Query 025287
Match_columns 255
No_of_seqs 160 out of 1145
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 04:18:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025287.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025287hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1603 Copper chaperone [Inor 99.5 3.5E-14 7.5E-19 106.0 8.5 67 6-76 4-70 (73)
2 PF00403 HMA: Heavy-metal-asso 99.5 1.4E-13 3.1E-18 97.6 7.9 58 10-67 1-61 (62)
3 COG2608 CopZ Copper chaperone 99.4 2E-12 4.2E-17 96.4 8.3 63 6-68 1-66 (71)
4 KOG4656 Copper chaperone for s 98.8 1.3E-08 2.7E-13 91.8 7.9 76 1-81 1-76 (247)
5 PRK10671 copA copper exporting 98.2 3.6E-06 7.9E-11 86.9 7.7 59 7-68 3-62 (834)
6 PLN02957 copper, zinc superoxi 98.1 1.9E-05 4.2E-10 71.0 10.1 66 8-78 7-72 (238)
7 TIGR00003 copper ion binding p 97.9 0.00012 2.6E-09 46.7 8.5 61 7-67 2-65 (68)
8 COG2217 ZntA Cation transport 97.3 0.0006 1.3E-08 70.7 7.5 61 7-68 2-66 (713)
9 PTZ00449 104 kDa microneme/rho 96.9 0.0054 1.2E-07 62.7 9.8 10 59-68 485-494 (943)
10 PTZ00449 104 kDa microneme/rho 96.7 0.0092 2E-07 61.0 9.8 69 89-157 577-654 (943)
11 PRK10671 copA copper exporting 96.7 0.005 1.1E-07 64.1 7.7 60 8-68 100-160 (834)
12 KOG0207 Cation transport ATPas 96.5 0.0063 1.4E-07 64.6 7.0 62 7-68 146-210 (951)
13 PRK11033 zntA zinc/cadmium/mer 96.2 0.014 3.1E-07 60.3 7.9 61 8-68 54-115 (741)
14 KOG0207 Cation transport ATPas 95.5 0.024 5.2E-07 60.4 5.8 61 14-78 2-63 (951)
15 COG1888 Uncharacterized protei 93.2 0.39 8.5E-06 38.8 6.7 72 5-77 4-83 (97)
16 PF02680 DUF211: Uncharacteriz 92.9 0.35 7.7E-06 39.1 6.1 73 5-78 3-82 (95)
17 TIGR02052 MerP mercuric transp 90.2 3 6.4E-05 29.4 8.1 59 8-66 24-85 (92)
18 cd00371 HMA Heavy-metal-associ 85.9 4.4 9.6E-05 22.7 7.7 37 14-50 6-42 (63)
19 PF13732 DUF4162: Domain of un 80.0 5.6 0.00012 29.3 5.4 47 28-78 26-74 (84)
20 PRK13748 putative mercuric red 79.8 6.8 0.00015 38.5 7.5 57 10-66 3-61 (561)
21 PF01883 DUF59: Domain of unkn 76.0 5 0.00011 29.1 4.1 32 8-39 35-72 (72)
22 PF04972 BON: BON domain; Int 75.2 4.3 9.3E-05 28.5 3.5 41 22-64 2-45 (64)
23 PF01206 TusA: Sulfurtransfera 74.5 11 0.00023 27.2 5.5 50 10-68 2-53 (70)
24 cd04883 ACT_AcuB C-terminal AC 71.3 30 0.00066 24.2 7.1 59 10-68 3-67 (72)
25 PRK11198 LysM domain/BON super 70.4 12 0.00027 31.4 5.7 47 21-68 28-75 (147)
26 smart00362 RRM_2 RNA recogniti 68.1 30 0.00066 22.5 7.5 54 11-66 2-60 (72)
27 PRK10553 assembly protein for 68.1 23 0.0005 27.9 6.4 44 21-64 19-62 (87)
28 PF03927 NapD: NapD protein; 67.3 30 0.00065 26.4 6.7 44 20-64 16-59 (79)
29 PF14437 MafB19-deam: MafB19-l 66.8 13 0.00028 32.2 5.2 41 8-49 101-143 (146)
30 PF05046 Img2: Mitochondrial l 65.6 28 0.00061 27.1 6.4 60 6-67 27-87 (87)
31 PF09580 Spore_YhcN_YlaJ: Spor 65.3 7.2 0.00016 32.9 3.3 48 20-67 76-127 (177)
32 PF08777 RRM_3: RNA binding mo 64.6 42 0.00092 26.8 7.4 57 9-65 2-60 (105)
33 cd04888 ACT_PheB-BS C-terminal 63.3 22 0.00048 25.1 5.1 34 6-39 40-74 (76)
34 PRK06418 transcription elongat 62.8 44 0.00095 29.4 7.7 69 7-78 6-98 (166)
35 PF08260 Kinin: Insect kinin p 60.3 4.6 0.0001 19.3 0.7 8 219-226 1-8 (8)
36 COG0425 SirA Predicted redox p 58.9 48 0.001 25.3 6.5 57 8-73 5-63 (78)
37 PRK11018 hypothetical protein; 58.8 43 0.00094 25.2 6.2 51 9-68 9-61 (78)
38 cd04920 ACT_AKiii-DAPDC_2 ACT 58.6 63 0.0014 22.9 6.8 51 14-65 9-60 (63)
39 PRK11023 outer membrane lipopr 57.2 30 0.00065 30.3 5.9 46 21-67 51-99 (191)
40 PF13740 ACT_6: ACT domain; PD 56.0 63 0.0014 23.7 6.6 60 8-67 2-67 (76)
41 PF13192 Thioredoxin_3: Thiore 55.9 15 0.00033 26.9 3.3 10 13-22 6-15 (76)
42 PF13291 ACT_4: ACT domain; PD 53.3 34 0.00075 24.8 4.8 34 5-38 46-79 (80)
43 PRK10568 periplasmic protein; 52.1 42 0.0009 29.7 5.9 46 18-64 59-106 (203)
44 smart00749 BON bacterial OsmY 49.0 76 0.0016 21.0 6.8 42 22-63 2-45 (62)
45 PF08002 DUF1697: Protein of u 48.0 70 0.0015 26.7 6.4 43 21-65 21-63 (137)
46 PF14535 AMP-binding_C_2: AMP- 45.4 94 0.002 23.9 6.3 57 22-79 7-80 (96)
47 PF07837 FTCD_N: Formiminotran 45.1 32 0.00069 30.7 4.0 52 21-73 18-71 (178)
48 TIGR03406 FeS_long_SufT probab 44.9 29 0.00063 30.5 3.8 34 8-41 114-153 (174)
49 TIGR02945 SUF_assoc FeS assemb 44.3 29 0.00063 26.7 3.3 21 22-42 58-78 (99)
50 cd02410 archeal_CPSF_KH The ar 43.4 76 0.0017 27.5 6.0 57 19-78 53-114 (145)
51 PF14492 EFG_II: Elongation Fa 43.0 1.4E+02 0.003 22.2 7.1 58 10-67 7-68 (75)
52 KOG4034 Uncharacterized conser 42.9 50 0.0011 29.3 4.8 59 7-67 110-169 (169)
53 COG2151 PaaD Predicted metal-s 41.8 46 0.001 27.5 4.2 33 9-41 51-89 (111)
54 COG3062 NapD Uncharacterized p 41.2 87 0.0019 25.5 5.6 46 19-65 18-63 (94)
55 PRK14440 acylphosphatase; Prov 40.8 1.7E+02 0.0037 22.7 7.8 69 6-76 2-76 (90)
56 PF05137 PilN: Fimbrial assemb 39.8 1.4E+02 0.003 21.3 6.2 47 32-78 12-59 (78)
57 cd00590 RRM RRM (RNA recogniti 39.5 1.1E+02 0.0023 19.9 7.4 53 11-65 2-60 (74)
58 cd04879 ACT_3PGDH-like ACT_3PG 39.2 54 0.0012 21.9 3.7 18 21-38 52-69 (71)
59 PRK14054 methionine sulfoxide 38.9 69 0.0015 28.2 5.2 47 18-64 10-77 (172)
60 PF01849 NAC: NAC domain; Int 38.8 34 0.00073 24.5 2.7 29 22-50 2-35 (58)
61 cd03421 SirA_like_N SirA_like_ 38.6 65 0.0014 23.0 4.2 48 11-68 2-51 (67)
62 PF05258 DUF721: Protein of un 37.7 52 0.0011 23.9 3.7 36 40-75 45-89 (89)
63 PF12685 SpoIIIAH: SpoIIIAH-li 36.9 1.4E+02 0.003 26.1 6.8 53 22-75 138-195 (196)
64 PRK10819 transport protein Ton 36.7 3.1E+02 0.0067 25.3 9.2 8 72-79 49-56 (246)
65 TIGR02898 spore_YhcN_YlaJ spor 36.3 1.1E+02 0.0024 26.6 6.0 33 19-51 54-86 (158)
66 PRK14425 acylphosphatase; Prov 36.0 2.1E+02 0.0046 22.4 8.1 74 1-77 1-80 (94)
67 PF13193 AMP-binding_C: AMP-bi 35.5 1.3E+02 0.0028 21.4 5.4 45 24-68 2-50 (73)
68 PF03958 Secretin_N: Bacterial 35.2 72 0.0016 23.1 4.1 16 36-51 47-62 (82)
69 PRK10555 aminoglycoside/multid 35.2 58 0.0013 35.5 5.0 45 21-65 159-210 (1037)
70 PF00679 EFG_C: Elongation fac 33.4 2.1E+02 0.0045 21.5 8.9 57 8-68 8-67 (89)
71 PRK11023 outer membrane lipopr 32.3 1.1E+02 0.0023 26.9 5.3 38 20-58 128-167 (191)
72 cd04878 ACT_AHAS N-terminal AC 31.5 94 0.002 20.8 3.9 31 6-37 41-71 (72)
73 PF01037 AsnC_trans_reg: AsnC 31.4 1.8E+02 0.0039 20.2 8.5 46 19-64 10-55 (74)
74 TIGR00412 redox_disulf_2 small 31.2 2E+02 0.0044 20.9 5.9 22 11-32 3-28 (76)
75 COG3643 Glutamate formiminotra 31.0 83 0.0018 30.1 4.6 54 14-68 10-68 (302)
76 PRK09577 multidrug efflux prot 30.7 79 0.0017 34.5 5.1 46 21-66 158-210 (1032)
77 cd03423 SirA SirA (also known 30.1 1.8E+02 0.0039 21.1 5.4 46 14-68 6-52 (69)
78 PRK00435 ef1B elongation facto 29.7 86 0.0019 24.8 3.9 36 5-40 47-83 (88)
79 TIGR00915 2A0602 The (Largely 29.6 82 0.0018 34.4 5.0 45 21-65 159-210 (1044)
80 PRK01192 50S ribosomal protein 29.4 1.9E+02 0.0041 23.1 5.7 54 1-68 1-64 (89)
81 PRK14435 acylphosphatase; Prov 29.3 2.7E+02 0.0059 21.6 7.7 68 7-76 2-75 (90)
82 PRK15127 multidrug efflux syst 29.3 87 0.0019 34.3 5.1 44 22-65 160-210 (1049)
83 PRK14447 acylphosphatase; Prov 28.9 2.8E+02 0.0062 21.7 7.5 68 8-76 5-78 (95)
84 PRK15078 polysaccharide export 28.8 1.2E+02 0.0025 29.6 5.4 59 10-68 133-204 (379)
85 cd02973 TRX_GRX_like Thioredox 28.6 1E+02 0.0022 21.2 3.8 22 9-31 3-24 (67)
86 PRK00299 sulfur transfer prote 28.3 2.5E+02 0.0053 21.2 6.1 51 9-68 10-62 (81)
87 cd04887 ACT_MalLac-Enz ACT_Mal 28.3 1.7E+02 0.0038 20.4 5.0 34 6-39 39-72 (74)
88 PRK11152 ilvM acetolactate syn 28.1 1.2E+02 0.0027 23.2 4.4 34 5-40 43-76 (76)
89 TIGR02024 FtcD glutamate formi 28.0 78 0.0017 30.4 3.9 53 20-73 19-73 (298)
90 PRK13763 putative RNA-processi 27.9 1.8E+02 0.0039 25.3 5.9 41 8-49 4-48 (180)
91 COG2097 RPL31A Ribosomal prote 27.7 2.3E+02 0.005 22.8 6.0 53 1-68 1-63 (89)
92 COG2177 FtsX Cell division pro 27.6 1.6E+02 0.0034 28.0 5.9 46 9-68 63-108 (297)
93 TIGR00489 aEF-1_beta translati 27.6 1.1E+02 0.0023 24.3 4.1 22 19-40 62-83 (88)
94 PRK10568 periplasmic protein; 27.2 2.1E+02 0.0045 25.3 6.3 33 21-54 141-175 (203)
95 PRK10509 bacterioferritin-asso 27.2 32 0.0007 25.4 1.0 22 10-31 32-53 (64)
96 PF00708 Acylphosphatase: Acyl 27.0 2.8E+02 0.0061 21.0 7.8 70 7-77 4-78 (91)
97 PF02983 Pro_Al_protease: Alph 26.8 1.7E+02 0.0037 21.3 4.8 29 23-51 8-42 (62)
98 TIGR02189 GlrX-like_plant Glut 25.8 2.9E+02 0.0063 21.4 6.3 49 9-67 10-58 (99)
99 PF04459 DUF512: Protein of un 25.5 1.6E+02 0.0034 26.5 5.3 25 40-65 135-159 (204)
100 KOG3432 Vacuolar H+-ATPase V1 25.5 1.1E+02 0.0024 25.9 3.9 43 31-76 24-66 (121)
101 cd03420 SirA_RHOD_Pry_redox Si 25.3 1.7E+02 0.0037 21.2 4.6 49 11-68 2-52 (69)
102 PRK05528 methionine sulfoxide 25.2 1.8E+02 0.0039 25.2 5.4 47 18-64 8-70 (156)
103 PRK14451 acylphosphatase; Prov 25.2 3.3E+02 0.0071 21.1 7.6 58 6-64 2-63 (89)
104 PRK00058 methionine sulfoxide 24.6 1.5E+02 0.0033 27.1 5.1 48 18-65 52-120 (213)
105 KOG1924 RhoA GTPase effector D 24.2 2.6E+02 0.0057 30.9 7.3 7 224-230 630-636 (1102)
106 PF12229 PG_binding_4: Putativ 24.1 2.3E+02 0.005 21.1 5.3 45 22-67 53-107 (114)
107 TIGR03027 pepcterm_export puta 24.0 2.3E+02 0.0049 23.9 5.7 68 10-77 38-124 (165)
108 TIGR03028 EpsE polysaccharide 23.5 2.6E+02 0.0057 25.0 6.3 58 10-67 39-110 (239)
109 PRK00378 nucleoid-associated p 23.4 83 0.0018 29.5 3.2 29 35-66 303-331 (334)
110 TIGR00268 conserved hypothetic 23.3 3E+02 0.0064 24.8 6.7 47 21-68 187-240 (252)
111 cd03422 YedF YedF is a bacteri 23.3 2.4E+02 0.0051 20.5 5.0 46 14-68 6-52 (69)
112 cd00291 SirA_YedF_YeeD SirA, Y 23.1 2.7E+02 0.0058 19.4 5.5 46 14-68 6-52 (69)
113 COG2092 EFB1 Translation elong 23.1 1.3E+02 0.0029 24.1 3.8 36 5-40 47-83 (88)
114 TIGR00914 2A0601 heavy metal e 23.0 1.2E+02 0.0025 33.2 4.6 49 19-67 698-755 (1051)
115 cd04902 ACT_3PGDH-xct C-termin 22.9 1.6E+02 0.0034 20.3 3.9 16 23-38 54-69 (73)
116 cd00292 EF1B Elongation factor 22.4 1.4E+02 0.0031 23.5 3.9 22 19-40 62-83 (88)
117 PF08712 Nfu_N: Scaffold prote 22.3 1.4E+02 0.0031 23.1 3.9 45 22-68 37-82 (87)
118 PF00873 ACR_tran: AcrB/AcrD/A 21.8 1.5E+02 0.0033 31.9 5.2 51 18-68 686-745 (1021)
119 KOG0921 Dosage compensation co 21.7 1E+02 0.0022 34.5 3.8 14 197-210 1184-1197(1282)
120 TIGR01676 GLDHase galactonolac 21.6 1.1E+02 0.0025 31.4 4.0 37 30-67 109-146 (541)
121 PF08478 POTRA_1: POTRA domain 21.5 85 0.0018 22.0 2.3 30 21-50 36-66 (69)
122 cd06407 PB1_NLP A PB1 domain i 21.4 3.1E+02 0.0068 21.1 5.6 56 8-64 11-70 (82)
123 PRK13014 methionine sulfoxide 21.3 1.5E+02 0.0033 26.5 4.3 46 19-64 16-82 (186)
124 PF09122 DUF1930: Domain of un 21.3 1.1E+02 0.0024 23.5 2.9 44 6-49 18-62 (68)
125 TIGR03143 AhpF_homolog putativ 20.9 3.9E+02 0.0084 26.9 7.6 32 9-40 480-514 (555)
126 PF01565 FAD_binding_4: FAD bi 20.5 1.4E+02 0.0031 23.5 3.6 33 34-67 53-86 (139)
127 TIGR02200 GlrX_actino Glutared 20.4 2.2E+02 0.0049 19.5 4.3 30 9-40 2-31 (77)
128 cd02429 PTH2_like Peptidyl-tRN 20.3 4.9E+02 0.011 21.5 6.8 57 5-64 54-111 (116)
129 cd04876 ACT_RelA-SpoT ACT dom 20.2 2.4E+02 0.0052 17.8 4.9 17 21-37 53-69 (71)
No 1
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.53 E-value=3.5e-14 Score=106.05 Aligned_cols=67 Identities=33% Similarity=0.500 Sum_probs=62.1
Q ss_pred ceEEEEEEeccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcCCccceeEEe
Q 025287 6 VTTMVLKVDLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGEGSIKSIAIL 76 (255)
Q Consensus 6 vtt~vLKV~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKggk~IK~IEIV 76 (255)
+++.+|+|+|||+||+.+|++.|+.+.||.++.+|.++++|||.|. ++++.|+++|++.+++ ++++|
T Consensus 4 ~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~-~~p~~vl~~l~k~~~k---~~~~~ 70 (73)
T KOG1603|consen 4 IKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGN-VDPVKLLKKLKKTGGK---RAELW 70 (73)
T ss_pred ccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEe-cCHHHHHHHHHhcCCC---ceEEe
Confidence 5689999999999999999999999999999999999999999999 9999999999997756 56555
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=99.48 E-value=1.4e-13 Score=97.61 Aligned_cols=58 Identities=34% Similarity=0.470 Sum_probs=53.5
Q ss_pred EEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEee--cCHHHHHHHHHHhcC
Q 025287 10 VLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVC--CSPEKIRDKLCCKGE 67 (255)
Q Consensus 10 vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~--vdpekLv~aL~kKgg 67 (255)
+|+| +|+|.+|+++|+++|.+++||+++++|+.+++|+|+++. ++.++|+++|++.|+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy 61 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGY 61 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTS
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCc
Confidence 6899 999999999999999999999999999999999999972 356999999999876
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.38 E-value=2e-12 Score=96.40 Aligned_cols=63 Identities=22% Similarity=0.290 Sum_probs=56.8
Q ss_pred ceEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe--ecCHHHHHHHHHHhcCC
Q 025287 6 VTTMVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV--CCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 6 vtt~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~--~vdpekLv~aL~kKggk 68 (255)
|+++.|+| +|+|+||+++|+++|.+++||.+|++|+..++++|+.+ .++.++|+++|.+.|++
T Consensus 1 ~~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~ 66 (71)
T COG2608 1 MMKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYK 66 (71)
T ss_pred CceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCC
Confidence 45789999 99999999999999999999999999999966666654 37999999999999987
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.81 E-value=1.3e-08 Score=91.81 Aligned_cols=76 Identities=22% Similarity=0.389 Sum_probs=64.5
Q ss_pred CCCCCceEEEEEEeccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcCCccceeEEeCCCC
Q 025287 1 MGEKKVTTMVLKVDLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGEGSIKSIAILEPEK 80 (255)
Q Consensus 1 Ma~k~vtt~vLKV~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKggk~IK~IEIVspep 80 (255)
|+.+-..+++|.|.|+|.+|++.|+++|..+.||++|+||+.++.|.|.+. +.+..|.++|+..|+ ++-|.-...
T Consensus 1 mtSd~~~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts-~p~s~i~~~le~tGr----~Avl~G~G~ 75 (247)
T KOG4656|consen 1 MTSDDTYEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETS-VPPSEIQNTLENTGR----DAVLRGAGK 75 (247)
T ss_pred CCcCCceeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEcc-CChHHHHHHHHhhCh----heEEecCCc
Confidence 455445678999999999999999999999999999999999999999998 899999999997554 455555543
Q ss_pred C
Q 025287 81 P 81 (255)
Q Consensus 81 p 81 (255)
+
T Consensus 76 p 76 (247)
T KOG4656|consen 76 P 76 (247)
T ss_pred h
Confidence 3
No 5
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.19 E-value=3.6e-06 Score=86.91 Aligned_cols=59 Identities=22% Similarity=0.377 Sum_probs=52.9
Q ss_pred eEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcCC
Q 025287 7 TTMVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 7 tt~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKggk 68 (255)
++++|+| +|+|.+|+++|+++|.+++||.++.+|++ +++|++. .+.+.|.++|++.|++
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~-~~~~~i~~~i~~~Gy~ 62 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGT-ASAEALIETIKQAGYD 62 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEec-CCHHHHHHHHHhcCCc
Confidence 4689999 99999999999999999999999999994 5666666 7899999999988875
No 6
>PLN02957 copper, zinc superoxide dismutase
Probab=98.12 E-value=1.9e-05 Score=70.98 Aligned_cols=66 Identities=18% Similarity=0.273 Sum_probs=58.6
Q ss_pred EEEEEEeccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcCCccceeEEeCC
Q 025287 8 TMVLKVDLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGEGSIKSIAILEP 78 (255)
Q Consensus 8 t~vLKV~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKggk~IK~IEIVsp 78 (255)
++.|.|+|+|.+|+++|+++|.+++||.++.+|+.+++++|.+. .+...|+.+|++.++. ++++..
T Consensus 7 ~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~-~~~~~I~~aIe~~Gy~----a~~~~~ 72 (238)
T PLN02957 7 LTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGS-SPVKAMTAALEQTGRK----ARLIGQ 72 (238)
T ss_pred EEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEec-CCHHHHHHHHHHcCCc----EEEecC
Confidence 67788899999999999999999999999999999999999986 7888899999987764 566654
No 7
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.93 E-value=0.00012 Score=46.70 Aligned_cols=61 Identities=13% Similarity=0.310 Sum_probs=50.3
Q ss_pred eEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe--ecCHHHHHHHHHHhcC
Q 025287 7 TTMVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV--CCSPEKIRDKLCCKGE 67 (255)
Q Consensus 7 tt~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~--~vdpekLv~aL~kKgg 67 (255)
+++.|.| +|+|..|...|++.|..+.++..+.+++..+++.|... ..+...+...|...++
T Consensus 2 ~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ 65 (68)
T TIGR00003 2 QKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGY 65 (68)
T ss_pred cEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCC
Confidence 4578999 99999999999999999999999999999999998753 1356667666665554
No 8
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.30 E-value=0.0006 Score=70.68 Aligned_cols=61 Identities=18% Similarity=0.342 Sum_probs=54.6
Q ss_pred eEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEee--cC-HHHHHHHHHHhcCC
Q 025287 7 TTMVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVC--CS-PEKIRDKLCCKGEG 68 (255)
Q Consensus 7 tt~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~--vd-pekLv~aL~kKggk 68 (255)
.+..|.| +|||..|+.+|+ +|.+++||.++.+|+.+++++|..+. .+ .+.+..+++..|+.
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~ 66 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYS 66 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCcc
Confidence 3578999 999999999999 99999999999999999999998751 45 68899999998886
No 9
>PTZ00449 104 kDa microneme/rhoptry antigen; Provisional
Probab=96.92 E-value=0.0054 Score=62.68 Aligned_cols=10 Identities=30% Similarity=0.172 Sum_probs=4.2
Q ss_pred HHHHHHhcCC
Q 025287 59 RDKLCCKGEG 68 (255)
Q Consensus 59 v~aL~kKggk 68 (255)
+++|.++..+
T Consensus 485 ikklikkskk 494 (943)
T PTZ00449 485 IKKLIKKSKK 494 (943)
T ss_pred HHHHHHHhhc
Confidence 3344444444
No 10
>PTZ00449 104 kDa microneme/rhoptry antigen; Provisional
Probab=96.74 E-value=0.0092 Score=61.04 Aligned_cols=69 Identities=46% Similarity=1.041 Sum_probs=31.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---------CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025287 89 KEPEKPKAPEKPKEPEKPKQPEKPKEPEKPKQPEKPKEPE---------KPKEPEKPKEPEKPKEPAKPKEPEKPKEP 157 (255)
Q Consensus 89 ~~pe~p~~pe~p~~p~~p~~pe~P~~pe~P~~pekpk~pe---------~p~~pekp~~pe~p~~pe~p~~p~~p~~~ 157 (255)
+.|+-|+.|+-|++|+.|+.|+.|+.++.|..|..|+.|| .|..++.||.|..|..|+.|+.|+.|+-+
T Consensus 577 K~Pe~PK~Pk~PKdPksPK~PK~Prspq~P~~PkSPk~Pe~~d~PkSPK~PespksPKsP~sPqrP~SPkRPEsPKiP 654 (943)
T PTZ00449 577 KKPEFPKDPKHPKDPEEPKKPKRPRSAQRPTRPKSPKLPELLDIPKSPKRPESPKSPKRPPPPQRPSSPERPEGPKII 654 (943)
T ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCC
Confidence 4455555555555555555555555444444444333222 22222333344444444444444444433
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.67 E-value=0.005 Score=64.06 Aligned_cols=60 Identities=18% Similarity=0.359 Sum_probs=52.8
Q ss_pred EEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcCC
Q 025287 8 TMVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 8 t~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKggk 68 (255)
.+.|.| +|+|.+|...|++.|.+++||.++.+++.++++.|.+. .+.+.+.+.|.+.|+.
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~-~s~~~I~~~I~~~Gy~ 160 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGS-ASPQDLVQAVEKAGYG 160 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEcc-CCHHHHHHHHHhcCCC
Confidence 567889 99999999999999999999999999999999998765 6788888888876554
No 12
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.48 E-value=0.0063 Score=64.63 Aligned_cols=62 Identities=18% Similarity=0.314 Sum_probs=56.2
Q ss_pred eEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe--ecCHHHHHHHHHHhcCC
Q 025287 7 TTMVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV--CCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 7 tt~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~--~vdpekLv~aL~kKggk 68 (255)
.++.|.| +|.|.+|..+|++.|.+++||+++++|+.++++.|..+ ...+-++++.|...+..
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~ 210 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFE 210 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhccc
Confidence 4789999 99999999999999999999999999999999999875 26788999999987765
No 13
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.24 E-value=0.014 Score=60.33 Aligned_cols=61 Identities=13% Similarity=0.206 Sum_probs=48.5
Q ss_pred EEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcCC
Q 025287 8 TMVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 8 t~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKggk 68 (255)
.+.|+| +|+|.+|..+|+++|.+++||.++.+++.++++.|..+....+.+.+.+...|+.
T Consensus 54 r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~ 115 (741)
T PRK11033 54 RYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFS 115 (741)
T ss_pred eEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccc
Confidence 567889 9999999999999999999999999999999988875411125555666655443
No 14
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=95.45 E-value=0.024 Score=60.42 Aligned_cols=61 Identities=20% Similarity=0.373 Sum_probs=54.0
Q ss_pred eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-ecCHHHHHHHHHHhcCCccceeEEeCC
Q 025287 14 DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-CCSPEKIRDKLCCKGEGSIKSIAILEP 78 (255)
Q Consensus 14 ~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-~vdpekLv~aL~kKggk~IK~IEIVsp 78 (255)
+|+|..|.+.|+++|...+||.++.|++.++..+|..+ .++++.|++.|+..|++ +++++.
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ied~gf~----~~~~~~ 63 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIEDMGFE----ASLLSD 63 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhhcccce----eeeccc
Confidence 79999999999999999999999999999999888764 47999999999998775 666554
No 15
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=93.18 E-value=0.39 Score=38.82 Aligned_cols=72 Identities=15% Similarity=0.172 Sum_probs=51.0
Q ss_pred CceEEEEEE-eccChhhHHHHHHHHhcCCCceeEEE-------EcCCCeEEEEEeecCHHHHHHHHHHhcCCccceeEEe
Q 025287 5 KVTTMVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIF-------DEKTNTVRIKVVCCSPEKIRDKLCCKGEGSIKSIAIL 76 (255)
Q Consensus 5 ~vtt~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~V-------Dlk~~kVTVeG~~vdpekLv~aL~kKggk~IK~IEIV 76 (255)
+...++|-| -=|-+-=.-.+-+.|++|+||+.|.+ +-.+=++||+|+.+|-+.|.+.|.+.|+ +|.+|.-|
T Consensus 4 ~iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg-~IHSiDev 82 (97)
T COG1888 4 GIRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGG-AIHSIDEV 82 (97)
T ss_pred cceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCC-eeeehhhh
Confidence 355566666 33334455667788999999877654 2346678889977999999999999766 67777544
Q ss_pred C
Q 025287 77 E 77 (255)
Q Consensus 77 s 77 (255)
-
T Consensus 83 v 83 (97)
T COG1888 83 V 83 (97)
T ss_pred h
Confidence 3
No 16
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=92.91 E-value=0.35 Score=39.07 Aligned_cols=73 Identities=18% Similarity=0.167 Sum_probs=49.5
Q ss_pred CceEEEEEEeccChhhHHHHHHHHhcCCCceeEEE-----EcCC--CeEEEEEeecCHHHHHHHHHHhcCCccceeEEeC
Q 025287 5 KVTTMVLKVDLQCSKCYKKVKKVLCKFPQIQDQIF-----DEKT--NTVRIKVVCCSPEKIRDKLCCKGEGSIKSIAILE 77 (255)
Q Consensus 5 ~vtt~vLKV~M~C~gCakKIkKAL~kI~GV~sV~V-----Dlk~--~kVTVeG~~vdpekLv~aL~kKggk~IK~IEIVs 77 (255)
+++.++|-|-.-=+==.-.+-++|++++||..|.+ |..+ =+|||+|..+|.+.|.++|.+.|+ +|.+|.-|.
T Consensus 3 ~irRlVLDVlKP~~p~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg-~IHSIDeVv 81 (95)
T PF02680_consen 3 GIRRLVLDVLKPHEPSIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGG-VIHSIDEVV 81 (95)
T ss_dssp SEEEEEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT--EEEEEEEEE
T ss_pred ceeEEEEEeecCCCCCHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCC-eEEeeeeee
Confidence 45667777733333445678899999999888774 3333 346667876999999999998766 688886554
Q ss_pred C
Q 025287 78 P 78 (255)
Q Consensus 78 p 78 (255)
.
T Consensus 82 a 82 (95)
T PF02680_consen 82 A 82 (95)
T ss_dssp E
T ss_pred e
Confidence 4
No 17
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=90.21 E-value=3 Score=29.35 Aligned_cols=59 Identities=19% Similarity=0.248 Sum_probs=43.2
Q ss_pred EEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe--ecCHHHHHHHHHHhc
Q 025287 8 TMVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV--CCSPEKIRDKLCCKG 66 (255)
Q Consensus 8 t~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~--~vdpekLv~aL~kKg 66 (255)
.+.+.+ +++|.+|...++..+....|+....+++....+.+... ..+...+...+...+
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g 85 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAG 85 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcC
Confidence 456777 99999999999999999999999999888887666521 134444444444433
No 18
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=85.89 E-value=4.4 Score=22.67 Aligned_cols=37 Identities=24% Similarity=0.531 Sum_probs=31.6
Q ss_pred eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEE
Q 025287 14 DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKV 50 (255)
Q Consensus 14 ~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG 50 (255)
+++|.+|...++..+..+.++....+++....+.+..
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 42 (63)
T cd00371 6 GMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEY 42 (63)
T ss_pred CeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEE
Confidence 8899999999999999999988888887777766654
No 19
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=80.01 E-value=5.6 Score=29.25 Aligned_cols=47 Identities=28% Similarity=0.347 Sum_probs=34.8
Q ss_pred HhcCCCceeEEEEcCCCeEEEE--EeecCHHHHHHHHHHhcCCccceeEEeCC
Q 025287 28 LCKFPQIQDQIFDEKTNTVRIK--VVCCSPEKIRDKLCCKGEGSIKSIAILEP 78 (255)
Q Consensus 28 L~kI~GV~sV~VDlk~~kVTVe--G~~vdpekLv~aL~kKggk~IK~IEIVsp 78 (255)
|..++||.++..+. ++.++|. .. .+..+|++.|...|. |.++++..|
T Consensus 26 l~~~~~v~~v~~~~-~~~~~i~l~~~-~~~~~ll~~l~~~g~--I~~f~~~~P 74 (84)
T PF13732_consen 26 LEELPGVESVEQDG-DGKLRIKLEDE-ETANELLQELIEKGI--IRSFEEEEP 74 (84)
T ss_pred HhhCCCeEEEEEeC-CcEEEEEECCc-ccHHHHHHHHHhCCC--eeEEEEcCC
Confidence 88999999998763 4435554 33 678999999998754 888877654
No 20
>PRK13748 putative mercuric reductase; Provisional
Probab=79.81 E-value=6.8 Score=38.54 Aligned_cols=57 Identities=23% Similarity=0.446 Sum_probs=44.1
Q ss_pred EEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-ecCHHHHHHHHHHhc
Q 025287 10 VLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-CCSPEKIRDKLCCKG 66 (255)
Q Consensus 10 vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-~vdpekLv~aL~kKg 66 (255)
.|.+ +|+|.+|..+++..+..++++....+++..+.+.+... ..+...+...+...+
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g 61 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLG 61 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcC
Confidence 4667 99999999999999999999999999999998777742 134555555555433
No 21
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=76.04 E-value=5 Score=29.10 Aligned_cols=32 Identities=13% Similarity=0.410 Sum_probs=22.7
Q ss_pred EEEEEEeccChhhH------HHHHHHHhcCCCceeEEE
Q 025287 8 TMVLKVDLQCSKCY------KKVKKVLCKFPQIQDQIF 39 (255)
Q Consensus 8 t~vLKV~M~C~gCa------kKIkKAL~kI~GV~sV~V 39 (255)
++.|.+.+...+|. ..|+++|..|+||.+|+|
T Consensus 35 ~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 35 KVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp EEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 46666666666664 788999999999999986
No 22
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=75.24 E-value=4.3 Score=28.49 Aligned_cols=41 Identities=17% Similarity=0.195 Sum_probs=21.3
Q ss_pred HHHHHHHhc---CCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHH
Q 025287 22 KKVKKVLCK---FPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCC 64 (255)
Q Consensus 22 kKIkKAL~k---I~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~k 64 (255)
.+|+.+|.. +++- ++.+...++.|++.|. ++-...++++..
T Consensus 2 ~~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~-v~s~~~~~~a~~ 45 (64)
T PF04972_consen 2 TKVRAALRADPWLPDS-NISVSVENGVVTLSGE-VPSQEQRDAAER 45 (64)
T ss_dssp -----------CTT-T-TEEEEEECTEEEEEEE-ESSCHHHHHHHH
T ss_pred cccccccccccccCCC-eEEEEEECCEEEEEee-CcHHHHHHhHHh
Confidence 467788877 4455 7899999999999998 543334444433
No 23
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=74.52 E-value=11 Score=27.15 Aligned_cols=50 Identities=24% Similarity=0.252 Sum_probs=36.9
Q ss_pred EEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-ecCHHHHHHHHHHhcCC
Q 025287 10 VLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-CCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 10 vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-~vdpekLv~aL~kKggk 68 (255)
+|-+ ++.|-...-+++++|.+++. ++.+.|..+ ....++|...+.+.|++
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~---------G~~l~v~~d~~~~~~di~~~~~~~g~~ 53 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPP---------GEVLEVLVDDPAAVEDIPRWCEENGYE 53 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGT---------T-EEEEEESSTTHHHHHHHHHHHHTEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCC---------CCEEEEEECCccHHHHHHHHHHHCCCE
Confidence 5677 99999999999999999963 345555554 24567788889888775
No 24
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=71.29 E-value=30 Score=24.18 Aligned_cols=59 Identities=12% Similarity=0.121 Sum_probs=38.0
Q ss_pred EEEEeccC-hhhHHHHHHHHhcCCC-ceeEEEEcC----CCeEEEEEeecCHHHHHHHHHHhcCC
Q 025287 10 VLKVDLQC-SKCYKKVKKVLCKFPQ-IQDQIFDEK----TNTVRIKVVCCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 10 vLKV~M~C-~gCakKIkKAL~kI~G-V~sV~VDlk----~~kVTVeG~~vdpekLv~aL~kKggk 68 (255)
.|.|.|.- .|-..+|.+.|.+... |.++..... ...|+|.....+.+.+++.|+++|.+
T Consensus 3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L~~~G~~ 67 (72)
T cd04883 3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNPRPIIEDLRRAGYE 67 (72)
T ss_pred EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCHHHHHHHHHHCCCe
Confidence 34444443 3678888888887753 666654332 23355554435777999999999876
No 25
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=70.35 E-value=12 Score=31.42 Aligned_cols=47 Identities=9% Similarity=0.041 Sum_probs=34.0
Q ss_pred HHHHHHHHhcCC-CceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcCC
Q 025287 21 YKKVKKVLCKFP-QIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 21 akKIkKAL~kI~-GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKggk 68 (255)
+.+|.++|.+.. ++.++.|...++.|++.|. +.-...+.+|....+.
T Consensus 28 ~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~-v~s~~~~~~~~~aa~~ 75 (147)
T PRK11198 28 ADALKEHISKQGLGDADVNVQVEDGKATVSGD-AASQEAKEKILLAVGN 75 (147)
T ss_pred HHHHHHHHHhcCCCcCCceEEEeCCEEEEEEE-eCCHHHHHHHHHHhcc
Confidence 466777776642 4666777888999999998 7666677777766654
No 26
>smart00362 RRM_2 RNA recognition motif.
Probab=68.13 E-value=30 Score=22.50 Aligned_cols=54 Identities=19% Similarity=0.197 Sum_probs=40.4
Q ss_pred EEE-eccChhhHHHHHHHHhcCCCceeEEEEcCC----CeEEEEEeecCHHHHHHHHHHhc
Q 025287 11 LKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKT----NTVRIKVVCCSPEKIRDKLCCKG 66 (255)
Q Consensus 11 LKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~----~kVTVeG~~vdpekLv~aL~kKg 66 (255)
|.| ++...-....|++.|.....|..+.+.... +.+.|+.. +.+....+|...-
T Consensus 2 v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~--~~~~a~~a~~~~~ 60 (72)
T smart00362 2 LFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFE--SEEDAEKAIEALN 60 (72)
T ss_pred EEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeC--CHHHHHHHHHHhC
Confidence 456 788888889999999999999999887766 67777753 4555556665543
No 27
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=68.10 E-value=23 Score=27.88 Aligned_cols=44 Identities=14% Similarity=0.205 Sum_probs=33.6
Q ss_pred HHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHH
Q 025287 21 YKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCC 64 (255)
Q Consensus 21 akKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~k 64 (255)
...|+++|..++|++=...|..+||+.|+-..-+...+.+.|..
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~~ 62 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIES 62 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHHH
Confidence 78899999999999888888878887776543456666665554
No 28
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=67.28 E-value=30 Score=26.41 Aligned_cols=44 Identities=18% Similarity=0.277 Sum_probs=32.6
Q ss_pred hHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHH
Q 025287 20 CYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCC 64 (255)
Q Consensus 20 CakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~k 64 (255)
=...|+.+|..++|++=...|.+ +++.|+-..-+...+.+.|..
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~ 59 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDA 59 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHH
Confidence 35789999999999966666766 777776543566777777765
No 29
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=66.77 E-value=13 Score=32.19 Aligned_cols=41 Identities=17% Similarity=0.257 Sum_probs=33.7
Q ss_pred EEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcC-CCeEEEE
Q 025287 8 TMVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEK-TNTVRIK 49 (255)
Q Consensus 8 t~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk-~~kVTVe 49 (255)
.|+|.| .-.|+.|...|.+...++ |+.+++|... ++++.+.
T Consensus 101 ~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~~~ 143 (146)
T PF14437_consen 101 SMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVYYW 143 (146)
T ss_pred eEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEEEe
Confidence 688999 677999999998888777 8999999776 7766553
No 30
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=65.65 E-value=28 Score=27.08 Aligned_cols=60 Identities=25% Similarity=0.212 Sum_probs=44.9
Q ss_pred ceEEEEEEeccChhhHHHHHHHHhcCCC-ceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcC
Q 025287 6 VTTMVLKVDLQCSKCYKKVKKVLCKFPQ-IQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGE 67 (255)
Q Consensus 6 vtt~vLKV~M~C~gCakKIkKAL~kI~G-V~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKgg 67 (255)
..|++=+|+=+=...++.++++|....+ -.++.|+..++.|.|.|+ . .+.|.++|.++|+
T Consensus 27 ~~T~IrkI~GD~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~-~-~~~Vk~wL~~~GF 87 (87)
T PF05046_consen 27 KITVIRKIEGDIWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGD-H-VEEVKKWLLEKGF 87 (87)
T ss_pred eEEEEEeecCCHHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCc-c-HHHHHHHHHHCcC
Confidence 3455566744446788888888876654 357889999999999997 3 6779999988764
No 31
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=65.35 E-value=7.2 Score=32.94 Aligned_cols=48 Identities=15% Similarity=0.172 Sum_probs=35.0
Q ss_pred hHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe----ecCHHHHHHHHHHhcC
Q 025287 20 CYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV----CCSPEKIRDKLCCKGE 67 (255)
Q Consensus 20 CakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~----~vdpekLv~aL~kKgg 67 (255)
=+.+|.+.|.+++||+++.+-..++.|.|-.. .....+|.+.|.++..
T Consensus 76 ~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~~~~~~~~~~~i~~~V~~~v~ 127 (177)
T PF09580_consen 76 LADRIANRVKKVPGVEDATVVVTDDNAYVAVDLDFNRFNTKKIKKKVEKAVK 127 (177)
T ss_pred HHHHHHHHHhcCCCceEEEEEEECCEEEEEEEecccccchhHHHHHHHHHHH
Confidence 36789999999999999999999999888654 1234445555544433
No 32
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=64.56 E-value=42 Score=26.82 Aligned_cols=57 Identities=16% Similarity=0.195 Sum_probs=34.5
Q ss_pred EEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEee-cCHHHHHHHHHHh
Q 025287 9 MVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVC-CSPEKIRDKLCCK 65 (255)
Q Consensus 9 ~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~-vdpekLv~aL~kK 65 (255)
++|+| +++=+-+...|+.+|+.+..|.-|++...+..-.|.-.. -++..++.++...
T Consensus 2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhc
Confidence 35677 577666799999999999999999998877777776431 3467788888776
No 33
>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=63.27 E-value=22 Score=25.09 Aligned_cols=34 Identities=6% Similarity=0.114 Sum_probs=24.3
Q ss_pred ceEEEEEEeccChh-hHHHHHHHHhcCCCceeEEE
Q 025287 6 VTTMVLKVDLQCSK-CYKKVKKVLCKFPQIQDQIF 39 (255)
Q Consensus 6 vtt~vLKV~M~C~g-CakKIkKAL~kI~GV~sV~V 39 (255)
...+.|.|..+=.. --+.|.++|.+++||.+|.+
T Consensus 40 ~~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 40 RANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred eEEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 34455666555544 77888889999999988875
No 34
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=62.77 E-value=44 Score=29.41 Aligned_cols=69 Identities=23% Similarity=0.301 Sum_probs=44.4
Q ss_pred eEEEEEEeccChhhHHHH------------HHHHhcC------CCceeEEEEcCCCeEEEEEe---ec---CHHHHHHHH
Q 025287 7 TTMVLKVDLQCSKCYKKV------------KKVLCKF------PQIQDQIFDEKTNTVRIKVV---CC---SPEKIRDKL 62 (255)
Q Consensus 7 tt~vLKV~M~C~gCakKI------------kKAL~kI------~GV~sV~VDlk~~kVTVeG~---~v---dpekLv~aL 62 (255)
..+=+|-++-|.+|.++| .++|.+| .+++-.+.-..+++|.+... .. ---+.+++|
T Consensus 6 ~~~c~kt~ilC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gdg~aIGk~G~~ik~l 85 (166)
T PRK06418 6 CEVCVKTGLLCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGPRIPIGKGGKIAKAL 85 (166)
T ss_pred eeEEeccCccChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCCcccccccchHHHHH
Confidence 345566699999999975 5788887 33333333233577666532 00 123688899
Q ss_pred HHhcCCccceeEEeCC
Q 025287 63 CCKGEGSIKSIAILEP 78 (255)
Q Consensus 63 ~kKggk~IK~IEIVsp 78 (255)
+++.|| +|+||.-
T Consensus 86 ~~~lgk---~VevVE~ 98 (166)
T PRK06418 86 SRKLGK---KVRVVEK 98 (166)
T ss_pred HHHhCC---cEEEEEc
Confidence 999998 7777764
No 35
>PF08260 Kinin: Insect kinin peptide; InterPro: IPR013202 This entry represents neuropeptides that are the first members of the insect kinin-family isolated from the American cockroach. Their occurrence in the retrocerebral complex suggests a physiological role as a neurohormone. The C-terminal sequence Phe-X-Ser-Trp-Gly-NH2 characterised the peptides as members of the insect kinin family. Data suggest a possible involvement of insect kinins in water-balance by regulating the osmoregulation. Insect kinins also mediate visceral muscle contractile activity (myotropic activity) []. These peptides have lengths ranging from 6 to 14 amino acids [].
Probab=60.32 E-value=4.6 Score=19.28 Aligned_cols=8 Identities=25% Similarity=1.186 Sum_probs=5.5
Q ss_pred CCCccCCC
Q 025287 219 RPVYEGWA 226 (255)
Q Consensus 219 ~p~y~~~~ 226 (255)
+|+|++||
T Consensus 1 ~pafnswg 8 (8)
T PF08260_consen 1 DPAFNSWG 8 (8)
T ss_pred CccccccC
Confidence 36778875
No 36
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=58.87 E-value=48 Score=25.32 Aligned_cols=57 Identities=19% Similarity=0.229 Sum_probs=41.7
Q ss_pred EEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-ecCHHHHHHHHHHhcCCcccee
Q 025287 8 TMVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-CCSPEKIRDKLCCKGEGSIKSI 73 (255)
Q Consensus 8 t~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-~vdpekLv~aL~kKggk~IK~I 73 (255)
..+|-+ |++|-.=.-.++++|.+|+ .+..+.|..+ .....+|-..+++.|+-.+..+
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~---------~Ge~LeV~~ddp~~~~dIp~~~~~~~~~~ll~~ 63 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLK---------PGEILEVIADDPAAKEDIPAWAKKEGGHELLEV 63 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCC---------CCCEEEEEecCcchHHHHHHHHHHcCCcEEEEE
Confidence 568888 9999999999999999997 4555666554 2455778888887775333333
No 37
>PRK11018 hypothetical protein; Provisional
Probab=58.83 E-value=43 Score=25.21 Aligned_cols=51 Identities=12% Similarity=0.005 Sum_probs=38.5
Q ss_pred EEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-ecCHHHHHHHHHHhcCC
Q 025287 9 MVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-CCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 9 ~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-~vdpekLv~aL~kKggk 68 (255)
.+|-+ |+.|-.=.-+.+++|.++.. ++.+.|..+ ..+...|...+++.|++
T Consensus 9 ~~lD~rG~~CP~Pvl~~kk~l~~l~~---------G~~L~V~~d~~~a~~di~~~~~~~G~~ 61 (78)
T PRK11018 9 YRLDMVGEPCPYPAVATLEALPQLKK---------GEILEVVSDCPQSINNIPLDARNHGYT 61 (78)
T ss_pred eeEECCCCcCCHHHHHHHHHHHhCCC---------CCEEEEEeCCccHHHHHHHHHHHcCCE
Confidence 67778 99999999999999999963 334444443 14567888888888776
No 38
>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=58.65 E-value=63 Score=22.93 Aligned_cols=51 Identities=8% Similarity=-0.037 Sum_probs=37.7
Q ss_pred ec-cChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHh
Q 025287 14 DL-QCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCK 65 (255)
Q Consensus 14 ~M-~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kK 65 (255)
+| ...+...++-++|... +|.-+.....+..+++-.+.-|.++++++|.++
T Consensus 9 g~~~~~gv~~~~~~~L~~~-~i~~i~~~~s~~~is~vv~~~d~~~av~~LH~~ 60 (63)
T cd04920 9 GIRSLLHKLGPALEVFGKK-PVHLVSQAANDLNLTFVVDEDQADGLCARLHFQ 60 (63)
T ss_pred CcccCccHHHHHHHHHhcC-CceEEEEeCCCCeEEEEEeHHHHHHHHHHHHHH
Confidence 56 6788999999999875 888888888777887764434556666666654
No 39
>PRK11023 outer membrane lipoprotein; Provisional
Probab=57.25 E-value=30 Score=30.27 Aligned_cols=46 Identities=13% Similarity=0.039 Sum_probs=35.2
Q ss_pred HHHHHHHHhcCCCce---eEEEEcCCCeEEEEEeecCHHHHHHHHHHhcC
Q 025287 21 YKKVKKVLCKFPQIQ---DQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGE 67 (255)
Q Consensus 21 akKIkKAL~kI~GV~---sV~VDlk~~kVTVeG~~vdpekLv~aL~kKgg 67 (255)
..+|+.+|..-+++. ++.|+..++.|++.|. ++-+..+.+..+...
T Consensus 51 ~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~-V~~~~~k~~A~~ia~ 99 (191)
T PRK11023 51 ELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQ-SPNAELSERAKQIAM 99 (191)
T ss_pred HHHHHHHHhhCcccCcCceEEEEEECCEEEEEEE-eCCHHHHHHHHHHHh
Confidence 568888998877774 5888889999999998 766666666655444
No 40
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=56.01 E-value=63 Score=23.69 Aligned_cols=60 Identities=18% Similarity=0.096 Sum_probs=41.9
Q ss_pred EEEEEE-eccChhhHHHHHHHHhcCCC-ceeEEEEcCCCeEEEEE----eecCHHHHHHHHHHhcC
Q 025287 8 TMVLKV-DLQCSKCYKKVKKVLCKFPQ-IQDQIFDEKTNTVRIKV----VCCSPEKIRDKLCCKGE 67 (255)
Q Consensus 8 t~vLKV-~M~C~gCakKIkKAL~kI~G-V~sV~VDlk~~kVTVeG----~~vdpekLv~aL~kKgg 67 (255)
.++|.| +.+..|-...|.++|.+..+ |.+++...-.+..+..- ..-+.++|.+.|...+.
T Consensus 2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~~~~~~~l~~~L~~l~~ 67 (76)
T PF13740_consen 2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIPEDSLERLESALEELAE 67 (76)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEESHHHHHHHHHHHHHHHH
T ss_pred EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeCcccHHHHHHHHHHHHH
Confidence 578898 99999999999999999987 77777776667666543 21245566677766543
No 41
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=55.86 E-value=15 Score=26.86 Aligned_cols=10 Identities=20% Similarity=0.557 Sum_probs=8.2
Q ss_pred EeccChhhHH
Q 025287 13 VDLQCSKCYK 22 (255)
Q Consensus 13 V~M~C~gCak 22 (255)
++.+|..|..
T Consensus 6 ~~~~C~~C~~ 15 (76)
T PF13192_consen 6 FSPGCPYCPE 15 (76)
T ss_dssp ECSSCTTHHH
T ss_pred eCCCCCCcHH
Confidence 5888999983
No 42
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=53.26 E-value=34 Score=24.83 Aligned_cols=34 Identities=12% Similarity=0.223 Sum_probs=27.4
Q ss_pred CceEEEEEEeccChhhHHHHHHHHhcCCCceeEE
Q 025287 5 KVTTMVLKVDLQCSKCYKKVKKVLCKFPQIQDQI 38 (255)
Q Consensus 5 ~vtt~vLKV~M~C~gCakKIkKAL~kI~GV~sV~ 38 (255)
+...+.|.|.+.--.=-+.|.+.|.+++||.+|.
T Consensus 46 ~~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 46 GTARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp TEEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred CEEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 4566777777777777788999999999998874
No 43
>PRK10568 periplasmic protein; Provisional
Probab=52.11 E-value=42 Score=29.69 Aligned_cols=46 Identities=17% Similarity=0.168 Sum_probs=32.1
Q ss_pred hhhHHHHHHHHhcCCCce--eEEEEcCCCeEEEEEeecCHHHHHHHHHH
Q 025287 18 SKCYKKVKKVLCKFPQIQ--DQIFDEKTNTVRIKVVCCSPEKIRDKLCC 64 (255)
Q Consensus 18 ~gCakKIkKAL~kI~GV~--sV~VDlk~~kVTVeG~~vdpekLv~aL~k 64 (255)
..=..+|+.+|..-+++. ++.|...++.|++.|. ++-...++++..
T Consensus 59 ~~I~~~v~~~L~~~~~i~~~~I~V~v~~G~V~L~G~-V~s~~~~~~a~~ 106 (203)
T PRK10568 59 SAITAKVKAALVDHDNIKSTDISVKTHQKVVTLSGF-VESQAQAEEAVK 106 (203)
T ss_pred HHHHHHHHHHHHhCCCCCCCceEEEEECCEEEEEEE-eCCHHHHHHHHH
Confidence 344678888988777764 6778888999999998 553333333333
No 44
>smart00749 BON bacterial OsmY and nodulation domain.
Probab=48.99 E-value=76 Score=20.96 Aligned_cols=42 Identities=19% Similarity=0.090 Sum_probs=29.0
Q ss_pred HHHHHHHhcCCCcee--EEEEcCCCeEEEEEeecCHHHHHHHHH
Q 025287 22 KKVKKVLCKFPQIQD--QIFDEKTNTVRIKVVCCSPEKIRDKLC 63 (255)
Q Consensus 22 kKIkKAL~kI~GV~s--V~VDlk~~kVTVeG~~vdpekLv~aL~ 63 (255)
.+|+.+|...+.+.. +.+....+.|++.|.-.+.+.+..++.
T Consensus 2 ~~v~~~l~~~~~~~~~~~~v~~~~~~vvL~g~~~~~~~~~~~~~ 45 (62)
T smart00749 2 EKVKKALAKDGLIKADSIVVVTDGGVVVLLGGVVDNAEAAAAAA 45 (62)
T ss_pred hhHHHHHhhCCCCCcCceEEEEECCEEEEeeecCCHHHHHHHHH
Confidence 578999988887775 667778888988886234444444433
No 45
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=48.03 E-value=70 Score=26.67 Aligned_cols=43 Identities=9% Similarity=0.102 Sum_probs=32.6
Q ss_pred HHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHh
Q 025287 21 YKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCK 65 (255)
Q Consensus 21 akKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kK 65 (255)
-..++.+|.++ |.++|+.=+.+|.|.++.. .+.+.|..+|.+.
T Consensus 21 MaeLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~-~~~~~l~~~ie~~ 63 (137)
T PF08002_consen 21 MAELREALEDL-GFTNVRTYIQSGNVVFESD-RDPAELAAKIEKA 63 (137)
T ss_dssp HHHHHHHHHHC-T-EEEEEETTTTEEEEEES-S-HHHHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCceEEEeeCCEEEecC-CChHHHHHHHHHH
Confidence 45677788887 9999999999999999955 7777777666554
No 46
>PF14535 AMP-binding_C_2: AMP-binding enzyme C-terminal domain; PDB: 2Y27_A 2Y4N_A 3QOV_B 3S89_D 3LAX_A 2Y4O_B.
Probab=45.43 E-value=94 Score=23.85 Aligned_cols=57 Identities=18% Similarity=0.359 Sum_probs=34.2
Q ss_pred HHHHHHHhcCCCce-eEE--EE--cCCCeEEEEEee---cC---------HHHHHHHHHHhcCCccceeEEeCCC
Q 025287 22 KKVKKVLCKFPQIQ-DQI--FD--EKTNTVRIKVVC---CS---------PEKIRDKLCCKGEGSIKSIAILEPE 79 (255)
Q Consensus 22 kKIkKAL~kI~GV~-sV~--VD--lk~~kVTVeG~~---vd---------pekLv~aL~kKggk~IK~IEIVspe 79 (255)
..|+.+|.+++|+. ... ++ ...+.++|.... ++ .++|.++|+++.|=. -.|+|+++.
T Consensus 7 ~~Ie~vl~~~~~~~~~y~i~v~~~~~~D~l~v~vE~~~~~~~~~~~~~~l~~~i~~~lk~~lgv~-~~V~lv~~g 80 (96)
T PF14535_consen 7 SQIEEVLREFPEVSPEYQIVVTREGGLDELTVRVELRPGFSDDAEDLEALAERIAERLKERLGVR-PEVELVPPG 80 (96)
T ss_dssp HHHHHHHCTSTTEEEEEEEEEEEETTEEEEEEEEEESTTCCTTHHHHHHHHHHHHHHHHHHHSS--EEEEEE-TT
T ss_pred HHHHHHHHhCcCCCCcEEEEEEcCCCCcEEEEEEEECCccCcchHHHHHHHHHHHHHHHhhcCce-EEEEEECCC
Confidence 46899999999988 333 33 334555555431 21 245666677776633 378888865
No 47
>PF07837 FTCD_N: Formiminotransferase domain, N-terminal subdomain; InterPro: IPR012886 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. This entry represents the N-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 2PFD_C 1QD1_B.
Probab=45.10 E-value=32 Score=30.68 Aligned_cols=52 Identities=17% Similarity=0.191 Sum_probs=35.0
Q ss_pred HHHHHHHHhcCCCceeEE--EEcCCCeEEEEEeecCHHHHHHHHHHhcCCcccee
Q 025287 21 YKKVKKVLCKFPQIQDQI--FDEKTNTVRIKVVCCSPEKIRDKLCCKGEGSIKSI 73 (255)
Q Consensus 21 akKIkKAL~kI~GV~sV~--VDlk~~kVTVeG~~vdpekLv~aL~kKggk~IK~I 73 (255)
..+|.+++...+||.-+. .|...|+..|+-. -+++.|.+++.....+++..|
T Consensus 18 ie~I~~a~~~~~gv~ll~~~~D~~~NRsv~T~v-G~p~~v~~a~~~~~~~A~~~I 71 (178)
T PF07837_consen 18 IEAIAKAARNVPGVKLLDVFSDADYNRSVITLV-GEPEAVAEAAFAAIRKALELI 71 (178)
T ss_dssp HHHHHHHCCTSTTEEEEEEEEETTTTEEEEEEE-E-HHHHHHHHHHHHHHHHCC-
T ss_pred HHHHHHHHHcCCCCEEEecCCCCCCCCCeEEEe-eChHHHHHHHHHHHHHHHHhc
Confidence 456666777777866555 4778888888765 568888888887765544444
No 48
>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=44.87 E-value=29 Score=30.47 Aligned_cols=34 Identities=12% Similarity=0.308 Sum_probs=25.0
Q ss_pred EEEEEEeccChhhH------HHHHHHHhcCCCceeEEEEc
Q 025287 8 TMVLKVDLQCSKCY------KKVKKVLCKFPQIQDQIFDE 41 (255)
Q Consensus 8 t~vLKV~M~C~gCa------kKIkKAL~kI~GV~sV~VDl 41 (255)
.+.|+|.|+-.+|. ..|+.+|..++||++|+|++
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 35566655555554 55899999999999998874
No 49
>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=44.31 E-value=29 Score=26.66 Aligned_cols=21 Identities=10% Similarity=0.166 Sum_probs=17.9
Q ss_pred HHHHHHHhcCCCceeEEEEcC
Q 025287 22 KKVKKVLCKFPQIQDQIFDEK 42 (255)
Q Consensus 22 kKIkKAL~kI~GV~sV~VDlk 42 (255)
+.|+.+|..+.|+++|.|++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 468889999999999998864
No 50
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=43.39 E-value=76 Score=27.53 Aligned_cols=57 Identities=14% Similarity=0.130 Sum_probs=38.5
Q ss_pred hhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEee----c-CHHHHHHHHHHhcCCccceeEEeCC
Q 025287 19 KCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVC----C-SPEKIRDKLCCKGEGSIKSIAILEP 78 (255)
Q Consensus 19 gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~----v-dpekLv~aL~kKggk~IK~IEIVsp 78 (255)
.=.+.|++.+=+-.||+++.||..+|.|+|+... . --...++.|..++|= ...|+..
T Consensus 53 ~A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW---~p~vvRt 114 (145)
T cd02410 53 EAIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGW---APKVVRT 114 (145)
T ss_pred HHHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCC---eeEEEec
Confidence 3344555555555799999999999999998631 1 235566777777775 5555553
No 51
>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=42.98 E-value=1.4e+02 Score=22.20 Aligned_cols=58 Identities=14% Similarity=0.060 Sum_probs=41.1
Q ss_pred EEEEeccChhhHHHHHHHHhcC---CCceeEEEEcCCCeEEEEEee-cCHHHHHHHHHHhcC
Q 025287 10 VLKVDLQCSKCYKKVKKVLCKF---PQIQDQIFDEKTNTVRIKVVC-CSPEKIRDKLCCKGE 67 (255)
Q Consensus 10 vLKV~M~C~gCakKIkKAL~kI---~GV~sV~VDlk~~kVTVeG~~-vdpekLv~aL~kKgg 67 (255)
.+.|.-.=.+=..++..+|.+| +---.+..|..++.+.|.|.+ +-.+-++++|+++.+
T Consensus 7 ~~~i~p~~~~d~~kl~~aL~~l~~eDP~l~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~ 68 (75)
T PF14492_consen 7 SVAIEPKNKEDEPKLSEALQKLSEEDPSLRVERDEETGELILSGMGELHLEVLLERLKRRFG 68 (75)
T ss_dssp EEEEEESSHHHHHHHHHHHHHHHHH-TTSEEEEETTTSEEEEEESSHHHHHHHHHHHHHTTC
T ss_pred EEEEEECCHhHHHHHHHHHHHHHhcCCeEEEEEcchhceEEEEECCHHHHHHHHHHHHHHHC
Confidence 3344334455677888888777 445588899999999999742 667788888888754
No 52
>KOG4034 consensus Uncharacterized conserved protein NOF (Neighbor of FAU) [Function unknown]
Probab=42.90 E-value=50 Score=29.34 Aligned_cols=59 Identities=19% Similarity=0.157 Sum_probs=45.5
Q ss_pred eEEEEEEeccChhhHHHHHHHHhcCCCce-eEEEEcCCCeEEEEEeecCHHHHHHHHHHhcC
Q 025287 7 TTMVLKVDLQCSKCYKKVKKVLCKFPQIQ-DQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGE 67 (255)
Q Consensus 7 tt~vLKV~M~C~gCakKIkKAL~kI~GV~-sV~VDlk~~kVTVeG~~vdpekLv~aL~kKgg 67 (255)
.+++=||+-+=--|.+.++..|..+.|-. ...||.-+++|.+.|+ -.+.|.+.|.+||+
T Consensus 110 lT~IRkVeGDi~aLe~DL~s~L~~~~~~s~~t~VnelsgqI~~~g~--~v~~vr~~L~eKGF 169 (169)
T KOG4034|consen 110 LTVIRKVEGDIWALENDLRSTLEMSPKKSYATHVNELSGQIVLKGN--HVDTVREWLQEKGF 169 (169)
T ss_pred EEEEEeecccHHHHHHHHHHHHhhccCCChhhhhhhhcceEEEeCC--hHHHHHHHHHHccC
Confidence 34455677777889999999999987733 3458999999998876 23489999999874
No 53
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=41.77 E-value=46 Score=27.45 Aligned_cols=33 Identities=21% Similarity=0.411 Sum_probs=25.2
Q ss_pred EEEEEeccChhh------HHHHHHHHhcCCCceeEEEEc
Q 025287 9 MVLKVDLQCSKC------YKKVKKVLCKFPQIQDQIFDE 41 (255)
Q Consensus 9 ~vLKV~M~C~gC------akKIkKAL~kI~GV~sV~VDl 41 (255)
+.+++.++=.+| ...|+.+|..+.||++++|++
T Consensus 51 v~v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 51 VKVKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred EEEEEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEEE
Confidence 444455555566 688999999999999998873
No 54
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=41.22 E-value=87 Score=25.49 Aligned_cols=46 Identities=13% Similarity=0.110 Sum_probs=34.1
Q ss_pred hhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHh
Q 025287 19 KCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCK 65 (255)
Q Consensus 19 gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kK 65 (255)
.=...|+.+|+.|+|++=-.-|.. |++.|.-..-+-+.|.+.|...
T Consensus 18 e~l~av~~~L~~ip~~EV~~~d~~-GKlVVVie~~~~~~l~~tie~i 63 (94)
T COG3062 18 ERLSAVKTALLAIPGCEVYGEDAE-GKLVVVIEAEDSETLLETIESI 63 (94)
T ss_pred HHHHHHHHHHhcCCCcEeeccCCC-ceEEEEEEcCchHHHHHHHHHH
Confidence 446789999999999987777776 5555544335778888888764
No 55
>PRK14440 acylphosphatase; Provisional
Probab=40.80 E-value=1.7e+02 Score=22.72 Aligned_cols=69 Identities=13% Similarity=0.092 Sum_probs=46.8
Q ss_pred ceEEEEEE--eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEE--EeecCHHHHHHHHHHhcCC-c-cceeEEe
Q 025287 6 VTTMVLKV--DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIK--VVCCSPEKIRDKLCCKGEG-S-IKSIAIL 76 (255)
Q Consensus 6 vtt~vLKV--~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVe--G~~vdpekLv~aL~kKggk-~-IK~IEIV 76 (255)
|..+.|.| ..+--|-..-+.+.-.++ |++-..-|+.+++|.|. |..-+.+.++++|++ +.. + |.++++-
T Consensus 2 m~~~~~~v~G~VQGVGFR~~v~~~A~~~-gl~G~V~N~~dG~Vei~~~G~~~~v~~f~~~l~~-gp~~a~V~~i~~~ 76 (90)
T PRK14440 2 LKRMYARVYGLVQGVGFRKFVQIHAIRL-GIKGYAKNLPDGSVEVVAEGYEEALSKLLERIKQ-GPPAAEVEKVDFS 76 (90)
T ss_pred cEEEEEEEEEeEeccCchHHHHHHHHHc-CCEEEEEECCCCCEEEEEEcCHHHHHHHHHHHhh-CCCCcEEEEEEEE
Confidence 34567777 677788888888777666 58888889999977775 432345777788874 432 2 5555553
No 56
>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=39.78 E-value=1.4e+02 Score=21.29 Aligned_cols=47 Identities=11% Similarity=-0.027 Sum_probs=30.8
Q ss_pred CCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcC-CccceeEEeCC
Q 025287 32 PQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGE-GSIKSIAILEP 78 (255)
Q Consensus 32 ~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKgg-k~IK~IEIVsp 78 (255)
+||.=-++...+++|+|+|...+.+.|.+.++.... .-+..+.|.+.
T Consensus 12 ~~v~l~~l~~~~~~l~i~G~a~~~~~v~~f~~~L~~~~~f~~v~l~~~ 59 (78)
T PF05137_consen 12 EGVWLTSLSINGNTLSISGYADSYQSVAAFLRNLEQSPFFSDVSLSSI 59 (78)
T ss_pred CCEEEEEEEEeCCEEEEEEEECCHHHHHHHHHHHhhCCCccceEEEEE
Confidence 677777778889999999985566666655554322 12456665554
No 57
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=39.52 E-value=1.1e+02 Score=19.93 Aligned_cols=53 Identities=13% Similarity=0.161 Sum_probs=38.2
Q ss_pred EEE-eccChhhHHHHHHHHhcCCCceeEEEEcCC-----CeEEEEEeecCHHHHHHHHHHh
Q 025287 11 LKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKT-----NTVRIKVVCCSPEKIRDKLCCK 65 (255)
Q Consensus 11 LKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~-----~kVTVeG~~vdpekLv~aL~kK 65 (255)
|.| +|.-......|+..|+.+..|.++.+.... +.+.|+-. +.+....++...
T Consensus 2 i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~--s~~~a~~a~~~~ 60 (74)
T cd00590 2 LFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFE--DEEDAEKALEAL 60 (74)
T ss_pred EEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEEC--CHHHHHHHHHHh
Confidence 456 888888899999999999889998887653 45555543 455555566543
No 58
>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=39.22 E-value=54 Score=21.87 Aligned_cols=18 Identities=22% Similarity=0.135 Sum_probs=10.7
Q ss_pred HHHHHHHHhcCCCceeEE
Q 025287 21 YKKVKKVLCKFPQIQDQI 38 (255)
Q Consensus 21 akKIkKAL~kI~GV~sV~ 38 (255)
...|.+.|.+++||.+|.
T Consensus 52 ~~~l~~~l~~~~~V~~v~ 69 (71)
T cd04879 52 PEEVLEELKALPGIIRVR 69 (71)
T ss_pred CHHHHHHHHcCCCeEEEE
Confidence 345666666666666554
No 59
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=38.92 E-value=69 Score=28.18 Aligned_cols=47 Identities=9% Similarity=0.082 Sum_probs=34.9
Q ss_pred hhhHHHHHHHHhcCCCceeEEEEcCCCe-------------------EEEEEe--ecCHHHHHHHHHH
Q 025287 18 SKCYKKVKKVLCKFPQIQDQIFDEKTNT-------------------VRIKVV--CCSPEKIRDKLCC 64 (255)
Q Consensus 18 ~gCakKIkKAL~kI~GV~sV~VDlk~~k-------------------VTVeG~--~vdpekLv~aL~k 64 (255)
+||-=-++..+.+|+||.++.+-..++. |.|+.+ .++-++|++.+.+
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~~ 77 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFFQ 77 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHHH
Confidence 3566667788889999999999887775 555543 2677788887765
No 60
>PF01849 NAC: NAC domain; InterPro: IPR002715 Nascent polypeptide-associated complex (NAC) is among the first ribosome-associated entities to bind the nascent polypeptide after peptide bond formation. The nascent polypeptide-associated complex (NAC) of yeast functions in the targeting process of ribosomes to the ER membrane []. NAC may prevent binding of ribosome nascent chains (RNCs) without a signal sequence to yeast membranes.; PDB: 3MCE_D 3MCB_A 3LKX_B 1TR8_B.
Probab=38.85 E-value=34 Score=24.47 Aligned_cols=29 Identities=31% Similarity=0.425 Sum_probs=18.4
Q ss_pred HHHHHHHhcC-----CCceeEEEEcCCCeEEEEE
Q 025287 22 KKVKKVLCKF-----PQIQDQIFDEKTNTVRIKV 50 (255)
Q Consensus 22 kKIkKAL~kI-----~GV~sV~VDlk~~kVTVeG 50 (255)
++++++|.+| +||+.|.+-..++++.+-.
T Consensus 2 kk~~~~l~klgl~~i~~i~eV~i~~~dg~~~~~~ 35 (58)
T PF01849_consen 2 KKLQKMLKKLGLKEIPGIEEVTIRKDDGTVFVFN 35 (58)
T ss_dssp ------GHHCT-EEETTEEEEEEEETTTEEEEEE
T ss_pred HHHHHHHHHcCCcccCCcEEEEEEECCceEEEEc
Confidence 4566666555 7999999999998887753
No 61
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=38.56 E-value=65 Score=22.97 Aligned_cols=48 Identities=19% Similarity=0.263 Sum_probs=34.1
Q ss_pred EEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-ecCHHHHHHHHHHhcCC
Q 025287 11 LKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-CCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 11 LKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-~vdpekLv~aL~kKggk 68 (255)
|-+ |+.|-.=.-+++++| ++.. ++.+.|..+ ..+.+.|...+++.|++
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~~~s~~~i~~~~~~~G~~ 51 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEA---------GGEIEVLVDNEVAKENVSRFAESRGYE 51 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCC---------CCEEEEEEcChhHHHHHHHHHHHcCCE
Confidence 445 899999999999999 7642 334445443 14457888899888775
No 62
>PF05258 DUF721: Protein of unknown function (DUF721); InterPro: IPR007922 This family contains several actinomycete proteins of unknown function, and related sequences from other species.
Probab=37.68 E-value=52 Score=23.86 Aligned_cols=36 Identities=28% Similarity=0.148 Sum_probs=26.8
Q ss_pred EcCCCeEEEEEee--------cCHHHHHHHHHHhcC-CccceeEE
Q 025287 40 DEKTNTVRIKVVC--------CSPEKIRDKLCCKGE-GSIKSIAI 75 (255)
Q Consensus 40 Dlk~~kVTVeG~~--------vdpekLv~aL~kKgg-k~IK~IEI 75 (255)
++++++++|..+. +-..+|+++|...++ ..|++|.|
T Consensus 45 ~i~~g~L~i~v~~~~~~~~L~~~~~~il~~l~~~~g~~~i~~I~~ 89 (89)
T PF05258_consen 45 SIKDGTLVIEVDSSAWAQELRYMKPQILKKLNEFLGFPAIKDIRF 89 (89)
T ss_pred EEECCEEEEEECCHHHHHHHHHHHHHHHHHHHHHcCCCCccEeeC
Confidence 4468999997641 346788999999888 66887765
No 63
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=36.89 E-value=1.4e+02 Score=26.13 Aligned_cols=53 Identities=15% Similarity=0.229 Sum_probs=35.6
Q ss_pred HHHHHHHhcCCCceeEEEEcCCCeEEEEEee-----cCHHHHHHHHHHhcCCccceeEE
Q 025287 22 KKVKKVLCKFPQIQDQIFDEKTNTVRIKVVC-----CSPEKIRDKLCCKGEGSIKSIAI 75 (255)
Q Consensus 22 kKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~-----vdpekLv~aL~kKggk~IK~IEI 75 (255)
..|+..| +-.|-.++.+.+.+++|+|.... .+..+|++.+.+.++-...+|.|
T Consensus 138 ~~iE~ll-kakGf~davv~~~~~~v~VvV~~~~L~~~~~~~I~diV~~~~~v~~~~I~V 195 (196)
T PF12685_consen 138 MEIENLL-KAKGFEDAVVFIEDDSVDVVVKADKLSDAEAAQIIDIVMRETGVPAENISV 195 (196)
T ss_dssp HHHHHHH-HTTS-SEEEEE-SSSEEEEEEE-S---HHHHHHHHHHHHHHHC-STSEEEE
T ss_pred HHHHHHH-HhCCCCceEEEeeCCEEEEEEeCCCCCHHHHHHHHHHHHHHhCCCcCeEEe
Confidence 3455544 44699999999999999998641 35677888888888754555554
No 64
>PRK10819 transport protein TonB; Provisional
Probab=36.66 E-value=3.1e+02 Score=25.29 Aligned_cols=8 Identities=25% Similarity=0.742 Sum_probs=4.2
Q ss_pred eeEEeCCC
Q 025287 72 SIAILEPE 79 (255)
Q Consensus 72 ~IEIVspe 79 (255)
+|++|.+.
T Consensus 49 sV~mv~pa 56 (246)
T PRK10819 49 SVTMVAPA 56 (246)
T ss_pred EEEEeccc
Confidence 55555543
No 65
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic 40-residue C-terminal domain that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=36.28 E-value=1.1e+02 Score=26.58 Aligned_cols=33 Identities=12% Similarity=0.069 Sum_probs=29.0
Q ss_pred hhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe
Q 025287 19 KCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV 51 (255)
Q Consensus 19 gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~ 51 (255)
.=+.+|.+.+.+|+||.++.+-..++.+.|-..
T Consensus 54 ~~A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vgv~ 86 (158)
T TIGR02898 54 DVADEIASEAAKVKGVKDATVVITGNYAYVGVD 86 (158)
T ss_pred HHHHHHHHHHhcCCCCceEEEEEECCEEEEEEE
Confidence 557899999999999999999999999888654
No 66
>PRK14425 acylphosphatase; Provisional
Probab=36.00 E-value=2.1e+02 Score=22.38 Aligned_cols=74 Identities=8% Similarity=0.163 Sum_probs=49.2
Q ss_pred CCCCCceEEEEEE--eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe--ecCHHHHHHHHHHhcC-Cc-cceeE
Q 025287 1 MGEKKVTTMVLKV--DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV--CCSPEKIRDKLCCKGE-GS-IKSIA 74 (255)
Q Consensus 1 Ma~k~vtt~vLKV--~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~--~vdpekLv~aL~kKgg-k~-IK~IE 74 (255)
|.+. ...+.|.| ....-|-..-+.+.-.++ |+.-..-|+.++.|.|... .-+.++++++|++ +- .+ |.+++
T Consensus 1 m~~~-~~~~~~~v~G~VQGVGFR~~v~~~A~~~-gl~G~V~N~~dGsVei~~qG~~~~le~f~~~l~~-gp~~a~V~~i~ 77 (94)
T PRK14425 1 MSDH-REAVRVRITGRVQGVGFRDWTRDEAERL-GLTGWVRNESDGSVTALIAGPDSAISAMIERFRR-GPPGASVSGVE 77 (94)
T ss_pred CCCc-ceEEEEEEEEeEecccchHHHHHHHHHh-CCEEEEEECCCCeEEEEEEeCHHHHHHHHHHHhh-CCCceEEEEEE
Confidence 4443 33566777 666777777777666555 6888889999999988643 2456778888884 42 22 56665
Q ss_pred EeC
Q 025287 75 ILE 77 (255)
Q Consensus 75 IVs 77 (255)
+-.
T Consensus 78 ~~~ 80 (94)
T PRK14425 78 TEA 80 (94)
T ss_pred EEE
Confidence 543
No 67
>PF13193 AMP-binding_C: AMP-binding enzyme C-terminal domain; PDB: 3L8C_B 2VSQ_A 3R44_A 3RG2_B 3A9U_A 3A9V_A 3NI2_A 1V26_B 1ULT_B 1V25_B ....
Probab=35.52 E-value=1.3e+02 Score=21.43 Aligned_cols=45 Identities=27% Similarity=0.316 Sum_probs=28.5
Q ss_pred HHHHHhcCCCceeEEE----EcCCCeEEEEEeecCHHHHHHHHHHhcCC
Q 025287 24 VKKVLCKFPQIQDQIF----DEKTNTVRIKVVCCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 24 IkKAL~kI~GV~sV~V----Dlk~~kVTVeG~~vdpekLv~aL~kKggk 68 (255)
|+.+|.+++||.++-+ |...+...+-....+.+.|++.|+.+..+
T Consensus 2 IE~~l~~~~~V~~~~V~~~~d~~~g~~l~a~vv~~~~~i~~~~~~~l~~ 50 (73)
T PF13193_consen 2 IESVLRQHPGVAEAAVVGVPDEDWGERLVAFVVLDEEEIRDHLRDKLPP 50 (73)
T ss_dssp HHHHHHTSTTEEEEEEEEEEETTTEEEEEEEEEEHHHHHHHHHHHHS-G
T ss_pred HHHHHhcCCCccEEEEEEEEcccccccceeEEEeeecccccchhhhCCC
Confidence 7899999999999886 22223222222113558888888886553
No 68
>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=35.23 E-value=72 Score=23.09 Aligned_cols=16 Identities=25% Similarity=0.403 Sum_probs=15.1
Q ss_pred eEEEEcCCCeEEEEEe
Q 025287 36 DQIFDEKTNTVRIKVV 51 (255)
Q Consensus 36 sV~VDlk~~kVTVeG~ 51 (255)
.|.+|..+|.|.|.|.
T Consensus 47 ~i~~d~~tNsliv~g~ 62 (82)
T PF03958_consen 47 RIVADERTNSLIVRGT 62 (82)
T ss_dssp EEEEECTTTEEEEEEE
T ss_pred EEEEECCCCEEEEEeC
Confidence 8889999999999997
No 69
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=35.22 E-value=58 Score=35.49 Aligned_cols=45 Identities=11% Similarity=0.126 Sum_probs=36.0
Q ss_pred HHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-------ecCHHHHHHHHHHh
Q 025287 21 YKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-------CCSPEKIRDKLCCK 65 (255)
Q Consensus 21 akKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-------~vdpekLv~aL~kK 65 (255)
++.|+..|..++||.+|+++-....+.|+-+ .++.++|.++|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 4679999999999999999866666777652 26788888999864
No 70
>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=33.44 E-value=2.1e+02 Score=21.53 Aligned_cols=57 Identities=19% Similarity=0.056 Sum_probs=38.7
Q ss_pred EEEEEEeccChhhHHHHHHHHhcCCC-ceeEEEEcCCCeEEEEEe--ecCHHHHHHHHHHhcCC
Q 025287 8 TMVLKVDLQCSKCYKKVKKVLCKFPQ-IQDQIFDEKTNTVRIKVV--CCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 8 t~vLKV~M~C~gCakKIkKAL~kI~G-V~sV~VDlk~~kVTVeG~--~vdpekLv~aL~kKggk 68 (255)
.+.|.+. .....+|...|++..| |.+...+ .++.+.|+|. ......+...|+..+..
T Consensus 8 ~~~I~~p---~~~~g~v~~~l~~r~g~i~~~~~~-~~~~~~i~~~iP~~~~~gf~~~Lr~~T~G 67 (89)
T PF00679_consen 8 SVEISVP---EEYLGKVISDLSKRRGEILSMDPI-GGDRVVIEAEIPVRELFGFRSELRSLTSG 67 (89)
T ss_dssp EEEEEEE---GGGHHHHHHHHHHTT-EEEEEEEE-STTEEEEEEEEEGGGHTTHHHHHHHHTTT
T ss_pred EEEEEEC---HHHHHHHHHHhcccccEEEechhh-hhhheeEEEEEChhhhhhHHHHhhccCCC
Confidence 3444444 7788999999999888 4455555 6889999986 13444566777777664
No 71
>PRK11023 outer membrane lipoprotein; Provisional
Probab=32.33 E-value=1.1e+02 Score=26.88 Aligned_cols=38 Identities=11% Similarity=0.099 Sum_probs=28.9
Q ss_pred hHHHHHHHHhcCCCceeE--EEEcCCCeEEEEEeecCHHHH
Q 025287 20 CYKKVKKVLCKFPQIQDQ--IFDEKTNTVRIKVVCCSPEKI 58 (255)
Q Consensus 20 CakKIkKAL~kI~GV~sV--~VDlk~~kVTVeG~~vdpekL 58 (255)
=..+|+.+|..-+.|... +|...++.|++.|. ++.++.
T Consensus 128 It~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~-v~~~e~ 167 (191)
T PRK11023 128 ITTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGL-VTQREA 167 (191)
T ss_pred HHHHHHHHHhcCCCCCcceEEEEEECcEEEEEEE-eCHHHH
Confidence 556899999888877654 45666999999998 665544
No 72
>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=31.52 E-value=94 Score=20.80 Aligned_cols=31 Identities=13% Similarity=0.257 Sum_probs=19.2
Q ss_pred ceEEEEEEeccChhhHHHHHHHHhcCCCceeE
Q 025287 6 VTTMVLKVDLQCSKCYKKVKKVLCKFPQIQDQ 37 (255)
Q Consensus 6 vtt~vLKV~M~C~gCakKIkKAL~kI~GV~sV 37 (255)
+..+.|.++.. +.=...+.+.|.++.||.+|
T Consensus 41 ~~~~~~~~~~~-~~~~~~l~~~l~~~~~v~~v 71 (72)
T cd04878 41 ISRITIVVEGD-DDVIEQIVKQLNKLVDVLKV 71 (72)
T ss_pred eEEEEEEEECC-HHHHHHHHHHHhCCccEEEe
Confidence 44566666542 24456667777777777766
No 73
>PF01037 AsnC_trans_reg: AsnC family; InterPro: IPR019887 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily []. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes []. Members of the Lrp family are small DNA-binding proteins with molecular masses of around 15 kDa. Target promoters often contain a number of binding sites that typically lack obvious inverted repeat elements, and to which binding is usually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure has been solved. In the crystal structure LrpA forms an octamer consisting of four dimers. The structure revealed that the N-terminal part of the protein consists of a helix-turn-helix (HTH) domain, a fold generally involved in DNA binding. The C terminus of Lrp-like proteins has a beta-fold, where the two alpha-helices are located at one side of the four-stranded antiparallel beta-sheet. LrpA forms a homodimer mainly through interactions between the beta-strands of this C-terminal domain, and an octamer through further interactions between the second alpha-helix and fourth beta-strand of the motif. Hence, the C-terminal domain of Lrp-like proteins appears to be involved in ligand-response and activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2DJW_F 2GQQ_A 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2CG4_B 2DBB_B 1I1G_A ....
Probab=31.36 E-value=1.8e+02 Score=20.17 Aligned_cols=46 Identities=13% Similarity=0.208 Sum_probs=37.2
Q ss_pred hhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHH
Q 025287 19 KCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCC 64 (255)
Q Consensus 19 gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~k 64 (255)
.-..++.+.|.++++|..+-.-....-+.+....-|.+.|.+.|.+
T Consensus 10 ~~~~~~~~~l~~~p~V~~~~~vtG~~d~~~~v~~~d~~~l~~~i~~ 55 (74)
T PF01037_consen 10 DAYDEFAEALAEIPEVVECYSVTGEYDLILKVRARDMEELEEFIRE 55 (74)
T ss_dssp THHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHH
T ss_pred chHHHHHHHHHcCCCEEEEEEEeCCCCEEEEEEECCHHHHHHHHHH
Confidence 4788999999999999999988777777777764577777777665
No 74
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=31.20 E-value=2e+02 Score=20.89 Aligned_cols=22 Identities=23% Similarity=0.567 Sum_probs=14.0
Q ss_pred EEE-eccChhhHHH---HHHHHhcCC
Q 025287 11 LKV-DLQCSKCYKK---VKKVLCKFP 32 (255)
Q Consensus 11 LKV-~M~C~gCakK---IkKAL~kI~ 32 (255)
|.+ .-.|..|... +++++.++.
T Consensus 3 i~~~a~~C~~C~~~~~~~~~~~~e~~ 28 (76)
T TIGR00412 3 IQIYGTGCANCQMTEKNVKKAVEELG 28 (76)
T ss_pred EEEECCCCcCHHHHHHHHHHHHHHcC
Confidence 444 5778888775 555665554
No 75
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=31.05 E-value=83 Score=30.05 Aligned_cols=54 Identities=13% Similarity=0.153 Sum_probs=35.4
Q ss_pred eccChhhH---HHHHHHHhcCCCceeEEEE--cCCCeEEEEEeecCHHHHHHHHHHhcCC
Q 025287 14 DLQCSKCY---KKVKKVLCKFPQIQDQIFD--EKTNTVRIKVVCCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 14 ~M~C~gCa---kKIkKAL~kI~GV~sV~VD--lk~~kVTVeG~~vdpekLv~aL~kKggk 68 (255)
+.+=++=. .+|..+...+++|.=++++ .+.|+-+|+.. .|++++++++....+.
T Consensus 10 NfSEG~~~~~ie~i~a~~~~~~~v~ildve~danhNRsViT~v-gdp~~~~~A~f~~ik~ 68 (302)
T COG3643 10 NFSEGRDLEKIEKIVAAAKSIPTVKILDVEMDANHNRSVITLV-GDPSKVVNAAFALIKK 68 (302)
T ss_pred CccccccHHHHHHHHHHHhcCCceEEEEeccCCCCCceEEEEe-cChHHHHHHHHHHHHH
Confidence 55444444 4555566677887766664 45566666666 7899999998876555
No 76
>PRK09577 multidrug efflux protein; Reviewed
Probab=30.69 E-value=79 Score=34.49 Aligned_cols=46 Identities=13% Similarity=0.068 Sum_probs=36.4
Q ss_pred HHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-------ecCHHHHHHHHHHhc
Q 025287 21 YKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-------CCSPEKIRDKLCCKG 66 (255)
Q Consensus 21 akKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-------~vdpekLv~aL~kKg 66 (255)
.+.|+..|.+++||.+|+++-...+|.|.-+ .++..+|.++|+...
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n 210 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAHN 210 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhC
Confidence 4679999999999999999876666777531 267788889998754
No 77
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=30.07 E-value=1.8e+02 Score=21.06 Aligned_cols=46 Identities=15% Similarity=0.177 Sum_probs=34.0
Q ss_pred eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-ecCHHHHHHHHHHhcCC
Q 025287 14 DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-CCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 14 ~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-~vdpekLv~aL~kKggk 68 (255)
++.|..=.-+++++|.++. .++.++|..+ ..+...|.+.+++.|++
T Consensus 6 G~~CP~P~i~~k~~l~~l~---------~G~~l~V~~dd~~s~~di~~~~~~~g~~ 52 (69)
T cd03423 6 GLRCPEPVMMLHKKVRKMK---------PGDTLLVLATDPSTTRDIPKFCTFLGHE 52 (69)
T ss_pred CCcCCHHHHHHHHHHHcCC---------CCCEEEEEeCCCchHHHHHHHHHHcCCE
Confidence 7889888899999999985 2334444443 25677889999988776
No 78
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=29.70 E-value=86 Score=24.82 Aligned_cols=36 Identities=8% Similarity=0.103 Sum_probs=23.6
Q ss_pred CceEEEEEEeccC-hhhHHHHHHHHhcCCCceeEEEE
Q 025287 5 KVTTMVLKVDLQC-SKCYKKVKKVLCKFPQIQDQIFD 40 (255)
Q Consensus 5 ~vtt~vLKV~M~C-~gCakKIkKAL~kI~GV~sV~VD 40 (255)
|+..+.+.+-|-. .+=...|..+|++++||++++|.
T Consensus 47 GLkaL~i~~vv~D~~~~td~lee~i~~~e~Vqsvei~ 83 (88)
T PRK00435 47 GLKALKLYVIMPDEEGGTEPVEEAFANVEGVESVEVE 83 (88)
T ss_pred cceeEEEEEEEEcCCcCcHHHHHHHhccCCCcEEEEE
Confidence 3344444443333 46668888888899888888874
No 79
>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=29.57 E-value=82 Score=34.41 Aligned_cols=45 Identities=9% Similarity=0.131 Sum_probs=36.5
Q ss_pred HHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-------ecCHHHHHHHHHHh
Q 025287 21 YKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-------CCSPEKIRDKLCCK 65 (255)
Q Consensus 21 akKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-------~vdpekLv~aL~kK 65 (255)
.+.|+..|.+++||.+|+++-....+.|+-+ .++..+|.++|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~~~ 210 (1044)
T TIGR00915 159 ASNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQAQ 210 (1044)
T ss_pred HHHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 3579999999999999999877667888752 26788889999873
No 80
>PRK01192 50S ribosomal protein L31e; Reviewed
Probab=29.40 E-value=1.9e+02 Score=23.05 Aligned_cols=54 Identities=20% Similarity=0.348 Sum_probs=29.6
Q ss_pred CCCCCceEEEEEEeccChh----------hHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcCC
Q 025287 1 MGEKKVTTMVLKVDLQCSK----------CYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 1 Ma~k~vtt~vLKV~M~C~g----------CakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKggk 68 (255)
|++. +.+.++.|+|+.-+ =.+.|++.|.+.=+.. ...|.|. ..|-++|+++|.+
T Consensus 1 ~~~~-~~~r~yTInLrk~~~~~~~kRA~rAik~Ir~f~~k~mkt~-------~~~V~iD------~~lN~~IW~rGi~ 64 (89)
T PRK01192 1 SAKE-VEERIYTIPLRDVKKVPRTKRADRAVKLVREFLARHFKAD-------EDKVKID------PSINEKIWERGRE 64 (89)
T ss_pred CCCc-ceEEEEEEeCeeccCCCccccCHHHHHHHHHHHHHHhCCC-------CCcEEEC------hHHHHHHHHccCC
Confidence 3444 55677777776532 2233444444443333 1133333 4588999998876
No 81
>PRK14435 acylphosphatase; Provisional
Probab=29.27 E-value=2.7e+02 Score=21.56 Aligned_cols=68 Identities=9% Similarity=0.156 Sum_probs=44.2
Q ss_pred eEEEEEE--eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe--ecCHHHHHHHHHHhcCCc--cceeEEe
Q 025287 7 TTMVLKV--DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV--CCSPEKIRDKLCCKGEGS--IKSIAIL 76 (255)
Q Consensus 7 tt~vLKV--~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~--~vdpekLv~aL~kKggk~--IK~IEIV 76 (255)
..+.|.| ..+.-|-..-+.+.-.++ |++-..-|+.++.|.|... ..+.++++++|.+ +-.. |.++++-
T Consensus 2 ~~~~~~v~G~VQGVGFR~~v~~~A~~~-gl~G~V~N~~dG~Vei~~~G~~~~i~~f~~~l~~-gp~~a~V~~v~~~ 75 (90)
T PRK14435 2 KALKIRVEGIVQGVGFRYFTRRVAKSL-GVKGYVMNMDDGSVFIHAEGDENALRRFLNEVAK-GPPAAVVTNVSVE 75 (90)
T ss_pred eEEEEEEEEEeCCcCChHHHHHHHHHh-CCEEEEEECCCCCEEEEEEECHHHHHHHHHHHhh-CCCCcEEEEEEEE
Confidence 3556666 666777777777766555 6888888999998888643 2345677777763 4321 4444443
No 82
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=29.27 E-value=87 Score=34.27 Aligned_cols=44 Identities=11% Similarity=0.158 Sum_probs=34.7
Q ss_pred HHHHHHHhcCCCceeEEEEcCCCeEEEEEe-------ecCHHHHHHHHHHh
Q 025287 22 KKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-------CCSPEKIRDKLCCK 65 (255)
Q Consensus 22 kKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-------~vdpekLv~aL~kK 65 (255)
+.|+..|.+++||.+|++.-....+.|+-+ .++..+|.++|+..
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~~~ 210 (1049)
T PRK15127 160 ANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIKAQ 210 (1049)
T ss_pred HHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 579999999999999999766666777642 26777888888854
No 83
>PRK14447 acylphosphatase; Provisional
Probab=28.90 E-value=2.8e+02 Score=21.66 Aligned_cols=68 Identities=9% Similarity=0.071 Sum_probs=39.5
Q ss_pred EEEEEEeccChh-hHHHHHHHHhcCCCceeEEEEcCCC-eEEE--EEeecCHHHHHHHHHHhcCC-c-cceeEEe
Q 025287 8 TMVLKVDLQCSK-CYKKVKKVLCKFPQIQDQIFDEKTN-TVRI--KVVCCSPEKIRDKLCCKGEG-S-IKSIAIL 76 (255)
Q Consensus 8 t~vLKV~M~C~g-CakKIkKAL~kI~GV~sV~VDlk~~-kVTV--eG~~vdpekLv~aL~kKggk-~-IK~IEIV 76 (255)
.+.|.|.=...| -.....+.+..--||+-..-|+.++ +|.| .|..-+.+++++.|+. +-. + |.++++.
T Consensus 5 ~~~~~v~G~VQGVGFR~~~~~~A~~~gl~G~V~N~~dG~~Vei~~qG~~~~l~~f~~~l~~-gp~~a~V~~v~~~ 78 (95)
T PRK14447 5 RAHLFIRGKVQGVFFRQSMKEVANRNGVRGWVRNRSDGRTVEAVLEGPRDAVLKVIEWARV-GPPGARVEDVEVK 78 (95)
T ss_pred EEEEEEEEecCCccchHHHHHHHhhcCeEEEEEECCCCCEEEEEEEeCHHHHHHHHHHHhh-CCCCeEEEEEEEE
Confidence 455555333322 2334444555556788888899999 6877 5653456777777773 432 1 5555543
No 84
>PRK15078 polysaccharide export protein Wza; Provisional
Probab=28.82 E-value=1.2e+02 Score=29.59 Aligned_cols=59 Identities=17% Similarity=0.229 Sum_probs=43.4
Q ss_pred EEEE-eccChhhHHHHHHHHhcC---CCceeEEEEcCCCeEEEEEee-------cC--HHHHHHHHHHhcCC
Q 025287 10 VLKV-DLQCSKCYKKVKKVLCKF---PQIQDQIFDEKTNTVRIKVVC-------CS--PEKIRDKLCCKGEG 68 (255)
Q Consensus 10 vLKV-~M~C~gCakKIkKAL~kI---~GV~sV~VDlk~~kVTVeG~~-------vd--pekLv~aL~kKggk 68 (255)
.++| ||+-..=.+.|+++|.++ +.|.=-..+..+++|+|.|.. ++ ...|+++|...||=
T Consensus 133 ~V~vaG~T~~e~~~~I~~~L~~~~~~PqV~V~v~~~~s~~V~V~GeV~~PG~~~l~~~~~tlldaIa~AGG~ 204 (379)
T PRK15078 133 KVHVAGKTVTEIRSDITGRLAKYIESPQVDVNIAAFRSQKAYVTGEVNKSGQQAITNVPLTILDAINAAGGL 204 (379)
T ss_pred eEEECCCCHHHHHHHHHHHHHHhccCCeEEEEEccCCceEEEEEceecCCeEEEecCCCccHHHHHHHccCC
Confidence 4678 999999999999999876 334322335567899999851 22 57899999988874
No 85
>cd02973 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacteri
Probab=28.59 E-value=1e+02 Score=21.17 Aligned_cols=22 Identities=14% Similarity=0.344 Sum_probs=13.8
Q ss_pred EEEEEeccChhhHHHHHHHHhcC
Q 025287 9 MVLKVDLQCSKCYKKVKKVLCKF 31 (255)
Q Consensus 9 ~vLKV~M~C~gCakKIkKAL~kI 31 (255)
++|...-.|..| +.++..|..+
T Consensus 3 v~~f~~~~C~~C-~~~~~~l~~l 24 (67)
T cd02973 3 IEVFVSPTCPYC-PDAVQAANRI 24 (67)
T ss_pred EEEEECCCCCCc-HHHHHHHHHH
Confidence 344446689999 4455666655
No 86
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=28.34 E-value=2.5e+02 Score=21.23 Aligned_cols=51 Identities=16% Similarity=0.139 Sum_probs=36.9
Q ss_pred EEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-ecCHHHHHHHHHHhcCC
Q 025287 9 MVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-CCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 9 ~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-~vdpekLv~aL~kKggk 68 (255)
.+|-+ |+.|..=.-+++++|.++.. ++.+.|..+ ....++|....+..|++
T Consensus 10 ~~lD~~Gl~CP~Pll~~kk~l~~l~~---------G~~l~V~~dd~~~~~di~~~~~~~G~~ 62 (81)
T PRK00299 10 HTLDALGLRCPEPVMMVRKTVRNMQP---------GETLLIIADDPATTRDIPSFCRFMDHE 62 (81)
T ss_pred eEEecCCCCCCHHHHHHHHHHHcCCC---------CCEEEEEeCCccHHHHHHHHHHHcCCE
Confidence 56777 99999999999999999962 334444433 24567788887877765
No 87
>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=28.26 E-value=1.7e+02 Score=20.38 Aligned_cols=34 Identities=12% Similarity=0.156 Sum_probs=19.2
Q ss_pred ceEEEEEEeccChhhHHHHHHHHhcCCCceeEEE
Q 025287 6 VTTMVLKVDLQCSKCYKKVKKVLCKFPQIQDQIF 39 (255)
Q Consensus 6 vtt~vLKV~M~C~gCakKIkKAL~kI~GV~sV~V 39 (255)
+..+.|.|...=..=.+.|.+.|.+++||...++
T Consensus 39 ~~~~~~~vev~~~~~l~~i~~~L~~i~gV~~~~~ 72 (74)
T cd04887 39 YTVRDITVDAPSEEHAETIVAAVRALPEVKVLSV 72 (74)
T ss_pred EEEEEEEEEcCCHHHHHHHHHHHhcCCCeEEEEe
Confidence 4444455544444445557777777777665444
No 88
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=28.13 E-value=1.2e+02 Score=23.16 Aligned_cols=34 Identities=12% Similarity=0.078 Sum_probs=26.7
Q ss_pred CceEEEEEEeccChhhHHHHHHHHhcCCCceeEEEE
Q 025287 5 KVTTMVLKVDLQCSKCYKKVKKVLCKFPQIQDQIFD 40 (255)
Q Consensus 5 ~vtt~vLKV~M~C~gCakKIkKAL~kI~GV~sV~VD 40 (255)
++..|+|.|+ -++....|.+.|.+|..|..|+++
T Consensus 43 ~~sriti~v~--~~~~i~ql~kQL~KL~dV~~V~~~ 76 (76)
T PRK11152 43 QNINIELTVA--SERPIDLLSSQLNKLVDVAHVEIL 76 (76)
T ss_pred CEEEEEEEEC--CCchHHHHHHHHhcCcCeEEEEEC
Confidence 5666777774 488888899999999888888763
No 89
>TIGR02024 FtcD glutamate formiminotransferase. This model covers enzymes from metazoa as well as gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype. The crystal structure of the enzyme has been studied in the context of the catalytic mechanism.
Probab=27.96 E-value=78 Score=30.44 Aligned_cols=53 Identities=17% Similarity=0.142 Sum_probs=37.2
Q ss_pred hHHHHHHHHhcCCCceeEEE--EcCCCeEEEEEeecCHHHHHHHHHHhcCCcccee
Q 025287 20 CYKKVKKVLCKFPQIQDQIF--DEKTNTVRIKVVCCSPEKIRDKLCCKGEGSIKSI 73 (255)
Q Consensus 20 CakKIkKAL~kI~GV~sV~V--Dlk~~kVTVeG~~vdpekLv~aL~kKggk~IK~I 73 (255)
=..+|.+++...+||.=+++ |...|+..|+-. -+++.|.+++....++++..|
T Consensus 19 vie~I~~a~~~~~gv~lld~~~D~d~NRsv~Tlv-g~pe~v~eaa~~~~~~A~elI 73 (298)
T TIGR02024 19 VIEKIVDAIIKTDNVKLLDVDMDPDHNRSVITFV-GEPECVVNAALKLAKKAAELI 73 (298)
T ss_pred HHHHHHHHHhcCCCcEEEeCCCCCCCCceEEEEe-cChHHHHHHHHHHHHHHHHhc
Confidence 34566777777788877776 556677777765 578999998888766644333
No 90
>PRK13763 putative RNA-processing protein; Provisional
Probab=27.89 E-value=1.8e+02 Score=25.31 Aligned_cols=41 Identities=17% Similarity=0.127 Sum_probs=28.7
Q ss_pred EEEEEEeccChhhH----HHHHHHHhcCCCceeEEEEcCCCeEEEE
Q 025287 8 TMVLKVDLQCSKCY----KKVKKVLCKFPQIQDQIFDEKTNTVRIK 49 (255)
Q Consensus 8 t~vLKV~M~C~gCa----kKIkKAL~kI~GV~sV~VDlk~~kVTVe 49 (255)
+..|+|.-+--+=. .++.+.|.+.-|++ +++|.++++|+|.
T Consensus 4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~-I~i~~~~g~V~I~ 48 (180)
T PRK13763 4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVK-LEIDSETGEVIIE 48 (180)
T ss_pred eEEEEcCHHHhhhHhccchhHHHHHHHHHCcE-EEEECCCCeEEEE
Confidence 34555555444333 56677777777876 8899888999997
No 91
>COG2097 RPL31A Ribosomal protein L31E [Translation, ribosomal structure and biogenesis]
Probab=27.68 E-value=2.3e+02 Score=22.80 Aligned_cols=53 Identities=17% Similarity=0.346 Sum_probs=33.8
Q ss_pred CCCCCceEEEEEEeccC----------hhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcCC
Q 025287 1 MGEKKVTTMVLKVDLQC----------SKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 1 Ma~k~vtt~vLKV~M~C----------~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKggk 68 (255)
|+++-+.+..+.|+|+= ..=.+-|++.|++.=.++.|.+| ..|-++|+++|.+
T Consensus 1 M~~~~~~er~ytI~LR~~~~v~r~kRA~rAVk~ir~fv~rHmk~e~V~id---------------~~lNe~iW~rG~e 63 (89)
T COG2097 1 MADKVVVERIYTIPLRRAKKVPRTKRAPRAVKIIRKFVARHMKAEEVRID---------------PSLNEKIWERGIE 63 (89)
T ss_pred CCccccceEEEEEEchhhccCCccccchHHHHHHHHHHHHHhCCceEEEC---------------HHHhHHHHHhhcc
Confidence 67765677888888871 12234566666665444433333 5599999999875
No 92
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=27.64 E-value=1.6e+02 Score=27.99 Aligned_cols=46 Identities=17% Similarity=0.089 Sum_probs=37.2
Q ss_pred EEEEEeccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcCC
Q 025287 9 MVLKVDLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 9 ~vLKV~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKggk 68 (255)
+.|+++.+ +.|.+.|++.|..++||.++++- +.++-.+.|++..|.
T Consensus 63 vyL~~~~~-~~~~~~v~~~i~~~~gV~~v~~~-------------sre~~l~~L~~~lg~ 108 (297)
T COG2177 63 VYLQIDAD-QDDAALVREKIEGIPGVKSVRFI-------------SREEALKELQPWLGF 108 (297)
T ss_pred EEEecCCC-hHHHHHHHHHHhcCCCcceEEEe-------------CHHHHHHHHHHHcCc
Confidence 45556666 99999999999999999998874 557777888877774
No 93
>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=27.61 E-value=1.1e+02 Score=24.29 Aligned_cols=22 Identities=5% Similarity=0.018 Sum_probs=18.7
Q ss_pred hhHHHHHHHHhcCCCceeEEEE
Q 025287 19 KCYKKVKKVLCKFPQIQDQIFD 40 (255)
Q Consensus 19 gCakKIkKAL~kI~GV~sV~VD 40 (255)
+=...|+.+|++++||++++|.
T Consensus 62 g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 62 GGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred cChHHHHHHHhcCCCccEEEEE
Confidence 4458999999999999999875
No 94
>PRK10568 periplasmic protein; Provisional
Probab=27.25 E-value=2.1e+02 Score=25.30 Aligned_cols=33 Identities=9% Similarity=0.086 Sum_probs=26.2
Q ss_pred HHHHHHHHhcCCCc--eeEEEEcCCCeEEEEEeecC
Q 025287 21 YKKVKKVLCKFPQI--QDQIFDEKTNTVRIKVVCCS 54 (255)
Q Consensus 21 akKIkKAL~kI~GV--~sV~VDlk~~kVTVeG~~vd 54 (255)
..+|+.+|..-..+ .+++|+..+|.|++.|. ++
T Consensus 141 t~~vk~~L~~~~~v~~~~I~V~v~~G~V~L~G~-V~ 175 (203)
T PRK10568 141 TSEIKAKLLADDIVPSRKVKVETTDGVVQLSGT-VD 175 (203)
T ss_pred HHHHHHHHhhCCCCCcceeEEEEeCcEEEEEEE-EC
Confidence 67788888766665 46788889999999998 63
No 95
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=27.19 E-value=32 Score=25.39 Aligned_cols=22 Identities=27% Similarity=0.563 Sum_probs=18.7
Q ss_pred EEEEeccChhhHHHHHHHHhcC
Q 025287 10 VLKVDLQCSKCYKKVKKVLCKF 31 (255)
Q Consensus 10 vLKV~M~C~gCakKIkKAL~kI 31 (255)
.|+++-.|++|...|++.|...
T Consensus 32 ~~~~g~~CG~C~~~i~~il~~~ 53 (64)
T PRK10509 32 FVPVGNQCGKCIRAAREVMQDE 53 (64)
T ss_pred hcCCCCCccchHHHHHHHHHHH
Confidence 4677899999999999998655
No 96
>PF00708 Acylphosphatase: Acylphosphatase; InterPro: IPR001792 Acylphosphatase (3.6.1.7 from EC) is an enzyme of approximately 98 amino acid residues that specifically catalyses the hydrolysis of the carboxyl-phosphate bond of acylphosphates [], its substrates including 1,3-diphosphoglycerate and carbamyl phosphate []. The enzyme has a mainly beta-sheet structure with 2 short alpha-helical segments. It is distributed in a tissue-specific manner in a wide variety of species, although its physiological role is as yet unknown []: it may, however, play a part in the regulation of the glycolytic pathway and pyrimidine biosynthesis []. There are two known isozymes. One seems to be specific to muscular tissues, the other, called 'organ-common type', is found in many different tissues. While bacterial and archebacterial hypothetical proteins that are highly similar to that enzyme and that probably possess the same activity. These proteins include: Escherichia coli putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (gene yccX). Bacillus subtilis putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (gene yflL). Archaeoglobus fulgidus putative acylphosphatase (3.6.1.7 from EC) (acylphosphate phosphohydrolase) (O29440 from SWISSPROT). An acylphosphatase-like domain is also found in some prokaryotic hydrogenase maturation HypF carbamoyltransferases [, ].; PDB: 1APS_A 1GXT_A 1GXU_A 2HLT_A 2FHM_A 2HLU_A 3BR8_A 1ULR_A 3TRG_A 2BJD_A ....
Probab=27.04 E-value=2.8e+02 Score=20.98 Aligned_cols=70 Identities=16% Similarity=0.075 Sum_probs=40.4
Q ss_pred eEEEEEE--eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEE--eecCHHHHHHHHHHhcCCc-cceeEEeC
Q 025287 7 TTMVLKV--DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKV--VCCSPEKIRDKLCCKGEGS-IKSIAILE 77 (255)
Q Consensus 7 tt~vLKV--~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG--~~vdpekLv~aL~kKggk~-IK~IEIVs 77 (255)
..+.|.| .++=-|=..-|.+.-.++ ||+-..-|+.+++|.|.. ..-+.+.++++|++....+ |.++++-.
T Consensus 4 ~~~~i~v~G~VQGVgFR~~v~~~A~~~-gl~G~V~N~~dg~V~i~~~G~~~~l~~f~~~l~~g~p~a~V~~i~~~~ 78 (91)
T PF00708_consen 4 KRYRIIVSGRVQGVGFRPFVKRIARKL-GLTGWVRNLPDGSVEIEAEGEEEQLEEFIKWLKKGPPPARVDEIEVEE 78 (91)
T ss_dssp EEEEEEEEEETSSSSHHHHHHHHHHHT-T-EEEEEE-TTSEEEEEEEEEHHHHHHHHHHHHHSSTTSEEEEEEEEE
T ss_pred EEEEEEEEEEECcCChhHHHHHHHHHh-CCceEEEECCCCEEEEEEEeCHHHHHHHHHHHHhCCCCcEEEEEEEEE
Confidence 3455555 344333334444444444 688888899999888864 4345678888888754333 55665543
No 97
>PF02983 Pro_Al_protease: Alpha-lytic protease prodomain; InterPro: IPR004236 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. The alpha-lytic protease prodomain is associated with serine peptidases, specifically the alpha-lytic endopeptidases and streptogrisin A, B, C, D and E, which are bacterial enzymes and which belong to MEROPS peptidase subfamily S1A (IPR001316 from INTERPRO). The protease precursor in Gram-negative bacterial proteases may be a general property of extracellular bacterial proteases []. The proteases are encoded with a large (166 amino acid) N-terminal pro region that is required transiently both in vivo and in vitro for the correct folding of the protease domain [, ]. The pro region also acts as a potent inhibitor of the mature enzyme []. ; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis, 0005576 extracellular region; PDB: 3PRO_C 2PRO_B 4PRO_C.
Probab=26.77 E-value=1.7e+02 Score=21.29 Aligned_cols=29 Identities=21% Similarity=0.189 Sum_probs=22.8
Q ss_pred HHHHHH------hcCCCceeEEEEcCCCeEEEEEe
Q 025287 23 KVKKVL------CKFPQIQDQIFDEKTNTVRIKVV 51 (255)
Q Consensus 23 KIkKAL------~kI~GV~sV~VDlk~~kVTVeG~ 51 (255)
.++..| ..-.++...-||..+|+|+|+..
T Consensus 8 aak~~L~da~~~~~~~~~~~WyvD~~tn~VVV~a~ 42 (62)
T PF02983_consen 8 AAKAALDDAAAAAAPVAVTSWYVDPRTNKVVVTAD 42 (62)
T ss_dssp HHHHHHHHCHHHHGGGCEEEEEEECCCTEEEEEEE
T ss_pred HHHHHHHhhhhccCCCCcceEEEeCCCCeEEEEEC
Confidence 455666 23457999999999999999976
No 98
>TIGR02189 GlrX-like_plant Glutaredoxin-like family. This family of glutaredoxin-like proteins is aparrently limited to plants. Multiple isoforms are found in A. thaliana and O.sativa.
Probab=25.84 E-value=2.9e+02 Score=21.39 Aligned_cols=49 Identities=18% Similarity=0.315 Sum_probs=29.7
Q ss_pred EEEEEeccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcC
Q 025287 9 MVLKVDLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGE 67 (255)
Q Consensus 9 ~vLKV~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKgg 67 (255)
++|-.--.|..|. ++++.|.++ ||.-..+|++. . -+...++++|.+.+|
T Consensus 10 Vvvysk~~Cp~C~-~ak~~L~~~-~i~~~~vdid~-------~-~~~~~~~~~l~~~tg 58 (99)
T TIGR02189 10 VVIFSRSSCCMCH-VVKRLLLTL-GVNPAVHEIDK-------E-PAGKDIENALSRLGC 58 (99)
T ss_pred EEEEECCCCHHHH-HHHHHHHHc-CCCCEEEEcCC-------C-ccHHHHHHHHHHhcC
Confidence 4555578899998 667788777 56544444332 1 233456666665544
No 99
>PF04459 DUF512: Protein of unknown function (DUF512); InterPro: IPR007549 This is a domain of uncharacterised prokaryotic proteins. It is often found C-terminal to the radical SAM domain (IPR007197 from INTERPRO).
Probab=25.55 E-value=1.6e+02 Score=26.53 Aligned_cols=25 Identities=16% Similarity=0.098 Sum_probs=21.2
Q ss_pred EcCCCeEEEEEeecCHHHHHHHHHHh
Q 025287 40 DEKTNTVRIKVVCCSPEKIRDKLCCK 65 (255)
Q Consensus 40 Dlk~~kVTVeG~~vdpekLv~aL~kK 65 (255)
++=.++|||.|- +.-.+|+++|+.+
T Consensus 135 ~fFG~~ItVaGL-LTg~Dii~~L~~~ 159 (204)
T PF04459_consen 135 RFFGGTITVAGL-LTGQDIIEQLKGK 159 (204)
T ss_pred CCCCCCeEEeeC-ccHHHHHHHhCcC
Confidence 445789999998 8899999999874
No 100
>KOG3432 consensus Vacuolar H+-ATPase V1 sector, subunit F [Energy production and conversion]
Probab=25.46 E-value=1.1e+02 Score=25.86 Aligned_cols=43 Identities=16% Similarity=0.195 Sum_probs=34.1
Q ss_pred CCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHHhcCCccceeEEe
Q 025287 31 FPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKGEGSIKSIAIL 76 (255)
Q Consensus 31 I~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKggk~IK~IEIV 76 (255)
|.||.++.-+.+.|-+.|... ...++|.+++.+-+.| ..|.||
T Consensus 24 laGvg~v~~~r~~Nf~vv~~~-Tt~~eiedaF~~f~~R--dDIaIi 66 (121)
T KOG3432|consen 24 LAGVGEVNENREPNFLVVDSK-TTVEEIEDAFKSFTAR--DDIAII 66 (121)
T ss_pred eecccccccCCCCCEEEEecc-CCHHHHHHHHHhhccc--cCeEEE
Confidence 578999998899999999876 7889999999887765 444443
No 101
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=25.27 E-value=1.7e+02 Score=21.25 Aligned_cols=49 Identities=18% Similarity=0.196 Sum_probs=35.4
Q ss_pred EEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-ecCHHHHHHHHHHhcCC
Q 025287 11 LKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-CCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 11 LKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-~vdpekLv~aL~kKggk 68 (255)
|-+ |+.|-.=.-+++++|.++. .++.+.|..+ ....+.|.+..++.|+.
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~---------~G~~l~V~~d~~~a~~di~~~~~~~G~~ 52 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQ---------DGEQLEVKASDPGFARDAQAWCKSTGNT 52 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCC---------CCCEEEEEECCccHHHHHHHHHHHcCCE
Confidence 445 8889888899999999986 2344555543 25567888888887775
No 102
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=25.22 E-value=1.8e+02 Score=25.21 Aligned_cols=47 Identities=13% Similarity=0.128 Sum_probs=32.9
Q ss_pred hhhHHHHHHHHhcCCCceeEEEEcCCCe--------------EEEEEe--ecCHHHHHHHHHH
Q 025287 18 SKCYKKVKKVLCKFPQIQDQIFDEKTNT--------------VRIKVV--CCSPEKIRDKLCC 64 (255)
Q Consensus 18 ~gCakKIkKAL~kI~GV~sV~VDlk~~k--------------VTVeG~--~vdpekLv~aL~k 64 (255)
+||-=-++..+.+|+||.++++-..++. |.|+.+ .++-++|++.+.+
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~~ 70 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLFE 70 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHHH
Confidence 4566667788899999999998776544 333332 2577788877765
No 103
>PRK14451 acylphosphatase; Provisional
Probab=25.19 E-value=3.3e+02 Score=21.11 Aligned_cols=58 Identities=14% Similarity=-0.059 Sum_probs=40.7
Q ss_pred ceEEEEEE--eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEE--eecCHHHHHHHHHH
Q 025287 6 VTTMVLKV--DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKV--VCCSPEKIRDKLCC 64 (255)
Q Consensus 6 vtt~vLKV--~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG--~~vdpekLv~aL~k 64 (255)
|.++.+.| ...--|-..-+.+.-.++ |++-..-|+.+++|.|.. +.-+.+++++.|++
T Consensus 2 ~~~~~~~V~G~VQGVGFR~~~~~~A~~~-gl~G~V~N~~dG~Vei~~qG~~~~i~~f~~~l~~ 63 (89)
T PRK14451 2 ELCMRCYISGRVQGVWFRASAKKLAEQL-MISGWARNLADGRVEVFACGKEDKLEEFYTWLQK 63 (89)
T ss_pred cEEEEEEEEEeeCCcCchHHHHHHHHHh-CCEEEEEECCCCCEEEEEEECHHHHHHHHHHHhh
Confidence 55666667 555666667776666655 688888899999988864 33456777777774
No 104
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=24.59 E-value=1.5e+02 Score=27.06 Aligned_cols=48 Identities=13% Similarity=0.205 Sum_probs=34.0
Q ss_pred hhhHHHHHHHHhcCCCceeEEEEcCCCe-------------------EEEEEe--ecCHHHHHHHHHHh
Q 025287 18 SKCYKKVKKVLCKFPQIQDQIFDEKTNT-------------------VRIKVV--CCSPEKIRDKLCCK 65 (255)
Q Consensus 18 ~gCakKIkKAL~kI~GV~sV~VDlk~~k-------------------VTVeG~--~vdpekLv~aL~kK 65 (255)
+||.=-++..+.+|+||.++++-..++. |.|+.+ .++-++|++.+.+.
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff~~ 120 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFWEN 120 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHHHh
Confidence 4566667777888999999999887552 444443 25677888877753
No 105
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=24.20 E-value=2.6e+02 Score=30.91 Aligned_cols=7 Identities=14% Similarity=0.449 Sum_probs=3.0
Q ss_pred CCCCCCC
Q 025287 224 GWAGGCD 230 (255)
Q Consensus 224 ~~~~g~~ 230 (255)
.|+.-+|
T Consensus 630 nW~kI~p 636 (1102)
T KOG1924|consen 630 NWSKIVP 636 (1102)
T ss_pred CccccCc
Confidence 4544333
No 106
>PF12229 PG_binding_4: Putative peptidoglycan binding domain; InterPro: IPR022029 This domain is found associated with the L,D-transpeptidase domain PF03734 from PFAM. The structure of this domain has been solved and shows a mixed alpha-beta fold composed of nine beta strands and four alpha helices. This domain is usually found to be duplicated. Therefore, it seems likely that this domain acts to bind the two unlinked peptidoglycan chains and bring them into close association so they can be cross linked by the transpeptidase domain. ; PDB: 2HKL_C 1ZAT_A.
Probab=24.06 E-value=2.3e+02 Score=21.05 Aligned_cols=45 Identities=11% Similarity=0.138 Sum_probs=27.8
Q ss_pred HHHHHHHhcC------CCceeEEEEcCCCeEEEE----EeecCHHHHHHHHHHhcC
Q 025287 22 KKVKKVLCKF------PQIQDQIFDEKTNTVRIK----VVCCSPEKIRDKLCCKGE 67 (255)
Q Consensus 22 kKIkKAL~kI------~GV~sV~VDlk~~kVTVe----G~~vdpekLv~aL~kKgg 67 (255)
.++...|..+ .++ +..|.+++++++|. |..+|.+++++.|.....
T Consensus 53 ~~l~~~v~~~~~~~~~~~~-na~~~~~~~~~~i~~~~~G~~id~~~~~~~i~~al~ 107 (114)
T PF12229_consen 53 EKLEQYVDELAKEYNTPPV-NASISIDGGTFTITPGQYGWKIDVDKLAEAIKKALK 107 (114)
T ss_dssp HHHHHHHHHHHHHH-TTTS--EEEE-SSCEEEE---SS-EEE-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCcCCc-ceEEEEeCCEEEEcCCcCeEEEcHHHHHHHHHHHHH
Confidence 3444555443 344 77777799999995 445899999988887654
No 107
>TIGR03027 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by Pfam model pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system.
Probab=24.03 E-value=2.3e+02 Score=23.87 Aligned_cols=68 Identities=12% Similarity=0.118 Sum_probs=46.7
Q ss_pred EEEE-eccChhhHHHHHHHHhcCC--CceeEEEEc----CCCeEEEEEee--------cCHHHHHHHHHHhcCCc----c
Q 025287 10 VLKV-DLQCSKCYKKVKKVLCKFP--QIQDQIFDE----KTNTVRIKVVC--------CSPEKIRDKLCCKGEGS----I 70 (255)
Q Consensus 10 vLKV-~M~C~gCakKIkKAL~kI~--GV~sV~VDl----k~~kVTVeG~~--------vdpekLv~aL~kKggk~----I 70 (255)
.++| ||+-.-=.+.|+++|+++= -.-+|.+.. .+++|+|.|.. -+...|.++|...||=+ .
T Consensus 38 ~v~v~G~T~~e~~~~I~~~l~~~~~~p~v~V~v~~~~~~~~~~V~V~GeV~~PG~y~~~~~~tl~~ai~~AGG~~~~a~~ 117 (165)
T TIGR03027 38 DLVASGKTPTQLARDIEEKLAKYVRNPVVTVIVTGFIGPFSEQIRVVGAAANPQALPYREGMTLLDVMIAVGGLTDFADG 117 (165)
T ss_pred eEEECCCCHHHHHHHHHHHHHHhccCCeEEEEEeecccCCCcEEEEEEEeCCCceeeeCCCCcHHHHHHHcCCCCcccCC
Confidence 4677 9999999999999998852 122233321 35899999852 24577999999988733 3
Q ss_pred ceeEEeC
Q 025287 71 KSIAILE 77 (255)
Q Consensus 71 K~IEIVs 77 (255)
.+|.|+-
T Consensus 118 ~~v~i~R 124 (165)
T TIGR03027 118 NRAVIVR 124 (165)
T ss_pred CeEEEEE
Confidence 4666664
No 108
>TIGR03028 EpsE polysaccharide export protein EpsE. Sequences in this family of proteins are members of a polysaccharide export protein family (pfam02563) which includes the wza protein from E.coli. This family of proteins are homologous to the EpsE protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=23.53 E-value=2.6e+02 Score=24.99 Aligned_cols=58 Identities=17% Similarity=0.243 Sum_probs=41.7
Q ss_pred EEEE-eccChhhHHHHHHHHhc---C--CCceeEEEEcCCCeEEEEEee--------cCHHHHHHHHHHhcC
Q 025287 10 VLKV-DLQCSKCYKKVKKVLCK---F--PQIQDQIFDEKTNTVRIKVVC--------CSPEKIRDKLCCKGE 67 (255)
Q Consensus 10 vLKV-~M~C~gCakKIkKAL~k---I--~GV~sV~VDlk~~kVTVeG~~--------vdpekLv~aL~kKgg 67 (255)
.++| +|+-..=.+.|++.|.+ + +.|+=....+..++|+|.|.. -....|.++|...||
T Consensus 39 ~v~v~G~T~~e~~~~I~~~l~~~~~~~~p~V~V~v~~~~~~~V~V~GeV~~PG~~~l~~~~tl~~ai~~AGG 110 (239)
T TIGR03028 39 EVKLGGETPAAAERKIASRLSKGGFVKQPQVTINVLQYRGQQVSVLGQVNRPGRYPLETAGRVSDVLALAGG 110 (239)
T ss_pred eEEECCCCHHHHHHHHHHHHhhcCcccCCEEEEEEEeccceEEEEEEEecCCceEEcCCCCcHHHHHHHcCC
Confidence 4677 89988889999999986 2 233322335568899999852 123689999998886
No 109
>PRK00378 nucleoid-associated protein NdpA; Validated
Probab=23.41 E-value=83 Score=29.52 Aligned_cols=29 Identities=31% Similarity=0.477 Sum_probs=24.5
Q ss_pred eeEEEEcCCCeEEEEEeecCHHHHHHHHHHhc
Q 025287 35 QDQIFDEKTNTVRIKVVCCSPEKIRDKLCCKG 66 (255)
Q Consensus 35 ~sV~VDlk~~kVTVeG~~vdpekLv~aL~kKg 66 (255)
+.|.+|..++++||+|. |..|++.|.+..
T Consensus 303 ~~i~yd~~~~~ltI~~~---p~~l~~ql~r~~ 331 (334)
T PRK00378 303 ERIFYDPATDTLTIKGT---PPNLRDQLQRRL 331 (334)
T ss_pred CceEEcCCCCEEEEeCC---CHHHHHHHHHHh
Confidence 38899999999999986 677999887754
No 110
>TIGR00268 conserved hypothetical protein TIGR00268. The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server.
Probab=23.29 E-value=3e+02 Score=24.76 Aligned_cols=47 Identities=21% Similarity=0.165 Sum_probs=34.5
Q ss_pred HHHHHHHHhcCCCceeEEEEcCCCeEEEEEee------c-CHHHHHHHHHHhcCC
Q 025287 21 YKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVC------C-SPEKIRDKLCCKGEG 68 (255)
Q Consensus 21 akKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~------v-dpekLv~aL~kKggk 68 (255)
..+.+..|..+ |+..+.|...++.+.|+... + ..+.|.+.|++.|++
T Consensus 187 v~~~E~~l~~~-g~~~~rvr~~~~~a~ie~~~~~~~~~~~~~~~i~~~~~~~gf~ 240 (252)
T TIGR00268 187 VDEAEEVLRNA-GVGQVRVRNYDNLAVIEVPEDELSKLLNEAEEVRDKFKDIGFR 240 (252)
T ss_pred HHHHHHHHHHc-CCCeEEEEecCCeEEEEECHHHHHHHHhhHHHHHHHHHHcCCC
Confidence 45677778885 89999999999999999631 1 125566777777776
No 111
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=23.26 E-value=2.4e+02 Score=20.52 Aligned_cols=46 Identities=11% Similarity=-0.049 Sum_probs=33.6
Q ss_pred eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-ecCHHHHHHHHHHhcCC
Q 025287 14 DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-CCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 14 ~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-~vdpekLv~aL~kKggk 68 (255)
|+.|-.=.-+.+++|.++.. ++.+.|..+ ..+.+.|.+.++..|++
T Consensus 6 G~~CP~Pvi~~kkal~~l~~---------G~~l~V~~d~~~s~~ni~~~~~~~g~~ 52 (69)
T cd03422 6 GEPCPYPAIATLEALPSLKP---------GEILEVISDCPQSINNIPIDARNHGYK 52 (69)
T ss_pred CCcCCHHHHHHHHHHHcCCC---------CCEEEEEecCchHHHHHHHHHHHcCCE
Confidence 78888888999999999962 333444443 25678888888887775
No 112
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=23.14 E-value=2.7e+02 Score=19.42 Aligned_cols=46 Identities=22% Similarity=0.159 Sum_probs=33.5
Q ss_pred eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe-ecCHHHHHHHHHHhcCC
Q 025287 14 DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-CCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 14 ~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-~vdpekLv~aL~kKggk 68 (255)
++.|..=.-+++++|.++.. ++.+.|..+ ......|...++..|++
T Consensus 6 g~~CP~Pl~~~~~~l~~l~~---------g~~l~v~~d~~~~~~~i~~~~~~~g~~ 52 (69)
T cd00291 6 GLPCPLPVLKTKKALEKLKS---------GEVLEVLLDDPGAVEDIPAWAKETGHE 52 (69)
T ss_pred CCcCCHHHHHHHHHHhcCCC---------CCEEEEEecCCcHHHHHHHHHHHcCCE
Confidence 78888888889999988763 344455443 14578888889988876
No 113
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=23.14 E-value=1.3e+02 Score=24.12 Aligned_cols=36 Identities=8% Similarity=0.090 Sum_probs=26.7
Q ss_pred CceEEEEEEeccC-hhhHHHHHHHHhcCCCceeEEEE
Q 025287 5 KVTTMVLKVDLQC-SKCYKKVKKVLCKFPQIQDQIFD 40 (255)
Q Consensus 5 ~vtt~vLKV~M~C-~gCakKIkKAL~kI~GV~sV~VD 40 (255)
|+..+.|.|-|.- .|=...|+.+|+.++||+++++.
T Consensus 47 GLkal~l~vvv~D~Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 47 GLKALKLYVVVEDKEGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred eeeeEEEEEEEcccccCcHHHHHHHhhccCcceEEEE
Confidence 5556666665533 45578899999999999999874
No 114
>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium). This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=22.96 E-value=1.2e+02 Score=33.22 Aligned_cols=49 Identities=14% Similarity=0.188 Sum_probs=36.9
Q ss_pred hhHHHHHHHHhcCCCceeEEEEcCC--CeEEEEEe-------ecCHHHHHHHHHHhcC
Q 025287 19 KCYKKVKKVLCKFPQIQDQIFDEKT--NTVRIKVV-------CCSPEKIRDKLCCKGE 67 (255)
Q Consensus 19 gCakKIkKAL~kI~GV~sV~VDlk~--~kVTVeG~-------~vdpekLv~aL~kKgg 67 (255)
.=+++|+..|..++||.+|..|... ..+.|+-+ .++.++|.+.|+....
T Consensus 698 ~~a~~v~~~l~~~pgv~~v~~~~~~~~~e~~i~id~~~~~~~Glt~~~v~~~l~~~~~ 755 (1051)
T TIGR00914 698 ATAEKISAVLKGVPGAADVKVEQTTGLPYLTVEIDREKAARYGLTVGDVQDTVATAVG 755 (1051)
T ss_pred HHHHHHHHHHhcCCCceeeeccccCCCceEEEEECHHHHHHcCCCHHHHHHHHHHHhC
Confidence 4467899999999999999998754 45555532 2678888899887654
No 115
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from 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. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=22.93 E-value=1.6e+02 Score=20.31 Aligned_cols=16 Identities=25% Similarity=0.260 Sum_probs=8.2
Q ss_pred HHHHHHhcCCCceeEE
Q 025287 23 KVKKVLCKFPQIQDQI 38 (255)
Q Consensus 23 KIkKAL~kI~GV~sV~ 38 (255)
.+.+.|.+++||..+.
T Consensus 54 ~~~~~l~~~~~v~~v~ 69 (73)
T cd04902 54 EVLEELRALPGILSAK 69 (73)
T ss_pred HHHHHHHcCCCccEEE
Confidence 4555555555555444
No 116
>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=22.37 E-value=1.4e+02 Score=23.46 Aligned_cols=22 Identities=5% Similarity=0.053 Sum_probs=16.9
Q ss_pred hhHHHHHHHHhcCCCceeEEEE
Q 025287 19 KCYKKVKKVLCKFPQIQDQIFD 40 (255)
Q Consensus 19 gCakKIkKAL~kI~GV~sV~VD 40 (255)
+=...|..+|+.++||++++|.
T Consensus 62 ~~td~lee~i~~~d~VqsveI~ 83 (88)
T cd00292 62 GGTDELEEAISEEDGVQSVDVE 83 (88)
T ss_pred cCcHHHHHHHhccCCceEEEEE
Confidence 3347888888888888888875
No 117
>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=22.27 E-value=1.4e+02 Score=23.06 Aligned_cols=45 Identities=7% Similarity=0.093 Sum_probs=33.0
Q ss_pred HHHHHHHhcCCCceeEEEEcCCCeEEEEEe-ecCHHHHHHHHHHhcCC
Q 025287 22 KKVKKVLCKFPQIQDQIFDEKTNTVRIKVV-CCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 22 kKIkKAL~kI~GV~sV~VDlk~~kVTVeG~-~vdpekLv~aL~kKggk 68 (255)
.-+-++|-.|+||++|-+. .+-|||+-. .++=+.|+..|......
T Consensus 37 spLA~~Lf~i~gV~~Vf~~--~dfItVtK~~~~~W~~l~~~I~~~I~~ 82 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFIG--DDFITVTKNPDADWEDLKPEIREVIME 82 (87)
T ss_dssp -HHHHHHHTSTTEEEEEEE--TTEEEEEE-TTS-HHHHHHHHHHHTH-
T ss_pred CHHHHHhcCCCCEeEEEEE--CCEEEEeeCCCCCHHHHHHHHHHHHhh
Confidence 6677888899999999987 668888743 37888888888876543
No 118
>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=21.82 E-value=1.5e+02 Score=31.93 Aligned_cols=51 Identities=24% Similarity=0.268 Sum_probs=39.5
Q ss_pred hhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEe---------ecCHHHHHHHHHHhcCC
Q 025287 18 SKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVV---------CCSPEKIRDKLCCKGEG 68 (255)
Q Consensus 18 ~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~---------~vdpekLv~aL~kKggk 68 (255)
..=+++|++.|++++|+.+|..|...++-.+.-. .++.++|.+.|+...+.
T Consensus 686 ~~~a~~v~~~l~~~pgv~dv~~~~~~~~~el~i~~dreka~~~Gls~~~va~~l~~a~~G 745 (1021)
T PF00873_consen 686 RKAAEKVKAKLAEIPGVTDVRDDWEDGQPELRIDPDREKAARLGLSPADVARTLRTAFSG 745 (1021)
T ss_dssp HHHHHHHHHHHHHSTTEEEEEESSSSBEEEEEEEE-HHHHHHTTB-HHHHHHHHHHHHS-
T ss_pred HHHHHHHHHHHHhCCCcccccccccccCcceEEEecHHHHHHcCCCHHHHHHHHHHHhcc
Confidence 4567899999999999999999999887777653 25677788888876654
No 119
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=21.73 E-value=1e+02 Score=34.53 Aligned_cols=14 Identities=43% Similarity=0.736 Sum_probs=7.5
Q ss_pred CCCCccccCCCCCC
Q 025287 197 RGGGPCYDLGYGQT 210 (255)
Q Consensus 197 ~~~~~c~~~g~g~~ 210 (255)
+++++-..+|||++
T Consensus 1184 RGgssysgGGYGgg 1197 (1282)
T KOG0921|consen 1184 RGGSSYSGGGYGGG 1197 (1282)
T ss_pred cCCCCCCCCCcCCC
Confidence 34455555556655
No 120
>TIGR01676 GLDHase galactonolactone dehydrogenase. This model represents L-Galactono-gamma-lactone dehydrogenase (EC 1.3.2.3). This enzyme catalyzes the final step in ascorbic acid biosynthesis in higher plants. This protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD.
Probab=21.64 E-value=1.1e+02 Score=31.45 Aligned_cols=37 Identities=16% Similarity=0.226 Sum_probs=28.7
Q ss_pred cCCCcee-EEEEcCCCeEEEEEeecCHHHHHHHHHHhcC
Q 025287 30 KFPQIQD-QIFDEKTNTVRIKVVCCSPEKIRDKLCCKGE 67 (255)
Q Consensus 30 kI~GV~s-V~VDlk~~kVTVeG~~vdpekLv~aL~kKgg 67 (255)
.|...+. ++||..+++|||.+. +.-.+|.++|...|.
T Consensus 109 dL~~ln~Vl~vD~~~~tVtV~AG-~~l~~L~~~L~~~Gl 146 (541)
T TIGR01676 109 NLALMDKVLEVDEEKKRVRVQAG-IRVQQLVDAIKEYGI 146 (541)
T ss_pred EhhhCCCCEEEcCCCCEEEEcCC-CCHHHHHHHHHHcCC
Confidence 3344444 478889999999987 889999999998764
No 121
>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=21.50 E-value=85 Score=21.98 Aligned_cols=30 Identities=33% Similarity=0.512 Sum_probs=24.5
Q ss_pred HHHHHHHHhcCCCceeEEEEcC-CCeEEEEE
Q 025287 21 YKKVKKVLCKFPQIQDQIFDEK-TNTVRIKV 50 (255)
Q Consensus 21 akKIkKAL~kI~GV~sV~VDlk-~~kVTVeG 50 (255)
.+++++.|.+++.|++++|... -+++.|..
T Consensus 36 ~~~~~~~l~~~p~V~~v~V~r~~P~~l~I~V 66 (69)
T PF08478_consen 36 LKKIEQRLEKLPWVKSVSVSRRFPNTLEIKV 66 (69)
T ss_dssp HHHHHHCCCCTTTEEEEEEEEETTTEEEEEE
T ss_pred HHHHHHHHHcCCCEEEEEEEEeCCCEEEEEE
Confidence 4678889999999999999754 77888764
No 122
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=21.41 E-value=3.1e+02 Score=21.08 Aligned_cols=56 Identities=11% Similarity=0.061 Sum_probs=33.4
Q ss_pred EEEEEE--eccChhhHHHHHHHHhcCC-CceeEE-EEcCCCeEEEEEeecCHHHHHHHHHH
Q 025287 8 TMVLKV--DLQCSKCYKKVKKVLCKFP-QIQDQI-FDEKTNTVRIKVVCCSPEKIRDKLCC 64 (255)
Q Consensus 8 t~vLKV--~M~C~gCakKIkKAL~kI~-GV~sV~-VDlk~~kVTVeG~~vdpekLv~aL~k 64 (255)
++.|+| ++.-..=...|.+.|.--+ +--.++ .|..+..|+|+.+ .|.+.-++..+.
T Consensus 11 ~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd-~DL~eai~i~~~ 70 (82)
T cd06407 11 KIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCD-ADLEECIDVYRS 70 (82)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecH-HHHHHHHHHHHH
Confidence 566776 5555555566666665333 344444 3778999999987 444444443333
No 123
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=21.32 E-value=1.5e+02 Score=26.48 Aligned_cols=46 Identities=17% Similarity=0.211 Sum_probs=32.3
Q ss_pred hhHHHHHHHHhcCCCceeEEEEcCCCe-------------------EEEEEe--ecCHHHHHHHHHH
Q 025287 19 KCYKKVKKVLCKFPQIQDQIFDEKTNT-------------------VRIKVV--CCSPEKIRDKLCC 64 (255)
Q Consensus 19 gCakKIkKAL~kI~GV~sV~VDlk~~k-------------------VTVeG~--~vdpekLv~aL~k 64 (255)
||-=-++..+.+|+||.++++-..++. |.|+.+ .++-++|++.+.+
T Consensus 16 GCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff~ 82 (186)
T PRK13014 16 GCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFFS 82 (186)
T ss_pred CCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHHH
Confidence 444446667778999999999887775 445443 2577788877765
No 124
>PF09122 DUF1930: Domain of unknown function (DUF1930); InterPro: IPR015206 This entry represents a domain found in 3-mercaptopyruvate sulphurtransferase which has no known function. This domain adopts a structure consisting of a four-stranded antiparallel beta-sheet and an alpha-helix, arranged in a beta(2)-alpha-beta(2) fashion, and bearing a remarkable structural similarity to the FK506-binding protein class of peptidylprolyl cis/trans-isomerase []. ; PDB: 1OKG_A.
Probab=21.29 E-value=1.1e+02 Score=23.50 Aligned_cols=44 Identities=14% Similarity=0.027 Sum_probs=31.4
Q ss_pred ceEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEE
Q 025287 6 VTTMVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIK 49 (255)
Q Consensus 6 vtt~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVe 49 (255)
..+++|+| |--|..=-.-++.||..|.--+...|-+++++|.+.
T Consensus 18 ~~~~tl~vDg~~v~~PD~El~sA~~HlH~GEkA~V~FkS~Rv~~i 62 (68)
T PF09122_consen 18 LDNATLIVDGEIVENPDAELKSALVHLHIGEKAQVFFKSQRVAVI 62 (68)
T ss_dssp TTT--EEETTEEESS--HHHHHHHTT-BTT-EEEEEETTS-EEEE
T ss_pred ccceEEEEcCeEcCCCCHHHHHHHHHhhcCceeEEEEecCcEEEE
Confidence 35689999 888988889999999999988899999998887664
No 125
>TIGR03143 AhpF_homolog putative alkyl hydroperoxide reductase F subunit. This family of thioredoxin reductase homologs is found adjacent to alkylhydroperoxide reductase C subunit predominantly in cases where there is only one C subunit in the genome and that genome is lacking the F subunit partner (also a thioredcxin reductase homolog) that is usually found (TIGR03140).
Probab=20.87 E-value=3.9e+02 Score=26.86 Aligned_cols=32 Identities=22% Similarity=0.544 Sum_probs=19.4
Q ss_pred EEEEEeccChhhHHHHH---HHHhcCCCceeEEEE
Q 025287 9 MVLKVDLQCSKCYKKVK---KVLCKFPQIQDQIFD 40 (255)
Q Consensus 9 ~vLKV~M~C~gCakKIk---KAL~kI~GV~sV~VD 40 (255)
+.+.|..+|..|-+.++ +++...++|+.-.+|
T Consensus 480 i~v~~~~~C~~Cp~~~~~~~~~~~~~~~i~~~~i~ 514 (555)
T TIGR03143 480 IKIGVSLSCTLCPDVVLAAQRIASLNPNVEAEMID 514 (555)
T ss_pred EEEEECCCCCCcHHHHHHHHHHHHhCCCceEEEEE
Confidence 44555999999996332 333344566655555
No 126
>PF01565 FAD_binding_4: FAD binding domain This is only a subset of the Pfam family; InterPro: IPR006094 Various enzymes use FAD as a co-factor, most of these enzymes are oxygen-dependent oxidoreductases, containing a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. One of the enzymes Vanillyl-alcohol oxidase (VAO, 1.1.3.38 from EC) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 []. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging from aromatic amines to 4-alkylphenols. ; GO: 0008762 UDP-N-acetylmuramate dehydrogenase activity, 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZR6_A 3HSU_A 2AXR_A 3D2J_A 3D2H_A 3FW9_A 3FW8_A 3FW7_A 3GSY_A 3FWA_A ....
Probab=20.48 E-value=1.4e+02 Score=23.52 Aligned_cols=33 Identities=15% Similarity=0.190 Sum_probs=27.3
Q ss_pred cee-EEEEcCCCeEEEEEeecCHHHHHHHHHHhcC
Q 025287 34 IQD-QIFDEKTNTVRIKVVCCSPEKIRDKLCCKGE 67 (255)
Q Consensus 34 V~s-V~VDlk~~kVTVeG~~vdpekLv~aL~kKgg 67 (255)
.+. +++|.++++|+|... +.-.+|.++|...+.
T Consensus 53 l~~i~~id~~~~~v~v~aG-~~~~~l~~~l~~~g~ 86 (139)
T PF01565_consen 53 LNKIIEIDPENGTVTVGAG-VTWGDLYEALAPRGL 86 (139)
T ss_dssp CGCEEEEETTTTEEEEETT-SBHHHHHHHHHHHTE
T ss_pred ccccccccccceeEEEecc-ccchhcccccccccc
Confidence 444 778889999999977 888999999987754
No 127
>TIGR02200 GlrX_actino Glutaredoxin-like protein. This family of glutaredoxin-like proteins is limited to the Actinobacteria and contains the conserved CxxC motif.
Probab=20.43 E-value=2.2e+02 Score=19.51 Aligned_cols=30 Identities=17% Similarity=0.274 Sum_probs=18.6
Q ss_pred EEEEEeccChhhHHHHHHHHhcCCCceeEEEE
Q 025287 9 MVLKVDLQCSKCYKKVKKVLCKFPQIQDQIFD 40 (255)
Q Consensus 9 ~vLKV~M~C~gCakKIkKAL~kI~GV~sV~VD 40 (255)
++|--.-+|..|.+ ++..|.++ |+.-..+|
T Consensus 2 v~ly~~~~C~~C~~-~~~~L~~~-~~~~~~id 31 (77)
T TIGR02200 2 ITVYGTTWCGYCAQ-LMRTLDKL-GAAYEWVD 31 (77)
T ss_pred EEEEECCCChhHHH-HHHHHHHc-CCceEEEe
Confidence 34444778999987 56677666 44433333
No 128
>cd02429 PTH2_like Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported to encode such activity, Pth present in bacteria and eukaryotes and Pth2 present in archaea and eukaryotes. There is no functional information for this eukaryote-specific subgroup.
Probab=20.35 E-value=4.9e+02 Score=21.51 Aligned_cols=57 Identities=14% Similarity=0.108 Sum_probs=32.9
Q ss_pred CceEEEEEE-eccChhhHHHHHHHHhcCCCceeEEEEcCCCeEEEEEeecCHHHHHHHHHH
Q 025287 5 KVTTMVLKV-DLQCSKCYKKVKKVLCKFPQIQDQIFDEKTNTVRIKVVCCSPEKIRDKLCC 64 (255)
Q Consensus 5 ~vtt~vLKV-~M~C~gCakKIkKAL~kI~GV~sV~VDlk~~kVTVeG~~vdpekLv~aL~k 64 (255)
||.+++|+| +. .=-..+.+.+....=...+-+....|+.|+-|..=.+..+++.|.+
T Consensus 54 g~~KVVLkv~~e---~eL~~L~~~a~~~gi~~~l~te~p~gt~T~LaigP~~~~~id~it~ 111 (116)
T cd02429 54 NMHKVVLEVPDE---AALKNLSSKLTENSIKHKLWIEQPENIPTCIALKPYPKETVASYLK 111 (116)
T ss_pred CCceEEEEeCCH---HHHHHHHHHHHHcCCCeEEEEEcCCCCceEEEeCCCCHHHHHHHhC
Confidence 677888888 33 1223344444444334555567777778887754455556665543
No 129
>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains. ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i
Probab=20.24 E-value=2.4e+02 Score=17.75 Aligned_cols=17 Identities=18% Similarity=0.399 Sum_probs=9.0
Q ss_pred HHHHHHHHhcCCCceeE
Q 025287 21 YKKVKKVLCKFPQIQDQ 37 (255)
Q Consensus 21 akKIkKAL~kI~GV~sV 37 (255)
...+.+.|.++.||..|
T Consensus 53 ~~~~~~~l~~~~~v~~v 69 (71)
T cd04876 53 LARIMRKLRQIPGVIDV 69 (71)
T ss_pred HHHHHHHHhCCCCcEEE
Confidence 44555555555555443
Done!