Query 033623
Match_columns 115
No_of_seqs 272 out of 1447
Neff 9.4
Searched_HMMs 46136
Date Fri Mar 29 04:24:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033623.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033623hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.5 8.4E-14 1.8E-18 76.1 7.1 53 1-53 7-62 (62)
2 KOG4656 Copper chaperone for s 99.5 8.2E-14 1.8E-18 91.1 4.8 86 1-86 15-101 (247)
3 COG2608 CopZ Copper chaperone 99.4 2.3E-12 4.9E-17 72.3 7.7 57 1-57 11-70 (71)
4 KOG1603 Copper chaperone [Inor 99.3 8.2E-12 1.8E-16 70.4 6.8 58 1-58 13-71 (73)
5 PLN02957 copper, zinc superoxi 98.7 1.9E-07 4.1E-12 63.7 8.2 63 1-63 14-76 (238)
6 PRK10671 copA copper exporting 98.3 1.7E-06 3.6E-11 68.3 6.8 56 1-58 12-67 (834)
7 COG2217 ZntA Cation transport 98.2 4.6E-06 9.9E-11 64.6 6.8 55 1-56 11-69 (713)
8 KOG0207 Cation transport ATPas 97.8 6.9E-05 1.5E-09 58.9 6.4 61 1-61 3-65 (951)
9 TIGR00003 copper ion binding p 97.7 0.00059 1.3E-08 35.3 7.1 54 1-54 11-67 (68)
10 KOG0207 Cation transport ATPas 97.6 0.00018 3.9E-09 56.7 6.3 60 1-60 155-217 (951)
11 PRK10671 copA copper exporting 97.4 0.00072 1.6E-08 53.7 7.1 58 1-58 108-165 (834)
12 PRK11033 zntA zinc/cadmium/mer 97.1 0.0023 5E-08 50.3 6.8 57 1-57 62-119 (741)
13 COG1888 Uncharacterized protei 94.0 0.35 7.5E-06 28.2 5.6 49 10-58 24-80 (97)
14 TIGR02052 MerP mercuric transp 93.9 0.58 1.3E-05 25.9 7.6 56 1-56 32-90 (92)
15 PF02680 DUF211: Uncharacteriz 93.0 0.4 8.6E-06 28.2 4.8 50 9-58 21-78 (95)
16 PRK13748 putative mercuric red 88.7 3.2 6.9E-05 31.7 7.5 59 1-59 9-69 (561)
17 PRK14054 methionine sulfoxide 85.5 2 4.3E-05 28.1 4.1 44 4-47 10-75 (172)
18 cd00371 HMA Heavy-metal-associ 85.4 2.4 5.3E-05 19.2 7.2 52 1-52 7-60 (63)
19 PRK10553 assembly protein for 82.5 7.4 0.00016 22.5 6.2 43 7-49 19-62 (87)
20 PRK05528 methionine sulfoxide 78.3 6.5 0.00014 25.3 4.5 44 4-47 8-68 (156)
21 PRK00058 methionine sulfoxide 76.4 5.7 0.00012 26.9 4.0 44 4-47 52-117 (213)
22 PF03927 NapD: NapD protein; 75.4 12 0.00027 21.0 6.5 43 7-50 17-60 (79)
23 PF13732 DUF4162: Domain of un 75.1 12 0.00025 20.8 4.6 42 13-56 25-68 (84)
24 PRK13014 methionine sulfoxide 73.7 5.2 0.00011 26.5 3.2 44 4-47 15-80 (186)
25 PF01883 DUF59: Domain of unkn 72.5 5.8 0.00013 21.5 2.8 19 7-25 54-72 (72)
26 PF09580 Spore_YhcN_YlaJ: Spor 68.4 29 0.00062 22.3 6.0 29 7-35 77-105 (177)
27 PF01206 TusA: Sulfurtransfera 67.5 17 0.00037 19.4 4.4 48 1-57 8-57 (70)
28 PF04972 BON: BON domain; Int 64.9 7.8 0.00017 20.3 2.3 31 8-38 2-34 (64)
29 PRK09577 multidrug efflux prot 62.4 36 0.00079 28.5 6.5 46 7-52 158-211 (1032)
30 PF08712 Nfu_N: Scaffold prote 59.8 29 0.00064 19.9 4.2 39 10-50 39-79 (87)
31 PF04805 Pox_E10: E10-like pro 58.6 9.6 0.00021 20.9 1.8 20 1-20 16-35 (70)
32 PRK10555 aminoglycoside/multid 58.1 41 0.00088 28.2 6.1 44 7-50 159-210 (1037)
33 PRK05550 bifunctional methioni 57.6 21 0.00046 25.3 3.9 27 4-30 134-160 (283)
34 KOG3411 40S ribosomal protein 57.4 11 0.00025 23.5 2.3 44 4-50 97-141 (143)
35 TIGR00489 aEF-1_beta translati 56.9 14 0.0003 21.4 2.5 20 7-26 64-83 (88)
36 PF01625 PMSR: Peptide methion 55.5 15 0.00033 23.5 2.7 45 4-48 7-73 (155)
37 PRK11023 outer membrane lipopr 55.2 46 0.00099 22.0 5.0 41 7-47 51-94 (191)
38 PF02672 CP12: CP12 domain; I 54.9 2.8 6.1E-05 23.3 -0.6 15 100-114 52-68 (71)
39 cd04888 ACT_PheB-BS C-terminal 54.5 19 0.0004 19.3 2.7 19 7-25 56-74 (76)
40 TIGR02945 SUF_assoc FeS assemb 53.6 17 0.00037 21.0 2.6 21 8-28 58-78 (99)
41 COG4004 Uncharacterized protei 53.5 28 0.0006 20.4 3.3 22 15-36 37-58 (96)
42 TIGR00401 msrA methionine-S-su 52.8 11 0.00024 24.0 1.8 27 4-30 7-33 (149)
43 PRK11198 LysM domain/BON super 50.6 56 0.0012 20.6 4.7 42 7-48 28-70 (147)
44 PRK15127 multidrug efflux syst 50.5 66 0.0014 27.1 6.2 43 8-50 160-210 (1049)
45 COG2092 EFB1 Translation elong 50.0 18 0.0004 21.0 2.2 20 7-26 64-83 (88)
46 PRK11023 outer membrane lipopr 49.6 74 0.0016 21.0 5.6 37 7-43 129-167 (191)
47 TIGR00915 2A0602 The (Largely 49.4 69 0.0015 27.0 6.1 43 8-50 160-210 (1044)
48 PRK09019 translation initiatio 48.9 23 0.00051 21.4 2.6 10 39-48 59-68 (108)
49 cd02410 archeal_CPSF_KH The ar 48.2 71 0.0015 20.4 5.8 54 8-61 56-116 (145)
50 PRK00435 ef1B elongation facto 47.1 24 0.00052 20.4 2.4 20 7-26 64-83 (88)
51 PRK07451 translation initiatio 46.8 18 0.00039 22.1 1.9 9 39-47 66-74 (115)
52 PHA03005 sulfhydryl oxidase; P 46.5 19 0.00041 21.1 1.9 20 1-20 41-60 (96)
53 PF05046 Img2: Mitochondrial l 46.2 57 0.0012 18.7 5.6 30 22-52 58-87 (87)
54 PF08002 DUF1697: Protein of u 46.2 72 0.0016 19.9 5.9 48 9-57 23-75 (137)
55 PF11491 DUF3213: Protein of u 46.1 44 0.00095 19.2 3.3 47 8-54 14-63 (88)
56 PRK06824 translation initiatio 46.0 31 0.00067 21.2 2.9 10 39-48 69-78 (118)
57 COG3062 NapD Uncharacterized p 45.5 63 0.0014 19.0 5.3 42 7-49 20-62 (94)
58 PF15643 Tox-PL-2: Papain fold 44.9 30 0.00065 20.6 2.6 19 2-21 20-38 (100)
59 TIGR01676 GLDHase galactonolac 44.4 54 0.0012 25.5 4.6 39 14-54 110-148 (541)
60 COG2151 PaaD Predicted metal-s 43.7 33 0.00071 20.8 2.7 21 7-27 69-89 (111)
61 PF03434 DUF276: DUF276 ; Int 42.8 48 0.001 23.1 3.6 28 7-34 89-116 (291)
62 KOG4730 D-arabinono-1, 4-lacto 40.2 49 0.0011 25.4 3.6 34 23-56 105-138 (518)
63 cd04885 ACT_ThrD-I Tandem C-te 39.3 32 0.0007 18.3 2.1 17 38-54 50-66 (68)
64 cd03421 SirA_like_N SirA_like_ 39.0 62 0.0013 17.1 5.2 48 1-58 7-56 (67)
65 TIGR03406 FeS_long_SufT probab 38.5 45 0.00098 21.9 3.0 21 7-27 133-153 (174)
66 PRK11018 hypothetical protein; 38.4 72 0.0016 17.7 5.2 47 2-57 17-65 (78)
67 PF01514 YscJ_FliF: Secretory 38.2 45 0.00098 22.3 3.0 21 7-27 117-137 (206)
68 PF00352 TBP: Transcription fa 38.2 76 0.0016 17.9 3.7 23 27-49 55-77 (86)
69 TIGR00914 2A0601 heavy metal e 38.2 65 0.0014 27.1 4.4 44 7-50 700-753 (1051)
70 COG0225 MsrA Peptide methionin 38.2 27 0.00059 22.9 1.9 28 4-31 13-40 (174)
71 COG0841 AcrB Cation/multidrug 38.0 1.6E+02 0.0034 25.0 6.5 45 7-51 157-210 (1009)
72 PRK11670 antiporter inner memb 37.8 1.2E+02 0.0027 22.2 5.4 57 7-63 67-148 (369)
73 TIGR01158 SUI1_rel translation 36.4 54 0.0012 19.4 2.8 21 29-49 37-62 (101)
74 cd06167 LabA_like LabA_like pr 36.4 56 0.0012 20.0 3.1 29 32-60 104-132 (149)
75 TIGR02830 spore_III_AG stage I 35.9 41 0.00088 22.4 2.5 28 7-34 63-92 (186)
76 PF13193 AMP-binding_C: AMP-bi 35.9 46 0.001 17.8 2.4 41 9-49 1-46 (73)
77 PRK10614 multidrug efflux syst 35.8 1.5E+02 0.0032 25.1 6.0 43 8-50 160-211 (1025)
78 PRK11282 glcE glycolate oxidas 35.6 83 0.0018 23.0 4.2 37 15-53 44-80 (352)
79 PRK10503 multidrug efflux syst 35.3 1.5E+02 0.0032 25.1 6.0 43 8-50 169-220 (1040)
80 PRK09579 multidrug efflux prot 35.1 1.5E+02 0.0033 25.0 6.0 43 7-49 158-209 (1017)
81 COG0277 GlcD FAD/FMN-containin 35.0 50 0.0011 24.4 3.1 34 24-57 89-122 (459)
82 PF08478 POTRA_1: POTRA domain 34.7 73 0.0016 16.6 3.1 28 7-34 36-64 (69)
83 COG2331 Uncharacterized protei 34.1 24 0.00052 19.9 1.0 16 2-17 35-50 (82)
84 COG4669 EscJ Type III secretor 33.9 53 0.0012 22.8 2.8 21 7-27 111-131 (246)
85 cd04908 ACT_Bt0572_1 N-termina 33.9 76 0.0016 16.6 5.7 48 7-55 15-65 (66)
86 COG3643 Glutamate formiminotra 33.7 92 0.002 21.9 3.9 41 7-47 20-62 (302)
87 PF10934 DUF2634: Protein of u 33.3 1.1E+02 0.0024 18.3 4.0 31 7-37 71-104 (112)
88 cd00292 EF1B Elongation factor 33.1 56 0.0012 18.9 2.5 20 7-26 64-83 (88)
89 TIGR02544 III_secr_YscJ type I 32.8 56 0.0012 21.7 2.8 21 7-27 109-129 (193)
90 PF13216 DUF4024: Protein of u 32.5 17 0.00036 16.7 0.2 11 101-111 9-19 (35)
91 PLN00204 CP12 gene family prot 32.3 12 0.00026 23.1 -0.4 16 99-114 106-123 (126)
92 PF01849 NAC: NAC domain; Int 32.2 71 0.0015 16.6 2.6 19 16-34 15-33 (58)
93 PF00873 ACR_tran: AcrB/AcrD/A 31.8 1.2E+02 0.0025 25.5 4.9 44 7-50 689-742 (1021)
94 cd03420 SirA_RHOD_Pry_redox Si 31.8 89 0.0019 16.7 5.6 49 1-58 7-57 (69)
95 PRK07334 threonine dehydratase 31.5 2.1E+02 0.0047 21.1 5.9 50 8-57 341-402 (403)
96 PHA01634 hypothetical protein 31.4 15 0.00031 23.3 -0.2 13 1-13 98-110 (156)
97 PRK15348 type III secretion sy 31.2 62 0.0013 22.6 2.8 21 7-27 109-129 (249)
98 PRK10568 periplasmic protein; 31.2 1.6E+02 0.0035 19.6 5.2 33 7-39 62-96 (203)
99 KOG1635 Peptide methionine sul 30.6 52 0.0011 21.8 2.2 28 4-31 31-58 (191)
100 cd04877 ACT_TyrR N-terminal AC 30.5 66 0.0014 17.3 2.4 17 8-24 52-68 (74)
101 cd04886 ACT_ThrD-II-like C-ter 30.4 42 0.0009 17.3 1.6 17 39-55 56-72 (73)
102 KOG4034 Uncharacterized conser 29.9 1.5E+02 0.0033 19.3 4.2 47 5-52 122-169 (169)
103 TIGR03527 selenium_YedF seleni 29.8 1.7E+02 0.0037 19.4 5.4 49 1-58 6-56 (194)
104 PF00873 ACR_tran: AcrB/AcrD/A 29.4 2E+02 0.0044 24.1 5.9 41 7-47 62-106 (1021)
105 KOG3782 Predicted membrane pro 29.0 1.7E+02 0.0038 19.2 4.4 46 2-47 26-84 (189)
106 cd08032 LARP_7 La RNA-binding 28.6 18 0.0004 20.6 -0.1 7 102-108 15-21 (82)
107 PF00736 EF1_GNE: EF-1 guanine 28.4 77 0.0017 18.3 2.5 20 7-26 64-84 (89)
108 TIGR01677 pln_FAD_oxido plant- 28.3 1.3E+02 0.0028 23.6 4.4 34 23-56 92-125 (557)
109 KOG3302 TATA-box binding prote 28.3 72 0.0016 21.4 2.6 34 27-60 74-114 (200)
110 PF11360 DUF3110: Protein of u 27.9 73 0.0016 18.3 2.4 23 38-60 55-77 (86)
111 cd04883 ACT_AcuB C-terminal AC 27.8 1E+02 0.0022 16.1 5.9 50 5-54 13-68 (72)
112 TIGR02898 spore_YhcN_YlaJ spor 27.8 1.7E+02 0.0038 18.8 6.2 29 7-35 56-84 (158)
113 TIGR00288 conserved hypothetic 27.5 89 0.0019 20.2 2.9 28 32-59 110-137 (160)
114 PRK11200 grxA glutaredoxin 1; 27.4 1.2E+02 0.0025 16.7 3.4 26 2-28 10-39 (85)
115 TIGR01679 bact_FAD_ox FAD-link 27.3 1.4E+02 0.003 22.3 4.3 32 24-55 65-96 (419)
116 PF13299 CPSF100_C: Cleavage a 27.2 71 0.0015 20.5 2.5 24 36-59 98-121 (161)
117 PRK10614 multidrug efflux syst 27.2 1.2E+02 0.0026 25.6 4.2 44 7-50 677-730 (1025)
118 PF14056 DUF4250: Domain of un 26.8 75 0.0016 16.7 2.1 19 37-55 31-49 (55)
119 COG2177 FtsX Cell division pro 26.6 89 0.0019 22.3 3.1 38 4-53 71-109 (297)
120 COG3603 Uncharacterized conser 26.6 1.7E+02 0.0036 18.2 5.0 45 8-54 81-126 (128)
121 cd03422 YedF YedF is a bacteri 26.6 1.1E+02 0.0025 16.3 5.1 47 2-57 8-56 (69)
122 COG3870 Uncharacterized protei 26.6 1.2E+02 0.0026 18.2 3.1 24 34-57 7-30 (109)
123 PHA02119 hypothetical protein 26.3 98 0.0021 17.2 2.5 20 38-57 54-73 (87)
124 COG0217 Uncharacterized conser 26.2 1.3E+02 0.0029 20.9 3.7 45 7-51 110-160 (241)
125 PF01565 FAD_binding_4: FAD bi 26.0 1.4E+02 0.003 18.0 3.6 32 23-54 57-88 (139)
126 cd04879 ACT_3PGDH-like ACT_3PG 25.7 1E+02 0.0022 15.5 2.7 16 9-24 54-69 (71)
127 PF03698 UPF0180: Uncharacteri 25.4 1.1E+02 0.0024 17.4 2.8 21 39-59 9-29 (80)
128 PF09158 MotCF: Bacteriophage 25.1 1.6E+02 0.0035 17.6 4.5 40 17-57 40-79 (103)
129 KOG3476 Microtubule-associated 24.7 37 0.0008 19.7 0.7 14 1-14 1-14 (100)
130 TIGR00914 2A0601 heavy metal e 24.5 3E+02 0.0065 23.4 6.1 43 9-51 170-221 (1051)
131 PRK15324 type III secretion sy 24.4 95 0.0021 21.7 2.8 21 7-27 110-130 (252)
132 PRK10503 multidrug efflux syst 24.4 1.5E+02 0.0033 25.0 4.4 44 7-50 691-744 (1040)
133 PF07837 FTCD_N: Formiminotran 24.1 2.2E+02 0.0048 18.8 5.4 41 7-47 18-60 (178)
134 PLN02465 L-galactono-1,4-lacto 24.0 1.8E+02 0.004 22.9 4.5 32 24-55 153-184 (573)
135 TIGR01678 FAD_lactone_ox sugar 23.9 2.1E+02 0.0046 21.5 4.8 32 24-55 71-102 (438)
136 cd04906 ACT_ThrD-I_1 First of 23.9 1.4E+02 0.0031 16.6 6.7 50 9-59 17-74 (85)
137 PF01936 NYN: NYN domain; Int 23.7 60 0.0013 19.6 1.6 28 32-59 100-127 (146)
138 PF04312 DUF460: Protein of un 23.6 2E+02 0.0044 18.2 4.4 36 24-59 47-84 (138)
139 TIGR00915 2A0602 The (Largely 23.4 1.7E+02 0.0036 24.8 4.4 44 7-50 699-752 (1044)
140 cd04909 ACT_PDH-BS C-terminal 22.9 1.3E+02 0.0028 15.6 5.1 49 6-54 14-69 (69)
141 TIGR03675 arCOG00543 arCOG0054 22.9 3.1E+02 0.0067 21.9 5.6 55 7-61 72-133 (630)
142 KOG2874 rRNA processing protei 22.7 2.8E+02 0.0061 20.0 4.8 41 5-47 73-122 (356)
143 TIGR00268 conserved hypothetic 22.6 2.6E+02 0.0057 19.1 6.7 52 7-59 187-246 (252)
144 PRK10555 aminoglycoside/multid 22.4 1.8E+02 0.0038 24.7 4.4 44 7-50 698-751 (1037)
145 COG1432 Uncharacterized conser 22.3 1.2E+02 0.0027 19.7 3.0 30 32-61 115-144 (181)
146 PF07582 AP_endonuc_2_N: AP en 22.3 89 0.0019 16.4 1.8 17 40-56 2-18 (55)
147 PRK10509 bacterioferritin-asso 22.1 59 0.0013 17.5 1.2 16 2-17 38-53 (64)
148 PRK14018 trifunctional thiored 21.7 72 0.0016 24.8 1.9 27 4-30 205-231 (521)
149 PRK15367 type III secretion sy 21.6 2.2E+02 0.0049 21.4 4.4 18 8-25 241-258 (395)
150 COG1094 Predicted RNA-binding 21.6 2.6E+02 0.0057 18.8 4.8 36 9-45 28-66 (194)
151 cd03423 SirA SirA (also known 21.5 1.5E+02 0.0032 15.8 5.4 48 2-58 8-57 (69)
152 PF13721 SecD-TM1: SecD export 21.4 1.9E+02 0.0041 17.0 4.2 29 8-37 49-77 (101)
153 cd00291 SirA_YedF_YeeD SirA, Y 21.4 1.4E+02 0.0031 15.5 5.6 48 2-58 8-57 (69)
154 PF02983 Pro_Al_protease: Alph 20.6 1.5E+02 0.0033 15.6 3.9 21 17-37 22-42 (62)
155 smart00874 B5 tRNA synthetase 20.6 1.2E+02 0.0025 16.1 2.2 19 38-56 19-37 (71)
156 COG5561 Predicted metal-bindin 20.5 1.3E+02 0.0028 17.7 2.4 8 3-10 7-14 (101)
157 cd04874 ACT_Af1403 N-terminal 20.3 1.4E+02 0.0031 15.1 2.6 17 9-25 55-71 (72)
158 cd06482 ACD_HspB10 Alpha cryst 20.2 1.2E+02 0.0026 17.3 2.3 22 16-37 15-38 (87)
159 PF04461 DUF520: Protein of un 20.2 2.3E+02 0.005 18.5 3.7 44 7-52 105-150 (160)
160 PF13383 Methyltransf_22: Meth 20.1 1.6E+02 0.0035 20.3 3.3 50 1-58 173-226 (242)
No 1
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.52 E-value=8.4e-14 Score=76.05 Aligned_cols=53 Identities=36% Similarity=0.631 Sum_probs=49.8
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee---CCHHHHHHHHHHcCCC
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY---VDPNKVLKKVKSTGKR 53 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~---~~~~~i~~~i~~~G~~ 53 (115)
|+|++|+++|+++|.+++||.++++|+.+++++|.++ +++++|.++|+++||+
T Consensus 7 m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 7 MTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGYE 62 (62)
T ss_dssp TTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTSE
T ss_pred cccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCcC
Confidence 8999999999999999999999999999999999976 4669999999999984
No 2
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.46 E-value=8.2e-14 Score=91.06 Aligned_cols=86 Identities=28% Similarity=0.418 Sum_probs=72.8
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEeeCCHHHHHHHHHHcCCCceecCCCCCccccCCCccccc-CCCCC
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGYVDPNKVLKKVKSTGKRAEFWPYVPYNLVAYPYVAQAY-DKKAP 79 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 79 (115)
|+|++|+..|++.|..++||.++++|+.++.+.|.+...+.+|..+|+.+|.++.+.+.+..+.++-...-+.| .+..+
T Consensus 15 M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G~psaval~at~a~~~~~~~v 94 (247)
T KOG4656|consen 15 MTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAGKPSAVALLATVAKYTGPQAV 94 (247)
T ss_pred chhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCCchhHHHHHHHHHHhcCCccc
Confidence 89999999999999999999999999999999999999999999999999999999998877665444333333 22367
Q ss_pred CCccccc
Q 033623 80 SGYVKNV 86 (115)
Q Consensus 80 ~g~~~~~ 86 (115)
+|++|+.
T Consensus 95 ~GvvRf~ 101 (247)
T KOG4656|consen 95 QGVVRFV 101 (247)
T ss_pred eeEEEEE
Confidence 7777774
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.41 E-value=2.3e-12 Score=72.29 Aligned_cols=57 Identities=28% Similarity=0.490 Sum_probs=51.3
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee---CCHHHHHHHHHHcCCCceec
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY---VDPNKVLKKVKSTGKRAEFW 57 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~---~~~~~i~~~i~~~G~~~~~~ 57 (115)
|+|.+|+.+|+++|.+++||.++++++..+.+.|..+ ++.++|.++|+.+||.+..+
T Consensus 11 MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~~ 70 (71)
T COG2608 11 MTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEEI 70 (71)
T ss_pred cCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeeec
Confidence 8999999999999999999999999999977776643 79999999999999987654
No 4
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.33 E-value=8.2e-12 Score=70.40 Aligned_cols=58 Identities=52% Similarity=0.993 Sum_probs=54.1
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEeeCCHHHHHHHHHHcC-CCceecC
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGYVDPNKVLKKVKSTG-KRAEFWP 58 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~~~~~~i~~~i~~~G-~~~~~~~ 58 (115)
|+|.+|..+|++.|..++||.++++|..+++++|.|.+++..|++.|++.| .+..+|.
T Consensus 13 ~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 13 MHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred cccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEec
Confidence 799999999999999999999999999999999999999999999999888 6666654
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.66 E-value=1.9e-07 Score=63.67 Aligned_cols=63 Identities=27% Similarity=0.469 Sum_probs=57.2
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEeeCCHHHHHHHHHHcCCCceecCCCCCc
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGYVDPNKVLKKVKSTGKRAEFWPYVPYN 63 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~~~~~~~~~~~ 63 (115)
|+|..|+.+|++.|.+++||.++.+++..++++|........+.+.|++.||.+++++.+..+
T Consensus 14 MsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 14 MKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQGDPE 76 (238)
T ss_pred ccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCCCcc
Confidence 789999999999999999999999999999999987778889999999999999888765544
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.33 E-value=1.7e-06 Score=68.26 Aligned_cols=56 Identities=18% Similarity=0.415 Sum_probs=50.0
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEeeCCHHHHHHHHHHcCCCceecC
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGYVDPNKVLKKVKSTGKRAEFWP 58 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~~~~~~ 58 (115)
|+|.+|+.+|+++|++++||.++++++. +.++.+..+.+.+.+.+++.||+++...
T Consensus 12 mtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 12 LSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred cccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 8999999999999999999999999994 5566666788999999999999998753
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.22 E-value=4.6e-06 Score=64.64 Aligned_cols=55 Identities=29% Similarity=0.560 Sum_probs=50.2
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee---CC-HHHHHHHHHHcCCCcee
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY---VD-PNKVLKKVKSTGKRAEF 56 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~---~~-~~~i~~~i~~~G~~~~~ 56 (115)
|+|..|+++|| +|++++||..+.+|+.++++.|..+ .+ .+++..++++.||.+..
T Consensus 11 m~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 11 MTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred cCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 89999999999 9999999999999999999998854 45 78899999999998775
No 8
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.80 E-value=6.9e-05 Score=58.93 Aligned_cols=61 Identities=25% Similarity=0.456 Sum_probs=56.1
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHHcCCCceecCCCC
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY--VDPNKVLKKVKSTGKRAEFWPYVP 61 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~--~~~~~i~~~i~~~G~~~~~~~~~~ 61 (115)
|+|..|.+.+++++...+|+.++.+++.++..+|..+ .+++.+.+.++..||.+++.....
T Consensus 3 mtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ied~gf~~~~~~~~~ 65 (951)
T KOG0207|consen 3 MTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIEDMGFEASLLSDSE 65 (951)
T ss_pred ccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhhcccceeeecccCc
Confidence 8999999999999999999999999999999998865 889999999999999999887543
No 9
>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=97.67 E-value=0.00059 Score=35.25 Aligned_cols=54 Identities=20% Similarity=0.354 Sum_probs=44.1
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee---CCHHHHHHHHHHcCCCc
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY---VDPNKVLKKVKSTGKRA 54 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~---~~~~~i~~~i~~~G~~~ 54 (115)
+.|..|...+++.+...+++....+++...++.+..+ .+...+...+...|+.+
T Consensus 11 ~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 11 MTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYEV 67 (68)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCCc
Confidence 4699999999999999999999999999998887642 46667767777777653
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.62 E-value=0.00018 Score=56.66 Aligned_cols=60 Identities=28% Similarity=0.517 Sum_probs=54.8
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee---CCHHHHHHHHHHcCCCceecCCC
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY---VDPNKVLKKVKSTGKRAEFWPYV 60 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~---~~~~~i~~~i~~~G~~~~~~~~~ 60 (115)
|.|..|..+|++.|.+++||.++++++.++++.|..+ ..+.++.+.|+.+|+.+......
T Consensus 155 ~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~~~ 217 (951)
T KOG0207|consen 155 MTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRPYG 217 (951)
T ss_pred ccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeeecc
Confidence 7899999999999999999999999999999998754 78999999999999998877643
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.40 E-value=0.00072 Score=53.71 Aligned_cols=58 Identities=29% Similarity=0.518 Sum_probs=50.9
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEeeCCHHHHHHHHHHcCCCceecC
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGYVDPNKVLKKVKSTGKRAEFWP 58 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~~~~~~ 58 (115)
|+|..|...+++.+.+++||.++.+++.++++.+.+..+.+++.+.+++.||.+.+..
T Consensus 108 m~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~~~ 165 (834)
T PRK10671 108 MSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEAIE 165 (834)
T ss_pred cCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCccccc
Confidence 7899999999999999999999999999998888755678888888999999876543
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.07 E-value=0.0023 Score=50.33 Aligned_cols=57 Identities=30% Similarity=0.373 Sum_probs=47.2
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee-CCHHHHHHHHHHcCCCceec
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY-VDPNKVLKKVKSTGKRAEFW 57 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~-~~~~~i~~~i~~~G~~~~~~ 57 (115)
|+|.+|..++++.+.+++||.++.+++.++++.+..+ ...+++.+.+++.||.+...
T Consensus 62 m~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~~~ 119 (741)
T PRK11033 62 MDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLRDE 119 (741)
T ss_pred CCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccccccc
Confidence 7899999999999999999999999999999877643 12266777888899987644
No 13
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=94.04 E-value=0.35 Score=28.15 Aligned_cols=49 Identities=14% Similarity=0.300 Sum_probs=35.4
Q ss_pred HHHHHhCCCCceEEEEec-----cC--CEEEEEee-CCHHHHHHHHHHcCCCceecC
Q 033623 10 VRNAVSSIRGAKSVEVNR-----KQ--SRVTVTGY-VDPNKVLKKVKSTGKRAEFWP 58 (115)
Q Consensus 10 v~~~l~~~~gv~~~~v~~-----~~--~~v~v~~~-~~~~~i~~~i~~~G~~~~~~~ 58 (115)
+-+.|++++||..+++.+ .+ -+++|.|. ++-++|.+.|++.|...+-+.
T Consensus 24 ~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHSiD 80 (97)
T COG1888 24 LALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHSID 80 (97)
T ss_pred HHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeeehh
Confidence 456688888888776543 22 34566664 999999999999997766554
No 14
>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=93.90 E-value=0.58 Score=25.89 Aligned_cols=56 Identities=21% Similarity=0.329 Sum_probs=40.9
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEe---eCCHHHHHHHHHHcCCCcee
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTG---YVDPNKVLKKVKSTGKRAEF 56 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~---~~~~~~i~~~i~~~G~~~~~ 56 (115)
+.|..|...++..+....++....++....+..+.. ..+...+...+.+.|+..++
T Consensus 32 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 32 MTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 458999999999999999988888888777755542 13555555666777776554
No 15
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=92.99 E-value=0.4 Score=28.17 Aligned_cols=50 Identities=16% Similarity=0.340 Sum_probs=34.8
Q ss_pred HHHHHHhCCCCceEEEEec-----cCCE--EEEEee-CCHHHHHHHHHHcCCCceecC
Q 033623 9 KVRNAVSSIRGAKSVEVNR-----KQSR--VTVTGY-VDPNKVLKKVKSTGKRAEFWP 58 (115)
Q Consensus 9 ~v~~~l~~~~gv~~~~v~~-----~~~~--v~v~~~-~~~~~i~~~i~~~G~~~~~~~ 58 (115)
.+-+.|.+++||..+++.. .+.. ++|+|+ ++.++|.++|++.|-..+-+.
T Consensus 21 e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHSID 78 (95)
T PF02680_consen 21 ELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHSID 78 (95)
T ss_dssp HHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEEEE
T ss_pred HHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEeee
Confidence 3567789999998877654 3333 455675 999999999999997665443
No 16
>PRK13748 putative mercuric reductase; Provisional
Probab=88.72 E-value=3.2 Score=31.69 Aligned_cols=59 Identities=24% Similarity=0.436 Sum_probs=44.9
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEe--eCCHHHHHHHHHHcCCCceecCC
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTG--YVDPNKVLKKVKSTGKRAEFWPY 59 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~--~~~~~~i~~~i~~~G~~~~~~~~ 59 (115)
|+|..|..+++..+...+++....+++......+.. ..+...+...+...|+..+....
T Consensus 9 ~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~~~ 69 (561)
T PRK13748 9 MTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLADA 69 (561)
T ss_pred eecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeeccCc
Confidence 579999999999999999998888888888766653 23556666667777877655544
No 17
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=85.50 E-value=2 Score=28.13 Aligned_cols=44 Identities=18% Similarity=0.291 Sum_probs=34.5
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeccCCE-------------------EEEEee---CCHHHHHHHH
Q 033623 4 DGCERKVRNAVSSIRGAKSVEVNRKQSR-------------------VTVTGY---VDPNKVLKKV 47 (115)
Q Consensus 4 ~~C~~~v~~~l~~~~gv~~~~v~~~~~~-------------------v~v~~~---~~~~~i~~~i 47 (115)
.+|-+.++..+.+++||.++.+-...+. |.|..+ ++.++|++..
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f 75 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELF 75 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHH
Confidence 5799999999999999999998876654 455543 7777777754
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=85.36 E-value=2.4 Score=19.24 Aligned_cols=52 Identities=33% Similarity=0.638 Sum_probs=33.4
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHHcCC
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY--VDPNKVLKKVKSTGK 52 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~--~~~~~i~~~i~~~G~ 52 (115)
+.|..|...++..+....++.....++......+... .....+...+...++
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 (63)
T cd00371 7 MTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIEDAGY 60 (63)
T ss_pred eEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHHHcCC
Confidence 3588999999988888888777777776666555432 244444334444443
No 19
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=82.48 E-value=7.4 Score=22.51 Aligned_cols=43 Identities=12% Similarity=0.227 Sum_probs=30.2
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEEee-CCHHHHHHHHHH
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY-VDPNKVLKKVKS 49 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~-~~~~~i~~~i~~ 49 (115)
...|.+.|..++|++-...|...+|+.|+-+ .+...+.+.|..
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~~ 62 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIES 62 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHHH
Confidence 5678899999999987777777788776532 355555555543
No 20
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=78.28 E-value=6.5 Score=25.33 Aligned_cols=44 Identities=20% Similarity=0.289 Sum_probs=33.3
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeccCCE--------------EEEEee---CCHHHHHHHH
Q 033623 4 DGCERKVRNAVSSIRGAKSVEVNRKQSR--------------VTVTGY---VDPNKVLKKV 47 (115)
Q Consensus 4 ~~C~~~v~~~l~~~~gv~~~~v~~~~~~--------------v~v~~~---~~~~~i~~~i 47 (115)
.+|-+-+|..+.+++||.++.+-...+. |.|..+ ++.++|++..
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f 68 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYL 68 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHH
Confidence 5799999999999999999998765533 344443 6777777754
No 21
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=76.42 E-value=5.7 Score=26.93 Aligned_cols=44 Identities=18% Similarity=0.163 Sum_probs=34.1
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeccCC-------------------EEEEEee---CCHHHHHHHH
Q 033623 4 DGCERKVRNAVSSIRGAKSVEVNRKQS-------------------RVTVTGY---VDPNKVLKKV 47 (115)
Q Consensus 4 ~~C~~~v~~~l~~~~gv~~~~v~~~~~-------------------~v~v~~~---~~~~~i~~~i 47 (115)
.+|-+.+|..+.+++||.++.+-...+ .|.|..+ ++.++|++..
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~F 117 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVF 117 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHH
Confidence 579999999999999999999987744 2445543 7778887755
No 22
>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=75.38 E-value=12 Score=21.03 Aligned_cols=43 Identities=16% Similarity=0.248 Sum_probs=30.1
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEEee-CCHHHHHHHHHHc
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY-VDPNKVLKKVKST 50 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~-~~~~~i~~~i~~~ 50 (115)
...+.++|.+++|++-...+.. +|+.|+-+ .+..++.+.+...
T Consensus 17 ~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~i 60 (79)
T PF03927_consen 17 LEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDAI 60 (79)
T ss_dssp HHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHHH
Confidence 4578899999999976666655 88766533 4666666666543
No 23
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=75.08 E-value=12 Score=20.79 Aligned_cols=42 Identities=17% Similarity=0.310 Sum_probs=29.6
Q ss_pred HHhCCCCceEEEEeccCCEEE--EEeeCCHHHHHHHHHHcCCCcee
Q 033623 13 AVSSIRGAKSVEVNRKQSRVT--VTGYVDPNKVLKKVKSTGKRAEF 56 (115)
Q Consensus 13 ~l~~~~gv~~~~v~~~~~~v~--v~~~~~~~~i~~~i~~~G~~~~~ 56 (115)
.|..++||.++...- .+.+. +.......+|+..|...|. +.-
T Consensus 25 ~l~~~~~v~~v~~~~-~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~ 68 (84)
T PF13732_consen 25 ELEELPGVESVEQDG-DGKLRIKLEDEETANELLQELIEKGI-IRS 68 (84)
T ss_pred HHhhCCCeEEEEEeC-CcEEEEEECCcccHHHHHHHHHhCCC-eeE
Confidence 377889999887643 44344 4445678899999998887 543
No 24
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=73.71 E-value=5.2 Score=26.54 Aligned_cols=44 Identities=23% Similarity=0.264 Sum_probs=33.9
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeccCCE-------------------EEEEee---CCHHHHHHHH
Q 033623 4 DGCERKVRNAVSSIRGAKSVEVNRKQSR-------------------VTVTGY---VDPNKVLKKV 47 (115)
Q Consensus 4 ~~C~~~v~~~l~~~~gv~~~~v~~~~~~-------------------v~v~~~---~~~~~i~~~i 47 (115)
.+|-+-+|..+.+++||.++.+-...+. |.|..+ ++.++|++..
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~F 80 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIF 80 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHH
Confidence 4788999999999999999998876653 445543 6777777754
No 25
>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=72.45 E-value=5.8 Score=21.54 Aligned_cols=19 Identities=37% Similarity=0.669 Sum_probs=15.2
Q ss_pred HHHHHHHHhCCCCceEEEE
Q 033623 7 ERKVRNAVSSIRGAKSVEV 25 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v 25 (115)
...++++|..++||.+++|
T Consensus 54 ~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 54 REEIREALKALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHHTSTT-SEEEE
T ss_pred HHHHHHHHHhCCCCceEeC
Confidence 4678999999999998875
No 26
>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=68.39 E-value=29 Score=22.32 Aligned_cols=29 Identities=17% Similarity=0.295 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEE
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQSRVTVT 35 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~~v~v~ 35 (115)
+..|.+.+.+++||.++.+-.....+.|.
T Consensus 77 a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 77 ADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 56788999999999999988888887664
No 27
>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=67.51 E-value=17 Score=19.44 Aligned_cols=48 Identities=10% Similarity=0.061 Sum_probs=34.0
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHHcCCCceec
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY--VDPNKVLKKVKSTGKRAEFW 57 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~--~~~~~i~~~i~~~G~~~~~~ 57 (115)
+.|+....+++++|.+++.- +.+.|..+ .....|...+++.|+....+
T Consensus 8 ~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 8 LSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp -STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred CCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHCCCEEEEE
Confidence 36999999999999997432 34445443 45677888999999975444
No 28
>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=64.91 E-value=7.8 Score=20.33 Aligned_cols=31 Identities=29% Similarity=0.310 Sum_probs=15.2
Q ss_pred HHHHHHHhCCCCce--EEEEeccCCEEEEEeeC
Q 033623 8 RKVRNAVSSIRGAK--SVEVNRKQSRVTVTGYV 38 (115)
Q Consensus 8 ~~v~~~l~~~~gv~--~~~v~~~~~~v~v~~~~ 38 (115)
.+|+++|...+.+. .+.+....+.+++.|.+
T Consensus 2 ~~v~~~L~~~~~~~~~~i~v~v~~g~v~L~G~v 34 (64)
T PF04972_consen 2 TKVRAALRADPWLPDSNISVSVENGVVTLSGEV 34 (64)
T ss_dssp -----------CTT-TTEEEEEECTEEEEEEEE
T ss_pred cccccccccccccCCCeEEEEEECCEEEEEeeC
Confidence 35666776633222 57888889999999875
No 29
>PRK09577 multidrug efflux protein; Reviewed
Probab=62.37 E-value=36 Score=28.49 Aligned_cols=46 Identities=11% Similarity=0.162 Sum_probs=34.9
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEEe--------eCCHHHHHHHHHHcCC
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQSRVTVTG--------YVDPNKVLKKVKSTGK 52 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~--------~~~~~~i~~~i~~~G~ 52 (115)
...++..|++++||.++++.-....+.|.- .++..+|.++|+..+.
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n~ 211 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAHNA 211 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhCC
Confidence 357899999999999999987555555541 2788888899977553
No 30
>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=59.82 E-value=29 Score=19.86 Aligned_cols=39 Identities=26% Similarity=0.304 Sum_probs=27.4
Q ss_pred HHHHHhCCCCceEEEEeccCCEEEEE--eeCCHHHHHHHHHHc
Q 033623 10 VRNAVSSIRGAKSVEVNRKQSRVTVT--GYVDPNKVLKKVKST 50 (115)
Q Consensus 10 v~~~l~~~~gv~~~~v~~~~~~v~v~--~~~~~~~i~~~i~~~ 50 (115)
+-+.|-.++||.+|-+. .+=++|+ .+.+++.|...|...
T Consensus 39 LA~~Lf~i~gV~~Vf~~--~dfItVtK~~~~~W~~l~~~I~~~ 79 (87)
T PF08712_consen 39 LAQALFAIPGVKSVFIG--DDFITVTKNPDADWEDLKPEIREV 79 (87)
T ss_dssp HHHHHHTSTTEEEEEEE--TTEEEEEE-TTS-HHHHHHHHHHH
T ss_pred HHHHhcCCCCEeEEEEE--CCEEEEeeCCCCCHHHHHHHHHHH
Confidence 44556689999887664 6677776 348999998887643
No 31
>PF04805 Pox_E10: E10-like protein conserved region; InterPro: IPR006890 This entry represents a family of probable FAD-linked sulphydryl oxidases found in poxviruses.; GO: 0016972 thiol oxidase activity, 0055114 oxidation-reduction process
Probab=58.64 E-value=9.6 Score=20.94 Aligned_cols=20 Identities=15% Similarity=0.401 Sum_probs=15.8
Q ss_pred CCcHhHHHHHHHHHhCCCCc
Q 033623 1 MDCDGCERKVRNAVSSIRGA 20 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv 20 (115)
+.|..|.....+++++-.=.
T Consensus 16 LPC~~Cr~HA~~ai~kNNiM 35 (70)
T PF04805_consen 16 LPCPECRIHAKEAIQKNNIM 35 (70)
T ss_pred CCCHHHHHHHHHHHHhcCcc
Confidence 46999999999999875433
No 32
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=58.13 E-value=41 Score=28.23 Aligned_cols=44 Identities=11% Similarity=0.243 Sum_probs=33.6
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEEe--------eCCHHHHHHHHHHc
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQSRVTVTG--------YVDPNKVLKKVKST 50 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~--------~~~~~~i~~~i~~~ 50 (115)
...++..|++++||.++++......+.|.- .++..++..+|+..
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 356889999999999999986555465652 27888888888754
No 33
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=57.60 E-value=21 Score=25.31 Aligned_cols=27 Identities=26% Similarity=0.309 Sum_probs=23.5
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeccCC
Q 033623 4 DGCERKVRNAVSSIRGAKSVEVNRKQS 30 (115)
Q Consensus 4 ~~C~~~v~~~l~~~~gv~~~~v~~~~~ 30 (115)
.+|-+.+|..+.+++||.++.+-...+
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG 160 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGG 160 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCC
Confidence 579999999999999999999877554
No 34
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=57.37 E-value=11 Score=23.52 Aligned_cols=44 Identities=27% Similarity=0.373 Sum_probs=27.3
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeccCCE-EEEEeeCCHHHHHHHHHHc
Q 033623 4 DGCERKVRNAVSSIRGAKSVEVNRKQSR-VTVTGYVDPNKVLKKVKST 50 (115)
Q Consensus 4 ~~C~~~v~~~l~~~~gv~~~~v~~~~~~-v~v~~~~~~~~i~~~i~~~ 50 (115)
.+|.+++-++| +.+.-++.+...++ ++-.|.-+.++|...|...
T Consensus 97 ~~i~rkvlQ~L---e~~~~ve~hp~gGR~lt~~GqrdldrIa~~i~~~ 141 (143)
T KOG3411|consen 97 GGIARKVLQAL---EKMGIVEKHPKGGRRLTEQGQRDLDRIAGQIREE 141 (143)
T ss_pred cHHHHHHHHHH---HhCCceeeCCCCcceeCcccchhHHHHHHHHHhc
Confidence 34555555555 45555666665554 4455778888898887643
No 35
>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=56.86 E-value=14 Score=21.42 Aligned_cols=20 Identities=35% Similarity=0.537 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCCCceEEEEe
Q 033623 7 ERKVRNAVSSIRGAKSVEVN 26 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~ 26 (115)
...++.++++++||+++++.
T Consensus 64 td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 64 TEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred hHHHHHHHhcCCCccEEEEE
Confidence 46789999999999999875
No 36
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=55.45 E-value=15 Score=23.54 Aligned_cols=45 Identities=24% Similarity=0.246 Sum_probs=33.1
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeccCC-------------------EEEEEee---CCHHHHHHHHH
Q 033623 4 DGCERKVRNAVSSIRGAKSVEVNRKQS-------------------RVTVTGY---VDPNKVLKKVK 48 (115)
Q Consensus 4 ~~C~~~v~~~l~~~~gv~~~~v~~~~~-------------------~v~v~~~---~~~~~i~~~i~ 48 (115)
.+|-+.++..+.+++||.++.+-...+ .|.|..+ ++.++|++..-
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~is~~~Ll~~f~ 73 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVISYEELLDVFF 73 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS-HHHHHHHHH
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcccHHHHHHHHH
Confidence 479999999999999999999877554 2344443 67777777653
No 37
>PRK11023 outer membrane lipoprotein; Provisional
Probab=55.22 E-value=46 Score=21.98 Aligned_cols=41 Identities=27% Similarity=0.328 Sum_probs=29.4
Q ss_pred HHHHHHHHhCCCCce---EEEEeccCCEEEEEeeCCHHHHHHHH
Q 033623 7 ERKVRNAVSSIRGAK---SVEVNRKQSRVTVTGYVDPNKVLKKV 47 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~---~~~v~~~~~~v~v~~~~~~~~i~~~i 47 (115)
..+|+.+|...+++. .+++....+.|++.|.++.+......
T Consensus 51 ~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~V~~~~~k~~A 94 (191)
T PRK11023 51 ELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQSPNAELSERA 94 (191)
T ss_pred HHHHHHHHhhCcccCcCceEEEEEECCEEEEEEEeCCHHHHHHH
Confidence 467888887777664 57777889999999986555444333
No 38
>PF02672 CP12: CP12 domain; InterPro: IPR003823 This entry represents an uncharacterised domain in proteins of unknown function. This domain is found associated with CBS domains in some proteins IPR000644 from INTERPRO.; PDB: 3B1K_I 3B1J_D 3RVD_N 3QV1_I 2LJ9_A.
Probab=54.92 E-value=2.8 Score=23.29 Aligned_cols=15 Identities=47% Similarity=0.953 Sum_probs=12.3
Q ss_pred cccCCccCCCCC--ccc
Q 033623 100 LTTLFSDENPNA--CSI 114 (115)
Q Consensus 100 ~~~~FsDenp~a--CsI 114 (115)
..-.|.|+||.| |.|
T Consensus 52 ~lE~yC~~nPea~Ecrv 68 (71)
T PF02672_consen 52 PLELYCDENPEADECRV 68 (71)
T ss_dssp CHHHHHHHSTTSTTTTT
T ss_pred HHHHHHHHCCCcHHhhh
Confidence 458899999998 865
No 39
>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=54.55 E-value=19 Score=19.30 Aligned_cols=19 Identities=21% Similarity=0.370 Sum_probs=15.5
Q ss_pred HHHHHHHHhCCCCceEEEE
Q 033623 7 ERKVRNAVSSIRGAKSVEV 25 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v 25 (115)
...+.+.|++++||.++.+
T Consensus 56 l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 56 IDELLEELREIDGVEKVEL 74 (76)
T ss_pred HHHHHHHHhcCCCeEEEEE
Confidence 4677888999999998865
No 40
>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=53.56 E-value=17 Score=21.04 Aligned_cols=21 Identities=38% Similarity=0.449 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCCceEEEEecc
Q 033623 8 RKVRNAVSSIRGAKSVEVNRK 28 (115)
Q Consensus 8 ~~v~~~l~~~~gv~~~~v~~~ 28 (115)
..++.+|.+++|+.++++++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 467888999999998888754
No 41
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=53.53 E-value=28 Score=20.40 Aligned_cols=22 Identities=18% Similarity=0.365 Sum_probs=19.1
Q ss_pred hCCCCceEEEEeccCCEEEEEe
Q 033623 15 SSIRGAKSVEVNRKQSRVTVTG 36 (115)
Q Consensus 15 ~~~~gv~~~~v~~~~~~v~v~~ 36 (115)
...+|++.+++...++++.|.+
T Consensus 37 as~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 37 ASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EecCCceEEEEecccceEEEec
Confidence 4568899999999999999875
No 42
>TIGR00401 msrA methionine-S-sulfoxide reductase. This model describes peptide methionine sulfoxide reductase (MsrA), a repair enzyme for proteins that have been inactivated by oxidation. The enzyme from E. coli is coextensive with this model and has enzymatic activity. However, in all completed genomes in which this module is present, a second protein module, described in TIGR00357, is also found, and in several cases as part of the same polypeptide chain: N-terminal to this module in Helicobacter pylori and Haemophilus influenzae (as in PilB of Neisseria gonorrhoeae) but C-terminal to it in Treponema pallidum. PilB, containing both domains, has been shown to be important for the expression of adhesins in certain pathogens.
Probab=52.80 E-value=11 Score=24.00 Aligned_cols=27 Identities=26% Similarity=0.250 Sum_probs=23.2
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeccCC
Q 033623 4 DGCERKVRNAVSSIRGAKSVEVNRKQS 30 (115)
Q Consensus 4 ~~C~~~v~~~l~~~~gv~~~~v~~~~~ 30 (115)
.+|-+.++..+.+++||.++.+-...+
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG 33 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGG 33 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCC
Confidence 479999999999999999998876554
No 43
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=50.62 E-value=56 Score=20.59 Aligned_cols=42 Identities=19% Similarity=0.329 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCC-CceEEEEeccCCEEEEEeeCCHHHHHHHHH
Q 033623 7 ERKVRNAVSSIR-GAKSVEVNRKQSRVTVTGYVDPNKVLKKVK 48 (115)
Q Consensus 7 ~~~v~~~l~~~~-gv~~~~v~~~~~~v~v~~~~~~~~i~~~i~ 48 (115)
...|.++|.+.. +...++|....+.|++.|.+.......++.
T Consensus 28 ~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~~~~~ 70 (147)
T PRK11198 28 ADALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAKEKIL 70 (147)
T ss_pred HHHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHHHHHH
Confidence 356677776532 344566777799999999855444444443
No 44
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=50.53 E-value=66 Score=27.11 Aligned_cols=43 Identities=16% Similarity=0.296 Sum_probs=33.0
Q ss_pred HHHHHHHhCCCCceEEEEeccCCEEEEEe--------eCCHHHHHHHHHHc
Q 033623 8 RKVRNAVSSIRGAKSVEVNRKQSRVTVTG--------YVDPNKVLKKVKST 50 (115)
Q Consensus 8 ~~v~~~l~~~~gv~~~~v~~~~~~v~v~~--------~~~~~~i~~~i~~~ 50 (115)
..++..|.+++||.++++.-....+.|.- .++..+|..+|+..
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 46889999999999999876655466652 27788888888754
No 45
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=49.98 E-value=18 Score=20.97 Aligned_cols=20 Identities=30% Similarity=0.531 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCCCceEEEEe
Q 033623 7 ERKVRNAVSSIRGAKSVEVN 26 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~ 26 (115)
...++++|++++||.++++-
T Consensus 64 td~~ee~l~~vegV~sveve 83 (88)
T COG2092 64 TDALEEALEEVEGVESVEVE 83 (88)
T ss_pred cHHHHHHHhhccCcceEEEE
Confidence 45789999999999998874
No 46
>PRK11023 outer membrane lipoprotein; Provisional
Probab=49.62 E-value=74 Score=21.00 Aligned_cols=37 Identities=27% Similarity=0.369 Sum_probs=23.1
Q ss_pred HHHHHHHHhCCCCceE--EEEeccCCEEEEEeeCCHHHH
Q 033623 7 ERKVRNAVSSIRGAKS--VEVNRKQSRVTVTGYVDPNKV 43 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~--~~v~~~~~~v~v~~~~~~~~i 43 (115)
..+|+.+|...+++.. +++...++.|++.|.++.++.
T Consensus 129 t~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~ 167 (191)
T PRK11023 129 TTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREA 167 (191)
T ss_pred HHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHH
Confidence 3567777776666654 344445777777777665544
No 47
>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=49.39 E-value=69 Score=26.97 Aligned_cols=43 Identities=14% Similarity=0.283 Sum_probs=33.5
Q ss_pred HHHHHHHhCCCCceEEEEeccCCEEEEEe--------eCCHHHHHHHHHHc
Q 033623 8 RKVRNAVSSIRGAKSVEVNRKQSRVTVTG--------YVDPNKVLKKVKST 50 (115)
Q Consensus 8 ~~v~~~l~~~~gv~~~~v~~~~~~v~v~~--------~~~~~~i~~~i~~~ 50 (115)
..++..|.+++||.++++......+.|.- .++..++..+|+..
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~~~ 210 (1044)
T TIGR00915 160 SNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQAQ 210 (1044)
T ss_pred HHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 46889999999999999987744466652 27888888888763
No 48
>PRK09019 translation initiation factor Sui1; Validated
Probab=48.88 E-value=23 Score=21.35 Aligned_cols=10 Identities=20% Similarity=0.361 Sum_probs=5.0
Q ss_pred CHHHHHHHHH
Q 033623 39 DPNKVLKKVK 48 (115)
Q Consensus 39 ~~~~i~~~i~ 48 (115)
+..+|++.|.
T Consensus 59 dlk~l~K~lK 68 (108)
T PRK09019 59 ELKKLAAELK 68 (108)
T ss_pred HHHHHHHHHH
Confidence 4445555553
No 49
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=48.17 E-value=71 Score=20.39 Aligned_cols=54 Identities=11% Similarity=0.140 Sum_probs=35.8
Q ss_pred HHHHHHHhCCCCceEEEEeccCCEEEEEee-------CCHHHHHHHHHHcCCCceecCCCC
Q 033623 8 RKVRNAVSSIRGAKSVEVNRKQSRVTVTGY-------VDPNKVLKKVKSTGKRAEFWPYVP 61 (115)
Q Consensus 8 ~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~-------~~~~~i~~~i~~~G~~~~~~~~~~ 61 (115)
..|++.+-.-.|+.++.+|..++.|.|... .....+.+-..++|....+....|
T Consensus 56 ~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 56 KIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred HHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 345555544469999999999999988632 222333444578998888766433
No 50
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=47.10 E-value=24 Score=20.43 Aligned_cols=20 Identities=35% Similarity=0.564 Sum_probs=17.0
Q ss_pred HHHHHHHHhCCCCceEEEEe
Q 033623 7 ERKVRNAVSSIRGAKSVEVN 26 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~ 26 (115)
...++.++++++||+++++.
T Consensus 64 td~lee~i~~~e~Vqsvei~ 83 (88)
T PRK00435 64 TEPVEEAFANVEGVESVEVE 83 (88)
T ss_pred cHHHHHHHhccCCCcEEEEE
Confidence 45688999999999999875
No 51
>PRK07451 translation initiation factor Sui1; Validated
Probab=46.82 E-value=18 Score=22.11 Aligned_cols=9 Identities=33% Similarity=0.479 Sum_probs=4.4
Q ss_pred CHHHHHHHH
Q 033623 39 DPNKVLKKV 47 (115)
Q Consensus 39 ~~~~i~~~i 47 (115)
+..+|++.|
T Consensus 66 dlk~LaK~L 74 (115)
T PRK07451 66 TLAKLLKQL 74 (115)
T ss_pred HHHHHHHHH
Confidence 344455555
No 52
>PHA03005 sulfhydryl oxidase; Provisional
Probab=46.48 E-value=19 Score=21.15 Aligned_cols=20 Identities=20% Similarity=0.541 Sum_probs=15.6
Q ss_pred CCcHhHHHHHHHHHhCCCCc
Q 033623 1 MDCDGCERKVRNAVSSIRGA 20 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv 20 (115)
+-|..|.....+++++-.=.
T Consensus 41 LPC~~Cr~HA~~ai~knnim 60 (96)
T PHA03005 41 LPCPACRRHAKEAIEKNNIM 60 (96)
T ss_pred CCCHHHHHHHHHHHhhcCcc
Confidence 46999999999999874333
No 53
>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=46.22 E-value=57 Score=18.69 Aligned_cols=30 Identities=23% Similarity=0.288 Sum_probs=23.8
Q ss_pred EEEEeccCCEEEEEeeCCHHHHHHHHHHcCC
Q 033623 22 SVEVNRKQSRVTVTGYVDPNKVLKKVKSTGK 52 (115)
Q Consensus 22 ~~~v~~~~~~v~v~~~~~~~~i~~~i~~~G~ 52 (115)
.+.++..++.+.|.|+ ...+|.+-|...||
T Consensus 58 ~~~V~~~~g~i~IkG~-~~~~Vk~wL~~~GF 87 (87)
T PF05046_consen 58 DVRVNELTGHIEIKGD-HVEEVKKWLLEKGF 87 (87)
T ss_pred ceEEeecCCEEEEcCc-cHHHHHHHHHHCcC
Confidence 5788888999999987 46677777777775
No 54
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=46.16 E-value=72 Score=19.87 Aligned_cols=48 Identities=19% Similarity=0.296 Sum_probs=31.0
Q ss_pred HHHHHHhCCCCceEEEEeccCCEEEEEeeCCHHHHHHHH-----HHcCCCceec
Q 033623 9 KVRNAVSSIRGAKSVEVNRKQSRVTVTGYVDPNKVLKKV-----KSTGKRAEFW 57 (115)
Q Consensus 9 ~v~~~l~~~~gv~~~~v~~~~~~v~v~~~~~~~~i~~~i-----~~~G~~~~~~ 57 (115)
.++..|.++ |..+|+.-+.++.+.++.+.+.+++...| ...|+.+.+.
T Consensus 23 eLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~fG~~v~v~ 75 (137)
T PF08002_consen 23 ELREALEDL-GFTNVRTYIQSGNVVFESDRDPAELAAKIEKALEERFGFDVPVI 75 (137)
T ss_dssp HHHHHHHHC-T-EEEEEETTTTEEEEEESS-HHHHHHHHHHHHHHH-TT---EE
T ss_pred HHHHHHHHc-CCCCceEEEeeCCEEEecCCChHHHHHHHHHHHHHhcCCCeEEE
Confidence 345666665 89999999999999998767777776555 3567765543
No 55
>PF11491 DUF3213: Protein of unknown function (DUF3213) ; InterPro: IPR021583 The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold []. ; PDB: 2F40_A.
Probab=46.15 E-value=44 Score=19.24 Aligned_cols=47 Identities=11% Similarity=-0.021 Sum_probs=23.9
Q ss_pred HHHHHHHhCCCCceEEEEeccCCEEEEEee---CCHHHHHHHHHHcCCCc
Q 033623 8 RKVRNAVSSIRGAKSVEVNRKQSRVTVTGY---VDPNKVLKKVKSTGKRA 54 (115)
Q Consensus 8 ~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~---~~~~~i~~~i~~~G~~~ 54 (115)
..++=.|++..+|-.+-+|.-.....|.++ +..++|++.+++.+..+
T Consensus 14 ~~~QYeLsk~~~vyRvFiNgYar~g~VifDe~kl~~e~lL~~le~~kpEV 63 (88)
T PF11491_consen 14 MVKQYELSKNEAVYRVFINGYARNGFVIFDESKLSKEELLEMLEEFKPEV 63 (88)
T ss_dssp HHHHHTTTTTTTB------TTSS--EEE--B-S-SHHHH---HHHTTT-S
T ss_pred HHHHHHhhcccceeeeeecccccceEEEECcccCCHHHHHHHHHhcChhh
Confidence 344556888899999999987776666643 78899999998877543
No 56
>PRK06824 translation initiation factor Sui1; Validated
Probab=45.95 E-value=31 Score=21.19 Aligned_cols=10 Identities=20% Similarity=0.315 Sum_probs=4.6
Q ss_pred CHHHHHHHHH
Q 033623 39 DPNKVLKKVK 48 (115)
Q Consensus 39 ~~~~i~~~i~ 48 (115)
+..+|.+.|.
T Consensus 69 dlk~l~K~LK 78 (118)
T PRK06824 69 ALKELAKELK 78 (118)
T ss_pred HHHHHHHHHH
Confidence 3344555553
No 57
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=45.53 E-value=63 Score=19.00 Aligned_cols=42 Identities=19% Similarity=0.281 Sum_probs=28.3
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEEe-eCCHHHHHHHHHH
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQSRVTVTG-YVDPNKVLKKVKS 49 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~-~~~~~~i~~~i~~ 49 (115)
...|+++|..++|++--.-+.. +|+.|.- ..+...+.+.++.
T Consensus 20 l~av~~~L~~ip~~EV~~~d~~-GKlVVVie~~~~~~l~~tie~ 62 (94)
T COG3062 20 LSAVKTALLAIPGCEVYGEDAE-GKLVVVIEAEDSETLLETIES 62 (94)
T ss_pred HHHHHHHHhcCCCcEeeccCCC-ceEEEEEEcCchHHHHHHHHH
Confidence 4578999999999875555544 6766543 2466667776654
No 58
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=44.88 E-value=30 Score=20.59 Aligned_cols=19 Identities=16% Similarity=0.513 Sum_probs=15.8
Q ss_pred CcHhHHHHHHHHHhCCCCce
Q 033623 2 DCDGCERKVRNAVSSIRGAK 21 (115)
Q Consensus 2 ~C~~C~~~v~~~l~~~~gv~ 21 (115)
.|..|+..+++.|.+ .||.
T Consensus 20 qC~~cA~Al~~~L~~-~gI~ 38 (100)
T PF15643_consen 20 QCVECASALKQFLKQ-AGIP 38 (100)
T ss_pred ehHHHHHHHHHHHHH-CCCC
Confidence 699999999999976 4664
No 59
>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=44.37 E-value=54 Score=25.54 Aligned_cols=39 Identities=18% Similarity=0.331 Sum_probs=30.2
Q ss_pred HhCCCCceEEEEeccCCEEEEEeeCCHHHHHHHHHHcCCCc
Q 033623 14 VSSIRGAKSVEVNRKQSRVTVTGYVDPNKVLKKVKSTGKRA 54 (115)
Q Consensus 14 l~~~~gv~~~~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~~ 54 (115)
|..+++| +++|..+++++|..-+...+|.+.|.+.|+..
T Consensus 110 L~~ln~V--l~vD~~~~tVtV~AG~~l~~L~~~L~~~Glal 148 (541)
T TIGR01676 110 LALMDKV--LEVDEEKKRVRVQAGIRVQQLVDAIKEYGITL 148 (541)
T ss_pred hhhCCCC--EEEcCCCCEEEEcCCCCHHHHHHHHHHcCCEe
Confidence 3445555 35677788899988789999999999999754
No 60
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=43.68 E-value=33 Score=20.83 Aligned_cols=21 Identities=33% Similarity=0.476 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCCCceEEEEec
Q 033623 7 ERKVRNAVSSIRGAKSVEVNR 27 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~ 27 (115)
...++.+|..++||.++++++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 567899999999999887753
No 61
>PF03434 DUF276: DUF276 ; InterPro: IPR005096 This family is specific to Borrelia burgdorferi (Lyme disease spirochete). The protein is encoded on extrachromosomal DNA and is of unknown function.
Probab=42.77 E-value=48 Score=23.13 Aligned_cols=28 Identities=11% Similarity=0.354 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEE
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQSRVTV 34 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~~v~v 34 (115)
-..|+++|.+++||..+++--..+++.+
T Consensus 89 y~Avk~aLL~~~gv~haNI~SsaGtini 116 (291)
T PF03434_consen 89 YEAVKSALLNLNGVEHANIKSSAGTINI 116 (291)
T ss_pred HHHHHHHhcCCCCceeeeeecCCCeeEE
Confidence 3578999999999999999888888765
No 62
>KOG4730 consensus D-arabinono-1, 4-lactone oxidase [Defense mechanisms]
Probab=40.17 E-value=49 Score=25.36 Aligned_cols=34 Identities=18% Similarity=0.224 Sum_probs=27.9
Q ss_pred EEEeccCCEEEEEeeCCHHHHHHHHHHcCCCcee
Q 033623 23 VEVNRKQSRVTVTGYVDPNKVLKKVKSTGKRAEF 56 (115)
Q Consensus 23 ~~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~~~~ 56 (115)
+++|.+..++||+.-+...+|++.+.+.|+....
T Consensus 105 v~~dpe~~tvTV~aGirlrQLie~~~~~GlsL~~ 138 (518)
T KOG4730|consen 105 VEFDPELKTVTVQAGIRLRQLIEELAKLGLSLPN 138 (518)
T ss_pred eeeCchhceEEeccCcCHHHHHHHHHhcCccccC
Confidence 4557777888888889999999999999987543
No 63
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=39.34 E-value=32 Score=18.26 Aligned_cols=17 Identities=12% Similarity=0.182 Sum_probs=13.7
Q ss_pred CCHHHHHHHHHHcCCCc
Q 033623 38 VDPNKVLKKVKSTGKRA 54 (115)
Q Consensus 38 ~~~~~i~~~i~~~G~~~ 54 (115)
...++|.++|++.||..
T Consensus 50 ~~~~~i~~~L~~~G~~~ 66 (68)
T cd04885 50 EDLAELKERLEALGYPY 66 (68)
T ss_pred HHHHHHHHHHHHcCCCc
Confidence 45677889999999965
No 64
>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=39.03 E-value=62 Score=17.09 Aligned_cols=48 Identities=17% Similarity=0.191 Sum_probs=31.8
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHHcCCCceecC
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY--VDPNKVLKKVKSTGKRAEFWP 58 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~--~~~~~i~~~i~~~G~~~~~~~ 58 (115)
+.|+.-.-+++++| ++.. .+.+.|..+ .....|...+++.|+......
T Consensus 7 ~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~~~s~~~i~~~~~~~G~~~~~~~ 56 (67)
T cd03421 7 LACPQPVIKTKKAL-ELEA---------GGEIEVLVDNEVAKENVSRFAESRGYEVSVEE 56 (67)
T ss_pred CCCCHHHHHHHHHH-hcCC---------CCEEEEEEcChhHHHHHHHHHHHcCCEEEEEe
Confidence 35888888899998 5532 223444333 445678888899999885443
No 65
>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=38.49 E-value=45 Score=21.86 Aligned_cols=21 Identities=24% Similarity=0.311 Sum_probs=16.9
Q ss_pred HHHHHHHHhCCCCceEEEEec
Q 033623 7 ERKVRNAVSSIRGAKSVEVNR 27 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~ 27 (115)
...|+.+|.+++||.++++++
T Consensus 133 ~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 133 VEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred HHHHHHHHHhCCCceeEEEEE
Confidence 356889999999999887764
No 66
>PRK11018 hypothetical protein; Provisional
Probab=38.42 E-value=72 Score=17.69 Aligned_cols=47 Identities=11% Similarity=0.062 Sum_probs=32.9
Q ss_pred CcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHHcCCCceec
Q 033623 2 DCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY--VDPNKVLKKVKSTGKRAEFW 57 (115)
Q Consensus 2 ~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~--~~~~~i~~~i~~~G~~~~~~ 57 (115)
.|+.-.-+.+++|.+++.- +.+.|..+ .....|...+++.|+.+...
T Consensus 17 ~CP~Pvl~~kk~l~~l~~G---------~~L~V~~d~~~a~~di~~~~~~~G~~v~~~ 65 (78)
T PRK11018 17 PCPYPAVATLEALPQLKKG---------EILEVVSDCPQSINNIPLDARNHGYTVLDI 65 (78)
T ss_pred cCCHHHHHHHHHHHhCCCC---------CEEEEEeCCccHHHHHHHHHHHcCCEEEEE
Confidence 5888889999999988532 23344332 55667888889999987543
No 67
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=38.24 E-value=45 Score=22.34 Aligned_cols=21 Identities=29% Similarity=0.463 Sum_probs=17.7
Q ss_pred HHHHHHHHhCCCCceEEEEec
Q 033623 7 ERKVRNAVSSIRGAKSVEVNR 27 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~ 27 (115)
...+++.|..++||.+++|++
T Consensus 117 e~eL~~tI~~i~gV~~A~V~l 137 (206)
T PF01514_consen 117 EGELERTIESIDGVESARVHL 137 (206)
T ss_dssp HHHHHHHHTTSTTEEEEEEEE
T ss_pred HHHHHHHHHcCCCeeEEEEEE
Confidence 356889999999999988874
No 68
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=38.22 E-value=76 Score=17.88 Aligned_cols=23 Identities=13% Similarity=0.276 Sum_probs=17.1
Q ss_pred ccCCEEEEEeeCCHHHHHHHHHH
Q 033623 27 RKQSRVTVTGYVDPNKVLKKVKS 49 (115)
Q Consensus 27 ~~~~~v~v~~~~~~~~i~~~i~~ 49 (115)
+.++++.++|..+.+++..++++
T Consensus 55 F~sGki~itGaks~~~~~~a~~~ 77 (86)
T PF00352_consen 55 FSSGKIVITGAKSEEEAKKAIEK 77 (86)
T ss_dssp ETTSEEEEEEESSHHHHHHHHHH
T ss_pred EcCCEEEEEecCCHHHHHHHHHH
Confidence 47899999987777776666543
No 69
>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=38.20 E-value=65 Score=27.08 Aligned_cols=44 Identities=20% Similarity=0.278 Sum_probs=32.1
Q ss_pred HHHHHHHHhCCCCceEEEEeccCC--EEEEEe--------eCCHHHHHHHHHHc
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQS--RVTVTG--------YVDPNKVLKKVKST 50 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~--~v~v~~--------~~~~~~i~~~i~~~ 50 (115)
+.++++.|.+++|+.+++.+...+ .+.|.- .++++++...|+..
T Consensus 700 a~~v~~~l~~~pgv~~v~~~~~~~~~e~~i~id~~~~~~~Glt~~~v~~~l~~~ 753 (1051)
T TIGR00914 700 AEKISAVLKGVPGAADVKVEQTTGLPYLTVEIDREKAARYGLTVGDVQDTVATA 753 (1051)
T ss_pred HHHHHHHHhcCCCceeeeccccCCCceEEEEECHHHHHHcCCCHHHHHHHHHHH
Confidence 467899999999999999887543 344432 16778888888643
No 70
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=38.16 E-value=27 Score=22.94 Aligned_cols=28 Identities=21% Similarity=0.223 Sum_probs=23.6
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeccCCE
Q 033623 4 DGCERKVRNAVSSIRGAKSVEVNRKQSR 31 (115)
Q Consensus 4 ~~C~~~v~~~l~~~~gv~~~~v~~~~~~ 31 (115)
.+|-+-+++.+.+++||.++.+-...+.
T Consensus 13 gGCFWg~E~~f~~i~GV~~t~~GYagG~ 40 (174)
T COG0225 13 GGCFWGVEAYFEQIPGVLSTVSGYAGGH 40 (174)
T ss_pred ccCccchHHHHhhCCCeEEEeeeEcCCC
Confidence 4789999999999999999988766553
No 71
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=38.05 E-value=1.6e+02 Score=25.01 Aligned_cols=45 Identities=20% Similarity=0.294 Sum_probs=34.2
Q ss_pred HHHHHHHHhCCCCceEEEEeccC-CEEEEEe--------eCCHHHHHHHHHHcC
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQ-SRVTVTG--------YVDPNKVLKKVKSTG 51 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~-~~v~v~~--------~~~~~~i~~~i~~~G 51 (115)
...++..|.+++||.++++.-.. ..+.|.- .+++.++..+|+...
T Consensus 157 ~~~l~~~L~~v~GV~~V~~~G~~~~~~rI~ldp~kLa~~gLt~~dV~~ai~~qN 210 (1009)
T COG0841 157 ASNVRDELSRVPGVGSVQLFGAQEYAMRIWLDPAKLAAYGLTPSDVQSAIRAQN 210 (1009)
T ss_pred HHHHHHHHhcCCCceEEEEcCCCceeEEEEeCHHHHHHcCCCHHHHHHHHHHhC
Confidence 45689999999999999998764 4455652 278888888987644
No 72
>PRK11670 antiporter inner membrane protein; Provisional
Probab=37.80 E-value=1.2e+02 Score=22.21 Aligned_cols=57 Identities=14% Similarity=0.228 Sum_probs=37.0
Q ss_pred HHHHHHHHhCCCCceEEEEeccC------------------CEEEEE---ee----CCHHHHHHHHHHcCCCceecCCCC
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQ------------------SRVTVT---GY----VDPNKVLKKVKSTGKRAEFWPYVP 61 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~------------------~~v~v~---~~----~~~~~i~~~i~~~G~~~~~~~~~~ 61 (115)
...++++|+.++|+.++++.+.. ..+.|. |- .....|..++.+.|+++-+++..+
T Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avNLA~aLA~~G~rVlLID~D~ 146 (369)
T PRK11670 67 KEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVNLALALAAEGAKVGILDADI 146 (369)
T ss_pred HHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCC
Confidence 35688899999999877765432 112232 11 233446667888999998887665
Q ss_pred Cc
Q 033623 62 YN 63 (115)
Q Consensus 62 ~~ 63 (115)
+.
T Consensus 147 qg 148 (369)
T PRK11670 147 YG 148 (369)
T ss_pred CC
Confidence 54
No 73
>TIGR01158 SUI1_rel translation initation factor SUI1, putative, prokaryotic. This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met.
Probab=36.43 E-value=54 Score=19.43 Aligned_cols=21 Identities=29% Similarity=0.360 Sum_probs=11.7
Q ss_pred CCEEEEEe-----eCCHHHHHHHHHH
Q 033623 29 QSRVTVTG-----YVDPNKVLKKVKS 49 (115)
Q Consensus 29 ~~~v~v~~-----~~~~~~i~~~i~~ 49 (115)
...||+.. ..+.+++.+.|.+
T Consensus 37 gK~VTvV~Gl~~~~~~l~~l~k~LKk 62 (101)
T TIGR01158 37 GKGVTIIEGLDLSDIDLKELAKELKS 62 (101)
T ss_pred CCEEEEEeCCcCchhhHHHHHHHHHH
Confidence 34566542 2456667777753
No 74
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=36.37 E-value=56 Score=20.02 Aligned_cols=29 Identities=24% Similarity=0.344 Sum_probs=23.7
Q ss_pred EEEEeeCCHHHHHHHHHHcCCCceecCCC
Q 033623 32 VTVTGYVDPNKVLKKVKSTGKRAEFWPYV 60 (115)
Q Consensus 32 v~v~~~~~~~~i~~~i~~~G~~~~~~~~~ 60 (115)
+.++++.+...+++.+++.|+++.++...
T Consensus 104 vLvSgD~Df~~~i~~lr~~G~~V~v~~~~ 132 (149)
T cd06167 104 VLVSGDSDFVPLVERLRELGKRVIVVGFE 132 (149)
T ss_pred EEEECCccHHHHHHHHHHcCCEEEEEccC
Confidence 34567788888999999999999988864
No 75
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=35.94 E-value=41 Score=22.38 Aligned_cols=28 Identities=29% Similarity=0.424 Sum_probs=20.1
Q ss_pred HHHHHHHHhCCCCceEEEE--eccCCEEEE
Q 033623 7 ERKVRNAVSSIRGAKSVEV--NRKQSRVTV 34 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v--~~~~~~v~v 34 (115)
..+++..|.++.||..++| .+..+.-.|
T Consensus 63 E~~L~~iL~~I~GvG~V~VmItl~s~~e~v 92 (186)
T TIGR02830 63 ENELKEILEKIEGVGDVTVMVNLDSSEEKV 92 (186)
T ss_pred HHHHHHHHHhccCcceeEEEEEECCCceEE
Confidence 5688999999999987654 555554433
No 76
>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=35.86 E-value=46 Score=17.76 Aligned_cols=41 Identities=10% Similarity=0.141 Sum_probs=23.4
Q ss_pred HHHHHHhCCCCceEEEEecc----CCEEEEEe-eCCHHHHHHHHHH
Q 033623 9 KVRNAVSSIRGAKSVEVNRK----QSRVTVTG-YVDPNKVLKKVKS 49 (115)
Q Consensus 9 ~v~~~l~~~~gv~~~~v~~~----~~~v~v~~-~~~~~~i~~~i~~ 49 (115)
.||.+|.+++||.++-+-.. .+...+.. ..+.++|.+.+++
T Consensus 1 EIE~~l~~~~~V~~~~V~~~~d~~~g~~l~a~vv~~~~~i~~~~~~ 46 (73)
T PF13193_consen 1 EIESVLRQHPGVAEAAVVGVPDEDWGERLVAFVVLDEEEIRDHLRD 46 (73)
T ss_dssp HHHHHHHTSTTEEEEEEEEEEETTTEEEEEEEEEEHHHHHHHHHHH
T ss_pred CHHHHHhcCCCccEEEEEEEEcccccccceeEEEeeecccccchhh
Confidence 37899999999987655321 12211111 1244667776654
No 77
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=35.76 E-value=1.5e+02 Score=25.07 Aligned_cols=43 Identities=21% Similarity=0.265 Sum_probs=31.6
Q ss_pred HHHHHHHhCCCCceEEEEeccCC-EEEEEe--------eCCHHHHHHHHHHc
Q 033623 8 RKVRNAVSSIRGAKSVEVNRKQS-RVTVTG--------YVDPNKVLKKVKST 50 (115)
Q Consensus 8 ~~v~~~l~~~~gv~~~~v~~~~~-~v~v~~--------~~~~~~i~~~i~~~ 50 (115)
..++..|++++||.++++.-..+ .+.|.- .++..++.++|+..
T Consensus 160 ~~l~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~~ 211 (1025)
T PRK10614 160 TQLAQTISQIDGVGDVDVGGSSLPAVRVGLNPQALFNQGVSLDDVRQAISNA 211 (1025)
T ss_pred HHHHHHhcCCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 56899999999999999876433 345542 27778888888654
No 78
>PRK11282 glcE glycolate oxidase FAD binding subunit; Provisional
Probab=35.64 E-value=83 Score=23.04 Aligned_cols=37 Identities=11% Similarity=0.113 Sum_probs=28.1
Q ss_pred hCCCCceEEEEeccCCEEEEEeeCCHHHHHHHHHHcCCC
Q 033623 15 SSIRGAKSVEVNRKQSRVTVTGYVDPNKVLKKVKSTGKR 53 (115)
Q Consensus 15 ~~~~gv~~~~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~ 53 (115)
.++++|. ++|.....++|..-+...+|.+.|.+.|..
T Consensus 44 ~~ln~Il--e~d~~~~~vtV~AG~~l~el~~~L~~~G~~ 80 (352)
T PRK11282 44 RAHRGIV--SYDPTELVITARAGTPLAELEAALAEAGQM 80 (352)
T ss_pred ccCCCcE--EEcCCCCEEEECCCCCHHHHHHHHHHcCCe
Confidence 3445553 567778888888778999999999998864
No 79
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=35.27 E-value=1.5e+02 Score=25.10 Aligned_cols=43 Identities=19% Similarity=0.238 Sum_probs=32.0
Q ss_pred HHHHHHHhCCCCceEEEEeccC-CEEEEEe--------eCCHHHHHHHHHHc
Q 033623 8 RKVRNAVSSIRGAKSVEVNRKQ-SRVTVTG--------YVDPNKVLKKVKST 50 (115)
Q Consensus 8 ~~v~~~l~~~~gv~~~~v~~~~-~~v~v~~--------~~~~~~i~~~i~~~ 50 (115)
..++..|++++||.++++.-.. ..+.|.- .+++.++.++|+..
T Consensus 169 ~~l~~~L~~i~gV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~~v~~ai~~~ 220 (1040)
T PRK10503 169 TRVAQKISQVSGVGLVTLSGGQRPAVRVKLNAQAIAALGLTSETVRTAITGA 220 (1040)
T ss_pred HHHHHHhcCCCCceEEEecCCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 4689999999999999888643 3455542 27778888888654
No 80
>PRK09579 multidrug efflux protein; Reviewed
Probab=35.06 E-value=1.5e+02 Score=24.99 Aligned_cols=43 Identities=12% Similarity=0.180 Sum_probs=0.0
Q ss_pred HHHHHHHHhCCCCceEEEEec-cCCEEEEEee--------CCHHHHHHHHHH
Q 033623 7 ERKVRNAVSSIRGAKSVEVNR-KQSRVTVTGY--------VDPNKVLKKVKS 49 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~-~~~~v~v~~~--------~~~~~i~~~i~~ 49 (115)
...++..|++++||.++++.- ....+.|.-+ ++..+|.++|+.
T Consensus 158 ~~~i~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~ 209 (1017)
T PRK09579 158 SRVIQPKLATLPGMAEAEILGNQVFAMRLWLDPVKLAGFGLSAGDVTQAVRR 209 (1017)
T ss_pred HHHHHHHhhcCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHH
No 81
>COG0277 GlcD FAD/FMN-containing dehydrogenases [Energy production and conversion]
Probab=34.98 E-value=50 Score=24.37 Aligned_cols=34 Identities=18% Similarity=0.131 Sum_probs=27.6
Q ss_pred EEeccCCEEEEEeeCCHHHHHHHHHHcCCCceec
Q 033623 24 EVNRKQSRVTVTGYVDPNKVLKKVKSTGKRAEFW 57 (115)
Q Consensus 24 ~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~~~~~ 57 (115)
++|..+.+++|..-+...+|.+.+++.|+..-..
T Consensus 89 ~id~~~~~~~v~aGv~l~~l~~~l~~~G~~~p~~ 122 (459)
T COG0277 89 EIDPEDGTATVQAGVTLEDLEKALAPHGLFLPVD 122 (459)
T ss_pred ccCcCCCEEEEcCCccHHHHHHHHHHcCCccCCC
Confidence 6777888999987788999999999888764433
No 82
>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=34.66 E-value=73 Score=16.65 Aligned_cols=28 Identities=21% Similarity=0.320 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCCCceEEEEec-cCCEEEE
Q 033623 7 ERKVRNAVSSIRGAKSVEVNR-KQSRVTV 34 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~-~~~~v~v 34 (115)
...+++.|.+++.|.++++.. --+++.|
T Consensus 36 ~~~~~~~l~~~p~V~~v~V~r~~P~~l~I 64 (69)
T PF08478_consen 36 LKKIEQRLEKLPWVKSVSVSRRFPNTLEI 64 (69)
T ss_dssp HHHHHHCCCCTTTEEEEEEEEETTTEEEE
T ss_pred HHHHHHHHHcCCCEEEEEEEEeCCCEEEE
Confidence 356788888999999999875 3445554
No 83
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.06 E-value=24 Score=19.94 Aligned_cols=16 Identities=13% Similarity=0.775 Sum_probs=13.6
Q ss_pred CcHhHHHHHHHHHhCC
Q 033623 2 DCDGCERKVRNAVSSI 17 (115)
Q Consensus 2 ~C~~C~~~v~~~l~~~ 17 (115)
.|+.|..++++.|+..
T Consensus 35 ~ce~c~a~~kk~l~~v 50 (82)
T COG2331 35 TCEECGARLKKLLNAV 50 (82)
T ss_pred cChhhChHHHHhhccc
Confidence 5999999999988763
No 84
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=33.88 E-value=53 Score=22.82 Aligned_cols=21 Identities=24% Similarity=0.412 Sum_probs=16.9
Q ss_pred HHHHHHHHhCCCCceEEEEec
Q 033623 7 ERKVRNAVSSIRGAKSVEVNR 27 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~ 27 (115)
+..+++.|++++||.+++|..
T Consensus 111 eQ~le~tLs~mDGVi~ArV~I 131 (246)
T COG4669 111 EQQLEQTLSKMDGVISARVHI 131 (246)
T ss_pred HHHHHHHHHhcCceEEEEEEE
Confidence 567899999999998766543
No 85
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=33.85 E-value=76 Score=16.56 Aligned_cols=48 Identities=15% Similarity=0.185 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCC-CceEEEEeccCCEEE--EEeeCCHHHHHHHHHHcCCCce
Q 033623 7 ERKVRNAVSSIR-GAKSVEVNRKQSRVT--VTGYVDPNKVLKKVKSTGKRAE 55 (115)
Q Consensus 7 ~~~v~~~l~~~~-gv~~~~v~~~~~~v~--v~~~~~~~~i~~~i~~~G~~~~ 55 (115)
-.+|-+.|.+.. .|.++-+....++.. +.. .+.+.+.+.|++.||++.
T Consensus 15 La~v~~~l~~~~inI~~i~~~~~~~~~~~rl~~-~~~~~~~~~L~~~G~~v~ 65 (66)
T cd04908 15 LAAVTEILSEAGINIRALSIADTSEFGILRLIV-SDPDKAKEALKEAGFAVK 65 (66)
T ss_pred HHHHHHHHHHCCCCEEEEEEEecCCCCEEEEEE-CCHHHHHHHHHHCCCEEE
Confidence 345555555432 133443332222333 334 467789999999999764
No 86
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=33.69 E-value=92 Score=21.91 Aligned_cols=41 Identities=29% Similarity=0.348 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCCceEEEEec--cCCEEEEEeeCCHHHHHHHH
Q 033623 7 ERKVRNAVSSIRGAKSVEVNR--KQSRVTVTGYVDPNKVLKKV 47 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~--~~~~v~v~~~~~~~~i~~~i 47 (115)
..+|..+..+.++|.-++++. ..++-.++..-++++++++.
T Consensus 20 ie~i~a~~~~~~~v~ildve~danhNRsViT~vgdp~~~~~A~ 62 (302)
T COG3643 20 IEKIVAAAKSIPTVKILDVEMDANHNRSVITLVGDPSKVVNAA 62 (302)
T ss_pred HHHHHHHHhcCCceEEEEeccCCCCCceEEEEecChHHHHHHH
Confidence 346667777888887655544 44555555445666665544
No 87
>PF10934 DUF2634: Protein of unknown function (DUF2634); InterPro: IPR020288 This entry is represented by the Bacteriophage EJ-1, Orf60. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Bacteriophage EJ-1, Orf60 function has not been characterised. It has been shown to be simialr to XkdS (P54331 from SWISSPROT), which is encoded on a phage-like element (prophage) of PSBX found in Bacillus subtilis.
Probab=33.30 E-value=1.1e+02 Score=18.34 Aligned_cols=31 Identities=13% Similarity=0.139 Sum_probs=22.3
Q ss_pred HHHHHHHHhCC---CCceEEEEeccCCEEEEEee
Q 033623 7 ERKVRNAVSSI---RGAKSVEVNRKQSRVTVTGY 37 (115)
Q Consensus 7 ~~~v~~~l~~~---~gv~~~~v~~~~~~v~v~~~ 37 (115)
.+.|+.+|... .+|.+..+....+++.|...
T Consensus 71 ~r~I~EaL~~d~rI~~V~~f~f~~~~~~l~v~f~ 104 (112)
T PF10934_consen 71 EREIEEALLQDPRITSVENFSFEWEGDSLYVSFT 104 (112)
T ss_pred HHHHHHHHhcCCCcceEEEEEEEEECCEEEEEEE
Confidence 46778888555 45667778888888877654
No 88
>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=33.07 E-value=56 Score=18.85 Aligned_cols=20 Identities=30% Similarity=0.494 Sum_probs=16.6
Q ss_pred HHHHHHHHhCCCCceEEEEe
Q 033623 7 ERKVRNAVSSIRGAKSVEVN 26 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~ 26 (115)
...++.++++.+||+++++.
T Consensus 64 td~lee~i~~~d~VqsveI~ 83 (88)
T cd00292 64 TDELEEAISEEDGVQSVDVE 83 (88)
T ss_pred cHHHHHHHhccCCceEEEEE
Confidence 35678889999999999875
No 89
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=32.80 E-value=56 Score=21.71 Aligned_cols=21 Identities=29% Similarity=0.463 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCCCceEEEEec
Q 033623 7 ERKVRNAVSSIRGAKSVEVNR 27 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~ 27 (115)
...+++.|..++||.+++|++
T Consensus 109 e~EL~rtI~~i~~V~~ArVhl 129 (193)
T TIGR02544 109 EQRLEQTLSQIDGVISARVHV 129 (193)
T ss_pred HHHHHHHHHhcCCeeeeEEEE
Confidence 356788999999999887765
No 90
>PF13216 DUF4024: Protein of unknown function (DUF4024)
Probab=32.49 E-value=17 Score=16.69 Aligned_cols=11 Identities=45% Similarity=0.546 Sum_probs=9.0
Q ss_pred ccCCccCCCCC
Q 033623 101 TTLFSDENPNA 111 (115)
Q Consensus 101 ~~~FsDenp~a 111 (115)
..+|-||+.|.
T Consensus 9 lhlfrde~vnf 19 (35)
T PF13216_consen 9 LHLFRDEKVNF 19 (35)
T ss_pred EEEeecCCccE
Confidence 47899999984
No 91
>PLN00204 CP12 gene family protein; Provisional
Probab=32.26 E-value=12 Score=23.13 Aligned_cols=16 Identities=19% Similarity=0.526 Sum_probs=12.5
Q ss_pred ccccCCccCCCCC--ccc
Q 033623 99 RLTTLFSDENPNA--CSI 114 (115)
Q Consensus 99 ~~~~~FsDenp~a--CsI 114 (115)
.....|+||||.+ |.|
T Consensus 106 t~lE~YCdeNPeA~ECRv 123 (126)
T PLN00204 106 DPLEEYCKDNPETDECRT 123 (126)
T ss_pred ChHHHHHHHCCCchhhhc
Confidence 3458999999998 764
No 92
>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=32.22 E-value=71 Score=16.62 Aligned_cols=19 Identities=26% Similarity=0.459 Sum_probs=13.8
Q ss_pred CCCCceEEEEeccCCEEEE
Q 033623 16 SIRGAKSVEVNRKQSRVTV 34 (115)
Q Consensus 16 ~~~gv~~~~v~~~~~~v~v 34 (115)
.++||..|.+-...+++.+
T Consensus 15 ~i~~i~eV~i~~~dg~~~~ 33 (58)
T PF01849_consen 15 EIPGIEEVTIRKDDGTVFV 33 (58)
T ss_dssp EETTEEEEEEEETTTEEEE
T ss_pred ccCCcEEEEEEECCceEEE
Confidence 3478888888887766654
No 93
>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=31.81 E-value=1.2e+02 Score=25.47 Aligned_cols=44 Identities=16% Similarity=0.320 Sum_probs=33.4
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEEee----------CCHHHHHHHHHHc
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY----------VDPNKVLKKVKST 50 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~----------~~~~~i~~~i~~~ 50 (115)
+.++++.|++.+|+.++..+....+-++.-. ++.++|...|+.+
T Consensus 689 a~~v~~~l~~~pgv~dv~~~~~~~~~el~i~~dreka~~~Gls~~~va~~l~~a 742 (1021)
T PF00873_consen 689 AEKVKAKLAEIPGVTDVRDDWEDGQPELRIDPDREKAARLGLSPADVARTLRTA 742 (1021)
T ss_dssp HHHHHHHHHHSTTEEEEEESSSSBEEEEEEEE-HHHHHHTTB-HHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCcccccccccccCcceEEEecHHHHHHcCCCHHHHHHHHHHH
Confidence 5788999999999999999998877655422 6677777777644
No 94
>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=31.81 E-value=89 Score=16.74 Aligned_cols=49 Identities=16% Similarity=0.201 Sum_probs=33.8
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHHcCCCceecC
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY--VDPNKVLKKVKSTGKRAEFWP 58 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~--~~~~~i~~~i~~~G~~~~~~~ 58 (115)
+.|+.=.-+.+++|.+++. .+.+.|..+ .....|....++.|+......
T Consensus 7 ~~CP~Pvl~~kkal~~l~~---------G~~l~V~~d~~~a~~di~~~~~~~G~~~~~~~ 57 (69)
T cd03420 7 LQCPGPILKLKKEIDKLQD---------GEQLEVKASDPGFARDAQAWCKSTGNTLISLE 57 (69)
T ss_pred CcCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHHHcCCEEEEEE
Confidence 3577778889999988753 223444432 566778888899999876443
No 95
>PRK07334 threonine dehydratase; Provisional
Probab=31.49 E-value=2.1e+02 Score=21.11 Aligned_cols=50 Identities=12% Similarity=0.131 Sum_probs=29.2
Q ss_pred HHHHHHHhCCC-CceEEEEecc-----CCEEEEE--ee----CCHHHHHHHHHHcCCCceec
Q 033623 8 RKVRNAVSSIR-GAKSVEVNRK-----QSRVTVT--GY----VDPNKVLKKVKSTGKRAEFW 57 (115)
Q Consensus 8 ~~v~~~l~~~~-gv~~~~v~~~-----~~~v~v~--~~----~~~~~i~~~i~~~G~~~~~~ 57 (115)
..|-+.|++.+ .|.+++.... .+...+. .+ ...+.|+..|++.||.++++
T Consensus 341 ~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~~~L~~vi~~Lr~~g~~~~~~ 402 (403)
T PRK07334 341 ARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDAAHLQEVIAALRAAGFEARLV 402 (403)
T ss_pred HHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCHHHHHHHHHHHHHcCCeeEeC
Confidence 45556665542 3445554422 3443333 22 34557889999999998875
No 96
>PHA01634 hypothetical protein
Probab=31.45 E-value=15 Score=23.27 Aligned_cols=13 Identities=54% Similarity=1.267 Sum_probs=10.0
Q ss_pred CCcHhHHHHHHHH
Q 033623 1 MDCDGCERKVRNA 13 (115)
Q Consensus 1 m~C~~C~~~v~~~ 13 (115)
|+|++|..++.-.
T Consensus 98 iDCeGCE~~l~v~ 110 (156)
T PHA01634 98 MDCEGCEEKLNVS 110 (156)
T ss_pred EEccchHHhcCHH
Confidence 6899999887543
No 97
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=31.21 E-value=62 Score=22.56 Aligned_cols=21 Identities=19% Similarity=0.420 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCCceEEEEec
Q 033623 7 ERKVRNAVSSIRGAKSVEVNR 27 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~ 27 (115)
...+++.|..++||.+++|++
T Consensus 109 egELarTI~~idgV~~ArVhL 129 (249)
T PRK15348 109 EQRIEGMLSQMEGVINAKVTI 129 (249)
T ss_pred HHHHHHHHHhCCCeeEeEEEE
Confidence 356889999999999988865
No 98
>PRK10568 periplasmic protein; Provisional
Probab=31.16 E-value=1.6e+02 Score=19.58 Aligned_cols=33 Identities=30% Similarity=0.491 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCCCce--EEEEeccCCEEEEEeeCC
Q 033623 7 ERKVRNAVSSIRGAK--SVEVNRKQSRVTVTGYVD 39 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~--~~~v~~~~~~v~v~~~~~ 39 (115)
..+|+.+|...+++. .+++...++.+++.|.++
T Consensus 62 ~~~v~~~L~~~~~i~~~~I~V~v~~G~V~L~G~V~ 96 (203)
T PRK10568 62 TAKVKAALVDHDNIKSTDISVKTHQKVVTLSGFVE 96 (203)
T ss_pred HHHHHHHHHhCCCCCCCceEEEEECCEEEEEEEeC
Confidence 467788887776665 566777899999998754
No 99
>KOG1635 consensus Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=30.62 E-value=52 Score=21.76 Aligned_cols=28 Identities=25% Similarity=0.266 Sum_probs=23.9
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeccCCE
Q 033623 4 DGCERKVRNAVSSIRGAKSVEVNRKQSR 31 (115)
Q Consensus 4 ~~C~~~v~~~l~~~~gv~~~~v~~~~~~ 31 (115)
.+|-+.+|.+...++||...+|-.+.++
T Consensus 31 ~GCFWg~E~a~~~l~gV~~T~vGYagG~ 58 (191)
T KOG1635|consen 31 AGCFWGVELAYQRLPGVVRTEVGYAGGI 58 (191)
T ss_pred ccchhhHHHHHhhcCCeEEEeecccCCc
Confidence 4799999999999999999988776553
No 100
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=30.54 E-value=66 Score=17.29 Aligned_cols=17 Identities=18% Similarity=0.397 Sum_probs=13.4
Q ss_pred HHHHHHHhCCCCceEEE
Q 033623 8 RKVRNAVSSIRGAKSVE 24 (115)
Q Consensus 8 ~~v~~~l~~~~gv~~~~ 24 (115)
..+-+.|.+++||.++.
T Consensus 52 ~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 52 QTLMPEIRRIDGVEDVK 68 (74)
T ss_pred HHHHHHHhCCCCceEEE
Confidence 45677889999998875
No 101
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=30.43 E-value=42 Score=17.26 Aligned_cols=17 Identities=6% Similarity=0.296 Sum_probs=12.9
Q ss_pred CHHHHHHHHHHcCCCce
Q 033623 39 DPNKVLKKVKSTGKRAE 55 (115)
Q Consensus 39 ~~~~i~~~i~~~G~~~~ 55 (115)
+.+.+.+.|++.||++.
T Consensus 56 ~l~~l~~~l~~~g~~~~ 72 (73)
T cd04886 56 HIEEIIAALREAGYDVR 72 (73)
T ss_pred HHHHHHHHHHHcCCEEe
Confidence 34588899999998653
No 102
>KOG4034 consensus Uncharacterized conserved protein NOF (Neighbor of FAU) [Function unknown]
Probab=29.88 E-value=1.5e+02 Score=19.25 Aligned_cols=47 Identities=15% Similarity=0.227 Sum_probs=31.3
Q ss_pred hHHHHHHHHHhCCCCc-eEEEEeccCCEEEEEeeCCHHHHHHHHHHcCC
Q 033623 5 GCERKVRNAVSSIRGA-KSVEVNRKQSRVTVTGYVDPNKVLKKVKSTGK 52 (115)
Q Consensus 5 ~C~~~v~~~l~~~~gv-~~~~v~~~~~~v~v~~~~~~~~i~~~i~~~G~ 52 (115)
.|.+.++..|...+|- -...||..++++.+.+. ..+.|.+-|.+.||
T Consensus 122 aLe~DL~s~L~~~~~~s~~t~VnelsgqI~~~g~-~v~~vr~~L~eKGF 169 (169)
T KOG4034|consen 122 ALENDLRSTLEMSPKKSYATHVNELSGQIVLKGN-HVDTVREWLQEKGF 169 (169)
T ss_pred HHHHHHHHHHhhccCCChhhhhhhhcceEEEeCC-hHHHHHHHHHHccC
Confidence 4667777777777653 33568888888887765 23366667777765
No 103
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=29.83 E-value=1.7e+02 Score=19.44 Aligned_cols=49 Identities=18% Similarity=0.130 Sum_probs=34.4
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEe--eCCHHHHHHHHHHcCCCceecC
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTG--YVDPNKVLKKVKSTGKRAEFWP 58 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~--~~~~~~i~~~i~~~G~~~~~~~ 58 (115)
+.|+.-.-+.+++|.+++.- +.++|.. ....+.|.+.+++.|+......
T Consensus 6 l~CP~Pvi~tKkal~~l~~g---------~~L~VlvD~~~a~~nV~~~~~~~G~~v~~~e 56 (194)
T TIGR03527 6 LACPQPVILTKKALDELGEE---------GVLTVIVDNEAAKENVSKFATSLGYEVEVEE 56 (194)
T ss_pred CCCCHHHHHHHHHHHcCCCC---------CEEEEEECCccHHHHHHHHHHHcCCEEEEEE
Confidence 35888899999999988521 2333332 3566778888899999887543
No 104
>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=29.42 E-value=2e+02 Score=24.09 Aligned_cols=41 Identities=22% Similarity=0.396 Sum_probs=28.5
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEE--ee--CCHHHHHHHH
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQSRVTVT--GY--VDPNKVLKKV 47 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~~v~v~--~~--~~~~~i~~~i 47 (115)
...+|++|..++|++.++-.-..+...|. .. .+.++....+
T Consensus 62 t~plE~~l~~v~gv~~i~S~s~~g~s~i~v~f~~~~d~~~a~~~v 106 (1021)
T PF00873_consen 62 TKPLEEALSSVEGVKEIRSTSREGSSSITVEFDDGTDIDEALQEV 106 (1021)
T ss_dssp HHHHHHTHCSSTTEEEEEEEETTSEEEEEEEESTTS-HHHHHHHH
T ss_pred HHHHHHHHcCCCCeEEEEEEecCCcEEEEEEeccccCHHHHHHHH
Confidence 35789999999999999888877776554 32 4555433333
No 105
>KOG3782 consensus Predicted membrane protein, contains type II SA sequence [General function prediction only]
Probab=29.04 E-value=1.7e+02 Score=19.22 Aligned_cols=46 Identities=15% Similarity=0.462 Sum_probs=27.1
Q ss_pred CcHhHHHHH---HHHHhCCC-----CceEEEEeccCCEEE--EE---eeCCHHHHHHHH
Q 033623 2 DCDGCERKV---RNAVSSIR-----GAKSVEVNRKQSRVT--VT---GYVDPNKVLKKV 47 (115)
Q Consensus 2 ~C~~C~~~v---~~~l~~~~-----gv~~~~v~~~~~~v~--v~---~~~~~~~i~~~i 47 (115)
.|..|...| |-++.+.. .|.+.+++...+... |. ++....+|++.|
T Consensus 26 ~CgaC~alVtelE~~IA~vDPkK~i~vgsFR~~p~G~q~~~kV~yarSE~hLTEl~E~i 84 (189)
T KOG3782|consen 26 KCGACKALVTELEEAIAKVDPKKMIDVGSFRLDPQGNQISKKVRYARSEMHLTELMEKI 84 (189)
T ss_pred ccchHHHHHHHHHHHHHhcCchheeeecceEECCCCCeeeeeeccchhHHHHHHHHHHH
Confidence 688897666 45555542 467888887655443 32 234455555554
No 106
>cd08032 LARP_7 La RNA-binding domain of La-related protein 7. LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.
Probab=28.63 E-value=18 Score=20.65 Aligned_cols=7 Identities=43% Similarity=0.529 Sum_probs=5.6
Q ss_pred cCCccCC
Q 033623 102 TLFSDEN 108 (115)
Q Consensus 102 ~~FsDen 108 (115)
.+|||+|
T Consensus 15 fYFSd~N 21 (82)
T cd08032 15 FWFGDVN 21 (82)
T ss_pred hhcchhh
Confidence 5788887
No 107
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=28.41 E-value=77 Score=18.28 Aligned_cols=20 Identities=30% Similarity=0.454 Sum_probs=16.7
Q ss_pred HHHHHHHH-hCCCCceEEEEe
Q 033623 7 ERKVRNAV-SSIRGAKSVEVN 26 (115)
Q Consensus 7 ~~~v~~~l-~~~~gv~~~~v~ 26 (115)
...++.++ +..+||+++++.
T Consensus 64 ~d~lee~i~~~~e~Vqsvei~ 84 (89)
T PF00736_consen 64 TDDLEEAIESFEEGVQSVEIE 84 (89)
T ss_dssp HHHHHHHHTTCTTTEEEEEEE
T ss_pred hHHHHHHHHhcCCCccEEEEE
Confidence 45788888 899999999875
No 108
>TIGR01677 pln_FAD_oxido plant-specific FAD-dependent oxidoreductase. This model represents an uncharacterized plant-specific family of FAD-dependent oxidoreductases. At least seven distinct members are found in Arabidopsis thaliana. The family shows considerable sequence similarity to three different enzymes of ascorbic acid biosynthesis: L-galactono-1,4-lactone dehydrogenase (EC 1.3.2.3) from higher plants, D-arabinono-1,4-lactone oxidase (EC 1.1.3.37 from Saccharomyces cerevisiae, and L-gulonolactone oxidase (EC 1.1.3.8) from mouse, as well as to a bacterial sorbitol oxidase. The class of compound acted on by members of this family is unknown.
Probab=28.31 E-value=1.3e+02 Score=23.61 Aligned_cols=34 Identities=18% Similarity=0.266 Sum_probs=25.8
Q ss_pred EEEeccCCEEEEEeeCCHHHHHHHHHHcCCCcee
Q 033623 23 VEVNRKQSRVTVTGYVDPNKVLKKVKSTGKRAEF 56 (115)
Q Consensus 23 ~~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~~~~ 56 (115)
+++|..+.+++|..-+...+|.+.|.+.|+....
T Consensus 92 l~iD~~~~tVtV~AG~~l~~L~~~L~~~Glal~~ 125 (557)
T TIGR01677 92 VAVDATAMTVTVESGMSLRELIVEAEKAGLALPY 125 (557)
T ss_pred EEEeCCCCEEEECCCCcHHHHHHHHHHcCCEecc
Confidence 4556666778887778899999999999875433
No 109
>KOG3302 consensus TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=28.31 E-value=72 Score=21.45 Aligned_cols=34 Identities=15% Similarity=0.273 Sum_probs=23.8
Q ss_pred ccCCEEEEEee-------CCHHHHHHHHHHcCCCceecCCC
Q 033623 27 RKQSRVTVTGY-------VDPNKVLKKVKSTGKRAEFWPYV 60 (115)
Q Consensus 27 ~~~~~v~v~~~-------~~~~~i~~~i~~~G~~~~~~~~~ 60 (115)
+..+++..+|. ....++++.|++.||.+.+..+.
T Consensus 74 ~ssGKi~ctgA~se~~ar~aark~aRilqkLgf~~~f~~fk 114 (200)
T KOG3302|consen 74 FSSGKIVCTGAKSEDSARLAARKYARILQKLGFPVKFRDFK 114 (200)
T ss_pred ecCCcEEEeccCCHHHHHHHHHHHHHHHHHcCCCceehhee
Confidence 35666666653 33445778889999999988753
No 110
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=27.89 E-value=73 Score=18.31 Aligned_cols=23 Identities=26% Similarity=0.394 Sum_probs=14.6
Q ss_pred CCHHHHHHHHHHcCCCceecCCC
Q 033623 38 VDPNKVLKKVKSTGKRAEFWPYV 60 (115)
Q Consensus 38 ~~~~~i~~~i~~~G~~~~~~~~~ 60 (115)
++.++|....++.||.+++++.+
T Consensus 55 id~~~i~~fC~~~gy~~~iv~~g 77 (86)
T PF11360_consen 55 IDPEEIEEFCRSAGYEYEIVPPG 77 (86)
T ss_pred ECHHHHHHHHHHCCceEEEECCC
Confidence 45555666666777777776654
No 111
>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=27.84 E-value=1e+02 Score=16.08 Aligned_cols=50 Identities=12% Similarity=0.200 Sum_probs=28.0
Q ss_pred hHHHHHHHHHhCCC-CceEEEEecc--CCE--EEEEee-CCHHHHHHHHHHcCCCc
Q 033623 5 GCERKVRNAVSSIR-GAKSVEVNRK--QSR--VTVTGY-VDPNKVLKKVKSTGKRA 54 (115)
Q Consensus 5 ~C~~~v~~~l~~~~-gv~~~~v~~~--~~~--v~v~~~-~~~~~i~~~i~~~G~~~ 54 (115)
+...++.+.|.+.. .+.++..... .+. +.+..+ .+.+++.+.|++.||++
T Consensus 13 G~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L~~~G~~v 68 (72)
T cd04883 13 GQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNPRPIIEDLRRAGYEV 68 (72)
T ss_pred CHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCHHHHHHHHHHCCCee
Confidence 34455666665542 3344433322 222 334332 46779999999999864
No 112
>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=27.81 E-value=1.7e+02 Score=18.84 Aligned_cols=29 Identities=14% Similarity=0.224 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEE
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQSRVTVT 35 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~~v~v~ 35 (115)
+.+|.+.+.+++||.++.+-.....+.|-
T Consensus 56 A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vg 84 (158)
T TIGR02898 56 ADEIASEAAKVKGVKDATVVITGNYAYVG 84 (158)
T ss_pred HHHHHHHHhcCCCCceEEEEEECCEEEEE
Confidence 56788889999999999888777777664
No 113
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=27.52 E-value=89 Score=20.25 Aligned_cols=28 Identities=29% Similarity=0.182 Sum_probs=23.1
Q ss_pred EEEEeeCCHHHHHHHHHHcCCCceecCC
Q 033623 32 VTVTGYVDPNKVLKKVKSTGKRAEFWPY 59 (115)
Q Consensus 32 v~v~~~~~~~~i~~~i~~~G~~~~~~~~ 59 (115)
+.+.++-|-..|+..|++.|..+...+.
T Consensus 110 vLvSgD~DF~~Lv~~lre~G~~V~v~g~ 137 (160)
T TIGR00288 110 ALVTRDADFLPVINKAKENGKETIVIGA 137 (160)
T ss_pred EEEeccHhHHHHHHHHHHCCCEEEEEeC
Confidence 4456778889999999999998888874
No 114
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=27.44 E-value=1.2e+02 Score=16.70 Aligned_cols=26 Identities=15% Similarity=0.285 Sum_probs=15.1
Q ss_pred CcHhHHHHHHHHHhCC----CCceEEEEecc
Q 033623 2 DCDGCERKVRNAVSSI----RGAKSVEVNRK 28 (115)
Q Consensus 2 ~C~~C~~~v~~~l~~~----~gv~~~~v~~~ 28 (115)
.|..|.+ +++.|..+ .|+.-..+|..
T Consensus 10 ~C~~C~~-a~~~L~~l~~~~~~i~~~~idi~ 39 (85)
T PRK11200 10 GCPYCVR-AKELAEKLSEERDDFDYRYVDIH 39 (85)
T ss_pred CChhHHH-HHHHHHhhcccccCCcEEEEECC
Confidence 5888974 45556654 45554444443
No 115
>TIGR01679 bact_FAD_ox FAD-linked oxidoreductase. This model represents a family of bacterial oxidoreductases with covalently linked FAD, closely related to two different eukaryotic oxidases, L-gulonolactone oxidase (EC 1.1.3.8) from rat and D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) from Saccharomyces cerevisiae.
Probab=27.33 E-value=1.4e+02 Score=22.29 Aligned_cols=32 Identities=16% Similarity=0.135 Sum_probs=26.3
Q ss_pred EEeccCCEEEEEeeCCHHHHHHHHHHcCCCce
Q 033623 24 EVNRKQSRVTVTGYVDPNKVLKKVKSTGKRAE 55 (115)
Q Consensus 24 ~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~~~ 55 (115)
++|..+++++|..-+...+|.+.|.+.|+...
T Consensus 65 ~~d~~~~~v~v~aG~~l~~l~~~L~~~G~~l~ 96 (419)
T TIGR01679 65 DVDQPTGLATVEAGTRLGALGPQLAQRGLGLE 96 (419)
T ss_pred eecCCCCEEEEcCCCCHHHHHHHHHHcCCccc
Confidence 56777888888877899999999999997543
No 116
>PF13299 CPSF100_C: Cleavage and polyadenylation factor 2 C-terminal
Probab=27.21 E-value=71 Score=20.53 Aligned_cols=24 Identities=25% Similarity=0.340 Sum_probs=21.3
Q ss_pred eeCCHHHHHHHHHHcCCCceecCC
Q 033623 36 GYVDPNKVLKKVKSTGKRAEFWPY 59 (115)
Q Consensus 36 ~~~~~~~i~~~i~~~G~~~~~~~~ 59 (115)
|++...++.+.|.+.|+.+++.+.
T Consensus 98 Gd~rL~~lk~~L~~~g~~aEF~g~ 121 (161)
T PF13299_consen 98 GDLRLSDLKQALQSAGIQAEFRGE 121 (161)
T ss_pred CcccHHHHHHHHHHCCCceEEeeC
Confidence 678899999999999999999953
No 117
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=27.18 E-value=1.2e+02 Score=25.57 Aligned_cols=44 Identities=16% Similarity=0.265 Sum_probs=32.6
Q ss_pred HHHHHHHHhCCCCceEEEEeccCC--EEEEEe--------eCCHHHHHHHHHHc
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQS--RVTVTG--------YVDPNKVLKKVKST 50 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~--~v~v~~--------~~~~~~i~~~i~~~ 50 (115)
+.++++.|.+.+|+.+++.+...+ .+.|.- .++..++...|+..
T Consensus 677 a~~i~~~L~~~pgv~~v~~~~~~~~~el~i~id~~ka~~~Gls~~~v~~~l~~~ 730 (1025)
T PRK10614 677 EPKIRKALAALPELADVNSDQQDKGAEMALTYDRDTMARLGIDVQAANSLLNNA 730 (1025)
T ss_pred HHHHHHHHhcCCCeEEeecCCCCCCceEEEEECHHHHHHcCCCHHHHHHHHHHH
Confidence 567899999999999999887554 444442 27778888888654
No 118
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=26.81 E-value=75 Score=16.70 Aligned_cols=19 Identities=21% Similarity=0.323 Sum_probs=15.8
Q ss_pred eCCHHHHHHHHHHcCCCce
Q 033623 37 YVDPNKVLKKVKSTGKRAE 55 (115)
Q Consensus 37 ~~~~~~i~~~i~~~G~~~~ 55 (115)
+++.++|.+.|...||...
T Consensus 31 ~id~~~l~~kL~~~Gy~Y~ 49 (55)
T PF14056_consen 31 DIDKEELEEKLASIGYEYD 49 (55)
T ss_pred CCCHHHHHHHHHHcCCeEc
Confidence 4788999999999998643
No 119
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=26.64 E-value=89 Score=22.34 Aligned_cols=38 Identities=26% Similarity=0.289 Sum_probs=27.5
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeccCCEEEEEeeCCHHHHHHHH-HHcCCC
Q 033623 4 DGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGYVDPNKVLKKV-KSTGKR 53 (115)
Q Consensus 4 ~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~~~~~~i~~~i-~~~G~~ 53 (115)
..|...+++.+.+.+||.++++- +.++-.+.+ +..|+.
T Consensus 71 ~~~~~~v~~~i~~~~gV~~v~~~------------sre~~l~~L~~~lg~~ 109 (297)
T COG2177 71 QDDAALVREKIEGIPGVKSVRFI------------SREEALKELQPWLGFG 109 (297)
T ss_pred hHHHHHHHHHHhcCCCcceEEEe------------CHHHHHHHHHHHcCch
Confidence 56888899999999999987664 444555544 456654
No 120
>COG3603 Uncharacterized conserved protein [Function unknown]
Probab=26.61 E-value=1.7e+02 Score=18.20 Aligned_cols=45 Identities=20% Similarity=0.296 Sum_probs=29.4
Q ss_pred HHHHHHHhCCCCceEEEEe-ccCCEEEEEeeCCHHHHHHHHHHcCCCc
Q 033623 8 RKVRNAVSSIRGAKSVEVN-RKQSRVTVTGYVDPNKVLKKVKSTGKRA 54 (115)
Q Consensus 8 ~~v~~~l~~~~gv~~~~v~-~~~~~v~v~~~~~~~~i~~~i~~~G~~~ 54 (115)
.+|-+.|+. +||.-..++ +.++-+.|... +.++-+++|+.+|+++
T Consensus 81 asV~~pLsd-~gigIFavStydtDhiLVr~~-dLekAv~~L~eaGhev 126 (128)
T COG3603 81 ASVSQPLSD-NGIGIFAVSTYDTDHILVREE-DLEKAVKALEEAGHEV 126 (128)
T ss_pred hhhhhhHhh-CCccEEEEEeccCceEEEehh-hHHHHHHHHHHcCCcc
Confidence 455565554 566555544 35666666654 7788888999999865
No 121
>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=26.60 E-value=1.1e+02 Score=16.33 Aligned_cols=47 Identities=13% Similarity=0.099 Sum_probs=32.7
Q ss_pred CcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEe--eCCHHHHHHHHHHcCCCceec
Q 033623 2 DCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTG--YVDPNKVLKKVKSTGKRAEFW 57 (115)
Q Consensus 2 ~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~--~~~~~~i~~~i~~~G~~~~~~ 57 (115)
.|+.=.-+.+++|++++.- +.+.|.. ......|...++..|+.....
T Consensus 8 ~CP~Pvi~~kkal~~l~~G---------~~l~V~~d~~~s~~ni~~~~~~~g~~v~~~ 56 (69)
T cd03422 8 PCPYPAIATLEALPSLKPG---------EILEVISDCPQSINNIPIDARNHGYKVLAI 56 (69)
T ss_pred cCCHHHHHHHHHHHcCCCC---------CEEEEEecCchHHHHHHHHHHHcCCEEEEE
Confidence 5777788899999987532 2334433 256677888889999987643
No 122
>COG3870 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.59 E-value=1.2e+02 Score=18.17 Aligned_cols=24 Identities=17% Similarity=0.134 Sum_probs=19.3
Q ss_pred EEeeCCHHHHHHHHHHcCCCceec
Q 033623 34 VTGYVDPNKVLKKVKSTGKRAEFW 57 (115)
Q Consensus 34 v~~~~~~~~i~~~i~~~G~~~~~~ 57 (115)
|.-+.+..++.++|.+.+|++.-+
T Consensus 7 ivqd~da~~l~~~L~d~~fraTkL 30 (109)
T COG3870 7 IVQDQDANELEDALTDKNFRATKL 30 (109)
T ss_pred EEecccHHHHHHHHHhCCceeEEe
Confidence 345678999999999999998643
No 123
>PHA02119 hypothetical protein
Probab=26.35 E-value=98 Score=17.16 Aligned_cols=20 Identities=20% Similarity=0.293 Sum_probs=16.5
Q ss_pred CCHHHHHHHHHHcCCCceec
Q 033623 38 VDPNKVLKKVKSTGKRAEFW 57 (115)
Q Consensus 38 ~~~~~i~~~i~~~G~~~~~~ 57 (115)
+-+.+|+..|+..||.+.--
T Consensus 54 i~~~divdylr~lgy~~~~~ 73 (87)
T PHA02119 54 IMPKDIVDYLRSLGYDAKSD 73 (87)
T ss_pred cccHHHHHHHHHccchhccc
Confidence 67889999999999986543
No 124
>COG0217 Uncharacterized conserved protein [Function unknown]
Probab=26.18 E-value=1.3e+02 Score=20.91 Aligned_cols=45 Identities=24% Similarity=0.311 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCCCc----eEEEEeccCCEE-EEEee-CCHHHHHHHHHHcC
Q 033623 7 ERKVRNAVSSIRGA----KSVEVNRKQSRV-TVTGY-VDPNKVLKKVKSTG 51 (115)
Q Consensus 7 ~~~v~~~l~~~~gv----~~~~v~~~~~~v-~v~~~-~~~~~i~~~i~~~G 51 (115)
+..|+.++.+..|- .+|...|...-+ ++... .+.++|.+++-.+|
T Consensus 110 as~vR~~F~K~GG~lg~~GSV~~mF~~kGvi~~~~~~~~ed~l~e~~ieag 160 (241)
T COG0217 110 ASNVRSAFNKNGGNLGEPGSVSYMFDRKGVIVVEKNEIDEDELLEAAIEAG 160 (241)
T ss_pred HHHHHHHHHhcCCccCCCceEEEEEeccEEEEECCCCCCHHHHHHHHHHCC
Confidence 34566666665542 245555544333 34333 46666666665554
No 125
>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=26.04 E-value=1.4e+02 Score=18.00 Aligned_cols=32 Identities=19% Similarity=0.241 Sum_probs=25.9
Q ss_pred EEEeccCCEEEEEeeCCHHHHHHHHHHcCCCc
Q 033623 23 VEVNRKQSRVTVTGYVDPNKVLKKVKSTGKRA 54 (115)
Q Consensus 23 ~~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~~ 54 (115)
+++|.....++|..-+...+|.+.|...|...
T Consensus 57 ~~id~~~~~v~v~aG~~~~~l~~~l~~~g~~~ 88 (139)
T PF01565_consen 57 IEIDPENGTVTVGAGVTWGDLYEALAPRGLML 88 (139)
T ss_dssp EEEETTTTEEEEETTSBHHHHHHHHHHHTEEE
T ss_pred ccccccceeEEEeccccchhcccccccccccc
Confidence 56777788888887789999999998877543
No 126
>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=25.74 E-value=1e+02 Score=15.51 Aligned_cols=16 Identities=19% Similarity=0.324 Sum_probs=12.2
Q ss_pred HHHHHHhCCCCceEEE
Q 033623 9 KVRNAVSSIRGAKSVE 24 (115)
Q Consensus 9 ~v~~~l~~~~gv~~~~ 24 (115)
.+.+.|++++||.++.
T Consensus 54 ~l~~~l~~~~~V~~v~ 69 (71)
T cd04879 54 EVLEELKALPGIIRVR 69 (71)
T ss_pred HHHHHHHcCCCeEEEE
Confidence 5667788888888765
No 127
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=25.41 E-value=1.1e+02 Score=17.36 Aligned_cols=21 Identities=10% Similarity=0.041 Sum_probs=17.8
Q ss_pred CHHHHHHHHHHcCCCceecCC
Q 033623 39 DPNKVLKKVKSTGKRAEFWPY 59 (115)
Q Consensus 39 ~~~~i~~~i~~~G~~~~~~~~ 59 (115)
....|.+.|++.||.+..+..
T Consensus 9 ~Ls~v~~~L~~~GyeVv~l~~ 29 (80)
T PF03698_consen 9 GLSNVKEALREKGYEVVDLEN 29 (80)
T ss_pred CchHHHHHHHHCCCEEEecCC
Confidence 566899999999999888774
No 128
>PF09158 MotCF: Bacteriophage T4 MotA, C-terminal; InterPro: IPR015241 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the C-terminal domain of MotA factors, which adopts a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. It contains a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [].; PDB: 1KAF_B.
Probab=25.14 E-value=1.6e+02 Score=17.62 Aligned_cols=40 Identities=20% Similarity=0.403 Sum_probs=27.3
Q ss_pred CCCceEEEEeccCCEEEEEeeCCHHHHHHHHHHcCCCceec
Q 033623 17 IRGAKSVEVNRKQSRVTVTGYVDPNKVLKKVKSTGKRAEFW 57 (115)
Q Consensus 17 ~~gv~~~~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~~~~~ 57 (115)
..|+...++. ..+...|-+.--.+++++.+.+.|..+...
T Consensus 40 t~GirqfEi~-n~G~~RI~gYk~se~~~~~f~slG~~~K~~ 79 (103)
T PF09158_consen 40 TKGIRQFEIR-NKGEFRIFGYKMSEEIIKKFTSLGMEVKQK 79 (103)
T ss_dssp ETTEEEEEEE-TTSEEEEEEES--HHHHHHHHHTT-EEEE-
T ss_pred cCceeEEEEe-cCCcEEEEEEcCCHHHHHHHHhcCcEEEEc
Confidence 3567666664 566777777777888999999999877663
No 129
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=24.67 E-value=37 Score=19.69 Aligned_cols=14 Identities=36% Similarity=0.978 Sum_probs=10.6
Q ss_pred CCcHhHHHHHHHHH
Q 033623 1 MDCDGCERKVRNAV 14 (115)
Q Consensus 1 m~C~~C~~~v~~~l 14 (115)
|-|+.|..++.+.+
T Consensus 1 MVC~kCEkKLskvi 14 (100)
T KOG3476|consen 1 MVCEKCEKKLSKVI 14 (100)
T ss_pred CchhHHHHHhcccc
Confidence 77999987776654
No 130
>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium). This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=24.52 E-value=3e+02 Score=23.36 Aligned_cols=43 Identities=12% Similarity=0.159 Sum_probs=30.9
Q ss_pred HHHHHHhCCCCceEEEEeccCC-EEEEEe--------eCCHHHHHHHHHHcC
Q 033623 9 KVRNAVSSIRGAKSVEVNRKQS-RVTVTG--------YVDPNKVLKKVKSTG 51 (115)
Q Consensus 9 ~v~~~l~~~~gv~~~~v~~~~~-~v~v~~--------~~~~~~i~~~i~~~G 51 (115)
.++..|++++||.++++....+ .+.|.- .++..++..+|+...
T Consensus 170 ~l~~~L~~i~GV~~V~~~G~~~~ei~V~iD~~kl~~~glt~~dV~~~l~~~~ 221 (1051)
T TIGR00914 170 IIRPQLRTVPGVAEVNSIGGYVKQFLVAPDPEKLAAYGLSLADVVNALERNN 221 (1051)
T ss_pred HHHHHHhcCCCceEeeecCCceEEEEEEECHHHHHHcCCCHHHHHHHHHHhC
Confidence 3778899999999999876443 344542 277888888887654
No 131
>PRK15324 type III secretion system lipoprotein PrgK; Provisional
Probab=24.35 E-value=95 Score=21.68 Aligned_cols=21 Identities=19% Similarity=0.441 Sum_probs=17.2
Q ss_pred HHHHHHHHhCCCCceEEEEec
Q 033623 7 ERKVRNAVSSIRGAKSVEVNR 27 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~ 27 (115)
...+++.|++++||.+++|.+
T Consensus 110 e~ELarTI~~IdgV~~ARVHl 130 (252)
T PRK15324 110 EQRLEQSLQTMEGVLSARVHI 130 (252)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 356788999999999888765
No 132
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=24.35 E-value=1.5e+02 Score=25.02 Aligned_cols=44 Identities=9% Similarity=0.036 Sum_probs=31.5
Q ss_pred HHHHHHHHhCCCCceEEEEeccCC--EEEEEe--------eCCHHHHHHHHHHc
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQS--RVTVTG--------YVDPNKVLKKVKST 50 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~--~v~v~~--------~~~~~~i~~~i~~~ 50 (115)
+.+++..|++++|+.+++.+...+ .+.|.- .++.+++...|+..
T Consensus 691 a~~l~~~l~~~pgv~~v~~~~~~~~~e~~v~id~~k~~~~Gls~~~v~~~l~~~ 744 (1040)
T PRK10503 691 VPKLMEKLQQLPQLSDVSSDWQDKGLVAYVNVDRDSASRLGISMADVDNALYNA 744 (1040)
T ss_pred HHHHHHHHhcCCCeEEEEccccCCCceEEEEECHHHHHHcCCCHHHHHHHHHHH
Confidence 457889999999999998765443 444432 27788888888653
No 133
>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=24.13 E-value=2.2e+02 Score=18.83 Aligned_cols=41 Identities=20% Similarity=0.229 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCCceE--EEEeccCCEEEEEeeCCHHHHHHHH
Q 033623 7 ERKVRNAVSSIRGAKS--VEVNRKQSRVTVTGYVDPNKVLKKV 47 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~--~~v~~~~~~v~v~~~~~~~~i~~~i 47 (115)
..+|.+++.+.+||.- +..|...++..++..-+++.|.+++
T Consensus 18 ie~I~~a~~~~~gv~ll~~~~D~~~NRsv~T~vG~p~~v~~a~ 60 (178)
T PF07837_consen 18 IEAIAKAARNVPGVKLLDVFSDADYNRSVITLVGEPEAVAEAA 60 (178)
T ss_dssp HHHHHHHCCTSTTEEEEEEEEETTTTEEEEEEEE-HHHHHHHH
T ss_pred HHHHHHHHHcCCCCEEEecCCCCCCCCCeEEEeeChHHHHHHH
Confidence 4567788888888764 4455677776665433455555443
No 134
>PLN02465 L-galactono-1,4-lactone dehydrogenase
Probab=23.97 E-value=1.8e+02 Score=22.94 Aligned_cols=32 Identities=25% Similarity=0.426 Sum_probs=26.2
Q ss_pred EEeccCCEEEEEeeCCHHHHHHHHHHcCCCce
Q 033623 24 EVNRKQSRVTVTGYVDPNKVLKKVKSTGKRAE 55 (115)
Q Consensus 24 ~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~~~ 55 (115)
++|..+++++|.+-+...+|.+.|.+.|....
T Consensus 153 ~vD~e~~~VtV~AG~~l~~L~~~L~~~GLal~ 184 (573)
T PLN02465 153 EVDKEKKRVTVQAGARVQQVVEALRPHGLTLQ 184 (573)
T ss_pred EEeCCCCEEEEccCCCHHHHHHHHHHcCCEec
Confidence 56777788888877899999999999997644
No 135
>TIGR01678 FAD_lactone_ox sugar 1,4-lactone oxidases. This model represents a family of at least two different sugar 1,4 lactone oxidases, both involved in synthesizing ascorbic acid or a derivative. These include L-gulonolactone oxidase (EC 1.1.3.8) from rat and D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) from Saccharomyces cerevisiae. Members are proposed to have the cofactor FAD covalently bound at a site specified by Prosite motif PS00862; OX2_COVAL_FAD; 1.
Probab=23.93 E-value=2.1e+02 Score=21.55 Aligned_cols=32 Identities=9% Similarity=0.268 Sum_probs=25.8
Q ss_pred EEeccCCEEEEEeeCCHHHHHHHHHHcCCCce
Q 033623 24 EVNRKQSRVTVTGYVDPNKVLKKVKSTGKRAE 55 (115)
Q Consensus 24 ~v~~~~~~v~v~~~~~~~~i~~~i~~~G~~~~ 55 (115)
++|..++.++|..-+...+|.+.|.+.|+...
T Consensus 71 ~id~~~~~vtV~aG~~l~~L~~~L~~~Gl~l~ 102 (438)
T TIGR01678 71 QFDKEKKQITVEAGIRLYQLHEQLDEHGYSMS 102 (438)
T ss_pred EEcCCCCEEEEcCCCCHHHHHHHHHHcCCEec
Confidence 56666778888877889999999999997644
No 136
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.89 E-value=1.4e+02 Score=16.55 Aligned_cols=50 Identities=16% Similarity=0.127 Sum_probs=28.6
Q ss_pred HHHHHHhCCCCceEEEEec---cCCEEEEEee-----CCHHHHHHHHHHcCCCceecCC
Q 033623 9 KVRNAVSSIRGAKSVEVNR---KQSRVTVTGY-----VDPNKVLKKVKSTGKRAEFWPY 59 (115)
Q Consensus 9 ~v~~~l~~~~gv~~~~v~~---~~~~v~v~~~-----~~~~~i~~~i~~~G~~~~~~~~ 59 (115)
++-..|. -.+|..+..+. ....+.+.-+ .+.+++.+.|++.||+......
T Consensus 17 ~ll~~l~-~anI~~~~y~~~~~~~~~v~i~ie~~~~~~~~~~i~~~L~~~G~~~~~~~~ 74 (85)
T cd04906 17 KFCELIG-PRNITEFNYRYADEKDAHIFVGVSVANGAEELAELLEDLKSAGYEVVDLSD 74 (85)
T ss_pred HHHHHhC-CCceeEEEEEccCCCeeEEEEEEEeCCcHHHHHHHHHHHHHCCCCeEECCC
Confidence 4444454 23455555544 2333433222 2367889999999998876553
No 137
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=23.65 E-value=60 Score=19.59 Aligned_cols=28 Identities=29% Similarity=0.351 Sum_probs=18.3
Q ss_pred EEEEeeCCHHHHHHHHHHcCCCceecCC
Q 033623 32 VTVTGYVDPNKVLKKVKSTGKRAEFWPY 59 (115)
Q Consensus 32 v~v~~~~~~~~i~~~i~~~G~~~~~~~~ 59 (115)
+.|+|+.+...++..|+..|+++.++..
T Consensus 100 vLvSgD~Df~~~v~~l~~~g~~V~v~~~ 127 (146)
T PF01936_consen 100 VLVSGDSDFAPLVRKLRERGKRVIVVGA 127 (146)
T ss_dssp EEE---GGGHHHHHHHHHH--EEEEEE-
T ss_pred EEEECcHHHHHHHHHHHHcCCEEEEEEe
Confidence 4456788888899999999998888873
No 138
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=23.57 E-value=2e+02 Score=18.19 Aligned_cols=36 Identities=8% Similarity=0.077 Sum_probs=27.5
Q ss_pred EEeccCCEEEEEe--eCCHHHHHHHHHHcCCCceecCC
Q 033623 24 EVNRKQSRVTVTG--YVDPNKVLKKVKSTGKRAEFWPY 59 (115)
Q Consensus 24 ~v~~~~~~v~v~~--~~~~~~i~~~i~~~G~~~~~~~~ 59 (115)
-+|+..+-+.+.+ .++..++++.|.+.|..+.+...
T Consensus 47 ildL~G~~l~l~S~R~~~~~evi~~I~~~G~PviVAtD 84 (138)
T PF04312_consen 47 ILDLDGELLDLKSSRNMSRSEVIEWISEYGKPVIVATD 84 (138)
T ss_pred EEecCCcEEEEEeecCCCHHHHHHHHHHcCCEEEEEec
Confidence 4566666666664 38999999999999998877653
No 139
>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=23.35 E-value=1.7e+02 Score=24.83 Aligned_cols=44 Identities=7% Similarity=0.034 Sum_probs=32.3
Q ss_pred HHHHHHHHhCCCCceEEEEeccCC--EEEEEe--------eCCHHHHHHHHHHc
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQS--RVTVTG--------YVDPNKVLKKVKST 50 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~--~v~v~~--------~~~~~~i~~~i~~~ 50 (115)
+.++++.|++.+|+.+++.+...+ .+.+.- .++.++|...|+.+
T Consensus 699 a~~l~~~l~~~pg~~~v~~~~~~~~~~~~i~~d~~k~~~~Gls~~~v~~~l~~~ 752 (1044)
T TIGR00915 699 RNQLLGLAAQNPALTRVRPNGLEDEPQFKLNIDDEKAQALGVSIADINTTLSTA 752 (1044)
T ss_pred HHHHHHHHhcCCCeEEeeccccCCCceEEEEECHHHHHHcCCCHHHHHHHHHHH
Confidence 457889999999999998887544 455542 17778888888653
No 140
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.95 E-value=1.3e+02 Score=15.60 Aligned_cols=49 Identities=12% Similarity=0.138 Sum_probs=26.5
Q ss_pred HHHHHHHHHhCCC-CceEEEEecc----CCEEEEEee--CCHHHHHHHHHHcCCCc
Q 033623 6 CERKVRNAVSSIR-GAKSVEVNRK----QSRVTVTGY--VDPNKVLKKVKSTGKRA 54 (115)
Q Consensus 6 C~~~v~~~l~~~~-gv~~~~v~~~----~~~v~v~~~--~~~~~i~~~i~~~G~~~ 54 (115)
...++-+.|.+.. .+.++..... .+.+.+... .+.+++.+.|++.||++
T Consensus 14 ~L~~l~~~l~~~~i~i~~~~~~~~~~~~~~~~~i~v~~~~~~~~~~~~L~~~G~~v 69 (69)
T cd04909 14 VIAEVTQILGDAGISIKNIEILEIREGIGGILRISFKTQEDRERAKEILKEAGYEV 69 (69)
T ss_pred HHHHHHHHHHHcCCCceeeEeEEeecCCcEEEEEEECCHHHHHHHHHHHHHcCCcC
Confidence 3445566665542 2334433221 233333332 35778999999999863
No 141
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=22.86 E-value=3.1e+02 Score=21.92 Aligned_cols=55 Identities=13% Similarity=0.140 Sum_probs=37.1
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEEee-------CCHHHHHHHHHHcCCCceecCCCC
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY-------VDPNKVLKKVKSTGKRAEFWPYVP 61 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~-------~~~~~i~~~i~~~G~~~~~~~~~~ 61 (115)
...|++.+-.-.||.++.++..++.|.|... .....+.+-..++|...+++...|
T Consensus 72 ~~~i~~~~~~~~~~~~~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 72 IEKIKEIVPEEAGITDIYFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred HHHHHHhCCCcCCceeEEecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 3455666655579999999999999988732 133334445578898887765433
No 142
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=22.68 E-value=2.8e+02 Score=20.00 Aligned_cols=41 Identities=15% Similarity=0.205 Sum_probs=29.9
Q ss_pred hHHHHHHHHHhCCCCceEEEEeccCCEEEEEee---------CCHHHHHHHH
Q 033623 5 GCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY---------VDPNKVLKKV 47 (115)
Q Consensus 5 ~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~---------~~~~~i~~~i 47 (115)
.|...|+++|... +| ...+|+..+.++|.++ +.+.++++.|
T Consensus 73 e~wp~v~raL~e~-~i-~c~lDL~egsm~V~TtRkT~DPyIiikArdlIKLl 122 (356)
T KOG2874|consen 73 ECWPLVERALDEH-HI-KCVLDLVEGSMTVKTTRKTRDPYIIIKARDLIKLL 122 (356)
T ss_pred HHHHHHHHHHHhc-Cc-ceEEeeccceeEEeecccccCceeeeeHHHHHHHH
Confidence 4788999999864 44 5788999999988631 5566666655
No 143
>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=22.56 E-value=2.6e+02 Score=19.11 Aligned_cols=52 Identities=15% Similarity=0.195 Sum_probs=36.7
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEEee-------C-CHHHHHHHHHHcCCCceecCC
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY-------V-DPNKVLKKVKSTGKRAEFWPY 59 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~-------~-~~~~i~~~i~~~G~~~~~~~~ 59 (115)
....|+.|..+ |...+.|-...+.+.|+-. . ..+.|...+++.||.-..++.
T Consensus 187 v~~~E~~l~~~-g~~~~rvr~~~~~a~ie~~~~~~~~~~~~~~~i~~~~~~~gf~~v~ldl 246 (252)
T TIGR00268 187 VDEAEEVLRNA-GVGQVRVRNYDNLAVIEVPEDELSKLLNEAEEVRDKFKDIGFRKVLIDL 246 (252)
T ss_pred HHHHHHHHHHc-CCCeEEEEecCCeEEEEECHHHHHHHHhhHHHHHHHHHHcCCCeEEEcc
Confidence 34567778774 8888888877777777631 1 236678889999998776654
No 144
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=22.45 E-value=1.8e+02 Score=24.67 Aligned_cols=44 Identities=7% Similarity=0.060 Sum_probs=33.0
Q ss_pred HHHHHHHHhCCCCceEEEEeccC--CEEEEEe--------eCCHHHHHHHHHHc
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQ--SRVTVTG--------YVDPNKVLKKVKST 50 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~--~~v~v~~--------~~~~~~i~~~i~~~ 50 (115)
+..+++.|++++|+.+++.+... ..+.|.- .++..+|...|+..
T Consensus 698 a~~l~~~l~~~~gv~~v~~~~~~~~~~l~i~id~~k~~~~Gls~~~v~~~l~~~ 751 (1037)
T PRK10555 698 RNQLLALAAKNPELTRVRHNGLDDSPQLQIDIDQRKAQALGVSIDDINDTLQTA 751 (1037)
T ss_pred HHHHHHHHhcCCCeEEEecCCcCCCceEEEEECHHHHHHcCCCHHHHHHHHHHH
Confidence 45688999999999999988765 3455542 27888888888754
No 145
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=22.30 E-value=1.2e+02 Score=19.74 Aligned_cols=30 Identities=27% Similarity=0.308 Sum_probs=25.0
Q ss_pred EEEEeeCCHHHHHHHHHHcCCCceecCCCC
Q 033623 32 VTVTGYVDPNKVLKKVKSTGKRAEFWPYVP 61 (115)
Q Consensus 32 v~v~~~~~~~~i~~~i~~~G~~~~~~~~~~ 61 (115)
+.+.++.+...++++++..|.++++.+..+
T Consensus 115 vl~SgD~DF~p~v~~~~~~G~rv~v~~~~~ 144 (181)
T COG1432 115 VLFSGDGDFIPLVEAARDKGKRVEVAGIEP 144 (181)
T ss_pred EEEcCCccHHHHHHHHHHcCCEEEEEecCC
Confidence 345678888889999999999999988765
No 146
>PF07582 AP_endonuc_2_N: AP endonuclease family 2 C terminus; InterPro: IPR011418 DNA damaging agents such as the anti-tumour drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3' termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3' terminus of DNA strand breaks. AP endonucleases can be classified into two families based on sequence similarity []. This entry represents a highly-conserved sequence found at the C terminus of several apurinic/apyrimidinic (AP) endonucleases in a range of Gram-positive and Gram-negative bacteria. ; PDB: 3LMZ_A 2ZDS_D.
Probab=22.26 E-value=89 Score=16.36 Aligned_cols=17 Identities=6% Similarity=0.194 Sum_probs=11.7
Q ss_pred HHHHHHHHHHcCCCcee
Q 033623 40 PNKVLKKVKSTGKRAEF 56 (115)
Q Consensus 40 ~~~i~~~i~~~G~~~~~ 56 (115)
...++.+|+..||.--+
T Consensus 2 w~~i~~~L~~~GYdG~~ 18 (55)
T PF07582_consen 2 WKRIFSALREIGYDGWL 18 (55)
T ss_dssp HHHHHHHHHHTT--SEE
T ss_pred HHHHHHHHHHcCCCceE
Confidence 56789999999997443
No 147
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=22.14 E-value=59 Score=17.47 Aligned_cols=16 Identities=25% Similarity=0.623 Sum_probs=12.3
Q ss_pred CcHhHHHHHHHHHhCC
Q 033623 2 DCDGCERKVRNAVSSI 17 (115)
Q Consensus 2 ~C~~C~~~v~~~l~~~ 17 (115)
.|..|...+++.|...
T Consensus 38 ~CG~C~~~i~~il~~~ 53 (64)
T PRK10509 38 QCGKCIRAAREVMQDE 53 (64)
T ss_pred CccchHHHHHHHHHHH
Confidence 4888988888887543
No 148
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=21.68 E-value=72 Score=24.78 Aligned_cols=27 Identities=15% Similarity=0.213 Sum_probs=23.7
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeccCC
Q 033623 4 DGCERKVRNAVSSIRGAKSVEVNRKQS 30 (115)
Q Consensus 4 ~~C~~~v~~~l~~~~gv~~~~v~~~~~ 30 (115)
.+|-+-+|..+.+++||.++.+-...+
T Consensus 205 gGCFWg~e~~f~~~~GV~~t~~GYagG 231 (521)
T PRK14018 205 GGCFWGLEAYFQRIDGVVDAVSGYANG 231 (521)
T ss_pred cCCchhhHHHHccCCCEEEEEEeeCCC
Confidence 479999999999999999999877655
No 149
>PRK15367 type III secretion system protein SsaD; Provisional
Probab=21.63 E-value=2.2e+02 Score=21.37 Aligned_cols=18 Identities=28% Similarity=0.418 Sum_probs=11.2
Q ss_pred HHHHHHHhCCCCceEEEE
Q 033623 8 RKVRNAVSSIRGAKSVEV 25 (115)
Q Consensus 8 ~~v~~~l~~~~gv~~~~v 25 (115)
.+|+..|..++|...+++
T Consensus 241 ~~V~~lL~~vpGL~gW~v 258 (395)
T PRK15367 241 RKVQPLLADIPGLLHWQI 258 (395)
T ss_pred HHHHHHHHhCcCcceEEE
Confidence 466666666666665544
No 150
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=21.61 E-value=2.6e+02 Score=18.78 Aligned_cols=36 Identities=28% Similarity=0.473 Sum_probs=25.6
Q ss_pred HHHHHHhCCCCceEEEEeccCCEEEEEee---CCHHHHHH
Q 033623 9 KVRNAVSSIRGAKSVEVNRKQSRVTVTGY---VDPNKVLK 45 (115)
Q Consensus 9 ~v~~~l~~~~gv~~~~v~~~~~~v~v~~~---~~~~~i~~ 45 (115)
.+.+.|....|+ .+.+|..++.++|... .|+-.+.+
T Consensus 28 ~v~k~ie~~~~~-~~~iD~~~~~V~i~~~~~t~Dp~~~~k 66 (194)
T COG1094 28 EVKKAIEEKTGV-KLRIDSKTGSVTIRTTRKTEDPLALLK 66 (194)
T ss_pred cchHHHHhhcCe-EEEEECCCCeEEEEecCCCCChHHHHH
Confidence 456777776666 4899999999999753 46655544
No 151
>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=21.52 E-value=1.5e+02 Score=15.82 Aligned_cols=48 Identities=10% Similarity=0.039 Sum_probs=33.1
Q ss_pred CcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEe--eCCHHHHHHHHHHcCCCceecC
Q 033623 2 DCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTG--YVDPNKVLKKVKSTGKRAEFWP 58 (115)
Q Consensus 2 ~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~--~~~~~~i~~~i~~~G~~~~~~~ 58 (115)
.|+.=.-+++++|.+++- .+.+.|.. ......|...+++.|+......
T Consensus 8 ~CP~P~i~~k~~l~~l~~---------G~~l~V~~dd~~s~~di~~~~~~~g~~~~~~~ 57 (69)
T cd03423 8 RCPEPVMMLHKKVRKMKP---------GDTLLVLATDPSTTRDIPKFCTFLGHELLAQE 57 (69)
T ss_pred cCCHHHHHHHHHHHcCCC---------CCEEEEEeCCCchHHHHHHHHHHcCCEEEEEE
Confidence 577777888999988742 12334432 2567788889999999876443
No 152
>PF13721 SecD-TM1: SecD export protein N-terminal TM region
Probab=21.39 E-value=1.9e+02 Score=17.01 Aligned_cols=29 Identities=10% Similarity=0.139 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCCceEEEEeccCCEEEEEee
Q 033623 8 RKVRNAVSSIRGAKSVEVNRKQSRVTVTGY 37 (115)
Q Consensus 8 ~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~ 37 (115)
.+|++.|++ .||.-..+....+++.|...
T Consensus 49 ~~v~~~L~~-~~I~~k~i~~~~~~llirf~ 77 (101)
T PF13721_consen 49 FQVEQALKA-AGIAVKSIEQEGDSLLIRFD 77 (101)
T ss_pred HHHHHHHHH-CCCCcceEEeeCCEEEEEEC
Confidence 355666654 46655556666666666654
No 153
>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=21.37 E-value=1.4e+02 Score=15.53 Aligned_cols=48 Identities=15% Similarity=0.046 Sum_probs=32.3
Q ss_pred CcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHHcCCCceecC
Q 033623 2 DCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY--VDPNKVLKKVKSTGKRAEFWP 58 (115)
Q Consensus 2 ~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~--~~~~~i~~~i~~~G~~~~~~~ 58 (115)
.|+.=..+++++|.+++. .+.+.|..+ .....|...++..|+......
T Consensus 8 ~CP~Pl~~~~~~l~~l~~---------g~~l~v~~d~~~~~~~i~~~~~~~g~~~~~~~ 57 (69)
T cd00291 8 PCPLPVLKTKKALEKLKS---------GEVLEVLLDDPGAVEDIPAWAKETGHEVLEVE 57 (69)
T ss_pred cCCHHHHHHHHHHhcCCC---------CCEEEEEecCCcHHHHHHHHHHHcCCEEEEEE
Confidence 577777788888887643 234444433 457788888999999865443
No 154
>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=20.65 E-value=1.5e+02 Score=15.65 Aligned_cols=21 Identities=24% Similarity=0.177 Sum_probs=17.7
Q ss_pred CCCceEEEEeccCCEEEEEee
Q 033623 17 IRGAKSVEVNRKQSRVTVTGY 37 (115)
Q Consensus 17 ~~gv~~~~v~~~~~~v~v~~~ 37 (115)
-.++.++-+|..+++|.|+..
T Consensus 22 ~~~~~~WyvD~~tn~VVV~a~ 42 (62)
T PF02983_consen 22 PVAVTSWYVDPRTNKVVVTAD 42 (62)
T ss_dssp GGCEEEEEEECCCTEEEEEEE
T ss_pred CCCcceEEEeCCCCeEEEEEC
Confidence 357889999999999998754
No 155
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=20.55 E-value=1.2e+02 Score=16.09 Aligned_cols=19 Identities=16% Similarity=0.267 Sum_probs=16.7
Q ss_pred CCHHHHHHHHHHcCCCcee
Q 033623 38 VDPNKVLKKVKSTGKRAEF 56 (115)
Q Consensus 38 ~~~~~i~~~i~~~G~~~~~ 56 (115)
++.+++.+.|++.|+.++.
T Consensus 19 i~~~ei~~~L~~lg~~~~~ 37 (71)
T smart00874 19 LSAEEIEEILKRLGFEVEV 37 (71)
T ss_pred CCHHHHHHHHHHCCCeEEe
Confidence 6888999999999998865
No 156
>COG5561 Predicted metal-binding protein [Function unknown]
Probab=20.50 E-value=1.3e+02 Score=17.68 Aligned_cols=8 Identities=38% Similarity=0.605 Sum_probs=3.6
Q ss_pred cHhHHHHH
Q 033623 3 CDGCERKV 10 (115)
Q Consensus 3 C~~C~~~v 10 (115)
|++|++=.
T Consensus 7 CPG~v~Cf 14 (101)
T COG5561 7 CPGEVRCF 14 (101)
T ss_pred CCchHHHH
Confidence 55544333
No 157
>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.33 E-value=1.4e+02 Score=15.12 Aligned_cols=17 Identities=18% Similarity=0.319 Sum_probs=12.3
Q ss_pred HHHHHHhCCCCceEEEE
Q 033623 9 KVRNAVSSIRGAKSVEV 25 (115)
Q Consensus 9 ~v~~~l~~~~gv~~~~v 25 (115)
.+.+.|.+++||..+.+
T Consensus 55 ~~~~~L~~~~~v~~v~~ 71 (72)
T cd04874 55 ELVEELRSLPIVREVEI 71 (72)
T ss_pred HHHHHHhCCCCeEEEEe
Confidence 56677888888877654
No 158
>cd06482 ACD_HspB10 Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB10, also known as sperm outer dense fiber protein (ODFP), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB10 occurs exclusively in the axoneme of sperm cells and may have a cytoskeletal role.
Probab=20.25 E-value=1.2e+02 Score=17.34 Aligned_cols=22 Identities=27% Similarity=0.413 Sum_probs=16.8
Q ss_pred CCCCce--EEEEeccCCEEEEEee
Q 033623 16 SIRGAK--SVEVNRKQSRVTVTGY 37 (115)
Q Consensus 16 ~~~gv~--~~~v~~~~~~v~v~~~ 37 (115)
.++|+. +++|.+..+.++|.+.
T Consensus 15 dlPG~~kedI~V~v~~~~L~I~ge 38 (87)
T cd06482 15 DVCGFEPDQVKVKVKDGKVQVSAE 38 (87)
T ss_pred ECCCCCHHHeEEEEECCEEEEEEE
Confidence 357775 5778888899999886
No 159
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=20.20 E-value=2.3e+02 Score=18.45 Aligned_cols=44 Identities=23% Similarity=0.284 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCCceEEEEeccCCEEEEEee--CCHHHHHHHHHHcCC
Q 033623 7 ERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY--VDPNKVLKKVKSTGK 52 (115)
Q Consensus 7 ~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~--~~~~~i~~~i~~~G~ 52 (115)
+.+|-+.+... +.. |+.......+.|+|. -+..++++.|+...+
T Consensus 105 AKkIvK~IKd~-klK-Vqa~IQgd~vRVtgKkrDDLQ~viallk~~d~ 150 (160)
T PF04461_consen 105 AKKIVKLIKDS-KLK-VQAQIQGDQVRVTGKKRDDLQEVIALLKEQDL 150 (160)
T ss_dssp HHHHHHHHHHH---S-EEEEEETTEEEEEES-HHHHHHHHHHHHHS--
T ss_pred HHHHHHHHHhc-CCc-eeEEecCcEEEEecCCHHHHHHHHHHHHcccC
Confidence 34455554432 222 666677788888874 466667777766544
No 160
>PF13383 Methyltransf_22: Methyltransferase domain
Probab=20.11 E-value=1.6e+02 Score=20.32 Aligned_cols=50 Identities=20% Similarity=0.322 Sum_probs=28.4
Q ss_pred CCcHhHHHHHHHHHhCCCCceEEEEeccCCEEEEEee----CCHHHHHHHHHHcCCCceecC
Q 033623 1 MDCDGCERKVRNAVSSIRGAKSVEVNRKQSRVTVTGY----VDPNKVLKKVKSTGKRAEFWP 58 (115)
Q Consensus 1 m~C~~C~~~v~~~l~~~~gv~~~~v~~~~~~v~v~~~----~~~~~i~~~i~~~G~~~~~~~ 58 (115)
|+|++|...+-..+.. .++..+ -+.|-+. ....++++.|++.||..--..
T Consensus 173 iDIEG~Ew~~L~~~l~-~~~~Qi-------~iEiH~~~~~~~~~~~~l~~l~~~gfr~F~~e 226 (242)
T PF13383_consen 173 IDIEGAEWTVLEPLLE-SGVCQI-------LIEIHGWPSEHREWYKLLQELEKAGFRLFNVE 226 (242)
T ss_pred EEcCccHHHHHHHHHh-cCCcEE-------EEEEEeCccchhHHHHHHHHHHHCCcEEEEec
Confidence 5788888888666643 344211 1122222 123468889999998654443
Done!