)
89 PF07338 DUF1471: Protein of u 24.6 91 0.002 21.5 2.8 23 36-58 6-28 (56)
90 PF15643 Tox-PL-2: Papain fold 24.5 64 0.0014 25.4 2.3 20 6-26 18-37 (100)
91 PF00873 ACR_tran: AcrB/AcrD/A 24.5 1.1E+02 0.0023 31.9 4.5 49 11-59 687-744 (1021)
92 PF05046 Img2: Mitochondrial l 24.2 2.4E+02 0.0052 21.0 5.3 43 11-55 40-83 (87)
93 cd06482 ACD_HspB10 Alpha cryst 24.1 58 0.0013 24.4 1.9 22 22-43 15-38 (87)
94 COG0841 AcrB Cation/multidrug 23.8 1.9E+02 0.0041 30.9 6.2 43 13-55 157-207 (1009)
95 PF00873 ACR_tran: AcrB/AcrD/A 23.0 2E+02 0.0044 29.9 6.2 45 13-57 62-109 (1021)
96 PF05258 DUF721: Protein of un 23.0 1.2E+02 0.0027 21.0 3.4 39 29-67 42-89 (89)
97 PF01565 FAD_binding_4: FAD bi 22.8 1.4E+02 0.0031 22.6 3.9 28 29-57 57-84 (139)
98 smart00749 BON bacterial OsmY 21.5 2.2E+02 0.0048 17.9 6.8 41 14-54 2-44 (62)
99 cd04877 ACT_TyrR N-terminal AC 21.2 1.7E+02 0.0036 20.2 3.7 15 45-59 49-63 (74)
100 TIGR03665 arCOG04150 arCOG0415 21.2 1.8E+02 0.0039 24.1 4.5 39 15-54 18-56 (172)
101 PF03434 DUF276: DUF276 ; Int 21.1 1.3E+02 0.0029 27.5 3.9 29 12-40 88-116 (291)
102 PRK00435 ef1B elongation facto 21.0 93 0.002 23.7 2.5 24 10-33 61-84 (88)
103 PRK10614 multidrug efflux syst 21.0 1.2E+02 0.0026 31.8 4.1 48 12-59 676-732 (1025)
104 COG2092 EFB1 Translation elong 20.8 87 0.0019 24.1 2.3 22 11-32 62-83 (88)
105 PRK15078 polysaccharide export 20.3 1.9E+02 0.0042 27.0 5.0 68 2-70 133-218 (379)
106 PRK13625 bis(5'-nucleosyl)-tet 20.2 2.2E+02 0.0048 24.5 5.0 53 1-55 1-61 (245)
107 TIGR03527 selenium_YedF seleni 20.1 2.7E+02 0.0059 23.7 5.5 44 6-59 5-49 (194)
No 1
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.47 E-value=3.6e-13 Score=92.48 Aligned_cols=57 Identities=35% Similarity=0.543 Sum_probs=52.9
Q ss_pred EEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee--cCCHHHHHHHHHhhcC
Q 046486 2 VLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV--SCSPEEIRDKLCCKGE 59 (202)
Q Consensus 2 vLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~--~vdpekL~~kL~~KtG 59 (202)
+|+| +|+|++|+++|+++|.+++||.++++|+.+++|+|.++ ..++++|.++|+ ++|
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~-~~G 60 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIE-KAG 60 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHH-HTT
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHH-HhC
Confidence 6899 99999999999999999999999999999999999985 245799999999 788
No 2
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.46 E-value=2.1e-13 Score=98.49 Aligned_cols=63 Identities=37% Similarity=0.577 Sum_probs=57.3
Q ss_pred EEEEcccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcCCceeeEEEc
Q 046486 2 VLKVDLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGEGVIKTIEIL 68 (202)
Q Consensus 2 vLKV~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtGk~iK~aEIV 68 (202)
+++|+|||++|+.+|+++|+.+.||.++.+|.++++|||.| .+++..|+++|++.++ +.+++|
T Consensus 8 v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g-~~~p~~vl~~l~k~~~---k~~~~~ 70 (73)
T KOG1603|consen 8 VLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKG-NVDPVKLLKKLKKTGG---KRAELW 70 (73)
T ss_pred EEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEE-ecCHHHHHHHHHhcCC---CceEEe
Confidence 68889999999999999999999999999999999999999 6999999999996554 555555
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.29 E-value=1.7e-11 Score=88.35 Aligned_cols=58 Identities=24% Similarity=0.375 Sum_probs=52.7
Q ss_pred CEEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee--cCCHHHHHHHHHhhcC
Q 046486 1 MVLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV--SCSPEEIRDKLCCKGE 59 (202)
Q Consensus 1 mvLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~--~vdpekL~~kL~~KtG 59 (202)
+.|+| +|+|++|+++|+++|.+++||.+++||++.++++|..+ .++.++|+++|. ++|
T Consensus 4 ~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~-~aG 64 (71)
T COG2608 4 TTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIE-DAG 64 (71)
T ss_pred EEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHH-HcC
Confidence 36889 99999999999999999999999999999977777655 379999999999 888
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.11 E-value=1.8e-10 Score=100.19 Aligned_cols=69 Identities=22% Similarity=0.390 Sum_probs=65.4
Q ss_pred CEEEEcccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcCCceeeEEEcCCCCCC
Q 046486 1 MVLKVDLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGEGVIKTIEILKPDEKR 74 (202)
Q Consensus 1 mvLKV~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtGk~iK~aEIVsp~kpk 74 (202)
++|.|+|+|++|++.|+..|..++||.+|+||++++.|.|.+ ++.+.+|.++|+ .+| +++.|...+++.
T Consensus 9 ~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~t-s~p~s~i~~~le-~tG---r~Avl~G~G~ps 77 (247)
T KOG4656|consen 9 AEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVET-SVPPSEIQNTLE-NTG---RDAVLRGAGKPS 77 (247)
T ss_pred EEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEc-cCChHHHHHHHH-hhC---hheEEecCCchh
Confidence 368999999999999999999999999999999999999999 899999999999 899 999999998864
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.27 E-value=5.1e-06 Score=72.19 Aligned_cols=67 Identities=16% Similarity=0.285 Sum_probs=59.8
Q ss_pred CEEEEcccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcCCceeeEEEcCCCC
Q 046486 1 MVLKVDLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGEGVIKTIEILKPDE 72 (202)
Q Consensus 1 mvLKV~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtGk~iK~aEIVsp~k 72 (202)
+.|.|+|+|+.|+++|+++|.+++||.++.+|+.+++++|.. ..+.+.|+++|+ ++| +.+++++...
T Consensus 8 ~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~-~~~~~~I~~aIe-~~G---y~a~~~~~~~ 74 (238)
T PLN02957 8 TEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLG-SSPVKAMTAALE-QTG---RKARLIGQGD 74 (238)
T ss_pred EEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEe-cCCHHHHHHHHH-HcC---CcEEEecCCC
Confidence 357789999999999999999999999999999999999998 678999999999 888 7788887654
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.12 E-value=7.6e-06 Score=81.71 Aligned_cols=62 Identities=19% Similarity=0.378 Sum_probs=54.2
Q ss_pred CEEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcCCceeeEEEcC
Q 046486 1 MVLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGEGVIKTIEILK 69 (202)
Q Consensus 1 mvLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtGk~iK~aEIVs 69 (202)
++|+| +|+|.+|+++|+++|.+++||.+++||++ +++|++ ..+.+.|.++|+ +.| +.+++.+
T Consensus 5 ~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~-~~~~~~i~~~i~-~~G---y~~~~~~ 67 (834)
T PRK10671 5 IDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTG-TASAEALIETIK-QAG---YDASVSH 67 (834)
T ss_pred EEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEe-cCCHHHHHHHHH-hcC---Ccccccc
Confidence 36889 99999999999999999999999999994 566666 579999999999 889 6777765
No 7
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.42 E-value=0.0017 Score=39.93 Aligned_cols=57 Identities=12% Similarity=0.339 Sum_probs=47.1
Q ss_pred EEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee--cCCHHHHHHHHHhhcC
Q 046486 2 VLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV--SCSPEEIRDKLCCKGE 59 (202)
Q Consensus 2 vLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~--~vdpekL~~kL~~KtG 59 (202)
.|.| +|+|..|+..|++.|..+.++..+.+++..+++.|..+ ..+...+...|. ..|
T Consensus 5 ~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g 64 (68)
T TIGR00003 5 TVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAIL-DAG 64 (68)
T ss_pred EEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHH-HcC
Confidence 4677 89999999999999999999999999999999988752 246677777665 445
No 8
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.11 E-value=0.0012 Score=66.06 Aligned_cols=56 Identities=23% Similarity=0.474 Sum_probs=50.5
Q ss_pred EEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee--cCC-HHHHHHHHHhhcC
Q 046486 2 VLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV--SCS-PEEIRDKLCCKGE 59 (202)
Q Consensus 2 vLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~--~vd-pekL~~kL~~KtG 59 (202)
.|.| +|+|..|+.+|+ +|.+++||.++.|++.+.+++|..+ ..+ .+.+..+++ +.|
T Consensus 5 ~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~-~~g 64 (713)
T COG2217 5 SLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVE-KAG 64 (713)
T ss_pred EEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHH-hcC
Confidence 5788 999999999999 9999999999999999999999864 245 788999999 778
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.41 E-value=0.0073 Score=62.03 Aligned_cols=64 Identities=19% Similarity=0.371 Sum_probs=58.4
Q ss_pred cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcCCceeeEEEcCCCCC
Q 046486 6 DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGEGVIKTIEILKPDEK 73 (202)
Q Consensus 6 ~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtGk~iK~aEIVsp~kp 73 (202)
+|+|..|.+.|+++|++.+||.+++|++.+++.+|.-+ .++++.|++.|+ ..| ..+++++....
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ie-d~g---f~~~~~~~~~~ 66 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIE-DMG---FEASLLSDSEI 66 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhh-ccc---ceeeecccCcc
Confidence 69999999999999999999999999999999999765 689999999999 777 89999887654
No 10
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.41 E-value=0.0085 Score=60.22 Aligned_cols=56 Identities=21% Similarity=0.417 Sum_probs=50.6
Q ss_pred EEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcC
Q 046486 2 VLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGE 59 (202)
Q Consensus 2 vLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtG 59 (202)
.|.| +|+|.+|+..|++.|.+++||.++.+++..+++.|.+ ..+.+.+.+.|. +.|
T Consensus 102 ~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~-~~s~~~I~~~I~-~~G 158 (834)
T PRK10671 102 QLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMG-SASPQDLVQAVE-KAG 158 (834)
T ss_pred EEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEc-cCCHHHHHHHHH-hcC
Confidence 4778 9999999999999999999999999999999999876 578888888888 777
No 11
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.01 E-value=0.016 Score=59.55 Aligned_cols=58 Identities=19% Similarity=0.381 Sum_probs=52.2
Q ss_pred CEEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee--cCCHHHHHHHHHhhcC
Q 046486 1 MVLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV--SCSPEEIRDKLCCKGE 59 (202)
Q Consensus 1 mvLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~--~vdpekL~~kL~~KtG 59 (202)
++|.| +|.|.+|..+|++.|.+++||+++.+|+.++++.|.-+ ...+-++.+.|+ .+|
T Consensus 148 i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie-~~~ 208 (951)
T KOG0207|consen 148 IYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIE-ETG 208 (951)
T ss_pred EEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHH-hhc
Confidence 36888 99999999999999999999999999999999999875 467888999998 666
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=95.49 E-value=0.041 Score=55.02 Aligned_cols=57 Identities=14% Similarity=0.292 Sum_probs=46.5
Q ss_pred EEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcC
Q 046486 2 VLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGE 59 (202)
Q Consensus 2 vLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtG 59 (202)
.|+| +|+|.+|+.+|+++|.+++||.++.+++.++++.|..+....+.+.+.++ ..|
T Consensus 56 ~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~-~~G 113 (741)
T PRK11033 56 SWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQ-KAG 113 (741)
T ss_pred EEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHH-hcc
Confidence 4778 89999999999999999999999999999999888753112256666666 566
No 13
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=95.48 E-value=0.038 Score=42.92 Aligned_cols=59 Identities=15% Similarity=0.236 Sum_probs=47.1
Q ss_pred HHHHHHhcCCCceEE-------EEEcCCCEEEEEeecCCHHHHHHHHHhhcCCceeeEEEcCCCCCC
Q 046486 15 KVKKVLCKFPQIQEQ-------SFDEKTNTVTIKVVSCSPEEIRDKLCCKGEGVIKTIEILKPDEKR 74 (202)
Q Consensus 15 KIkKaL~ki~GV~~V-------eVDlk~~tVtV~G~~vdpekL~~kL~~KtGk~iK~aEIVsp~kpk 74 (202)
.+.+.|++++||+.| +++..+=+|||.|.++|-+.|.+.|+ ..|..|.+|.-+-.++.-
T Consensus 23 e~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE-~~Gg~IHSiDevvaGk~i 88 (97)
T COG1888 23 ELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIE-ELGGAIHSIDEVVAGKRI 88 (97)
T ss_pred HHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHH-HcCCeeeehhhhhhccee
Confidence 456789999997654 33444667888998899999999999 888899999888777654
No 14
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=95.40 E-value=0.035 Score=43.18 Aligned_cols=59 Identities=20% Similarity=0.321 Sum_probs=44.0
Q ss_pred HHHHHHHhcCCCceEEE-----EEcCCC--EEEEEeecCCHHHHHHHHHhhcCCceeeEEEcCCCCC
Q 046486 14 KKVKKVLCKFPQIQEQS-----FDEKTN--TVTIKVVSCSPEEIRDKLCCKGEGVIKTIEILKPDEK 73 (202)
Q Consensus 14 kKIkKaL~ki~GV~~Ve-----VDlk~~--tVtV~G~~vdpekL~~kL~~KtGk~iK~aEIVsp~kp 73 (202)
-.+.++|.+++||..|. +|.++. +|||.|+++|.+.|.++|+ +.|..|.++.-|..++.
T Consensus 20 ~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie-~~Gg~IHSIDeVvaG~~ 85 (95)
T PF02680_consen 20 VELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIE-ELGGVIHSIDEVVAGKR 85 (95)
T ss_dssp HHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHH-HTT-EEEEEEEEEEESS
T ss_pred HHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHH-HcCCeEEeeeeeeecce
Confidence 35678999999988754 344433 4566787899999999999 88889999998877654
No 15
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=89.40 E-value=4.7 Score=27.31 Aligned_cols=56 Identities=16% Similarity=0.295 Sum_probs=41.9
Q ss_pred EEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee--cCCHHHHHHHHHhhcC
Q 046486 3 LKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV--SCSPEEIRDKLCCKGE 59 (202)
Q Consensus 3 LKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~--~vdpekL~~kL~~KtG 59 (202)
+.+ +++|..|...++..+....++....++.....+.+..+ ..+...+...+. ..|
T Consensus 27 ~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g 85 (92)
T TIGR02052 27 LEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATT-DAG 85 (92)
T ss_pred EEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHH-hcC
Confidence 456 78999999999999999999998999988887666521 235555555555 445
No 16
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=84.49 E-value=4.8 Score=28.53 Aligned_cols=49 Identities=16% Similarity=0.236 Sum_probs=35.0
Q ss_pred HHhcCCCceEEEEEcCC-CEEEEEeecCCHHHHHHHHHhhcCCceeeEEEcCC
Q 046486 19 VLCKFPQIQEQSFDEKT-NTVTIKVVSCSPEEIRDKLCCKGEGVIKTIEILKP 70 (202)
Q Consensus 19 aL~ki~GV~~VeVDlk~-~tVtV~G~~vdpekL~~kL~~KtGk~iK~aEIVsp 70 (202)
.|..++||.++..+... -++.|.. ..+...|++.|. ..|. |.+.++..|
T Consensus 25 ~l~~~~~v~~v~~~~~~~~~i~l~~-~~~~~~ll~~l~-~~g~-I~~f~~~~P 74 (84)
T PF13732_consen 25 ELEELPGVESVEQDGDGKLRIKLED-EETANELLQELI-EKGI-IRSFEEEEP 74 (84)
T ss_pred HHhhCCCeEEEEEeCCcEEEEEECC-cccHHHHHHHHH-hCCC-eeEEEEcCC
Confidence 38889999999876433 3444444 577889999999 6575 777777655
No 17
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=83.92 E-value=4.3 Score=28.12 Aligned_cols=49 Identities=24% Similarity=0.260 Sum_probs=35.9
Q ss_pred EEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcCC
Q 046486 2 VLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGEG 60 (202)
Q Consensus 2 vLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtGk 60 (202)
+|.+ ++.|..-.-+++++|.+++ ..+.+.|..+ ....+.|...++ ..|.
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~---------~G~~l~v~~d~~~~~~di~~~~~-~~g~ 52 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELP---------PGEVLEVLVDDPAAVEDIPRWCE-ENGY 52 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSG---------TT-EEEEEESSTTHHHHHHHHHH-HHTE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcC---------CCCEEEEEECCccHHHHHHHHHH-HCCC
Confidence 5677 8999999999999999985 2456666664 345677888888 7783
No 18
>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=78.38 E-value=21 Score=26.26 Aligned_cols=54 Identities=17% Similarity=0.257 Sum_probs=34.6
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcC--CceeeEEEc
Q 046486 13 RKKVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGE--GVIKTIEIL 68 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtG--k~iK~aEIV 68 (202)
...|+++|..++|++=...|.+ ++++|+-...+...+.+.|. ... .-+.++.++
T Consensus 17 ~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~-~i~~l~GVlsa~lv 72 (79)
T PF03927_consen 17 LEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLID-AINALPGVLSASLV 72 (79)
T ss_dssp HHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHH-HHCCSTTEEEEEES
T ss_pred HHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHH-HHHcCCCceEEEEE
Confidence 4689999999999966666666 66665543456666666665 221 224555554
No 19
>PRK13748 putative mercuric reductase; Provisional
Probab=78.34 E-value=14 Score=35.07 Aligned_cols=57 Identities=21% Similarity=0.443 Sum_probs=44.9
Q ss_pred EEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcC
Q 046486 2 VLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGE 59 (202)
Q Consensus 2 vLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtG 59 (202)
.+.+ +|+|.+|..+++..+..++++....+++..+.+.+... ..+...+...+. ..|
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~-~~g 61 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVA-GLG 61 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHH-HcC
Confidence 3567 89999999999999999999999999999998877641 235566666665 555
No 20
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=75.48 E-value=13 Score=28.28 Aligned_cols=55 Identities=11% Similarity=0.161 Sum_probs=37.1
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHH---HHHhhcCCceeeEEEcC
Q 046486 13 RKKVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRD---KLCCKGEGVIKTIEILK 69 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~---kL~~KtGk~iK~aEIVs 69 (202)
...|+++|..++|++=.-.|.++++++|+-..-+...+.+ +|+.--| +.++.+|-
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~~I~~l~G--Vlsa~lVY 76 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIESVRNVEG--VLAVSLVY 76 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHHHHHcCCC--ceEEEEEE
Confidence 5789999999999977777777777766543345554444 4453334 66666664
No 21
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=71.77 E-value=5.3 Score=27.90 Aligned_cols=29 Identities=17% Similarity=0.563 Sum_probs=19.5
Q ss_pred EEEcccChhh------HHHHHHHHhcCCCceEEEE
Q 046486 3 LKVDLSCSKC------RKKVKKVLCKFPQIQEQSF 31 (202)
Q Consensus 3 LKV~M~C~gC------akKIkKaL~ki~GV~~VeV 31 (202)
|.+.+.-.+| ...|+++|..++||.+|+|
T Consensus 38 v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 38 VSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp EEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred EEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 4444554444 4789999999999999886
No 22
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=71.38 E-value=14 Score=19.78 Aligned_cols=52 Identities=29% Similarity=0.547 Sum_probs=37.2
Q ss_pred EE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHH
Q 046486 4 KV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLC 55 (202)
Q Consensus 4 KV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~ 55 (202)
.+ ++.|..|...++..+..+.++....+++....+.+... ..+...+...+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIE 56 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHH
Confidence 35 78999999999999999999888888877777666541 124444433443
No 23
>PF14535 AMP-binding_C_2: AMP-binding enzyme C-terminal domain; PDB: 2Y27_A 2Y4N_A 3QOV_B 3S89_D 3LAX_A 2Y4O_B.
Probab=67.20 E-value=18 Score=26.88 Aligned_cols=59 Identities=22% Similarity=0.366 Sum_probs=36.8
Q ss_pred HHHHHHHhcCCCce-EEE--EE--cCCCEEEEEee---cCC---------HHHHHHHHHhhcCCceeeEEEcCCCCC
Q 046486 14 KKVKKVLCKFPQIQ-EQS--FD--EKTNTVTIKVV---SCS---------PEEIRDKLCCKGEGVIKTIEILKPDEK 73 (202)
Q Consensus 14 kKIkKaL~ki~GV~-~Ve--VD--lk~~tVtV~G~---~vd---------pekL~~kL~~KtGk~iK~aEIVsp~kp 73 (202)
..|+.+|.+++|+. ... ++ ...+.++|... ..+ .+.|.++|+.++|-.. +|++++++.=
T Consensus 7 ~~Ie~vl~~~~~~~~~y~i~v~~~~~~D~l~v~vE~~~~~~~~~~~~~~l~~~i~~~lk~~lgv~~-~V~lv~~gtL 82 (96)
T PF14535_consen 7 SQIEEVLREFPEVSPEYQIVVTREGGLDELTVRVELRPGFSDDAEDLEALAERIAERLKERLGVRP-EVELVPPGTL 82 (96)
T ss_dssp HHHHHHHCTSTTEEEEEEEEEEEETTEEEEEEEEEESTTCCTTHHHHHHHHHHHHHHHHHHHSS-E-EEEEE-TT-S
T ss_pred HHHHHHHHhCcCCCCcEEEEEEcCCCCcEEEEEEEECCccCcchHHHHHHHHHHHHHHHhhcCceE-EEEEECCCCc
Confidence 46899999999998 433 33 33555666532 121 3467777887887444 8888988653
No 24
>PRK11018 hypothetical protein; Provisional
Probab=65.55 E-value=40 Score=24.41 Aligned_cols=54 Identities=13% Similarity=0.037 Sum_probs=37.1
Q ss_pred EEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcCCceeeE
Q 046486 2 VLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGEGVIKTI 65 (202)
Q Consensus 2 vLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtGk~iK~a 65 (202)
+|.+ ++.|..=.-+.+++|.+++ ..+.++|..+ ......|...++ +.|..+.++
T Consensus 10 ~lD~rG~~CP~Pvl~~kk~l~~l~---------~G~~L~V~~d~~~a~~di~~~~~-~~G~~v~~~ 65 (78)
T PRK11018 10 RLDMVGEPCPYPAVATLEALPQLK---------KGEILEVVSDCPQSINNIPLDAR-NHGYTVLDI 65 (78)
T ss_pred eEECCCCcCCHHHHHHHHHHHhCC---------CCCEEEEEeCCccHHHHHHHHHH-HcCCEEEEE
Confidence 4566 8899999999999999986 2344555553 345566777777 778444433
No 25
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=64.02 E-value=31 Score=28.02 Aligned_cols=30 Identities=10% Similarity=0.271 Sum_probs=26.4
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCCEEEEEe
Q 046486 13 RKKVKKVLCKFPQIQEQSFDEKTNTVTIKV 42 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeVDlk~~tVtV~G 42 (202)
+.+|.+.|.+++||+++.|=...+.+.|-.
T Consensus 77 a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav 106 (177)
T PF09580_consen 77 ADRIANRVKKVPGVEDATVVVTDDNAYVAV 106 (177)
T ss_pred HHHHHHHHhcCCCceEEEEEEECCEEEEEE
Confidence 678999999999999999888888887754
No 26
>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=61.91 E-value=5.6 Score=26.87 Aligned_cols=31 Identities=23% Similarity=0.295 Sum_probs=16.7
Q ss_pred HHHHHHHhc---CCCceEEEEEcCCCEEEEEeecCC
Q 046486 14 KKVKKVLCK---FPQIQEQSFDEKTNTVTIKVVSCS 46 (202)
Q Consensus 14 kKIkKaL~k---i~GV~~VeVDlk~~tVtV~G~~vd 46 (202)
.+|+.+|.. +++- ++.|...++.|++.| .++
T Consensus 2 ~~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G-~v~ 35 (64)
T PF04972_consen 2 TKVRAALRADPWLPDS-NISVSVENGVVTLSG-EVP 35 (64)
T ss_dssp -----------CTT-T-TEEEEEECTEEEEEE-EES
T ss_pred cccccccccccccCCC-eEEEEEECCEEEEEe-eCc
Confidence 467888888 4444 789999999999999 453
No 27
>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=61.02 E-value=37 Score=24.31 Aligned_cols=54 Identities=17% Similarity=0.161 Sum_probs=39.4
Q ss_pred hhHHHHHHHHhcCCC---ceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcCCceeeEEE
Q 046486 11 KCRKKVKKVLCKFPQ---IQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGEGVIKTIEI 67 (202)
Q Consensus 11 gCakKIkKaL~ki~G---V~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtGk~iK~aEI 67 (202)
+=..++..+|.+|.- --++..|.+++.+.|.|. .+-.+.++++|+.+.| ..|++
T Consensus 16 ~d~~kl~~aL~~l~~eDP~l~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~---v~v~~ 73 (75)
T PF14492_consen 16 EDEPKLSEALQKLSEEDPSLRVERDEETGELILSGMGELHLEVLLERLKRRFG---VEVEF 73 (75)
T ss_dssp HHHHHHHHHHHHHHHH-TTSEEEEETTTSEEEEEESSHHHHHHHHHHHHHTTC---EBEEE
T ss_pred hHHHHHHHHHHHHHhcCCeEEEEEcchhceEEEEECCHHHHHHHHHHHHHHHC---CeeEe
Confidence 335566666666543 338999999999999864 5778889999998877 55543
No 28
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=59.88 E-value=14 Score=29.86 Aligned_cols=46 Identities=11% Similarity=0.125 Sum_probs=33.4
Q ss_pred HHHHHHHHhcCC-CceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcC
Q 046486 13 RKKVKKVLCKFP-QIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGE 59 (202)
Q Consensus 13 akKIkKaL~ki~-GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtG 59 (202)
+++|.++|.+.. ++.++.|..+++.|++.| .+.-+..+++|...++
T Consensus 28 ~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G-~v~s~~~~~~~~~aa~ 74 (147)
T PRK11198 28 ADALKEHISKQGLGDADVNVQVEDGKATVSG-DAASQEAKEKILLAVG 74 (147)
T ss_pred HHHHHHHHHhcCCCcCCceEEEeCCEEEEEE-EeCCHHHHHHHHHHhc
Confidence 567888887632 355677888899999999 6777777777764555
No 29
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=56.77 E-value=33 Score=26.80 Aligned_cols=56 Identities=13% Similarity=0.123 Sum_probs=36.9
Q ss_pred hHHHHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcC-CceeeEEEc
Q 046486 12 CRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGE-GVIKTIEIL 68 (202)
Q Consensus 12 CakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtG-k~iK~aEIV 68 (202)
=..+|+.+|..|+|++-..-|.+.+.|+|.- .-+.+.|.+.|+.--. .-+.+|-+|
T Consensus 19 ~l~av~~~L~~ip~~EV~~~d~~GKlVVVie-~~~~~~l~~tie~i~nl~gVlav~lV 75 (94)
T COG3062 19 RLSAVKTALLAIPGCEVYGEDAEGKLVVVIE-AEDSETLLETIESIRNLPGVLAVSLV 75 (94)
T ss_pred HHHHHHHHHhcCCCcEeeccCCCceEEEEEE-cCchHHHHHHHHHHhcCCceeEEEEE
Confidence 3578999999999997777777745554432 4678888887762211 224455555
No 30
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=56.29 E-value=82 Score=24.21 Aligned_cols=57 Identities=16% Similarity=0.260 Sum_probs=34.8
Q ss_pred CEEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhh
Q 046486 1 MVLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCK 57 (202)
Q Consensus 1 mvLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~K 57 (202)
++|++ +++=+-....|+.+|+.+..|.-|++..-...-.|... ...+..+++++...
T Consensus 2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhc
Confidence 36777 57766669999999999999999999988888888763 23477888888733
No 31
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=56.08 E-value=11 Score=34.35 Aligned_cols=54 Identities=15% Similarity=0.219 Sum_probs=37.4
Q ss_pred HHHHHHHHhcCCCceEEEE--EcCCCEEEEEeecCCHHHHHHHHHhhcCCceeeEEEcCC
Q 046486 13 RKKVKKVLCKFPQIQEQSF--DEKTNTVTIKVVSCSPEEIRDKLCCKGEGVIKTIEILKP 70 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeV--Dlk~~tVtV~G~~vdpekL~~kL~~KtGk~iK~aEIVsp 70 (202)
..+|..+..++++|.-+++ |...|+-+|+. --+++++++++..-++ +.+++++-
T Consensus 20 ie~i~a~~~~~~~v~ildve~danhNRsViT~-vgdp~~~~~A~f~~ik---~AaelIDM 75 (302)
T COG3643 20 IEKIVAAAKSIPTVKILDVEMDANHNRSVITL-VGDPSKVVNAAFALIK---KAAELIDM 75 (302)
T ss_pred HHHHHHHHhcCCceEEEEeccCCCCCceEEEE-ecChHHHHHHHHHHHH---HHHHhhch
Confidence 4567777888898875555 44566766665 3589999888874555 66777763
No 32
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=55.73 E-value=79 Score=23.16 Aligned_cols=56 Identities=21% Similarity=0.264 Sum_probs=39.4
Q ss_pred EEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcCCceeeEE
Q 046486 2 VLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGEGVIKTIE 66 (202)
Q Consensus 2 vLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtGk~iK~aE 66 (202)
+|.+ +++|..=.-.++++|.+|+ ....+.|..+ .....+|-..++..+|..+-.++
T Consensus 7 ~LD~rG~~CP~Pv~~~kk~l~~m~---------~Ge~LeV~~ddp~~~~dIp~~~~~~~~~~ll~~e 64 (78)
T COG0425 7 VLDLRGLRCPGPVVETKKALAKLK---------PGEILEVIADDPAAKEDIPAWAKKEGGHELLEVE 64 (78)
T ss_pred EEeccCCcCCccHHHHHHHHHcCC---------CCCEEEEEecCcchHHHHHHHHHHcCCcEEEEEE
Confidence 5777 8999999999999999987 4566666654 34556777777744443444433
No 33
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=55.15 E-value=50 Score=22.65 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=33.5
Q ss_pred EEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcCCce
Q 046486 3 LKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGEGVI 62 (202)
Q Consensus 3 LKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtGk~i 62 (202)
|.+ ++.|..=.-+++++| ++.. .+.+.|..+ ....+.|...++ +.|..+
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~~~s~~~i~~~~~-~~G~~~ 52 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEA---------GGEIEVLVDNEVAKENVSRFAE-SRGYEV 52 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCC---------CCEEEEEEcChhHHHHHHHHHH-HcCCEE
Confidence 456 889999999999999 6642 345555553 344567888888 778333
No 34
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=55.10 E-value=60 Score=22.72 Aligned_cols=53 Identities=13% Similarity=0.169 Sum_probs=36.7
Q ss_pred EEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcCCceeeE
Q 046486 3 LKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGEGVIKTI 65 (202)
Q Consensus 3 LKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtGk~iK~a 65 (202)
|.+ ++.|..=.-+.+++|.++. ..+.++|..+ ....+.|....+ ..|..+..+
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~---------~G~~l~V~~d~~~a~~di~~~~~-~~G~~~~~~ 56 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQ---------DGEQLEVKASDPGFARDAQAWCK-STGNTLISL 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCC---------CCCEEEEEECCccHHHHHHHHHH-HcCCEEEEE
Confidence 455 7889888899999999986 2445566553 455677777777 778444433
No 35
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=53.50 E-value=68 Score=21.69 Aligned_cols=49 Identities=20% Similarity=0.175 Sum_probs=34.4
Q ss_pred EEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcCCc
Q 046486 3 LKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGEGV 61 (202)
Q Consensus 3 LKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtGk~ 61 (202)
|.+ ++.|..=.-+++++|.++. ..+.+.|..+ ......|...++ ..|..
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~---------~g~~l~v~~d~~~~~~~i~~~~~-~~g~~ 52 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLK---------SGEVLEVLLDDPGAVEDIPAWAK-ETGHE 52 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCC---------CCCEEEEEecCCcHHHHHHHHHH-HcCCE
Confidence 445 7888888888999998875 3455566654 345777888888 77733
No 36
>PF08260 Kinin: Insect kinin peptide; InterPro: IPR013202 This entry represents neuropeptides that are the first members of the insect kinin-family isolated from the American cockroach. Their occurrence in the retrocerebral complex suggests a physiological role as a neurohormone. The C-terminal sequence Phe-X-Ser-Trp-Gly-NH2 characterised the peptides as members of the insect kinin family. Data suggest a possible involvement of insect kinins in water-balance by regulating the osmoregulation. Insect kinins also mediate visceral muscle contractile activity (myotropic activity) []. These peptides have lengths ranging from 6 to 14 amino acids [].
Probab=52.35 E-value=6.2 Score=18.03 Aligned_cols=7 Identities=43% Similarity=1.274 Sum_probs=4.9
Q ss_pred ccccccC
Q 046486 151 LVYESWG 157 (202)
Q Consensus 151 p~yd~~~ 157 (202)
|.|.|||
T Consensus 2 pafnswg 8 (8)
T PF08260_consen 2 PAFNSWG 8 (8)
T ss_pred ccccccC
Confidence 5677776
No 37
>PF07837 FTCD_N: Formiminotransferase domain, N-terminal subdomain; InterPro: IPR012886 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. This entry represents the N-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 2PFD_C 1QD1_B.
Probab=51.23 E-value=13 Score=31.83 Aligned_cols=53 Identities=17% Similarity=0.278 Sum_probs=35.4
Q ss_pred HHHHHHHHhcCCCce--EEEEEcCCCEEEEEeecCCHHHHHHHHHhhcCCceeeEEEcC
Q 046486 13 RKKVKKVLCKFPQIQ--EQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGEGVIKTIEILK 69 (202)
Q Consensus 13 akKIkKaL~ki~GV~--~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtGk~iK~aEIVs 69 (202)
..+|.+++.+.+||. ++..|.+.|+..|+. --+++.|.+++-.... +.+++|+
T Consensus 18 ie~I~~a~~~~~gv~ll~~~~D~~~NRsv~T~-vG~p~~v~~a~~~~~~---~A~~~ID 72 (178)
T PF07837_consen 18 IEAIAKAARNVPGVKLLDVFSDADYNRSVITL-VGEPEAVAEAAFAAIR---KALELID 72 (178)
T ss_dssp HHHHHHHCCTSTTEEEEEEEEETTTTEEEEEE-EE-HHHHHHHHHHHHH---HHHCC--
T ss_pred HHHHHHHHHcCCCCEEEecCCCCCCCCCeEEE-eeChHHHHHHHHHHHH---HHHHhcc
Confidence 467888888888876 677788889887775 2367888877764544 4444444
No 38
>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=48.99 E-value=35 Score=23.12 Aligned_cols=8 Identities=25% Similarity=0.526 Sum_probs=3.9
Q ss_pred HHHHHHHH
Q 046486 48 EEIRDKLC 55 (202)
Q Consensus 48 ekL~~kL~ 55 (202)
+.|+++|+
T Consensus 57 ~~l~~~L~ 64 (76)
T cd04888 57 DELLEELR 64 (76)
T ss_pred HHHHHHHh
Confidence 44445554
No 39
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=48.65 E-value=91 Score=21.74 Aligned_cols=50 Identities=14% Similarity=0.138 Sum_probs=35.1
Q ss_pred EEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcCCce
Q 046486 3 LKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGEGVI 62 (202)
Q Consensus 3 LKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtGk~i 62 (202)
|.+ ++.|..=.-+++++|.+++ ..+.++|..+ ......|.+.++ +.|..+
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~---------~G~~l~V~~dd~~s~~di~~~~~-~~g~~~ 53 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMK---------PGDTLLVLATDPSTTRDIPKFCT-FLGHEL 53 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCC---------CCCEEEEEeCCCchHHHHHHHHH-HcCCEE
Confidence 345 7888888889999999986 2344555543 466778888888 778333
No 40
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=48.14 E-value=58 Score=27.18 Aligned_cols=55 Identities=13% Similarity=0.142 Sum_probs=36.6
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCCEEEEEeec-----CCHHHHHHHHHhhcCCceeeEEEcCC
Q 046486 13 RKKVKKVLCKFPQIQEQSFDEKTNTVTIKVVS-----CSPEEIRDKLCCKGEGVIKTIEILKP 70 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~-----vdpekL~~kL~~KtGk~iK~aEIVsp 70 (202)
.+.|++.+-.-.||+++.||.+++.|+|.... -.....++.|..++| =..+++..
T Consensus 55 ~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tg---W~p~vvRt 114 (145)
T cd02410 55 IKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETG---WAPKVVRT 114 (145)
T ss_pred HHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhC---CeeEEEec
Confidence 44555555555799999999999999997520 123455566666888 45555543
No 41
>PRK11023 outer membrane lipoprotein; Provisional
Probab=48.11 E-value=56 Score=27.54 Aligned_cols=40 Identities=13% Similarity=0.095 Sum_probs=31.2
Q ss_pred hhhHHHHHHHHhcCCCce--EEEEEcCCCEEEEEeecCCHHHH
Q 046486 10 SKCRKKVKKVLCKFPQIQ--EQSFDEKTNTVTIKVVSCSPEEI 50 (202)
Q Consensus 10 ~gCakKIkKaL~ki~GV~--~VeVDlk~~tVtV~G~~vdpekL 50 (202)
..=..+|+.+|..-+.|. +++|...++.|++.| .++.++.
T Consensus 126 ~~It~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G-~v~~~e~ 167 (191)
T PRK11023 126 TWITTKVRSQLLTSDSVKSSNVKVTTENGEVFLLG-LVTQREA 167 (191)
T ss_pred HHHHHHHHHHHhcCCCCCcceEEEEEECcEEEEEE-EeCHHHH
Confidence 335679999998877766 577777899999999 6776554
No 42
>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=47.58 E-value=27 Score=24.41 Aligned_cols=28 Identities=25% Similarity=0.334 Sum_probs=20.6
Q ss_pred EEEEEcCCCEEEEEeecCCHHHHHHHHH
Q 046486 28 EQSFDEKTNTVTIKVVSCSPEEIRDKLC 55 (202)
Q Consensus 28 ~VeVDlk~~tVtV~G~~vdpekL~~kL~ 55 (202)
.|.+|..+|.+.|.|...+.+.|.+.|+
T Consensus 47 ~i~~d~~tNsliv~g~~~~~~~i~~li~ 74 (82)
T PF03958_consen 47 RIVADERTNSLIVRGTPEDLEQIRELIK 74 (82)
T ss_dssp EEEEECTTTEEEEEEEHHHHHHHHHHHH
T ss_pred EEEEECCCCEEEEEeCHHHHHHHHHHHH
Confidence 8999999999999984344444555444
No 43
>smart00362 RRM_2 RNA recognition motif.
Probab=46.43 E-value=71 Score=19.89 Aligned_cols=53 Identities=19% Similarity=0.246 Sum_probs=40.6
Q ss_pred EEE-cccChhhHHHHHHHHhcCCCceEEEEEcCC----CEEEEEeecCCHHHHHHHHHhh
Q 046486 3 LKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKT----NTVTIKVVSCSPEEIRDKLCCK 57 (202)
Q Consensus 3 LKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~----~tVtV~G~~vdpekL~~kL~~K 57 (202)
|.| ++.-.--...|++.|..+..|..+.+-... +.+.|+. .+.+...++|...
T Consensus 2 v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f--~~~~~a~~a~~~~ 59 (72)
T smart00362 2 LFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEF--ESEEDAEKAIEAL 59 (72)
T ss_pred EEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEe--CCHHHHHHHHHHh
Confidence 445 777777788999999999999999888876 7788886 4666666666633
No 44
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=46.15 E-value=48 Score=34.84 Aligned_cols=45 Identities=7% Similarity=0.154 Sum_probs=36.6
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCCEEEEEee-------cCCHHHHHHHHHhh
Q 046486 13 RKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-------SCSPEEIRDKLCCK 57 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-------~vdpekL~~kL~~K 57 (202)
++.|+..|.+++||.+|++.-....+.|..| .++..+|.++|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 4679999999999999999977666777653 37788899999843
No 45
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=45.63 E-value=61 Score=27.42 Aligned_cols=64 Identities=25% Similarity=0.369 Sum_probs=39.7
Q ss_pred EEcccChhhHHHH------------HHHHhcC------CCceEEEEEcCCCEEEEEeecCC------HHHHHHHHHhhcC
Q 046486 4 KVDLSCSKCRKKV------------KKVLCKF------PQIQEQSFDEKTNTVTIKVVSCS------PEEIRDKLCCKGE 59 (202)
Q Consensus 4 KV~M~C~gCakKI------------kKaL~ki------~GV~~VeVDlk~~tVtV~G~~vd------pekL~~kL~~KtG 59 (202)
|-++-|.+|.++| .++|.+| .+++-.+.=...++|++....-+ --.++++|+++.|
T Consensus 11 kt~ilC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gdg~aIGk~G~~ik~l~~~lg 90 (166)
T PRK06418 11 KTGLLCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGPRIPIGKGGKIAKALSRKLG 90 (166)
T ss_pred ccCccChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCCcccccccchHHHHHHHHhC
Confidence 3378899999875 5778776 33333222222466655421111 2257888888899
Q ss_pred CceeeEEEcCC
Q 046486 60 GVIKTIEILKP 70 (202)
Q Consensus 60 k~iK~aEIVsp 70 (202)
|+|++|+-
T Consensus 91 ---k~VevVE~ 98 (166)
T PRK06418 91 ---KKVRVVEK 98 (166)
T ss_pred ---CcEEEEEc
Confidence 88888874
No 46
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=44.80 E-value=1.1e+02 Score=21.47 Aligned_cols=51 Identities=10% Similarity=-0.022 Sum_probs=34.7
Q ss_pred EEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcCCcee
Q 046486 3 LKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGEGVIK 63 (202)
Q Consensus 3 LKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtGk~iK 63 (202)
|.+ ++.|..=.-+.+++|.++. ..+.+.|..+ ....+.|...++ ..|..+.
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~---------~G~~l~V~~d~~~s~~ni~~~~~-~~g~~v~ 54 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLK---------PGEILEVISDCPQSINNIPIDAR-NHGYKVL 54 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCC---------CCCEEEEEecCchHHHHHHHHHH-HcCCEEE
Confidence 344 7788888889999999986 2344555543 456677777777 7783433
No 47
>PF02983 Pro_Al_protease: Alpha-lytic protease prodomain; InterPro: IPR004236 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. The alpha-lytic protease prodomain is associated with serine peptidases, specifically the alpha-lytic endopeptidases and streptogrisin A, B, C, D and E, which are bacterial enzymes and which belong to MEROPS peptidase subfamily S1A (IPR001316 from INTERPRO). The protease precursor in Gram-negative bacterial proteases may be a general property of extracellular bacterial proteases []. The proteases are encoded with a large (166 amino acid) N-terminal pro region that is required transiently both in vivo and in vitro for the correct folding of the protease domain [, ]. The pro region also acts as a potent inhibitor of the mature enzyme []. ; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis, 0005576 extracellular region; PDB: 3PRO_C 2PRO_B 4PRO_C.
Probab=44.49 E-value=51 Score=23.11 Aligned_cols=29 Identities=21% Similarity=0.195 Sum_probs=22.7
Q ss_pred HHHHHH------hcCCCceEEEEEcCCCEEEEEee
Q 046486 15 KVKKVL------CKFPQIQEQSFDEKTNTVTIKVV 43 (202)
Q Consensus 15 KIkKaL------~ki~GV~~VeVDlk~~tVtV~G~ 43 (202)
.++..| ..-.++..+-||..+|+|+|+.+
T Consensus 8 aak~~L~da~~~~~~~~~~~WyvD~~tn~VVV~a~ 42 (62)
T PF02983_consen 8 AAKAALDDAAAAAAPVAVTSWYVDPRTNKVVVTAD 42 (62)
T ss_dssp HHHHHHHHCHHHHGGGCEEEEEEECCCTEEEEEEE
T ss_pred HHHHHHHhhhhccCCCCcceEEEeCCCCeEEEEEC
Confidence 455666 23457999999999999999974
No 48
>PRK09577 multidrug efflux protein; Reviewed
Probab=43.36 E-value=56 Score=34.32 Aligned_cols=44 Identities=11% Similarity=0.095 Sum_probs=35.8
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCCEEEEEee-------cCCHHHHHHHHHh
Q 046486 13 RKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-------SCSPEEIRDKLCC 56 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-------~vdpekL~~kL~~ 56 (202)
++.|+..|.+++||.+|+++-...+|.|..| .++..+|.++|+.
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~ 208 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRA 208 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHH
Confidence 4679999999999999999987777777532 3778889999984
No 49
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=41.56 E-value=1.1e+02 Score=20.50 Aligned_cols=57 Identities=11% Similarity=0.134 Sum_probs=35.4
Q ss_pred EEEEcccC-hhhHHHHHHHHhcCC-CceEEEEEcC----CCEEEEEeecCCHHHHHHHHHhhcC
Q 046486 2 VLKVDLSC-SKCRKKVKKVLCKFP-QIQEQSFDEK----TNTVTIKVVSCSPEEIRDKLCCKGE 59 (202)
Q Consensus 2 vLKV~M~C-~gCakKIkKaL~ki~-GV~~VeVDlk----~~tVtV~G~~vdpekL~~kL~~KtG 59 (202)
.|.|.|.- .+--.+|.+.|.+.. .|.++..... ...++|..+..+.+.+.+.|+ +.|
T Consensus 3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L~-~~G 65 (72)
T cd04883 3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNPRPIIEDLR-RAG 65 (72)
T ss_pred EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCHHHHHHHHH-HCC
Confidence 35555543 367778888887754 3555543332 333566653467889999999 667
No 50
>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=40.66 E-value=65 Score=33.90 Aligned_cols=44 Identities=5% Similarity=0.135 Sum_probs=36.8
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCCEEEEEee-------cCCHHHHHHHHHh
Q 046486 13 RKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-------SCSPEEIRDKLCC 56 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-------~vdpekL~~kL~~ 56 (202)
...|+..|.+++||.+|+++-.+..+.|.-| .+++.+|.++|+.
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~~ 209 (1044)
T TIGR00915 159 ASNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQA 209 (1044)
T ss_pred HHHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHHH
Confidence 3579999999999999999988777788753 3788889999984
No 51
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=39.62 E-value=93 Score=28.40 Aligned_cols=43 Identities=21% Similarity=0.174 Sum_probs=34.2
Q ss_pred EEEcccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcC
Q 046486 3 LKVDLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGE 59 (202)
Q Consensus 3 LKV~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtG 59 (202)
|+.+.+ +.+.+.|++.|..++||+++.+- +.++-.+.|+++.|
T Consensus 65 L~~~~~-~~~~~~v~~~i~~~~gV~~v~~~-------------sre~~l~~L~~~lg 107 (297)
T COG2177 65 LQIDAD-QDDAALVREKIEGIPGVKSVRFI-------------SREEALKELQPWLG 107 (297)
T ss_pred EecCCC-hHHHHHHHHHHhcCCCcceEEEe-------------CHHHHHHHHHHHcC
Confidence 334555 88999999999999999887653 67888888887888
No 52
>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=39.48 E-value=25 Score=26.03 Aligned_cols=38 Identities=11% Similarity=0.212 Sum_probs=25.2
Q ss_pred HHHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhh
Q 046486 14 KKVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCK 57 (202)
Q Consensus 14 kKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~K 57 (202)
+.|+.+|.+++|+++|+|++. ..- ...++.|-+.-+.+
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~-----~~~-~~~~~~~~~~~~~~ 95 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV-----WDP-PWTPERMSEEARLE 95 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE-----eeC-CCChHHCCHHHHHH
Confidence 568899999999999998864 222 34455555444433
No 53
>KOG0559 consensus Dihydrolipoamide succinyltransferase (2-oxoglutarate dehydrogenase, E2 subunit) [Energy production and conversion]
Probab=39.41 E-value=50 Score=31.89 Aligned_cols=15 Identities=27% Similarity=0.364 Sum_probs=9.3
Q ss_pred EEEEEcCCCEEEEEe
Q 046486 28 EQSFDEKTNTVTIKV 42 (202)
Q Consensus 28 ~VeVDlk~~tVtV~G 42 (202)
++....++++++|..
T Consensus 104 E~va~IETDK~tv~V 118 (457)
T KOG0559|consen 104 EAVAEIETDKTTVEV 118 (457)
T ss_pred hhheeeeccceeeec
Confidence 344555667777765
No 54
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=38.51 E-value=75 Score=33.52 Aligned_cols=42 Identities=7% Similarity=0.150 Sum_probs=34.9
Q ss_pred HHHHHHHhcCCCceEEEEEcCCCEEEEEee-------cCCHHHHHHHHH
Q 046486 14 KKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-------SCSPEEIRDKLC 55 (202)
Q Consensus 14 kKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-------~vdpekL~~kL~ 55 (202)
+.|+..|.+++||.+|++.-....+.|..| .++..+|.++|+
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~ 208 (1049)
T PRK15127 160 ANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIK 208 (1049)
T ss_pred HHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHH
Confidence 579999999999999999877666777653 377888889998
No 55
>PRK11023 outer membrane lipoprotein; Provisional
Probab=38.09 E-value=59 Score=27.36 Aligned_cols=44 Identities=16% Similarity=0.170 Sum_probs=33.6
Q ss_pred hhHHHHHHHHhcCCCce---EEEEEcCCCEEEEEeecCCHHHHHHHHH
Q 046486 11 KCRKKVKKVLCKFPQIQ---EQSFDEKTNTVTIKVVSCSPEEIRDKLC 55 (202)
Q Consensus 11 gCakKIkKaL~ki~GV~---~VeVDlk~~tVtV~G~~vdpekL~~kL~ 55 (202)
.=..+|+.+|.+-+.+. ++.|+..++.|+++| .++-+...+...
T Consensus 49 ~i~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G-~V~~~~~k~~A~ 95 (191)
T PRK11023 49 TLELRVNNALSKDEQIKKEARINVTAYQGKVLLTG-QSPNAELSERAK 95 (191)
T ss_pred HHHHHHHHHHhhCcccCcCceEEEEEECCEEEEEE-EeCCHHHHHHHH
Confidence 34678999998877774 688999999999999 677665555444
No 56
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=38.02 E-value=42 Score=26.64 Aligned_cols=30 Identities=20% Similarity=0.478 Sum_probs=23.3
Q ss_pred EEcccChhh------HHHHHHHHhcCCCceEEEEEc
Q 046486 4 KVDLSCSKC------RKKVKKVLCKFPQIQEQSFDE 33 (202)
Q Consensus 4 KV~M~C~gC------akKIkKaL~ki~GV~~VeVDl 33 (202)
++.++=.+| ...|+.+|..++||++++|++
T Consensus 54 ~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 54 KMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred EEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEEE
Confidence 334555555 678999999999999988875
No 57
>PF01849 NAC: NAC domain; InterPro: IPR002715 Nascent polypeptide-associated complex (NAC) is among the first ribosome-associated entities to bind the nascent polypeptide after peptide bond formation. The nascent polypeptide-associated complex (NAC) of yeast functions in the targeting process of ribosomes to the ER membrane []. NAC may prevent binding of ribosome nascent chains (RNCs) without a signal sequence to yeast membranes.; PDB: 3MCE_D 3MCB_A 3LKX_B 1TR8_B.
Probab=37.07 E-value=28 Score=23.90 Aligned_cols=29 Identities=34% Similarity=0.460 Sum_probs=18.5
Q ss_pred HHHHHHHhc-----CCCceEEEEEcCCCEEEEEe
Q 046486 14 KKVKKVLCK-----FPQIQEQSFDEKTNTVTIKV 42 (202)
Q Consensus 14 kKIkKaL~k-----i~GV~~VeVDlk~~tVtV~G 42 (202)
++++++|.+ ++||++|.+-..++++.+-.
T Consensus 2 kk~~~~l~klgl~~i~~i~eV~i~~~dg~~~~~~ 35 (58)
T PF01849_consen 2 KKLQKMLKKLGLKEIPGIEEVTIRKDDGTVFVFN 35 (58)
T ss_dssp ------GHHCT-EEETTEEEEEEEETTTEEEEEE
T ss_pred HHHHHHHHHcCCcccCCcEEEEEEECCceEEEEc
Confidence 455666655 67999999999998887754
No 58
>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=36.33 E-value=37 Score=22.94 Aligned_cols=30 Identities=37% Similarity=0.523 Sum_probs=24.9
Q ss_pred HHHHHHHHhcCCCceEEEEEcC-CCEEEEEe
Q 046486 13 RKKVKKVLCKFPQIQEQSFDEK-TNTVTIKV 42 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeVDlk-~~tVtV~G 42 (202)
.+++++.|.+++.|++++|... -+++.|..
T Consensus 36 ~~~~~~~l~~~p~V~~v~V~r~~P~~l~I~V 66 (69)
T PF08478_consen 36 LKKIEQRLEKLPWVKSVSVSRRFPNTLEIKV 66 (69)
T ss_dssp HHHHHHCCCCTTTEEEEEEEEETTTEEEEEE
T ss_pred HHHHHHHHHcCCCEEEEEEEEeCCCEEEEEE
Confidence 4678899999999999999866 77887764
No 59
>TIGR02024 FtcD glutamate formiminotransferase. This model covers enzymes from metazoa as well as gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype. The crystal structure of the enzyme has been studied in the context of the catalytic mechanism.
Probab=34.97 E-value=27 Score=32.26 Aligned_cols=55 Identities=16% Similarity=0.190 Sum_probs=38.2
Q ss_pred HHHHHHHHhcCCCceEEEE--EcCCCEEEEEeecCCHHHHHHHHHhhcCCceeeEEEcCCC
Q 046486 13 RKKVKKVLCKFPQIQEQSF--DEKTNTVTIKVVSCSPEEIRDKLCCKGEGVIKTIEILKPD 71 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeV--Dlk~~tVtV~G~~vdpekL~~kL~~KtGk~iK~aEIVsp~ 71 (202)
..+|.+++.+.+||.=+++ |.+.|+..|+- --+++.|.+++-..+. +.+++|+=.
T Consensus 20 ie~I~~a~~~~~gv~lld~~~D~d~NRsv~Tl-vg~pe~v~eaa~~~~~---~A~elIDm~ 76 (298)
T TIGR02024 20 IEKIVDAIIKTDNVKLLDVDMDPDHNRSVITF-VGEPECVVNAALKLAK---KAAELIDMR 76 (298)
T ss_pred HHHHHHHHhcCCCcEEEeCCCCCCCCceEEEE-ecChHHHHHHHHHHHH---HHHHhcCcc
Confidence 4678888889999885555 45577777765 2468888888775655 566666543
No 60
>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=34.93 E-value=92 Score=23.19 Aligned_cols=41 Identities=10% Similarity=0.233 Sum_probs=30.1
Q ss_pred HHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHh
Q 046486 14 KKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCC 56 (202)
Q Consensus 14 kKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~ 56 (202)
.-+-++|-+++||++|-+.. +-|||+=. .++++.|...|..
T Consensus 37 spLA~~Lf~i~gV~~Vf~~~--dfItVtK~~~~~W~~l~~~I~~ 78 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFIGD--DFITVTKNPDADWEDLKPEIRE 78 (87)
T ss_dssp -HHHHHHHTSTTEEEEEEET--TEEEEEE-TTS-HHHHHHHHHH
T ss_pred CHHHHHhcCCCCEeEEEEEC--CEEEEeeCCCCCHHHHHHHHHH
Confidence 45667788999999988874 57777532 6899999988873
No 61
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=34.85 E-value=86 Score=27.35 Aligned_cols=38 Identities=26% Similarity=0.355 Sum_probs=28.6
Q ss_pred HHHHHHHhcCCCceEEEEEcCCCEEEEEee--cCCHHHHHH
Q 046486 14 KKVKKVLCKFPQIQEQSFDEKTNTVTIKVV--SCSPEEIRD 52 (202)
Q Consensus 14 kKIkKaL~ki~GV~~VeVDlk~~tVtV~G~--~vdpekL~~ 52 (202)
..|+++|...-|| .+.+|.+++.|+|+.. +.||..++.
T Consensus 27 g~v~k~ie~~~~~-~~~iD~~~~~V~i~~~~~t~Dp~~~~k 66 (194)
T COG1094 27 GEVKKAIEEKTGV-KLRIDSKTGSVTIRTTRKTEDPLALLK 66 (194)
T ss_pred ccchHHHHhhcCe-EEEEECCCCeEEEEecCCCCChHHHHH
Confidence 3578888888877 8999999999999862 246655443
No 62
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic 40-residue C-terminal domain that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=34.40 E-value=2e+02 Score=24.07 Aligned_cols=32 Identities=9% Similarity=0.118 Sum_probs=27.3
Q ss_pred hhHHHHHHHHhcCCCceEEEEEcCCCEEEEEe
Q 046486 11 KCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKV 42 (202)
Q Consensus 11 gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G 42 (202)
.=+.+|.+.+.+++||.++.+=...+.+.|-.
T Consensus 54 ~~A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vgv 85 (158)
T TIGR02898 54 DVADEIASEAAKVKGVKDATVVITGNYAYVGV 85 (158)
T ss_pred HHHHHHHHHHhcCCCCceEEEEEECCEEEEEE
Confidence 44789999999999999999888888887754
No 63
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=33.60 E-value=68 Score=22.34 Aligned_cols=24 Identities=8% Similarity=0.135 Sum_probs=14.1
Q ss_pred ccChhhHHHHHHHHhcCCCceEEE
Q 046486 7 LSCSKCRKKVKKVLCKFPQIQEQS 30 (202)
Q Consensus 7 M~C~gCakKIkKaL~ki~GV~~Ve 30 (202)
+.--.=-+.|.+.|.+++||.+|.
T Consensus 56 V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 56 VKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp ESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred ECCHHHHHHHHHHHHCCCCeeEEE
Confidence 333344456667777777776653
No 64
>PRK03195 hypothetical protein; Provisional
Probab=32.95 E-value=94 Score=26.73 Aligned_cols=43 Identities=14% Similarity=0.248 Sum_probs=32.5
Q ss_pred EEcCCCEEEEEeec--------CCHHHHHHHHHhhcC-CceeeEEEcCCCCC
Q 046486 31 FDEKTNTVTIKVVS--------CSPEEIRDKLCCKGE-GVIKTIEILKPDEK 73 (202)
Q Consensus 31 VDlk~~tVtV~G~~--------vdpekL~~kL~~KtG-k~iK~aEIVsp~kp 73 (202)
+.+++++++|..++ +--.+|+++|...+| ..|++|.|+.|..|
T Consensus 116 ~~i~~gvL~V~~~SsaWAteL~~~k~~Ii~rLN~~lG~~vV~~I~i~GP~~p 167 (186)
T PRK03195 116 TALNDGVLSVSAESTAWATQLRMMQAQLLAKIAAAVGDGVVTSLKITGPAAP 167 (186)
T ss_pred eEEECCEEEEEeCCHHHHHHHHhhHHHHHHHHHHHhCccceeEEEEeCCCCC
Confidence 34458999997631 334568899988888 89999999999754
No 65
>PRK04021 hypothetical protein; Reviewed
Probab=31.98 E-value=1.3e+02 Score=22.91 Aligned_cols=46 Identities=24% Similarity=0.239 Sum_probs=32.6
Q ss_pred ccChhhHHHHHHHHhcCCCceEEEEEc----CCCEEEEEeecCCHHHHHHHHH
Q 046486 7 LSCSKCRKKVKKVLCKFPQIQEQSFDE----KTNTVTIKVVSCSPEEIRDKLC 55 (202)
Q Consensus 7 M~C~gCakKIkKaL~ki~GV~~VeVDl----k~~tVtV~G~~vdpekL~~kL~ 55 (202)
..=+..-+.+-+.|.+.=|+ +|++.- ..++|.|.| .+++.+.++|.
T Consensus 42 P~~GkAN~ali~~LAk~l~~-~I~I~~G~~sr~K~v~i~g--~~~e~l~~~L~ 91 (92)
T PRK04021 42 PVKGKANKELVKFFSKLLGA-EVEIIRGETSREKDLLVKG--ISLEEVKKKLK 91 (92)
T ss_pred CCCChHHHHHHHHHHHHhCC-CEEEEecCCcCceEEEEec--CCHHHHHHHhc
Confidence 44566677888888888887 555532 256677776 79999988774
No 66
>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium). This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=30.64 E-value=66 Score=33.75 Aligned_cols=47 Identities=15% Similarity=0.269 Sum_probs=35.9
Q ss_pred hHHHHHHHHhcCCCceEEEEEcCC--CEEEEEee-------cCCHHHHHHHHHhhc
Q 046486 12 CRKKVKKVLCKFPQIQEQSFDEKT--NTVTIKVV-------SCSPEEIRDKLCCKG 58 (202)
Q Consensus 12 CakKIkKaL~ki~GV~~VeVDlk~--~tVtV~G~-------~vdpekL~~kL~~Kt 58 (202)
=+++|+..|.+++||.+|..|... .++.|.-+ .+++++|.+.|+...
T Consensus 699 ~a~~v~~~l~~~pgv~~v~~~~~~~~~e~~i~id~~~~~~~Glt~~~v~~~l~~~~ 754 (1051)
T TIGR00914 699 TAEKISAVLKGVPGAADVKVEQTTGLPYLTVEIDREKAARYGLTVGDVQDTVATAV 754 (1051)
T ss_pred HHHHHHHHHhcCCCceeeeccccCCCceEEEEECHHHHHHcCCCHHHHHHHHHHHh
Confidence 367899999999999999998764 45555532 377888989887553
No 67
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=30.61 E-value=1.8e+02 Score=24.47 Aligned_cols=53 Identities=11% Similarity=0.131 Sum_probs=33.3
Q ss_pred HHHHHHHhcCCCceEEEEEcCCCEEEEEee--cC---CHHHHHHHHHhhcCCceeeEEE
Q 046486 14 KKVKKVLCKFPQIQEQSFDEKTNTVTIKVV--SC---SPEEIRDKLCCKGEGVIKTIEI 67 (202)
Q Consensus 14 kKIkKaL~ki~GV~~VeVDlk~~tVtV~G~--~v---dpekL~~kL~~KtGk~iK~aEI 67 (202)
..|+..|.. .|-.++.|.+++++|+|..- .+ +..+|.+.+.+.+|-...+|.|
T Consensus 138 ~~iE~llka-kGf~davv~~~~~~v~VvV~~~~L~~~~~~~I~diV~~~~~v~~~~I~V 195 (196)
T PF12685_consen 138 MEIENLLKA-KGFEDAVVFIEDDSVDVVVKADKLSDAEAAQIIDIVMRETGVPAENISV 195 (196)
T ss_dssp HHHHHHHHT-TS-SEEEEE-SSSEEEEEEE-S---HHHHHHHHHHHHHHHC-STSEEEE
T ss_pred HHHHHHHHh-CCCCceEEEeeCCEEEEEEeCCCCCHHHHHHHHHHHHHHhCCCcCeEEe
Confidence 345555554 69999999999999988752 22 3556788887777744444443
No 68
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=30.18 E-value=2e+02 Score=23.05 Aligned_cols=44 Identities=14% Similarity=0.153 Sum_probs=32.1
Q ss_pred HHHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHH----HHhhcC
Q 046486 14 KKVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDK----LCCKGE 59 (202)
Q Consensus 14 kKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~k----L~~KtG 59 (202)
+.++.+|.++ |.++|+.=++++-|+++. ..+++.|..+ |....|
T Consensus 22 aeLr~~l~~~-Gf~~V~Tyi~SGNvvf~~-~~~~~~l~~~ie~~l~~~fG 69 (137)
T PF08002_consen 22 AELREALEDL-GFTNVRTYIQSGNVVFES-DRDPAELAAKIEKALEERFG 69 (137)
T ss_dssp HHHHHHHHHC-T-EEEEEETTTTEEEEEE-SS-HHHHHHHHHHHHHHH-T
T ss_pred HHHHHHHHHc-CCCCceEEEeeCCEEEec-CCChHHHHHHHHHHHHHhcC
Confidence 4577788887 899999999999999996 6777766544 455566
No 69
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=29.36 E-value=2e+02 Score=23.84 Aligned_cols=40 Identities=13% Similarity=0.089 Sum_probs=30.6
Q ss_pred EEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcCCceeeEEEcCCC
Q 046486 28 EQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGEGVIKTIEILKPD 71 (202)
Q Consensus 28 ~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtGk~iK~aEIVsp~ 71 (202)
-..+|++.+-+.+.+. +++..+|++.|. +.| +-+.|-...
T Consensus 45 iAildL~G~~l~l~S~R~~~~~evi~~I~-~~G---~PviVAtDV 85 (138)
T PF04312_consen 45 IAILDLDGELLDLKSSRNMSRSEVIEWIS-EYG---KPVIVATDV 85 (138)
T ss_pred EEEEecCCcEEEEEeecCCCHHHHHHHHH-HcC---CEEEEEecC
Confidence 3678999999998765 799999999999 778 444444433
No 70
>PRK09579 multidrug efflux protein; Reviewed
Probab=29.11 E-value=1.3e+02 Score=31.79 Aligned_cols=44 Identities=9% Similarity=0.157 Sum_probs=33.7
Q ss_pred HHHHHHHHhcCCCceEEEEEcC-CCEEEEEee-------cCCHHHHHHHHHh
Q 046486 13 RKKVKKVLCKFPQIQEQSFDEK-TNTVTIKVV-------SCSPEEIRDKLCC 56 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeVDlk-~~tVtV~G~-------~vdpekL~~kL~~ 56 (202)
++.|+..|.+++||.+|++.-. ..++.|..+ .++.++|.++|+.
T Consensus 158 ~~~i~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~ 209 (1017)
T PRK09579 158 SRVIQPKLATLPGMAEAEILGNQVFAMRLWLDPVKLAGFGLSAGDVTQAVRR 209 (1017)
T ss_pred HHHHHHHhhcCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHH
Confidence 3569999999999999988765 345566532 3778889999984
No 71
>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=28.79 E-value=61 Score=24.65 Aligned_cols=23 Identities=4% Similarity=0.118 Sum_probs=19.6
Q ss_pred hhHHHHHHHHhcCCCceEEEEEc
Q 046486 11 KCRKKVKKVLCKFPQIQEQSFDE 33 (202)
Q Consensus 11 gCakKIkKaL~ki~GV~~VeVDl 33 (202)
+=...|+.+|++++||++++|..
T Consensus 62 g~td~lee~i~~ve~V~svev~~ 84 (88)
T TIGR00489 62 GGTEAAEESLSGIEGVESVEVTD 84 (88)
T ss_pred cChHHHHHHHhcCCCccEEEEEE
Confidence 44589999999999999998863
No 72
>COG0217 Uncharacterized conserved protein [Function unknown]
Probab=28.35 E-value=1.1e+02 Score=27.68 Aligned_cols=50 Identities=8% Similarity=0.111 Sum_probs=27.6
Q ss_pred HHHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcCCceeeEEE
Q 046486 14 KKVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGEGVIKTIEI 67 (202)
Q Consensus 14 kKIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtGk~iK~aEI 67 (202)
.+|..+|... |+++|+.+ .+..+|...--+..+|.++|+ ..|..+.++||
T Consensus 150 d~l~e~~iea-gaeDv~~~--~~~~~V~t~p~~~~~V~~~L~-~~g~~~~~ael 199 (241)
T COG0217 150 DELLEAAIEA-GAEDVEED--EGSIEVYTEPEDFNKVKEALE-AAGYEIESAEL 199 (241)
T ss_pred HHHHHHHHHC-CchhhhcC--CCeEEEEEChHHHHHHHHHHH-HcCCceeeeeE
Confidence 3444444433 66666666 445555443345666777777 55556655444
No 73
>PRK10568 periplasmic protein; Provisional
Probab=28.02 E-value=1.2e+02 Score=25.78 Aligned_cols=38 Identities=24% Similarity=0.218 Sum_probs=29.7
Q ss_pred cChhhHHHHHHHHhcCCCce--EEEEEcCCCEEEEEeecCC
Q 046486 8 SCSKCRKKVKKVLCKFPQIQ--EQSFDEKTNTVTIKVVSCS 46 (202)
Q Consensus 8 ~C~gCakKIkKaL~ki~GV~--~VeVDlk~~tVtV~G~~vd 46 (202)
.-..=..+|+.+|..-+++. ++.|...++.|++.| .++
T Consensus 57 ~D~~I~~~v~~~L~~~~~i~~~~I~V~v~~G~V~L~G-~V~ 96 (203)
T PRK10568 57 DDSAITAKVKAALVDHDNIKSTDISVKTHQKVVTLSG-FVE 96 (203)
T ss_pred cHHHHHHHHHHHHHhCCCCCCCceEEEEECCEEEEEE-EeC
Confidence 33445678999998877765 688888999999999 555
No 74
>PRK06719 precorrin-2 dehydrogenase; Validated
Probab=27.82 E-value=1.2e+02 Score=24.64 Aligned_cols=39 Identities=13% Similarity=0.088 Sum_probs=27.5
Q ss_pred EEEEcCCCEEEEEeecCCHHHHHHHHHhhcCCceeeEEEcCCC
Q 046486 29 QSFDEKTNTVTIKVVSCSPEEIRDKLCCKGEGVIKTIEILKPD 71 (202)
Q Consensus 29 VeVDlk~~tVtV~G~~vdpekL~~kL~~KtGk~iK~aEIVsp~ 71 (202)
+-+|+++++|.|.|-.--.....+.|. +.| .+|.+|+++
T Consensus 7 ~~l~l~~~~vlVvGGG~va~rka~~Ll-~~g---a~V~VIsp~ 45 (157)
T PRK06719 7 LMFNLHNKVVVIIGGGKIAYRKASGLK-DTG---AFVTVVSPE 45 (157)
T ss_pred eEEEcCCCEEEEECCCHHHHHHHHHHH-hCC---CEEEEEcCc
Confidence 578999999999973222344556666 567 789999754
No 75
>TIGR02515 IV_pilus_PilQ type IV pilus secretin (or competence protein) PilQ. A number of proteins homologous to PilQ are involved in type IV pilus formation, competence for transformation, type III secretion, and type II secretion (also called the main terminal branch of the general secretion pathway). Members of this family include PilQ itself, which is a component of the type IV pilus structure, from a number of species. In Haemophilus influenzae, the member of this family is associated with competence for transformation with exogenous DNA rather than with formation of a type IV pilus; the surface structure required for competence may be considered an unusual, incomplete type IV pilus structure.
Probab=27.58 E-value=1.7e+02 Score=27.33 Aligned_cols=57 Identities=19% Similarity=0.240 Sum_probs=33.5
Q ss_pred HHHHHHHHhcC--------CCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcC----CceeeEEEcCC
Q 046486 13 RKKVKKVLCKF--------PQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGE----GVIKTIEILKP 70 (202)
Q Consensus 13 akKIkKaL~ki--------~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtG----k~iK~aEIVsp 70 (202)
+..|.++|..+ .....+.+|..+|.++|++..-..+.|.+.|+ +.. -...+|.|++.
T Consensus 109 a~~v~~~l~~~~~~~~~~l~~~~~v~~d~~~n~lvv~~~~~~~~~i~~~i~-~lD~~~~QV~Iea~IveV 177 (418)
T TIGR02515 109 ASDIAKVLTGDDGGKGSLLSPRGSVTVDPRTNTLIVTDIPENLARIRKLIA-ELDIPVKQVLIEARIVEA 177 (418)
T ss_pred HHHHHHHHhhcccccccccCCCeeEEEECCcCeEEEEeCHHHHHHHHHHHH-HhCCCccEEEEEEEEEEE
Confidence 56677777754 12347899999999999983222333444443 332 33345555554
No 76
>PF01709 Transcrip_reg: Transcriptional regulator; InterPro: IPR002876 This entry represents the core region of several hypothetical proteins found in bacteria, plants, and yeast proteins. This core region can be subdivided into three domains: a 3-helical bundle domain, and two alpha+beta domains with different folds, where domain 3 (ferredoxin-like fold) is inserted within domain 2. This core region is found in the following hypothetical proteins: YebC from Escherichia coli, HP0162 from Helicobacter pylori (Campylobacter pylori) and aq1575 from Aquifex aeolicus []. The crystal structure of a conserved hypothetical protein, Aq1575, from Aquifex aeolicus has been determined. A structural homology search reveals that this protein has a new fold with no obvious similarity to those of other proteins of known three-dimensional structure. The protein reveals a monomer consisting of three domains arranged along a pseudo threefold symmetry axis. There is a large cleft with approximate dimensions of 10 A x 10 A x 20 A in the centre of the three domains along the symmetry axis. Two possible active sites are suggested based on the structure and multiple sequence alignment. There are several highly conserved residues in these putative active sites [].; PDB: 1LFP_A 1MW7_A 1KON_A.
Probab=27.09 E-value=1.7e+02 Score=25.66 Aligned_cols=48 Identities=10% Similarity=0.046 Sum_probs=33.0
Q ss_pred HHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcCCceeeEEEcC
Q 046486 17 KKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGEGVIKTIEILK 69 (202)
Q Consensus 17 kKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtGk~iK~aEIVs 69 (202)
+-+|. + |+++|+.| .+.+.|..+-.+...|.++|. +.|..+.++++.-
T Consensus 150 e~aIe-~-GaeDve~~--d~~~~~~c~p~~~~~v~~~L~-~~g~~i~~~e~~~ 197 (234)
T PF01709_consen 150 EDAIE-A-GAEDVEED--DGEFEFICDPSDLSAVKKALE-KKGYEIESAELEY 197 (234)
T ss_dssp HHHHH-H-TESEEEEC--TSEEEEEEEGGGHHHHHHHHH-HTT---SEEEEEE
T ss_pred HHHHh-C-CCcEeeec--CCeEEEEECHHHHHHHHHHHH-HcCCCeeEEEEEE
Confidence 34444 3 99999844 566888765678899999999 5587888888753
No 77
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=26.98 E-value=1e+02 Score=20.37 Aligned_cols=34 Identities=21% Similarity=0.255 Sum_probs=22.3
Q ss_pred HHHhcCCCceEEEEEcC--CCEEEEEeecCCHHHHHHHHH
Q 046486 18 KVLCKFPQIQEQSFDEK--TNTVTIKVVSCSPEEIRDKLC 55 (202)
Q Consensus 18 KaL~ki~GV~~VeVDlk--~~tVtV~G~~vdpekL~~kL~ 55 (202)
+.|.+.-|+. +.++.+ ...|+|.| +.+.|.++++
T Consensus 23 ~~I~~~t~~~-I~i~~~~~~~~v~I~G---~~~~v~~A~~ 58 (60)
T PF00013_consen 23 KEIEEETGVK-IQIPDDDERDIVTISG---SPEQVEKAKK 58 (60)
T ss_dssp HHHHHHHTSE-EEEESTTEEEEEEEEE---SHHHHHHHHH
T ss_pred HHhhhhcCeE-EEEcCCCCcEEEEEEe---CHHHHHHHHh
Confidence 3444444664 666654 45888898 7888887765
No 78
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=26.94 E-value=2e+02 Score=19.30 Aligned_cols=33 Identities=21% Similarity=0.237 Sum_probs=28.2
Q ss_pred hhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEe
Q 046486 10 SKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKV 42 (202)
Q Consensus 10 ~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G 42 (202)
.++...|.+.+..+-.|.++.++...+.+.|+-
T Consensus 11 ~~~~~~vl~~F~~fGeI~~~~~~~~~~~~~l~y 43 (53)
T PF14605_consen 11 PDLAEEVLEHFASFGEIVDIYVPESTNWMYLKY 43 (53)
T ss_pred chHHHHHHHHHHhcCCEEEEEcCCCCcEEEEEE
Confidence 567788888999999999999998888888885
No 79
>TIGR01676 GLDHase galactonolactone dehydrogenase. This model represents L-Galactono-gamma-lactone dehydrogenase (EC 1.3.2.3). This enzyme catalyzes the final step in ascorbic acid biosynthesis in higher plants. This protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD.
Probab=26.92 E-value=95 Score=30.82 Aligned_cols=35 Identities=11% Similarity=0.220 Sum_probs=28.2
Q ss_pred hcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcC
Q 046486 21 CKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGE 59 (202)
Q Consensus 21 ~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtG 59 (202)
.+|.+| ++||.++++|||.+ .+...+|.+.|. +.|
T Consensus 111 ~~ln~V--l~vD~~~~tVtV~A-G~~l~~L~~~L~-~~G 145 (541)
T TIGR01676 111 ALMDKV--LEVDEEKKRVRVQA-GIRVQQLVDAIK-EYG 145 (541)
T ss_pred hhCCCC--EEEcCCCCEEEEcC-CCCHHHHHHHHH-HcC
Confidence 344444 47889999999998 799999999998 555
No 80
>COG4892 Predicted heme/steroid binding protein [General function prediction only]
Probab=26.90 E-value=24 Score=26.61 Aligned_cols=16 Identities=38% Similarity=0.792 Sum_probs=11.3
Q ss_pred CCCC-Cccccc-----ccCCCCC
Q 046486 145 DWCY-ARLVYE-----SWGGSCH 161 (202)
Q Consensus 145 y~~y-~rp~yd-----~~~~~~~ 161 (202)
|=.| |+ ||| +|++|.|
T Consensus 20 YiA~~G~-VYDvS~s~~W~dGtH 41 (81)
T COG4892 20 YIAVNGT-VYDVSLSPSWGDGTH 41 (81)
T ss_pred EEEECCE-EEeeccCcccCCCcc
Confidence 4444 55 676 8999988
No 81
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=26.75 E-value=1.5e+02 Score=31.21 Aligned_cols=45 Identities=7% Similarity=0.218 Sum_probs=34.5
Q ss_pred HHHHHHHHhcCCCceEEEEEcC-CCEEEEEee-------cCCHHHHHHHHHhh
Q 046486 13 RKKVKKVLCKFPQIQEQSFDEK-TNTVTIKVV-------SCSPEEIRDKLCCK 57 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeVDlk-~~tVtV~G~-------~vdpekL~~kL~~K 57 (202)
+..|+..|.+++||.+|.+.-. ...+.|..| .+++++|.++|...
T Consensus 159 ~~~l~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~~ 211 (1025)
T PRK10614 159 STQLAQTISQIDGVGDVDVGGSSLPAVRVGLNPQALFNQGVSLDDVRQAISNA 211 (1025)
T ss_pred HHHHHHHhcCCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 3579999999999999999865 345666643 37778888888833
No 82
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=26.68 E-value=2.5e+02 Score=20.32 Aligned_cols=51 Identities=16% Similarity=0.157 Sum_probs=34.7
Q ss_pred EEEE-cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcCCce
Q 046486 2 VLKV-DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGEGVI 62 (202)
Q Consensus 2 vLKV-~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtGk~i 62 (202)
+|.+ ++.|..=.-+++++|.+++ ..+.+.|..+ ....+.|....+ ..|..+
T Consensus 11 ~lD~~Gl~CP~Pll~~kk~l~~l~---------~G~~l~V~~dd~~~~~di~~~~~-~~G~~~ 63 (81)
T PRK00299 11 TLDALGLRCPEPVMMVRKTVRNMQ---------PGETLLIIADDPATTRDIPSFCR-FMDHEL 63 (81)
T ss_pred EEecCCCCCCHHHHHHHHHHHcCC---------CCCEEEEEeCCccHHHHHHHHHH-HcCCEE
Confidence 4556 7889998999999999986 2345555543 345666766666 777333
No 83
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=26.46 E-value=89 Score=26.76 Aligned_cols=44 Identities=16% Similarity=0.194 Sum_probs=34.3
Q ss_pred hhhHHHHHHHHhc-CCCceEEEEEcC-----CCEEEEEeecCCHHHHHHHHH
Q 046486 10 SKCRKKVKKVLCK-FPQIQEQSFDEK-----TNTVTIKVVSCSPEEIRDKLC 55 (202)
Q Consensus 10 ~gCakKIkKaL~k-i~GV~~VeVDlk-----~~tVtV~G~~vdpekL~~kL~ 55 (202)
+.--.+|++.|.+ ++++.++-++.. ++.+=|.. ++++.|+++|.
T Consensus 57 D~~GekIRk~i~~~vp~~khafi~~~~a~~~~~~iGVE~--As~e~I~~AL~ 106 (174)
T TIGR00334 57 DFPGEKIRKKIEQHLPGYENCFIPKHLAKPNKKKIGVEE--ASVEAIIAALE 106 (174)
T ss_pred CCchHHHHHHHHHHCCCCeEEeeeHHhcCcCCCCcccCC--CCHHHHHHHHH
Confidence 3345789999988 899998888854 23466664 89999999999
No 84
>PRK13568 hofQ putative outer membrane porin HofQ; Provisional
Probab=26.17 E-value=1.9e+02 Score=26.84 Aligned_cols=58 Identities=17% Similarity=0.149 Sum_probs=33.5
Q ss_pred HHHHHHHHhcCC-----CceEEEEEcCCCEEEEEeecCCHHHHHHHHHhhcCC----ceeeEEEcCCC
Q 046486 13 RKKVKKVLCKFP-----QIQEQSFDEKTNTVTIKVVSCSPEEIRDKLCCKGEG----VIKTIEILKPD 71 (202)
Q Consensus 13 akKIkKaL~ki~-----GV~~VeVDlk~~tVtV~G~~vdpekL~~kL~~KtGk----~iK~aEIVsp~ 71 (202)
+..|.+.|..+. .-.+|.+|..+|+++|++.....+.|.+.|. +... ...+|.|++..
T Consensus 94 a~~v~~~L~~~~~~~ls~~g~v~~d~~tNsLiV~~~~~~~~~i~~lI~-~lD~p~~QV~Iea~Ivev~ 160 (381)
T PRK13568 94 AEEVADSLQSQRGGLLSPRGSVTADKRTNTLLIRDTPAALAQLKNWLI-ELDLPLQQVQLAAHIVTIS 160 (381)
T ss_pred HHHHHHHHhhccccccCCCceEEEeCCCCEEEEEeCHHHHHHHHHHHH-HhCCCCcEEEEEEEEEEEE
Confidence 355666665432 2348999999999999983223334444444 4442 33444555543
No 85
>PRK13763 putative RNA-processing protein; Provisional
Probab=26.16 E-value=1.4e+02 Score=24.99 Aligned_cols=38 Identities=18% Similarity=0.226 Sum_probs=25.4
Q ss_pred HHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHH
Q 046486 15 KVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDK 53 (202)
Q Consensus 15 KIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~k 53 (202)
++-+.|.+.-|++ +++|.++++|+|... ..|++.+..+
T Consensus 23 k~Ik~I~e~tg~~-I~i~~~~g~V~I~~~~~~d~~~i~kA 61 (180)
T PRK13763 23 ETKKEIEERTGVK-LEIDSETGEVIIEPTDGEDPLAVLKA 61 (180)
T ss_pred hHHHHHHHHHCcE-EEEECCCCeEEEEeCCCCCHHHHHHH
Confidence 5566677777774 999988899999711 1355555433
No 86
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=26.12 E-value=92 Score=26.12 Aligned_cols=24 Identities=25% Similarity=0.295 Sum_probs=18.2
Q ss_pred CCHHHHHHHHHhhcCCceeeEEEcCC
Q 046486 45 CSPEEIRDKLCCKGEGVIKTIEILKP 70 (202)
Q Consensus 45 vdpekL~~kL~~KtGk~iK~aEIVsp 70 (202)
-+.++|+++|+ +. ..+.+|||++.
T Consensus 126 ~~V~~ii~kl~-k~-e~V~kVeivgs 149 (150)
T COG4492 126 KDVDKIIEKLR-KV-EGVEKVEIVGS 149 (150)
T ss_pred hhHHHHHHHHh-cc-cceeEEEEeec
Confidence 46788999998 43 35888998864
No 87
>PF10934 DUF2634: Protein of unknown function (DUF2634); InterPro: IPR020288 This entry is represented by the Bacteriophage EJ-1, Orf60. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Bacteriophage EJ-1, Orf60 function has not been characterised. It has been shown to be simialr to XkdS (P54331 from SWISSPROT), which is encoded on a phage-like element (prophage) of PSBX found in Bacillus subtilis.
Probab=25.63 E-value=1.1e+02 Score=23.70 Aligned_cols=31 Identities=10% Similarity=0.343 Sum_probs=25.3
Q ss_pred hHHHHHHHHhc---CCCceEEEEEcCCCEEEEEe
Q 046486 12 CRKKVKKVLCK---FPQIQEQSFDEKTNTVTIKV 42 (202)
Q Consensus 12 CakKIkKaL~k---i~GV~~VeVDlk~~tVtV~G 42 (202)
-.+.|+.||.. +.+|++++++.+++++.|+.
T Consensus 70 i~r~I~EaL~~d~rI~~V~~f~f~~~~~~l~v~f 103 (112)
T PF10934_consen 70 IEREIEEALLQDPRITSVENFSFEWEGDSLYVSF 103 (112)
T ss_pred HHHHHHHHHhcCCCcceEEEEEEEEECCEEEEEE
Confidence 35678999955 77888999999999998864
No 88
>PRK11670 antiporter inner membrane protein; Provisional
Probab=25.46 E-value=1.4e+02 Score=27.78 Aligned_cols=55 Identities=15% Similarity=0.232 Sum_probs=36.5
Q ss_pred HHHHHHHHhcCCCceEEEEEcCC------------------CEEEEE---e-e--cCCHHHHHHHHHhhcCCceeeEEEc
Q 046486 13 RKKVKKVLCKFPQIQEQSFDEKT------------------NTVTIK---V-V--SCSPEEIRDKLCCKGEGVIKTIEIL 68 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeVDlk~------------------~tVtV~---G-~--~vdpekL~~kL~~KtGk~iK~aEIV 68 (202)
.+.++.+|..++||+++++++.. +.+.|. | + +.....|...|. +.| +++-+|
T Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avNLA~aLA-~~G---~rVlLI 142 (369)
T PRK11670 67 KEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVNLALALA-AEG---AKVGIL 142 (369)
T ss_pred HHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHHHHHHHH-HCC---CcEEEE
Confidence 45799999999999987765532 334443 1 1 233455666777 668 888888
Q ss_pred CCC
Q 046486 69 KPD 71 (202)
Q Consensus 69 sp~ 71 (202)
+..
T Consensus 143 D~D 145 (369)
T PRK11670 143 DAD 145 (369)
T ss_pred eCC
Confidence 765
No 89
>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=24.59 E-value=91 Score=21.50 Aligned_cols=23 Identities=22% Similarity=0.333 Sum_probs=17.2
Q ss_pred CEEEEEeecCCHHHHHHHHHhhc
Q 046486 36 NTVTIKVVSCSPEEIRDKLCCKG 58 (202)
Q Consensus 36 ~tVtV~G~~vdpekL~~kL~~Kt 58 (202)
++|+|.+...+++++.++|.+|+
T Consensus 6 G~Isvs~~~~s~~d~~~~la~kA 28 (56)
T PF07338_consen 6 GTISVSGNFGSPDDAEEALAKKA 28 (56)
T ss_dssp EEEEEEEECSSHHHHHHHHHHHH
T ss_pred EEEEEccccCCHHHHHHHHHHHH
Confidence 46788874478999988887553
No 90
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=24.49 E-value=64 Score=25.44 Aligned_cols=20 Identities=25% Similarity=0.556 Sum_probs=17.2
Q ss_pred cccChhhHHHHHHHHhcCCCc
Q 046486 6 DLSCSKCRKKVKKVLCKFPQI 26 (202)
Q Consensus 6 ~M~C~gCakKIkKaL~ki~GV 26 (202)
.++|..|+.+|++.|.+ .||
T Consensus 18 ~~qC~~cA~Al~~~L~~-~gI 37 (100)
T PF15643_consen 18 IFQCVECASALKQFLKQ-AGI 37 (100)
T ss_pred ceehHHHHHHHHHHHHH-CCC
Confidence 58899999999999987 355
No 91
>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=24.47 E-value=1.1e+02 Score=31.89 Aligned_cols=49 Identities=20% Similarity=0.276 Sum_probs=37.9
Q ss_pred hhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee---------cCCHHHHHHHHHhhcC
Q 046486 11 KCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV---------SCSPEEIRDKLCCKGE 59 (202)
Q Consensus 11 gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~---------~vdpekL~~kL~~KtG 59 (202)
.=+++|++.|.+++|+.++..|.+.++-.++-+ .++.++|.+.|+...+
T Consensus 687 ~~a~~v~~~l~~~pgv~dv~~~~~~~~~el~i~~dreka~~~Gls~~~va~~l~~a~~ 744 (1021)
T PF00873_consen 687 KAAEKVKAKLAEIPGVTDVRDDWEDGQPELRIDPDREKAARLGLSPADVARTLRTAFS 744 (1021)
T ss_dssp HHHHHHHHHHHHSTTEEEEEESSSSBEEEEEEEE-HHHHHHTTB-HHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHhCCCcccccccccccCcceEEEecHHHHHHcCCCHHHHHHHHHHHhc
Confidence 457899999999999999999999887766531 2667778888875544
No 92
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=24.19 E-value=2.4e+02 Score=20.98 Aligned_cols=43 Identities=26% Similarity=0.305 Sum_probs=31.0
Q ss_pred hhHHHHHHHHhcCCC-ceEEEEEcCCCEEEEEeecCCHHHHHHHHH
Q 046486 11 KCRKKVKKVLCKFPQ-IQEQSFDEKTNTVTIKVVSCSPEEIRDKLC 55 (202)
Q Consensus 11 gCakKIkKaL~ki~G-V~~VeVDlk~~tVtV~G~~vdpekL~~kL~ 55 (202)
..++.++++|....+ -.++.|+..+++|.|+|+ -.+.|.+.|.
T Consensus 40 aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~--~~~~Vk~wL~ 83 (87)
T PF05046_consen 40 ALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGD--HVEEVKKWLL 83 (87)
T ss_pred HHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCc--cHHHHHHHHH
Confidence 345566666655443 237889999999999993 4677888887
No 93
>cd06482 ACD_HspB10 Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB10, also known as sperm outer dense fiber protein (ODFP), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB10 occurs exclusively in the axoneme of sperm cells and may have a cytoskeletal role.
Probab=24.09 E-value=58 Score=24.38 Aligned_cols=22 Identities=9% Similarity=0.104 Sum_probs=18.4
Q ss_pred cCCCce--EEEEEcCCCEEEEEee
Q 046486 22 KFPQIQ--EQSFDEKTNTVTIKVV 43 (202)
Q Consensus 22 ki~GV~--~VeVDlk~~tVtV~G~ 43 (202)
.|+|++ +++|++++++++|.|.
T Consensus 15 dlPG~~kedI~V~v~~~~L~I~ge 38 (87)
T cd06482 15 DVCGFEPDQVKVKVKDGKVQVSAE 38 (87)
T ss_pred ECCCCCHHHeEEEEECCEEEEEEE
Confidence 468876 5888999999999994
No 94
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=23.84 E-value=1.9e+02 Score=30.86 Aligned_cols=43 Identities=12% Similarity=0.249 Sum_probs=36.0
Q ss_pred HHHHHHHHhcCCCceEEEEEcC-CCEEEEEee-------cCCHHHHHHHHH
Q 046486 13 RKKVKKVLCKFPQIQEQSFDEK-TNTVTIKVV-------SCSPEEIRDKLC 55 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeVDlk-~~tVtV~G~-------~vdpekL~~kL~ 55 (202)
++.|+..|++++||.+|++--. +..|.|+-| .+++++|.++|+
T Consensus 157 ~~~l~~~L~~v~GV~~V~~~G~~~~~~rI~ldp~kLa~~gLt~~dV~~ai~ 207 (1009)
T COG0841 157 ASNVRDELSRVPGVGSVQLFGAQEYAMRIWLDPAKLAAYGLTPSDVQSAIR 207 (1009)
T ss_pred HHHHHHHHhcCCCceEEEEcCCCceeEEEEeCHHHHHHcCCCHHHHHHHHH
Confidence 4679999999999999999988 667778753 377888999998
No 95
>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=22.97 E-value=2e+02 Score=29.89 Aligned_cols=45 Identities=16% Similarity=0.199 Sum_probs=34.1
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCCEEEEEee---cCCHHHHHHHHHhh
Q 046486 13 RKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV---SCSPEEIRDKLCCK 57 (202)
Q Consensus 13 akKIkKaL~ki~GV~~VeVDlk~~tVtV~G~---~vdpekL~~kL~~K 57 (202)
.+.|+++|..++||++++-.-..+..+|+.. ..|.+.....++.+
T Consensus 62 t~plE~~l~~v~gv~~i~S~s~~g~s~i~v~f~~~~d~~~a~~~v~~~ 109 (1021)
T PF00873_consen 62 TKPLEEALSSVEGVKEIRSTSREGSSSITVEFDDGTDIDEALQEVREK 109 (1021)
T ss_dssp HHHHHHTHCSSTTEEEEEEEETTSEEEEEEEESTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCeEEEEEEecCCcEEEEEEeccccCHHHHHHHHHHH
Confidence 4689999999999999999999888877643 46666666655533
No 96
>PF05258 DUF721: Protein of unknown function (DUF721); InterPro: IPR007922 This family contains several actinomycete proteins of unknown function, and related sequences from other species.
Probab=22.96 E-value=1.2e+02 Score=21.00 Aligned_cols=39 Identities=28% Similarity=0.187 Sum_probs=26.6
Q ss_pred EEEEcCCCEEEEEeec--------CCHHHHHHHHHhhcC-CceeeEEE
Q 046486 29 QSFDEKTNTVTIKVVS--------CSPEEIRDKLCCKGE-GVIKTIEI 67 (202)
Q Consensus 29 VeVDlk~~tVtV~G~~--------vdpekL~~kL~~KtG-k~iK~aEI 67 (202)
.-+++++++++|..++ .-..+|+++|....| ..|++|+|
T Consensus 42 ~~~~i~~g~L~i~v~~~~~~~~L~~~~~~il~~l~~~~g~~~i~~I~~ 89 (89)
T PF05258_consen 42 RPVSIKDGTLVIEVDSSAWAQELRYMKPQILKKLNEFLGFPAIKDIRF 89 (89)
T ss_pred EEEEEECCEEEEEECCHHHHHHHHHHHHHHHHHHHHHcCCCCccEeeC
Confidence 3455568999997631 234568888987777 77777764
No 97
>PF01565 FAD_binding_4: FAD binding domain This is only a subset of the Pfam family; InterPro: IPR006094 Various enzymes use FAD as a co-factor, most of these enzymes are oxygen-dependent oxidoreductases, containing a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. One of the enzymes Vanillyl-alcohol oxidase (VAO, 1.1.3.38 from EC) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 []. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging from aromatic amines to 4-alkylphenols. ; GO: 0008762 UDP-N-acetylmuramate dehydrogenase activity, 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZR6_A 3HSU_A 2AXR_A 3D2J_A 3D2H_A 3FW9_A 3FW8_A 3FW7_A 3GSY_A 3FWA_A ....
Probab=22.81 E-value=1.4e+02 Score=22.62 Aligned_cols=28 Identities=18% Similarity=0.267 Sum_probs=24.8
Q ss_pred EEEEcCCCEEEEEeecCCHHHHHHHHHhh
Q 046486 29 QSFDEKTNTVTIKVVSCSPEEIRDKLCCK 57 (202)
Q Consensus 29 VeVDlk~~tVtV~G~~vdpekL~~kL~~K 57 (202)
+++|.+.++|+|.. .+...+|.+.|..+
T Consensus 57 ~~id~~~~~v~v~a-G~~~~~l~~~l~~~ 84 (139)
T PF01565_consen 57 IEIDPENGTVTVGA-GVTWGDLYEALAPR 84 (139)
T ss_dssp EEEETTTTEEEEET-TSBHHHHHHHHHHH
T ss_pred ccccccceeEEEec-cccchhcccccccc
Confidence 78899999999997 79999999999734
No 98
>smart00749 BON bacterial OsmY and nodulation domain.
Probab=21.53 E-value=2.2e+02 Score=17.87 Aligned_cols=41 Identities=22% Similarity=0.085 Sum_probs=28.7
Q ss_pred HHHHHHHhcCCCceE--EEEEcCCCEEEEEeecCCHHHHHHHH
Q 046486 14 KKVKKVLCKFPQIQE--QSFDEKTNTVTIKVVSCSPEEIRDKL 54 (202)
Q Consensus 14 kKIkKaL~ki~GV~~--VeVDlk~~tVtV~G~~vdpekL~~kL 54 (202)
.+|+.+|...+.+.. +.+....+.+++.|...+.+....+.
T Consensus 2 ~~v~~~l~~~~~~~~~~~~v~~~~~~vvL~g~~~~~~~~~~~~ 44 (62)
T smart00749 2 EKVKKALAKDGLIKADSIVVVTDGGVVVLLGGVVDNAEAAAAA 44 (62)
T ss_pred hhHHHHHhhCCCCCcCceEEEEECCEEEEeeecCCHHHHHHHH
Confidence 578899988777764 77888889998887434444444443
No 99
>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=21.20 E-value=1.7e+02 Score=20.21 Aligned_cols=15 Identities=0% Similarity=-0.139 Sum_probs=7.8
Q ss_pred CCHHHHHHHHHhhcC
Q 046486 45 CSPEEIRDKLCCKGE 59 (202)
Q Consensus 45 vdpekL~~kL~~KtG 59 (202)
...+.|+++|+.--|
T Consensus 49 ~~L~~li~~L~~i~g 63 (74)
T cd04877 49 EKLQTLMPEIRRIDG 63 (74)
T ss_pred HHHHHHHHHHhCCCC
Confidence 345566666663333
No 100
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=21.15 E-value=1.8e+02 Score=24.10 Aligned_cols=39 Identities=18% Similarity=0.198 Sum_probs=25.3
Q ss_pred HHHHHHhcCCCceEEEEEcCCCEEEEEeecCCHHHHHHHH
Q 046486 15 KVKKVLCKFPQIQEQSFDEKTNTVTIKVVSCSPEEIRDKL 54 (202)
Q Consensus 15 KIkKaL~ki~GV~~VeVDlk~~tVtV~G~~vdpekL~~kL 54 (202)
++.+.|.+.-|++ +++|.+++.|+|+....|++.+..+.
T Consensus 18 ~~Ik~I~~~tgv~-I~Id~~~g~V~I~~~t~d~~~i~kA~ 56 (172)
T TIGR03665 18 ETKKEIEERTGVK-LDIDSETGEVKIEEEDEDPLAVMKAR 56 (172)
T ss_pred hHHHHHHHHhCcE-EEEEcCCceEEEecCCCCHHHHHHHH
Confidence 3455666666774 88888889999931135666655543
No 101
>PF03434 DUF276: DUF276 ; InterPro: IPR005096 This family is specific to Borrelia burgdorferi (Lyme disease spirochete). The protein is encoded on extrachromosomal DNA and is of unknown function.
Probab=21.08 E-value=1.3e+02 Score=27.53 Aligned_cols=29 Identities=17% Similarity=0.318 Sum_probs=26.0
Q ss_pred hHHHHHHHHhcCCCceEEEEEcCCCEEEE
Q 046486 12 CRKKVKKVLCKFPQIQEQSFDEKTNTVTI 40 (202)
Q Consensus 12 CakKIkKaL~ki~GV~~VeVDlk~~tVtV 40 (202)
-..+|+++|..++||+.+.+--..+++.+
T Consensus 88 Ty~Avk~aLL~~~gv~haNI~SsaGtini 116 (291)
T PF03434_consen 88 TYEAVKSALLNLNGVEHANIKSSAGTINI 116 (291)
T ss_pred hHHHHHHHhcCCCCceeeeeecCCCeeEE
Confidence 35789999999999999999988898876
No 102
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=21.02 E-value=93 Score=23.65 Aligned_cols=24 Identities=8% Similarity=0.216 Sum_probs=20.1
Q ss_pred hhhHHHHHHHHhcCCCceEEEEEc
Q 046486 10 SKCRKKVKKVLCKFPQIQEQSFDE 33 (202)
Q Consensus 10 ~gCakKIkKaL~ki~GV~~VeVDl 33 (202)
.+=...|+.+|++++||++++|..
T Consensus 61 ~~~td~lee~i~~~e~Vqsvei~~ 84 (88)
T PRK00435 61 EGGTEPVEEAFANVEGVESVEVEE 84 (88)
T ss_pred CcCcHHHHHHHhccCCCcEEEEEE
Confidence 355688999999999999998863
No 103
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=21.01 E-value=1.2e+02 Score=31.84 Aligned_cols=48 Identities=13% Similarity=0.208 Sum_probs=37.3
Q ss_pred hHHHHHHHHhcCCCceEEEEEcCCC--EEEEEee-------cCCHHHHHHHHHhhcC
Q 046486 12 CRKKVKKVLCKFPQIQEQSFDEKTN--TVTIKVV-------SCSPEEIRDKLCCKGE 59 (202)
Q Consensus 12 CakKIkKaL~ki~GV~~VeVDlk~~--tVtV~G~-------~vdpekL~~kL~~KtG 59 (202)
=+++|++.|.+++||.++..|...+ ++.|+-| .+++.+|.+.|+...+
T Consensus 676 ~a~~i~~~L~~~pgv~~v~~~~~~~~~el~i~id~~ka~~~Gls~~~v~~~l~~~~~ 732 (1025)
T PRK10614 676 WEPKIRKALAALPELADVNSDQQDKGAEMALTYDRDTMARLGIDVQAANSLLNNAFG 732 (1025)
T ss_pred HHHHHHHHHhcCCCeEEeecCCCCCCceEEEEECHHHHHHcCCCHHHHHHHHHHHhC
Confidence 3678999999999999999887644 6666532 3788889999986644
No 104
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=20.76 E-value=87 Score=24.15 Aligned_cols=22 Identities=5% Similarity=0.130 Sum_probs=18.8
Q ss_pred hhHHHHHHHHhcCCCceEEEEE
Q 046486 11 KCRKKVKKVLCKFPQIQEQSFD 32 (202)
Q Consensus 11 gCakKIkKaL~ki~GV~~VeVD 32 (202)
+=...|+++|++++||+++++.
T Consensus 62 g~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 62 GGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred cCcHHHHHHHhhccCcceEEEE
Confidence 3457899999999999999875
No 105
>PRK15078 polysaccharide export protein Wza; Provisional
Probab=20.26 E-value=1.9e+02 Score=27.01 Aligned_cols=68 Identities=15% Similarity=0.273 Sum_probs=43.9
Q ss_pred EEEE-cccChhhHHHHHHHHhcC---CCceEEEEEcCCCEEEEEee-------cCC--HHHHHHHHHhhcCCce-----e
Q 046486 2 VLKV-DLSCSKCRKKVKKVLCKF---PQIQEQSFDEKTNTVTIKVV-------SCS--PEEIRDKLCCKGEGVI-----K 63 (202)
Q Consensus 2 vLKV-~M~C~gCakKIkKaL~ki---~GV~~VeVDlk~~tVtV~G~-------~vd--pekL~~kL~~KtGk~i-----K 63 (202)
.++| +|+=+.=.+.|++.|.++ +.|.--..+...++|+|.|. .++ +..|+++|. .+|+.- .
T Consensus 133 ~V~vaG~T~~e~~~~I~~~L~~~~~~PqV~V~v~~~~s~~V~V~GeV~~PG~~~l~~~~~tlldaIa-~AGG~~~~a~~~ 211 (379)
T PRK15078 133 KVHVAGKTVTEIRSDITGRLAKYIESPQVDVNIAAFRSQKAYVTGEVNKSGQQAITNVPLTILDAIN-AAGGLTDDADWR 211 (379)
T ss_pred eEEECCCCHHHHHHHHHHHHHHhccCCeEEEEEccCCceEEEEEceecCCeEEEecCCCccHHHHHH-HccCCCcccccc
Confidence 3677 888888899999999874 33332223334678999884 122 578999998 655332 4
Q ss_pred eEEEcCC
Q 046486 64 TIEILKP 70 (202)
Q Consensus 64 ~aEIVsp 70 (202)
.|+|.--
T Consensus 212 ~V~l~R~ 218 (379)
T PRK15078 212 NVVLTHN 218 (379)
T ss_pred eEEEEEC
Confidence 4555543
No 106
>PRK13625 bis(5'-nucleosyl)-tetraphosphatase PrpE; Provisional
Probab=20.17 E-value=2.2e+02 Score=24.52 Aligned_cols=53 Identities=8% Similarity=0.096 Sum_probs=33.4
Q ss_pred CEEEE--cccChhhHHHHHHHHhcCCC--ceEEEEEcCCCEEEEEeecC----CHHHHHHHHH
Q 046486 1 MVLKV--DLSCSKCRKKVKKVLCKFPQ--IQEQSFDEKTNTVTIKVVSC----SPEEIRDKLC 55 (202)
Q Consensus 1 mvLKV--~M~C~gCakKIkKaL~ki~G--V~~VeVDlk~~tVtV~G~~v----dpekL~~kL~ 55 (202)
|.+.| |+| ||....+++|.++.- ...+.+..++.++.+.||-+ +...+++.|.
T Consensus 1 ~~~~vIGDIH--G~~~~L~~lL~~~~~~~~~~~~~~~~~d~li~lGDliDRGp~S~~vl~~~~ 61 (245)
T PRK13625 1 MKYDIIGDIH--GCYQEFQALTEKLGYNWSSGLPVHPDQRKLAFVGDLTDRGPHSLRMIEIVW 61 (245)
T ss_pred CceEEEEECc--cCHHHHHHHHHHcCCCcccCcccCCCCCEEEEECcccCCCcChHHHHHHHH
Confidence 45555 888 899999999988642 11222234567888888622 3455555554
No 107
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=20.11 E-value=2.7e+02 Score=23.71 Aligned_cols=44 Identities=18% Similarity=0.191 Sum_probs=32.2
Q ss_pred cccChhhHHHHHHHHhcCCCceEEEEEcCCCEEEEEee-cCCHHHHHHHHHhhcC
Q 046486 6 DLSCSKCRKKVKKVLCKFPQIQEQSFDEKTNTVTIKVV-SCSPEEIRDKLCCKGE 59 (202)
Q Consensus 6 ~M~C~gCakKIkKaL~ki~GV~~VeVDlk~~tVtV~G~-~vdpekL~~kL~~KtG 59 (202)
++.|..=.-+.+++|.+++. .+.++|..+ ....+.|.+.++ ..|
T Consensus 5 Gl~CP~Pvi~tKkal~~l~~---------g~~L~VlvD~~~a~~nV~~~~~-~~G 49 (194)
T TIGR03527 5 GLACPQPVILTKKALDELGE---------EGVLTVIVDNEAAKENVSKFAT-SLG 49 (194)
T ss_pred CCCCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHH-HcC
Confidence 68899999999999999862 234555543 455667777777 777
Done!