Query 047835
Match_columns 101
No_of_seqs 105 out of 669
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 03:36:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047835.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047835hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1603 Copper chaperone [Inor 99.7 9.5E-18 2.1E-22 107.2 8.8 67 2-70 4-71 (73)
2 PF00403 HMA: Heavy-metal-asso 99.2 4.2E-11 9E-16 72.8 7.0 56 6-63 1-60 (62)
3 COG2608 CopZ Copper chaperone 98.4 3E-06 6.5E-11 53.7 7.9 59 3-63 2-64 (71)
4 KOG4656 Copper chaperone for s 98.4 1.8E-06 4E-11 66.4 7.8 67 4-72 8-74 (247)
5 PLN02957 copper, zinc superoxi 98.1 4.2E-05 9E-10 58.4 9.3 71 3-75 6-76 (238)
6 PRK10671 copA copper exporting 97.7 0.00013 2.7E-09 63.9 7.3 66 1-70 1-67 (834)
7 COG2217 ZntA Cation transport 94.6 0.15 3.2E-06 45.0 7.3 63 3-68 2-69 (713)
8 TIGR00003 copper ion binding p 94.4 0.39 8.5E-06 25.6 7.5 57 3-61 2-62 (68)
9 PRK10671 copA copper exporting 92.9 0.41 9E-06 42.2 7.1 62 4-67 100-162 (834)
10 KOG0207 Cation transport ATPas 91.7 0.81 1.8E-05 41.7 7.4 66 3-70 146-215 (951)
11 cd04098 eEF2_C_snRNP eEF2_C_sn 84.7 7.4 0.00016 24.6 6.6 62 6-68 3-69 (80)
12 PF02680 DUF211: Uncharacteriz 84.4 4.1 8.8E-05 27.8 5.5 60 4-64 6-72 (95)
13 KOG0207 Cation transport ATPas 84.0 2.8 6.1E-05 38.4 5.8 61 10-72 2-64 (951)
14 PF00679 EFG_C: Elongation fac 83.3 5.5 0.00012 25.5 5.7 61 6-68 6-71 (89)
15 smart00838 EFG_C Elongation fa 82.0 9.7 0.00021 24.0 6.4 63 6-70 5-71 (85)
16 PRK11033 zntA zinc/cadmium/mer 81.6 4.3 9.3E-05 35.7 6.0 56 3-61 53-111 (741)
17 COG1888 Uncharacterized protei 78.8 5.3 0.00011 27.3 4.4 44 20-64 23-74 (97)
18 PF01883 DUF59: Domain of unkn 77.3 6 0.00013 24.1 4.2 32 4-36 35-72 (72)
19 PF13732 DUF4162: Domain of un 72.3 13 0.00028 23.0 4.8 39 25-63 26-64 (84)
20 cd04096 eEF2_snRNP_like_C eEF2 72.3 20 0.00044 22.1 6.1 63 6-69 3-70 (80)
21 cd03711 Tet_C Tet_C: C-terminu 71.5 21 0.00046 22.1 6.4 61 6-68 3-67 (78)
22 cd03713 EFG_mtEFG_C EFG_mtEFG_ 70.9 22 0.00047 21.9 6.3 61 6-69 3-68 (78)
23 cd04888 ACT_PheB-BS C-terminal 69.3 19 0.00041 21.4 4.9 31 5-36 43-74 (76)
24 PF13291 ACT_4: ACT domain; PD 68.2 18 0.0004 22.1 4.8 31 4-35 49-79 (80)
25 PF03927 NapD: NapD protein; 68.0 20 0.00043 23.0 5.0 33 4-37 40-72 (79)
26 PF04972 BON: BON domain; Int 62.0 5.2 0.00011 23.6 1.4 33 20-54 3-38 (64)
27 cd01514 Elongation_Factor_C El 61.0 36 0.00078 20.8 6.7 63 6-70 3-70 (79)
28 COG2092 EFB1 Translation elong 57.9 16 0.00035 24.5 3.3 35 4-38 50-84 (88)
29 cd04097 mtEFG1_C mtEFG1_C: C-t 57.1 44 0.00095 20.6 6.4 61 6-69 3-68 (78)
30 cd03710 BipA_TypA_C BipA_TypA_ 54.4 50 0.0011 20.5 6.0 62 6-69 3-69 (79)
31 PF08712 Nfu_N: Scaffold prote 50.4 56 0.0012 21.2 4.9 41 19-62 37-79 (87)
32 cd04877 ACT_TyrR N-terminal AC 49.8 49 0.0011 20.0 4.4 30 6-36 40-69 (74)
33 PF09358 UBA_e1_C: Ubiquitin-a 49.6 29 0.00063 24.1 3.7 38 34-73 29-67 (125)
34 PRK11023 outer membrane lipopr 49.5 24 0.00052 25.9 3.4 44 15-59 48-94 (191)
35 PF05193 Peptidase_M16_C: Pept 49.3 16 0.00035 24.1 2.3 23 42-64 20-42 (184)
36 PF02107 FlgH: Flagellar L-rin 49.1 13 0.00027 27.4 1.9 29 27-56 110-138 (179)
37 PRK09577 multidrug efflux prot 46.0 39 0.00084 31.0 4.8 43 18-63 158-210 (1032)
38 PRK10555 aminoglycoside/multid 45.6 41 0.00089 30.8 4.9 43 17-62 158-210 (1037)
39 TIGR00489 aEF-1_beta translati 43.9 38 0.00082 22.4 3.4 32 7-38 53-84 (88)
40 cd06167 LabA_like LabA_like pr 43.1 38 0.00083 22.8 3.4 30 43-72 103-132 (149)
41 PRK00435 ef1B elongation facto 43.0 35 0.00077 22.6 3.1 34 5-38 51-84 (88)
42 COG1432 Uncharacterized conser 43.0 36 0.00079 24.8 3.5 31 43-73 114-144 (181)
43 TIGR00288 conserved hypothetic 41.8 44 0.00096 24.5 3.7 30 43-72 109-138 (160)
44 COG0612 PqqL Predicted Zn-depe 41.5 33 0.00071 27.5 3.3 23 42-64 199-221 (438)
45 PRK15127 multidrug efflux syst 40.8 53 0.0011 30.2 4.8 41 18-61 159-209 (1049)
46 TIGR00915 2A0602 The (Largely 39.3 56 0.0012 30.0 4.7 41 18-61 159-209 (1044)
47 PF01936 NYN: NYN domain; Int 38.6 40 0.00086 22.3 2.9 30 42-71 98-127 (146)
48 PF07338 DUF1471: Protein of u 38.0 40 0.00088 20.2 2.6 32 42-73 6-43 (56)
49 PHA00514 dsDNA binding protein 37.4 62 0.0013 22.0 3.6 34 42-75 32-67 (98)
50 PRK09579 multidrug efflux prot 37.4 65 0.0014 29.5 4.8 43 18-62 158-210 (1017)
51 PRK10553 assembly protein for 36.7 1.2E+02 0.0027 19.9 5.8 55 15-70 16-76 (87)
52 PRK11198 LysM domain/BON super 36.4 77 0.0017 22.3 4.2 54 15-70 25-80 (147)
53 PRK13760 putative RNA-associat 36.1 1.7E+02 0.0037 22.7 6.4 61 4-68 163-227 (231)
54 smart00653 eIF2B_5 domain pres 35.8 67 0.0015 22.0 3.7 29 34-64 50-78 (110)
55 COG4004 Uncharacterized protei 35.7 40 0.00086 23.0 2.5 38 23-61 34-76 (96)
56 PF05922 Inhibitor_I9: Peptida 35.2 51 0.0011 19.8 2.8 19 20-38 59-77 (82)
57 TIGR02945 SUF_assoc FeS assemb 34.4 73 0.0016 20.4 3.6 34 4-38 38-77 (99)
58 PF05137 PilN: Fimbrial assemb 33.9 1.1E+02 0.0023 18.3 4.4 42 31-75 16-63 (78)
59 PRK11023 outer membrane lipopr 33.7 1.4E+02 0.003 21.9 5.3 40 15-55 126-167 (191)
60 PRK10503 multidrug efflux syst 31.6 93 0.002 28.6 4.9 36 18-55 168-203 (1040)
61 PF12164 SporV_AA: Stage V spo 31.4 60 0.0013 21.5 2.8 51 18-75 32-82 (93)
62 PLN00116 translation elongatio 31.4 1E+02 0.0022 27.7 5.0 62 6-68 729-795 (843)
63 PRK13351 elongation factor G; 31.2 1.3E+02 0.0028 26.1 5.5 61 6-68 601-666 (687)
64 TIGR03406 FeS_long_SufT probab 31.1 86 0.0019 23.1 3.9 34 4-38 114-153 (174)
65 PF14492 EFG_II: Elongation Fa 30.3 1.4E+02 0.003 18.5 4.6 46 18-64 18-68 (75)
66 cd07422 MPP_ApaH Escherichia c 30.3 1.2E+02 0.0027 23.3 4.8 42 15-63 8-54 (257)
67 COG0841 AcrB Cation/multidrug 30.2 1E+02 0.0022 28.6 4.9 37 17-55 156-192 (1009)
68 PF00873 ACR_tran: AcrB/AcrD/A 30.0 58 0.0013 29.5 3.3 37 17-55 157-193 (1021)
69 PRK00007 elongation factor G; 30.0 1.2E+02 0.0026 26.5 5.1 61 6-68 605-669 (693)
70 PRK12698 flgH flagellar basal 29.5 40 0.00087 25.9 1.9 29 27-56 153-181 (224)
71 COG2151 PaaD Predicted metal-s 29.5 97 0.0021 21.4 3.7 50 5-61 51-106 (111)
72 COG2177 FtsX Cell division pro 29.5 1.8E+02 0.004 23.1 5.7 38 15-65 71-108 (297)
73 cd04879 ACT_3PGDH-like ACT_3PG 29.5 68 0.0015 17.9 2.5 19 18-36 52-70 (71)
74 PF00736 EF1_GNE: EF-1 guanine 28.9 1.6E+02 0.0036 19.2 4.6 35 5-39 51-86 (89)
75 PRK12788 flgH flagellar basal 28.8 41 0.00089 26.1 1.9 29 27-56 164-192 (234)
76 cd03309 CmuC_like CmuC_like. P 28.4 63 0.0014 25.7 2.9 45 9-55 215-269 (321)
77 cd00141 NT_POLXc Nucleotidyltr 28.4 89 0.0019 24.6 3.8 47 17-63 146-205 (307)
78 PRK00249 flgH flagellar basal 28.0 45 0.00097 25.5 2.0 29 27-56 152-180 (222)
79 PF03927 NapD: NapD protein; 27.9 1.7E+02 0.0036 18.6 6.3 44 16-61 15-59 (79)
80 PRK12697 flgH flagellar basal 27.8 44 0.00095 25.8 1.9 29 27-56 156-184 (226)
81 cd04910 ACT_AK-Ectoine_1 ACT d 27.8 1.4E+02 0.0031 18.8 4.0 52 15-68 15-69 (71)
82 KOG3411 40S ribosomal protein 27.7 46 0.00099 24.2 1.8 45 14-61 96-140 (143)
83 cd02643 R3H_NF-X1 R3H domain o 27.6 1.2E+02 0.0025 19.1 3.6 29 18-46 44-72 (74)
84 PRK12407 flgH flagellar basal 27.5 45 0.00097 25.6 1.9 29 27-56 150-178 (221)
85 PF03958 Secretin_N: Bacterial 26.9 1.5E+02 0.0033 17.8 4.0 24 33-57 47-71 (82)
86 PRK13748 putative mercuric red 26.8 2.6E+02 0.0057 23.1 6.4 50 10-61 8-59 (561)
87 PRK10614 multidrug efflux syst 26.8 1.5E+02 0.0032 27.2 5.3 36 18-55 159-194 (1025)
88 COG3643 Glutamate formiminotra 26.6 1.1E+02 0.0023 24.7 3.8 42 18-61 20-64 (302)
89 cd06471 ACD_LpsHSP_like Group 26.1 44 0.00095 21.1 1.4 24 27-51 17-42 (93)
90 PRK10568 periplasmic protein; 25.5 1.7E+02 0.0037 21.6 4.7 36 15-51 59-96 (203)
91 PRK12739 elongation factor G; 25.5 2E+02 0.0043 25.2 5.7 60 6-68 602-666 (691)
92 PRK00166 apaH diadenosine tetr 25.2 1.4E+02 0.0031 23.2 4.4 40 16-62 11-55 (275)
93 PRK12701 flgH flagellar basal 25.1 53 0.0011 25.4 1.9 29 27-56 159-187 (230)
94 cd00292 EF1B Elongation factor 24.8 1.2E+02 0.0026 19.9 3.3 34 6-39 52-85 (88)
95 PF07683 CobW_C: Cobalamin syn 24.7 92 0.002 19.3 2.7 21 41-61 71-92 (94)
96 PRK12696 flgH flagellar basal 24.7 52 0.0011 25.5 1.8 29 27-56 166-194 (236)
97 PF07744 SPOC: SPOC domain; I 24.7 90 0.002 20.2 2.8 30 42-71 39-72 (119)
98 PRK12700 flgH flagellar basal 24.1 58 0.0012 25.2 1.9 29 27-56 160-188 (230)
99 cd04920 ACT_AKiii-DAPDC_2 ACT 23.8 1.7E+02 0.0036 17.2 4.8 46 15-62 14-60 (63)
100 smart00749 BON bacterial OsmY 23.7 1.4E+02 0.003 16.4 3.6 38 19-57 2-41 (62)
101 PF10369 ALS_ss_C: Small subun 23.7 1.9E+02 0.0042 18.0 5.8 63 4-71 4-67 (75)
102 PF08478 POTRA_1: POTRA domain 23.6 1E+02 0.0022 18.0 2.7 28 19-46 37-64 (69)
103 cd04887 ACT_MalLac-Enz ACT_Mal 23.6 1.6E+02 0.0036 17.1 5.0 29 7-36 44-72 (74)
104 cd04901 ACT_3PGDH C-terminal A 23.5 1E+02 0.0022 17.7 2.6 18 19-36 51-68 (69)
105 cd06475 ACD_HspB1_like Alpha c 23.5 65 0.0014 20.6 1.8 23 27-50 17-41 (86)
106 TIGR00668 apaH bis(5'-nucleosy 22.8 1.8E+02 0.0039 23.1 4.5 45 15-66 10-59 (279)
107 COG0071 IbpA Molecular chapero 22.5 40 0.00088 23.4 0.8 28 24-52 54-83 (146)
108 cd04903 ACT_LSD C-terminal ACT 22.4 1E+02 0.0022 17.2 2.4 19 18-36 52-70 (71)
109 PRK12699 flgH flagellar basal 22.2 64 0.0014 25.2 1.9 29 27-56 177-205 (246)
110 PRK05096 guanosine 5'-monophos 22.0 3E+02 0.0065 22.8 5.8 53 10-69 102-155 (346)
111 PRK11439 pphA serine/threonine 21.5 1.1E+02 0.0025 22.4 3.0 41 15-62 26-71 (218)
112 TIGR00484 EF-G translation elo 21.5 2.8E+02 0.0061 24.2 5.8 61 6-68 602-666 (689)
113 cd04881 ACT_HSDH-Hom ACT_HSDH_ 21.4 1.6E+02 0.0036 16.7 3.2 28 6-34 45-72 (79)
114 PF08923 MAPKK1_Int: Mitogen-a 21.2 1.9E+02 0.0041 19.9 3.9 29 18-48 4-32 (119)
115 cd00474 SUI1_eIF1 The SUI1/eIF 21.1 1.6E+02 0.0035 18.7 3.3 26 43-68 14-45 (77)
116 cd04878 ACT_AHAS N-terminal AC 21.1 87 0.0019 17.5 1.9 29 5-35 44-72 (72)
117 PRK13625 bis(5'-nucleosyl)-tet 20.9 1.3E+02 0.0029 22.5 3.4 46 15-61 10-62 (245)
118 PF01424 R3H: R3H domain; Int 20.8 1.7E+02 0.0037 17.0 3.2 33 15-47 29-61 (63)
119 smart00683 DM16 Repeats in sea 20.6 54 0.0012 20.0 1.0 25 24-48 3-27 (55)
No 1
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.75 E-value=9.5e-18 Score=107.18 Aligned_cols=67 Identities=21% Similarity=0.344 Sum_probs=61.8
Q ss_pred cceEEEEEeCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHHHHHHHHhcc-CceEEEe
Q 047835 2 RKKILYRLDNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKI-GYVETMK 70 (101)
Q Consensus 2 ~q~vvlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l~~~LrKk~-~~aeivs 70 (101)
.++.+++|+||| +||.+++.+.+.++.||+++.+|.++ ++|||.|++||..|+++|+|.+ +.+++|.
T Consensus 4 ~~~~v~kv~~~C-~gc~~kV~~~l~~~~GV~~v~id~~~-~kvtV~g~~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 4 IKTVVLKVNMHC-EGCARKVKRVLQKLKGVESVDIDIKK-QKVTVKGNVDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred ccEEEEEECccc-ccHHHHHHHHhhccCCeEEEEecCCC-CEEEEEEecCHHHHHHHHHhcCCCceEEec
Confidence 578999999999 99999999999999999999999987 8999999999999999999977 4666653
No 2
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.24 E-value=4.2e-11 Score=72.76 Aligned_cols=56 Identities=16% Similarity=0.259 Sum_probs=50.4
Q ss_pred EEEE-eCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc
Q 047835 6 LYRL-DNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDI---DEVALANMLRRKI 63 (101)
Q Consensus 6 vlKV-~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~ 63 (101)
.|+| +|+| ++|.+++.++|.+++||.++.+|... ++++|.++. ++.++.++|++.+
T Consensus 1 t~~v~~m~C-~~C~~~v~~~l~~~~GV~~v~vd~~~-~~v~v~~~~~~~~~~~i~~~i~~~G 60 (62)
T PF00403_consen 1 TFKVPGMTC-EGCAKKVEKALSKLPGVKSVKVDLET-KTVTVTYDPDKTSIEKIIEAIEKAG 60 (62)
T ss_dssp EEEEESTTS-HHHHHHHHHHHHTSTTEEEEEEETTT-TEEEEEESTTTSCHHHHHHHHHHTT
T ss_pred CEEECCccc-HHHHHHHHHHHhcCCCCcEEEEECCC-CEEEEEEecCCCCHHHHHHHHHHhC
Confidence 4677 7999 99999999999999999999999987 899999994 5699999998843
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.39 E-value=3e-06 Score=53.72 Aligned_cols=59 Identities=14% Similarity=0.144 Sum_probs=48.6
Q ss_pred ceEEEEE-eCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEE--EEEE-ccHHHHHHHHHhcc
Q 047835 3 KKILYRL-DNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHME--VIGD-IDEVALANMLRRKI 63 (101)
Q Consensus 3 q~vvlKV-~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvt--V~G~-vDp~~l~~~LrKk~ 63 (101)
++..|++ +|+| .+|...+.++|.+++||.++.+|... ++.+ +.+. ++..++...+...+
T Consensus 2 ~~~~l~v~~MtC-~~C~~~V~~al~~v~gv~~v~v~l~~-~~~~V~~d~~~~~~~~i~~ai~~aG 64 (71)
T COG2608 2 MKTTLKVEGMTC-GHCVKTVEKALEEVDGVASVDVDLEK-GTATVTFDSNKVDIEAIIEAIEDAG 64 (71)
T ss_pred ceEEEEECCcCc-HHHHHHHHHHHhcCCCeeEEEEEccc-CeEEEEEcCCcCCHHHHHHHHHHcC
Confidence 3556777 6999 99999999999999999999999965 4444 4553 89999999998744
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.37 E-value=1.8e-06 Score=66.36 Aligned_cols=67 Identities=13% Similarity=0.164 Sum_probs=61.3
Q ss_pred eEEEEEeCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHHHHHHHHhccCceEEEecC
Q 047835 4 KILYRLDNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKIGYVETMKLD 72 (101)
Q Consensus 4 ~vvlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l~~~LrKk~~~aeivsv~ 72 (101)
++.+-|.|+| +.|...++..|..++||++|++|.++ +.|.|-+.+-+..+...|+..++.|-|.-.+
T Consensus 8 ~~efaV~M~c-escvnavk~~L~~V~Gi~~vevdle~-q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G 74 (247)
T KOG4656|consen 8 EAEFAVQMTC-ESCVNAVKACLKGVPGINSVEVDLEQ-QIVSVETSVPPSEIQNTLENTGRDAVLRGAG 74 (247)
T ss_pred eEEEEEechh-HHHHHHHHHHhccCCCcceEEEEhhh-cEEEEEccCChHHHHHHHHhhChheEEecCC
Confidence 6788999999 99999999999999999999999987 8999999999999999999977788776554
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.06 E-value=4.2e-05 Score=58.36 Aligned_cols=71 Identities=11% Similarity=0.110 Sum_probs=62.3
Q ss_pred ceEEEEEeCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHHHHHHHHhccCceEEEecCCCC
Q 047835 3 KKILYRLDNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKIGYVETMKLDILD 75 (101)
Q Consensus 3 q~vvlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l~~~LrKk~~~aeivsv~p~k 75 (101)
+++.+.+.|+| +.|..++.+.+.+++||.++.++... ++++|.+..++..++..+++....+++++.+...
T Consensus 6 ~~~~~~VgMsC-~~Ca~~Iek~L~~~~GV~~v~vn~~~-~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 6 LLTEFMVDMKC-EGCVAAVKNKLETLEGVKAVEVDLSN-QVVRVLGSSPVKAMTAALEQTGRKARLIGQGDPE 76 (238)
T ss_pred EEEEEEECccC-HHHHHHHHHHHhcCCCeEEEEEEcCC-CEEEEEecCCHHHHHHHHHHcCCcEEEecCCCcc
Confidence 56788999999 99999999999999999999999987 7999999889999999998855578888776654
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.70 E-value=0.00013 Score=63.88 Aligned_cols=66 Identities=15% Similarity=0.136 Sum_probs=57.8
Q ss_pred CcceEEEEEe-CCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHHHHHHHHhccCceEEEe
Q 047835 1 MRKKILYRLD-NMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKIGYVETMK 70 (101)
Q Consensus 1 M~q~vvlKV~-m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l~~~LrKk~~~aeivs 70 (101)
|++++.++|. |+| ..|.+++.+.+.+++||.++.+|.+ +.+|.+..|+..+...+..-+-.+++.+
T Consensus 1 ~~~~~~l~V~gmtC-~~C~~~i~~al~~~~gv~~v~v~~~---~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 1 MSQTIDLTLDGLSC-GHCVKRVKESLEQRPDVEQADVSIT---EAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred CCeEEEEEECCccc-HHHHHHHHHHHhcCCCcceEEEeee---EEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 8899999995 999 9999999999999999999999982 5677888999999999987555777654
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=94.60 E-value=0.15 Score=45.04 Aligned_cols=63 Identities=10% Similarity=0.171 Sum_probs=51.5
Q ss_pred ceEEEEE-eCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEE---cc-HHHHHHHHHhccCceEE
Q 047835 3 KKILYRL-DNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD---ID-EVALANMLRRKIGYVET 68 (101)
Q Consensus 3 q~vvlKV-~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~---vD-p~~l~~~LrKk~~~aei 68 (101)
++..|.+ .||| ..|.+++. .+.+++||.+..++... ++++|..+ .+ +..+...+++.+-.+..
T Consensus 2 ~~~~l~v~Gm~C-a~C~~~ie-~l~~~~gV~~~~vn~~t-~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 2 RETSLSVEGMTC-AACASRIE-ALNKLPGVEEARVNLAT-ERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred ceeEEeecCcCc-HHHHHHHH-HHhcCCCeeEEEeeccc-ceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 3556677 4999 99999999 99999999999999976 79998865 56 78899998885544444
No 8
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=94.36 E-value=0.39 Score=25.61 Aligned_cols=57 Identities=19% Similarity=0.258 Sum_probs=43.3
Q ss_pred ceEEEEEe-CCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEE---ccHHHHHHHHHh
Q 047835 3 KKILYRLD-NMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD---IDEVALANMLRR 61 (101)
Q Consensus 3 q~vvlKV~-m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~---vDp~~l~~~LrK 61 (101)
++..+.++ ++| ..|...+.+.+....|+.+..++... +.+++..+ .+...+...+..
T Consensus 2 ~~~~~~v~~~~~-~~c~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 62 (68)
T TIGR00003 2 QKFTVQVMSMTC-QHCVDKIEKFVGELEGVSKVQVKLEK-ASVKVEFDAPQATEICIAEAILD 62 (68)
T ss_pred cEEEEEECCeEc-HHHHHHHHHHHhcCCCEEEEEEEcCC-CEEEEEeCCCCCCHHHHHHHHHH
Confidence 34557774 778 99999999999999999999999866 67777642 567776665543
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=92.94 E-value=0.41 Score=42.20 Aligned_cols=62 Identities=15% Similarity=0.186 Sum_probs=49.6
Q ss_pred eEEEEE-eCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHHHHHHHHhccCceE
Q 047835 4 KILYRL-DNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKIGYVE 67 (101)
Q Consensus 4 ~vvlKV-~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l~~~LrKk~~~ae 67 (101)
++.+.+ .|+| ..|...+.+.+.+++||.++.++... ++..+.+..++..+...++...-.+.
T Consensus 100 ~~~l~V~Gm~C-a~Ca~~Ie~~L~~~~GV~~a~vnl~t-~~~~V~~~~s~~~I~~~I~~~Gy~a~ 162 (834)
T PRK10671 100 SQQLLLSGMSC-ASCVSRVQNALQSVPGVTQARVNLAE-RTALVMGSASPQDLVQAVEKAGYGAE 162 (834)
T ss_pred eEEEEeCCcCc-HHHHHHHHHHHhcCCCceeeeeecCC-CeEEEEccCCHHHHHHHHHhcCCCcc
Confidence 345656 5899 99999999999999999999999876 67888777888888888876332443
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=91.66 E-value=0.81 Score=41.73 Aligned_cols=66 Identities=14% Similarity=0.088 Sum_probs=52.1
Q ss_pred ceEEEEEe-CCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEE---ccHHHHHHHHHhccCceEEEe
Q 047835 3 KKILYRLD-NMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD---IDEVALANMLRRKIGYVETMK 70 (101)
Q Consensus 3 q~vvlKV~-m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~---vDp~~l~~~LrKk~~~aeivs 70 (101)
++++|.|. |.| +.|..++.+++.+++||.+++++... +++.|.=+ .-|.++.+.|-...-.+.+..
T Consensus 146 ~~i~L~v~g~~c-~s~~~~ie~~l~~l~gV~~~sv~~~t-~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~ 215 (951)
T KOG0207|consen 146 QKIYLDVLGMTC-ASCVSKIESILERLRGVKSFSVSLAT-DTAIVVYDPEITGPRDIIKAIEETGFEASVRP 215 (951)
T ss_pred CcEEEEeecccc-cchhhhhHHHHhhccCeeEEEEeccC-CceEEEecccccChHHHHHHHHhhcccceeee
Confidence 57888885 777 99999999999999999999999977 88888655 567777777765443444444
No 11
>cd04098 eEF2_C_snRNP eEF2_C_snRNP: This family includes a C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to the C-terminal domain of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=84.67 E-value=7.4 Score=24.58 Aligned_cols=62 Identities=13% Similarity=0.180 Sum_probs=44.9
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCC-eeEEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEE
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPG-LLSVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVET 68 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~G-V~sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aei 68 (101)
+++|+++|.+.+-.+++..|++..| |.+.+..... ...+|.|.+ +...+...||..+ |.+..
T Consensus 3 i~~~ei~~p~~~~g~v~~~L~~rrg~i~~~~~~~~~-~~~~i~a~vP~~e~~~~~~~Lrs~T~G~~~~ 69 (80)
T cd04098 3 IYEVEITCPADAVSAVYEVLSRRRGHVIYDTPIPGT-PLYEVKAFIPVIESFGFETDLRVHTQGQAFC 69 (80)
T ss_pred EEEEEEEECHHHHhHHHHHHhhCCcEEeeeeccCCC-CcEEEEEECCHHHHhChHHHHHhhCCCceEE
Confidence 4677777778899999999999999 4444432211 238899994 6677888999877 46654
No 12
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=84.41 E-value=4.1 Score=27.76 Aligned_cols=60 Identities=15% Similarity=0.216 Sum_probs=39.8
Q ss_pred eEEEEEeCCChHhhHHHHHHHHcCCCCeeEEEe-----cCCCC-CcEEEEEE-ccHHHHHHHHHhccC
Q 047835 4 KILYRLDNMHSPKCRTKAFKIIAGFPGLLSVAM-----KGDDL-RHMEVIGD-IDEVALANMLRRKIG 64 (101)
Q Consensus 4 ~vvlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~i-----d~~~k-~kvtV~G~-vDp~~l~~~LrKk~~ 64 (101)
.+||-|.-.- +=-.-.+-+.|++++||+.|.+ |.+-. =++||.|+ +|-..+.+.+.+.++
T Consensus 6 RlVLDVlKP~-~p~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg 72 (95)
T PF02680_consen 6 RLVLDVLKPH-EPSIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGG 72 (95)
T ss_dssp EEEEEEEEES-SS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-
T ss_pred EEEEEeecCC-CCCHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCC
Confidence 3455554333 4445566788999999998765 33221 27899999 999999999998665
No 13
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=84.02 E-value=2.8 Score=38.40 Aligned_cols=61 Identities=11% Similarity=0.113 Sum_probs=50.0
Q ss_pred eCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEE--ccHHHHHHHHHhccCceEEEecC
Q 047835 10 DNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD--IDEVALANMLRRKIGYVETMKLD 72 (101)
Q Consensus 10 ~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~--vDp~~l~~~LrKk~~~aeivsv~ 72 (101)
.|.| ..|.+.+.+.+++.+||.+++++..+ +..+|.=+ +++..+...+.--+..+++++-.
T Consensus 2 gmtc-~ac~~si~~~~~~~~g~~~i~vsl~~-~~~~v~~~~~~~~~~i~~~ied~gf~~~~~~~~ 64 (951)
T KOG0207|consen 2 GMTC-SACSNSIEKAISRKPGVQKIEVSLAQ-KRANVSYDNIVSPESIKETIEDMGFEASLLSDS 64 (951)
T ss_pred CccH-HHHhhhHHHHHhcCCCceeEEEEecc-ccceEEEeeccCHHHHHHHhhcccceeeecccC
Confidence 4789 99999999999999999999999876 56555443 89999999988766677776643
No 14
>PF00679 EFG_C: Elongation factor G C-terminus; InterPro: IPR000640 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. This entry represents the C-terminal domain found in EF2 (or EF-G) of both prokaryotes and eukaryotes (also known as eEF2), as well as in some tetracycline-resistance proteins. This domain adopts a ferredoxin-like fold consisting of an alpha/beta sandwich with anti-parallel beta-sheets. It resembles the topology of domain III found in these elongation factors, with which it forms the C-terminal block, but these two domains cannot be superimposed []. This domain is often found associated with (IPR000795 from INTERPRO), which contains the signatures for the N terminus of the proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1WDT_A 2DY1_A 3CB4_F 3DEG_C 2EFG_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y ....
Probab=83.34 E-value=5.5 Score=25.46 Aligned_cols=61 Identities=13% Similarity=0.150 Sum_probs=44.6
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCC-eeEEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEE
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPG-LLSVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVET 68 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~G-V~sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aei 68 (101)
++++.+.+.+.+..+|...|++..| |.+...+ .+ +...|.|.+ .-..+...||..+ |+|.+
T Consensus 6 ~~~~~I~~p~~~~g~v~~~l~~r~g~i~~~~~~-~~-~~~~i~~~iP~~~~~gf~~~Lr~~T~G~a~~ 71 (89)
T PF00679_consen 6 IMSVEISVPEEYLGKVISDLSKRRGEILSMDPI-GG-DRVVIEAEIPVRELFGFRSELRSLTSGRASF 71 (89)
T ss_dssp EEEEEEEEEGGGHHHHHHHHHHTT-EEEEEEEE-ST-TEEEEEEEEEGGGHTTHHHHHHHHTTTS-EE
T ss_pred EEEEEEEECHHHHHHHHHHhcccccEEEechhh-hh-hheeEEEEEChhhhhhHHHHhhccCCCEEEE
Confidence 4566666668899999999999999 5566666 23 799999994 6667788888777 46654
No 15
>smart00838 EFG_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.
Probab=82.01 E-value=9.7 Score=23.98 Aligned_cols=63 Identities=10% Similarity=0.099 Sum_probs=46.1
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEEEe
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVETMK 70 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aeivs 70 (101)
++.+.+.|.+.+...++..|++..|.-. +++..+ +.+.+.|.+ ....+.+.||..+ |++.+..
T Consensus 5 i~~~~I~~p~~~~g~v~~~l~~rrG~i~-~~~~~~-~~~~i~~~iP~~~~~~~~~~Lrs~T~G~~~~~~ 71 (85)
T smart00838 5 IMKVEVTVPEEYMGDVIGDLNSRRGKIE-GMEQRG-GAQVIKAKVPLSEMFGYATDLRSATQGRATWSM 71 (85)
T ss_pred EEEEEEEeCHHHHHHHHHHHHHcCCEEE-CeeccC-CcEEEEEECCHHHHhchHHHHHHhcCCeEEEEE
Confidence 4677778878899999999999999442 333334 578999995 5566788888777 4666543
No 16
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=81.56 E-value=4.3 Score=35.71 Aligned_cols=56 Identities=14% Similarity=0.271 Sum_probs=41.5
Q ss_pred ceEEEEEe-CCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEE--ccHHHHHHHHHh
Q 047835 3 KKILYRLD-NMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD--IDEVALANMLRR 61 (101)
Q Consensus 3 q~vvlKV~-m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~--vDp~~l~~~LrK 61 (101)
+++.+++. |+| ..|..++.+.+.+++||.++.++... +++.+..+ .+ ..+...++.
T Consensus 53 ~r~~l~V~Gm~C-~sCa~~Ie~aL~~~~GV~~v~Vn~at-~k~~V~~d~~~~-~~I~~aI~~ 111 (741)
T PRK11033 53 TRYSWKVSGMDC-PSCARKVENAVRQLAGVNQVQVLFAT-EKLVVDADNDIR-AQVESAVQK 111 (741)
T ss_pred ceEEEEECCCCc-HHHHHHHHHHHhcCCCeeeEEEEcCC-CeEEEEecccch-HHHHHHHHh
Confidence 34566664 889 99999999999999999999999866 57666533 22 445555554
No 17
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=78.82 E-value=5.3 Score=27.29 Aligned_cols=44 Identities=11% Similarity=0.247 Sum_probs=33.6
Q ss_pred HHHHHHcCCCCeeEEEe-------cCCCCCcEEEEEE-ccHHHHHHHHHhccC
Q 047835 20 KAFKIIAGFPGLLSVAM-------KGDDLRHMEVIGD-IDEVALANMLRRKIG 64 (101)
Q Consensus 20 Kv~k~l~~~~GV~sV~i-------d~~~k~kvtV~G~-vDp~~l~~~LrKk~~ 64 (101)
..-+.|++++||+.|.+ +... =++||-|+ +|=..+.+.|-..++
T Consensus 23 e~A~~lskl~gVegVNItv~eiD~et~~-~~itIeG~~ldydei~~~iE~~Gg 74 (97)
T COG1888 23 ELALELSKLEGVEGVNITVTEIDVETEN-LKITIEGTNLDYDEIEEVIEELGG 74 (97)
T ss_pred HHHHHHhhcCCcceEEEEEEEeeehhcc-eEEEEEcCCCCHHHHHHHHHHcCC
Confidence 34567788888887654 3333 48999999 999999999998666
No 18
>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=77.31 E-value=6 Score=24.11 Aligned_cols=32 Identities=28% Similarity=0.526 Sum_probs=22.9
Q ss_pred eEEEEEeCCChHhh------HHHHHHHHcCCCCeeEEEe
Q 047835 4 KILYRLDNMHSPKC------RTKAFKIIAGFPGLLSVAM 36 (101)
Q Consensus 4 ~vvlKV~m~C~e~C------~~Kv~k~l~~~~GV~sV~i 36 (101)
++.+.+.+.. .+| +..+..+|..++||.+|.+
T Consensus 35 ~V~v~l~l~~-~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 35 KVSVSLELPT-PACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp EEEEEE--SS-TTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred EEEEEEEECC-CCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 4566666666 666 6889999999999999875
No 19
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=72.35 E-value=13 Score=22.97 Aligned_cols=39 Identities=23% Similarity=0.283 Sum_probs=30.5
Q ss_pred HcCCCCeeEEEecCCCCCcEEEEEEccHHHHHHHHHhcc
Q 047835 25 IAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKI 63 (101)
Q Consensus 25 l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l~~~LrKk~ 63 (101)
+..++||.++..+....=.+.+.+..++.+|++.|...+
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~~~g 64 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDEETANELLQELIEKG 64 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHHhCC
Confidence 778899999998663323677777789999999998854
No 20
>cd04096 eEF2_snRNP_like_C eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=72.25 E-value=20 Score=22.14 Aligned_cols=63 Identities=14% Similarity=0.199 Sum_probs=43.5
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCCee-EEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEEE
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPGLL-SVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVETM 69 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~GV~-sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aeiv 69 (101)
++++.++|.+.+..++...|++..|.- +.+..... +.+.+.|.+ .-..+...||..+ |.+.+.
T Consensus 3 i~~~~I~~p~~~~g~V~~~l~~rrg~i~~~~~~~~~-~~~~i~~~iP~~e~~~~~~~Lrs~T~G~~~~~ 70 (80)
T cd04096 3 IYLVEIQCPEDALGKVYSVLSKRRGHVLSEEPKEGT-PLFEIKAYLPVIESFGFETDLRSATSGQAFPQ 70 (80)
T ss_pred EEEEEEEEcHHHhhHHHHhhhhCeeEEeEEeecCCC-ccEEEEEEEeHHHHhCcHHHHHhhCCCCcEEE
Confidence 456677776788999999999999944 33332222 468899995 5566778888766 466543
No 21
>cd03711 Tet_C Tet_C: C-terminus of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to the C terminal domains of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=71.50 E-value=21 Score=22.05 Aligned_cols=61 Identities=11% Similarity=0.055 Sum_probs=44.9
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEE
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVET 68 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aei 68 (101)
++++.+.|.+....++...|++..|.-. .++..+ +...+.|.+ +...+...||..+ |.+.+
T Consensus 3 i~~~~i~~p~~~~g~v~~~l~~rrg~i~-~~~~~~-~~~~i~~~~P~~~~~g~~~~Lr~~T~G~~~~ 67 (78)
T cd03711 3 YLRFELEVPQDALGRAMSDLAKMGATFE-DPQIKG-DEVTLEGTIPVATSQDYQSELPSYTHGEGVL 67 (78)
T ss_pred eEEEEEEcCHHHHHHHHHHHHHcCCEee-CcEecC-CEEEEEEEECHHHHhhHHHHhHhhcCCeEEE
Confidence 4567777778899999999999999443 233334 688999994 6667788888877 46654
No 22
>cd03713 EFG_mtEFG_C EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide
Probab=70.89 E-value=22 Score=21.86 Aligned_cols=61 Identities=7% Similarity=0.070 Sum_probs=45.2
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCCee-EEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEEE
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPGLL-SVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVETM 69 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~GV~-sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aeiv 69 (101)
++++.++|.+....+++..|++..|.- +.+. . . +...+.|.+ ....+...||..+ |+|.+.
T Consensus 3 i~~~~I~~p~~~~g~v~~~l~~rrg~i~~~~~-~-~-~~~~i~~~iP~~e~~~~~~~Lr~~T~G~a~~~ 68 (78)
T cd03713 3 IMKVEVTVPEEYMGDVIGDLSSRRGQILGTES-R-G-GWKVIKAEVPLAEMFGYSTDLRSLTQGRGSFT 68 (78)
T ss_pred EEEEEEEcCHHHHHHHHHHHHHcCCceEceec-c-C-CcEEEEEEcCHHHHhChHHHHHhhcCCeEEEE
Confidence 467888887889999999999999943 3332 2 3 578999994 5666788888877 466553
No 23
>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=69.27 E-value=19 Score=21.39 Aligned_cols=31 Identities=10% Similarity=0.154 Sum_probs=23.2
Q ss_pred EEEEEeCCChHh-hHHHHHHHHcCCCCeeEEEe
Q 047835 5 ILYRLDNMHSPK-CRTKAFKIIAGFPGLLSVAM 36 (101)
Q Consensus 5 vvlKV~m~C~e~-C~~Kv~k~l~~~~GV~sV~i 36 (101)
+.+-+..+. .. --..+++.|.+++||.+|.+
T Consensus 43 i~~~v~v~~-~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 43 VTISIDTST-MNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEcCc-hHHHHHHHHHHHhcCCCeEEEEE
Confidence 445555565 44 77889999999999999875
No 24
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=68.22 E-value=18 Score=22.08 Aligned_cols=31 Identities=16% Similarity=0.338 Sum_probs=25.5
Q ss_pred eEEEEEeCCChHhhHHHHHHHHcCCCCeeEEE
Q 047835 4 KILYRLDNMHSPKCRTKAFKIIAGFPGLLSVA 35 (101)
Q Consensus 4 ~vvlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~ 35 (101)
.+.|.+.+.. -.--..+++.|.+++||.+|+
T Consensus 49 ~~~l~v~V~d-~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 49 RITLTVEVKD-LEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEEEEESS-HHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEEEEECC-HHHHHHHHHHHHCCCCeeEEE
Confidence 4566777777 777889999999999999885
No 25
>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=67.96 E-value=20 Score=22.97 Aligned_cols=33 Identities=21% Similarity=0.409 Sum_probs=26.5
Q ss_pred eEEEEEeCCChHhhHHHHHHHHcCCCCeeEEEec
Q 047835 4 KILYRLDNMHSPKCRTKAFKIIAGFPGLLSVAMK 37 (101)
Q Consensus 4 ~vvlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id 37 (101)
++|+-+.-.. .+-....++.|..++||.|+.+-
T Consensus 40 KiVVtiE~~~-~~~~~~~~~~i~~l~GVlsa~lv 72 (79)
T PF03927_consen 40 KIVVTIEAES-SEEEVDLIDAINALPGVLSASLV 72 (79)
T ss_dssp EEEEEEEESS-HHHHHHHHHHHCCSTTEEEEEES
T ss_pred eEEEEEEeCC-hHHHHHHHHHHHcCCCceEEEEE
Confidence 5666677677 78888889999999999998763
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=62.01 E-value=5.2 Score=23.61 Aligned_cols=33 Identities=9% Similarity=0.269 Sum_probs=16.6
Q ss_pred HHHHHHcC---CCCeeEEEecCCCCCcEEEEEEccHHH
Q 047835 20 KAFKIIAG---FPGLLSVAMKGDDLRHMEVIGDIDEVA 54 (101)
Q Consensus 20 Kv~k~l~~---~~GV~sV~id~~~k~kvtV~G~vDp~~ 54 (101)
+++..|.. +++- .|.+...+ +.|+++|.++-..
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v~~-g~v~L~G~v~s~~ 38 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSVEN-GVVTLSGEVPSQE 38 (64)
T ss_dssp ----------CTT-T-TEEEEEEC-TEEEEEEEESSCH
T ss_pred ccccccccccccCCC-eEEEEEEC-CEEEEEeeCcHHH
Confidence 44455554 4554 56666655 8999999984333
No 27
>cd01514 Elongation_Factor_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p. This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain. EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the
Probab=61.03 E-value=36 Score=20.84 Aligned_cols=63 Identities=11% Similarity=0.152 Sum_probs=45.6
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCCe-eEEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEEEe
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPGL-LSVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVETMK 70 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~GV-~sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aeivs 70 (101)
++.+.++|.+....++...|++..|. .+..... . +...+.|.+ +...+-..||..+ |.+.+.+
T Consensus 3 i~~~~I~~p~~~~g~v~~~l~~rrg~v~~~~~~~-~-~~~~i~~~iP~~e~~g~~~~lr~~T~G~~~~~~ 70 (79)
T cd01514 3 IMKVEITVPEEYLGAVIGDLSKRRGEILGMEPRG-T-GRVVIKAELPLAEMFGFATDLRSLTQGRASFSM 70 (79)
T ss_pred EEEEEEEcCHHHHHHHHHHHHhcCCeeEeeEecC-C-CeEEEEEECCHHHHcCcHHHhhhhcCCeEEEEE
Confidence 45677777788899999999999994 4444333 2 588999994 5566778888777 4666543
No 28
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=57.85 E-value=16 Score=24.53 Aligned_cols=35 Identities=9% Similarity=0.010 Sum_probs=27.8
Q ss_pred eEEEEEeCCChHhhHHHHHHHHcCCCCeeEEEecC
Q 047835 4 KILYRLDNMHSPKCRTKAFKIIAGFPGLLSVAMKG 38 (101)
Q Consensus 4 ~vvlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id~ 38 (101)
.+.|.+-|...+|--..+...++.++||+|+++-.
T Consensus 50 al~l~vvv~D~Eg~td~~ee~l~~vegV~sveve~ 84 (88)
T COG2092 50 ALKLYVVVEDKEGGTDALEEALEEVEGVESVEVEN 84 (88)
T ss_pred eEEEEEEEcccccCcHHHHHHHhhccCcceEEEEE
Confidence 34555666665787889999999999999999854
No 29
>cd04097 mtEFG1_C mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals (desig
Probab=57.15 E-value=44 Score=20.60 Aligned_cols=61 Identities=10% Similarity=0.200 Sum_probs=44.3
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCCee-EEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEEE
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPGLL-SVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVETM 69 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~GV~-sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aeiv 69 (101)
++++.+.|.+....+++..|++..|.- +.+ ..+ +.+.+.|.+ +...+.+.||..+ |.+.+.
T Consensus 3 i~~~~I~~p~~~~g~v~~~l~~rrg~i~~~~--~~~-~~~~i~~~~P~~e~~g~~~~Lr~~T~G~~~~~ 68 (78)
T cd04097 3 IMKVEVTAPTEFQGNVIGLLNKRKGTIVDTD--TGE-DEFTLEAEVPLNDMFGYSTELRSMTQGKGEFS 68 (78)
T ss_pred EEEEEEEecHHHHHHHHHHHHHCCCEEeceE--ecC-CeEEEEEEECHHHhhChHHHHHhhCCCcEEEE
Confidence 456777776788999999999999943 433 223 578899994 6666788888877 466543
No 30
>cd03710 BipA_TypA_C BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secreti
Probab=54.39 E-value=50 Score=20.47 Aligned_cols=62 Identities=8% Similarity=0.050 Sum_probs=43.7
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCC-eeEEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEEE
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPG-LLSVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVETM 69 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~G-V~sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aeiv 69 (101)
+++|.+.|.+.+..+|+..|++..| +.+.+... + +...+.|.+ ....+...||..+ |.+.+-
T Consensus 3 i~~v~I~~P~~~~g~V~~~l~~rrg~i~~~~~~~-~-~~~~i~~~~P~~~~~~~~~~Lrs~T~G~a~~~ 69 (79)
T cd03710 3 IEELTIDVPEEYSGAVIEKLGKRKGEMVDMEPDG-N-GRTRLEFKIPSRGLIGFRSEFLTDTRGTGIMN 69 (79)
T ss_pred EEEEEEEeCchhhHHHHHHHHhCCCEEEccEECC-C-CEEEEEEEECHHHHcCcHHHHHhhCCCeEEEE
Confidence 3566667767888899999999999 44555432 2 578899995 5556678888766 466543
No 31
>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=50.37 E-value=56 Score=21.19 Aligned_cols=41 Identities=20% Similarity=0.238 Sum_probs=29.6
Q ss_pred HHHHHHHcCCCCeeEEEecCCCCCcEEEEEE--ccHHHHHHHHHhc
Q 047835 19 TKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD--IDEVALANMLRRK 62 (101)
Q Consensus 19 ~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~--vDp~~l~~~LrKk 62 (101)
.-.-+.|-.++||.+|-+.. +=+||+-. +|=..|...++..
T Consensus 37 spLA~~Lf~i~gV~~Vf~~~---dfItVtK~~~~~W~~l~~~I~~~ 79 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFIGD---DFITVTKNPDADWEDLKPEIREV 79 (87)
T ss_dssp -HHHHHHHTSTTEEEEEEET---TEEEEEE-TTS-HHHHHHHHHHH
T ss_pred CHHHHHhcCCCCEeEEEEEC---CEEEEeeCCCCCHHHHHHHHHHH
Confidence 33445555999999999976 68899877 8888888777653
No 32
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=49.83 E-value=49 Score=19.98 Aligned_cols=30 Identities=10% Similarity=0.067 Sum_probs=19.6
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCCeeEEEe
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPGLLSVAM 36 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~i 36 (101)
-+.+.... -.--..+++.|.+++||.+|+-
T Consensus 40 ~l~i~v~~-~~~L~~li~~L~~i~gV~~V~R 69 (74)
T cd04877 40 YLNFPTIE-FEKLQTLMPEIRRIDGVEDVKT 69 (74)
T ss_pred EEEeEecC-HHHHHHHHHHHhCCCCceEEEE
Confidence 34444444 4445778888888888887753
No 33
>PF09358 UBA_e1_C: Ubiquitin-activating enzyme e1 C-terminal domain; InterPro: IPR018965 This presumed domain found at the C terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterised. ; PDB: 3CMM_A.
Probab=49.59 E-value=29 Score=24.07 Aligned_cols=38 Identities=21% Similarity=0.249 Sum_probs=29.0
Q ss_pred EEecCCCCCcEEEEEEccHHHHHHHHHhccC-ceEEEecCC
Q 047835 34 VAMKGDDLRHMEVIGDIDEVALANMLRRKIG-YVETMKLDI 73 (101)
Q Consensus 34 V~id~~~k~kvtV~G~vDp~~l~~~LrKk~~-~aeivsv~p 73 (101)
.++... +++.|.|++.-.++++.++++++ .+..++.+.
T Consensus 29 ~~~T~W--Dr~~v~~~~Tl~~li~~~~~~~~lev~ml~~g~ 67 (125)
T PF09358_consen 29 KEWTLW--DRIEVNGDMTLQELIDYFKEKYGLEVTMLSQGV 67 (125)
T ss_dssp EEETTT---EEEEES--BHHHHHHHHHHTTS-EEEEEEETT
T ss_pred ccccce--eEEEEcCCCCHHHHHHHHHHHhCceEEEEEeCC
Confidence 345555 59999999999999999999987 888888764
No 34
>PRK11023 outer membrane lipoprotein; Provisional
Probab=49.50 E-value=24 Score=25.95 Aligned_cols=44 Identities=5% Similarity=0.040 Sum_probs=31.9
Q ss_pred HhhHHHHHHHHcCCCCee---EEEecCCCCCcEEEEEEccHHHHHHHH
Q 047835 15 PKCRTKAFKIIAGFPGLL---SVAMKGDDLRHMEVIGDIDEVALANML 59 (101)
Q Consensus 15 e~C~~Kv~k~l~~~~GV~---sV~id~~~k~kvtV~G~vDp~~l~~~L 59 (101)
..=..++...|..-+++. .|.+...+ +.|+.+|.|+-.....+.
T Consensus 48 ~~i~~~V~~aL~~~~~l~~~~~I~V~v~~-G~V~L~G~V~~~~~k~~A 94 (191)
T PRK11023 48 GTLELRVNNALSKDEQIKKEARINVTAYQ-GKVLLTGQSPNAELSERA 94 (191)
T ss_pred HHHHHHHHHHHhhCcccCcCceEEEEEEC-CEEEEEEEeCCHHHHHHH
Confidence 445778888887777664 58888876 899999998665544333
No 35
>PF05193 Peptidase_M16_C: Peptidase M16 inactive domain; InterPro: IPR007863 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. The peptidases in this group of sequences include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The mitochondrial processing peptidase consists of two structurally related domains. One is the active peptidase whereas the other, the C-terminal region, is inactive. The two domains hold the substrate like a clamp [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B 1SQX_B 1NU1_B 1L0L_B 2FYU_B ....
Probab=49.32 E-value=16 Score=24.13 Aligned_cols=23 Identities=26% Similarity=0.590 Sum_probs=19.5
Q ss_pred CcEEEEEEccHHHHHHHHHhccC
Q 047835 42 RHMEVIGDIDEVALANMLRRKIG 64 (101)
Q Consensus 42 ~kvtV~G~vDp~~l~~~LrKk~~ 64 (101)
-.+.++|++|+..+.+.+.+.++
T Consensus 20 ~~l~i~Gd~~~~~~~~~i~~~~~ 42 (184)
T PF05193_consen 20 MTLVIVGDIDPDELEKLIEKYFG 42 (184)
T ss_dssp EEEEEEESSGHHHHHHHHHHHHT
T ss_pred eEEEEEcCccHHHHHHHHHhhhh
Confidence 37889999999999999987654
No 36
>PF02107 FlgH: Flagellar L-ring protein; InterPro: IPR000527 The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body []. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament []. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have an extensive beta-sheet structure, in keeping with other outer membrane proteins [].; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0009427 bacterial-type flagellum basal body, distal rod, L ring
Probab=49.12 E-value=13 Score=27.37 Aligned_cols=29 Identities=10% Similarity=0.273 Sum_probs=25.8
Q ss_pred CCCCeeEEEecCCCCCcEEEEEEccHHHHH
Q 047835 27 GFPGLLSVAMKGDDLRHMEVIGDIDEVALA 56 (101)
Q Consensus 27 ~~~GV~sV~id~~~k~kvtV~G~vDp~~l~ 56 (101)
.++|-+.|.++.+. +.+++.|.|.|.++.
T Consensus 110 ~I~G~k~i~vn~e~-~~i~lsGiVRp~DI~ 138 (179)
T PF02107_consen 110 VIEGEKQIRVNGEE-QYIRLSGIVRPEDID 138 (179)
T ss_pred EEEEEEEEEECCCE-EEEEEEEEECHHHCC
Confidence 57889999999976 899999999999975
No 37
>PRK09577 multidrug efflux protein; Reviewed
Probab=46.04 E-value=39 Score=30.97 Aligned_cols=43 Identities=19% Similarity=0.257 Sum_probs=32.0
Q ss_pred HHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHH----------HHHHHHhcc
Q 047835 18 RTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVA----------LANMLRRKI 63 (101)
Q Consensus 18 ~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~----------l~~~LrKk~ 63 (101)
...+...|.+++||.+|++++.+ ..+.| ++||.+ +.+.|+...
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e-~~v~V--~vD~~kl~~~Gls~~~V~~~l~~~n 210 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAE-YAMRI--WPDPVKLAALGLTASDIASAVRAHN 210 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCc-eEEEE--EeCHHHHHHcCCCHHHHHHHHHHhC
Confidence 56789999999999999999854 45555 355554 667787643
No 38
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=45.62 E-value=41 Score=30.82 Aligned_cols=43 Identities=9% Similarity=0.220 Sum_probs=31.9
Q ss_pred hHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccH----------HHHHHHHHhc
Q 047835 17 CRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDE----------VALANMLRRK 62 (101)
Q Consensus 17 C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp----------~~l~~~LrKk 62 (101)
-++.++..|.+++||.+|++.+.. ..+.|. +|| .++.+.|+..
T Consensus 158 ~~~~l~~~L~~v~GV~~V~~~G~~-~ei~V~--vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 158 VASNIQDPLSRVNGVGDIDAYGSQ-YSMRIW--LDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHHhhcCCCeEEEEEcCCc-eEEEEE--ECHHHHHHcCCCHHHHHHHHHHh
Confidence 356788999999999999999854 455554 555 5567788753
No 39
>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=43.91 E-value=38 Score=22.45 Aligned_cols=32 Identities=16% Similarity=0.101 Sum_probs=24.1
Q ss_pred EEEeCCChHhhHHHHHHHHcCCCCeeEEEecC
Q 047835 7 YRLDNMHSPKCRTKAFKIIAGFPGLLSVAMKG 38 (101)
Q Consensus 7 lKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id~ 38 (101)
+-+-|...++--..+..++++++||+|+++..
T Consensus 53 ~~~vv~D~~g~td~lee~i~~ve~V~svev~~ 84 (88)
T TIGR00489 53 VMVVMGDAEGGTEAAEESLSGIEGVESVEVTD 84 (88)
T ss_pred EEEEEecCCcChHHHHHHHhcCCCccEEEEEE
Confidence 33444442466789999999999999999865
No 40
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=43.14 E-value=38 Score=22.79 Aligned_cols=30 Identities=30% Similarity=0.235 Sum_probs=26.3
Q ss_pred cEEEEEEccHHHHHHHHHhccCceEEEecC
Q 047835 43 HMEVIGDIDEVALANMLRRKIGYVETMKLD 72 (101)
Q Consensus 43 kvtV~G~vDp~~l~~~LrKk~~~aeivsv~ 72 (101)
-+.|+|+-|=.-++++||..+..+.+++..
T Consensus 103 ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~ 132 (149)
T cd06167 103 IVLVSGDSDFVPLVERLRELGKRVIVVGFE 132 (149)
T ss_pred EEEEECCccHHHHHHHHHHcCCEEEEEccC
Confidence 567799999999999999988888888876
No 41
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=42.99 E-value=35 Score=22.59 Aligned_cols=34 Identities=12% Similarity=0.018 Sum_probs=25.1
Q ss_pred EEEEEeCCChHhhHHHHHHHHcCCCCeeEEEecC
Q 047835 5 ILYRLDNMHSPKCRTKAFKIIAGFPGLLSVAMKG 38 (101)
Q Consensus 5 vvlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id~ 38 (101)
+.+.+-+.+.++-...+...+++++||+|+++..
T Consensus 51 L~i~~vv~D~~~~td~lee~i~~~e~Vqsvei~~ 84 (88)
T PRK00435 51 LKLYVIMPDEEGGTEPVEEAFANVEGVESVEVEE 84 (88)
T ss_pred EEEEEEEEcCCcCcHHHHHHHhccCCCcEEEEEE
Confidence 3344444442477788999999999999999865
No 42
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=42.97 E-value=36 Score=24.78 Aligned_cols=31 Identities=26% Similarity=0.188 Sum_probs=27.2
Q ss_pred cEEEEEEccHHHHHHHHHhccCceEEEecCC
Q 047835 43 HMEVIGDIDEVALANMLRRKIGYVETMKLDI 73 (101)
Q Consensus 43 kvtV~G~vDp~~l~~~LrKk~~~aeivsv~p 73 (101)
-+.++|+-|=.-+++.++.+++.+.++++++
T Consensus 114 ivl~SgD~DF~p~v~~~~~~G~rv~v~~~~~ 144 (181)
T COG1432 114 IVLFSGDGDFIPLVEAARDKGKRVEVAGIEP 144 (181)
T ss_pred EEEEcCCccHHHHHHHHHHcCCEEEEEecCC
Confidence 5667899888888999999999999999887
No 43
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=41.77 E-value=44 Score=24.49 Aligned_cols=30 Identities=13% Similarity=0.015 Sum_probs=26.1
Q ss_pred cEEEEEEccHHHHHHHHHhccCceEEEecC
Q 047835 43 HMEVIGDIDEVALANMLRRKIGYVETMKLD 72 (101)
Q Consensus 43 kvtV~G~vDp~~l~~~LrKk~~~aeivsv~ 72 (101)
=+.|+|+-|=.-|+.+||..+..+..++++
T Consensus 109 ~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~ 138 (160)
T TIGR00288 109 VALVTRDADFLPVINKAKENGKETIVIGAE 138 (160)
T ss_pred EEEEeccHhHHHHHHHHHHCCCEEEEEeCC
Confidence 567899999999999999988788888863
No 44
>COG0612 PqqL Predicted Zn-dependent peptidases [General function prediction only]
Probab=41.47 E-value=33 Score=27.49 Aligned_cols=23 Identities=22% Similarity=0.550 Sum_probs=20.5
Q ss_pred CcEEEEEEccHHHHHHHHHhccC
Q 047835 42 RHMEVIGDIDEVALANMLRRKIG 64 (101)
Q Consensus 42 ~kvtV~G~vDp~~l~~~LrKk~~ 64 (101)
=.|.|+|++|+.++...+.+.++
T Consensus 199 ~~l~vvGdi~~~~v~~~~~~~f~ 221 (438)
T COG0612 199 MVLVVVGDVDAEEVVELIEKYFG 221 (438)
T ss_pred eEEEEecCCCHHHHHHHHHHHHc
Confidence 37888999999999999999775
No 45
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=40.79 E-value=53 Score=30.23 Aligned_cols=41 Identities=15% Similarity=0.218 Sum_probs=30.4
Q ss_pred HHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHH----------HHHHHHh
Q 047835 18 RTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVA----------LANMLRR 61 (101)
Q Consensus 18 ~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~----------l~~~LrK 61 (101)
...++..|.+++||.+|++.+.. ..+.|. +||.+ +.+.|+.
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~-~ei~V~--vDp~kl~~~gls~~~V~~~l~~ 209 (1049)
T PRK15127 159 AANMKDPISRTSGVGDVQLFGSQ-YAMRIW--MNPNELNKFQLTPVDVINAIKA 209 (1049)
T ss_pred HHHHHHHHhcCCCceEEEEcCCc-eEEEEE--eCHHHHHHcCCCHHHHHHHHHH
Confidence 35688999999999999998863 455554 56655 5666774
No 46
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=39.26 E-value=56 Score=30.00 Aligned_cols=41 Identities=15% Similarity=0.265 Sum_probs=31.4
Q ss_pred HHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccH----------HHHHHHHHh
Q 047835 18 RTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDE----------VALANMLRR 61 (101)
Q Consensus 18 ~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp----------~~l~~~LrK 61 (101)
...+...|.+++||.+|++.+. ...+.|. +|| .++.+.|+.
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~-~~ei~V~--vD~~kl~~~gls~~dV~~~i~~ 209 (1044)
T TIGR00915 159 ASNMVDPISRLEGVGDVQLFGS-QYAMRIW--LDPAKLNSYQLTPADVISAIQA 209 (1044)
T ss_pred HHHHHHHHhCCCCceEEEecCC-ceEEEEE--ECHHHHHHcCCCHHHHHHHHHH
Confidence 4578999999999999999987 4566664 555 556677776
No 47
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=38.64 E-value=40 Score=22.27 Aligned_cols=30 Identities=27% Similarity=0.181 Sum_probs=20.9
Q ss_pred CcEEEEEEccHHHHHHHHHhccCceEEEec
Q 047835 42 RHMEVIGDIDEVALANMLRRKIGYVETMKL 71 (101)
Q Consensus 42 ~kvtV~G~vDp~~l~~~LrKk~~~aeivsv 71 (101)
.-+.|+|+-|=.-++++||.++..+.++..
T Consensus 98 ~ivLvSgD~Df~~~v~~l~~~g~~V~v~~~ 127 (146)
T PF01936_consen 98 TIVLVSGDSDFAPLVRKLRERGKRVIVVGA 127 (146)
T ss_dssp EEEEE---GGGHHHHHHHHHH--EEEEEE-
T ss_pred EEEEEECcHHHHHHHHHHHHcCCEEEEEEe
Confidence 467789999999999999987778888874
No 48
>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=37.98 E-value=40 Score=20.23 Aligned_cols=32 Identities=19% Similarity=0.218 Sum_probs=23.6
Q ss_pred CcEEEEEE-ccHHHHHHHHHhcc---C--ceEEEecCC
Q 047835 42 RHMEVIGD-IDEVALANMLRRKI---G--YVETMKLDI 73 (101)
Q Consensus 42 ~kvtV~G~-vDp~~l~~~LrKk~---~--~aeivsv~p 73 (101)
+.++|+|. -+|.++...|.++. | +-.|+++..
T Consensus 6 G~Isvs~~~~s~~d~~~~la~kAd~~GA~~y~I~~~~~ 43 (56)
T PF07338_consen 6 GTISVSGNFGSPDDAEEALAKKADEKGAKYYRITSASE 43 (56)
T ss_dssp EEEEEEEECSSHHHHHHHHHHHHHHTT-SEEEEEEEEE
T ss_pred EEEEEccccCCHHHHHHHHHHHHHHcCCCEEEEEEEEc
Confidence 58999999 79999999998765 2 344555543
No 49
>PHA00514 dsDNA binding protein
Probab=37.38 E-value=62 Score=22.00 Aligned_cols=34 Identities=12% Similarity=0.246 Sum_probs=28.4
Q ss_pred CcEEEEEEccHHHHHHHHHhcc--CceEEEecCCCC
Q 047835 42 RHMEVIGDIDEVALANMLRRKI--GYVETMKLDILD 75 (101)
Q Consensus 42 ~kvtV~G~vDp~~l~~~LrKk~--~~aeivsv~p~k 75 (101)
+-.|..|+..-..--+.|.|+. +.+.++|++|.-
T Consensus 32 ~~~Tl~GNLtiEqAQ~e~~k~~k~~pvqVvsVEpnt 67 (98)
T PHA00514 32 NEQTLLGNLTIEQAQKELSKQYKHGPVQVVSVEPNT 67 (98)
T ss_pred CcceeecceeHHHHHHHHhhcccCCCeeEEEecCCC
Confidence 4668999998889889998885 589999998864
No 50
>PRK09579 multidrug efflux protein; Reviewed
Probab=37.38 E-value=65 Score=29.53 Aligned_cols=43 Identities=19% Similarity=0.297 Sum_probs=30.9
Q ss_pred HHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccH----------HHHHHHHHhc
Q 047835 18 RTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDE----------VALANMLRRK 62 (101)
Q Consensus 18 ~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp----------~~l~~~LrKk 62 (101)
.+.++..|.+++||.+|++.+.....+.| ++|| .++.+.|+..
T Consensus 158 ~~~i~~~L~~i~GV~~V~~~G~~~~ei~V--~vd~~kl~~~gls~~dV~~al~~~ 210 (1017)
T PRK09579 158 SRVIQPKLATLPGMAEAEILGNQVFAMRL--WLDPVKLAGFGLSAGDVTQAVRRY 210 (1017)
T ss_pred HHHHHHHhhcCCCceEEEecCCCceEEEE--EeCHHHHHHcCCCHHHHHHHHHHh
Confidence 45688999999999999998865334444 2555 5567778663
No 51
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=36.73 E-value=1.2e+02 Score=19.87 Aligned_cols=55 Identities=15% Similarity=0.155 Sum_probs=36.9
Q ss_pred HhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEE-ccHHH---HHHHHHhccC--ceEEEe
Q 047835 15 PKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD-IDEVA---LANMLRRKIG--YVETMK 70 (101)
Q Consensus 15 e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~-vDp~~---l~~~LrKk~~--~aeivs 70 (101)
..=...+.+.|..++|++=-..|.+. ||+.|+=+ -+... .++.|+.--| .|.++-
T Consensus 16 Pe~~~~V~~~l~~ipg~Evh~~d~~~-GKiVVtiE~~~~~~~~~~i~~I~~l~GVlsa~lVY 76 (87)
T PRK10553 16 SERISDISTQLNAFPGCEVAVSDAPS-GQLIVVVEAEDSETLLQTIESVRNVEGVLAVSLVY 76 (87)
T ss_pred hHHHHHHHHHHHcCCCcEEEeecCCC-CeEEEEEEeCChHHHHHHHHHHHcCCCceEEEEEE
Confidence 44467889999999999988887755 78887655 34444 4445554334 555554
No 52
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=36.37 E-value=77 Score=22.30 Aligned_cols=54 Identities=17% Similarity=0.212 Sum_probs=34.6
Q ss_pred HhhHHHHHHHHcCCCCee--EEEecCCCCCcEEEEEEccHHHHHHHHHhccCceEEEe
Q 047835 15 PKCRTKAFKIIAGFPGLL--SVAMKGDDLRHMEVIGDIDEVALANMLRRKIGYVETMK 70 (101)
Q Consensus 15 e~C~~Kv~k~l~~~~GV~--sV~id~~~k~kvtV~G~vDp~~l~~~LrKk~~~aeivs 70 (101)
+.-++++.+.|++ .|.. .+.+...+ |.||+.|.+.-..-..++....+++.-++
T Consensus 25 ~~~~~~i~~~i~~-~~~~~~~i~V~v~~-G~v~l~G~v~s~~~~~~~~~aa~~v~GV~ 80 (147)
T PRK11198 25 EDAADALKEHISK-QGLGDADVNVQVED-GKATVSGDAASQEAKEKILLAVGNIQGIA 80 (147)
T ss_pred HHHHHHHHHHHHh-cCCCcCCceEEEeC-CEEEEEEEeCCHHHHHHHHHHhccCCCcc
Confidence 3446677777765 4433 23444434 89999999877777777766565555443
No 53
>PRK13760 putative RNA-associated protein; Provisional
Probab=36.10 E-value=1.7e+02 Score=22.70 Aligned_cols=61 Identities=16% Similarity=0.132 Sum_probs=42.4
Q ss_pred eEEEEEeCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccH---HHHHHHHHhcc-CceEE
Q 047835 4 KILYRLDNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDE---VALANMLRRKI-GYVET 68 (101)
Q Consensus 4 ~vvlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp---~~l~~~LrKk~-~~aei 68 (101)
++.+.|.+.- .-..++...|.++-.|.+-+.+. + |.++.++.+|| ..+.+.|++.+ |.+++
T Consensus 163 ~~~~~v~iP~--~~~~~~~~~l~~~~~i~~eew~~-d-gs~~~v~~Ip~G~~~~~~~~~~~~tkG~~~~ 227 (231)
T PRK13760 163 KARIAVKIPP--EYAGKAYGELRKFGEIKKEEWQS-D-GSWIAVLEIPAGLQNEFYDKLNKLTKGEAET 227 (231)
T ss_pred eEEEEEEECH--HHHHHHHHHHHhhcccchhhccC-C-CcEEEEEEECCccHHHHHHHHHHhcCCcEEE
Confidence 4555666653 44778888888877777777765 3 57899999988 56778887766 35544
No 54
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=35.77 E-value=67 Score=21.99 Aligned_cols=29 Identities=28% Similarity=0.414 Sum_probs=23.6
Q ss_pred EEecCCCCCcEEEEEEccHHHHHHHHHhccC
Q 047835 34 VAMKGDDLRHMEVIGDIDEVALANMLRRKIG 64 (101)
Q Consensus 34 V~id~~~k~kvtV~G~vDp~~l~~~LrKk~~ 64 (101)
..+|.+ +++++.|.+++..+-+.|++...
T Consensus 50 g~id~~--~rlii~G~~~~~~i~~~l~~yI~ 78 (110)
T smart00653 50 GSIDGK--GRLIVNGRFTPKKLQDLLRRYIK 78 (110)
T ss_pred eeECCC--CeEEEEEeeCHHHHHHHHHHHHH
Confidence 355653 79999999999999999988553
No 55
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=35.70 E-value=40 Score=23.02 Aligned_cols=38 Identities=18% Similarity=0.359 Sum_probs=27.7
Q ss_pred HHHcCCCCeeEEEecCCCCCcEEEEEE-----ccHHHHHHHHHh
Q 047835 23 KIIAGFPGLLSVAMKGDDLRHMEVIGD-----IDEVALANMLRR 61 (101)
Q Consensus 23 k~l~~~~GV~sV~id~~~k~kvtV~G~-----vDp~~l~~~LrK 61 (101)
++++.++|+..|++..+. .++-|.|. .|..+.++.+++
T Consensus 34 ~ivas~pgis~ieik~E~-kkL~v~t~~~~~d~~~l~~~ktynd 76 (96)
T COG4004 34 RIVASSPGISRIEIKPEN-KKLLVNTTDYTDDETKLQTAKTYND 76 (96)
T ss_pred EEEEecCCceEEEEeccc-ceEEEecccccCchhHHHHHHHHHH
Confidence 567889999999999976 79999883 344444444444
No 56
>PF05922 Inhibitor_I9: Peptidase inhibitor I9; InterPro: IPR010259 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes []. The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route []. The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus. Proteinase propeptide inhibitors (sometimes refered to as activation peptides) are responsible for the modulation of folding and activity of the pro-enzyme or zymogen. The pro-segment docks into the enzyme moiety shielding the substrate binding site, thereby promoting inhibition of the enzyme. Several such propeptides share a similar topology [], despite often low sequence identities []. The propeptide region has an open-sandwich antiparallel-alpha/antiparallel-beta fold, with two alpha-helices and four beta-strands with a (beta/alpha/beta)x2 topology. This group of sequences contain the propeptide domain at the N terminus of peptidases belonging to MEROPS family S8A, subtilisins. A number of the members of this group of sequences belong to MEROPS inhibitor family I9, clan I-. The propeptide is removed by proteolytic cleavage; removal activating the enzyme.; GO: 0004252 serine-type endopeptidase activity, 0042802 identical protein binding, 0043086 negative regulation of catalytic activity; PDB: 3CNQ_P 1SPB_P 3CO0_P 1ITP_A 1V5I_B 1SCJ_B 3P5B_P 2XTJ_P 2W2M_P 2P4E_P ....
Probab=35.18 E-value=51 Score=19.78 Aligned_cols=19 Identities=21% Similarity=0.256 Sum_probs=16.2
Q ss_pred HHHHHHcCCCCeeEEEecC
Q 047835 20 KAFKIIAGFPGLLSVAMKG 38 (101)
Q Consensus 20 Kv~k~l~~~~GV~sV~id~ 38 (101)
...+.|++.+||.+|+-|.
T Consensus 59 ~~i~~L~~~p~V~~Ve~D~ 77 (82)
T PF05922_consen 59 EEIEKLRKDPGVKSVEPDQ 77 (82)
T ss_dssp HHHHHHHTSTTEEEEEEEC
T ss_pred HHHHHHHcCCCeEEEEeCc
Confidence 4568899999999999975
No 57
>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=34.44 E-value=73 Score=20.44 Aligned_cols=34 Identities=18% Similarity=0.330 Sum_probs=23.3
Q ss_pred eEEEEEeCCChHhh------HHHHHHHHcCCCCeeEEEecC
Q 047835 4 KILYRLDNMHSPKC------RTKAFKIIAGFPGLLSVAMKG 38 (101)
Q Consensus 4 ~vvlKV~m~C~e~C------~~Kv~k~l~~~~GV~sV~id~ 38 (101)
.+.+.+.+.. .+| ...+..+++.++|++++.+..
T Consensus 38 ~v~i~l~l~~-p~~~~~~~l~~~i~~al~~l~gv~~v~v~i 77 (99)
T TIGR02945 38 HVDIQMTLTA-PNCPVAGSMPGEVENAVRAVPGVGSVTVEL 77 (99)
T ss_pred eEEEEEEECC-CCCChHHHHHHHHHHHHHhCCCCceEEEEE
Confidence 3445555543 333 456888999999999998865
No 58
>PF05137 PilN: Fimbrial assembly protein (PilN); InterPro: IPR007813 PilN is a plasmid-encoded, lipoprotein which locates to the outer membrane of bacteria and are part of a thin pilus required only for liquid mating [].
Probab=33.94 E-value=1.1e+02 Score=18.28 Aligned_cols=42 Identities=19% Similarity=0.265 Sum_probs=25.6
Q ss_pred eeEEEecCCCCCcEEEEEE-ccHHHHHHHHH---hcc--CceEEEecCCCC
Q 047835 31 LLSVAMKGDDLRHMEVIGD-IDEVALANMLR---RKI--GYVETMKLDILD 75 (101)
Q Consensus 31 V~sV~id~~~k~kvtV~G~-vDp~~l~~~Lr---Kk~--~~aeivsv~p~k 75 (101)
+++++++. ++|++.|. -+...|...++ +.- ..+.+.++....
T Consensus 16 l~~l~~~~---~~l~i~G~a~~~~~v~~f~~~L~~~~~f~~v~l~~~~~~~ 63 (78)
T PF05137_consen 16 LTSLSING---NTLSISGYADSYQSVAAFLRNLEQSPFFSDVSLSSISRQE 63 (78)
T ss_pred EEEEEEeC---CEEEEEEEECCHHHHHHHHHHHhhCCCccceEEEEEEeec
Confidence 45666654 69999999 46666555444 322 366666665444
No 59
>PRK11023 outer membrane lipoprotein; Provisional
Probab=33.65 E-value=1.4e+02 Score=21.92 Aligned_cols=40 Identities=10% Similarity=0.073 Sum_probs=27.9
Q ss_pred HhhHHHHHHHHcCCCCee--EEEecCCCCCcEEEEEEccHHHH
Q 047835 15 PKCRTKAFKIIAGFPGLL--SVAMKGDDLRHMEVIGDIDEVAL 55 (101)
Q Consensus 15 e~C~~Kv~k~l~~~~GV~--sV~id~~~k~kvtV~G~vDp~~l 55 (101)
..-..+++..|..-+++. .|.+...+ |.|++.|.++..+.
T Consensus 126 ~~It~kik~~L~~~~~v~~~~I~V~t~~-G~V~L~G~v~~~e~ 167 (191)
T PRK11023 126 TWITTKVRSQLLTSDSVKSSNVKVTTEN-GEVFLLGLVTQREA 167 (191)
T ss_pred HHHHHHHHHHHhcCCCCCcceEEEEEEC-cEEEEEEEeCHHHH
Confidence 345677888887777766 44555555 89999999986543
No 60
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=31.59 E-value=93 Score=28.62 Aligned_cols=36 Identities=19% Similarity=0.321 Sum_probs=25.7
Q ss_pred HHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHHH
Q 047835 18 RTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVAL 55 (101)
Q Consensus 18 ~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l 55 (101)
...++..|.+++||.+|++.+.....+.| ++||.++
T Consensus 168 ~~~l~~~L~~i~gV~~V~~~G~~~~ei~V--~vd~~kl 203 (1040)
T PRK10503 168 ETRVAQKISQVSGVGLVTLSGGQRPAVRV--KLNAQAI 203 (1040)
T ss_pred HHHHHHHhcCCCCceEEEecCCCceEEEE--EECHHHH
Confidence 35788999999999999999864334444 3555544
No 61
>PF12164 SporV_AA: Stage V sporulation protein AA; InterPro: IPR021997 This domain family is found in bacteria - primarily Firmicutes, and is approximately 90 amino acids in length. There is a single completely conserved residue G that may be functionally important. Most annotation associated with this domain suggests that it is involved in the fifth stage of sporulation, however there is little publication to back this up. ; PDB: 3G74_B.
Probab=31.41 E-value=60 Score=21.47 Aligned_cols=51 Identities=8% Similarity=0.103 Sum_probs=30.9
Q ss_pred HHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHHHHHHHHhccCceEEEecCCCC
Q 047835 18 RTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKIGYVETMKLDILD 75 (101)
Q Consensus 18 ~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l~~~LrKk~~~aeivsv~p~k 75 (101)
...+...|..+ .=..++..+++++. +|..++++.+++.++++++-.+|+..
T Consensus 32 ~~~~~~klk~l---~i~~~~~~d~~r~V----isvm~II~~I~~~~p~l~I~~iGe~~ 82 (93)
T PF12164_consen 32 DDEIENKLKAL---PIYKIKKKDKNRYV----ISVMKIIEKIQEEYPNLDIQNIGETD 82 (93)
T ss_dssp SSHHHHHHHTS---EEEE-BTTT--EEE----EEHHHHHHHHHHH-SSEEEEE-S-SE
T ss_pred CHHHHHHhhcc---EeeeecCCCCCEEE----EEHHHHHHHHHHHCCCcEEEEcCCCc
Confidence 33555555554 23334555534433 48999999999999999999999864
No 62
>PLN00116 translation elongation factor EF-2 subunit; Provisional
Probab=31.38 E-value=1e+02 Score=27.71 Aligned_cols=62 Identities=8% Similarity=0.173 Sum_probs=46.6
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCC-eeEEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEE
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPG-LLSVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVET 68 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~G-V~sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aei 68 (101)
+++|.++|.+.+-.+|+..|++.+| |.+.+.+... +..+|.|.+ +-......||..+ |++..
T Consensus 729 i~~veI~~p~~~~G~V~~dL~~RRG~i~~~~~~~~t-~~~~I~A~vPl~e~~gy~~~LRs~T~G~g~~ 795 (843)
T PLN00116 729 VYLVEIQAPEQALGGIYSVLNQKRGHVFEEMQRPGT-PLYNIKAYLPVIESFGFSGTLRAATSGQAFP 795 (843)
T ss_pred eeEEEEEccHHHHhHHHHHHHhcCCccceeeecCCC-ceEEEEEEeeHHHHcCCCHHHHhhCCCCCeE
Confidence 5778888888999999999999999 4565554422 458899995 5556688899877 45543
No 63
>PRK13351 elongation factor G; Reviewed
Probab=31.18 E-value=1.3e+02 Score=26.06 Aligned_cols=61 Identities=15% Similarity=0.146 Sum_probs=45.1
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCC-eeEEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEE
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPG-LLSVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVET 68 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~G-V~sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aei 68 (101)
+++|+++|.+.+..+++..|++.+| |.+++... + +.++++|.+ +-......||..+ |.|.+
T Consensus 601 i~~~eI~~p~~~~g~v~~~l~~rrg~i~~~~~~~-~-~~~~i~a~vP~~e~~~~~~~Lrs~T~G~a~~ 666 (687)
T PRK13351 601 IMELEITVPTEHVGDVLGDLSQRRGRIEGTEPRG-D-GEVLVKAEAPLAELFGYATRLRSMTKGRGSF 666 (687)
T ss_pred eEEEEEEechHhhhhHHHHHHhCCcEEeceecCC-C-cEEEEEEEECHHHhhChHHHHHhhcCCceEE
Confidence 5678888878899999999999999 44554322 2 455699995 6666788899877 46654
No 64
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=31.14 E-value=86 Score=23.10 Aligned_cols=34 Identities=12% Similarity=0.210 Sum_probs=26.5
Q ss_pred eEEEEEeCCChHhh------HHHHHHHHcCCCCeeEEEecC
Q 047835 4 KILYRLDNMHSPKC------RTKAFKIIAGFPGLLSVAMKG 38 (101)
Q Consensus 4 ~vvlKV~m~C~e~C------~~Kv~k~l~~~~GV~sV~id~ 38 (101)
+|.+.+.+.. .+| +..+..+|..++||+++.++.
T Consensus 114 ~V~I~mtLt~-p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 114 RVDIEMTLTA-PGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEEeCC-CCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 5777777776 666 456889999999999988764
No 65
>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=30.30 E-value=1.4e+02 Score=18.49 Aligned_cols=46 Identities=17% Similarity=0.237 Sum_probs=30.6
Q ss_pred HHHHHHHHcCC---CCeeEEEecCCCCCcEEEEEE--ccHHHHHHHHHhccC
Q 047835 18 RTKAFKIIAGF---PGLLSVAMKGDDLRHMEVIGD--IDEVALANMLRRKIG 64 (101)
Q Consensus 18 ~~Kv~k~l~~~---~GV~sV~id~~~k~kvtV~G~--vDp~~l~~~LrKk~~ 64 (101)
..++..+|.++ +=--.+..|.+. +.+.|.|- +--.-+.++|+++++
T Consensus 18 ~~kl~~aL~~l~~eDP~l~~~~d~et-~e~~l~g~Gelhlev~~~~L~~~~~ 68 (75)
T PF14492_consen 18 EPKLSEALQKLSEEDPSLRVERDEET-GELILSGMGELHLEVLLERLKRRFG 68 (75)
T ss_dssp HHHHHHHHHHHHHH-TTSEEEEETTT-SEEEEEESSHHHHHHHHHHHHHTTC
T ss_pred HHHHHHHHHHHHhcCCeEEEEEcchh-ceEEEEECCHHHHHHHHHHHHHHHC
Confidence 34444444444 334477888765 67777665 788889999999885
No 66
>cd07422 MPP_ApaH Escherichia coli ApaH and related proteins, metallophosphatase domain. ApaH (also known as symmetrically cleaving Ap4A hydrolase and bis(5'nucleosyl)-tetraphosphatase) is a bacterial member of the PPP (phosphoprotein phosphatase) family of serine/threonine phosphatases that hydrolyzes the nucleotide-signaling molecule diadenosine tetraphosphate (Ap(4)A) into two ADP and also hydrolyzes Ap(5)A, Gp(4)G, and other extending compounds. Null mutations in apaH result in high intracellular levels of Ap(4)A which correlate with multiple phenotypes, including a decreased expression of catabolite-repressible genes, a reduction in the expression of flagellar operons, and an increased sensitivity to UV and heat. Ap4A hydrolase is important in responding to heat shock and oxidative stress via regulating the concentration of Ap4A in bacteria. Ap4A hydrolase is also thought to play a role in siderophore production, but the mechanism by which ApaH interacts with siderophore pathwa
Probab=30.25 E-value=1.2e+02 Score=23.35 Aligned_cols=42 Identities=7% Similarity=0.265 Sum_probs=30.7
Q ss_pred HhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEE-cc----HHHHHHHHHhcc
Q 047835 15 PKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD-ID----EVALANMLRRKI 63 (101)
Q Consensus 15 e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~-vD----p~~l~~~LrKk~ 63 (101)
.||.....+.+.++. .+... +++...|+ || +.++++.|+...
T Consensus 8 HG~~~~L~~LL~~i~------~~~~~-D~Li~lGDlVdRGp~s~evl~~l~~l~ 54 (257)
T cd07422 8 QGCYDELQRLLEKIN------FDPAK-DRLWLVGDLVNRGPDSLETLRFVKSLG 54 (257)
T ss_pred CCCHHHHHHHHHhcC------CCCCC-CEEEEecCcCCCCcCHHHHHHHHHhcC
Confidence 368888888777642 33333 79999999 65 999999998743
No 67
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=30.18 E-value=1e+02 Score=28.62 Aligned_cols=37 Identities=22% Similarity=0.285 Sum_probs=27.5
Q ss_pred hHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHHH
Q 047835 17 CRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVAL 55 (101)
Q Consensus 17 C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l 55 (101)
-.+.+...|++++||-+|.+-+.....+.| ++||.+|
T Consensus 156 ~~~~l~~~L~~v~GV~~V~~~G~~~~~~rI--~ldp~kL 192 (1009)
T COG0841 156 AASNVRDELSRVPGVGSVQLFGAQEYAMRI--WLDPAKL 192 (1009)
T ss_pred HHHHHHHHHhcCCCceEEEEcCCCceeEEE--EeCHHHH
Confidence 467789999999999999999864334444 3666554
No 68
>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=30.04 E-value=58 Score=29.48 Aligned_cols=37 Identities=19% Similarity=0.409 Sum_probs=25.5
Q ss_pred hHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHHH
Q 047835 17 CRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVAL 55 (101)
Q Consensus 17 C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l 55 (101)
....++..|.+++||.+|++.+.....+-| ++||.+|
T Consensus 157 ~~~~l~~~L~~i~gV~~v~~~G~~~~ei~i--~~d~~kl 193 (1021)
T PF00873_consen 157 AEEQLKPRLERIPGVARVDISGGREREIQI--ELDPEKL 193 (1021)
T ss_dssp HHHCTHHHHHTSTTEEEEEESSS--EEEEE--EE-HHHH
T ss_pred HHHHHHHhccceeEEEEEEeccchhhhhhh--eechhhh
Confidence 356788999999999999999865334433 4666654
No 69
>PRK00007 elongation factor G; Reviewed
Probab=30.00 E-value=1.2e+02 Score=26.54 Aligned_cols=61 Identities=10% Similarity=0.158 Sum_probs=46.0
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEE
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVET 68 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aei 68 (101)
+++|.++|.+.+..+++..|++.+|.-. .++... +..+|+|.+ +-......||..+ |.+.+
T Consensus 605 i~~~eI~~p~~~~g~v~~~L~~RRg~i~-~~~~~~-~~~~i~a~vP~~e~~g~~~~Lrs~T~G~a~~ 669 (693)
T PRK00007 605 IMKVEVVTPEEYMGDVIGDLNSRRGQIE-GMEDRG-GAKVIRAEVPLSEMFGYATDLRSMTQGRATY 669 (693)
T ss_pred cEEEEEEechhhhhhHHHHHHhCCCeEe-cccccC-CcEEEEEEcCHHHhhccHHHHHhhcCCceEE
Confidence 4678888888899999999999999442 333333 578899994 6667788898877 46654
No 70
>PRK12698 flgH flagellar basal body L-ring protein; Reviewed
Probab=29.52 E-value=40 Score=25.86 Aligned_cols=29 Identities=10% Similarity=0.228 Sum_probs=24.9
Q ss_pred CCCCeeEEEecCCCCCcEEEEEEccHHHHH
Q 047835 27 GFPGLLSVAMKGDDLRHMEVIGDIDEVALA 56 (101)
Q Consensus 27 ~~~GV~sV~id~~~k~kvtV~G~vDp~~l~ 56 (101)
.++|-+.|.++.+. +.+++.|.|.|.++-
T Consensus 153 ~I~GeK~i~vN~~~-e~I~lsGvVRP~DI~ 181 (224)
T PRK12698 153 VIRGEKWISINNGD-EFIRLTGIVRSQDIT 181 (224)
T ss_pred EEEEEEEEEECCCE-EEEEEEEEECHHHCC
Confidence 46788999999976 899999999998873
No 71
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=29.51 E-value=97 Score=21.38 Aligned_cols=50 Identities=14% Similarity=0.247 Sum_probs=33.4
Q ss_pred EEEEEeCCChHhh------HHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHHHHHHHHh
Q 047835 5 ILYRLDNMHSPKC------RTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRR 61 (101)
Q Consensus 5 vvlKV~m~C~e~C------~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l~~~LrK 61 (101)
+.+++.+.- .|| ...+..++..++||++++++. +-...-.+..+....|.
T Consensus 51 v~v~mtlT~-~gCP~~~~i~~~v~~al~~~~~v~~v~V~l------~~~p~Wt~~~ms~ear~ 106 (111)
T COG2151 51 VKVKMTLTS-PGCPLAEVIADQVEAALEEIPGVEDVEVEL------TLSPPWTPDRMSEEARR 106 (111)
T ss_pred EEEEEecCC-CCCCccHHHHHHHHHHHHhcCCcceEEEEE------EEcCCCchhhcCHHHHH
Confidence 556666666 788 788999999999999887743 22222445555555443
No 72
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=29.47 E-value=1.8e+02 Score=23.09 Aligned_cols=38 Identities=21% Similarity=0.282 Sum_probs=30.7
Q ss_pred HhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHHHHHHHHhccCc
Q 047835 15 PKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRRKIGY 65 (101)
Q Consensus 15 e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l~~~LrKk~~~ 65 (101)
+.|...+...+.+++||+|+.+- |.++-++.|++..|.
T Consensus 71 ~~~~~~v~~~i~~~~gV~~v~~~-------------sre~~l~~L~~~lg~ 108 (297)
T COG2177 71 QDDAALVREKIEGIPGVKSVRFI-------------SREEALKELQPWLGF 108 (297)
T ss_pred hHHHHHHHHHHhcCCCcceEEEe-------------CHHHHHHHHHHHcCc
Confidence 78899999999999999999884 445677777776663
No 73
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=29.45 E-value=68 Score=17.89 Aligned_cols=19 Identities=16% Similarity=0.543 Sum_probs=16.1
Q ss_pred HHHHHHHHcCCCCeeEEEe
Q 047835 18 RTKAFKIIAGFPGLLSVAM 36 (101)
Q Consensus 18 ~~Kv~k~l~~~~GV~sV~i 36 (101)
-..+++.|..++||.++..
T Consensus 52 ~~~l~~~l~~~~~V~~v~~ 70 (71)
T cd04879 52 PEEVLEELKALPGIIRVRL 70 (71)
T ss_pred CHHHHHHHHcCCCeEEEEE
Confidence 4589999999999999863
No 74
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=28.92 E-value=1.6e+02 Score=19.22 Aligned_cols=35 Identities=11% Similarity=-0.056 Sum_probs=25.5
Q ss_pred EEEEEeCCChHhhHHHHHHHH-cCCCCeeEEEecCC
Q 047835 5 ILYRLDNMHSPKCRTKAFKII-AGFPGLLSVAMKGD 39 (101)
Q Consensus 5 vvlKV~m~C~e~C~~Kv~k~l-~~~~GV~sV~id~~ 39 (101)
+.+.+-+...++--..+...+ +..+||+|+++...
T Consensus 51 L~v~~vv~D~~~~~d~lee~i~~~~e~Vqsvei~~~ 86 (89)
T PF00736_consen 51 LQVSCVVEDDEGSTDDLEEAIESFEEGVQSVEIESF 86 (89)
T ss_dssp EEEEEEECTTTCGHHHHHHHHTTCTTTEEEEEEEEE
T ss_pred EEEEEEEEcCccChHHHHHHHHhcCCCccEEEEEEE
Confidence 344445555246678888899 99999999998653
No 75
>PRK12788 flgH flagellar basal body L-ring protein; Reviewed
Probab=28.82 E-value=41 Score=26.12 Aligned_cols=29 Identities=17% Similarity=0.189 Sum_probs=25.0
Q ss_pred CCCCeeEEEecCCCCCcEEEEEEccHHHHH
Q 047835 27 GFPGLLSVAMKGDDLRHMEVIGDIDEVALA 56 (101)
Q Consensus 27 ~~~GV~sV~id~~~k~kvtV~G~vDp~~l~ 56 (101)
-++|-+.|.++.+. ..+.|.|.|.|.++-
T Consensus 164 vI~G~kev~vN~e~-~~i~vsGvVRP~DI~ 192 (234)
T PRK12788 164 LISGSQEVRVNYEM-RVLNVGGIVRPLDIT 192 (234)
T ss_pred EEEEEEEEEECCCE-EEEEEEEEECHHHCC
Confidence 46788999999976 799999999999874
No 76
>cd03309 CmuC_like CmuC_like. Proteins similar to the putative corrinoid methyltransferase CmuC. Its function has been inferred from sequence similarity to the methyltransferases CmuA and MtaA. Mutants of Methylobacterium sp. disrupted in cmuC and purU appear deficient in some step of chloromethane metabolism.
Probab=28.43 E-value=63 Score=25.70 Aligned_cols=45 Identities=20% Similarity=0.166 Sum_probs=31.4
Q ss_pred EeCCChHhhHHHHHHHHcCCCCeeEEEecCCC----------CCcEEEEEEccHHHH
Q 047835 9 LDNMHSPKCRTKAFKIIAGFPGLLSVAMKGDD----------LRHMEVIGDIDEVAL 55 (101)
Q Consensus 9 V~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~----------k~kvtV~G~vDp~~l 55 (101)
+-+|. .|....+...+..+ |++.+.+|... .+++++-|++||.-|
T Consensus 215 iilH~-cG~~~~~l~~~~e~-g~dvl~~d~~~~dl~eak~~~g~k~~l~GNlDp~~L 269 (321)
T cd03309 215 IVHHS-CGAAASLVPSMAEM-GVDSWNVVMTANNTAELRRLLGDKVVLAGAIDDVAL 269 (321)
T ss_pred eEEEe-CCCcHHHHHHHHHc-CCCEEEecCCCCCHHHHHHHhCCCeEEEcCCChHHh
Confidence 44566 56565677777666 88888887642 147899999998544
No 77
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=28.41 E-value=89 Score=24.60 Aligned_cols=47 Identities=21% Similarity=0.200 Sum_probs=36.0
Q ss_pred hHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEcc-------------HHHHHHHHHhcc
Q 047835 17 CRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDID-------------EVALANMLRRKI 63 (101)
Q Consensus 17 C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vD-------------p~~l~~~LrKk~ 63 (101)
=...+...+..++++..+++-+.=+..-...|+|| +.+|+..|++..
T Consensus 146 ~a~~i~~~l~~~~~~~~v~i~GS~RRg~et~gDiDilv~~~~~~~~~~~~~v~~~l~~~~ 205 (307)
T cd00141 146 IAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDATSRGLLEKVVDALVELG 205 (307)
T ss_pred HHHHHHHHHHhCCCceEEEEcccccCCCCccCCEEEEEecCCccccccHHHHHHHHHhCC
Confidence 35677888888999999999875555556777766 788999998744
No 78
>PRK00249 flgH flagellar basal body L-ring protein; Reviewed
Probab=27.98 E-value=45 Score=25.50 Aligned_cols=29 Identities=14% Similarity=0.182 Sum_probs=25.1
Q ss_pred CCCCeeEEEecCCCCCcEEEEEEccHHHHH
Q 047835 27 GFPGLLSVAMKGDDLRHMEVIGDIDEVALA 56 (101)
Q Consensus 27 ~~~GV~sV~id~~~k~kvtV~G~vDp~~l~ 56 (101)
.++|-+.|.++.+. ..+.+.|.|.|.++-
T Consensus 152 vI~G~K~i~vN~e~-~~i~lsGiVRP~DI~ 180 (222)
T PRK00249 152 VIRGEKEVRVNQGT-EFLRVSGVVRPRDIS 180 (222)
T ss_pred EEEEEEEEEECCCE-EEEEEEEEECHHHCC
Confidence 46788999999976 799999999999874
No 79
>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=27.85 E-value=1.7e+02 Score=18.60 Aligned_cols=44 Identities=14% Similarity=0.175 Sum_probs=31.3
Q ss_pred hhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEE-ccHHHHHHHHHh
Q 047835 16 KCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD-IDEVALANMLRR 61 (101)
Q Consensus 16 ~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~-vDp~~l~~~LrK 61 (101)
+=...+.+.|..++|++=-..+. + ||+.|+=+ -+...+.+.+..
T Consensus 15 ~~~~~v~~~l~~~~gvEVh~~~~-~-GKiVVtiE~~~~~~~~~~~~~ 59 (79)
T PF03927_consen 15 ERLEEVAEALAAIPGVEVHAVDE-D-GKIVVTIEAESSEEEVDLIDA 59 (79)
T ss_dssp CCHHHHHHHHCCSTTEEEEEEET-T-TEEEEEEEESSHHHHHHHHHH
T ss_pred hhHHHHHHHHHcCCCcEEEeeCC-C-CeEEEEEEeCChHHHHHHHHH
Confidence 34678999999999996556665 4 78888766 455666655554
No 80
>PRK12697 flgH flagellar basal body L-ring protein; Reviewed
Probab=27.77 E-value=44 Score=25.83 Aligned_cols=29 Identities=7% Similarity=0.180 Sum_probs=24.9
Q ss_pred CCCCeeEEEecCCCCCcEEEEEEccHHHHH
Q 047835 27 GFPGLLSVAMKGDDLRHMEVIGDIDEVALA 56 (101)
Q Consensus 27 ~~~GV~sV~id~~~k~kvtV~G~vDp~~l~ 56 (101)
.++|=+.|.++.+. +.+.+.|-|.|.++-
T Consensus 156 ~I~GeK~i~vN~e~-e~IrlsGvVRP~DI~ 184 (226)
T PRK12697 156 VVSGEKQMLINQGN-EFVRFSGVVNPNTIS 184 (226)
T ss_pred EEEEEEEEEECCCE-EEEEEEEEECHHHCC
Confidence 46788899999976 799999999999874
No 81
>cd04910 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase
Probab=27.77 E-value=1.4e+02 Score=18.81 Aligned_cols=52 Identities=12% Similarity=0.148 Sum_probs=37.3
Q ss_pred HhhHHHHHHHHcCCCCeeEEEecCCCCCcEEE--EEE-ccHHHHHHHHHhccCceEE
Q 047835 15 PKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEV--IGD-IDEVALANMLRRKIGYVET 68 (101)
Q Consensus 15 e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV--~G~-vDp~~l~~~LrKk~~~aei 68 (101)
.|=..+++.+|++. +|.=|.-+... +.+|. .|. -+-.+++..|.+.++.++|
T Consensus 15 ~g~d~~i~~~l~~~-~v~ii~K~~nA-Ntit~yl~~~~k~~~r~~~~Le~~~p~a~i 69 (71)
T cd04910 15 VGYDLEILELLQRF-KVSIIAKDTNA-NTITHYLAGSLKTIKRLTEDLENRFPNAEI 69 (71)
T ss_pred hhHHHHHHHHHHHc-CCeEEEEecCC-CeEEEEEEcCHHHHHHHHHHHHHhCccCcc
Confidence 45567888888765 55655566665 67776 555 3668899999888887776
No 82
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=27.74 E-value=46 Score=24.19 Aligned_cols=45 Identities=18% Similarity=0.136 Sum_probs=32.6
Q ss_pred hHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHHHHHHHHh
Q 047835 14 SPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVALANMLRR 61 (101)
Q Consensus 14 ~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l~~~LrK 61 (101)
+.+|.++++..|.++ .-|+.+.+.-.++|=.|.=|-..++.+++.
T Consensus 96 s~~i~rkvlQ~Le~~---~~ve~hp~gGR~lt~~GqrdldrIa~~i~~ 140 (143)
T KOG3411|consen 96 SGGIARKVLQALEKM---GIVEKHPKGGRRLTEQGQRDLDRIAGQIRE 140 (143)
T ss_pred ccHHHHHHHHHHHhC---CceeeCCCCcceeCcccchhHHHHHHHHHh
Confidence 356778777777665 445555544349999999999999998875
No 83
>cd02643 R3H_NF-X1 R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system and, the yeast homolog FAP1 encodes a dosage suppressor of rapamycin toxicity. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=27.55 E-value=1.2e+02 Score=19.12 Aligned_cols=29 Identities=17% Similarity=0.244 Sum_probs=22.1
Q ss_pred HHHHHHHHcCCCCeeEEEecCCCCCcEEE
Q 047835 18 RTKAFKIIAGFPGLLSVAMKGDDLRHMEV 46 (101)
Q Consensus 18 ~~Kv~k~l~~~~GV~sV~id~~~k~kvtV 46 (101)
.|++.-.++...||.|.+.|.+.+..|.|
T Consensus 44 eR~iIH~la~~~~l~S~S~G~ep~R~VvI 72 (74)
T cd02643 44 KRRIVHELAEHFGIESVSYDQEPKRNVVA 72 (74)
T ss_pred HHHHHHHHHhhCCCEEEecCCCCCceEEE
Confidence 46666667889999999999877545554
No 84
>PRK12407 flgH flagellar basal body L-ring protein; Reviewed
Probab=27.46 E-value=45 Score=25.62 Aligned_cols=29 Identities=21% Similarity=0.210 Sum_probs=24.8
Q ss_pred CCCCeeEEEecCCCCCcEEEEEEccHHHHH
Q 047835 27 GFPGLLSVAMKGDDLRHMEVIGDIDEVALA 56 (101)
Q Consensus 27 ~~~GV~sV~id~~~k~kvtV~G~vDp~~l~ 56 (101)
.++|-+.|.++.+. ..+.+.|-|.|.++-
T Consensus 150 ~I~GeK~i~vN~e~-e~i~~sGvVRP~DI~ 178 (221)
T PRK12407 150 VIRGEKWLTLNQGD-EYMRVTGLVRADDIA 178 (221)
T ss_pred EEEEEEEEEECCCE-EEEEEEEEECHHHCC
Confidence 46788999999976 799999999998863
No 85
>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=26.94 E-value=1.5e+02 Score=17.83 Aligned_cols=24 Identities=13% Similarity=0.138 Sum_probs=17.5
Q ss_pred EEEecCCCCCcEEEEEEc-cHHHHHH
Q 047835 33 SVAMKGDDLRHMEVIGDI-DEVALAN 57 (101)
Q Consensus 33 sV~id~~~k~kvtV~G~v-Dp~~l~~ 57 (101)
+|..|... |.|.|.|.- +-..+.+
T Consensus 47 ~i~~d~~t-Nsliv~g~~~~~~~i~~ 71 (82)
T PF03958_consen 47 RIVADERT-NSLIVRGTPEDLEQIRE 71 (82)
T ss_dssp EEEEECTT-TEEEEEEEHHHHHHHHH
T ss_pred EEEEECCC-CEEEEEeCHHHHHHHHH
Confidence 88999876 899999994 3333333
No 86
>PRK13748 putative mercuric reductase; Provisional
Probab=26.76 E-value=2.6e+02 Score=23.14 Aligned_cols=50 Identities=12% Similarity=0.128 Sum_probs=37.4
Q ss_pred eCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEE--EccHHHHHHHHHh
Q 047835 10 DNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIG--DIDEVALANMLRR 61 (101)
Q Consensus 10 ~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G--~vDp~~l~~~LrK 61 (101)
.++| ..|..++...+...+|+.....+... +...+.. ..+...+...+..
T Consensus 8 g~~C-~~c~~~ie~~l~~~~gv~~a~~~~~~-~~~~v~~~~~~~~~~i~~~i~~ 59 (561)
T PRK13748 8 GMTC-DSCAAHVKDALEKVPGVQSADVSYPK-GSAQLAIEVGTSPDALTAAVAG 59 (561)
T ss_pred Ceec-HHHHHHHHHHHhcCCCeeEEEEEcCC-CEEEEEECCCCCHHHHHHHHHH
Confidence 4778 99999999999999999988888765 5655553 2466666665544
No 87
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=26.75 E-value=1.5e+02 Score=27.23 Aligned_cols=36 Identities=22% Similarity=0.226 Sum_probs=26.7
Q ss_pred HHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEccHHHH
Q 047835 18 RTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDIDEVAL 55 (101)
Q Consensus 18 ~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~vDp~~l 55 (101)
...++..|.+++||..|++.+.. .=.+.=++||.+|
T Consensus 159 ~~~l~~~L~~i~GV~~V~~~G~~--~~ei~V~vd~~kl 194 (1025)
T PRK10614 159 STQLAQTISQIDGVGDVDVGGSS--LPAVRVGLNPQAL 194 (1025)
T ss_pred HHHHHHHhcCCCCceEEEecCCC--ceEEEEEeCHHHH
Confidence 46789999999999999998854 3344445666655
No 88
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=26.65 E-value=1.1e+02 Score=24.73 Aligned_cols=42 Identities=12% Similarity=0.180 Sum_probs=25.3
Q ss_pred HHHHHHHHcCCCCeeEEEe--cCCC-CCcEEEEEEccHHHHHHHHHh
Q 047835 18 RTKAFKIIAGFPGLLSVAM--KGDD-LRHMEVIGDIDEVALANMLRR 61 (101)
Q Consensus 18 ~~Kv~k~l~~~~GV~sV~i--d~~~-k~kvtV~G~vDp~~l~~~LrK 61 (101)
-.++...+.++++|.=+.+ |... +.-+|+.| ||.++++..-.
T Consensus 20 ie~i~a~~~~~~~v~ildve~danhNRsViT~vg--dp~~~~~A~f~ 64 (302)
T COG3643 20 IEKIVAAAKSIPTVKILDVEMDANHNRSVITLVG--DPSKVVNAAFA 64 (302)
T ss_pred HHHHHHHHhcCCceEEEEeccCCCCCceEEEEec--ChHHHHHHHHH
Confidence 3567777888899875555 4433 12345555 77777666543
No 89
>cd06471 ACD_LpsHSP_like Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Transcription of the genes encoding Lp HSP 18.5, 18.55 and 19.3 is regulated by a variety of stresses including heat, cold and ethanol. Early growing L. plantarum cells contain elevated levels of these mRNAs which rapidly fall of as the cells enter stationary phase. Also belonging to this group is Bifidobacterium breve (Bb) HSP20 and Oenococcus oenis (syn. Leuconostoc oenos) (Oo) HSP18. Transcription of the gene encoding BbHSP20 is strongly induced following heat or osmotic shock, and that of the gene encoding OoHSP18 following heat, ethanol or acid shock. OoHSP18 is peripherally associated with the cytoplasmic me
Probab=26.12 E-value=44 Score=21.11 Aligned_cols=24 Identities=17% Similarity=0.390 Sum_probs=16.6
Q ss_pred CCCCee--EEEecCCCCCcEEEEEEcc
Q 047835 27 GFPGLL--SVAMKGDDLRHMEVIGDID 51 (101)
Q Consensus 27 ~~~GV~--sV~id~~~k~kvtV~G~vD 51 (101)
.++||. .|.+...+ +.|+|.|.-.
T Consensus 17 ~lPGv~~edi~v~~~~-~~L~I~g~~~ 42 (93)
T cd06471 17 DLPGFKKEDIKLDYKD-GYLTISAKRD 42 (93)
T ss_pred ECCCCCHHHeEEEEEC-CEEEEEEEEc
Confidence 467773 56666655 7999999843
No 90
>PRK10568 periplasmic protein; Provisional
Probab=25.54 E-value=1.7e+02 Score=21.61 Aligned_cols=36 Identities=8% Similarity=0.198 Sum_probs=26.8
Q ss_pred HhhHHHHHHHHcCCCCee--EEEecCCCCCcEEEEEEcc
Q 047835 15 PKCRTKAFKIIAGFPGLL--SVAMKGDDLRHMEVIGDID 51 (101)
Q Consensus 15 e~C~~Kv~k~l~~~~GV~--sV~id~~~k~kvtV~G~vD 51 (101)
..=..++...|..-+++. .|.+...+ |.|++.|.|+
T Consensus 59 ~~I~~~v~~~L~~~~~i~~~~I~V~v~~-G~V~L~G~V~ 96 (203)
T PRK10568 59 SAITAKVKAALVDHDNIKSTDISVKTHQ-KVVTLSGFVE 96 (203)
T ss_pred HHHHHHHHHHHHhCCCCCCCceEEEEEC-CEEEEEEEeC
Confidence 455778878877666664 56666665 8999999986
No 91
>PRK12739 elongation factor G; Reviewed
Probab=25.51 E-value=2e+02 Score=25.17 Aligned_cols=60 Identities=10% Similarity=0.097 Sum_probs=45.8
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCC-eeEEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEE
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPG-LLSVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVET 68 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~G-V~sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aei 68 (101)
+++|+++|.+.+..+++..|++.+| |.+.+ ..+ +..+|+|.+ +-..+...||..+ |++.+
T Consensus 602 i~~~eI~~p~~~~g~v~~~L~~RRg~i~~~~--~~~-~~~~i~a~vP~~e~~g~~~~Lr~~T~G~a~~ 666 (691)
T PRK12739 602 IMKVEVVTPEEYMGDVIGDLNRRRGQIQGME--ARG-GAQIVKAFVPLSEMFGYATDLRSATQGRATF 666 (691)
T ss_pred eEEEEEEEchHhhhhHHHHHHhcCCeEECcc--ccC-CcEEEEEEeCHHHhhccHHHHHhhccCceEE
Confidence 5678888888899999999999999 44433 333 567899994 6677788899877 46654
No 92
>PRK00166 apaH diadenosine tetraphosphatase; Reviewed
Probab=25.22 E-value=1.4e+02 Score=23.21 Aligned_cols=40 Identities=8% Similarity=0.337 Sum_probs=29.9
Q ss_pred hhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEE-cc----HHHHHHHHHhc
Q 047835 16 KCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD-ID----EVALANMLRRK 62 (101)
Q Consensus 16 ~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~-vD----p~~l~~~LrKk 62 (101)
||.....+.+.++. .+... +++.+.|+ || +.++++.|++.
T Consensus 11 G~~~~l~~ll~~~~------~~~~~-D~li~lGDlVdrGp~s~~vl~~l~~l 55 (275)
T PRK00166 11 GCYDELQRLLEKID------FDPAK-DTLWLVGDLVNRGPDSLEVLRFVKSL 55 (275)
T ss_pred CCHHHHHHHHHhcC------CCCCC-CEEEEeCCccCCCcCHHHHHHHHHhc
Confidence 68888888887652 22223 78999999 65 99999999874
No 93
>PRK12701 flgH flagellar basal body L-ring protein; Reviewed
Probab=25.12 E-value=53 Score=25.36 Aligned_cols=29 Identities=10% Similarity=0.122 Sum_probs=24.7
Q ss_pred CCCCeeEEEecCCCCCcEEEEEEccHHHHH
Q 047835 27 GFPGLLSVAMKGDDLRHMEVIGDIDEVALA 56 (101)
Q Consensus 27 ~~~GV~sV~id~~~k~kvtV~G~vDp~~l~ 56 (101)
-++|-+.|.++.+. +.+++.|-|.|.++-
T Consensus 159 ~I~GeK~v~vN~e~-e~i~lsGvVRP~DI~ 187 (230)
T PRK12701 159 VVQGEKWVRINQGN-EFVRLSGIVRPQDIK 187 (230)
T ss_pred EEEEEEEEEECCCe-EEEEEEEEECHHHCC
Confidence 46788999999976 799999999998863
No 94
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=24.82 E-value=1.2e+02 Score=19.94 Aligned_cols=34 Identities=12% Similarity=-0.081 Sum_probs=24.0
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCCeeEEEecCC
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPGLLSVAMKGD 39 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~ 39 (101)
-+.+-+...++-...+...++..+||+|+++...
T Consensus 52 ~i~~vv~D~~~~td~lee~i~~~d~VqsveI~~~ 85 (88)
T cd00292 52 QIYCVVEDDEGGTDELEEAISEEDGVQSVDVEAF 85 (88)
T ss_pred EEEEEEEeCCcCcHHHHHHHhccCCceEEEEEEE
Confidence 3344444424556788889999999999998654
No 95
>PF07683 CobW_C: Cobalamin synthesis protein cobW C-terminal domain; InterPro: IPR011629 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [].; PDB: 1NIJ_A.
Probab=24.73 E-value=92 Score=19.28 Aligned_cols=21 Identities=29% Similarity=0.389 Sum_probs=15.5
Q ss_pred CCcEEEEEE-ccHHHHHHHHHh
Q 047835 41 LRHMEVIGD-IDEVALANMLRR 61 (101)
Q Consensus 41 k~kvtV~G~-vDp~~l~~~LrK 61 (101)
.++++++|. +|...|-+.|..
T Consensus 71 ~~~lV~IG~~ld~~~l~~~l~~ 92 (94)
T PF07683_consen 71 DSRLVFIGKNLDKEALREALDA 92 (94)
T ss_dssp -EEEEEEEES--HHHHHHHHHT
T ss_pred CeEEEEEECCCCHHHHHHHHHc
Confidence 479999999 999998888764
No 96
>PRK12696 flgH flagellar basal body L-ring protein; Reviewed
Probab=24.67 E-value=52 Score=25.46 Aligned_cols=29 Identities=10% Similarity=0.163 Sum_probs=24.8
Q ss_pred CCCCeeEEEecCCCCCcEEEEEEccHHHHH
Q 047835 27 GFPGLLSVAMKGDDLRHMEVIGDIDEVALA 56 (101)
Q Consensus 27 ~~~GV~sV~id~~~k~kvtV~G~vDp~~l~ 56 (101)
.++|-+.|.++.+. ..+.+.|.|.|.++-
T Consensus 166 vI~G~k~v~vN~e~-~~i~lsGvVRP~DI~ 194 (236)
T PRK12696 166 QVEGARETRVNDET-QYIVVSGLVRPRDIG 194 (236)
T ss_pred EEEEEEEEEECCCE-EEEEEEEEECHHHCC
Confidence 46788999999976 799999999998863
No 97
>PF07744 SPOC: SPOC domain; InterPro: IPR012921 Spen (split end) proteins regulate the expression of key transcriptional effectors in diverse signalling pathways. They are large proteins characterised by N-terminal RNA-binding motifs and a highly conserved C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The function of the SPOC domain is unknown, but the SPOC domain of the SHARP Spen protein has been implicated in the interaction of SHARP with the SMRT/NcoR corepressor, where SHARP plays an essential role in the repressor complex []. The SPOC domain is folded into a single compact domain consisting of a beta-barrel with seven strands framed by six alpha helices. A number of deep grooves and clefts in the surface, plus two nonpolar loops, render the SPOC domain well suited to protein-protein interactions; most of the conserved residues occur on the protein surface rather than in the core. Other proteins containing a SPOC domain include drosophila Split ends, which promotes sclerite development in the head and restricts it in the thorax, and mouse MINT (homologue of SHARP), which is involved in skeletal and neuronal development via its repression of Msx2.; PDB: 1OW1_A.
Probab=24.67 E-value=90 Score=20.23 Aligned_cols=30 Identities=20% Similarity=0.310 Sum_probs=20.7
Q ss_pred CcEEEEEEccHHHHHHHHHhccC----ceEEEec
Q 047835 42 RHMEVIGDIDEVALANMLRRKIG----YVETMKL 71 (101)
Q Consensus 42 ~kvtV~G~vDp~~l~~~LrKk~~----~aeivsv 71 (101)
.++.|.|.+|+..+-+.|++-.. .+-++.+
T Consensus 39 ~~i~i~gRl~~~~~~~yl~~i~~s~~~~v~v~~~ 72 (119)
T PF07744_consen 39 KKIDIRGRLDPEKVWDYLRQIRKSRSKDVCVVAL 72 (119)
T ss_dssp EEE-EEEE-SHHHHHHHHHHTSSTTT-EEEEEEE
T ss_pred cEEEEEeecCHHHHHHHHHhcccCCCceEEEEEE
Confidence 58999999999999999876442 4445544
No 98
>PRK12700 flgH flagellar basal body L-ring protein; Reviewed
Probab=24.07 E-value=58 Score=25.16 Aligned_cols=29 Identities=14% Similarity=0.261 Sum_probs=24.8
Q ss_pred CCCCeeEEEecCCCCCcEEEEEEccHHHHH
Q 047835 27 GFPGLLSVAMKGDDLRHMEVIGDIDEVALA 56 (101)
Q Consensus 27 ~~~GV~sV~id~~~k~kvtV~G~vDp~~l~ 56 (101)
-++|=+.|.++.+. ..+.+.|-|.|.++-
T Consensus 160 vI~GeK~i~vN~~~-e~irlsGiVRP~DI~ 188 (230)
T PRK12700 160 QIAGEKQIAINRGS-EYVRFSGVVDPRSIT 188 (230)
T ss_pred EEEEEEEEEECCCE-EEEEEEEEECHHHCC
Confidence 46788899999976 799999999999874
No 99
>cd04920 ACT_AKiii-DAPDC_2 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC). This CD includes the second of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.80 E-value=1.7e+02 Score=17.25 Aligned_cols=46 Identities=13% Similarity=0.132 Sum_probs=34.4
Q ss_pred HhhHHHHHHHHcCCCCeeEEEecCCCCCcEE-EEEEccHHHHHHHHHhc
Q 047835 15 PKCRTKAFKIIAGFPGLLSVAMKGDDLRHME-VIGDIDEVALANMLRRK 62 (101)
Q Consensus 15 e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvt-V~G~vDp~~l~~~LrKk 62 (101)
.+...++.++|+. .||.-+.....+ ..++ |+-+-|-.++++.|.+.
T Consensus 14 ~gv~~~~~~~L~~-~~i~~i~~~~s~-~~is~vv~~~d~~~av~~LH~~ 60 (63)
T cd04920 14 LHKLGPALEVFGK-KPVHLVSQAAND-LNLTFVVDEDQADGLCARLHFQ 60 (63)
T ss_pred ccHHHHHHHHHhc-CCceEEEEeCCC-CeEEEEEeHHHHHHHHHHHHHH
Confidence 6889999999977 489988887755 5663 45556777778777653
No 100
>smart00749 BON bacterial OsmY and nodulation domain.
Probab=23.67 E-value=1.4e+02 Score=16.35 Aligned_cols=38 Identities=18% Similarity=0.133 Sum_probs=22.4
Q ss_pred HHHHHHHcCCCCeeE--EEecCCCCCcEEEEEEccHHHHHH
Q 047835 19 TKAFKIIAGFPGLLS--VAMKGDDLRHMEVIGDIDEVALAN 57 (101)
Q Consensus 19 ~Kv~k~l~~~~GV~s--V~id~~~k~kvtV~G~vDp~~l~~ 57 (101)
.++...|..-+++.+ +.+.... +.+++.|.+++..-..
T Consensus 2 ~~v~~~l~~~~~~~~~~~~v~~~~-~~vvL~g~~~~~~~~~ 41 (62)
T smart00749 2 EKVKKALAKDGLIKADSIVVVTDG-GVVVLLGGVVDNAEAA 41 (62)
T ss_pred hhHHHHHhhCCCCCcCceEEEEEC-CEEEEeeecCCHHHHH
Confidence 356666665555543 4444444 7888888865554433
No 101
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=23.66 E-value=1.9e+02 Score=17.99 Aligned_cols=63 Identities=19% Similarity=0.305 Sum_probs=42.1
Q ss_pred eEEEEEeCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEE-ccHHHHHHHHHhccCceEEEec
Q 047835 4 KILYRLDNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD-IDEVALANMLRRKIGYVETMKL 71 (101)
Q Consensus 4 ~vvlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~-vDp~~l~~~LrKk~~~aeivsv 71 (101)
-+.+||.. - ..=+..+++++..+.| .=++++.+. =.+.++|+ =.-..+++.|++ ++-.+++.-
T Consensus 4 l~LiKV~~-~-~~~r~ei~~l~~~f~a-~ivd~~~~~-~iie~tG~~~kid~fi~~l~~-~gi~Ei~Rt 67 (75)
T PF10369_consen 4 LALIKVKA-T-PENRSEILQLAEIFRA-RIVDVSPDS-IIIELTGTPEKIDAFIKLLKP-FGILEIART 67 (75)
T ss_dssp EEEEEEE--S-CHHHHHHHHHHHHTT--EEEEEETTE-EEEEEEE-HHHHHHHHHHSTG-GGEEEEEEE
T ss_pred EEEEEEEC-C-ccCHHHHHHHHHHhCC-EEEEECCCE-EEEEEcCCHHHHHHHHHHhhh-cCCEEEEcc
Confidence 36788887 4 6788899999988887 444554433 46667998 566678888877 766676643
No 102
>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=23.62 E-value=1e+02 Score=17.99 Aligned_cols=28 Identities=18% Similarity=0.174 Sum_probs=20.9
Q ss_pred HHHHHHHcCCCCeeEEEecCCCCCcEEE
Q 047835 19 TKAFKIIAGFPGLLSVAMKGDDLRHMEV 46 (101)
Q Consensus 19 ~Kv~k~l~~~~GV~sV~id~~~k~kvtV 46 (101)
.++.+.|.+++.|+++.+...--+++.|
T Consensus 37 ~~~~~~l~~~p~V~~v~V~r~~P~~l~I 64 (69)
T PF08478_consen 37 KKIEQRLEKLPWVKSVSVSRRFPNTLEI 64 (69)
T ss_dssp HHHHHCCCCTTTEEEEEEEEETTTEEEE
T ss_pred HHHHHHHHcCCCEEEEEEEEeCCCEEEE
Confidence 5677888899999999997543356655
No 103
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.60 E-value=1.6e+02 Score=17.11 Aligned_cols=29 Identities=7% Similarity=0.170 Sum_probs=19.3
Q ss_pred EEEeCCChHhhHHHHHHHHcCCCCeeEEEe
Q 047835 7 YRLDNMHSPKCRTKAFKIIAGFPGLLSVAM 36 (101)
Q Consensus 7 lKV~m~C~e~C~~Kv~k~l~~~~GV~sV~i 36 (101)
+.+.... ..--..+++.|.+++||...++
T Consensus 44 ~~vev~~-~~~l~~i~~~L~~i~gV~~~~~ 72 (74)
T cd04887 44 ITVDAPS-EEHAETIVAAVRALPEVKVLSV 72 (74)
T ss_pred EEEEcCC-HHHHHHHHHHHhcCCCeEEEEe
Confidence 3444445 5556778888888888876554
No 104
>cd04901 ACT_3PGDH C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-
Probab=23.49 E-value=1e+02 Score=17.67 Aligned_cols=18 Identities=17% Similarity=0.503 Sum_probs=14.8
Q ss_pred HHHHHHHcCCCCeeEEEe
Q 047835 19 TKAFKIIAGFPGLLSVAM 36 (101)
Q Consensus 19 ~Kv~k~l~~~~GV~sV~i 36 (101)
..+++.+++++||.+|..
T Consensus 51 ~~li~~l~~~~~V~~v~~ 68 (69)
T cd04901 51 EELLEALRAIPGTIRVRL 68 (69)
T ss_pred HHHHHHHHcCCCeEEEEE
Confidence 477888889999998864
No 105
>cd06475 ACD_HspB1_like Alpha crystallin domain (ACD) found in mammalian small (s)heat shock protein (Hsp)-27 (also denoted HspB1 in human) and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Hsp27 shows enhanced synthesis in response to stress. It is a molecular chaperone which interacts with a large number of different proteins. It is found in many types of human cells including breast, uterus, cervix, platelets and cancer cells. Hsp27 has diverse cellular functions including, chaperoning, regulation of actin polymerization, keratinocyte differentiation, regulation of inflammatory pathways in keratinocytes, and protection from oxidative stress through modulating glutathione levels. It is also a subunit of AUF1-containing protein complexes. It has been linked to several transduction pathways regulating cellular functions including differentiat
Probab=23.45 E-value=65 Score=20.59 Aligned_cols=23 Identities=17% Similarity=0.281 Sum_probs=16.1
Q ss_pred CCCCee--EEEecCCCCCcEEEEEEc
Q 047835 27 GFPGLL--SVAMKGDDLRHMEVIGDI 50 (101)
Q Consensus 27 ~~~GV~--sV~id~~~k~kvtV~G~v 50 (101)
.++|+. .+.++..+ +.|+|.|.-
T Consensus 17 dlPG~~~edi~V~v~~-~~L~I~g~~ 41 (86)
T cd06475 17 DVNHFAPEELVVKTKD-GVVEITGKH 41 (86)
T ss_pred ECCCCCHHHEEEEEEC-CEEEEEEEE
Confidence 456765 56666655 799999983
No 106
>TIGR00668 apaH bis(5'-nucleosyl)-tetraphosphatase (symmetrical). Alternate names include diadenosine-tetraphosphatase and Ap4A hydrolase.
Probab=22.85 E-value=1.8e+02 Score=23.06 Aligned_cols=45 Identities=9% Similarity=0.191 Sum_probs=32.9
Q ss_pred HhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEE-c----cHHHHHHHHHhccCce
Q 047835 15 PKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD-I----DEVALANMLRRKIGYV 66 (101)
Q Consensus 15 e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~-v----Dp~~l~~~LrKk~~~a 66 (101)
.||.....+.|.++. .+... +++...|+ | |+.+++..|+.....+
T Consensus 10 HGc~daL~~LL~~i~------f~~~~-D~l~~lGDlVdRGP~slevL~~l~~l~~~~ 59 (279)
T TIGR00668 10 HGCYDELQALLERVE------FDPGQ-DTLWLTGDLVARGPGSLEVLRYVKSLGDAV 59 (279)
T ss_pred cCCHHHHHHHHHHhC------cCCCC-CEEEEeCCccCCCCCHHHHHHHHHhcCCCe
Confidence 478888888887763 34433 78999999 5 5999999998743333
No 107
>COG0071 IbpA Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=22.52 E-value=40 Score=23.40 Aligned_cols=28 Identities=21% Similarity=0.493 Sum_probs=19.8
Q ss_pred HHcCCCCee--EEEecCCCCCcEEEEEEccH
Q 047835 24 IIAGFPGLL--SVAMKGDDLRHMEVIGDIDE 52 (101)
Q Consensus 24 ~l~~~~GV~--sV~id~~~k~kvtV~G~vDp 52 (101)
+...++|++ .|.+.... +.|+|.|+...
T Consensus 54 I~~elPG~~kedI~I~~~~-~~l~I~g~~~~ 83 (146)
T COG0071 54 ITAELPGVDKEDIEITVEG-NTLTIRGEREE 83 (146)
T ss_pred EEEEcCCCChHHeEEEEEC-CEEEEEEEecc
Confidence 345678876 56666655 79999999643
No 108
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.36 E-value=1e+02 Score=17.22 Aligned_cols=19 Identities=16% Similarity=0.324 Sum_probs=15.5
Q ss_pred HHHHHHHHcCCCCeeEEEe
Q 047835 18 RTKAFKIIAGFPGLLSVAM 36 (101)
Q Consensus 18 ~~Kv~k~l~~~~GV~sV~i 36 (101)
-..+.+.|.+++||.++..
T Consensus 52 ~~~~i~~l~~~~~v~~v~~ 70 (71)
T cd04903 52 DEEVIEEIKKIPNIHQVIL 70 (71)
T ss_pred CHHHHHHHHcCCCceEEEE
Confidence 4578889999999988864
No 109
>PRK12699 flgH flagellar basal body L-ring protein; Reviewed
Probab=22.16 E-value=64 Score=25.22 Aligned_cols=29 Identities=10% Similarity=0.241 Sum_probs=25.3
Q ss_pred CCCCeeEEEecCCCCCcEEEEEEccHHHHH
Q 047835 27 GFPGLLSVAMKGDDLRHMEVIGDIDEVALA 56 (101)
Q Consensus 27 ~~~GV~sV~id~~~k~kvtV~G~vDp~~l~ 56 (101)
.++|=+.|.++.+. ..+.+.|.|.|.++.
T Consensus 177 vI~GeK~i~vN~~~-e~IrlsGvVRP~DI~ 205 (246)
T PRK12699 177 LVSGEKQIGINQGH-EFIRLSGVINPINVI 205 (246)
T ss_pred EEEEEEEEEECCCe-EEEEEEEEEChhhcc
Confidence 46788899999976 799999999999985
No 110
>PRK05096 guanosine 5'-monophosphate oxidoreductase; Provisional
Probab=22.01 E-value=3e+02 Score=22.76 Aligned_cols=53 Identities=17% Similarity=0.018 Sum_probs=34.5
Q ss_pred eCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEE-ccHHHHHHHHHhccCceEEE
Q 047835 10 DNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD-IDEVALANMLRRKIGYVETM 69 (101)
Q Consensus 10 ~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~-vDp~~l~~~LrKk~~~aeiv 69 (101)
.+-..+....++...+....|++-|.+|..+ |. .-..+.+++||+.+++..|+
T Consensus 102 avG~~~~d~er~~~L~~~~~g~D~iviD~Ah-------Ghs~~~i~~ik~ik~~~P~~~vI 155 (346)
T PRK05096 102 STGTSDADFEKTKQILALSPALNFICIDVAN-------GYSEHFVQFVAKAREAWPDKTIC 155 (346)
T ss_pred EecCCHHHHHHHHHHHhcCCCCCEEEEECCC-------CcHHHHHHHHHHHHHhCCCCcEE
Confidence 3334467788888888888999999999865 22 23344555555555554443
No 111
>PRK11439 pphA serine/threonine protein phosphatase 1; Provisional
Probab=21.55 E-value=1.1e+02 Score=22.39 Aligned_cols=41 Identities=12% Similarity=0.216 Sum_probs=30.5
Q ss_pred HhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEE-c----cHHHHHHHHHhc
Q 047835 15 PKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGD-I----DEVALANMLRRK 62 (101)
Q Consensus 15 e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~-v----Dp~~l~~~LrKk 62 (101)
.||....++.|.++. .+... +++...|+ | |+.++++.|++.
T Consensus 26 HG~~~~L~~lL~~i~------~~~~~-D~li~lGDlvDrGp~s~~vl~~l~~~ 71 (218)
T PRK11439 26 HGCFEQLMRKLRHCR------FDPWR-DLLISVGDLIDRGPQSLRCLQLLEEH 71 (218)
T ss_pred cCCHHHHHHHHHhcC------CCccc-CEEEEcCcccCCCcCHHHHHHHHHcC
Confidence 368888888888762 22223 78889999 5 699999999874
No 112
>TIGR00484 EF-G translation elongation factor EF-G. After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G.
Probab=21.47 E-value=2.8e+02 Score=24.16 Aligned_cols=61 Identities=10% Similarity=0.159 Sum_probs=45.9
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEEEEc---cHHHHHHHHHhcc-CceEE
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVIGDI---DEVALANMLRRKI-GYVET 68 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G~v---Dp~~l~~~LrKk~-~~aei 68 (101)
++++.++|.+.+..+++..|++.+|.-- .++... +..+|.|.+ +-......||..+ |++.+
T Consensus 602 i~~~eI~~p~~~~g~v~~~L~~rrg~i~-~~~~~~-~~~~I~a~vP~~e~~g~~~~Lrs~T~G~~~~ 666 (689)
T TIGR00484 602 IMKVEVEVPEEYMGDVMGDLSSRRGIIE-GMEARG-NVQKIKAEVPLSEMFGYATDLRSFTQGRGTY 666 (689)
T ss_pred cEEEEEEecHHHhHhHHHHHHhcCCeEe-cccccC-CcEEEEEEeCHHHHhChHHHHHHhcCCceEE
Confidence 4678888888999999999999999431 222323 578899994 6677788899877 46654
No 113
>cd04881 ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains. The ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) encoded by the hom gene of Bacillus subtilis and other related sequences. HSDH reduces aspartate semi-aldehyde to the amino acid homoserine, one that is required for the biosynthesis of Met, Thr, and Ile from Asp. Neither the enzyme nor the aspartate pathway is found in the animal kingdom. This mostly bacterial HSDH group has a C-terminal ACT domain and is believed to be involved in enzyme regulation. A C-terminal deletion in the Corynebacterium glutamicum HSDH abolished allosteric inhibition by L-threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.39 E-value=1.6e+02 Score=16.65 Aligned_cols=28 Identities=11% Similarity=0.090 Sum_probs=16.1
Q ss_pred EEEEeCCChHhhHHHHHHHHcCCCCeeEE
Q 047835 6 LYRLDNMHSPKCRTKAFKIIAGFPGLLSV 34 (101)
Q Consensus 6 vlKV~m~C~e~C~~Kv~k~l~~~~GV~sV 34 (101)
.+.++..- ..--+.+...|.+++||.++
T Consensus 45 ~i~~~~~~-~~~l~~~i~~L~~~~~V~~~ 72 (79)
T cd04881 45 VIVTHETS-EAALNAALAEIEALDAVQGV 72 (79)
T ss_pred EEEEccCC-HHHHHHHHHHHHcCccccCC
Confidence 33444444 55666666667777666654
No 114
>PF08923 MAPKK1_Int: Mitogen-activated protein kinase kinase 1 interacting; InterPro: IPR015019 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry represents Mitogen-activated protein kinase kinase 1 interacting protein, which is a small subcellular adaptor protein required for MAPK signalling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer []. ; PDB: 1VEU_A 1VET_A 1SKO_A 2ZL1_A 3CPT_A.
Probab=21.18 E-value=1.9e+02 Score=19.93 Aligned_cols=29 Identities=14% Similarity=0.294 Sum_probs=21.2
Q ss_pred HHHHHHHHcCCCCeeEEEecCCCCCcEEEEE
Q 047835 18 RTKAFKIIAGFPGLLSVAMKGDDLRHMEVIG 48 (101)
Q Consensus 18 ~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~G 48 (101)
.+-..+.+.+++|+.+|-+...+ | |-+..
T Consensus 4 ~~~L~~ll~~v~Gl~~I~itDrD-G-vpi~~ 32 (119)
T PF08923_consen 4 KRFLQKLLSRVDGLQAIVITDRD-G-VPIAK 32 (119)
T ss_dssp HHHHHHHGGGSTTEEEEEEEETT-S--EEEE
T ss_pred HHHHHHHHhccCCeEEEEEECCC-C-cEEEE
Confidence 35567889999999999998755 4 44444
No 115
>cd00474 SUI1_eIF1 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two antiparallel alpha helices packed against the same side of a five-strand beta sheet, is structurally similar to other RNA-binding domains suggesting that SUI1/eIF1 may bind RNA. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown.
Probab=21.14 E-value=1.6e+02 Score=18.74 Aligned_cols=26 Identities=19% Similarity=0.159 Sum_probs=19.1
Q ss_pred cEEEEEE-----ccHHHHHHHHHhccC-ceEE
Q 047835 43 HMEVIGD-----IDEVALANMLRRKIG-YVET 68 (101)
Q Consensus 43 kvtV~G~-----vDp~~l~~~LrKk~~-~aei 68 (101)
.||++.. +|+.+|++.|+++++ ...+
T Consensus 14 ~VT~I~Gl~~~~~dlk~l~k~lKk~~~cggtv 45 (77)
T cd00474 14 TVTTVQGLDLEYADLKKLAKELKKKCACGGTV 45 (77)
T ss_pred cEEEEECCCCchHhHHHHHHHHHHHcCCCcEE
Confidence 6777554 488999999999885 4443
No 116
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=21.06 E-value=87 Score=17.53 Aligned_cols=29 Identities=14% Similarity=0.195 Sum_probs=21.2
Q ss_pred EEEEEeCCChHhhHHHHHHHHcCCCCeeEEE
Q 047835 5 ILYRLDNMHSPKCRTKAFKIIAGFPGLLSVA 35 (101)
Q Consensus 5 vvlKV~m~C~e~C~~Kv~k~l~~~~GV~sV~ 35 (101)
+.+.++. . +.=-..+...|.+++||.+|+
T Consensus 44 ~~~~~~~-~-~~~~~~l~~~l~~~~~v~~v~ 72 (72)
T cd04878 44 ITIVVEG-D-DDVIEQIVKQLNKLVDVLKVS 72 (72)
T ss_pred EEEEEEC-C-HHHHHHHHHHHhCCccEEEeC
Confidence 5555664 4 355678889999999999874
No 117
>PRK13625 bis(5'-nucleosyl)-tetraphosphatase PrpE; Provisional
Probab=20.90 E-value=1.3e+02 Score=22.50 Aligned_cols=46 Identities=13% Similarity=0.288 Sum_probs=30.4
Q ss_pred HhhHHHHHHHHcCCCC--eeEEEecCCCCCcEEEEEE-cc----HHHHHHHHHh
Q 047835 15 PKCRTKAFKIIAGFPG--LLSVAMKGDDLRHMEVIGD-ID----EVALANMLRR 61 (101)
Q Consensus 15 e~C~~Kv~k~l~~~~G--V~sV~id~~~k~kvtV~G~-vD----p~~l~~~LrK 61 (101)
.||.....+.+.++.= ...+.....+ +++...|+ +| +..+++.|.+
T Consensus 10 HG~~~~L~~lL~~~~~~~~~~~~~~~~~-d~li~lGDliDRGp~S~~vl~~~~~ 62 (245)
T PRK13625 10 HGCYQEFQALTEKLGYNWSSGLPVHPDQ-RKLAFVGDLTDRGPHSLRMIEIVWE 62 (245)
T ss_pred ccCHHHHHHHHHHcCCCcccCcccCCCC-CEEEEECcccCCCcChHHHHHHHHH
Confidence 3688888888876531 1112222333 79999999 75 8888887765
No 118
>PF01424 R3H: R3H domain; InterPro: IPR001374 The R3H motif: a domain that binds single-stranded nucleic acids. The most prominent feature of the R3H motif is the presence of an invariant arginine residue and a highly conserved histidine residue that are separated by three residues. The motif also displays a conserved pattern of hydrophobic residues, prolines and glycines. The R3H motif is present in proteins from a diverse range of organisms that includes Eubacteria, green plants, fungi and various groups of metazoans. Intriguingly, it has not yet been identified in Archaea and Escherichia coli. The sequences that contain the R3H domain, many of which are hypothetical proteins predicted from genome sequencing projects, can be grouped into eight families on the basis of similarities outside the R3H region. Three of the families contain ATPase domains either upstream (families II and VII) or downstream of the R3H domain (family VIII). The N-terminal part of members of family VII contains an SF1 helicase domain5. The C-terminal part of family VIII contains an SF2 DEAH helicase domain5. The ATPase domain in the members of family II is similar to the stage-III sporulation protein AA (S3AA_BACSU), the proteasome ATPase, bacterial transcription-termination factor r and the mitochondrial F1-ATPase b subunit (the F5 helicase family5). Family VI contains Cys-rich repeats6, as well as a ring-type zinc finger upstream of the R3H domain. JAG bacterial proteins (family I) contain a KH domain N-terminal to the R3H domain. The functions of other domains in R3H proteins support the notion that the R3H domain might be involved in interactions with single-stranded nucleic acids [].; GO: 0003676 nucleic acid binding; PDB: 1WHR_A 1MSZ_A 1UG8_A 3GKU_B 2CPM_A.
Probab=20.76 E-value=1.7e+02 Score=17.03 Aligned_cols=33 Identities=21% Similarity=0.155 Sum_probs=22.4
Q ss_pred HhhHHHHHHHHcCCCCeeEEEecCCCCCcEEEE
Q 047835 15 PKCRTKAFKIIAGFPGLLSVAMKGDDLRHMEVI 47 (101)
Q Consensus 15 e~C~~Kv~k~l~~~~GV~sV~id~~~k~kvtV~ 47 (101)
..=.|++.-.++...|+.|-+.+.+.+..|+|.
T Consensus 29 ~~~~R~~iH~~a~~~gL~s~S~g~~~~R~vvv~ 61 (63)
T PF01424_consen 29 NSFERKLIHELAEYYGLKSKSEGEGPNRRVVVS 61 (63)
T ss_dssp -SHHHHHHHHHHHHCTEEEEEESSSSSSEEEEE
T ss_pred CHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEE
Confidence 344566666666799999999987663345553
No 119
>smart00683 DM16 Repeats in sea squirt COS41.4, worm R01H10.6, fly CG1126 etc.
Probab=20.58 E-value=54 Score=20.04 Aligned_cols=25 Identities=16% Similarity=0.211 Sum_probs=19.8
Q ss_pred HHcCCCCeeEEEecCCCCCcEEEEE
Q 047835 24 IIAGFPGLLSVAMKGDDLRHMEVIG 48 (101)
Q Consensus 24 ~l~~~~GV~sV~id~~~k~kvtV~G 48 (101)
.+.+++||+++.=|..+.|++.|+-
T Consensus 3 v~~~~~~Ved~kgn~G~~G~l~VTN 27 (55)
T smart00683 3 VLTRINGVEDTKGNNGDLGVFFVTN 27 (55)
T ss_pred EEeeecCeEecCCCCCCeeEEEEEe
Confidence 4568899999998887777887763
Done!