Query 035968
Match_columns 112
No_of_seqs 154 out of 1323
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 08:05:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035968.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035968hhsearch_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 99.6 8.3E-15 1.8E-19 86.9 8.0 57 7-63 2-62 (62)
2 COG2608 CopZ Copper chaperone 99.5 6.3E-14 1.4E-18 86.0 9.0 67 1-67 1-70 (71)
3 KOG1603 Copper chaperone [Inor 99.5 4.3E-13 9.4E-18 82.6 8.8 66 2-67 4-70 (73)
4 KOG4656 Copper chaperone for s 99.2 1.1E-10 2.5E-15 84.5 8.1 70 4-73 8-77 (247)
5 PRK10671 copA copper exporting 98.8 1.4E-08 3E-13 86.3 8.2 66 1-68 1-67 (834)
6 PLN02957 copper, zinc superoxi 98.8 1.1E-07 2.3E-12 70.5 10.1 70 4-73 7-76 (238)
7 COG2217 ZntA Cation transport 98.4 9.6E-07 2.1E-11 74.3 7.8 62 4-66 3-69 (713)
8 TIGR00003 copper ion binding p 98.2 3E-05 6.5E-10 42.8 8.7 63 1-64 1-67 (68)
9 KOG0207 Cation transport ATPas 97.7 7.8E-05 1.7E-09 63.9 6.4 65 9-73 1-67 (951)
10 KOG0207 Cation transport ATPas 97.7 0.00014 2.9E-09 62.5 7.5 68 3-70 146-217 (951)
11 PRK10671 copA copper exporting 97.7 0.00021 4.5E-09 61.1 8.3 64 5-68 101-165 (834)
12 PRK11033 zntA zinc/cadmium/mer 97.3 0.0013 2.8E-08 55.9 8.1 64 4-67 54-119 (741)
13 COG1888 Uncharacterized protei 93.8 0.34 7.4E-06 31.1 5.9 49 19-67 23-79 (97)
14 TIGR02052 MerP mercuric transp 93.7 0.83 1.8E-05 27.0 9.3 61 6-66 26-90 (92)
15 PF02680 DUF211: Uncharacteriz 93.4 0.26 5.7E-06 31.8 4.9 50 18-67 20-77 (95)
16 PRK14054 methionine sulfoxide 92.9 0.43 9.3E-06 33.9 5.9 54 2-60 3-78 (172)
17 PRK13748 putative mercuric red 91.2 1.9 4.1E-05 35.2 8.6 61 9-69 7-69 (561)
18 PF01206 TusA: Sulfurtransfera 91.0 1.5 3.4E-05 25.8 6.1 52 7-67 3-57 (70)
19 cd00371 HMA Heavy-metal-associ 88.8 1.7 3.7E-05 20.9 7.1 53 9-61 5-59 (63)
20 PRK11018 hypothetical protein; 87.4 4.8 0.0001 24.6 7.3 52 6-66 10-64 (78)
21 PRK05528 methionine sulfoxide 87.3 2.9 6.2E-05 29.3 6.1 46 14-59 8-70 (156)
22 PF13732 DUF4162: Domain of un 87.3 3 6.5E-05 25.2 5.6 47 24-72 26-74 (84)
23 PRK10553 assembly protein for 84.8 6 0.00013 25.0 6.1 46 15-60 17-63 (87)
24 COG0225 MsrA Peptide methionin 84.4 3.8 8.2E-05 29.3 5.5 54 2-60 6-81 (174)
25 PRK00058 methionine sulfoxide 84.1 4.1 9E-05 30.0 5.8 47 14-60 52-120 (213)
26 PRK13014 methionine sulfoxide 83.6 2.9 6.4E-05 30.1 4.8 47 14-60 15-83 (186)
27 cd03421 SirA_like_N SirA_like_ 83.3 6.9 0.00015 22.8 6.3 48 10-67 6-55 (67)
28 PF01883 DUF59: Domain of unkn 82.3 3 6.4E-05 24.7 3.8 31 5-35 36-72 (72)
29 PF03927 NapD: NapD protein; 80.8 11 0.00023 23.2 6.3 44 17-61 17-61 (79)
30 cd03423 SirA SirA (also known 78.7 11 0.00024 22.2 6.5 49 10-67 6-56 (69)
31 PRK00299 sulfur transfer prote 77.6 14 0.0003 22.7 7.4 54 4-66 9-65 (81)
32 cd03420 SirA_RHOD_Pry_redox Si 75.1 15 0.00031 21.7 6.5 49 10-67 6-56 (69)
33 PF01625 PMSR: Peptide methion 74.8 18 0.00039 25.1 6.4 47 14-60 7-75 (155)
34 cd03422 YedF YedF is a bacteri 74.1 16 0.00034 21.6 6.4 49 10-67 6-56 (69)
35 PRK05550 bifunctional methioni 73.7 12 0.00026 28.7 5.7 46 14-59 134-201 (283)
36 cd02410 archeal_CPSF_KH The ar 71.8 22 0.00047 24.7 6.1 56 16-71 54-116 (145)
37 cd00291 SirA_YedF_YeeD SirA, Y 68.1 21 0.00045 20.5 6.5 49 10-67 6-56 (69)
38 TIGR03527 selenium_YedF seleni 67.6 31 0.00068 24.8 6.5 50 10-68 5-56 (194)
39 COG3062 NapD Uncharacterized p 64.0 31 0.00068 22.2 5.2 47 14-61 17-64 (94)
40 PF04972 BON: BON domain; Int 63.6 6.9 0.00015 22.3 2.1 30 18-48 2-34 (64)
41 cd04908 ACT_Bt0572_1 N-termina 63.6 26 0.00056 20.0 5.7 52 14-65 12-65 (66)
42 PF09580 Spore_YhcN_YlaJ: Spor 62.5 32 0.00069 23.8 5.6 31 16-46 76-106 (177)
43 PF05046 Img2: Mitochondrial l 60.8 38 0.00083 21.1 6.7 55 7-62 32-87 (87)
44 PRK11023 outer membrane lipopr 54.0 40 0.00087 24.0 5.0 44 15-58 49-95 (191)
45 COG4004 Uncharacterized protei 53.8 30 0.00065 22.3 3.8 21 26-46 38-58 (96)
46 TIGR03406 FeS_long_SufT probab 53.6 18 0.00039 25.7 3.1 33 5-37 115-153 (174)
47 cd04888 ACT_PheB-BS C-terminal 53.3 17 0.00036 21.0 2.6 28 8-35 46-74 (76)
48 PF00539 Tat: Transactivating 52.7 7.6 0.00016 23.6 1.0 17 84-100 28-44 (68)
49 PRK14018 trifunctional thiored 52.7 43 0.00094 27.9 5.6 47 14-60 205-272 (521)
50 TIGR02945 SUF_assoc FeS assemb 52.3 18 0.00039 22.6 2.7 21 18-38 58-78 (99)
51 PRK09577 multidrug efflux prot 51.6 52 0.0011 29.5 6.3 47 17-63 158-212 (1032)
52 COG0425 SirA Predicted redox p 51.2 55 0.0012 20.0 7.1 48 5-61 6-56 (78)
53 TIGR00489 aEF-1_beta translati 50.8 19 0.0004 22.8 2.6 22 15-36 62-83 (88)
54 PF13740 ACT_6: ACT domain; PD 49.8 53 0.0012 19.4 5.2 57 4-60 2-65 (76)
55 PRK10555 aminoglycoside/multid 48.5 62 0.0013 29.0 6.3 44 17-60 159-210 (1037)
56 cd06167 LabA_like LabA_like pr 48.1 33 0.00071 22.6 3.7 29 42-70 104-132 (149)
57 cd04883 ACT_AcuB C-terminal AC 47.8 51 0.0011 18.7 6.1 51 14-64 12-68 (72)
58 TIGR01676 GLDHase galactonolac 46.9 39 0.00085 28.3 4.5 39 24-64 110-148 (541)
59 PRK11023 outer membrane lipopr 46.4 68 0.0015 22.8 5.2 40 15-54 127-168 (191)
60 TIGR02898 spore_YhcN_YlaJ spor 45.9 1E+02 0.0022 21.6 5.9 32 15-46 54-85 (158)
61 KOG4034 Uncharacterized conser 44.5 55 0.0012 23.2 4.3 56 6-62 113-169 (169)
62 cd04909 ACT_PDH-BS C-terminal 43.6 61 0.0013 18.3 4.8 51 14-64 12-69 (69)
63 PRK06418 transcription elongat 43.3 1.2E+02 0.0025 21.5 6.6 68 6-73 9-102 (166)
64 PF02983 Pro_Al_protease: Alph 42.2 69 0.0015 18.6 4.6 21 27-47 22-42 (62)
65 PRK00435 ef1B elongation facto 41.0 32 0.00069 21.8 2.5 23 14-36 61-83 (88)
66 KOG3411 40S ribosomal protein 40.9 35 0.00076 23.4 2.8 44 14-60 97-141 (143)
67 TIGR00288 conserved hypothetic 40.4 47 0.001 23.3 3.6 31 41-71 109-139 (160)
68 PRK10509 bacterioferritin-asso 40.1 19 0.00041 21.3 1.3 21 7-27 33-53 (64)
69 PRK15127 multidrug efflux syst 40.0 96 0.0021 27.9 6.2 43 18-60 160-210 (1049)
70 PF00352 TBP: Transcription fa 39.7 55 0.0012 20.0 3.5 23 37-59 55-77 (86)
71 PF08712 Nfu_N: Scaffold prote 39.1 88 0.0019 19.4 4.4 41 18-60 37-79 (87)
72 TIGR00915 2A0602 The (Largely 39.0 96 0.0021 27.8 6.0 43 18-60 160-210 (1044)
73 cd04882 ACT_Bt0572_2 C-termina 38.9 69 0.0015 17.5 6.0 50 15-64 11-64 (65)
74 TIGR00401 msrA methionine-S-su 38.7 26 0.00056 24.2 2.0 46 14-59 7-74 (149)
75 PF03958 Secretin_N: Bacterial 38.2 84 0.0018 18.4 4.2 29 32-60 47-76 (82)
76 PF13192 Thioredoxin_3: Thiore 37.8 62 0.0013 19.0 3.4 11 9-19 6-16 (76)
77 COG2177 FtsX Cell division pro 37.7 64 0.0014 24.8 4.2 45 5-62 63-108 (297)
78 TIGR03675 arCOG00543 arCOG0054 37.0 1.2E+02 0.0025 25.9 5.9 59 14-72 69-134 (630)
79 PF01936 NYN: NYN domain; Int 36.7 33 0.00071 22.2 2.2 29 41-69 99-127 (146)
80 PF11491 DUF3213: Protein of u 36.6 55 0.0012 20.7 3.0 47 18-64 14-63 (88)
81 PRK09579 multidrug efflux prot 36.1 1.2E+02 0.0025 27.3 6.0 44 17-60 158-210 (1017)
82 COG2092 EFB1 Translation elong 35.7 37 0.00081 21.6 2.2 23 14-36 61-83 (88)
83 PF13291 ACT_4: ACT domain; PD 35.3 86 0.0019 18.4 3.8 28 7-34 52-79 (80)
84 TIGR00914 2A0601 heavy metal e 35.2 64 0.0014 28.9 4.3 46 15-60 698-753 (1051)
85 COG2151 PaaD Predicted metal-s 35.2 45 0.00098 22.0 2.6 31 7-37 53-89 (111)
86 TIGR01709 typeII_sec_gspL gene 35.1 1.1E+02 0.0023 23.9 5.2 50 19-69 314-369 (384)
87 PRK10614 multidrug efflux syst 34.6 1.2E+02 0.0026 27.2 5.9 45 17-61 159-212 (1025)
88 PRK10568 periplasmic protein; 34.3 1.2E+02 0.0025 21.8 4.9 38 12-49 57-96 (203)
89 PRK11198 LysM domain/BON super 34.3 1.2E+02 0.0026 20.6 4.7 47 16-62 27-75 (147)
90 PRK10503 multidrug efflux syst 33.9 1.2E+02 0.0026 27.2 5.8 44 18-61 169-221 (1040)
91 TIGR01679 bact_FAD_ox FAD-link 33.7 84 0.0018 25.0 4.5 31 34-64 65-95 (419)
92 PF04805 Pox_E10: E10-like pro 33.6 37 0.0008 20.6 1.8 27 10-36 15-41 (70)
93 COG1432 Uncharacterized conser 33.5 68 0.0015 22.6 3.6 33 40-72 113-145 (181)
94 PF03434 DUF276: DUF276 ; Int 33.5 65 0.0014 24.5 3.5 50 17-66 89-150 (291)
95 PF00873 ACR_tran: AcrB/AcrD/A 33.3 93 0.002 27.7 5.0 47 14-60 686-742 (1021)
96 COG0277 GlcD FAD/FMN-containin 32.9 53 0.0012 25.7 3.2 36 27-64 84-119 (459)
97 PF09158 MotCF: Bacteriophage 32.3 1.5E+02 0.0032 19.4 4.8 39 27-66 40-78 (103)
98 TIGR02830 spore_III_AG stage I 32.1 46 0.001 24.0 2.5 29 16-44 62-92 (186)
99 PF01514 YscJ_FliF: Secretory 32.0 51 0.0011 23.8 2.7 21 17-37 117-137 (206)
100 PF10006 DUF2249: Uncharacteri 32.0 1.1E+02 0.0023 17.8 5.7 45 18-71 14-60 (69)
101 PRK11282 glcE glycolate oxidas 31.9 86 0.0019 24.7 4.2 37 25-63 44-80 (352)
102 cd04877 ACT_TyrR N-terminal AC 31.3 52 0.0011 19.2 2.3 20 15-34 49-68 (74)
103 cd00292 EF1B Elongation factor 31.2 56 0.0012 20.5 2.5 22 15-36 62-83 (88)
104 PF08777 RRM_3: RNA binding mo 31.2 1.5E+02 0.0032 19.0 6.1 54 7-60 4-60 (105)
105 COG0841 AcrB Cation/multidrug 30.9 1.8E+02 0.0039 26.4 6.3 47 17-63 157-212 (1009)
106 TIGR00334 5S_RNA_mat_M5 ribonu 30.5 90 0.002 22.3 3.7 48 14-62 57-110 (174)
107 TIGR01678 FAD_lactone_ox sugar 29.5 1.1E+02 0.0023 24.7 4.5 38 26-65 65-102 (438)
108 PF08478 POTRA_1: POTRA domain 29.4 77 0.0017 17.9 2.8 28 17-44 36-64 (69)
109 PRK11589 gcvR glycine cleavage 29.3 1.6E+02 0.0034 21.1 4.8 62 1-62 5-73 (190)
110 PRK10638 glutaredoxin 3; Provi 29.1 1.3E+02 0.0028 17.8 4.5 34 1-37 1-34 (83)
111 PF13193 AMP-binding_C: AMP-bi 28.6 64 0.0014 18.6 2.4 40 20-59 2-46 (73)
112 PF10934 DUF2634: Protein of u 28.4 1.1E+02 0.0024 19.9 3.6 33 15-47 69-104 (112)
113 TIGR01677 pln_FAD_oxido plant- 27.8 1.1E+02 0.0023 25.7 4.2 32 33-64 92-123 (557)
114 KOG4730 D-arabinono-1, 4-lacto 27.5 77 0.0017 26.3 3.3 32 33-64 105-136 (518)
115 PRK10614 multidrug efflux syst 27.3 1E+02 0.0022 27.7 4.2 46 15-60 675-730 (1025)
116 TIGR02159 PA_CoA_Oxy4 phenylac 27.3 81 0.0018 21.7 3.0 55 6-62 28-88 (146)
117 cd04879 ACT_3PGDH-like ACT_3PG 27.2 80 0.0017 17.2 2.6 18 17-34 52-69 (71)
118 PF04312 DUF460: Protein of un 26.8 2.2E+02 0.0047 19.6 6.5 38 32-69 45-84 (138)
119 COG1782 Predicted metal-depend 26.7 2.3E+02 0.005 24.1 5.8 59 15-73 76-141 (637)
120 PF00736 EF1_GNE: EF-1 guanine 26.7 74 0.0016 20.0 2.5 23 14-36 61-84 (89)
121 PLN02465 L-galactono-1,4-lacto 26.5 1.2E+02 0.0026 25.6 4.4 38 26-65 147-184 (573)
122 COG4669 EscJ Type III secretor 26.1 70 0.0015 24.1 2.6 20 17-36 111-130 (246)
123 PF07837 FTCD_N: Formiminotran 26.0 2.4E+02 0.0051 20.2 5.2 42 17-58 18-61 (178)
124 KOG3432 Vacuolar H+-ATPase V1 25.7 1.1E+02 0.0024 20.4 3.2 36 27-62 24-59 (121)
125 PRK11200 grxA glutaredoxin 1; 25.7 1.5E+02 0.0033 17.5 4.9 32 6-38 4-39 (85)
126 PF10892 DUF2688: Protein of u 25.7 40 0.00086 19.7 1.0 53 1-57 1-54 (60)
127 PF01565 FAD_binding_4: FAD bi 25.6 1.2E+02 0.0026 19.5 3.6 32 33-64 57-88 (139)
128 PF14056 DUF4250: Domain of un 25.5 72 0.0016 18.4 2.1 18 47-64 31-48 (55)
129 PF01963 TraB: TraB family; I 25.4 2E+02 0.0043 20.6 4.9 28 40-67 229-259 (259)
130 TIGR01158 SUI1_rel translation 24.9 1.2E+02 0.0025 19.5 3.2 39 28-66 23-70 (101)
131 PF14492 EFG_II: Elongation Fa 24.8 1.6E+02 0.0035 17.4 4.9 52 14-65 15-72 (75)
132 cd00652 TBP_TLF TATA box bindi 24.6 1.1E+02 0.0023 21.6 3.3 24 37-60 145-168 (174)
133 PF15643 Tox-PL-2: Papain fold 24.5 64 0.0014 21.0 1.9 17 10-26 18-34 (100)
134 cd04516 TBP_eukaryotes eukaryo 24.4 1.1E+02 0.0024 21.6 3.3 24 37-60 144-167 (174)
135 TIGR02544 III_secr_YscJ type I 24.1 86 0.0019 22.5 2.7 21 17-37 109-129 (193)
136 PF08002 DUF1697: Protein of u 23.9 2.3E+02 0.005 19.0 7.2 50 17-67 21-75 (137)
137 PRK07334 threonine dehydratase 23.8 3.7E+02 0.0079 21.2 6.9 55 13-67 336-402 (403)
138 PRK10503 multidrug efflux syst 23.5 1.4E+02 0.003 26.9 4.4 45 16-60 690-744 (1040)
139 COG1094 Predicted RNA-binding 23.4 2.3E+02 0.0051 20.6 4.8 36 19-55 28-66 (194)
140 TIGR00915 2A0602 The (Largely 23.4 1.4E+02 0.003 26.9 4.4 46 15-60 697-752 (1044)
141 PRK15348 type III secretion sy 23.2 91 0.002 23.5 2.8 21 17-37 109-129 (249)
142 cd04906 ACT_ThrD-I_1 First of 22.8 1.8E+02 0.004 17.4 6.7 57 14-71 12-76 (85)
143 cd04517 TLF TBP-like factors ( 22.7 1.3E+02 0.0028 21.2 3.3 24 37-60 145-168 (174)
144 PRK11670 antiporter inner memb 22.7 2.4E+02 0.0051 22.2 5.2 52 17-68 67-143 (369)
145 TIGR00268 conserved hypothetic 22.7 3.1E+02 0.0068 20.0 6.0 50 17-67 187-244 (252)
146 PRK06719 precorrin-2 dehydroge 22.6 2.1E+02 0.0045 19.5 4.4 38 33-70 7-45 (157)
147 TIGR00914 2A0601 heavy metal e 22.4 2.6E+02 0.0056 25.2 5.8 43 19-61 170-221 (1051)
148 cd04903 ACT_LSD C-terminal ACT 22.4 1.1E+02 0.0024 16.6 2.6 18 17-34 52-69 (71)
149 TIGR02190 GlrX-dom Glutaredoxi 22.0 1.8E+02 0.0039 17.0 4.5 31 5-37 10-40 (79)
150 COG0602 NrdG Organic radical a 21.9 1.5E+02 0.0033 21.4 3.7 33 38-70 71-108 (212)
151 cd04885 ACT_ThrD-I Tandem C-te 21.8 85 0.0018 18.0 2.0 17 48-64 50-66 (68)
152 cd04518 TBP_archaea archaeal T 21.7 1.3E+02 0.0029 21.2 3.3 24 37-60 144-167 (174)
153 PF12693 GspL_C: GspL periplas 21.4 2.6E+02 0.0056 18.6 4.7 48 19-67 86-139 (157)
154 cd02973 TRX_GRX_like Thioredox 21.4 1.6E+02 0.0035 16.2 3.3 18 9-27 7-24 (67)
155 cd04901 ACT_3PGDH C-terminal A 21.2 1.2E+02 0.0027 16.8 2.6 17 19-35 52-68 (69)
156 cd04874 ACT_Af1403 N-terminal 21.1 1.2E+02 0.0026 16.6 2.5 20 16-35 52-71 (72)
157 PRK04435 hypothetical protein; 20.9 2.5E+02 0.0053 19.0 4.4 20 16-35 124-143 (147)
158 PHA03005 sulfhydryl oxidase; P 20.9 81 0.0018 20.3 1.8 26 10-35 40-65 (96)
159 PF04324 Fer2_BFD: BFD-like [2 20.9 42 0.00091 18.6 0.5 18 9-26 36-53 (55)
160 cd03029 GRX_hybridPRX5 Glutare 20.6 1.8E+02 0.0039 16.5 4.6 32 5-38 3-34 (72)
161 TIGR03143 AhpF_homolog putativ 20.6 4.9E+02 0.011 21.4 7.1 23 9-31 484-509 (555)
162 COG1365 Predicted ATPase (PP-l 20.4 2.3E+02 0.005 21.3 4.3 53 12-64 134-204 (255)
163 PRK05412 putative nucleotide-b 20.3 3.1E+02 0.0067 19.4 4.8 54 6-62 95-150 (161)
164 PRK10555 aminoglycoside/multid 20.3 1.7E+02 0.0038 26.3 4.4 46 15-60 696-751 (1037)
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=99.60 E-value=8.3e-15 Score=86.91 Aligned_cols=57 Identities=33% Similarity=0.476 Sum_probs=53.1
Q ss_pred Eee-cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee---CCHHHHHHHHHhcCCc
Q 035968 7 VSV-KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD---ADPVKIIKKVREFRKS 63 (112)
Q Consensus 7 ~~v-gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~---~~~~~i~~~i~k~G~~ 63 (112)
|.+ ||+|++|+++|+++|.+++||.++.+|+.+++++|.++ .++++|.++|+++||+
T Consensus 2 ~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 2 FKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGYE 62 (62)
T ss_dssp EEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTSE
T ss_pred EEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCcC
Confidence 566 99999999999999999999999999999999999987 4569999999999984
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.55 E-value=6.3e-14 Score=86.03 Aligned_cols=67 Identities=27% Similarity=0.362 Sum_probs=57.4
Q ss_pred CceeEEEeecccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee---CCHHHHHHHHHhcCCceEEe
Q 035968 1 MAKKTIVSVKLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD---ADPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 1 m~~~~~~~vgm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~---~~~~~i~~~i~k~G~~~~~~ 67 (112)
||+..+...||+|++|+.+|+++|.+++||.++++|+..+++.|..+ ++.++|..+|.++||.+..+
T Consensus 1 ~~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~~ 70 (71)
T COG2608 1 MMKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEEI 70 (71)
T ss_pred CceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeeec
Confidence 55544444499999999999999999999999999999988777754 69999999999999988653
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.48 E-value=4.3e-13 Score=82.63 Aligned_cols=66 Identities=38% Similarity=0.651 Sum_probs=60.7
Q ss_pred ceeEEEeecccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhcC-CceEEe
Q 035968 2 AKKTIVSVKLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGDADPVKIIKKVREFR-KSAAIE 67 (112)
Q Consensus 2 ~~~~~~~vgm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G-~~~~~~ 67 (112)
++..+++++|+|.+|..+|++.|+.++||.++++|..+++++|.|++++..|++.|++.| .+..++
T Consensus 4 ~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~ 70 (73)
T KOG1603|consen 4 IKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELW 70 (73)
T ss_pred ccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEe
Confidence 456788899999999999999999999999999999999999999999999999999987 666554
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.18 E-value=1.1e-10 Score=84.49 Aligned_cols=70 Identities=21% Similarity=0.416 Sum_probs=65.9
Q ss_pred eEEEeecccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhcCCceEEecCCCCc
Q 035968 4 KTIVSVKLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGDADPVKIIKKVREFRKSAAIESIGPPK 73 (112)
Q Consensus 4 ~~~~~vgm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~~~~~~~~~~~ 73 (112)
++.|.+.|+|++|++.|++.|..++||.+|++|++.+.|.|.+...+.+|...|+.+|+++.+...+-++
T Consensus 8 ~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G~ps 77 (247)
T KOG4656|consen 8 EAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAGKPS 77 (247)
T ss_pred eEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCCchh
Confidence 4688999999999999999999999999999999999999999999999999999999999998876654
No 5
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.83 E-value=1.4e-08 Score=86.27 Aligned_cols=66 Identities=15% Similarity=0.315 Sum_probs=59.5
Q ss_pred CceeEEEee-cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhcCCceEEec
Q 035968 1 MAKKTIVSV-KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGDADPVKIIKKVREFRKSAAIES 68 (112)
Q Consensus 1 m~~~~~~~v-gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~~~~~~ 68 (112)
||+++.+.+ ||+|++|+.+|+++|++++||..+.+|+. +.+|.+..+.+.+...+++.||.+.+.+
T Consensus 1 ~~~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 1 MSQTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred CCeEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 788888998 99999999999999999999999999994 5566677889999999999999998764
No 6
>PLN02957 copper, zinc superoxide dismutase
Probab=98.76 E-value=1.1e-07 Score=70.51 Aligned_cols=70 Identities=23% Similarity=0.395 Sum_probs=62.8
Q ss_pred eEEEeecccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhcCCceEEecCCCCc
Q 035968 4 KTIVSVKLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGDADPVKIIKKVREFRKSAAIESIGPPK 73 (112)
Q Consensus 4 ~~~~~vgm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~~~~~~~~~~~ 73 (112)
++.+.++|+|..|+.+|+++|.+++||.++.+|+..++++|.+..+...+...+++.||.++++...+.+
T Consensus 7 ~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 7 LTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQGDPE 76 (238)
T ss_pred EEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCCCcc
Confidence 4567779999999999999999999999999999999999998788899999999999999888765543
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.42 E-value=9.6e-07 Score=74.28 Aligned_cols=62 Identities=27% Similarity=0.484 Sum_probs=55.8
Q ss_pred eEEEee-cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee---CC-HHHHHHHHHhcCCceEE
Q 035968 4 KTIVSV-KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD---AD-PVKIIKKVREFRKSAAI 66 (112)
Q Consensus 4 ~~~~~v-gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~---~~-~~~i~~~i~k~G~~~~~ 66 (112)
+..+.+ ||+|..|+++|+ +|++++||..+.+|+.++++.|.++ .+ .+.+...+++.||.+..
T Consensus 3 ~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 3 ETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred eeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 455676 999999999999 9999999999999999999999865 45 78999999999998876
No 8
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=98.21 E-value=3e-05 Score=42.82 Aligned_cols=63 Identities=25% Similarity=0.405 Sum_probs=51.5
Q ss_pred CceeEEEee-cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee---CCHHHHHHHHHhcCCce
Q 035968 1 MAKKTIVSV-KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD---ADPVKIIKKVREFRKSA 64 (112)
Q Consensus 1 m~~~~~~~v-gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~---~~~~~i~~~i~k~G~~~ 64 (112)
||+. .+.+ +++|..|...+++.+...+++....+++..+.+.+..+ .+...+...+...|+.+
T Consensus 1 ~~~~-~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 1 KQKF-TVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYEV 67 (68)
T ss_pred CcEE-EEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCCc
Confidence 5654 4566 99999999999999999999999999999999888753 46677777777777753
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.74 E-value=7.8e-05 Score=63.87 Aligned_cols=65 Identities=18% Similarity=0.309 Sum_probs=59.4
Q ss_pred ecccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee--CCHHHHHHHHHhcCCceEEecCCCCc
Q 035968 9 VKLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD--ADPVKIIKKVREFRKSAAIESIGPPK 73 (112)
Q Consensus 9 vgm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~--~~~~~i~~~i~k~G~~~~~~~~~~~~ 73 (112)
.||+|..|.+.|++++...+||.++.+++.+++.+|.++ .+++.|.+.++..||++.+.+.....
T Consensus 1 ~gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ied~gf~~~~~~~~~~~ 67 (951)
T KOG0207|consen 1 KGMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIEDMGFEASLLSDSEIT 67 (951)
T ss_pred CCccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhhcccceeeecccCccc
Confidence 389999999999999999999999999999999999876 79999999999999999998765543
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.71 E-value=0.00014 Score=62.45 Aligned_cols=68 Identities=26% Similarity=0.512 Sum_probs=60.9
Q ss_pred eeEEEee-cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee---CCHHHHHHHHHhcCCceEEecCC
Q 035968 3 KKTIVSV-KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD---ADPVKIIKKVREFRKSAAIESIG 70 (112)
Q Consensus 3 ~~~~~~v-gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~---~~~~~i~~~i~k~G~~~~~~~~~ 70 (112)
++++|.+ ||.|.+|..+|++.|.+++||.++.++..++++.|..+ ..+-++.+.|+..|+.+......
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~~~ 217 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRPYG 217 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeeecc
Confidence 3567787 99999999999999999999999999999999999875 68899999999999988776543
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.68 E-value=0.00021 Score=61.10 Aligned_cols=64 Identities=19% Similarity=0.382 Sum_probs=55.9
Q ss_pred EEEee-cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhcCCceEEec
Q 035968 5 TIVSV-KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGDADPVKIIKKVREFRKSAAIES 68 (112)
Q Consensus 5 ~~~~v-gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~~~~~~ 68 (112)
+.+.+ ||+|.+|+.+|++.|..++||.++.+++.++++.+.+..++..+.+.+.+.||.+.+..
T Consensus 101 ~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~~~ 165 (834)
T PRK10671 101 QQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEAIE 165 (834)
T ss_pred EEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCccccc
Confidence 34656 99999999999999999999999999999999888766788889899999999876543
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.30 E-value=0.0013 Score=55.86 Aligned_cols=64 Identities=19% Similarity=0.231 Sum_probs=52.5
Q ss_pred eEEEee-cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEeeC-CHHHHHHHHHhcCCceEEe
Q 035968 4 KTIVSV-KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGDA-DPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 4 ~~~~~v-gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~~-~~~~i~~~i~k~G~~~~~~ 67 (112)
+..+.+ ||+|.+|+.++++.+...+||.++.+++.++++.+..+. ..+.+...++..||.+...
T Consensus 54 r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~~~ 119 (741)
T PRK11033 54 RYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLRDE 119 (741)
T ss_pred eEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccccccc
Confidence 345666 999999999999999999999999999999998887541 2267778888899977543
No 13
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=93.83 E-value=0.34 Score=31.11 Aligned_cols=49 Identities=22% Similarity=0.288 Sum_probs=36.0
Q ss_pred HHHHHHHccCCccEEEE-----ec--CCCEEEEEee-CCHHHHHHHHHhcCCceEEe
Q 035968 19 KVMKLIAKLEGITSIVI-----DP--SKNTVTVIGD-ADPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 19 kI~k~L~~~~GV~~v~v-----d~--~~~~v~V~~~-~~~~~i~~~i~k~G~~~~~~ 67 (112)
-+-+.|.+++||..|.+ |. .+=+++|.|+ ++.++|.+.|++.|.-.+.+
T Consensus 23 e~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHSi 79 (97)
T COG1888 23 ELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHSI 79 (97)
T ss_pred HHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeeeh
Confidence 34456788888876543 33 3445567775 89999999999999877765
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=93.70 E-value=0.83 Score=26.99 Aligned_cols=61 Identities=13% Similarity=0.285 Sum_probs=45.5
Q ss_pred EEee-cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee---CCHHHHHHHHHhcCCceEE
Q 035968 6 IVSV-KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD---ADPVKIIKKVREFRKSAAI 66 (112)
Q Consensus 6 ~~~v-gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~---~~~~~i~~~i~k~G~~~~~ 66 (112)
.+.+ ++.|..|...++..+...+|+....++.......+... .+...+...+...|+..++
T Consensus 26 ~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 26 TLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred EEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 3445 89999999999999999999888888888877666521 3555565666677776543
No 15
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=93.37 E-value=0.26 Score=31.79 Aligned_cols=50 Identities=24% Similarity=0.349 Sum_probs=35.2
Q ss_pred HHHHHHHHccCCccEEEE-----ecCCCEE--EEEee-CCHHHHHHHHHhcCCceEEe
Q 035968 18 QKVMKLIAKLEGITSIVI-----DPSKNTV--TVIGD-ADPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 18 ~kI~k~L~~~~GV~~v~v-----d~~~~~v--~V~~~-~~~~~i~~~i~k~G~~~~~~ 67 (112)
-.+-++|.+++||..|.+ |..+..+ +|+|+ ++.+.|.++|++.|.-++.+
T Consensus 20 ~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHSI 77 (95)
T PF02680_consen 20 VELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHSI 77 (95)
T ss_dssp HHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEEE
T ss_pred HHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEee
Confidence 355678999999887654 3444444 45676 89999999999999877665
No 16
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=92.89 E-value=0.43 Score=33.94 Aligned_cols=54 Identities=9% Similarity=0.159 Sum_probs=42.1
Q ss_pred ceeEEEeecccChhHHHHHHHHHHccCCccEEEEecCCCE-------------------EEEEee---CCHHHHHHHHHh
Q 035968 2 AKKTIVSVKLLCLKCRQKVMKLIAKLEGITSIVIDPSKNT-------------------VTVIGD---ADPVKIIKKVRE 59 (112)
Q Consensus 2 ~~~~~~~vgm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~-------------------v~V~~~---~~~~~i~~~i~k 59 (112)
|++++|- +||-+-++..+.+++||.++.+-..++. |.|..| ++.++|++...+
T Consensus 3 ~~~a~fa-----gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~~ 77 (172)
T PRK14054 3 METAVLA-----GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFFQ 77 (172)
T ss_pred ceEEEEE-----cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHHH
Confidence 4555555 7888889999999999999998876665 667765 688888887765
Q ss_pred c
Q 035968 60 F 60 (112)
Q Consensus 60 ~ 60 (112)
.
T Consensus 78 ~ 78 (172)
T PRK14054 78 I 78 (172)
T ss_pred h
Confidence 4
No 17
>PRK13748 putative mercuric reductase; Provisional
Probab=91.20 E-value=1.9 Score=35.16 Aligned_cols=61 Identities=16% Similarity=0.299 Sum_probs=48.5
Q ss_pred ecccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee--CCHHHHHHHHHhcCCceEEecC
Q 035968 9 VKLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD--ADPVKIIKKVREFRKSAAIESI 69 (112)
Q Consensus 9 vgm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~--~~~~~i~~~i~k~G~~~~~~~~ 69 (112)
.+++|.+|..+++..+...+|+....+++..+.+.+... .+...+...+...|+..++...
T Consensus 7 ~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~~~ 69 (561)
T PRK13748 7 TGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLADA 69 (561)
T ss_pred CCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeeccCc
Confidence 399999999999999999999998899988888777642 4556666677778887665544
No 18
>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=91.00 E-value=1.5 Score=25.75 Aligned_cols=52 Identities=19% Similarity=0.092 Sum_probs=37.7
Q ss_pred Eee-cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee--CCHHHHHHHHHhcCCceEEe
Q 035968 7 VSV-KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD--ADPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 7 ~~v-gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~--~~~~~i~~~i~k~G~~~~~~ 67 (112)
+.. |+.|+...-+++++|.+++.- +.+.|..+ ....+|...+++.|+...-+
T Consensus 3 lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 3 LDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp EECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred EeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHCCCEEEEE
Confidence 444 999999999999999987532 44444443 55688999999999975443
No 19
>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=88.77 E-value=1.7 Score=20.95 Aligned_cols=53 Identities=25% Similarity=0.462 Sum_probs=36.8
Q ss_pred ecccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee--CCHHHHHHHHHhcC
Q 035968 9 VKLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD--ADPVKIIKKVREFR 61 (112)
Q Consensus 9 vgm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~--~~~~~i~~~i~k~G 61 (112)
.++.|..|...++..+...+|+.....++......+... .+...+...+...+
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 (63)
T cd00371 5 EGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIEDAG 59 (63)
T ss_pred CCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHHHcC
Confidence 378899999999999988899877777777666666543 24444444444444
No 20
>PRK11018 hypothetical protein; Provisional
Probab=87.40 E-value=4.8 Score=24.57 Aligned_cols=52 Identities=12% Similarity=0.083 Sum_probs=38.9
Q ss_pred EEee-cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee--CCHHHHHHHHHhcCCceEE
Q 035968 6 IVSV-KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD--ADPVKIIKKVREFRKSAAI 66 (112)
Q Consensus 6 ~~~v-gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~--~~~~~i~~~i~k~G~~~~~ 66 (112)
.+.. |+.|+.-.-+.+++|.+++.- +.+.|..+ .....|...+++.|+.+..
T Consensus 10 ~lD~rG~~CP~Pvl~~kk~l~~l~~G---------~~L~V~~d~~~a~~di~~~~~~~G~~v~~ 64 (78)
T PRK11018 10 RLDMVGEPCPYPAVATLEALPQLKKG---------EILEVVSDCPQSINNIPLDARNHGYTVLD 64 (78)
T ss_pred eEECCCCcCCHHHHHHHHHHHhCCCC---------CEEEEEeCCccHHHHHHHHHHHcCCEEEE
Confidence 4555 999999999999999987632 33333332 5667899999999998754
No 21
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=87.32 E-value=2.9 Score=29.30 Aligned_cols=46 Identities=15% Similarity=0.138 Sum_probs=35.9
Q ss_pred hhHHHHHHHHHHccCCccEEEEecCCCE--------------EEEEee---CCHHHHHHHHHh
Q 035968 14 LKCRQKVMKLIAKLEGITSIVIDPSKNT--------------VTVIGD---ADPVKIIKKVRE 59 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd~~~~~--------------v~V~~~---~~~~~i~~~i~k 59 (112)
+||-+-++..+.+++||.++.+-..++. |.|..| ++.++|++...+
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~~ 70 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLFE 70 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHHH
Confidence 6888889999999999999988765433 445655 688888887765
No 22
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=87.31 E-value=3 Score=25.18 Aligned_cols=47 Identities=13% Similarity=0.208 Sum_probs=34.3
Q ss_pred HHccCCccEEEEecCCCEEE--EEeeCCHHHHHHHHHhcCCceEEecCCCC
Q 035968 24 IAKLEGITSIVIDPSKNTVT--VIGDADPVKIIKKVREFRKSAAIESIGPP 72 (112)
Q Consensus 24 L~~~~GV~~v~vd~~~~~v~--V~~~~~~~~i~~~i~k~G~~~~~~~~~~~ 72 (112)
|..++||.++..+ ..+.+. +....+..+|+..|...|. +.-++...|
T Consensus 26 l~~~~~v~~v~~~-~~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~f~~~~P 74 (84)
T PF13732_consen 26 LEELPGVESVEQD-GDGKLRIKLEDEETANELLQELIEKGI-IRSFEEEEP 74 (84)
T ss_pred HhhCCCeEEEEEe-CCcEEEEEECCcccHHHHHHHHHhCCC-eeEEEEcCC
Confidence 8888999988764 345444 4455788999999999998 766655443
No 23
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=84.82 E-value=6 Score=25.00 Aligned_cols=46 Identities=11% Similarity=0.245 Sum_probs=32.2
Q ss_pred hHHHHHHHHHHccCCccEEEEecCCCEEEEEee-CCHHHHHHHHHhc
Q 035968 15 KCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD-ADPVKIIKKVREF 60 (112)
Q Consensus 15 ~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~-~~~~~i~~~i~k~ 60 (112)
.=...+.+.|.+++|++-...|..+||+.|+-. .+...+.+.|..+
T Consensus 17 e~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~~I 63 (87)
T PRK10553 17 ERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIESV 63 (87)
T ss_pred HHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHHHH
Confidence 336789999999999986666677888887633 4445555555543
No 24
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=84.41 E-value=3.8 Score=29.29 Aligned_cols=54 Identities=19% Similarity=0.172 Sum_probs=40.0
Q ss_pred ceeEEEeecccChhHHHHHHHHHHccCCccEEEEecCCCE-------------------EEEEee---CCHHHHHHHHHh
Q 035968 2 AKKTIVSVKLLCLKCRQKVMKLIAKLEGITSIVIDPSKNT-------------------VTVIGD---ADPVKIIKKVRE 59 (112)
Q Consensus 2 ~~~~~~~vgm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~-------------------v~V~~~---~~~~~i~~~i~k 59 (112)
|++++|- +||=+=+++.+.+++||.++.+-..+|. |.|.+| ++.++|++.+.+
T Consensus 6 ~~~a~fa-----gGCFWg~E~~f~~i~GV~~t~~GYagG~~~nptY~~Vcsg~TgHaE~V~V~yDp~~isy~~LL~~ff~ 80 (174)
T COG0225 6 MEKAYFA-----GGCFWGVEAYFEQIPGVLSTVSGYAGGHTPNPTYEEVCSGTTGHAEAVEVTYDPKVISYEELLEVFFE 80 (174)
T ss_pred cEEEEEe-----ccCccchHHHHhhCCCeEEEeeeEcCCCCCCCChhhccCCCCCceEEEEEEeCCccccHHHHHHHHhe
Confidence 4555555 6788888999999999999988766553 345554 677888888876
Q ss_pred c
Q 035968 60 F 60 (112)
Q Consensus 60 ~ 60 (112)
.
T Consensus 81 i 81 (174)
T COG0225 81 I 81 (174)
T ss_pred e
Confidence 5
No 25
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=84.14 E-value=4.1 Score=29.97 Aligned_cols=47 Identities=19% Similarity=0.232 Sum_probs=37.0
Q ss_pred hhHHHHHHHHHHccCCccEEEEecCCCE-------------------EEEEee---CCHHHHHHHHHhc
Q 035968 14 LKCRQKVMKLIAKLEGITSIVIDPSKNT-------------------VTVIGD---ADPVKIIKKVREF 60 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd~~~~~-------------------v~V~~~---~~~~~i~~~i~k~ 60 (112)
+||-+-++..+.+++||.++.+-+.++. |.|++| ++.++|++.+.+.
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff~~ 120 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFWEN 120 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHHHh
Confidence 6888889999999999999998876442 556665 6888888877653
No 26
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=83.56 E-value=2.9 Score=30.09 Aligned_cols=47 Identities=17% Similarity=0.154 Sum_probs=37.0
Q ss_pred hhHHHHHHHHHHccCCccEEEEecCCCE-------------------EEEEee---CCHHHHHHHHHhc
Q 035968 14 LKCRQKVMKLIAKLEGITSIVIDPSKNT-------------------VTVIGD---ADPVKIIKKVREF 60 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd~~~~~-------------------v~V~~~---~~~~~i~~~i~k~ 60 (112)
+||-+-++..+.+++||.++.+-..++. |.|..| ++.++|++...+.
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff~~ 83 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFFST 83 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHHHh
Confidence 6778888889999999999998876664 556665 6888888877653
No 27
>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=83.26 E-value=6.9 Score=22.77 Aligned_cols=48 Identities=19% Similarity=0.227 Sum_probs=35.2
Q ss_pred cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee--CCHHHHHHHHHhcCCceEEe
Q 035968 10 KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD--ADPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 10 gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~--~~~~~i~~~i~k~G~~~~~~ 67 (112)
|+.|+.-.-+++++| ++.. ++.+.|..+ .....|...+++.|+.....
T Consensus 6 G~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~~~s~~~i~~~~~~~G~~~~~~ 55 (67)
T cd03421 6 GLACPQPVIKTKKAL-ELEA---------GGEIEVLVDNEVAKENVSRFAESRGYEVSVE 55 (67)
T ss_pred CCCCCHHHHHHHHHH-hcCC---------CCEEEEEEcChhHHHHHHHHHHHcCCEEEEE
Confidence 899999999999999 5542 233444333 45678999999999988543
No 28
>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=82.32 E-value=3 Score=24.68 Aligned_cols=31 Identities=23% Similarity=0.455 Sum_probs=20.4
Q ss_pred EEEeecccChhHH------HHHHHHHHccCCccEEEE
Q 035968 5 TIVSVKLLCLKCR------QKVMKLIAKLEGITSIVI 35 (112)
Q Consensus 5 ~~~~vgm~C~~C~------~kI~k~L~~~~GV~~v~v 35 (112)
+.+.+.+..++|. ..|+++|..++||.+|+|
T Consensus 36 V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 36 VSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp EEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred EEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 4455555555554 778899999999998875
No 29
>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=80.78 E-value=11 Score=23.22 Aligned_cols=44 Identities=11% Similarity=0.225 Sum_probs=31.7
Q ss_pred HHHHHHHHHccCCccEEEEecCCCEEEEEe-eCCHHHHHHHHHhcC
Q 035968 17 RQKVMKLIAKLEGITSIVIDPSKNTVTVIG-DADPVKIIKKVREFR 61 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~-~~~~~~i~~~i~k~G 61 (112)
...+.++|.+++|++-...+.. |++.|+- ..+...+.+.+..+.
T Consensus 17 ~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~i~ 61 (79)
T PF03927_consen 17 LEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDAIN 61 (79)
T ss_dssp HHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHHHC
T ss_pred HHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHHHH
Confidence 4678899999999975556655 8887764 356677777776654
No 30
>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=78.67 E-value=11 Score=22.19 Aligned_cols=49 Identities=16% Similarity=0.156 Sum_probs=37.0
Q ss_pred cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEe--eCCHHHHHHHHHhcCCceEEe
Q 035968 10 KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIG--DADPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 10 gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~--~~~~~~i~~~i~k~G~~~~~~ 67 (112)
|..|+.=.-+.+++|.+++ ..+.+.|.. ......|.+..++.||.....
T Consensus 6 G~~CP~P~i~~k~~l~~l~---------~G~~l~V~~dd~~s~~di~~~~~~~g~~~~~~ 56 (69)
T cd03423 6 GLRCPEPVMMLHKKVRKMK---------PGDTLLVLATDPSTTRDIPKFCTFLGHELLAQ 56 (69)
T ss_pred CCcCCHHHHHHHHHHHcCC---------CCCEEEEEeCCCchHHHHHHHHHHcCCEEEEE
Confidence 8899999999999998875 223334332 366789999999999987654
No 31
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=77.61 E-value=14 Score=22.68 Aligned_cols=54 Identities=17% Similarity=0.150 Sum_probs=39.3
Q ss_pred eEEEee-cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEe--eCCHHHHHHHHHhcCCceEE
Q 035968 4 KTIVSV-KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIG--DADPVKIIKKVREFRKSAAI 66 (112)
Q Consensus 4 ~~~~~v-gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~--~~~~~~i~~~i~k~G~~~~~ 66 (112)
...+.. |+.|+.=.-+++++|.+++. .+.+.|.. .....+|....+..|+....
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~~---------G~~l~V~~dd~~~~~di~~~~~~~G~~~~~ 65 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQP---------GETLLIIADDPATTRDIPSFCRFMDHELLA 65 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCCC---------CCEEEEEeCCccHHHHHHHHHHHcCCEEEE
Confidence 345565 99999999999999998752 23333332 25667899999999997754
No 32
>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=75.08 E-value=15 Score=21.71 Aligned_cols=49 Identities=16% Similarity=0.046 Sum_probs=37.4
Q ss_pred cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee--CCHHHHHHHHHhcCCceEEe
Q 035968 10 KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD--ADPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 10 gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~--~~~~~i~~~i~k~G~~~~~~ 67 (112)
|+.|+.=.-+.+++|.++.. ++.+.|..+ ....+|....++.|+.....
T Consensus 6 G~~CP~Pvl~~kkal~~l~~---------G~~l~V~~d~~~a~~di~~~~~~~G~~~~~~ 56 (69)
T cd03420 6 GLQCPGPILKLKKEIDKLQD---------GEQLEVKASDPGFARDAQAWCKSTGNTLISL 56 (69)
T ss_pred CCcCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHHHcCCEEEEE
Confidence 89999999999999998762 233444432 56788999999999987643
No 33
>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=74.84 E-value=18 Score=25.14 Aligned_cols=47 Identities=17% Similarity=0.147 Sum_probs=35.6
Q ss_pred hhHHHHHHHHHHccCCccEEEEecCCC-------------------EEEEEee---CCHHHHHHHHHhc
Q 035968 14 LKCRQKVMKLIAKLEGITSIVIDPSKN-------------------TVTVIGD---ADPVKIIKKVREF 60 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd~~~~-------------------~v~V~~~---~~~~~i~~~i~k~ 60 (112)
+||-+.++..+.+++||.++.+-..++ -|.|..| ++.++|++...+.
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~is~~~Ll~~f~~~ 75 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVISYEELLDVFFRI 75 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS-HHHHHHHHHHH
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcccHHHHHHHHHHh
Confidence 578888999999999999999876544 2345565 6788888888754
No 34
>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=74.14 E-value=16 Score=21.61 Aligned_cols=49 Identities=12% Similarity=0.047 Sum_probs=37.0
Q ss_pred cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEe--eCCHHHHHHHHHhcCCceEEe
Q 035968 10 KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIG--DADPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 10 gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~--~~~~~~i~~~i~k~G~~~~~~ 67 (112)
|+.|+.=.-+.+++|++++. ++.+.|.. ......|.+..++.|+.+...
T Consensus 6 G~~CP~Pvi~~kkal~~l~~---------G~~l~V~~d~~~s~~ni~~~~~~~g~~v~~~ 56 (69)
T cd03422 6 GEPCPYPAIATLEALPSLKP---------GEILEVISDCPQSINNIPIDARNHGYKVLAI 56 (69)
T ss_pred CCcCCHHHHHHHHHHHcCCC---------CCEEEEEecCchHHHHHHHHHHHcCCEEEEE
Confidence 88999999999999998763 23333333 366788999999999987543
No 35
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=73.70 E-value=12 Score=28.73 Aligned_cols=46 Identities=24% Similarity=0.141 Sum_probs=35.5
Q ss_pred hhHHHHHHHHHHccCCccEEEEecCCCE-------------------EEEEee---CCHHHHHHHHHh
Q 035968 14 LKCRQKVMKLIAKLEGITSIVIDPSKNT-------------------VTVIGD---ADPVKIIKKVRE 59 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd~~~~~-------------------v~V~~~---~~~~~i~~~i~k 59 (112)
++|-+-++..+.+++||.++.+-..++. |.|+.+ ++.++|++...+
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~VcsG~tgH~EaV~V~yDp~~isy~~LL~~F~~ 201 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEFDPAKISYETLLKVFFE 201 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHHh
Confidence 6788889999999999999988765543 456665 677888887754
No 36
>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=71.79 E-value=22 Score=24.70 Aligned_cols=56 Identities=16% Similarity=0.262 Sum_probs=40.3
Q ss_pred HHHHHHHHHHccCCccEEEEecCCCEEEEEee-------CCHHHHHHHHHhcCCceEEecCCC
Q 035968 16 CRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD-------ADPVKIIKKVREFRKSAAIESIGP 71 (112)
Q Consensus 16 C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~-------~~~~~i~~~i~k~G~~~~~~~~~~ 71 (112)
=...|++.+-.-.||.++.+|..+|.|.|... -.-..+.+...++|+.+.++...|
T Consensus 54 A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 54 AIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred HHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 34456666655579999999999999998742 123345666669999999876555
No 37
>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=68.08 E-value=21 Score=20.52 Aligned_cols=49 Identities=22% Similarity=0.131 Sum_probs=36.5
Q ss_pred cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee--CCHHHHHHHHHhcCCceEEe
Q 035968 10 KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD--ADPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 10 gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~--~~~~~i~~~i~k~G~~~~~~ 67 (112)
|+.|+.=.-+++++|.+++ .++.+.|..+ .....|.+.++..||.....
T Consensus 6 g~~CP~Pl~~~~~~l~~l~---------~g~~l~v~~d~~~~~~~i~~~~~~~g~~~~~~ 56 (69)
T cd00291 6 GLPCPLPVLKTKKALEKLK---------SGEVLEVLLDDPGAVEDIPAWAKETGHEVLEV 56 (69)
T ss_pred CCcCCHHHHHHHHHHhcCC---------CCCEEEEEecCCcHHHHHHHHHHHcCCEEEEE
Confidence 8899999999999998755 3334444433 45788999999999986543
No 38
>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=67.58 E-value=31 Score=24.79 Aligned_cols=50 Identities=20% Similarity=0.205 Sum_probs=37.6
Q ss_pred cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEe--eCCHHHHHHHHHhcCCceEEec
Q 035968 10 KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIG--DADPVKIIKKVREFRKSAAIES 68 (112)
Q Consensus 10 gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~--~~~~~~i~~~i~k~G~~~~~~~ 68 (112)
|+.|+.-.-+.+++|.+++. .+.++|.. ....+.|.+.+++.||++....
T Consensus 5 Gl~CP~Pvi~tKkal~~l~~---------g~~L~VlvD~~~a~~nV~~~~~~~G~~v~~~e 56 (194)
T TIGR03527 5 GLACPQPVILTKKALDELGE---------EGVLTVIVDNEAAKENVSKFATSLGYEVEVEE 56 (194)
T ss_pred CCCCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHHHcCCEEEEEE
Confidence 88999999999999998762 22333332 3567789999999999886543
No 39
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=64.05 E-value=31 Score=22.19 Aligned_cols=47 Identities=13% Similarity=0.181 Sum_probs=32.5
Q ss_pred hhHHHHHHHHHHccCCccEEEEecCCCEEEEEe-eCCHHHHHHHHHhcC
Q 035968 14 LKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIG-DADPVKIIKKVREFR 61 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~-~~~~~~i~~~i~k~G 61 (112)
+.=...|+.+|..+||++-..-|.. |++.|.- .-+...|.+.+..+.
T Consensus 17 pe~l~av~~~L~~ip~~EV~~~d~~-GKlVVVie~~~~~~l~~tie~i~ 64 (94)
T COG3062 17 PERLSAVKTALLAIPGCEVYGEDAE-GKLVVVIEAEDSETLLETIESIR 64 (94)
T ss_pred HHHHHHHHHHHhcCCCcEeeccCCC-ceEEEEEEcCchHHHHHHHHHHh
Confidence 4446789999999999986656655 6666553 356667777776543
No 40
>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=63.61 E-value=6.9 Score=22.30 Aligned_cols=30 Identities=20% Similarity=0.238 Sum_probs=15.3
Q ss_pred HHHHHHHHcc---CCccEEEEecCCCEEEEEeeC
Q 035968 18 QKVMKLIAKL---EGITSIVIDPSKNTVTVIGDA 48 (112)
Q Consensus 18 ~kI~k~L~~~---~GV~~v~vd~~~~~v~V~~~~ 48 (112)
.+|+++|... ++- .+.+...++.|.+.|.+
T Consensus 2 ~~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v 34 (64)
T PF04972_consen 2 TKVRAALRADPWLPDS-NISVSVENGVVTLSGEV 34 (64)
T ss_dssp -----------CTT-T-TEEEEEECTEEEEEEEE
T ss_pred cccccccccccccCCC-eEEEEEECCEEEEEeeC
Confidence 4567777763 344 57888889999999975
No 41
>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=63.56 E-value=26 Score=20.02 Aligned_cols=52 Identities=13% Similarity=0.055 Sum_probs=33.2
Q ss_pred hhHHHHHHHHHHccCC-ccEEEEecCCCEEEEEee-CCHHHHHHHHHhcCCceE
Q 035968 14 LKCRQKVMKLIAKLEG-ITSIVIDPSKNTVTVIGD-ADPVKIIKKVREFRKSAA 65 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~G-V~~v~vd~~~~~v~V~~~-~~~~~i~~~i~k~G~~~~ 65 (112)
+|=-.+|.+.|.+... |.++.+....++..+.-. .+++.+.+.|++.||++.
T Consensus 12 pG~La~v~~~l~~~~inI~~i~~~~~~~~~~~rl~~~~~~~~~~~L~~~G~~v~ 65 (66)
T cd04908 12 PGRLAAVTEILSEAGINIRALSIADTSEFGILRLIVSDPDKAKEALKEAGFAVK 65 (66)
T ss_pred CChHHHHHHHHHHCCCCEEEEEEEecCCCCEEEEEECCHHHHHHHHHHCCCEEE
Confidence 5666788888876543 455554333333443322 567799999999999865
No 42
>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=62.53 E-value=32 Score=23.76 Aligned_cols=31 Identities=10% Similarity=0.213 Sum_probs=26.1
Q ss_pred HHHHHHHHHHccCCccEEEEecCCCEEEEEe
Q 035968 16 CRQKVMKLIAKLEGITSIVIDPSKNTVTVIG 46 (112)
Q Consensus 16 C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~ 46 (112)
=+.+|.+.+.+++||..+.+=.....+.|-.
T Consensus 76 ~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav 106 (177)
T PF09580_consen 76 LADRIANRVKKVPGVEDATVVVTDDNAYVAV 106 (177)
T ss_pred HHHHHHHHHhcCCCceEEEEEEECCEEEEEE
Confidence 3678999999999999999888888887653
No 43
>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=60.80 E-value=38 Score=21.11 Aligned_cols=55 Identities=9% Similarity=0.070 Sum_probs=37.8
Q ss_pred EeecccChhHHHHHHHHHHccCC-ccEEEEecCCCEEEEEeeCCHHHHHHHHHhcCC
Q 035968 7 VSVKLLCLKCRQKVMKLIAKLEG-ITSIVIDPSKNTVTVIGDADPVKIIKKVREFRK 62 (112)
Q Consensus 7 ~~vgm~C~~C~~kI~k~L~~~~G-V~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~ 62 (112)
-++.-.=.....-+.+.|....+ -..+.++..++.+.|.|+. ..+|.+.|.+.||
T Consensus 32 rkI~GD~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~-~~~Vk~wL~~~GF 87 (87)
T PF05046_consen 32 RKIEGDIWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGDH-VEEVKKWLLEKGF 87 (87)
T ss_pred EeecCCHHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCcc-HHHHHHHHHHCcC
Confidence 33433335566666666654443 2357889999999999985 6778888888886
No 44
>PRK11023 outer membrane lipoprotein; Provisional
Probab=53.99 E-value=40 Score=23.99 Aligned_cols=44 Identities=16% Similarity=0.268 Sum_probs=31.1
Q ss_pred hHHHHHHHHHHccCCcc---EEEEecCCCEEEEEeeCCHHHHHHHHH
Q 035968 15 KCRQKVMKLIAKLEGIT---SIVIDPSKNTVTVIGDADPVKIIKKVR 58 (112)
Q Consensus 15 ~C~~kI~k~L~~~~GV~---~v~vd~~~~~v~V~~~~~~~~i~~~i~ 58 (112)
.=..+|+.+|...+++. .+.+...++.|++.|.++.+.......
T Consensus 49 ~i~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~V~~~~~k~~A~ 95 (191)
T PRK11023 49 TLELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQSPNAELSERAK 95 (191)
T ss_pred HHHHHHHHHHhhCcccCcCceEEEEEECCEEEEEEEeCCHHHHHHHH
Confidence 34568888888777764 477778999999999865544444333
No 45
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=53.83 E-value=30 Score=22.27 Aligned_cols=21 Identities=29% Similarity=0.406 Sum_probs=18.8
Q ss_pred ccCCccEEEEecCCCEEEEEe
Q 035968 26 KLEGITSIVIDPSKNTVTVIG 46 (112)
Q Consensus 26 ~~~GV~~v~vd~~~~~v~V~~ 46 (112)
..+|++.++++++++++.|++
T Consensus 38 s~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 38 SSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred ecCCceEEEEecccceEEEec
Confidence 468999999999999999986
No 46
>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=53.65 E-value=18 Score=25.70 Aligned_cols=33 Identities=9% Similarity=0.251 Sum_probs=22.7
Q ss_pred EEEeecccChhHH------HHHHHHHHccCCccEEEEec
Q 035968 5 TIVSVKLLCLKCR------QKVMKLIAKLEGITSIVIDP 37 (112)
Q Consensus 5 ~~~~vgm~C~~C~------~kI~k~L~~~~GV~~v~vd~ 37 (112)
+.+.+-+.-++|. ..|+.+|..++||.++.|++
T Consensus 115 V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 115 VDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 4455555544444 45888999999999887764
No 47
>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=53.31 E-value=17 Score=21.02 Aligned_cols=28 Identities=7% Similarity=0.330 Sum_probs=20.6
Q ss_pred eecccChh-HHHHHHHHHHccCCccEEEE
Q 035968 8 SVKLLCLK-CRQKVMKLIAKLEGITSIVI 35 (112)
Q Consensus 8 ~vgm~C~~-C~~kI~k~L~~~~GV~~v~v 35 (112)
.+...-.. --..+.+.|++++||.+|.+
T Consensus 46 ~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 46 SIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 33333443 67889999999999998865
No 48
>PF00539 Tat: Transactivating regulatory protein (Tat); InterPro: IPR001831 Like other lentiviruses, Human immunodeficiency virus 1 (HIV-1) encodes a trans-activating regulatory protein (Tat), which is essential for efficient transcription of the viral genome [, ]. Tat acts by binding to an RNA stem-loop structure, the trans-activating response element (TAR), found at the 5' ends of nascent HIV-1 transcripts. In binding to TAR, Tat alters the properties of the transcription complex, recruits a positive transcription elongation complex (P-TEFb) and hence increases the production of full-length viral RNA []. Tat protein also associates with RNA polymerase II complexes during early transcription elongation after the promoter clearance and before the synthesis of full-length TAR RNA transcript. This interaction of Tat with RNA polymerase II elongation complexes is P-TEFb-independent. There are two Tat binding sites on each transcription elongation complex; one is located on TAR RNA and the other one on RNA polymerase II near the exit site for nascent mRNA transcripts which suggests that two Tat molecules are involved in performing various functions during a single round of HIV-1 mRNA synthesis []. The minimum Tat sequence that can mediate specific TAR binding in vitro has been mapped to a basic domain of 10 amino acids, comprising mostly Arg and Lys residues. Regulatory activity, however, also requires the 47 N-terminal residues, which interact with components of the transcription complex and function as a transcriptional activation domain [, , ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 2W2H_D 1ZBN_B 1TVS_A 1TVT_A 3O6L_C 3O6M_C 3MI9_C 3MIA_C 1JFW_A 1TBC_A ....
Probab=52.72 E-value=7.6 Score=23.55 Aligned_cols=17 Identities=18% Similarity=0.495 Sum_probs=13.7
Q ss_pred cccCCCCCCCCCcceEE
Q 035968 84 LVPVAPKACQRCDVWYV 100 (112)
Q Consensus 84 ~~~~~~~~~~~~~~~~~ 100 (112)
-.+|+.+.|+||.++++
T Consensus 28 n~CyCK~CcyHCqlCFl 44 (68)
T PF00539_consen 28 NKCYCKKCCYHCQLCFL 44 (68)
T ss_dssp SSSSSTTSTSSSSCCCC
T ss_pred CCcccCcceeeceeeee
Confidence 33588899999999865
No 49
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=52.66 E-value=43 Score=27.87 Aligned_cols=47 Identities=15% Similarity=0.157 Sum_probs=36.2
Q ss_pred hhHHHHHHHHHHccCCccEEEEecCCCE------------------EEEEee---CCHHHHHHHHHhc
Q 035968 14 LKCRQKVMKLIAKLEGITSIVIDPSKNT------------------VTVIGD---ADPVKIIKKVREF 60 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd~~~~~------------------v~V~~~---~~~~~i~~~i~k~ 60 (112)
+||-+-++..+.+++||.++.+-+.++. |.|+++ ++.++|++...+.
T Consensus 205 gGCFWg~e~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~gtgH~E~V~V~yDp~~is~~~Ll~~f~~~ 272 (521)
T PRK14018 205 GGCFWGLEAYFQRIDGVVDAVSGYANGNTKNPSYEDVYRHSGHAETVKVTYDADKLSLDTILQYYFRV 272 (521)
T ss_pred cCCchhhHHHHccCCCEEEEEEeeCCCCCCCCChhhccCCCCcEEEEEEEECCCcCcHHHHHHHHHHh
Confidence 6788888999999999999998776552 445555 6778888887653
No 50
>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=52.34 E-value=18 Score=22.64 Aligned_cols=21 Identities=14% Similarity=0.335 Sum_probs=17.1
Q ss_pred HHHHHHHHccCCccEEEEecC
Q 035968 18 QKVMKLIAKLEGITSIVIDPS 38 (112)
Q Consensus 18 ~kI~k~L~~~~GV~~v~vd~~ 38 (112)
..++++|.+++|+.++.+++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 457888999999999988763
No 51
>PRK09577 multidrug efflux protein; Reviewed
Probab=51.56 E-value=52 Score=29.47 Aligned_cols=47 Identities=13% Similarity=0.220 Sum_probs=36.4
Q ss_pred HHHHHHHHHccCCccEEEEecCCCEEEEE--------eeCCHHHHHHHHHhcCCc
Q 035968 17 RQKVMKLIAKLEGITSIVIDPSKNTVTVI--------GDADPVKIIKKVREFRKS 63 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd~~~~~v~V~--------~~~~~~~i~~~i~k~G~~ 63 (112)
...++..|.+++||.+|+++-...++.|. ..+++.+|.++|+..+..
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n~~ 212 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAHNAR 212 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhCCc
Confidence 46799999999999999988655556664 237888999999976543
No 52
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=51.15 E-value=55 Score=19.97 Aligned_cols=48 Identities=23% Similarity=0.248 Sum_probs=35.4
Q ss_pred EEEee-cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee--CCHHHHHHHHHhcC
Q 035968 5 TIVSV-KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD--ADPVKIIKKVREFR 61 (112)
Q Consensus 5 ~~~~v-gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~--~~~~~i~~~i~k~G 61 (112)
.++.+ |+.|+.=.-.++++|.+++ .++.+.|..+ ....+|....++.|
T Consensus 6 ~~LD~rG~~CP~Pv~~~kk~l~~m~---------~Ge~LeV~~ddp~~~~dIp~~~~~~~ 56 (78)
T COG0425 6 KVLDLRGLRCPGPVVETKKALAKLK---------PGEILEVIADDPAAKEDIPAWAKKEG 56 (78)
T ss_pred eEEeccCCcCCccHHHHHHHHHcCC---------CCCEEEEEecCcchHHHHHHHHHHcC
Confidence 35666 9999999999999999876 3444555433 45678888888565
No 53
>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=50.83 E-value=19 Score=22.84 Aligned_cols=22 Identities=14% Similarity=0.312 Sum_probs=19.2
Q ss_pred hHHHHHHHHHHccCCccEEEEe
Q 035968 15 KCRQKVMKLIAKLEGITSIVID 36 (112)
Q Consensus 15 ~C~~kI~k~L~~~~GV~~v~vd 36 (112)
+-...|+.+|++++||+++++.
T Consensus 62 g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 62 GGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred cChHHHHHHHhcCCCccEEEEE
Confidence 5568999999999999999874
No 54
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=49.77 E-value=53 Score=19.41 Aligned_cols=57 Identities=11% Similarity=-0.014 Sum_probs=37.4
Q ss_pred eEEEee-cccChhHHHHHHHHHHccCC-ccEEEEecCCCEEEE----Eee-CCHHHHHHHHHhc
Q 035968 4 KTIVSV-KLLCLKCRQKVMKLIAKLEG-ITSIVIDPSKNTVTV----IGD-ADPVKIIKKVREF 60 (112)
Q Consensus 4 ~~~~~v-gm~C~~C~~kI~k~L~~~~G-V~~v~vd~~~~~v~V----~~~-~~~~~i~~~i~k~ 60 (112)
.+++.+ |..-++-...+.+.|.+..+ +.+++...-.+..+. .++ .+.++|.+.|.+.
T Consensus 2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~~~~~~~l~~~L~~l 65 (76)
T PF13740_consen 2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIPEDSLERLESALEEL 65 (76)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEESHHHHHHHHHHHHHH
T ss_pred EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeCcccHHHHHHHHHHH
Confidence 345555 99999999999999999876 666666666666663 332 3455666666654
No 55
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=48.52 E-value=62 Score=29.02 Aligned_cols=44 Identities=7% Similarity=0.153 Sum_probs=34.6
Q ss_pred HHHHHHHHHccCCccEEEEecCCCEEEEEe--------eCCHHHHHHHHHhc
Q 035968 17 RQKVMKLIAKLEGITSIVIDPSKNTVTVIG--------DADPVKIIKKVREF 60 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~--------~~~~~~i~~~i~k~ 60 (112)
+..++..|.+++||.+|+++-....+.|.- .+++.+|..+|+..
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 467889999999999999885555566652 37888999999864
No 56
>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=48.08 E-value=33 Score=22.63 Aligned_cols=29 Identities=31% Similarity=0.516 Sum_probs=24.6
Q ss_pred EEEEeeCCHHHHHHHHHhcCCceEEecCC
Q 035968 42 VTVIGDADPVKIIKKVREFRKSAAIESIG 70 (112)
Q Consensus 42 v~V~~~~~~~~i~~~i~k~G~~~~~~~~~ 70 (112)
+.|+||.|...+++.+++.|+++.+++..
T Consensus 104 vLvSgD~Df~~~i~~lr~~G~~V~v~~~~ 132 (149)
T cd06167 104 VLVSGDSDFVPLVERLRELGKRVIVVGFE 132 (149)
T ss_pred EEEECCccHHHHHHHHHHcCCEEEEEccC
Confidence 34568888999999999999999998776
No 57
>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=47.78 E-value=51 Score=18.66 Aligned_cols=51 Identities=16% Similarity=0.212 Sum_probs=31.9
Q ss_pred hhHHHHHHHHHHccCC-ccEEEEecC--CCE--EEEEee-CCHHHHHHHHHhcCCce
Q 035968 14 LKCRQKVMKLIAKLEG-ITSIVIDPS--KNT--VTVIGD-ADPVKIIKKVREFRKSA 64 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~G-V~~v~vd~~--~~~--v~V~~~-~~~~~i~~~i~k~G~~~ 64 (112)
++-..++.+.|.+... +.++..... .+. +.+..+ .+++.+.+.|++.||++
T Consensus 12 pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L~~~G~~v 68 (72)
T cd04883 12 PGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNPRPIIEDLRRAGYEV 68 (72)
T ss_pred CCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCHHHHHHHHHHCCCee
Confidence 4566778888776543 445543332 223 344433 56779999999999965
No 58
>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=46.90 E-value=39 Score=28.26 Aligned_cols=39 Identities=15% Similarity=0.368 Sum_probs=31.6
Q ss_pred HHccCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhcCCce
Q 035968 24 IAKLEGITSIVIDPSKNTVTVIGDADPVKIIKKVREFRKSA 64 (112)
Q Consensus 24 L~~~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~~ 64 (112)
|..+.+| +.+|..+++|+|.+.+...+|.+.|.+.|+..
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 36788899999998899999999999999754
No 59
>PRK11023 outer membrane lipoprotein; Provisional
Probab=46.36 E-value=68 Score=22.79 Aligned_cols=40 Identities=13% Similarity=0.145 Sum_probs=25.9
Q ss_pred hHHHHHHHHHHccCCccE--EEEecCCCEEEEEeeCCHHHHH
Q 035968 15 KCRQKVMKLIAKLEGITS--IVIDPSKNTVTVIGDADPVKII 54 (112)
Q Consensus 15 ~C~~kI~k~L~~~~GV~~--v~vd~~~~~v~V~~~~~~~~i~ 54 (112)
.=..+|+.+|...+++.. +++...++.|++.|.++.++..
T Consensus 127 ~It~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~~ 168 (191)
T PRK11023 127 WITTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREAK 168 (191)
T ss_pred HHHHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHHH
Confidence 355677777777666654 4444567888888876555443
No 60
>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=45.93 E-value=1e+02 Score=21.58 Aligned_cols=32 Identities=16% Similarity=0.134 Sum_probs=26.4
Q ss_pred hHHHHHHHHHHccCCccEEEEecCCCEEEEEe
Q 035968 15 KCRQKVMKLIAKLEGITSIVIDPSKNTVTVIG 46 (112)
Q Consensus 15 ~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~ 46 (112)
.=+.+|.+.+.+++||.++.+=.....+.|-.
T Consensus 54 ~~A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vgv 85 (158)
T TIGR02898 54 DVADEIASEAAKVKGVKDATVVITGNYAYVGV 85 (158)
T ss_pred HHHHHHHHHHhcCCCCceEEEEEECCEEEEEE
Confidence 44678999999999999998877888887654
No 61
>KOG4034 consensus Uncharacterized conserved protein NOF (Neighbor of FAU) [Function unknown]
Probab=44.48 E-value=55 Score=23.15 Aligned_cols=56 Identities=7% Similarity=-0.010 Sum_probs=41.3
Q ss_pred EEeecccChhHHHHHHHHHHccCCcc-EEEEecCCCEEEEEeeCCHHHHHHHHHhcCC
Q 035968 6 IVSVKLLCLKCRQKVMKLIAKLEGIT-SIVIDPSKNTVTVIGDADPVKIIKKVREFRK 62 (112)
Q Consensus 6 ~~~vgm~C~~C~~kI~k~L~~~~GV~-~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~ 62 (112)
+-++.-.=-.|.+.++..|...+|=. .-.||.-++++.+.|+. .+.|.+.|.+.||
T Consensus 113 IRkVeGDi~aLe~DL~s~L~~~~~~s~~t~VnelsgqI~~~g~~-v~~vr~~L~eKGF 169 (169)
T KOG4034|consen 113 IRKVEGDIWALENDLRSTLEMSPKKSYATHVNELSGQIVLKGNH-VDTVREWLQEKGF 169 (169)
T ss_pred EEeecccHHHHHHHHHHHHhhccCCChhhhhhhhcceEEEeCCh-HHHHHHHHHHccC
Confidence 34455556789999999999887743 23588889999988763 2378888888876
No 62
>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=43.64 E-value=61 Score=18.31 Aligned_cols=51 Identities=12% Similarity=0.036 Sum_probs=31.4
Q ss_pred hhHHHHHHHHHHccCC-ccEEEEecC----CCEEEEEee--CCHHHHHHHHHhcCCce
Q 035968 14 LKCRQKVMKLIAKLEG-ITSIVIDPS----KNTVTVIGD--ADPVKIIKKVREFRKSA 64 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~G-V~~v~vd~~----~~~v~V~~~--~~~~~i~~~i~k~G~~~ 64 (112)
+|-..++.+.|.+... +.++..... .+.+.+..+ .+.+.+.+.|++.||.+
T Consensus 12 ~G~L~~l~~~l~~~~i~i~~~~~~~~~~~~~~~~~i~v~~~~~~~~~~~~L~~~G~~v 69 (69)
T cd04909 12 PGVIAEVTQILGDAGISIKNIEILEIREGIGGILRISFKTQEDRERAKEILKEAGYEV 69 (69)
T ss_pred CCHHHHHHHHHHHcCCCceeeEeEEeecCCcEEEEEEECCHHHHHHHHHHHHHcCCcC
Confidence 4566778888876543 444443321 334444432 36789999999999863
No 63
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=43.28 E-value=1.2e+02 Score=21.49 Aligned_cols=68 Identities=21% Similarity=0.288 Sum_probs=41.1
Q ss_pred EEeecccChhHHHHHH------------HHHHcc------CCccEEEEecCCCEEEE-E--ee---C-CHHHHHHHHH-h
Q 035968 6 IVSVKLLCLKCRQKVM------------KLIAKL------EGITSIVIDPSKNTVTV-I--GD---A-DPVKIIKKVR-E 59 (112)
Q Consensus 6 ~~~vgm~C~~C~~kI~------------k~L~~~------~GV~~v~vd~~~~~v~V-~--~~---~-~~~~i~~~i~-k 59 (112)
=++.|+-|++|.+++. ++|.++ .++...+.=...+++.+ . |+ + .--...++++ +
T Consensus 9 c~kt~ilC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gdg~aIGk~G~~ik~l~~~ 88 (166)
T PRK06418 9 CVKTGLLCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGPRIPIGKGGKIAKALSRK 88 (166)
T ss_pred EeccCccChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCCcccccccchHHHHHHHH
Confidence 3456999999999864 566655 34433332233566663 2 33 1 1124566666 7
Q ss_pred cCCceEEecCCCCc
Q 035968 60 FRKSAAIESIGPPK 73 (112)
Q Consensus 60 ~G~~~~~~~~~~~~ 73 (112)
.|++++++...++.
T Consensus 89 lgk~VevVE~s~d~ 102 (166)
T PRK06418 89 LGKKVRVVEKTNDI 102 (166)
T ss_pred hCCcEEEEEcCCCH
Confidence 89999998866553
No 64
>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=42.21 E-value=69 Score=18.57 Aligned_cols=21 Identities=38% Similarity=0.506 Sum_probs=18.1
Q ss_pred cCCccEEEEecCCCEEEEEee
Q 035968 27 LEGITSIVIDPSKNTVTVIGD 47 (112)
Q Consensus 27 ~~GV~~v~vd~~~~~v~V~~~ 47 (112)
-.++.++.+|..+++|.|+.+
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 457889999999999999864
No 65
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=40.97 E-value=32 Score=21.77 Aligned_cols=23 Identities=22% Similarity=0.361 Sum_probs=20.1
Q ss_pred hhHHHHHHHHHHccCCccEEEEe
Q 035968 14 LKCRQKVMKLIAKLEGITSIVID 36 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd 36 (112)
.+-...++.++++++||+++++-
T Consensus 61 ~~~td~lee~i~~~e~Vqsvei~ 83 (88)
T PRK00435 61 EGGTEPVEEAFANVEGVESVEVE 83 (88)
T ss_pred CcCcHHHHHHHhccCCCcEEEEE
Confidence 56778999999999999999874
No 66
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=40.86 E-value=35 Score=23.45 Aligned_cols=44 Identities=23% Similarity=0.274 Sum_probs=27.8
Q ss_pred hhHHHHHHHHHHccCCccEEEEecCCCE-EEEEeeCCHHHHHHHHHhc
Q 035968 14 LKCRQKVMKLIAKLEGITSIVIDPSKNT-VTVIGDADPVKIIKKVREF 60 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd~~~~~-v~V~~~~~~~~i~~~i~k~ 60 (112)
++|.+++-++| +.+.-|+-+...++ ++-.|.-+.+.|...|...
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 45555555555 45555666665554 4455778888988888753
No 67
>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=40.42 E-value=47 Score=23.33 Aligned_cols=31 Identities=29% Similarity=0.358 Sum_probs=24.7
Q ss_pred EEEEEeeCCHHHHHHHHHhcCCceEEecCCC
Q 035968 41 TVTVIGDADPVKIIKKVREFRKSAAIESIGP 71 (112)
Q Consensus 41 ~v~V~~~~~~~~i~~~i~k~G~~~~~~~~~~ 71 (112)
-+.|+|+-|...|+.+|++.|..+..++.+.
T Consensus 109 ~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~~ 139 (160)
T TIGR00288 109 VALVTRDADFLPVINKAKENGKETIVIGAEP 139 (160)
T ss_pred EEEEeccHhHHHHHHHHHHCCCEEEEEeCCC
Confidence 3446788888999999999999998887643
No 68
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=40.12 E-value=19 Score=21.25 Aligned_cols=21 Identities=24% Similarity=0.373 Sum_probs=17.4
Q ss_pred EeecccChhHHHHHHHHHHcc
Q 035968 7 VSVKLLCLKCRQKVMKLIAKL 27 (112)
Q Consensus 7 ~~vgm~C~~C~~kI~k~L~~~ 27 (112)
+..+-.|+.|...|++.|.+.
T Consensus 33 ~~~g~~CG~C~~~i~~il~~~ 53 (64)
T PRK10509 33 VPVGNQCGKCIRAAREVMQDE 53 (64)
T ss_pred cCCCCCccchHHHHHHHHHHH
Confidence 456889999999999998653
No 69
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=39.99 E-value=96 Score=27.89 Aligned_cols=43 Identities=14% Similarity=0.289 Sum_probs=33.7
Q ss_pred HHHHHHHHccCCccEEEEecCCCEEEEEe--------eCCHHHHHHHHHhc
Q 035968 18 QKVMKLIAKLEGITSIVIDPSKNTVTVIG--------DADPVKIIKKVREF 60 (112)
Q Consensus 18 ~kI~k~L~~~~GV~~v~vd~~~~~v~V~~--------~~~~~~i~~~i~k~ 60 (112)
+.++..|.+++||.++++.-....+.|.- .+++.+|..+|+..
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 56899999999999999875445566652 37888999999954
No 70
>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=39.67 E-value=55 Score=20.03 Aligned_cols=23 Identities=13% Similarity=0.211 Sum_probs=17.6
Q ss_pred cCCCEEEEEeeCCHHHHHHHHHh
Q 035968 37 PSKNTVTVIGDADPVKIIKKVRE 59 (112)
Q Consensus 37 ~~~~~v~V~~~~~~~~i~~~i~k 59 (112)
+.+|+++++|.-+.+++..++++
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 68999999997677766666554
No 71
>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=39.12 E-value=88 Score=19.42 Aligned_cols=41 Identities=24% Similarity=0.400 Sum_probs=29.0
Q ss_pred HHHHHHHHccCCccEEEEecCCCEEEEEe--eCCHHHHHHHHHhc
Q 035968 18 QKVMKLIAKLEGITSIVIDPSKNTVTVIG--DADPVKIIKKVREF 60 (112)
Q Consensus 18 ~kI~k~L~~~~GV~~v~vd~~~~~v~V~~--~~~~~~i~~~i~k~ 60 (112)
.-+-+.|-+++||.+|-+ ..+-++|+- +.+.+.|...|...
T Consensus 37 spLA~~Lf~i~gV~~Vf~--~~dfItVtK~~~~~W~~l~~~I~~~ 79 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFI--GDDFITVTKNPDADWEDLKPEIREV 79 (87)
T ss_dssp -HHHHHHHTSTTEEEEEE--ETTEEEEEE-TTS-HHHHHHHHHHH
T ss_pred CHHHHHhcCCCCEeEEEE--ECCEEEEeeCCCCCHHHHHHHHHHH
Confidence 345556669999998766 557888873 48889998888754
No 72
>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=38.97 E-value=96 Score=27.85 Aligned_cols=43 Identities=16% Similarity=0.336 Sum_probs=34.6
Q ss_pred HHHHHHHHccCCccEEEEecCCCEEEEEe--------eCCHHHHHHHHHhc
Q 035968 18 QKVMKLIAKLEGITSIVIDPSKNTVTVIG--------DADPVKIIKKVREF 60 (112)
Q Consensus 18 ~kI~k~L~~~~GV~~v~vd~~~~~v~V~~--------~~~~~~i~~~i~k~ 60 (112)
..++..|.+++||.+|++.-....+.|.- .+++.+|..+|+..
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 56899999999999999886655566663 37889999999973
No 73
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=38.87 E-value=69 Score=17.55 Aligned_cols=50 Identities=12% Similarity=0.038 Sum_probs=28.5
Q ss_pred hHHHHHHHHHHccCC-ccEEEEecC--CCEEEEEee-CCHHHHHHHHHhcCCce
Q 035968 15 KCRQKVMKLIAKLEG-ITSIVIDPS--KNTVTVIGD-ADPVKIIKKVREFRKSA 64 (112)
Q Consensus 15 ~C~~kI~k~L~~~~G-V~~v~vd~~--~~~v~V~~~-~~~~~i~~~i~k~G~~~ 64 (112)
|=-.++-+.|.+... |.++..... .+...+... -+.+.+.+.|++.||.+
T Consensus 11 G~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve~~~~~~~~L~~~G~~v 64 (65)
T cd04882 11 GGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTEDIEKAIEVLQERGVEL 64 (65)
T ss_pred cHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeCCHHHHHHHHHHCCceE
Confidence 334566666766544 433433222 234444322 24889999999999853
No 74
>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=38.72 E-value=26 Score=24.25 Aligned_cols=46 Identities=20% Similarity=0.140 Sum_probs=34.1
Q ss_pred hhHHHHHHHHHHccCCccEEEEecCCCE-------------------EEEEee---CCHHHHHHHHHh
Q 035968 14 LKCRQKVMKLIAKLEGITSIVIDPSKNT-------------------VTVIGD---ADPVKIIKKVRE 59 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd~~~~~-------------------v~V~~~---~~~~~i~~~i~k 59 (112)
+||-+-++..+.+++||.++.+-..++. |.|..| ++.++|++...+
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~g~tgh~E~V~V~yDp~~is~~~Ll~~f~~ 74 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGGYTPNPTYEEVCSGDTGHAEAVQVTYDPKVISYEELLDVFWE 74 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCCCCCCCChhhcccCCCCceEEEEEEECCCcCcHHHHHHHHHH
Confidence 6788888999999999999988654332 334554 677888887765
No 75
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=38.23 E-value=84 Score=18.41 Aligned_cols=29 Identities=28% Similarity=0.424 Sum_probs=21.7
Q ss_pred EEEEecCCCEEEEEee-CCHHHHHHHHHhc
Q 035968 32 SIVIDPSKNTVTVIGD-ADPVKIIKKVREF 60 (112)
Q Consensus 32 ~v~vd~~~~~v~V~~~-~~~~~i~~~i~k~ 60 (112)
.+.+|..++.+.|.|+ .+.+.|.+.|+++
T Consensus 47 ~i~~d~~tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 47 RIVADERTNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp EEEEECTTTEEEEEEEHHHHHHHHHHHHHH
T ss_pred EEEEECCCCEEEEEeCHHHHHHHHHHHHHH
Confidence 7889999999999987 4555566555543
No 76
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=37.76 E-value=62 Score=19.04 Aligned_cols=11 Identities=18% Similarity=0.329 Sum_probs=8.4
Q ss_pred ecccChhHHHH
Q 035968 9 VKLLCLKCRQK 19 (112)
Q Consensus 9 vgm~C~~C~~k 19 (112)
.+..|+.|...
T Consensus 6 ~~~~C~~C~~~ 16 (76)
T PF13192_consen 6 FSPGCPYCPEL 16 (76)
T ss_dssp ECSSCTTHHHH
T ss_pred eCCCCCCcHHH
Confidence 57779999943
No 77
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=37.67 E-value=64 Score=24.83 Aligned_cols=45 Identities=11% Similarity=0.104 Sum_probs=32.8
Q ss_pred EEEeecccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEeeCCHHHHHHHHH-hcCC
Q 035968 5 TIVSVKLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGDADPVKIIKKVR-EFRK 62 (112)
Q Consensus 5 ~~~~vgm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~-k~G~ 62 (112)
+++..+.+ ..|.+.+++.+.+.+||.++++ .+.++-.+.++ ..|+
T Consensus 63 vyL~~~~~-~~~~~~v~~~i~~~~gV~~v~~------------~sre~~l~~L~~~lg~ 108 (297)
T COG2177 63 VYLQIDAD-QDDAALVREKIEGIPGVKSVRF------------ISREEALKELQPWLGF 108 (297)
T ss_pred EEEecCCC-hHHHHHHHHHHhcCCCcceEEE------------eCHHHHHHHHHHHcCc
Confidence 45555666 8999999999999999998866 34455555555 5665
No 78
>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=36.95 E-value=1.2e+02 Score=25.89 Aligned_cols=59 Identities=15% Similarity=0.196 Sum_probs=43.8
Q ss_pred hhHHHHHHHHHHccCCccEEEEecCCCEEEEEee-------CCHHHHHHHHHhcCCceEEecCCCC
Q 035968 14 LKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD-------ADPVKIIKKVREFRKSAAIESIGPP 72 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~-------~~~~~i~~~i~k~G~~~~~~~~~~~ 72 (112)
+.-...|++.+-+-.||.++.+|..++.|.|+.. -.-..+.+..+++|+...++...|-
T Consensus 69 ~~~~~~i~~~~~~~~~~~~~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~~ 134 (630)
T TIGR03675 69 EEAIEKIKEIVPEEAGITDIYFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPPI 134 (630)
T ss_pred HHHHHHHHHhCCCcCCceeEEecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCCC
Confidence 4445567777766679999999999999998742 1345567777799999998765553
No 79
>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=36.69 E-value=33 Score=22.25 Aligned_cols=29 Identities=31% Similarity=0.423 Sum_probs=19.5
Q ss_pred EEEEEeeCCHHHHHHHHHhcCCceEEecC
Q 035968 41 TVTVIGDADPVKIIKKVREFRKSAAIESI 69 (112)
Q Consensus 41 ~v~V~~~~~~~~i~~~i~k~G~~~~~~~~ 69 (112)
-+.|+||.|...+++.++..|+++.++..
T Consensus 99 ivLvSgD~Df~~~v~~l~~~g~~V~v~~~ 127 (146)
T PF01936_consen 99 IVLVSGDSDFAPLVRKLRERGKRVIVVGA 127 (146)
T ss_dssp EEEE---GGGHHHHHHHHHH--EEEEEE-
T ss_pred EEEEECcHHHHHHHHHHHHcCCEEEEEEe
Confidence 34467888889999999999999998874
No 80
>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=36.56 E-value=55 Score=20.71 Aligned_cols=47 Identities=13% Similarity=0.127 Sum_probs=22.7
Q ss_pred HHHHHHHHccCCccEEEEecCCCEEEE--Eee-CCHHHHHHHHHhcCCce
Q 035968 18 QKVMKLIAKLEGITSIVIDPSKNTVTV--IGD-ADPVKIIKKVREFRKSA 64 (112)
Q Consensus 18 ~kI~k~L~~~~GV~~v~vd~~~~~v~V--~~~-~~~~~i~~~i~k~G~~~ 64 (112)
..++=.|+..++|-.|-+|.-.....| ... ++.++|++.+++.+..+
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 344556888899999999954444444 433 78999999999987654
No 81
>PRK09579 multidrug efflux protein; Reviewed
Probab=36.10 E-value=1.2e+02 Score=27.29 Aligned_cols=44 Identities=14% Similarity=0.163 Sum_probs=32.7
Q ss_pred HHHHHHHHHccCCccEEEEe-cCCCEEEEEe--------eCCHHHHHHHHHhc
Q 035968 17 RQKVMKLIAKLEGITSIVID-PSKNTVTVIG--------DADPVKIIKKVREF 60 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd-~~~~~v~V~~--------~~~~~~i~~~i~k~ 60 (112)
.+.|+..|.+++||.+|.+. ....++.|.- .+++++|.++|+..
T Consensus 158 ~~~i~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~~ 210 (1017)
T PRK09579 158 SRVIQPKLATLPGMAEAEILGNQVFAMRLWLDPVKLAGFGLSAGDVTQAVRRY 210 (1017)
T ss_pred HHHHHHHhhcCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 35689999999999999876 3334455542 37888999999864
No 82
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=35.69 E-value=37 Score=21.59 Aligned_cols=23 Identities=13% Similarity=0.326 Sum_probs=19.8
Q ss_pred hhHHHHHHHHHHccCCccEEEEe
Q 035968 14 LKCRQKVMKLIAKLEGITSIVID 36 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd 36 (112)
.+-...++++|+.++||+++++-
T Consensus 61 Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 61 EGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred ccCcHHHHHHHhhccCcceEEEE
Confidence 55678999999999999998764
No 83
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=35.26 E-value=86 Score=18.36 Aligned_cols=28 Identities=14% Similarity=0.394 Sum_probs=18.4
Q ss_pred EeecccChhHHHHHHHHHHccCCccEEE
Q 035968 7 VSVKLLCLKCRQKVMKLIAKLEGITSIV 34 (112)
Q Consensus 7 ~~vgm~C~~C~~kI~k~L~~~~GV~~v~ 34 (112)
|.+...-..=-..|.+.|++++||.+|.
T Consensus 52 l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 52 LTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 3344444555667778888888887663
No 84
>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=35.22 E-value=64 Score=28.89 Aligned_cols=46 Identities=11% Similarity=0.138 Sum_probs=34.3
Q ss_pred hHHHHHHHHHHccCCccEEEEecCC--CEEEEEe--------eCCHHHHHHHHHhc
Q 035968 15 KCRQKVMKLIAKLEGITSIVIDPSK--NTVTVIG--------DADPVKIIKKVREF 60 (112)
Q Consensus 15 ~C~~kI~k~L~~~~GV~~v~vd~~~--~~v~V~~--------~~~~~~i~~~i~k~ 60 (112)
.=+.+|++.|.+++||.+++.|... ..+.|.- .+++++|...++..
T Consensus 698 ~~a~~v~~~l~~~pgv~~v~~~~~~~~~e~~i~id~~~~~~~Glt~~~v~~~l~~~ 753 (1051)
T TIGR00914 698 ATAEKISAVLKGVPGAADVKVEQTTGLPYLTVEIDREKAARYGLTVGDVQDTVATA 753 (1051)
T ss_pred HHHHHHHHHHhcCCCceeeeccccCCCceEEEEECHHHHHHcCCCHHHHHHHHHHH
Confidence 3457889999999999999988643 4455542 26888999999854
No 85
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=35.19 E-value=45 Score=22.01 Aligned_cols=31 Identities=16% Similarity=0.418 Sum_probs=22.7
Q ss_pred EeecccChhH------HHHHHHHHHccCCccEEEEec
Q 035968 7 VSVKLLCLKC------RQKVMKLIAKLEGITSIVIDP 37 (112)
Q Consensus 7 ~~vgm~C~~C------~~kI~k~L~~~~GV~~v~vd~ 37 (112)
++..++-.+| ...++.+|..++||.++++++
T Consensus 53 v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 53 VKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred EEEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEEE
Confidence 3334444555 578999999999999887764
No 86
>TIGR01709 typeII_sec_gspL general secretion pathway protein L. This model represents GspL, protein L of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=35.15 E-value=1.1e+02 Score=23.90 Aligned_cols=50 Identities=14% Similarity=0.219 Sum_probs=33.3
Q ss_pred HHHHHHHccCCcc--EEEEecCCCEEEEEee----CCHHHHHHHHHhcCCceEEecC
Q 035968 19 KVMKLIAKLEGIT--SIVIDPSKNTVTVIGD----ADPVKIIKKVREFRKSAAIESI 69 (112)
Q Consensus 19 kI~k~L~~~~GV~--~v~vd~~~~~v~V~~~----~~~~~i~~~i~k~G~~~~~~~~ 69 (112)
.+-.+|...+|+. +++.|-..+.++++.. -+.+.+...++ .||.+++-+.
T Consensus 314 ~l~~al~~~~~~~l~sL~y~~~~~~L~l~l~a~~~~~le~l~~~l~-~g~~v~~~~~ 369 (384)
T TIGR01709 314 ALATALGQLPGLQLQSLDFDGARGELRLKLEAPSDADLEQLRSRLA-RGFQVALGQA 369 (384)
T ss_pred HHHHHhccCCCCceeEEeEcCCCCEEEEEEecCChHHHHHHHHHHh-hhceeccccc
Confidence 4455666666654 4555555777887754 35577888898 9998887543
No 87
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=34.64 E-value=1.2e+02 Score=27.23 Aligned_cols=45 Identities=11% Similarity=0.170 Sum_probs=33.7
Q ss_pred HHHHHHHHHccCCccEEEEec-CCCEEEEEe--------eCCHHHHHHHHHhcC
Q 035968 17 RQKVMKLIAKLEGITSIVIDP-SKNTVTVIG--------DADPVKIIKKVREFR 61 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd~-~~~~v~V~~--------~~~~~~i~~~i~k~G 61 (112)
...++..|.+++||.+|++.- ....+.|.- .+++++|..+|+...
T Consensus 159 ~~~l~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~~~ 212 (1025)
T PRK10614 159 STQLAQTISQIDGVGDVDVGGSSLPAVRVGLNPQALFNQGVSLDDVRQAISNAN 212 (1025)
T ss_pred HHHHHHHhcCCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhC
Confidence 357999999999999998873 334556652 368889999998543
No 88
>PRK10568 periplasmic protein; Provisional
Probab=34.30 E-value=1.2e+02 Score=21.79 Aligned_cols=38 Identities=18% Similarity=0.188 Sum_probs=28.5
Q ss_pred cChhHHHHHHHHHHccCCcc--EEEEecCCCEEEEEeeCC
Q 035968 12 LCLKCRQKVMKLIAKLEGIT--SIVIDPSKNTVTVIGDAD 49 (112)
Q Consensus 12 ~C~~C~~kI~k~L~~~~GV~--~v~vd~~~~~v~V~~~~~ 49 (112)
.-..=..+|+.+|..-+++. .+.+...+|.|++.|.++
T Consensus 57 ~D~~I~~~v~~~L~~~~~i~~~~I~V~v~~G~V~L~G~V~ 96 (203)
T PRK10568 57 DDSAITAKVKAALVDHDNIKSTDISVKTHQKVVTLSGFVE 96 (203)
T ss_pred cHHHHHHHHHHHHHhCCCCCCCceEEEEECCEEEEEEEeC
Confidence 34455678888888777764 466777899999999854
No 89
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=34.30 E-value=1.2e+02 Score=20.63 Aligned_cols=47 Identities=19% Similarity=0.184 Sum_probs=28.6
Q ss_pred HHHHHHHHHHccC-CccEEEEecCCCEEEEEeeCCH-HHHHHHHHhcCC
Q 035968 16 CRQKVMKLIAKLE-GITSIVIDPSKNTVTVIGDADP-VKIIKKVREFRK 62 (112)
Q Consensus 16 C~~kI~k~L~~~~-GV~~v~vd~~~~~v~V~~~~~~-~~i~~~i~k~G~ 62 (112)
=+.+|.++|.+.. +...+.|...++.|++.|.+.. +...+.+..+|.
T Consensus 27 ~~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~~~~~~aa~~ 75 (147)
T PRK11198 27 AADALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAKEKILLAVGN 75 (147)
T ss_pred HHHHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHHHHHHHHhcc
Confidence 3466777776521 3444566678999999998544 444444444443
No 90
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=33.87 E-value=1.2e+02 Score=27.25 Aligned_cols=44 Identities=11% Similarity=0.194 Sum_probs=33.4
Q ss_pred HHHHHHHHccCCccEEEEec-CCCEEEEEe--------eCCHHHHHHHHHhcC
Q 035968 18 QKVMKLIAKLEGITSIVIDP-SKNTVTVIG--------DADPVKIIKKVREFR 61 (112)
Q Consensus 18 ~kI~k~L~~~~GV~~v~vd~-~~~~v~V~~--------~~~~~~i~~~i~k~G 61 (112)
..|+..|.+++||.+|.+.- ....+.|.- .+++.+|.++|+...
T Consensus 169 ~~l~~~L~~i~gV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~~v~~ai~~~n 221 (1040)
T PRK10503 169 TRVAQKISQVSGVGLVTLSGGQRPAVRVKLNAQAIAALGLTSETVRTAITGAN 221 (1040)
T ss_pred HHHHHHhcCCCCceEEEecCCCceEEEEEECHHHHHHcCCCHHHHHHHHHHhC
Confidence 57899999999999988873 345566652 368889999998543
No 91
>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=33.73 E-value=84 Score=25.04 Aligned_cols=31 Identities=10% Similarity=-0.024 Sum_probs=27.2
Q ss_pred EEecCCCEEEEEeeCCHHHHHHHHHhcCCce
Q 035968 34 VIDPSKNTVTVIGDADPVKIIKKVREFRKSA 64 (112)
Q Consensus 34 ~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~~ 64 (112)
.+|..+++|+|.+.+...+|.+.|.+.|+..
T Consensus 65 ~~d~~~~~v~v~aG~~l~~l~~~L~~~G~~l 95 (419)
T TIGR01679 65 DVDQPTGLATVEAGTRLGALGPQLAQRGLGL 95 (419)
T ss_pred eecCCCCEEEEcCCCCHHHHHHHHHHcCCcc
Confidence 5777889999998899999999999999854
No 92
>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=33.55 E-value=37 Score=20.59 Aligned_cols=27 Identities=30% Similarity=0.407 Sum_probs=20.2
Q ss_pred cccChhHHHHHHHHHHccCCccEEEEe
Q 035968 10 KLLCLKCRQKVMKLIAKLEGITSIVID 36 (112)
Q Consensus 10 gm~C~~C~~kI~k~L~~~~GV~~v~vd 36 (112)
.|.|+.|+...++++++..=..+-++|
T Consensus 15 tLPC~~Cr~HA~~ai~kNNiMSs~DiN 41 (70)
T PF04805_consen 15 TLPCPECRIHAKEAIQKNNIMSSNDIN 41 (70)
T ss_pred cCCCHHHHHHHHHHHHhcCccccCCcc
Confidence 688999999999999875544443333
No 93
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=33.53 E-value=68 Score=22.58 Aligned_cols=33 Identities=24% Similarity=0.409 Sum_probs=27.5
Q ss_pred CEEEEEeeCCHHHHHHHHHhcCCceEEecCCCC
Q 035968 40 NTVTVIGDADPVKIIKKVREFRKSAAIESIGPP 72 (112)
Q Consensus 40 ~~v~V~~~~~~~~i~~~i~k~G~~~~~~~~~~~ 72 (112)
..|.++||.|...++++++..|.++.+++.++.
T Consensus 113 ~ivl~SgD~DF~p~v~~~~~~G~rv~v~~~~~~ 145 (181)
T COG1432 113 TIVLFSGDGDFIPLVEAARDKGKRVEVAGIEPM 145 (181)
T ss_pred EEEEEcCCccHHHHHHHHHHcCCEEEEEecCCc
Confidence 344567888889999999999999999988774
No 94
>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=33.52 E-value=65 Score=24.50 Aligned_cols=50 Identities=16% Similarity=0.166 Sum_probs=35.3
Q ss_pred HHHHHHHHHccCCccEEEEecCCCEEEEE----ee--------CCHHHHHHHHHhcCCceEE
Q 035968 17 RQKVMKLIAKLEGITSIVIDPSKNTVTVI----GD--------ADPVKIIKKVREFRKSAAI 66 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd~~~~~v~V~----~~--------~~~~~i~~~i~k~G~~~~~ 66 (112)
..+|+++|..++||+.+.+--..|++.+- .+ ....++...|+++-|-..+
T Consensus 89 y~Avk~aLL~~~gv~haNI~SsaGtiniYlIl~~d~~~~~k~~~~~~~~K~~iW~~~Y~T~P 150 (291)
T PF03434_consen 89 YEAVKSALLNLNGVEHANIKSSAGTINIYLILKDDCFNDDKTNIIDTEFKANIWQALYLTAP 150 (291)
T ss_pred HHHHHHHhcCCCCceeeeeecCCCeeEEEEEEhhhhhccccccccCHHHHHHHHHHHHccCC
Confidence 46899999999999999888888888752 11 2334566777776664433
No 95
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=33.33 E-value=93 Score=27.66 Aligned_cols=47 Identities=19% Similarity=0.247 Sum_probs=36.6
Q ss_pred hhHHHHHHHHHHccCCccEEEEecCCCEEEEEe----------eCCHHHHHHHHHhc
Q 035968 14 LKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIG----------DADPVKIIKKVREF 60 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~----------~~~~~~i~~~i~k~ 60 (112)
..=+.++++.|++.+|+..+..|...++-.+.- .+++++|...|+..
T Consensus 686 ~~~a~~v~~~l~~~pgv~dv~~~~~~~~~el~i~~dreka~~~Gls~~~va~~l~~a 742 (1021)
T PF00873_consen 686 RKAAEKVKAKLAEIPGVTDVRDDWEDGQPELRIDPDREKAARLGLSPADVARTLRTA 742 (1021)
T ss_dssp HHHHHHHHHHHHHSTTEEEEEESSSSBEEEEEEEE-HHHHHHTTB-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCcccccccccccCcceEEEecHHHHHHcCCCHHHHHHHHHHH
Confidence 445788999999999999999998877776542 26778888888854
No 96
>COG0277 GlcD FAD/FMN-containing dehydrogenases [Energy production and conversion]
Probab=32.87 E-value=53 Score=25.74 Aligned_cols=36 Identities=25% Similarity=0.207 Sum_probs=29.1
Q ss_pred cCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhcCCce
Q 035968 27 LEGITSIVIDPSKNTVTVIGDADPVKIIKKVREFRKSA 64 (112)
Q Consensus 27 ~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~~ 64 (112)
+.+|. ++|..+++++|...+...+|.+.+++.|+..
T Consensus 84 mn~i~--~id~~~~~~~v~aGv~l~~l~~~l~~~G~~~ 119 (459)
T COG0277 84 LNRIL--EIDPEDGTATVQAGVTLEDLEKALAPHGLFL 119 (459)
T ss_pred hcchh--ccCcCCCEEEEcCCccHHHHHHHHHHcCCcc
Confidence 44443 6888999999998888999999999888743
No 97
>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=32.29 E-value=1.5e+02 Score=19.43 Aligned_cols=39 Identities=23% Similarity=0.286 Sum_probs=28.2
Q ss_pred cCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhcCCceEE
Q 035968 27 LEGITSIVIDPSKNTVTVIGDADPVKIIKKVREFRKSAAI 66 (112)
Q Consensus 27 ~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~~~~ 66 (112)
..|+...++ ..+|.++|-|---.+++++.+..+|..+..
T Consensus 40 t~GirqfEi-~n~G~~RI~gYk~se~~~~~f~slG~~~K~ 78 (103)
T PF09158_consen 40 TKGIRQFEI-RNKGEFRIFGYKMSEEIIKKFTSLGMEVKQ 78 (103)
T ss_dssp ETTEEEEEE-ETTSEEEEEEES--HHHHHHHHHTT-EEEE
T ss_pred cCceeEEEE-ecCCcEEEEEEcCCHHHHHHHHhcCcEEEE
Confidence 467777777 367888887765678899999999998766
No 98
>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=32.12 E-value=46 Score=23.95 Aligned_cols=29 Identities=14% Similarity=0.424 Sum_probs=21.2
Q ss_pred HHHHHHHHHHccCCccEEEE--ecCCCEEEE
Q 035968 16 CRQKVMKLIAKLEGITSIVI--DPSKNTVTV 44 (112)
Q Consensus 16 C~~kI~k~L~~~~GV~~v~v--d~~~~~v~V 44 (112)
=..+++..|.++.||.+|+| .+.++.-.|
T Consensus 62 lE~~L~~iL~~I~GvG~V~VmItl~s~~e~v 92 (186)
T TIGR02830 62 YENELKEILEKIEGVGDVTVMVNLDSSEEKV 92 (186)
T ss_pred HHHHHHHHHHhccCcceeEEEEEECCCceEE
Confidence 35788999999999998764 455555544
No 99
>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=32.02 E-value=51 Score=23.81 Aligned_cols=21 Identities=14% Similarity=0.344 Sum_probs=17.4
Q ss_pred HHHHHHHHHccCCccEEEEec
Q 035968 17 RQKVMKLIAKLEGITSIVIDP 37 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd~ 37 (112)
...+++.|+.++||.+++|.+
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 356788999999999998873
No 100
>PF10006 DUF2249: Uncharacterized conserved protein (DUF2249); InterPro: IPR018720 This domain is found in a number of hypothetical bacterial and archaeal proteins with no known function. It is also found in proteins described as cupin 2 and hemerythrin. It represents a conserved region that shows distant similarity to the SirA protein (see IPR001455 from INTERPRO).
Probab=31.99 E-value=1.1e+02 Score=17.77 Aligned_cols=45 Identities=22% Similarity=0.417 Sum_probs=31.9
Q ss_pred HHHHHHHHccCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhc-CC-ceEEecCCC
Q 035968 18 QKVMKLIAKLEGITSIVIDPSKNTVTVIGDADPVKIIKKVREF-RK-SAAIESIGP 71 (112)
Q Consensus 18 ~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~-G~-~~~~~~~~~ 71 (112)
..|.+++.+++ ..+.+.+..+.+|.-|...+... |+ ..+....++
T Consensus 14 ~~il~~~~~L~---------~Ge~l~lv~d~~P~pL~~~l~~~~g~~~~~~~~~~~ 60 (69)
T PF10006_consen 14 ERILEALDELP---------PGETLELVNDHDPRPLYPQLEERRGFFSWEYEEQGP 60 (69)
T ss_pred HHHHHHHHcCC---------CCCEEEEEeCCCCHHHHHHHHHhCCCceEEEEEcCC
Confidence 44555555544 45667778889999999999988 98 666655444
No 101
>PRK11282 glcE glycolate oxidase FAD binding subunit; Provisional
Probab=31.87 E-value=86 Score=24.66 Aligned_cols=37 Identities=16% Similarity=0.201 Sum_probs=29.5
Q ss_pred HccCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhcCCc
Q 035968 25 AKLEGITSIVIDPSKNTVTVIGDADPVKIIKKVREFRKS 63 (112)
Q Consensus 25 ~~~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~ 63 (112)
.++.+|. ++|..+..++|...+...+|.+.|.+.|+.
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 3444553 678888999999889999999999998863
No 102
>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=31.32 E-value=52 Score=19.20 Aligned_cols=20 Identities=20% Similarity=0.414 Sum_probs=16.2
Q ss_pred hHHHHHHHHHHccCCccEEE
Q 035968 15 KCRQKVMKLIAKLEGITSIV 34 (112)
Q Consensus 15 ~C~~kI~k~L~~~~GV~~v~ 34 (112)
.=-..+.+.|++++||.+|.
T Consensus 49 ~~L~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 49 EKLQTLMPEIRRIDGVEDVK 68 (74)
T ss_pred HHHHHHHHHHhCCCCceEEE
Confidence 33578889999999998875
No 103
>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=31.23 E-value=56 Score=20.55 Aligned_cols=22 Identities=14% Similarity=0.345 Sum_probs=18.9
Q ss_pred hHHHHHHHHHHccCCccEEEEe
Q 035968 15 KCRQKVMKLIAKLEGITSIVID 36 (112)
Q Consensus 15 ~C~~kI~k~L~~~~GV~~v~vd 36 (112)
+-...++.++++.+||+++++.
T Consensus 62 ~~td~lee~i~~~d~VqsveI~ 83 (88)
T cd00292 62 GGTDELEEAISEEDGVQSVDVE 83 (88)
T ss_pred cCcHHHHHHHhccCCceEEEEE
Confidence 5558899999999999999875
No 104
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=31.20 E-value=1.5e+02 Score=19.04 Aligned_cols=54 Identities=11% Similarity=0.106 Sum_probs=32.1
Q ss_pred Eee-cccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee--CCHHHHHHHHHhc
Q 035968 7 VSV-KLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD--ADPVKIIKKVREF 60 (112)
Q Consensus 7 ~~v-gm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~--~~~~~i~~~i~k~ 60 (112)
+++ |+.=+-....|+..|+....|.-|++........|... -.+..++..+...
T Consensus 4 l~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 4 LKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp EEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred EEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhc
Confidence 444 56555569999999999998988888776677777764 4577888888866
No 105
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=30.92 E-value=1.8e+02 Score=26.36 Aligned_cols=47 Identities=11% Similarity=0.197 Sum_probs=36.1
Q ss_pred HHHHHHHHHccCCccEEEEecC-CCEEEEEe--------eCCHHHHHHHHHhcCCc
Q 035968 17 RQKVMKLIAKLEGITSIVIDPS-KNTVTVIG--------DADPVKIIKKVREFRKS 63 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd~~-~~~v~V~~--------~~~~~~i~~~i~k~G~~ 63 (112)
.+.|+..|..++||.+|.+.-. ...++|.- .++++++..+|+.....
T Consensus 157 ~~~l~~~L~~v~GV~~V~~~G~~~~~~rI~ldp~kLa~~gLt~~dV~~ai~~qN~~ 212 (1009)
T COG0841 157 ASNVRDELSRVPGVGSVQLFGAQEYAMRIWLDPAKLAAYGLTPSDVQSAIRAQNVQ 212 (1009)
T ss_pred HHHHHHHHhcCCCceEEEEcCCCceeEEEEeCHHHHHHcCCCHHHHHHHHHHhCcc
Confidence 4678999999999999998743 55666652 37889999999975543
No 106
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=30.48 E-value=90 Score=22.29 Aligned_cols=48 Identities=21% Similarity=0.175 Sum_probs=34.0
Q ss_pred hhHHHHHHHHHHc-cCCccEEEEecCC-----CEEEEEeeCCHHHHHHHHHhcCC
Q 035968 14 LKCRQKVMKLIAK-LEGITSIVIDPSK-----NTVTVIGDADPVKIIKKVREFRK 62 (112)
Q Consensus 14 ~~C~~kI~k~L~~-~~GV~~v~vd~~~-----~~v~V~~~~~~~~i~~~i~k~G~ 62 (112)
...-.+|++.|.+ +||+..+.++... +.+=|+. .+++.|.++|.+..-
T Consensus 57 D~~GekIRk~i~~~vp~~khafi~~~~a~~~~~~iGVE~-As~e~I~~AL~~~~~ 110 (174)
T TIGR00334 57 DFPGEKIRKKIEQHLPGYENCFIPKHLAKPNKKKIGVEE-ASVEAIIAALENVHE 110 (174)
T ss_pred CCchHHHHHHHHHHCCCCeEEeeeHHhcCcCCCCcccCC-CCHHHHHHHHHHhcc
Confidence 3445688888876 8999988887432 2333332 789999999998764
No 107
>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=29.54 E-value=1.1e+02 Score=24.73 Aligned_cols=38 Identities=18% Similarity=0.239 Sum_probs=29.9
Q ss_pred ccCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhcCCceE
Q 035968 26 KLEGITSIVIDPSKNTVTVIGDADPVKIIKKVREFRKSAA 65 (112)
Q Consensus 26 ~~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~~~ 65 (112)
++.+|. .+|..+++++|.+.+...+|.+.|.+.|+...
T Consensus 65 ~l~~i~--~id~~~~~vtV~aG~~l~~L~~~L~~~Gl~l~ 102 (438)
T TIGR01678 65 KMNKVL--QFDKEKKQITVEAGIRLYQLHEQLDEHGYSMS 102 (438)
T ss_pred hcCCce--EEcCCCCEEEEcCCCCHHHHHHHHHHcCCEec
Confidence 344442 57778889999988999999999999997643
No 108
>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=29.37 E-value=77 Score=17.93 Aligned_cols=28 Identities=21% Similarity=0.315 Sum_probs=20.7
Q ss_pred HHHHHHHHHccCCccEEEEec-CCCEEEE
Q 035968 17 RQKVMKLIAKLEGITSIVIDP-SKNTVTV 44 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd~-~~~~v~V 44 (112)
...+++.|.++|.|.+|.+.. --+++.|
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 457888899999999999873 3345554
No 109
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=29.33 E-value=1.6e+02 Score=21.13 Aligned_cols=62 Identities=5% Similarity=-0.071 Sum_probs=41.8
Q ss_pred CceeEEEee-cccChhHHHHHHHHHHccCC-ccEEEEecCCCEE----EEEee-CCHHHHHHHHHhcCC
Q 035968 1 MAKKTIVSV-KLLCLKCRQKVMKLIAKLEG-ITSIVIDPSKNTV----TVIGD-ADPVKIIKKVREFRK 62 (112)
Q Consensus 1 m~~~~~~~v-gm~C~~C~~kI~k~L~~~~G-V~~v~vd~~~~~v----~V~~~-~~~~~i~~~i~k~G~ 62 (112)
|++..++.+ |-.-+|-...|.+.|....+ +.+.+...-.+.. .|.+. ...+.|...|...+.
T Consensus 5 m~~~lviTviG~DrpGIVa~vs~~l~~~g~NI~ds~~t~lgg~Fa~i~lvs~~~~~~~~le~~L~~l~~ 73 (190)
T PRK11589 5 SQHYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLSGSWNAITLIESTLPLKGA 73 (190)
T ss_pred cccEEEEEEEcCCCChHHHHHHHHHHHcCCCeeehhhHhhCCceEEEEEEeCChhHHHHHHHHHHhhhh
Confidence 666777776 99999999999999998776 4444444333433 34443 355667777766553
No 110
>PRK10638 glutaredoxin 3; Provisional
Probab=29.09 E-value=1.3e+02 Score=17.78 Aligned_cols=34 Identities=24% Similarity=0.382 Sum_probs=21.2
Q ss_pred CceeEEEeecccChhHHHHHHHHHHccCCccEEEEec
Q 035968 1 MAKKTIVSVKLLCLKCRQKVMKLIAKLEGITSIVIDP 37 (112)
Q Consensus 1 m~~~~~~~vgm~C~~C~~kI~k~L~~~~GV~~v~vd~ 37 (112)
|. ++.+-.--.|+.|. ++++.|.. .|+.-..+|.
T Consensus 1 m~-~v~ly~~~~Cp~C~-~a~~~L~~-~gi~y~~~dv 34 (83)
T PRK10638 1 MA-NVEIYTKATCPFCH-RAKALLNS-KGVSFQEIPI 34 (83)
T ss_pred CC-cEEEEECCCChhHH-HHHHHHHH-cCCCcEEEEC
Confidence 44 45555567799998 56666665 4665544444
No 111
>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=28.56 E-value=64 Score=18.61 Aligned_cols=40 Identities=13% Similarity=0.140 Sum_probs=23.3
Q ss_pred HHHHHHccCCccEEEEe----cCCCEEEEEe-eCCHHHHHHHHHh
Q 035968 20 VMKLIAKLEGITSIVID----PSKNTVTVIG-DADPVKIIKKVRE 59 (112)
Q Consensus 20 I~k~L~~~~GV~~v~vd----~~~~~v~V~~-~~~~~~i~~~i~k 59 (112)
|+.+|.+.+||.++.+= ...+...+-. ..+.++|.+.+++
T Consensus 2 IE~~l~~~~~V~~~~V~~~~d~~~g~~l~a~vv~~~~~i~~~~~~ 46 (73)
T PF13193_consen 2 IESVLRQHPGVAEAAVVGVPDEDWGERLVAFVVLDEEEIRDHLRD 46 (73)
T ss_dssp HHHHHHTSTTEEEEEEEEEEETTTEEEEEEEEEEHHHHHHHHHHH
T ss_pred HHHHHhcCCCccEEEEEEEEcccccccceeEEEeeecccccchhh
Confidence 78999999999876532 1222222211 1144677777764
No 112
>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=28.39 E-value=1.1e+02 Score=19.93 Aligned_cols=33 Identities=3% Similarity=0.039 Sum_probs=24.2
Q ss_pred hHHHHHHHHHHccCC---ccEEEEecCCCEEEEEee
Q 035968 15 KCRQKVMKLIAKLEG---ITSIVIDPSKNTVTVIGD 47 (112)
Q Consensus 15 ~C~~kI~k~L~~~~G---V~~v~vd~~~~~v~V~~~ 47 (112)
--.+.|+.+|...+- |.+..+...++++.|+.+
T Consensus 69 Ei~r~I~EaL~~d~rI~~V~~f~f~~~~~~l~v~f~ 104 (112)
T PF10934_consen 69 EIEREIEEALLQDPRITSVENFSFEWEGDSLYVSFT 104 (112)
T ss_pred HHHHHHHHHHhcCCCcceEEEEEEEEECCEEEEEEE
Confidence 346789999976665 555677788898888754
No 113
>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=27.85 E-value=1.1e+02 Score=25.73 Aligned_cols=32 Identities=19% Similarity=0.200 Sum_probs=27.0
Q ss_pred EEEecCCCEEEEEeeCCHHHHHHHHHhcCCce
Q 035968 33 IVIDPSKNTVTVIGDADPVKIIKKVREFRKSA 64 (112)
Q Consensus 33 v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~~ 64 (112)
+.+|..+++|+|.+.+...+|.+.|.+.|+..
T Consensus 92 l~iD~~~~tVtV~AG~~l~~L~~~L~~~Glal 123 (557)
T TIGR01677 92 VAVDATAMTVTVESGMSLRELIVEAEKAGLAL 123 (557)
T ss_pred EEEeCCCCEEEECCCCcHHHHHHHHHHcCCEe
Confidence 46777788999998889999999999998753
No 114
>KOG4730 consensus D-arabinono-1, 4-lactone oxidase [Defense mechanisms]
Probab=27.53 E-value=77 Score=26.29 Aligned_cols=32 Identities=25% Similarity=0.330 Sum_probs=28.1
Q ss_pred EEEecCCCEEEEEeeCCHHHHHHHHHhcCCce
Q 035968 33 IVIDPSKNTVTVIGDADPVKIIKKVREFRKSA 64 (112)
Q Consensus 33 v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~~ 64 (112)
+++|.+..+|||+..+..-+|++.+++.|+..
T Consensus 105 v~~dpe~~tvTV~aGirlrQLie~~~~~GlsL 136 (518)
T KOG4730|consen 105 VEFDPELKTVTVQAGIRLRQLIEELAKLGLSL 136 (518)
T ss_pred eeeCchhceEEeccCcCHHHHHHHHHhcCccc
Confidence 46688889999998899999999999999864
No 115
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=27.32 E-value=1e+02 Score=27.68 Aligned_cols=46 Identities=13% Similarity=0.134 Sum_probs=35.0
Q ss_pred hHHHHHHHHHHccCCccEEEEecCCC--EEEEEe--------eCCHHHHHHHHHhc
Q 035968 15 KCRQKVMKLIAKLEGITSIVIDPSKN--TVTVIG--------DADPVKIIKKVREF 60 (112)
Q Consensus 15 ~C~~kI~k~L~~~~GV~~v~vd~~~~--~v~V~~--------~~~~~~i~~~i~k~ 60 (112)
.=+.+|++.|.+.+|+.+++.|+..+ ++.|.- .+++.+|...|+..
T Consensus 675 ~~a~~i~~~L~~~pgv~~v~~~~~~~~~el~i~id~~ka~~~Gls~~~v~~~l~~~ 730 (1025)
T PRK10614 675 EWEPKIRKALAALPELADVNSDQQDKGAEMALTYDRDTMARLGIDVQAANSLLNNA 730 (1025)
T ss_pred HHHHHHHHHHhcCCCeEEeecCCCCCCceEEEEECHHHHHHcCCCHHHHHHHHHHH
Confidence 34678999999999999999876544 555542 36888999999854
No 116
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=27.30 E-value=81 Score=21.66 Aligned_cols=55 Identities=18% Similarity=0.234 Sum_probs=28.2
Q ss_pred EEeecccChhHH------HHHHHHHHccCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhcCC
Q 035968 6 IVSVKLLCLKCR------QKVMKLIAKLEGITSIVIDPSKNTVTVIGDADPVKIIKKVREFRK 62 (112)
Q Consensus 6 ~~~vgm~C~~C~------~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~ 62 (112)
.+.+-++-.+|. ..|+++|.++ |+.+++|++.-.-.= +.+-=.++-.++|+..|.
T Consensus 28 ~VtIt~Ty~gcpa~e~L~~~I~~aL~~~-Gv~~V~V~i~~~p~W-t~d~it~~gr~~l~~~gi 88 (146)
T TIGR02159 28 VVKFTPTYSGCPALEVIRQDIRDAVRAL-GVEVVEVSTSLDPPW-TTDWITEDAREKLREYGI 88 (146)
T ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHhc-CCCeEEEeEeeCCCC-ChHHCCHHHHHHHHhcCc
Confidence 344444545554 3477888876 888777753100000 011111345677777774
No 117
>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=27.19 E-value=80 Score=17.16 Aligned_cols=18 Identities=22% Similarity=0.427 Sum_probs=15.0
Q ss_pred HHHHHHHHHccCCccEEE
Q 035968 17 RQKVMKLIAKLEGITSIV 34 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~ 34 (112)
...+.+.|++++||.++.
T Consensus 52 ~~~l~~~l~~~~~V~~v~ 69 (71)
T cd04879 52 PEEVLEELKALPGIIRVR 69 (71)
T ss_pred CHHHHHHHHcCCCeEEEE
Confidence 458888999999998875
No 118
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=26.84 E-value=2.2e+02 Score=19.63 Aligned_cols=38 Identities=11% Similarity=0.224 Sum_probs=30.5
Q ss_pred EEEEecCCCEEEEEee--CCHHHHHHHHHhcCCceEEecC
Q 035968 32 SIVIDPSKNTVTVIGD--ADPVKIIKKVREFRKSAAIESI 69 (112)
Q Consensus 32 ~v~vd~~~~~v~V~~~--~~~~~i~~~i~k~G~~~~~~~~ 69 (112)
-+-+|+..+-+.+... ++..+|++.|.+.|+.+-+...
T Consensus 45 iAildL~G~~l~l~S~R~~~~~evi~~I~~~G~PviVAtD 84 (138)
T PF04312_consen 45 IAILDLDGELLDLKSSRNMSRSEVIEWISEYGKPVIVATD 84 (138)
T ss_pred EEEEecCCcEEEEEeecCCCHHHHHHHHHHcCCEEEEEec
Confidence 3567888888887753 8999999999999998877544
No 119
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=26.70 E-value=2.3e+02 Score=24.12 Aligned_cols=59 Identities=17% Similarity=0.252 Sum_probs=42.9
Q ss_pred hHHHHHHHHHHccCCccEEEEecCCCEEEEEee-------CCHHHHHHHHHhcCCceEEecCCCCc
Q 035968 15 KCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD-------ADPVKIIKKVREFRKSAAIESIGPPK 73 (112)
Q Consensus 15 ~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~-------~~~~~i~~~i~k~G~~~~~~~~~~~~ 73 (112)
.-...|.+.+-+..||.++.+|..++.|.|... -.-..+....+++|+.++++...|-+
T Consensus 76 ~A~~~I~eivP~ea~i~~i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~PPi~ 141 (637)
T COG1782 76 EARKIILEIVPEEAGITDIYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTPPIQ 141 (637)
T ss_pred HHHHHHHHhCccccCceeEEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecCCCc
Confidence 334566666767789999999999999998742 13345666667999999988765543
No 120
>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=26.68 E-value=74 Score=19.99 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=19.7
Q ss_pred hhHHHHHHHHH-HccCCccEEEEe
Q 035968 14 LKCRQKVMKLI-AKLEGITSIVID 36 (112)
Q Consensus 14 ~~C~~kI~k~L-~~~~GV~~v~vd 36 (112)
.+-...|+.+| +..+||+++++.
T Consensus 61 ~~~~d~lee~i~~~~e~Vqsvei~ 84 (89)
T PF00736_consen 61 EGSTDDLEEAIESFEEGVQSVEIE 84 (89)
T ss_dssp TCGHHHHHHHHTTCTTTEEEEEEE
T ss_pred ccChHHHHHHHHhcCCCccEEEEE
Confidence 46778899999 999999999874
No 121
>PLN02465 L-galactono-1,4-lactone dehydrogenase
Probab=26.46 E-value=1.2e+02 Score=25.59 Aligned_cols=38 Identities=18% Similarity=0.315 Sum_probs=30.1
Q ss_pred ccCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhcCCceE
Q 035968 26 KLEGITSIVIDPSKNTVTVIGDADPVKIIKKVREFRKSAA 65 (112)
Q Consensus 26 ~~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~~~ 65 (112)
.+.+| +.+|..+++|+|.+.+...+|.+.+.+.|....
T Consensus 147 ~l~~I--l~vD~e~~~VtV~AG~~l~~L~~~L~~~GLal~ 184 (573)
T PLN02465 147 LMDKV--LEVDKEKKRVTVQAGARVQQVVEALRPHGLTLQ 184 (573)
T ss_pred CCCCc--EEEeCCCCEEEEccCCCHHHHHHHHHHcCCEec
Confidence 34444 367888899999988999999999999997543
No 122
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=26.12 E-value=70 Score=24.14 Aligned_cols=20 Identities=20% Similarity=0.488 Sum_probs=16.4
Q ss_pred HHHHHHHHHccCCccEEEEe
Q 035968 17 RQKVMKLIAKLEGITSIVID 36 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd 36 (112)
+..+++.|++++||.+++|.
T Consensus 111 eQ~le~tLs~mDGVi~ArV~ 130 (246)
T COG4669 111 EQQLEQTLSKMDGVISARVH 130 (246)
T ss_pred HHHHHHHHHhcCceEEEEEE
Confidence 56789999999999876654
No 123
>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=26.04 E-value=2.4e+02 Score=20.23 Aligned_cols=42 Identities=12% Similarity=0.183 Sum_probs=27.5
Q ss_pred HHHHHHHHHccCCccE--EEEecCCCEEEEEeeCCHHHHHHHHH
Q 035968 17 RQKVMKLIAKLEGITS--IVIDPSKNTVTVIGDADPVKIIKKVR 58 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~--v~vd~~~~~v~V~~~~~~~~i~~~i~ 58 (112)
..+|.+++++.+||.- +..|...+|..++.--+++.|.+++-
T Consensus 18 ie~I~~a~~~~~gv~ll~~~~D~~~NRsv~T~vG~p~~v~~a~~ 61 (178)
T PF07837_consen 18 IEAIAKAARNVPGVKLLDVFSDADYNRSVITLVGEPEAVAEAAF 61 (178)
T ss_dssp HHHHHHHCCTSTTEEEEEEEEETTTTEEEEEEEE-HHHHHHHHH
T ss_pred HHHHHHHHHcCCCCEEEecCCCCCCCCCeEEEeeChHHHHHHHH
Confidence 4578888888899764 45567888887775444555554443
No 124
>KOG3432 consensus Vacuolar H+-ATPase V1 sector, subunit F [Energy production and conversion]
Probab=25.75 E-value=1.1e+02 Score=20.44 Aligned_cols=36 Identities=17% Similarity=0.231 Sum_probs=30.3
Q ss_pred cCCccEEEEecCCCEEEEEeeCCHHHHHHHHHhcCC
Q 035968 27 LEGITSIVIDPSKNTVTVIGDADPVKIIKKVREFRK 62 (112)
Q Consensus 27 ~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~ 62 (112)
+.||..+.-+...+-+.|......++|.+++...-.
T Consensus 24 laGvg~v~~~r~~Nf~vv~~~Tt~~eiedaF~~f~~ 59 (121)
T KOG3432|consen 24 LAGVGEVNENREPNFLVVDSKTTVEEIEDAFKSFTA 59 (121)
T ss_pred eecccccccCCCCCEEEEeccCCHHHHHHHHHhhcc
Confidence 569998888888999999988889999999986443
No 125
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=25.71 E-value=1.5e+02 Score=17.50 Aligned_cols=32 Identities=19% Similarity=0.305 Sum_probs=20.6
Q ss_pred EEeecccChhHHHHHHHHHHcc----CCccEEEEecC
Q 035968 6 IVSVKLLCLKCRQKVMKLIAKL----EGITSIVIDPS 38 (112)
Q Consensus 6 ~~~vgm~C~~C~~kI~k~L~~~----~GV~~v~vd~~ 38 (112)
.+-.--.|+.|. ++++.|..+ .|+.-..+|..
T Consensus 4 ~iy~~~~C~~C~-~a~~~L~~l~~~~~~i~~~~idi~ 39 (85)
T PRK11200 4 VIFGRPGCPYCV-RAKELAEKLSEERDDFDYRYVDIH 39 (85)
T ss_pred EEEeCCCChhHH-HHHHHHHhhcccccCCcEEEEECC
Confidence 333455799998 566667665 57766666654
No 126
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=25.69 E-value=40 Score=19.74 Aligned_cols=53 Identities=23% Similarity=0.374 Sum_probs=31.9
Q ss_pred CceeEEEeecccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee-CCHHHHHHHH
Q 035968 1 MAKKTIVSVKLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD-ADPVKIIKKV 57 (112)
Q Consensus 1 m~~~~~~~vgm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~-~~~~~i~~~i 57 (112)
|+++-+..+.-+|..|-..|...=..+-|....+..+. -|-++ +.|++..+.+
T Consensus 1 M~~~kieIV~t~CrRCGk~i~tl~~SL~Gad~lr~klG----~IC~~CitpEE~~~I~ 54 (60)
T PF10892_consen 1 MSKGKIEIVETPCRRCGKSIRTLSRSLIGADDLRVKLG----GICGDCITPEEDREIL 54 (60)
T ss_pred CCCCceEeeeehhhhhCccHHHHHHHhhChHHHHHHHc----chhhccCCHHHHHHHH
Confidence 66665667789999999988877666666543332221 13333 5565554443
No 127
>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=25.64 E-value=1.2e+02 Score=19.53 Aligned_cols=32 Identities=25% Similarity=0.155 Sum_probs=27.0
Q ss_pred EEEecCCCEEEEEeeCCHHHHHHHHHhcCCce
Q 035968 33 IVIDPSKNTVTVIGDADPVKIIKKVREFRKSA 64 (112)
Q Consensus 33 v~vd~~~~~v~V~~~~~~~~i~~~i~k~G~~~ 64 (112)
+.+|.+..+++|...+...+|.+.+.+.|+..
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 56888899999998889999999998877643
No 128
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=25.51 E-value=72 Score=18.42 Aligned_cols=18 Identities=17% Similarity=0.171 Sum_probs=15.6
Q ss_pred eCCHHHHHHHHHhcCCce
Q 035968 47 DADPVKIIKKVREFRKSA 64 (112)
Q Consensus 47 ~~~~~~i~~~i~k~G~~~ 64 (112)
+++.+.|.+++..+||.-
T Consensus 31 ~id~~~l~~kL~~~Gy~Y 48 (55)
T PF14056_consen 31 DIDKEELEEKLASIGYEY 48 (55)
T ss_pred CCCHHHHHHHHHHcCCeE
Confidence 478899999999999964
No 129
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=25.36 E-value=2e+02 Score=20.59 Aligned_cols=28 Identities=11% Similarity=0.145 Sum_probs=20.5
Q ss_pred CEEEEEee---CCHHHHHHHHHhcCCceEEe
Q 035968 40 NTVTVIGD---ADPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 40 ~~v~V~~~---~~~~~i~~~i~k~G~~~~~~ 67 (112)
..+.|.|- .-+.-|++.|++.||.++.+
T Consensus 229 ~~fvvVGa~HL~G~~gvl~lLr~~Gy~V~~v 259 (259)
T PF01963_consen 229 TVFVVVGAGHLPGEDGVLDLLRKKGYTVEPV 259 (259)
T ss_pred CEEEEEcchhccchhhHHHHHHhCCceeecC
Confidence 34455553 46678999999999998754
No 130
>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=24.88 E-value=1.2e+02 Score=19.54 Aligned_cols=39 Identities=15% Similarity=0.264 Sum_probs=20.2
Q ss_pred CCccEEEEec---CCCEEEEEee-----CCHHHHHHHHHh-cCCceEE
Q 035968 28 EGITSIVIDP---SKNTVTVIGD-----ADPVKIIKKVRE-FRKSAAI 66 (112)
Q Consensus 28 ~GV~~v~vd~---~~~~v~V~~~-----~~~~~i~~~i~k-~G~~~~~ 66 (112)
.+...+.... ..+.||+... .++.++.+.|++ .|....+
T Consensus 23 ~~~i~i~~e~rgr~gK~VTvV~Gl~~~~~~l~~l~k~LKk~~gcGgtv 70 (101)
T TIGR01158 23 DQVVRIQRETRGRKGKGVTIIEGLDLSDIDLKELAKELKSKCGCGGTV 70 (101)
T ss_pred CceEEEEEEEecCCCCEEEEEeCCcCchhhHHHHHHHHHHHhcCCeeE
Confidence 4444444442 3566665422 456667777774 3444443
No 131
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=24.79 E-value=1.6e+02 Score=17.44 Aligned_cols=52 Identities=12% Similarity=0.218 Sum_probs=33.5
Q ss_pred hhHHHHHHHHHHcc---CCccEEEEecCCCEEEEEe--eCCHHHHHHHHHh-cCCceE
Q 035968 14 LKCRQKVMKLIAKL---EGITSIVIDPSKNTVTVIG--DADPVKIIKKVRE-FRKSAA 65 (112)
Q Consensus 14 ~~C~~kI~k~L~~~---~GV~~v~vd~~~~~v~V~~--~~~~~~i~~~i~k-~G~~~~ 65 (112)
.+=..++.++|.++ +---.+..|..++.+.|.| ++-.+-++.+|++ .|-.++
T Consensus 15 ~~d~~kl~~aL~~l~~eDP~l~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~ 72 (75)
T PF14492_consen 15 KEDEPKLSEALQKLSEEDPSLRVERDEETGELILSGMGELHLEVLLERLKRRFGVEVE 72 (75)
T ss_dssp HHHHHHHHHHHHHHHHH-TTSEEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEE
T ss_pred HhHHHHHHHHHHHHHhcCCeEEEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeE
Confidence 33445555555543 3344688999999999885 5677788888884 454443
No 132
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=24.59 E-value=1.1e+02 Score=21.55 Aligned_cols=24 Identities=13% Similarity=0.219 Sum_probs=20.0
Q ss_pred cCCCEEEEEeeCCHHHHHHHHHhc
Q 035968 37 PSKNTVTVIGDADPVKIIKKVREF 60 (112)
Q Consensus 37 ~~~~~v~V~~~~~~~~i~~~i~k~ 60 (112)
|.+|+++|+|.-+.+++..++++.
T Consensus 145 F~sGkvvitGaks~~~~~~a~~~i 168 (174)
T cd00652 145 FVSGKIVITGAKSREDIYEAVEKI 168 (174)
T ss_pred EcCCEEEEEecCCHHHHHHHHHHH
Confidence 689999999988888888777654
No 133
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=24.47 E-value=64 Score=20.99 Aligned_cols=17 Identities=12% Similarity=0.614 Sum_probs=15.6
Q ss_pred cccChhHHHHHHHHHHc
Q 035968 10 KLLCLKCRQKVMKLIAK 26 (112)
Q Consensus 10 gm~C~~C~~kI~k~L~~ 26 (112)
.+.|..|+..+++.|.+
T Consensus 18 ~~qC~~cA~Al~~~L~~ 34 (100)
T PF15643_consen 18 IFQCVECASALKQFLKQ 34 (100)
T ss_pred ceehHHHHHHHHHHHHH
Confidence 67899999999999986
No 134
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=24.39 E-value=1.1e+02 Score=21.57 Aligned_cols=24 Identities=8% Similarity=0.165 Sum_probs=19.7
Q ss_pred cCCCEEEEEeeCCHHHHHHHHHhc
Q 035968 37 PSKNTVTVIGDADPVKIIKKVREF 60 (112)
Q Consensus 37 ~~~~~v~V~~~~~~~~i~~~i~k~ 60 (112)
|.+|+++|+|.-+.+++.++++.+
T Consensus 144 F~sGkvvitGaks~~~~~~a~~~i 167 (174)
T cd04516 144 FVSGKIVLTGAKSREEIYQAFENI 167 (174)
T ss_pred eCCCEEEEEecCCHHHHHHHHHHH
Confidence 789999999987888888777653
No 135
>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=24.13 E-value=86 Score=22.47 Aligned_cols=21 Identities=14% Similarity=0.428 Sum_probs=16.8
Q ss_pred HHHHHHHHHccCCccEEEEec
Q 035968 17 RQKVMKLIAKLEGITSIVIDP 37 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd~ 37 (112)
...+.+.|..++||.+++|.+
T Consensus 109 e~EL~rtI~~i~~V~~ArVhl 129 (193)
T TIGR02544 109 EQRLEQTLSQIDGVISARVHV 129 (193)
T ss_pred HHHHHHHHHhcCCeeeeEEEE
Confidence 346788899999999888764
No 136
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=23.88 E-value=2.3e+02 Score=18.96 Aligned_cols=50 Identities=18% Similarity=0.306 Sum_probs=32.4
Q ss_pred HHHHHHHHHccCCccEEEEecCCCEEEEEeeCCHHHHHHHHH-----hcCCceEEe
Q 035968 17 RQKVMKLIAKLEGITSIVIDPSKNTVTVIGDADPVKIIKKVR-----EFRKSAAIE 67 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~~~~~~i~~~i~-----k~G~~~~~~ 67 (112)
...++..|.++ |-..|+.-+.+|-|.++.+.+++.|...|+ ..|+.+..+
T Consensus 21 MaeLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~fG~~v~v~ 75 (137)
T PF08002_consen 21 MAELREALEDL-GFTNVRTYIQSGNVVFESDRDPAELAAKIEKALEERFGFDVPVI 75 (137)
T ss_dssp HHHHHHHHHHC-T-EEEEEETTTTEEEEEESS-HHHHHHHHHHHHHHH-TT---EE
T ss_pred HHHHHHHHHHc-CCCCceEEEeeCCEEEecCCChHHHHHHHHHHHHHhcCCCeEEE
Confidence 45666777665 888899889999999997677776655554 468876543
No 137
>PRK07334 threonine dehydratase; Provisional
Probab=23.84 E-value=3.7e+02 Score=21.21 Aligned_cols=55 Identities=15% Similarity=0.097 Sum_probs=34.7
Q ss_pred ChhHHHHHHHHHHccCC-ccEEEEec-----CCCEEEEEe--e----CCHHHHHHHHHhcCCceEEe
Q 035968 13 CLKCRQKVMKLIAKLEG-ITSIVIDP-----SKNTVTVIG--D----ADPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 13 C~~C~~kI~k~L~~~~G-V~~v~vd~-----~~~~v~V~~--~----~~~~~i~~~i~k~G~~~~~~ 67 (112)
=.+=-..|.+.|++... |.++.... ..+.+.+.. . ...+.|+++|++.||.+.++
T Consensus 336 r~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~~~L~~vi~~Lr~~g~~~~~~ 402 (403)
T PRK07334 336 RPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDAAHLQEVIAALRAAGFEARLV 402 (403)
T ss_pred CCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCHHHHHHHHHHHHHcCCeeEeC
Confidence 34446778888876532 45555442 245554432 2 24468999999999998875
No 138
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=23.46 E-value=1.4e+02 Score=26.90 Aligned_cols=45 Identities=11% Similarity=0.048 Sum_probs=33.2
Q ss_pred HHHHHHHHHHccCCccEEEEecCC--CEEEEEe--------eCCHHHHHHHHHhc
Q 035968 16 CRQKVMKLIAKLEGITSIVIDPSK--NTVTVIG--------DADPVKIIKKVREF 60 (112)
Q Consensus 16 C~~kI~k~L~~~~GV~~v~vd~~~--~~v~V~~--------~~~~~~i~~~i~k~ 60 (112)
-+.+++..|.+++|+.++..++.. ..+.|.- .++++++...|+..
T Consensus 690 ~a~~l~~~l~~~pgv~~v~~~~~~~~~e~~v~id~~k~~~~Gls~~~v~~~l~~~ 744 (1040)
T PRK10503 690 WVPKLMEKLQQLPQLSDVSSDWQDKGLVAYVNVDRDSASRLGISMADVDNALYNA 744 (1040)
T ss_pred HHHHHHHHHhcCCCeEEEEccccCCCceEEEEECHHHHHHcCCCHHHHHHHHHHH
Confidence 456789999999999999866544 3455542 37888999999863
No 139
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=23.39 E-value=2.3e+02 Score=20.59 Aligned_cols=36 Identities=31% Similarity=0.538 Sum_probs=26.3
Q ss_pred HHHHHHHccCCccEEEEecCCCEEEEEee---CCHHHHHH
Q 035968 19 KVMKLIAKLEGITSIVIDPSKNTVTVIGD---ADPVKIIK 55 (112)
Q Consensus 19 kI~k~L~~~~GV~~v~vd~~~~~v~V~~~---~~~~~i~~ 55 (112)
.+.+.|....|+. +++|..++.|+|... .||..+.+
T Consensus 28 ~v~k~ie~~~~~~-~~iD~~~~~V~i~~~~~t~Dp~~~~k 66 (194)
T COG1094 28 EVKKAIEEKTGVK-LRIDSKTGSVTIRTTRKTEDPLALLK 66 (194)
T ss_pred cchHHHHhhcCeE-EEEECCCCeEEEEecCCCCChHHHHH
Confidence 5677777777775 899999999999753 46654433
No 140
>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=23.36 E-value=1.4e+02 Score=26.87 Aligned_cols=46 Identities=11% Similarity=0.096 Sum_probs=34.5
Q ss_pred hHHHHHHHHHHccCCccEEEEecCC--CEEEEEe--------eCCHHHHHHHHHhc
Q 035968 15 KCRQKVMKLIAKLEGITSIVIDPSK--NTVTVIG--------DADPVKIIKKVREF 60 (112)
Q Consensus 15 ~C~~kI~k~L~~~~GV~~v~vd~~~--~~v~V~~--------~~~~~~i~~~i~k~ 60 (112)
.=+.++++.|.+.+|+.+++.+... .+++|.- .+++++|...|+..
T Consensus 697 ~~a~~l~~~l~~~pg~~~v~~~~~~~~~~~~i~~d~~k~~~~Gls~~~v~~~l~~~ 752 (1044)
T TIGR00915 697 QARNQLLGLAAQNPALTRVRPNGLEDEPQFKLNIDDEKAQALGVSIADINTTLSTA 752 (1044)
T ss_pred HHHHHHHHHHhcCCCeEEeeccccCCCceEEEEECHHHHHHcCCCHHHHHHHHHHH
Confidence 3456789999999999999888644 4556552 26888999999853
No 141
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=23.16 E-value=91 Score=23.48 Aligned_cols=21 Identities=14% Similarity=0.452 Sum_probs=17.8
Q ss_pred HHHHHHHHHccCCccEEEEec
Q 035968 17 RQKVMKLIAKLEGITSIVIDP 37 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd~ 37 (112)
...+++.|..++||.+++|.+
T Consensus 109 egELarTI~~idgV~~ArVhL 129 (249)
T PRK15348 109 EQRIEGMLSQMEGVINAKVTI 129 (249)
T ss_pred HHHHHHHHHhCCCeeEeEEEE
Confidence 467889999999999988863
No 142
>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=22.84 E-value=1.8e+02 Score=17.43 Aligned_cols=57 Identities=14% Similarity=0.037 Sum_probs=34.8
Q ss_pred hhHHHHHHHHHHccCCccEEEEec---CCCEEEEEee-CC----HHHHHHHHHhcCCceEEecCCC
Q 035968 14 LKCRQKVMKLIAKLEGITSIVIDP---SKNTVTVIGD-AD----PVKIIKKVREFRKSAAIESIGP 71 (112)
Q Consensus 14 ~~C~~kI~k~L~~~~GV~~v~vd~---~~~~v~V~~~-~~----~~~i~~~i~k~G~~~~~~~~~~ 71 (112)
+|=-.++-+.|. -.+|..+.-+. ...++.+.-+ -+ .+.+.+.|++.||+....+..+
T Consensus 12 PG~L~~ll~~l~-~anI~~~~y~~~~~~~~~v~i~ie~~~~~~~~~~i~~~L~~~G~~~~~~~~~~ 76 (85)
T cd04906 12 PGSFKKFCELIG-PRNITEFNYRYADEKDAHIFVGVSVANGAEELAELLEDLKSAGYEVVDLSDDE 76 (85)
T ss_pred CcHHHHHHHHhC-CCceeEEEEEccCCCeeEEEEEEEeCCcHHHHHHHHHHHHHCCCCeEECCCCH
Confidence 455566666766 34455544443 3444444322 23 6789999999999887755443
No 143
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=22.72 E-value=1.3e+02 Score=21.24 Aligned_cols=24 Identities=25% Similarity=0.266 Sum_probs=19.7
Q ss_pred cCCCEEEEEeeCCHHHHHHHHHhc
Q 035968 37 PSKNTVTVIGDADPVKIIKKVREF 60 (112)
Q Consensus 37 ~~~~~v~V~~~~~~~~i~~~i~k~ 60 (112)
+.+|+++|+|.-+.+++.+++++.
T Consensus 145 F~sGkivitGaks~~~~~~a~~~i 168 (174)
T cd04517 145 FSTGSVTVTGARSMEDVREAVEKI 168 (174)
T ss_pred eCCCEEEEEecCCHHHHHHHHHHH
Confidence 689999999988888888777653
No 144
>PRK11670 antiporter inner membrane protein; Provisional
Probab=22.72 E-value=2.4e+02 Score=22.19 Aligned_cols=52 Identities=15% Similarity=0.221 Sum_probs=34.3
Q ss_pred HHHHHHHHHccCCccEEEEecCC------------------CEEEEE---ee----CCHHHHHHHHHhcCCceEEec
Q 035968 17 RQKVMKLIAKLEGITSIVIDPSK------------------NTVTVI---GD----ADPVKIIKKVREFRKSAAIES 68 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd~~~------------------~~v~V~---~~----~~~~~i~~~i~k~G~~~~~~~ 68 (112)
...++++|+.++|+.++.+.+.. ..+.|. |. .....|...+.+.|+++-++.
T Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avNLA~aLA~~G~rVlLID 143 (369)
T PRK11670 67 KEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVNLALALAAEGAKVGILD 143 (369)
T ss_pred HHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence 45689999999999887765432 122232 21 344567778888999887764
No 145
>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=22.70 E-value=3.1e+02 Score=20.03 Aligned_cols=50 Identities=6% Similarity=0.133 Sum_probs=35.4
Q ss_pred HHHHHHHHHccCCccEEEEecCCCEEEEEee-------C-CHHHHHHHHHhcCCceEEe
Q 035968 17 RQKVMKLIAKLEGITSIVIDPSKNTVTVIGD-------A-DPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~-------~-~~~~i~~~i~k~G~~~~~~ 67 (112)
....++.|..+ |...++|-...+.++|+-+ + ..+.|...+++.||.-..+
T Consensus 187 v~~~E~~l~~~-g~~~~rvr~~~~~a~ie~~~~~~~~~~~~~~~i~~~~~~~gf~~v~l 244 (252)
T TIGR00268 187 VDEAEEVLRNA-GVGQVRVRNYDNLAVIEVPEDELSKLLNEAEEVRDKFKDIGFRKVLI 244 (252)
T ss_pred HHHHHHHHHHc-CCCeEEEEecCCeEEEEECHHHHHHHHhhHHHHHHHHHHcCCCeEEE
Confidence 34566667763 7888888877888888732 1 2477889999999975443
No 146
>PRK06719 precorrin-2 dehydrogenase; Validated
Probab=22.59 E-value=2.1e+02 Score=19.52 Aligned_cols=38 Identities=11% Similarity=0.216 Sum_probs=27.4
Q ss_pred EEEecCCCEEEEEeeCC-HHHHHHHHHhcCCceEEecCC
Q 035968 33 IVIDPSKNTVTVIGDAD-PVKIIKKVREFRKSAAIESIG 70 (112)
Q Consensus 33 v~vd~~~~~v~V~~~~~-~~~i~~~i~k~G~~~~~~~~~ 70 (112)
+.+|+.+.++.|.|.-. .....+.|.+.|..+.++++.
T Consensus 7 ~~l~l~~~~vlVvGGG~va~rka~~Ll~~ga~V~VIsp~ 45 (157)
T PRK06719 7 LMFNLHNKVVVIIGGGKIAYRKASGLKDTGAFVTVVSPE 45 (157)
T ss_pred eEEEcCCCEEEEECCCHHHHHHHHHHHhCCCEEEEEcCc
Confidence 56788999999887532 344566777888888888643
No 147
>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium). This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=22.41 E-value=2.6e+02 Score=25.19 Aligned_cols=43 Identities=5% Similarity=0.067 Sum_probs=31.8
Q ss_pred HHHHHHHccCCccEEEEecC-CCEEEEEe--------eCCHHHHHHHHHhcC
Q 035968 19 KVMKLIAKLEGITSIVIDPS-KNTVTVIG--------DADPVKIIKKVREFR 61 (112)
Q Consensus 19 kI~k~L~~~~GV~~v~vd~~-~~~v~V~~--------~~~~~~i~~~i~k~G 61 (112)
.++..|.+++||.+|++.-. ...+.|.- .+++++|..+|+...
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 47789999999999998633 34455552 368889999998654
No 148
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.40 E-value=1.1e+02 Score=16.63 Aligned_cols=18 Identities=22% Similarity=0.492 Sum_probs=14.0
Q ss_pred HHHHHHHHHccCCccEEE
Q 035968 17 RQKVMKLIAKLEGITSIV 34 (112)
Q Consensus 17 ~~kI~k~L~~~~GV~~v~ 34 (112)
...+.+.|++++||.++.
T Consensus 52 ~~~~i~~l~~~~~v~~v~ 69 (71)
T cd04903 52 DEEVIEEIKKIPNIHQVI 69 (71)
T ss_pred CHHHHHHHHcCCCceEEE
Confidence 346778889999998775
No 149
>TIGR02190 GlrX-dom Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain.
Probab=22.03 E-value=1.8e+02 Score=17.01 Aligned_cols=31 Identities=23% Similarity=0.233 Sum_probs=20.2
Q ss_pred EEEeecccChhHHHHHHHHHHccCCccEEEEec
Q 035968 5 TIVSVKLLCLKCRQKVMKLIAKLEGITSIVIDP 37 (112)
Q Consensus 5 ~~~~vgm~C~~C~~kI~k~L~~~~GV~~v~vd~ 37 (112)
+.+-..-.|+.|. ++++.|.. .||.-..+|.
T Consensus 10 V~ly~~~~Cp~C~-~ak~~L~~-~gi~y~~idi 40 (79)
T TIGR02190 10 VVVFTKPGCPFCA-KAKATLKE-KGYDFEEIPL 40 (79)
T ss_pred EEEEECCCCHhHH-HHHHHHHH-cCCCcEEEEC
Confidence 4555577899998 66667764 4666554544
No 150
>COG0602 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=21.88 E-value=1.5e+02 Score=21.40 Aligned_cols=33 Identities=15% Similarity=0.343 Sum_probs=23.5
Q ss_pred CCCEEEEEee---C--CHHHHHHHHHhcCCceEEecCC
Q 035968 38 SKNTVTVIGD---A--DPVKIIKKVREFRKSAAIESIG 70 (112)
Q Consensus 38 ~~~~v~V~~~---~--~~~~i~~~i~k~G~~~~~~~~~ 70 (112)
...-|+++|. . +...|++.+++.|++..+-..+
T Consensus 71 ~~~~V~lTGGEP~~~~~l~~Ll~~l~~~g~~~~lETng 108 (212)
T COG0602 71 KARGVSLTGGEPLLQPNLLELLELLKRLGFRIALETNG 108 (212)
T ss_pred CcceEEEeCCcCCCcccHHHHHHHHHhCCceEEecCCC
Confidence 3346778863 1 5788999999999988775543
No 151
>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=21.77 E-value=85 Score=17.99 Aligned_cols=17 Identities=6% Similarity=0.151 Sum_probs=13.8
Q ss_pred CCHHHHHHHHHhcCCce
Q 035968 48 ADPVKIIKKVREFRKSA 64 (112)
Q Consensus 48 ~~~~~i~~~i~k~G~~~ 64 (112)
-..++|.+.|++.||..
T Consensus 50 ~~~~~i~~~L~~~G~~~ 66 (68)
T cd04885 50 EDLAELKERLEALGYPY 66 (68)
T ss_pred HHHHHHHHHHHHcCCCc
Confidence 35578999999999965
No 152
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=21.70 E-value=1.3e+02 Score=21.17 Aligned_cols=24 Identities=13% Similarity=0.196 Sum_probs=19.4
Q ss_pred cCCCEEEEEeeCCHHHHHHHHHhc
Q 035968 37 PSKNTVTVIGDADPVKIIKKVREF 60 (112)
Q Consensus 37 ~~~~~v~V~~~~~~~~i~~~i~k~ 60 (112)
|.+|++.++|.-+.+++..++++.
T Consensus 144 F~SGKvvitGaks~~~~~~a~~~i 167 (174)
T cd04518 144 FSSGKMVITGAKSEEDAKRAVEKL 167 (174)
T ss_pred eCCCEEEEEecCCHHHHHHHHHHH
Confidence 689999999987778777777654
No 153
>PF12693 GspL_C: GspL periplasmic domain; PDB: 2W7V_A.
Probab=21.43 E-value=2.6e+02 Score=18.62 Aligned_cols=48 Identities=6% Similarity=0.083 Sum_probs=31.2
Q ss_pred HHHHHHHccCCccE--EEEecCCCEEEEEee----CCHHHHHHHHHhcCCceEEe
Q 035968 19 KVMKLIAKLEGITS--IVIDPSKNTVTVIGD----ADPVKIIKKVREFRKSAAIE 67 (112)
Q Consensus 19 kI~k~L~~~~GV~~--v~vd~~~~~v~V~~~----~~~~~i~~~i~k~G~~~~~~ 67 (112)
.+..++...+|+.- ++.|...+.+++... .+.+.+...+.+. +.+++-
T Consensus 86 ~l~~~~~~~~~~~l~~l~y~~~~~~L~l~~~a~~~~~le~l~~~l~~~-~~v~~~ 139 (157)
T PF12693_consen 86 ALAPALQQVPGIQLQSLRYDAGRGELRLQLEAPSFQALEQLRAALAAQ-LQVEQG 139 (157)
T ss_dssp GHHHHHHTSTT-EEEEEEEETTTTEEEEEEEESSSHHHHHHHHHHHTT-EEEEE-
T ss_pred HHHHHhccCCCCceEEEEEcCCCcEEEEEeccCCHHHHHHHHHHHHhh-cCcccc
Confidence 45567777788654 444456667887632 2557888999988 888753
No 154
>cd02973 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacteri
Probab=21.41 E-value=1.6e+02 Score=16.23 Aligned_cols=18 Identities=17% Similarity=0.455 Sum_probs=11.0
Q ss_pred ecccChhHHHHHHHHHHcc
Q 035968 9 VKLLCLKCRQKVMKLIAKL 27 (112)
Q Consensus 9 vgm~C~~C~~kI~k~L~~~ 27 (112)
..-.|+.|. .++..|..+
T Consensus 7 ~~~~C~~C~-~~~~~l~~l 24 (67)
T cd02973 7 VSPTCPYCP-DAVQAANRI 24 (67)
T ss_pred ECCCCCCcH-HHHHHHHHH
Confidence 355799995 445555543
No 155
>cd04901 ACT_3PGDH C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-
Probab=21.19 E-value=1.2e+02 Score=16.78 Aligned_cols=17 Identities=6% Similarity=0.374 Sum_probs=13.0
Q ss_pred HHHHHHHccCCccEEEE
Q 035968 19 KVMKLIAKLEGITSIVI 35 (112)
Q Consensus 19 kI~k~L~~~~GV~~v~v 35 (112)
.+.+.|++++||.+|..
T Consensus 52 ~li~~l~~~~~V~~v~~ 68 (69)
T cd04901 52 ELLEALRAIPGTIRVRL 68 (69)
T ss_pred HHHHHHHcCCCeEEEEE
Confidence 56677888899988753
No 156
>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=21.10 E-value=1.2e+02 Score=16.62 Aligned_cols=20 Identities=10% Similarity=0.147 Sum_probs=15.0
Q ss_pred HHHHHHHHHHccCCccEEEE
Q 035968 16 CRQKVMKLIAKLEGITSIVI 35 (112)
Q Consensus 16 C~~kI~k~L~~~~GV~~v~v 35 (112)
=...+.+.|.+++||..+.+
T Consensus 52 ~~~~~~~~L~~~~~v~~v~~ 71 (72)
T cd04874 52 DIEELVEELRSLPIVREVEI 71 (72)
T ss_pred cHHHHHHHHhCCCCeEEEEe
Confidence 34477788999999987764
No 157
>PRK04435 hypothetical protein; Provisional
Probab=20.93 E-value=2.5e+02 Score=19.04 Aligned_cols=20 Identities=10% Similarity=0.395 Sum_probs=13.3
Q ss_pred HHHHHHHHHHccCCccEEEE
Q 035968 16 CRQKVMKLIAKLEGITSIVI 35 (112)
Q Consensus 16 C~~kI~k~L~~~~GV~~v~v 35 (112)
-...+...|++++||.+|++
T Consensus 124 ~L~~Li~~L~~i~gV~~V~i 143 (147)
T PRK04435 124 DIDELLEKLRNLDGVEKVEL 143 (147)
T ss_pred HHHHHHHHHHcCCCcEEEEE
Confidence 56666667777777766654
No 158
>PHA03005 sulfhydryl oxidase; Provisional
Probab=20.93 E-value=81 Score=20.33 Aligned_cols=26 Identities=27% Similarity=0.405 Sum_probs=19.4
Q ss_pred cccChhHHHHHHHHHHccCCccEEEE
Q 035968 10 KLLCLKCRQKVMKLIAKLEGITSIVI 35 (112)
Q Consensus 10 gm~C~~C~~kI~k~L~~~~GV~~v~v 35 (112)
.+.|+.|.....+++++..=+.+-++
T Consensus 40 tLPC~~Cr~HA~~ai~knnimSs~di 65 (96)
T PHA03005 40 TLPCPACRRHAKEAIEKNNIMSSNDL 65 (96)
T ss_pred cCCCHHHHHHHHHHHhhcCccccCCc
Confidence 78999999999999987443333333
No 159
>PF04324 Fer2_BFD: BFD-like [2Fe-2S] binding domain; InterPro: IPR007419 The two Fe ions are each coordinated by two conserved cysteine residues. This domain occurs alone in small proteins such as bacterioferritin-associated ferredoxin (BFD, P13655 from SWISSPROT). The function of BFD is not known, but it may be a general redox and/or regulatory component involved in the iron storage or mobilisation functions of bacterioferritin in bacteria []. This domain is also found in nitrate reductase proteins in association with the nitrite and sulphite reductase 4Fe-4S domain (IPR006067 from INTERPRO), nitrite/sulphite reductase ferredoxin-like half domain (IPR005117 from INTERPRO) and pyridine nucleotide-disulphide oxidoreductase (IPR001327 from INTERPRO). It is also found in NifU nitrogen fixation proteins, in association with NifU-like N-terminal domain (IPR002871 from INTERPRO) and C-terminal domain (IPR001075 from INTERPRO).; PDB: 2HU9_A.
Probab=20.90 E-value=42 Score=18.63 Aligned_cols=18 Identities=28% Similarity=0.444 Sum_probs=3.8
Q ss_pred ecccChhHHHHHHHHHHc
Q 035968 9 VKLLCLKCRQKVMKLIAK 26 (112)
Q Consensus 9 vgm~C~~C~~kI~k~L~~ 26 (112)
.|..|++|...|++.|..
T Consensus 36 ~g~~Cg~C~~~v~~ll~e 53 (55)
T PF04324_consen 36 AGTGCGSCVPEVKDLLAE 53 (55)
T ss_dssp TSS-TH------------
T ss_pred CCCCCCCccccccccccc
Confidence 377899999988887754
No 160
>cd03029 GRX_hybridPRX5 Glutaredoxin (GRX) family, PRX5 hybrid subfamily; composed of hybrid proteins containing peroxiredoxin (PRX) and GRX domains, which is found in some pathogenic bacteria and cyanobacteria. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins. PRX-GRX hybrid proteins from Haemophilus influenza and Neisseria meningitis exhibit GSH-dependent peroxidase activity. The flow of reducing equivalents in the catalytic cycle of the hybrid protein goes from NADPH - GSH reductase - GSH - GRX domain of hybrid - PRX domain of hybrid - peroxide substrate.
Probab=20.61 E-value=1.8e+02 Score=16.46 Aligned_cols=32 Identities=19% Similarity=0.218 Sum_probs=20.0
Q ss_pred EEEeecccChhHHHHHHHHHHccCCccEEEEecC
Q 035968 5 TIVSVKLLCLKCRQKVMKLIAKLEGITSIVIDPS 38 (112)
Q Consensus 5 ~~~~vgm~C~~C~~kI~k~L~~~~GV~~v~vd~~ 38 (112)
+.+-.--.|+.|.+ +++.|.. -||.-..+|..
T Consensus 3 v~lys~~~Cp~C~~-ak~~L~~-~~i~~~~~~v~ 34 (72)
T cd03029 3 VSLFTKPGCPFCAR-AKAALQE-NGISYEEIPLG 34 (72)
T ss_pred EEEEECCCCHHHHH-HHHHHHH-cCCCcEEEECC
Confidence 44445678999995 4677765 46655445443
No 161
>TIGR03143 AhpF_homolog putative alkyl hydroperoxide reductase F subunit. This family of thioredoxin reductase homologs is found adjacent to alkylhydroperoxide reductase C subunit predominantly in cases where there is only one C subunit in the genome and that genome is lacking the F subunit partner (also a thioredcxin reductase homolog) that is usually found (TIGR03140).
Probab=20.59 E-value=4.9e+02 Score=21.45 Aligned_cols=23 Identities=22% Similarity=0.481 Sum_probs=13.9
Q ss_pred ecccChhHHHHHH---HHHHccCCcc
Q 035968 9 VKLLCLKCRQKVM---KLIAKLEGIT 31 (112)
Q Consensus 9 vgm~C~~C~~kI~---k~L~~~~GV~ 31 (112)
++.+|+.|-..++ +.....++|.
T Consensus 484 ~~~~C~~Cp~~~~~~~~~~~~~~~i~ 509 (555)
T TIGR03143 484 VSLSCTLCPDVVLAAQRIASLNPNVE 509 (555)
T ss_pred ECCCCCCcHHHHHHHHHHHHhCCCce
Confidence 4999999996333 2233345554
No 162
>COG1365 Predicted ATPase (PP-loop superfamily) [General function prediction only]
Probab=20.40 E-value=2.3e+02 Score=21.33 Aligned_cols=53 Identities=6% Similarity=-0.025 Sum_probs=32.4
Q ss_pred cChhHHHHHHHHHHc---cCCccE-----------EEEecCCCEEEEEee----CCHHHHHHHHHhcCCce
Q 035968 12 LCLKCRQKVMKLIAK---LEGITS-----------IVIDPSKNTVTVIGD----ADPVKIIKKVREFRKSA 64 (112)
Q Consensus 12 ~C~~C~~kI~k~L~~---~~GV~~-----------v~vd~~~~~v~V~~~----~~~~~i~~~i~k~G~~~ 64 (112)
-|+.|.+.|++++.. .-++.- -.+..+.+.+.+.-. .+..++...+...|+..
T Consensus 134 pCGRCh~~I~~~V~~k~re~di~~vafGDlLs~G~~svy~eD~i~rlnlPAflAltK~Elr~il~~~~~e~ 204 (255)
T COG1365 134 PCGRCHSMIENAVMDKARELDIDVVAFGDLLSTGYGSVYREDGIFRLNLPAFLALTKDELRSILKWNGYEL 204 (255)
T ss_pred CcchHHHHHHHHHHHHHHhcCCeEEEEcccccccccceeccCCEEEEccHHHHhhCcHHHHHHHHhcCccc
Confidence 499999999999764 222222 233344555555421 35567777777777754
No 163
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=20.35 E-value=3.1e+02 Score=19.39 Aligned_cols=54 Identities=19% Similarity=0.233 Sum_probs=33.4
Q ss_pred EEeecccChhHHHHHHHHHHccCCccEEEEecCCCEEEEEee--CCHHHHHHHHHhcCC
Q 035968 6 IVSVKLLCLKCRQKVMKLIAKLEGITSIVIDPSKNTVTVIGD--ADPVKIIKKVREFRK 62 (112)
Q Consensus 6 ~~~vgm~C~~C~~kI~k~L~~~~GV~~v~vd~~~~~v~V~~~--~~~~~i~~~i~k~G~ 62 (112)
.++.|+. ..-+.+|.+.+.... . .|.+.....+|+|+|. -|...+...|+...+
T Consensus 95 ~lk~GI~-~e~AKkIvK~IKd~k-l-KVqa~IQGd~vRVtgKkrDDLQ~viallk~~d~ 150 (161)
T PRK05412 95 KLKQGID-QELAKKIVKLIKDSK-L-KVQAQIQGDQVRVTGKKRDDLQAVIALLRKADL 150 (161)
T ss_pred ehhhccC-HHHHHHHHHHHHhcC-C-ceeEEecCcEEEEecCCHhHHHHHHHHHHhccC
Confidence 3344553 334667777776422 2 3666778888888884 466777777775544
No 164
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=20.33 E-value=1.7e+02 Score=26.25 Aligned_cols=46 Identities=13% Similarity=0.095 Sum_probs=35.0
Q ss_pred hHHHHHHHHHHccCCccEEEEecCC--CEEEEEe--------eCCHHHHHHHHHhc
Q 035968 15 KCRQKVMKLIAKLEGITSIVIDPSK--NTVTVIG--------DADPVKIIKKVREF 60 (112)
Q Consensus 15 ~C~~kI~k~L~~~~GV~~v~vd~~~--~~v~V~~--------~~~~~~i~~~i~k~ 60 (112)
.=+..+++.|++.+|+.++..+... ..+.|.- .+++.+|...++..
T Consensus 696 ~~a~~l~~~l~~~~gv~~v~~~~~~~~~~l~i~id~~k~~~~Gls~~~v~~~l~~~ 751 (1037)
T PRK10555 696 AARNQLLALAAKNPELTRVRHNGLDDSPQLQIDIDQRKAQALGVSIDDINDTLQTA 751 (1037)
T ss_pred HHHHHHHHHHhcCCCeEEEecCCcCCCceEEEEECHHHHHHcCCCHHHHHHHHHHH
Confidence 3456788999999999999888654 5555552 37888999999964
Done!