Query psy16960
Match_columns 69
No_of_seqs 165 out of 1038
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 18:07:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16960.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16960hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00595 PDZ: PDZ domain (Also 99.3 8.7E-12 1.9E-16 72.5 5.5 57 11-68 9-72 (81)
2 cd00136 PDZ PDZ domain, also c 99.3 2.4E-11 5.3E-16 68.3 6.8 55 13-68 2-60 (70)
3 cd00988 PDZ_CTP_protease PDZ d 99.1 3.9E-10 8.4E-15 65.4 7.1 56 11-67 1-59 (85)
4 PF13180 PDZ_2: PDZ domain; PD 99.1 2.4E-10 5.1E-15 66.9 4.8 48 15-65 4-56 (82)
5 cd00992 PDZ_signaling PDZ doma 99.0 1.2E-09 2.5E-14 62.6 6.3 56 11-67 11-72 (82)
6 KOG3209|consensus 98.9 2.5E-09 5.3E-14 84.9 5.7 59 9-68 762-826 (984)
7 smart00228 PDZ Domain present 98.9 1.4E-08 3.1E-13 57.9 6.8 56 11-67 11-72 (85)
8 cd00991 PDZ_archaeal_metallopr 98.9 3.5E-09 7.7E-14 61.8 4.0 37 27-66 17-53 (79)
9 TIGR00225 prc C-terminal pepti 98.8 1.4E-08 3E-13 72.7 7.0 56 11-67 50-108 (334)
10 cd00989 PDZ_metalloprotease PD 98.8 8E-09 1.7E-13 59.0 4.7 36 27-65 19-54 (79)
11 COG0793 Prc Periplasmic protea 98.8 1.9E-08 4.2E-13 74.6 7.6 58 10-68 98-159 (406)
12 PLN00049 carboxyl-terminal pro 98.8 2.2E-08 4.7E-13 73.5 7.5 56 11-67 84-148 (389)
13 cd00990 PDZ_glycyl_aminopeptid 98.8 1.1E-08 2.4E-13 58.7 4.7 35 27-64 19-53 (80)
14 PRK11186 carboxy-terminal prot 98.7 4.5E-08 9.8E-13 76.7 6.4 57 11-68 243-308 (667)
15 cd00986 PDZ_LON_protease PDZ d 98.6 4.7E-08 1E-12 56.5 4.0 35 28-66 16-50 (79)
16 cd00987 PDZ_serine_protease PD 98.6 4.3E-08 9.3E-13 56.9 3.8 34 28-61 32-65 (90)
17 KOG3553|consensus 98.6 6.4E-08 1.4E-12 61.7 3.8 39 28-67 67-105 (124)
18 PRK10779 zinc metallopeptidase 98.5 1.2E-07 2.7E-12 70.5 3.8 32 27-58 133-164 (449)
19 TIGR00054 RIP metalloprotease 98.4 2.1E-07 4.6E-12 68.9 3.8 36 27-65 210-245 (420)
20 PRK10779 zinc metallopeptidase 98.4 2.6E-07 5.7E-12 68.7 3.8 36 27-65 228-263 (449)
21 TIGR03279 cyano_FeS_chp putati 98.4 3.2E-07 7E-12 69.2 3.9 36 27-65 5-40 (433)
22 PRK10139 serine endoprotease; 98.3 6.3E-07 1.4E-11 67.2 3.9 36 27-65 297-332 (455)
23 PRK10139 serine endoprotease; 98.3 6.4E-07 1.4E-11 67.2 3.8 37 27-66 397-433 (455)
24 TIGR01713 typeII_sec_gspC gene 98.3 1.9E-06 4E-11 60.9 5.9 38 28-65 199-236 (259)
25 TIGR02037 degP_htrA_DO peripla 98.3 7.2E-07 1.6E-11 65.7 3.5 36 27-62 264-299 (428)
26 TIGR02038 protease_degS peripl 98.2 1.2E-06 2.5E-11 63.6 3.7 34 28-61 286-319 (351)
27 TIGR00054 RIP metalloprotease 98.2 1.2E-06 2.7E-11 64.9 3.8 32 27-58 135-166 (420)
28 TIGR02037 degP_htrA_DO peripla 98.2 1.5E-06 3.2E-11 64.1 3.8 37 27-66 369-405 (428)
29 TIGR02860 spore_IV_B stage IV 98.2 4.4E-06 9.5E-11 62.6 6.2 33 30-65 123-155 (402)
30 PRK10898 serine endoprotease; 98.2 1.7E-06 3.6E-11 63.0 3.9 35 27-61 286-320 (353)
31 PRK10942 serine endoprotease; 98.2 1.6E-06 3.5E-11 65.3 3.9 34 27-60 318-351 (473)
32 KOG3580|consensus 98.2 2.6E-06 5.6E-11 67.6 4.9 59 8-67 413-475 (1027)
33 PRK10942 serine endoprotease; 98.1 2.3E-06 5E-11 64.5 3.8 37 27-66 415-451 (473)
34 KOG3209|consensus 98.1 2.5E-06 5.5E-11 68.2 3.8 56 11-67 908-970 (984)
35 KOG3550|consensus 98.1 3.2E-06 6.9E-11 57.5 3.8 56 11-67 100-162 (207)
36 KOG3542|consensus 97.9 8.8E-06 1.9E-10 65.4 2.5 50 11-67 559-608 (1283)
37 PF04495 GRASP55_65: GRASP55/6 97.7 0.00015 3.3E-09 47.2 5.9 51 12-65 28-86 (138)
38 KOG3552|consensus 97.6 3.5E-05 7.6E-10 63.2 2.8 54 12-67 67-120 (1298)
39 KOG3551|consensus 97.5 8.9E-05 1.9E-09 56.3 3.2 57 10-67 94-157 (506)
40 COG0265 DegQ Trypsin-like seri 97.4 0.00023 4.9E-09 51.0 3.8 36 27-65 277-312 (347)
41 KOG3129|consensus 97.3 0.00026 5.6E-09 49.8 3.3 35 27-61 146-180 (231)
42 KOG3651|consensus 97.2 0.00038 8.3E-09 51.7 3.6 40 27-67 37-77 (429)
43 PF12812 PDZ_1: PDZ-like domai 97.0 0.00094 2E-08 39.7 3.5 37 29-65 39-75 (78)
44 COG3975 Predicted protease wit 97.0 0.00087 1.9E-08 52.1 3.8 24 27-50 469-492 (558)
45 KOG3532|consensus 96.8 0.0016 3.5E-08 52.6 4.2 49 13-61 387-439 (1051)
46 KOG0609|consensus 96.8 0.0018 3.9E-08 50.3 4.1 53 15-68 137-194 (542)
47 KOG1892|consensus 96.7 0.0038 8.3E-08 52.1 5.7 60 8-68 939-1008(1629)
48 PF14685 Tricorn_PDZ: Tricorn 96.7 0.0029 6.3E-08 38.5 3.7 27 30-56 30-58 (88)
49 KOG0606|consensus 96.6 0.0015 3.2E-08 54.4 2.7 39 27-66 665-703 (1205)
50 KOG1320|consensus 96.6 0.002 4.4E-08 49.4 3.2 38 27-67 405-442 (473)
51 KOG3605|consensus 96.6 0.0056 1.2E-07 49.1 5.6 39 28-67 681-720 (829)
52 KOG3605|consensus 96.5 0.0023 5.1E-08 51.2 3.3 38 28-66 764-801 (829)
53 PRK09681 putative type II secr 96.5 0.0029 6.2E-08 45.6 3.4 39 27-65 211-252 (276)
54 KOG3549|consensus 96.5 0.003 6.5E-08 47.8 3.5 57 10-67 64-127 (505)
55 KOG3606|consensus 96.4 0.0051 1.1E-07 45.2 4.1 39 28-67 202-241 (358)
56 COG0750 Predicted membrane-ass 96.3 0.0058 1.3E-07 43.7 3.8 30 27-56 136-165 (375)
57 KOG3571|consensus 96.2 0.0048 1E-07 48.2 3.0 40 27-67 284-324 (626)
58 KOG3580|consensus 96.0 0.0058 1.3E-07 49.1 2.9 38 30-68 230-267 (1027)
59 KOG1738|consensus 95.4 0.029 6.4E-07 44.5 4.6 57 10-67 211-272 (638)
60 COG3480 SdrC Predicted secrete 94.2 0.069 1.5E-06 39.7 3.7 35 28-66 138-172 (342)
61 COG3031 PulC Type II secretory 93.4 0.12 2.6E-06 37.3 3.7 35 29-66 216-250 (275)
62 KOG2921|consensus 91.7 0.15 3.2E-06 39.2 2.5 47 4-56 208-257 (484)
63 KOG1421|consensus 88.9 0.28 6.1E-06 40.1 2.0 32 28-60 311-342 (955)
64 PF11874 DUF3394: Domain of un 88.6 0.68 1.5E-05 31.7 3.5 36 13-48 112-150 (183)
65 KOG3938|consensus 88.2 0.36 7.7E-06 35.5 2.0 40 28-68 157-197 (334)
66 PF07497 Rho_RNA_bind: Rho ter 85.2 0.82 1.8E-05 27.3 2.1 36 11-46 11-51 (78)
67 cd04459 Rho_CSD Rho_CSD: Rho p 84.0 1.6 3.4E-05 25.4 2.9 37 11-47 9-50 (68)
68 KOG4407|consensus 82.1 0.91 2E-05 39.6 1.9 40 27-67 150-189 (1973)
69 KOG3834|consensus 81.8 3.1 6.7E-05 32.2 4.5 30 27-56 22-52 (462)
70 PRK03760 hypothetical protein; 77.1 5.2 0.00011 25.2 3.8 18 28-45 96-113 (117)
71 COG5233 GRH1 Peripheral Golgi 72.4 2.4 5.3E-05 32.0 1.6 27 27-53 70-96 (417)
72 KOG1421|consensus 69.1 4.4 9.5E-05 33.5 2.5 34 29-66 871-904 (955)
73 COG2002 AbrB Regulators of sta 68.9 10 0.00023 22.4 3.6 34 15-48 5-38 (89)
74 smart00357 CSP Cold shock prot 65.6 15 0.00032 19.1 3.5 33 12-46 9-45 (64)
75 PF04014 Antitoxin-MazE: Antid 64.7 7 0.00015 20.4 2.0 25 22-46 5-29 (47)
76 TIGR02381 cspD cold shock doma 64.1 17 0.00037 20.5 3.7 42 5-46 5-50 (68)
77 PRK09937 stationary phase/star 60.6 22 0.00049 20.6 3.9 41 5-45 5-49 (74)
78 PRK14998 cold shock-like prote 60.5 21 0.00046 20.6 3.7 44 2-45 2-49 (73)
79 TIGR01439 lp_hng_hel_AbrB loop 59.5 12 0.00027 18.5 2.3 27 21-47 4-30 (43)
80 TIGR02851 spore_V_T stage V sp 59.2 13 0.00028 25.0 3.0 35 14-48 3-38 (180)
81 PRK10943 cold shock-like prote 55.2 20 0.00043 20.4 3.0 35 11-45 14-51 (69)
82 KOG3834|consensus 54.2 9.4 0.0002 29.6 1.9 36 27-65 116-152 (462)
83 PF06838 Met_gamma_lyase: Meth 53.9 6 0.00013 30.2 0.8 27 33-62 88-114 (403)
84 PRK08577 hypothetical protein; 52.3 24 0.00053 22.1 3.3 31 20-50 9-40 (136)
85 COG0207 ThyA Thymidylate synth 51.3 19 0.00042 26.1 3.0 37 30-67 190-226 (268)
86 PF04887 Pox_M2: Poxvirus M2 p 49.8 18 0.00039 25.2 2.5 42 3-45 27-78 (197)
87 COG1430 Uncharacterized conser 48.7 19 0.0004 23.3 2.4 18 29-46 102-119 (126)
88 PRK09890 cold shock protein Cs 48.4 27 0.00058 19.9 2.8 36 11-46 15-53 (70)
89 PRK10354 RNA chaperone/anti-te 47.5 26 0.00057 19.8 2.7 35 11-45 15-52 (70)
90 PF00313 CSD: 'Cold-shock' DNA 46.8 20 0.00044 19.5 2.1 39 7-45 7-48 (66)
91 PRK09507 cspE cold shock prote 46.4 35 0.00075 19.3 3.1 36 11-46 14-52 (69)
92 PRK15464 cold shock-like prote 44.2 39 0.00085 19.4 3.1 35 11-45 15-52 (70)
93 COG0260 PepB Leucyl aminopepti 43.3 16 0.00034 28.5 1.6 28 28-56 306-333 (485)
94 PRK09974 putative regulator Pr 42.9 31 0.00067 21.9 2.7 29 19-47 13-41 (111)
95 COG4100 Cystathionine beta-lya 42.5 14 0.0003 28.1 1.1 23 37-62 103-125 (416)
96 cd02791 MopB_CT_Nitrate-R-NapA 42.4 26 0.00057 20.8 2.3 19 31-49 42-60 (122)
97 PRK15463 cold shock-like prote 40.8 60 0.0013 18.5 3.5 36 11-46 15-53 (70)
98 PF07591 PT-HINT: Pretoxin HIN 40.8 18 0.00039 22.8 1.4 20 32-51 70-90 (130)
99 PF02362 B3: B3 DNA binding do 40.0 21 0.00046 20.5 1.5 13 33-45 69-81 (100)
100 TIGR00739 yajC preprotein tran 39.8 21 0.00046 21.2 1.5 16 35-50 35-50 (84)
101 PF02643 DUF192: Uncharacteriz 39.7 22 0.00047 21.7 1.6 18 28-45 88-105 (108)
102 PRK13821 thyA thymidylate synt 39.7 31 0.00068 25.6 2.6 38 30-68 234-271 (323)
103 PF01568 Molydop_binding: Moly 39.7 23 0.0005 20.7 1.7 18 31-48 37-54 (110)
104 cd02790 MopB_CT_Formate-Dh_H F 39.4 35 0.00077 20.0 2.5 19 31-49 42-60 (116)
105 PRK06531 yajC preprotein trans 39.4 20 0.00044 22.7 1.4 16 35-50 34-49 (113)
106 PRK05585 yajC preprotein trans 39.4 20 0.00044 22.2 1.4 17 34-50 49-65 (106)
107 cd00508 MopB_CT_Fdh-Nap-like T 39.3 35 0.00075 20.1 2.4 19 31-49 42-60 (120)
108 TIGR02876 spore_yqfD sporulati 38.7 44 0.00096 24.9 3.3 37 3-46 184-223 (382)
109 PRK00913 multifunctional amino 38.1 21 0.00046 27.7 1.6 27 28-55 307-333 (483)
110 PF06898 YqfD: Putative stage 37.9 46 0.00099 24.7 3.3 37 3-46 187-226 (385)
111 PF15057 DUF4537: Domain of un 37.0 29 0.00063 21.9 1.9 20 28-47 46-65 (124)
112 cd02792 MopB_CT_Formate-Dh-Na- 36.5 42 0.00091 19.9 2.5 18 31-48 42-59 (122)
113 TIGR00767 rho transcription te 36.4 38 0.00083 26.0 2.7 36 11-46 59-99 (415)
114 cd02787 MopB_CT_ydeP The MopB_ 36.4 33 0.00072 20.4 2.0 20 31-50 38-57 (112)
115 cd02786 MopB_CT_3 The MopB_CT_ 35.9 39 0.00085 20.0 2.3 19 30-48 37-55 (116)
116 COG4043 Preprotein translocase 35.4 30 0.00065 22.0 1.7 16 32-47 28-43 (111)
117 PRK05886 yajC preprotein trans 35.3 26 0.00056 22.1 1.4 16 35-50 36-51 (109)
118 PF00817 IMS: impB/mucB/samB f 35.1 54 0.0012 20.5 2.9 33 12-44 19-53 (149)
119 cd02775 MopB_CT Molybdopterin- 35.1 48 0.001 18.8 2.5 21 28-48 27-47 (101)
120 cd00433 Peptidase_M17 Cytosol 35.0 25 0.00054 27.1 1.6 27 28-55 293-319 (468)
121 cd06919 Asp_decarbox Aspartate 34.4 81 0.0017 20.1 3.6 19 29-48 70-88 (111)
122 TIGR03284 thym_sym thymidylate 34.3 39 0.00084 24.8 2.4 38 30-68 218-255 (296)
123 KOG0792|consensus 34.1 29 0.00063 29.8 1.9 39 29-68 757-797 (1144)
124 PRK12608 transcription termina 34.1 43 0.00092 25.4 2.6 36 11-46 27-67 (380)
125 PF01887 SAM_adeno_trans: S-ad 33.9 65 0.0014 22.8 3.4 19 27-45 239-257 (258)
126 cd02789 MopB_CT_FmdC-FwdD The 33.2 52 0.0011 19.7 2.5 19 31-49 38-56 (106)
127 PF00883 Peptidase_M17: Cytoso 33.1 18 0.00039 26.6 0.5 27 28-55 138-164 (311)
128 PRK09376 rho transcription ter 32.6 47 0.001 25.6 2.7 36 11-46 59-99 (416)
129 TIGR00223 panD L-aspartate-alp 32.5 88 0.0019 20.4 3.6 19 29-48 71-89 (126)
130 cd02779 MopB_CT_Arsenite-Ox Th 32.5 46 0.00099 19.9 2.2 21 29-49 38-58 (115)
131 PF14085 DUF4265: Domain of un 32.2 1E+02 0.0022 19.1 3.8 27 22-48 10-36 (117)
132 cd02794 MopB_CT_DmsA-EC The Mo 31.8 48 0.0011 19.9 2.3 18 31-48 37-54 (121)
133 cd02781 MopB_CT_Acetylene-hydr 31.7 56 0.0012 19.7 2.5 18 31-48 40-57 (130)
134 KOG1753|consensus 31.6 46 0.00099 22.1 2.2 35 31-66 17-51 (145)
135 COG1862 YajC Preprotein transl 31.3 34 0.00074 21.1 1.5 15 36-50 42-56 (97)
136 PRK05015 aminopeptidase B; Pro 31.2 32 0.00069 26.5 1.6 27 29-56 245-271 (424)
137 PRK00956 thyA thymidylate synt 31.1 46 0.00099 22.8 2.2 35 31-66 173-207 (208)
138 cd02777 MopB_CT_DMSOR-like The 30.9 53 0.0012 19.9 2.3 20 30-49 40-59 (127)
139 cd02785 MopB_CT_4 The MopB_CT_ 30.7 49 0.0011 20.0 2.1 18 31-48 39-56 (124)
140 cd04458 CSP_CDS Cold-Shock Pro 30.6 94 0.002 16.7 3.5 37 10-46 10-49 (65)
141 PRK05449 aspartate alpha-decar 30.3 1E+02 0.0022 20.1 3.6 19 29-48 71-89 (126)
142 cd02793 MopB_CT_DMSOR-BSOR-TMA 30.1 55 0.0012 20.0 2.3 19 31-49 40-58 (129)
143 TIGR03595 Obg_CgtA_exten Obg f 29.6 45 0.00098 19.0 1.7 17 33-50 49-65 (69)
144 KOG0820|consensus 29.2 48 0.001 24.7 2.1 19 30-48 48-66 (315)
145 PF14552 Tautomerase_2: Tautom 28.8 17 0.00037 21.5 -0.2 26 31-56 55-80 (82)
146 PF02699 YajC: Preprotein tran 28.6 21 0.00046 21.0 0.2 16 35-50 34-49 (82)
147 COG3127 Predicted ABC-type tra 28.4 51 0.0011 27.5 2.3 26 28-53 601-627 (829)
148 TIGR02828 putative membrane fu 28.4 36 0.00077 21.9 1.3 13 34-46 174-186 (188)
149 PF02353 CMAS: Mycolic acid cy 28.2 44 0.00096 23.6 1.8 18 31-48 53-70 (273)
150 PRK01827 thyA thymidylate synt 28.0 56 0.0012 23.4 2.3 36 31-67 187-222 (264)
151 PF09269 DUF1967: Domain of un 26.6 43 0.00093 19.0 1.3 14 32-45 48-61 (69)
152 cd02778 MopB_CT_Thiosulfate-R- 26.5 73 0.0016 18.9 2.4 18 31-48 37-54 (123)
153 PF02261 Asp_decarbox: Asparta 26.4 78 0.0017 20.3 2.5 17 30-47 72-88 (116)
154 COG1912 Uncharacterized conser 26.2 65 0.0014 23.5 2.4 19 27-45 246-264 (268)
155 PRK09570 rpoH DNA-directed RNA 26.1 59 0.0013 19.4 1.8 19 30-48 43-62 (79)
156 COG2012 RPB5 DNA-directed RNA 26.1 65 0.0014 19.4 2.0 18 30-47 46-64 (80)
157 cd02788 MopB_CT_NDH-1_NuoG2-N7 25.8 73 0.0016 18.6 2.2 18 31-48 36-53 (96)
158 COG1465 Predicted alternative 25.3 1.2E+02 0.0026 23.0 3.7 49 5-53 310-363 (376)
159 PF13509 S1_2: S1 domain; PDB: 25.3 1.3E+02 0.0027 16.4 3.2 38 8-46 9-46 (61)
160 KOG3369|consensus 25.0 38 0.00083 23.6 1.0 25 32-56 46-70 (199)
161 PF08206 OB_RNB: Ribonuclease 24.9 1.3E+02 0.0027 16.2 3.9 34 11-46 7-40 (58)
162 PF12700 HlyD_2: HlyD family s 24.9 1.1E+02 0.0024 20.9 3.3 11 35-45 317-327 (328)
163 PF01079 Hint: Hint module; I 24.5 48 0.001 22.9 1.4 19 30-48 24-42 (217)
164 PTZ00412 leucyl aminopeptidase 24.3 46 0.00099 26.7 1.4 26 29-55 353-378 (569)
165 PRK13669 hypothetical protein; 24.2 88 0.0019 18.7 2.3 32 34-66 38-69 (78)
166 cd02782 MopB_CT_1 The MopB_CT_ 24.1 88 0.0019 18.9 2.4 18 31-48 40-57 (129)
167 COG1158 Rho Transcription term 23.7 76 0.0016 24.5 2.4 36 11-46 62-102 (422)
168 PF05708 DUF830: Orthopoxvirus 23.5 43 0.00094 20.9 1.0 12 38-49 2-13 (158)
169 PF13624 SurA_N_3: SurA N-term 23.5 55 0.0012 20.2 1.4 28 35-63 33-60 (154)
170 cd04486 YhcR_OBF_like YhcR_OBF 23.5 1.6E+02 0.0034 16.9 3.7 12 35-46 42-53 (78)
171 TIGR02609 doc_partner putative 23.3 68 0.0015 18.3 1.7 20 26-45 12-31 (74)
172 cd02780 MopB_CT_Tetrathionate_ 23.3 78 0.0017 19.7 2.1 18 31-48 37-54 (143)
173 COG4273 Uncharacterized conser 23.2 42 0.0009 22.1 0.8 25 29-53 55-79 (135)
174 cd02783 MopB_CT_2 The MopB_CT_ 23.1 87 0.0019 20.1 2.4 19 30-48 38-56 (156)
175 COG1188 Ribosome-associated he 23.1 66 0.0014 20.1 1.7 23 23-45 33-56 (100)
176 PF01191 RNA_pol_Rpb5_C: RNA p 22.8 63 0.0014 19.0 1.5 19 29-47 39-58 (74)
177 PF09298 FAA_hydrolase_N: Fuma 22.6 25 0.00054 21.7 -0.3 16 31-46 13-28 (107)
178 PF14172 DUF4309: Domain of un 22.5 1E+02 0.0022 19.8 2.5 33 35-68 58-92 (134)
179 PF10844 DUF2577: Protein of u 22.5 58 0.0013 19.6 1.4 13 35-47 74-86 (100)
180 PF08121 Toxin_33: Waglerin fa 22.1 31 0.00068 15.8 0.1 7 4-10 11-17 (22)
181 PF13403 Hint_2: Hint domain 21.7 88 0.0019 20.1 2.2 25 26-50 9-33 (147)
182 PTZ00164 bifunctional dihydrof 21.7 1E+02 0.0022 24.1 2.9 38 30-68 436-473 (514)
183 PRK12678 transcription termina 21.5 97 0.0021 25.4 2.7 36 11-46 303-341 (672)
184 COG0853 PanD Aspartate 1-decar 21.4 1.6E+02 0.0035 19.2 3.3 19 29-48 70-88 (126)
185 cd02776 MopB_CT_Nitrate-R-NarG 21.2 94 0.002 19.7 2.2 18 31-48 38-55 (141)
186 PF01119 DNA_mis_repair: DNA m 21.1 1.4E+02 0.0031 18.0 3.0 24 39-63 38-61 (119)
187 PF03459 TOBE: TOBE domain; I 20.9 1.5E+02 0.0032 15.6 4.8 18 29-46 38-55 (64)
188 PF14250 AbrB-like: AbrB-like 20.6 1.8E+02 0.004 17.1 3.2 12 34-45 49-60 (71)
189 PRK00474 rps9p 30S ribosomal p 20.5 40 0.00086 21.9 0.3 30 35-65 17-46 (134)
190 KOG2597|consensus 20.3 66 0.0014 25.5 1.5 24 29-53 329-352 (513)
191 COG1582 FlgEa Uncharacterized 20.0 1.6E+02 0.0035 17.1 2.8 29 38-66 24-52 (67)
192 COG2230 Cfa Cyclopropane fatty 20.0 97 0.0021 22.5 2.3 17 32-48 64-80 (283)
193 PF01959 DHQS: 3-dehydroquinat 20.0 2.1E+02 0.0046 21.6 4.1 37 11-47 296-335 (354)
No 1
>PF00595 PDZ: PDZ domain (Also known as DHR or GLGF) Coordinates are not yet available; InterPro: IPR001478 PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [, ]. PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences []. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated. PDZ domains consist of 80 to 90 amino acids comprising six beta-strands (beta-A to beta-F) and two alpha-helices, A and B, compactly arranged in a globular structure. Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with the beta-B strand and the B helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands.; GO: 0005515 protein binding; PDB: 3AXA_A 1WF8_A 1QAV_B 1QAU_A 1B8Q_A 1MC7_A 2KAW_A 1I16_A 1VB7_A 1WI4_A ....
Probab=99.29 E-value=8.7e-12 Score=72.51 Aligned_cols=57 Identities=30% Similarity=0.543 Sum_probs=49.1
Q ss_pred cCCeEEEEEEcCCC---eE----EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcCC
Q psy16960 11 LKGYCIIIAETPDG---KV----KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 11 ~~g~~i~l~~~~~~---~i----v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~~ 68 (69)
..++||.+....+. .+ +.+++||+++||++||+|++|||+++.+|+ +++++.+++..
T Consensus 9 ~~~lG~~l~~~~~~~~~~~~V~~v~~~~~a~~~gl~~GD~Il~INg~~v~~~~-~~~~~~~l~~~ 72 (81)
T PF00595_consen 9 NGPLGFTLRGGSDNDEKGVFVSSVVPGSPAERAGLKVGDRILEINGQSVRGMS-HDEVVQLLKSA 72 (81)
T ss_dssp TSBSSEEEEEESTSSSEEEEEEEECTTSHHHHHTSSTTEEEEEETTEESTTSB-HHHHHHHHHHS
T ss_pred CCCcCEEEEecCCCCcCCEEEEEEeCCChHHhcccchhhhhheeCCEeCCCCC-HHHHHHHHHCC
Confidence 57788888887764 32 458999999999999999999999999999 99999988754
No 2
>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(pos
Probab=99.28 E-value=2.4e-11 Score=68.28 Aligned_cols=55 Identities=33% Similarity=0.474 Sum_probs=45.4
Q ss_pred CeEEEEEEcCC-CeE---EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcCC
Q psy16960 13 GYCIIIAETPD-GKV---KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 13 g~~i~l~~~~~-~~i---v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~~ 68 (69)
++||.+....+ +.+ +.+++||+++||++||+|++|||+++.+|+ ++++.++++..
T Consensus 2 ~~G~~~~~~~~~~~~V~~v~~~s~a~~~gl~~GD~I~~Ing~~v~~~~-~~~~~~~l~~~ 60 (70)
T cd00136 2 GLGFSIRGGTEGGVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLT-LEDVAELLKKE 60 (70)
T ss_pred CccEEEecCCCCCEEEEEeCCCCHHHHcCCCCCCEEEEECCEECCCCC-HHHHHHHHhhC
Confidence 56777766655 332 458999999999999999999999999998 88999988753
No 3
>cd00988 PDZ_CTP_protease PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=99.13 E-value=3.9e-10 Score=65.41 Aligned_cols=56 Identities=25% Similarity=0.433 Sum_probs=43.9
Q ss_pred cCCeEEEEEEcCCCeE---EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 11 LKGYCIIIAETPDGKV---KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 11 ~~g~~i~l~~~~~~~i---v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
|.|.|+.+.....+.+ +.+++||+++||++||+|++|||.++.+|. ++++...+++
T Consensus 1 ~~~lG~~~~~~~~~~~V~~v~~~s~a~~~gl~~GD~I~~vng~~i~~~~-~~~~~~~l~~ 59 (85)
T cd00988 1 FGGIGLELKYDDGGLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLS-LEDVVKLLRG 59 (85)
T ss_pred CeEEEEEEEEcCCeEEEEEecCCCCHHHcCCCCCCEEEEECCEEcCCCC-HHHHHHHhcC
Confidence 4567777765444333 458999999999999999999999999996 6688777743
No 4
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=99.08 E-value=2.4e-10 Score=66.90 Aligned_cols=48 Identities=33% Similarity=0.569 Sum_probs=36.6
Q ss_pred EEEEEEcCC--CeE---EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 15 CIIIAETPD--GKV---KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 15 ~i~l~~~~~--~~i---v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
|+.+....+ +.. +.++|||+++||++||+|++|||+++.++. ++.+.+
T Consensus 4 Gv~~~~~~~~~g~~V~~V~~~spA~~aGl~~GD~I~~ing~~v~~~~---~~~~~l 56 (82)
T PF13180_consen 4 GVTVQNLSDTGGVVVVSVIPGSPAAKAGLQPGDIILAINGKPVNSSE---DLVNIL 56 (82)
T ss_dssp SEEEEECSCSSSEEEEEESTTSHHHHTTS-TTEEEEEETTEESSSHH---HHHHHH
T ss_pred CeEEEEccCCCeEEEEEeCCCCcHHHCCCCCCcEEEEECCEEcCCHH---HHHHHH
Confidence 555555544 332 468999999999999999999999998777 666665
No 5
>cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
Probab=99.03 E-value=1.2e-09 Score=62.62 Aligned_cols=56 Identities=30% Similarity=0.490 Sum_probs=46.1
Q ss_pred cCCeEEEEEEcCC---CeE---EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 11 LKGYCIIIAETPD---GKV---KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 11 ~~g~~i~l~~~~~---~~i---v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
..++|+.+....+ +.+ +.+++||+++||++||+|++|||+++.+++ ++++...++.
T Consensus 11 ~~~~G~~~~~~~~~~~~~~V~~v~~~s~a~~~gl~~GD~I~~ing~~i~~~~-~~~~~~~l~~ 72 (82)
T cd00992 11 GGGLGFSLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLT-HEEAVELLKN 72 (82)
T ss_pred CCCcCEEEeCcccCCCCeEEEEECCCChHHhCCCCCCCEEEEECCEEcCccC-HHHHHHHHHh
Confidence 4678888876543 332 458999999999999999999999999887 8899988865
No 6
>KOG3209|consensus
Probab=98.90 E-value=2.5e-09 Score=84.88 Aligned_cols=59 Identities=31% Similarity=0.631 Sum_probs=50.8
Q ss_pred eccCCeEEEEEEcCCC---eE--EecCChHhhcC-CCCCCEEEEECCEEeCCCCChHHHHHhhcCC
Q psy16960 9 IDLKGYCIIIAETPDG---KV--KLYGSPADKSD-LEIGDEILEVNGKTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 9 ~~~~g~~i~l~~~~~~---~i--v~~gspA~~aG-Lk~GD~Il~Vng~~i~~~~~~~ev~~~i~~~ 68 (69)
.+-.||||++....+. .| +++||||++.| |++||+|++|||++|.+.+ |.+++++|+..
T Consensus 762 ~ENeGFGFVi~sS~~kp~sgiGrIieGSPAdRCgkLkVGDrilAVNG~sI~~ls-Hadiv~LIKda 826 (984)
T KOG3209|consen 762 KENEGFGFVIMSSQNKPESGIGRIIEGSPADRCGKLKVGDRILAVNGQSILNLS-HADIVSLIKDA 826 (984)
T ss_pred ccCCceeEEEEecccCCCCCccccccCChhHhhccccccceEEEecCeeeeccC-chhHHHHHHhc
Confidence 3467999999777542 24 68999999998 9999999999999999999 99999999864
No 7
>smart00228 PDZ Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
Probab=98.87 E-value=1.4e-08 Score=57.85 Aligned_cols=56 Identities=36% Similarity=0.513 Sum_probs=43.5
Q ss_pred cCCeEEEEEEcCC---CeE---EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 11 LKGYCIIIAETPD---GKV---KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 11 ~~g~~i~l~~~~~---~~i---v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
...+|+.+..... +.+ +.+++||+++||++||+|++|||+++.+++ ..+....++.
T Consensus 11 ~~~~G~~~~~~~~~~~~~~i~~v~~~s~a~~~gl~~GD~I~~In~~~v~~~~-~~~~~~~~~~ 72 (85)
T smart00228 11 GGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLKVGDVILEVNGTSVEGLT-HLEAVDLLKK 72 (85)
T ss_pred CCcccEEEECCCCCCCCEEEEEECCCCHHHHcCCCCCCEEEEECCEECCCCC-HHHHHHHHHh
Confidence 3577888766542 332 458999999999999999999999999998 7676666543
No 8
>cd00991 PDZ_archaeal_metalloprotease PDZ domain of archaeal zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.86 E-value=3.5e-09 Score=61.79 Aligned_cols=37 Identities=27% Similarity=0.492 Sum_probs=31.9
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
+.++|||+++||++||+|++|||+++.+|+ ++...+.
T Consensus 17 V~~~spa~~aGL~~GDiI~~Ing~~v~~~~---d~~~~l~ 53 (79)
T cd00991 17 VIVGSPAENAVLHTGDVIYSINGTPITTLE---DFMEALK 53 (79)
T ss_pred ECCCChHHhcCCCCCCEEEEECCEEcCCHH---HHHHHHh
Confidence 357999999999999999999999999888 6655554
No 9
>TIGR00225 prc C-terminal peptidase (prc). A C-terminal peptidase with different substrates in different species including processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in E.coli E.coli and H influenza have the most distal branch of the tree and their proteins have an N-terminal 200 amino acids that show no homology to other proteins in the database.
Probab=98.83 E-value=1.4e-08 Score=72.73 Aligned_cols=56 Identities=29% Similarity=0.505 Sum_probs=45.0
Q ss_pred cCCeEEEEEEcCCCeE---EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 11 LKGYCIIIAETPDGKV---KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 11 ~~g~~i~l~~~~~~~i---v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
+.|.|+.+....++.+ +.++|||+++||++||+|++|||+++.+|+ .+++...+++
T Consensus 50 ~~~lG~~~~~~~~~~~V~~V~~~spA~~aGL~~GD~I~~Ing~~v~~~~-~~~~~~~l~~ 108 (334)
T TIGR00225 50 LEGIGIQVGMDDGEIVIVSPFEGSPAEKAGIKPGDKIIKINGKSVAGMS-LDDAVALIRG 108 (334)
T ss_pred eEEEEEEEEEECCEEEEEEeCCCChHHHcCCCCCCEEEEECCEECCCCC-HHHHHHhccC
Confidence 4567888866544333 458999999999999999999999999997 7788777644
No 10
>cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.83 E-value=8e-09 Score=58.97 Aligned_cols=36 Identities=36% Similarity=0.622 Sum_probs=31.3
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
+.++|||+++||++||+|++|||+++.+|+ ++...+
T Consensus 19 v~~~s~a~~~gl~~GD~I~~ing~~i~~~~---~~~~~l 54 (79)
T cd00989 19 VVPGSPAAKAGLKAGDRILAINGQKIKSWE---DLVDAV 54 (79)
T ss_pred ECCCCHHHHcCCCCCCEEEEECCEECCCHH---HHHHHH
Confidence 458999999999999999999999999887 555554
No 11
>COG0793 Prc Periplasmic protease [Cell envelope biogenesis, outer membrane]
Probab=98.81 E-value=1.9e-08 Score=74.64 Aligned_cols=58 Identities=26% Similarity=0.438 Sum_probs=50.5
Q ss_pred ccCCeEEEEEEcC-CCeE---EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcCC
Q psy16960 10 DLKGYCIIIAETP-DGKV---KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 10 ~~~g~~i~l~~~~-~~~i---v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~~ 68 (69)
.|.|.|+.+...+ +... .++|+||+++||++||+|++|||+++.+.. .++++..|++.
T Consensus 98 ~~~GiG~~i~~~~~~~~~V~s~~~~~PA~kagi~~GD~I~~IdG~~~~~~~-~~~av~~irG~ 159 (406)
T COG0793 98 EFGGIGIELQMEDIGGVKVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVS-LDEAVKLIRGK 159 (406)
T ss_pred cccceeEEEEEecCCCcEEEecCCCChHHHcCCCCCCEEEEECCEEccCCC-HHHHHHHhCCC
Confidence 5889999998877 4433 357999999999999999999999999999 89999999864
No 12
>PLN00049 carboxyl-terminal processing protease; Provisional
Probab=98.80 E-value=2.2e-08 Score=73.48 Aligned_cols=56 Identities=21% Similarity=0.372 Sum_probs=45.4
Q ss_pred cCCeEEEEEEcCC------CeE---EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 11 LKGYCIIIAETPD------GKV---KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 11 ~~g~~i~l~~~~~------~~i---v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
+.|+|+.+...+. +.+ +.+||||+++||++||+|++|||+++.++. .+++..++++
T Consensus 84 ~~GiG~~~~~~~~~~~~~~g~~V~~V~~~SPA~~aGl~~GD~Iv~InG~~v~~~~-~~~~~~~l~g 148 (389)
T PLN00049 84 VTGVGLEVGYPTGSDGPPAGLVVVAPAPGGPAARAGIRPGDVILAIDGTSTEGLS-LYEAADRLQG 148 (389)
T ss_pred ceEEEEEEEEccCCCCccCcEEEEEeCCCChHHHcCCCCCCEEEEECCEECCCCC-HHHHHHHHhc
Confidence 6788888865443 222 458999999999999999999999999987 7788877754
No 13
>cd00990 PDZ_glycyl_aminopeptidase PDZ domain associated with archaeal and bacterial M61 glycyl-aminopeptidases. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand is presumed to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.80 E-value=1.1e-08 Score=58.72 Aligned_cols=35 Identities=34% Similarity=0.425 Sum_probs=30.1
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHh
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITH 64 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~ 64 (69)
+.++|||+++||++||+|++|||+++.+|. ++.+.
T Consensus 19 V~~~s~a~~aGl~~GD~I~~Ing~~v~~~~---~~l~~ 53 (80)
T cd00990 19 VRDDSPADKAGLVAGDELVAVNGWRVDALQ---DRLKE 53 (80)
T ss_pred ECCCChHHHhCCCCCCEEEEECCEEhHHHH---HHHHh
Confidence 468999999999999999999999999866 55544
No 14
>PRK11186 carboxy-terminal protease; Provisional
Probab=98.69 E-value=4.5e-08 Score=76.70 Aligned_cols=57 Identities=32% Similarity=0.480 Sum_probs=47.0
Q ss_pred cCCeEEEEEEcCCCeE---EecCChHhhc-CCCCCCEEEEEC--C---EEeCCCCChHHHHHhhcCC
Q psy16960 11 LKGYCIIIAETPDGKV---KLYGSPADKS-DLEIGDEILEVN--G---KTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 11 ~~g~~i~l~~~~~~~i---v~~gspA~~a-GLk~GD~Il~Vn--g---~~i~~~~~~~ev~~~i~~~ 68 (69)
+.|.|+.+....+..+ +++||||+++ ||++||+|++|| | .++.+|. +++++.+|+++
T Consensus 243 ~~GIGa~l~~~~~~~~V~~vipGsPA~ka~gLk~GD~IlaVn~~g~~~~dv~g~~-~~~vv~lirG~ 308 (667)
T PRK11186 243 LEGIGAVLQMDDDYTVINSLVAGGPAAKSKKLSVGDKIVGVGQDGKPIVDVIGWR-LDDVVALIKGP 308 (667)
T ss_pred eeEEEEEEEEeCCeEEEEEccCCChHHHhCCCCCCCEEEEECCCCCcccccccCC-HHHHHHHhcCC
Confidence 7789999977555433 4689999998 999999999999 4 3567898 99999999875
No 15
>cd00986 PDZ_LON_protease PDZ domain of ATP-dependent LON serine proteases. Most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this bacterial subfamily of protease-associated PDZ domains a C-terminal beta-strand is thought to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.64 E-value=4.7e-08 Score=56.52 Aligned_cols=35 Identities=43% Similarity=0.703 Sum_probs=29.5
Q ss_pred ecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 28 LYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
.+||||++ ||++||+|++|||+++.+|+ ++...+.
T Consensus 16 ~~~s~A~~-gL~~GD~I~~Ing~~v~~~~---~~~~~l~ 50 (79)
T cd00986 16 VEGMPAAG-KLKAGDHIIAVDGKPFKEAE---ELIDYIQ 50 (79)
T ss_pred CCCCchhh-CCCCCCEEEEECCEECCCHH---HHHHHHH
Confidence 57899987 79999999999999999888 5555543
No 16
>cd00987 PDZ_serine_protease PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.63 E-value=4.3e-08 Score=56.89 Aligned_cols=34 Identities=44% Similarity=0.551 Sum_probs=29.5
Q ss_pred ecCChHhhcCCCCCCEEEEECCEEeCCCCChHHH
Q psy16960 28 LYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEV 61 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev 61 (69)
.+++||+++||++||+|++|||+++.+|+++.++
T Consensus 32 ~~~s~a~~~gl~~GD~I~~Ing~~i~~~~~~~~~ 65 (90)
T cd00987 32 DPGSPAAKAGLKPGDVILAVNGKPVKSVADLRRA 65 (90)
T ss_pred CCCCHHHHcCCCcCCEEEEECCEECCCHHHHHHH
Confidence 5799999999999999999999999998834333
No 17
>KOG3553|consensus
Probab=98.58 E-value=6.4e-08 Score=61.65 Aligned_cols=39 Identities=38% Similarity=0.583 Sum_probs=35.9
Q ss_pred ecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 28 LYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
.+||||+.|||+.+|+|+.+||-.+.-.+ ++.+++.|+.
T Consensus 67 ~eGsPA~~AGLrihDKIlQvNG~DfTMvT-Hd~Avk~i~k 105 (124)
T KOG3553|consen 67 SEGSPAEIAGLRIHDKILQVNGWDFTMVT-HDQAVKRITK 105 (124)
T ss_pred ccCChhhhhcceecceEEEecCceeEEEE-hHHHHHHhhH
Confidence 57999999999999999999999998888 9999988864
No 18
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=98.49 E-value=1.2e-07 Score=70.46 Aligned_cols=32 Identities=22% Similarity=0.139 Sum_probs=29.4
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCCh
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNH 58 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~ 58 (69)
+.++|||++||||+||+|++|||+++.+|+|+
T Consensus 133 V~~~SpA~kAGLk~GDvI~~vnG~~V~~~~~l 164 (449)
T PRK10779 133 IAPNSIAAQAQIAPGTELKAVDGIETPDWDAV 164 (449)
T ss_pred cCCCCHHHHcCCCCCCEEEEECCEEcCCHHHH
Confidence 46899999999999999999999999999843
No 19
>TIGR00054 RIP metalloprotease RseP. A model that detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain.
Probab=98.43 E-value=2.1e-07 Score=68.89 Aligned_cols=36 Identities=28% Similarity=0.491 Sum_probs=31.6
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
+.++|||+++|||+||+|++|||+++.+|+ ++.+.+
T Consensus 210 V~~~SpA~~aGL~~GD~Iv~Vng~~V~s~~---dl~~~l 245 (420)
T TIGR00054 210 VTPNSPAEKAGLKEGDYIQSINGEKLRSWT---DFVSAV 245 (420)
T ss_pred ECCCCHHHHcCCCCCCEEEEECCEECCCHH---HHHHHH
Confidence 458999999999999999999999999998 555544
No 20
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=98.41 E-value=2.6e-07 Score=68.73 Aligned_cols=36 Identities=28% Similarity=0.418 Sum_probs=31.4
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
+.+||||++|||++||+|++|||+++.+|+ ++.+.+
T Consensus 228 V~~~SpA~~AGL~~GDvIl~Ing~~V~s~~---dl~~~l 263 (449)
T PRK10779 228 VQPNSAASKAGLQAGDRIVKVDGQPLTQWQ---TFVTLV 263 (449)
T ss_pred eCCCCHHHHcCCCCCCEEEEECCEEcCCHH---HHHHHH
Confidence 458999999999999999999999999998 555544
No 21
>TIGR03279 cyano_FeS_chp putative FeS-containing Cyanobacterial-specific oxidoreductase. Members of this protein family are predicted FeS-containing oxidoreductases of unknown function, apparently restricted to and universal across the Cyanobacteria. The high trusted cutoff score for this model, 700 bits, excludes homologs from other lineages. This exclusion seems justified because a significant number of sequence positions are simultaneously unique to and invariant across the Cyanobacteria, suggesting a specialized, conserved function, perhaps related to photosynthesis. A distantly related protein family, TIGR03278, in universal in and restricted to archaeal methanogens, and may be linked to methanogenesis.
Probab=98.39 E-value=3.2e-07 Score=69.17 Aligned_cols=36 Identities=28% Similarity=0.327 Sum_probs=31.5
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
+.+||||+++||++||+|++|||+++.+|. ++...+
T Consensus 5 V~pgSpAe~AGLe~GD~IlsING~~V~Dw~---D~~~~l 40 (433)
T TIGR03279 5 VLPGSIAEELGFEPGDALVSINGVAPRDLI---DYQFLC 40 (433)
T ss_pred cCCCCHHHHcCCCCCCEEEEECCEECCCHH---HHHHHh
Confidence 468999999999999999999999999998 554443
No 22
>PRK10139 serine endoprotease; Provisional
Probab=98.31 E-value=6.3e-07 Score=67.22 Aligned_cols=36 Identities=31% Similarity=0.412 Sum_probs=31.4
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
+.++|||+++|||+||+|++|||+++.+|+ ++...+
T Consensus 297 V~~~SpA~~AGL~~GDvIl~InG~~V~s~~---dl~~~l 332 (455)
T PRK10139 297 VLPNSGSAKAGVKAGDIITSLNGKPLNSFA---ELRSRI 332 (455)
T ss_pred ECCCChHHHCCCCCCCEEEEECCEECCCHH---HHHHHH
Confidence 458999999999999999999999999999 554444
No 23
>PRK10139 serine endoprotease; Provisional
Probab=98.30 E-value=6.4e-07 Score=67.19 Aligned_cols=37 Identities=27% Similarity=0.363 Sum_probs=31.9
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
+.++|||+++||++||+|++|||+++.+|+ ++.+.++
T Consensus 397 V~~~spA~~aGL~~GD~I~~Ing~~v~~~~---~~~~~l~ 433 (455)
T PRK10139 397 VVKGSPAAQAGLQKDDVIIGVNRDRVNSIA---EMRKVLA 433 (455)
T ss_pred eCCCChHHHcCCCCCCEEEEECCEEcCCHH---HHHHHHH
Confidence 357999999999999999999999999999 5555543
No 24
>TIGR01713 typeII_sec_gspC general secretion pathway protein C. This model represents GspC, protein C of the main terminal branch of the general secretion pathway, also called type II secretion. This system transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=98.30 E-value=1.9e-06 Score=60.87 Aligned_cols=38 Identities=24% Similarity=0.211 Sum_probs=31.4
Q ss_pred ecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 28 LYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
.+++||+++|||+||+|++|||+++.++++..++...+
T Consensus 199 ~~~s~a~~aGLr~GDvIv~ING~~i~~~~~~~~~l~~~ 236 (259)
T TIGR01713 199 KDPSLFYKSGLQDGDIAVALNGLDLRDPEQAFQALQML 236 (259)
T ss_pred CCCCHHHHcCCCCCCEEEEECCEEcCCHHHHHHHHHhc
Confidence 46899999999999999999999999998444444433
No 25
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=98.28 E-value=7.2e-07 Score=65.66 Aligned_cols=36 Identities=44% Similarity=0.633 Sum_probs=30.7
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHH
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVI 62 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~ 62 (69)
+.+||||+++||++||+|++|||+++.+|.++.+++
T Consensus 264 V~~~spA~~aGL~~GDvI~~Vng~~i~~~~~~~~~l 299 (428)
T TIGR02037 264 VLPGSPAEKAGLKAGDVILSVNGKPISSFADLRRAI 299 (428)
T ss_pred ccCCCChHHcCCCCCCEEEEECCEEcCCHHHHHHHH
Confidence 358999999999999999999999999988444433
No 26
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=98.23 E-value=1.2e-06 Score=63.58 Aligned_cols=34 Identities=21% Similarity=0.243 Sum_probs=29.7
Q ss_pred ecCChHhhcCCCCCCEEEEECCEEeCCCCChHHH
Q psy16960 28 LYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEV 61 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev 61 (69)
.+++||+++||++||+|++|||+++.+|+|+.+.
T Consensus 286 ~~~spA~~aGL~~GDvI~~Ing~~V~s~~dl~~~ 319 (351)
T TIGR02038 286 DPNGPAARAGILVRDVILKYDGKDVIGAEELMDR 319 (351)
T ss_pred CCCChHHHCCCCCCCEEEEECCEEcCCHHHHHHH
Confidence 5799999999999999999999999999844333
No 27
>TIGR00054 RIP metalloprotease RseP. A model that detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain.
Probab=98.23 E-value=1.2e-06 Score=64.86 Aligned_cols=32 Identities=34% Similarity=0.304 Sum_probs=29.3
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCCh
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNH 58 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~ 58 (69)
+.++|||++||||+||+|++|||+++.++.++
T Consensus 135 V~~~SpA~~AGL~~GDvI~~vng~~v~~~~dl 166 (420)
T TIGR00054 135 LDKNSIALEAGIEPGDEILSVNGNKIPGFKDV 166 (420)
T ss_pred cCCCCHHHHcCCCCCCEEEEECCEEcCCHHHH
Confidence 46899999999999999999999999999833
No 28
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=98.21 E-value=1.5e-06 Score=64.05 Aligned_cols=37 Identities=32% Similarity=0.473 Sum_probs=31.6
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
+.++|||+++||++||+|++|||+++.+++ ++.+.++
T Consensus 369 V~~~SpA~~aGL~~GDvI~~Ing~~V~s~~---d~~~~l~ 405 (428)
T TIGR02037 369 VVSGSPAARAGLQPGDVILSVNQQPVSSVA---ELRKVLD 405 (428)
T ss_pred eCCCCHHHHcCCCCCCEEEEECCEEcCCHH---HHHHHHH
Confidence 357999999999999999999999999888 5555443
No 29
>TIGR02860 spore_IV_B stage IV sporulation protein B. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else.
Probab=98.19 E-value=4.4e-06 Score=62.60 Aligned_cols=33 Identities=33% Similarity=0.662 Sum_probs=29.1
Q ss_pred CChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 30 GSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 30 gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
++||+++|||+||+|++|||+++.+|+ ++.+.+
T Consensus 123 ~SPAa~AGLq~GDiIvsING~~V~s~~---DL~~iL 155 (402)
T TIGR02860 123 HSPGEEAGIQIGDRILKINGEKIKNMD---DLANLI 155 (402)
T ss_pred CCHHHHcCCCCCCEEEEECCEECCCHH---HHHHHH
Confidence 599999999999999999999999999 555444
No 30
>PRK10898 serine endoprotease; Provisional
Probab=98.19 E-value=1.7e-06 Score=62.97 Aligned_cols=35 Identities=23% Similarity=0.282 Sum_probs=30.0
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHH
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEV 61 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev 61 (69)
+.++|||+++||++||+|++|||+++.+|.++.+.
T Consensus 286 V~~~spA~~aGL~~GDvI~~Ing~~V~s~~~l~~~ 320 (353)
T PRK10898 286 VSPDGPAAKAGIQVNDLIISVNNKPAISALETMDQ 320 (353)
T ss_pred ECCCChHHHcCCCCCCEEEEECCEEcCCHHHHHHH
Confidence 35899999999999999999999999998733333
No 31
>PRK10942 serine endoprotease; Provisional
Probab=98.19 E-value=1.6e-06 Score=65.34 Aligned_cols=34 Identities=29% Similarity=0.362 Sum_probs=30.0
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHH
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNE 60 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~e 60 (69)
+.++|||+++||+.||+|++|||+++.+|+++..
T Consensus 318 V~~~SpA~~AGL~~GDvIl~InG~~V~s~~dl~~ 351 (473)
T PRK10942 318 VLPNSSAAKAGIKAGDVITSLNGKPISSFAALRA 351 (473)
T ss_pred ECCCChHHHcCCCCCCEEEEECCEECCCHHHHHH
Confidence 4589999999999999999999999999984433
No 32
>KOG3580|consensus
Probab=98.18 E-value=2.6e-06 Score=67.56 Aligned_cols=59 Identities=25% Similarity=0.374 Sum_probs=49.8
Q ss_pred EeccCCeEEEEEEcCCCeE----EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 8 MIDLKGYCIIIAETPDGKV----KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 8 ~~~~~g~~i~l~~~~~~~i----v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
+.+...+|+.|...++-.| +.+|+||++.||+.||+|++||.+++.+.. .++++.++-+
T Consensus 413 F~KGdSvGLRLAGGNDVGIFVaGvqegspA~~eGlqEGDQIL~VN~vdF~nl~-REeAVlfLL~ 475 (1027)
T KOG3580|consen 413 FKKGDSVGLRLAGGNDVGIFVAGVQEGSPAEQEGLQEGDQILKVNTVDFRNLV-REEAVLFLLE 475 (1027)
T ss_pred eecCCeeeeEeccCCceeEEEeecccCCchhhccccccceeEEeccccchhhh-HHHHHHHHhc
Confidence 4456678888888777554 458999999999999999999999999999 9999987754
No 33
>PRK10942 serine endoprotease; Provisional
Probab=98.14 E-value=2.3e-06 Score=64.47 Aligned_cols=37 Identities=27% Similarity=0.371 Sum_probs=31.8
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
+.++|||+++||++||+|++|||+++.+|+ ++.+.++
T Consensus 415 V~~~S~A~~aGL~~GDvIv~VNg~~V~s~~---dl~~~l~ 451 (473)
T PRK10942 415 VKPGTPAAQIGLKKGDVIIGANQQPVKNIA---ELRKILD 451 (473)
T ss_pred eCCCChHHHcCCCCCCEEEEECCEEcCCHH---HHHHHHH
Confidence 357999999999999999999999999998 5555543
No 34
>KOG3209|consensus
Probab=98.12 E-value=2.5e-06 Score=68.17 Aligned_cols=56 Identities=27% Similarity=0.436 Sum_probs=48.0
Q ss_pred cCCeEEEEEEcCCCeE------EecCChHhhcC-CCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 11 LKGYCIIIAETPDGKV------KLYGSPADKSD-LEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 11 ~~g~~i~l~~~~~~~i------v~~gspA~~aG-Lk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
-+||||-+-..+.... ..+.+||.+.| +++||+|++|||++..+++ |++++++|++
T Consensus 908 ~kGFGFSiRGGreynM~LfVLRlAeDGPA~rdGrm~VGDqi~eINGesTkgmt-H~rAIelIk~ 970 (984)
T KOG3209|consen 908 AKGFGFSIRGGREYNMDLFVLRLAEDGPAIRDGRMRVGDQITEINGESTKGMT-HDRAIELIKQ 970 (984)
T ss_pred ccccceEeecccccccceEEEEeccCCCccccCceeecceEEEecCcccCCCc-HHHHHHHHHh
Confidence 5789998877654331 35799999998 9999999999999999999 9999999975
No 35
>KOG3550|consensus
Probab=98.12 E-value=3.2e-06 Score=57.47 Aligned_cols=56 Identities=21% Similarity=0.397 Sum_probs=46.1
Q ss_pred cCCeEEEEEEcCCC--eE----EecCChHhhc-CCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 11 LKGYCIIIAETPDG--KV----KLYGSPADKS-DLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 11 ~~g~~i~l~~~~~~--~i----v~~gspA~~a-GLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
-.|.||.+...+.. .| +++|+-|++- |||.||++++|||.++++-. ++.++++++.
T Consensus 100 deglgfnvmggkeqnspiyisriipggvadrhgglkrgdqllsvngvsvege~-hekavellka 162 (207)
T KOG3550|consen 100 DEGLGFNVMGGKEQNSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEH-HEKAVELLKA 162 (207)
T ss_pred ccccceeeccCcccCCceEEEeecCCccccccCcccccceeEeecceeecchh-hHHHHHHHHH
Confidence 56777777666532 23 5799999987 69999999999999999999 9999999864
No 36
>KOG3542|consensus
Probab=97.86 E-value=8.8e-06 Score=65.40 Aligned_cols=50 Identities=36% Similarity=0.584 Sum_probs=43.2
Q ss_pred cCCeEEEEEEcCCCeEEecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 11 LKGYCIIIAETPDGKVKLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 11 ~~g~~i~l~~~~~~~iv~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
.+||||++.+ +.+|+.|+++|||.||+|++|||+++++.+ ...+.++++.
T Consensus 559 EkGfgifV~~------V~pgskAa~~GlKRgDqilEVNgQnfenis-~~KA~eiLrn 608 (1283)
T KOG3542|consen 559 EKGFGIFVAE------VFPGSKAAREGLKRGDQILEVNGQNFENIS-AKKAEEILRN 608 (1283)
T ss_pred cccceeEEee------ecCCchHHHhhhhhhhhhhhccccchhhhh-HHHHHHHhcC
Confidence 5677777765 368999999999999999999999999998 8888888765
No 37
>PF04495 GRASP55_65: GRASP55/65 PDZ-like domain ; InterPro: IPR007583 GRASP55 (Golgi reassembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide-sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system [].; PDB: 3RLE_A 4EDJ_A.
Probab=97.69 E-value=0.00015 Score=47.21 Aligned_cols=51 Identities=24% Similarity=0.302 Sum_probs=31.4
Q ss_pred CCeEEEEEEcCC---C--eE--EecCChHhhcCCCC-CCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 12 KGYCIIIAETPD---G--KV--KLYGSPADKSDLEI-GDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 12 ~g~~i~l~~~~~---~--~i--v~~gspA~~aGLk~-GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
-|..+....... . +| |.+||||++|||++ .|.|+.+++..+.+.+ ++.+++
T Consensus 28 LG~sv~~~~~~~~~~~~~~Vl~V~p~SPA~~AGL~p~~DyIig~~~~~l~~~~---~l~~~v 86 (138)
T PF04495_consen 28 LGISVRFESFEGAEEEGWHVLRVAPNSPAAKAGLEPFFDYIIGIDGGLLDDED---DLFELV 86 (138)
T ss_dssp S-EEEEEEE-TTGCCCEEEEEEE-TTSHHHHTT--TTTEEEEEETTCE--STC---HHHHHH
T ss_pred CcEEEEEecccccccceEEEeEecCCCHHHHCCccccccEEEEccceecCCHH---HHHHHH
Confidence 355555555441 1 12 56999999999999 6999999999998766 555544
No 38
>KOG3552|consensus
Probab=97.64 E-value=3.5e-05 Score=63.19 Aligned_cols=54 Identities=28% Similarity=0.406 Sum_probs=41.6
Q ss_pred CCeEEEEEEcCCCeEEecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 12 KGYCIIIAETPDGKVKLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 12 ~g~~i~l~~~~~~~iv~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
=||||+-..----+.|.+|+|+.-. |++||+|++|||.++.+.. .|.++.+++.
T Consensus 67 lGFgfvagrPviVr~VT~GGps~GK-L~PGDQIl~vN~Epv~dap-rervIdlvRa 120 (1298)
T KOG3552|consen 67 LGFGFVAGRPVIVRFVTEGGPSIGK-LQPGDQILAVNGEPVKDAP-RERVIDLVRA 120 (1298)
T ss_pred ccceeecCCceEEEEecCCCCcccc-ccCCCeEEEecCccccccc-HHHHHHHHHH
Confidence 3788876511001125689998864 9999999999999999999 9999998863
No 39
>KOG3551|consensus
Probab=97.50 E-value=8.9e-05 Score=56.28 Aligned_cols=57 Identities=33% Similarity=0.550 Sum_probs=50.0
Q ss_pred ccCCeEEEEEEcCCCeE------EecCChHhhcC-CCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 10 DLKGYCIIIAETPDGKV------KLYGSPADKSD-LEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 10 ~~~g~~i~l~~~~~~~i------v~~gspA~~aG-Lk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
+.+|-||-+....+|+. +.+|-+|++.+ |..||.|++|||.+..+.+ |+++++.+++
T Consensus 94 d~gGLGISIKGGreNkMPIlISKIFkGlAADQt~aL~~gDaIlSVNG~dL~~At-HdeAVqaLKr 157 (506)
T KOG3551|consen 94 DAGGLGISIKGGRENKMPILISKIFKGLAADQTGALFLGDAILSVNGEDLRDAT-HDEAVQALKR 157 (506)
T ss_pred cCCcceEEeecCcccCCceehhHhccccccccccceeeccEEEEecchhhhhcc-hHHHHHHHHh
Confidence 37899999988888763 35799999886 9999999999999999999 9999998875
No 40
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=97.37 E-value=0.00023 Score=50.99 Aligned_cols=36 Identities=36% Similarity=0.570 Sum_probs=31.0
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
+.+++||+++|++.||.|+++||+++.+.. ++...+
T Consensus 277 v~~~spa~~agi~~Gdii~~vng~~v~~~~---~l~~~v 312 (347)
T COG0265 277 VLPGSPAAKAGIKAGDIITAVNGKPVASLS---DLVAAV 312 (347)
T ss_pred cCCCChHHHcCCCCCCEEEEECCEEccCHH---HHHHHH
Confidence 458999999999999999999999999887 555444
No 41
>KOG3129|consensus
Probab=97.30 E-value=0.00026 Score=49.81 Aligned_cols=35 Identities=31% Similarity=0.435 Sum_probs=27.8
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHH
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEV 61 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev 61 (69)
+.++|||++|||+.||+|+++.+..--++..+..+
T Consensus 146 V~~~SPA~~aGl~~gD~il~fGnV~sgn~~~lq~i 180 (231)
T KOG3129|consen 146 VVPGSPADEAGLCVGDEILKFGNVHSGNFLPLQNI 180 (231)
T ss_pred cCCCChhhhhCcccCceEEEecccccccchhHHHH
Confidence 46899999999999999999988776655533333
No 42
>KOG3651|consensus
Probab=97.22 E-value=0.00038 Score=51.72 Aligned_cols=40 Identities=35% Similarity=0.474 Sum_probs=35.8
Q ss_pred EecCChHhhcC-CCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 27 KLYGSPADKSD-LEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 27 v~~gspA~~aG-Lk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
+..++||++-| ++.||+|++|||.++.+.. -.++.++|+.
T Consensus 37 vFD~tPAa~dG~i~~GDEi~avNg~svKGkt-KveVAkmIQ~ 77 (429)
T KOG3651|consen 37 VFDKTPAAKDGRIRCGDEIVAVNGISVKGKT-KVEVAKMIQV 77 (429)
T ss_pred eccCCchhccCccccCCeeEEecceeecCcc-HHHHHHHHHH
Confidence 35799999987 9999999999999999999 8888888864
No 43
>PF12812 PDZ_1: PDZ-like domain
Probab=97.04 E-value=0.00094 Score=39.69 Aligned_cols=37 Identities=32% Similarity=0.256 Sum_probs=29.7
Q ss_pred cCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 29 YGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
.|+++.+.|+..|-.|.+||++++.+.+++.++++.|
T Consensus 39 ~g~~~~~~~i~~g~iI~~Vn~kpt~~Ld~f~~vvk~i 75 (78)
T PF12812_consen 39 GGSLAFAGGISKGFIITSVNGKPTPDLDDFIKVVKKI 75 (78)
T ss_pred CCChhhhCCCCCCeEEEeECCcCCcCHHHHHHHHHhC
Confidence 5788888889999999999999999877455544443
No 44
>COG3975 Predicted protease with the C-terminal PDZ domain [General function prediction only]
Probab=96.98 E-value=0.00087 Score=52.13 Aligned_cols=24 Identities=42% Similarity=0.655 Sum_probs=22.7
Q ss_pred EecCChHhhcCCCCCCEEEEECCE
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGK 50 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~ 50 (69)
|.+||||++|||.+||+|++|||.
T Consensus 469 V~~~gPA~~AGl~~Gd~ivai~G~ 492 (558)
T COG3975 469 VFPGGPAYKAGLSPGDKIVAINGI 492 (558)
T ss_pred cCCCChhHhccCCCccEEEEEcCc
Confidence 468999999999999999999999
No 45
>KOG3532|consensus
Probab=96.84 E-value=0.0016 Score=52.63 Aligned_cols=49 Identities=16% Similarity=0.250 Sum_probs=35.9
Q ss_pred CeEEEEEEcCCCeE----EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHH
Q psy16960 13 GYCIIIAETPDGKV----KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEV 61 (69)
Q Consensus 13 g~~i~l~~~~~~~i----v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev 61 (69)
..|++.-..-+..+ |.+++||.++.|++||.+++|||+||.+..+...+
T Consensus 387 ~ig~vf~~~~~~~v~v~tv~~ns~a~k~~~~~gdvlvai~~~pi~s~~q~~~~ 439 (1051)
T KOG3532|consen 387 PIGLVFDKNTNRAVKVCTVEDNSLADKAAFKPGDVLVAINNVPIRSERQATRF 439 (1051)
T ss_pred ceeEEEecCCceEEEEEEecCCChhhHhcCCCcceEEEecCccchhHHHHHHH
Confidence 34666644332222 45899999999999999999999999988733333
No 46
>KOG0609|consensus
Probab=96.80 E-value=0.0018 Score=50.32 Aligned_cols=53 Identities=34% Similarity=0.493 Sum_probs=42.3
Q ss_pred EEEEEEcCCCe-E---EecCChHhhcC-CCCCCEEEEECCEEeCCCCChHHHHHhhcCC
Q psy16960 15 CIIIAETPDGK-V---KLYGSPADKSD-LEIGDEILEVNGKTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 15 ~i~l~~~~~~~-i---v~~gspA~~aG-Lk~GD~Il~Vng~~i~~~~~~~ev~~~i~~~ 68 (69)
|+.+...+.+. + ++.|+.+++.| |+.||+|.+|||.++.+.+ .+++..+++..
T Consensus 137 G~Tik~~e~~~~~vARI~~GG~~~r~glL~~GD~i~EvNGi~v~~~~-~~e~q~~l~~~ 194 (542)
T KOG0609|consen 137 GATIRVEEDTKVVVARIMHGGMADRQGLLHVGDEILEVNGISVANKS-PEELQELLRNS 194 (542)
T ss_pred ceEEEeccCCccEEeeeccCCcchhccceeeccchheecCeecccCC-HHHHHHHHHhC
Confidence 55555544433 3 45799999998 9999999999999999998 99999888654
No 47
>KOG1892|consensus
Probab=96.72 E-value=0.0038 Score=52.12 Aligned_cols=60 Identities=22% Similarity=0.382 Sum_probs=46.6
Q ss_pred EeccCCeEEEEEEcCCC---e--E----EecCChHhhcC-CCCCCEEEEECCEEeCCCCChHHHHHhhcCC
Q psy16960 8 MIDLKGYCIIIAETPDG---K--V----KLYGSPADKSD-LEIGDEILEVNGKTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 8 ~~~~~g~~i~l~~~~~~---~--i----v~~gspA~~aG-Lk~GD~Il~Vng~~i~~~~~~~ev~~~i~~~ 68 (69)
+.|-+|.|+-++..+.. + | |++|+||+..| |++||++++|||++.-+.+ -|++..+|.+.
T Consensus 939 L~KnnGmGLSIVAAkGaGq~klGIYvKsVV~GgaAd~DGRL~aGDQLLsVdG~SLiGis-QErAA~lmtrt 1008 (1629)
T KOG1892|consen 939 LKKNNGMGLSIVAAKGAGQRKLGIYVKSVVEGGAADHDGRLEAGDQLLSVDGHSLIGIS-QERAARLMTRT 1008 (1629)
T ss_pred EeccCCceEEEEeeccCCccccceEEEEeccCCccccccccccCceeeeecCccccccc-HHHHHHHHhcc
Confidence 34457777766655431 1 2 57899999887 9999999999999999999 88988887553
No 48
>PF14685 Tricorn_PDZ: Tricorn protease PDZ domain; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A.
Probab=96.69 E-value=0.0029 Score=38.55 Aligned_cols=27 Identities=30% Similarity=0.533 Sum_probs=19.5
Q ss_pred CChHhhcC--CCCCCEEEEECCEEeCCCC
Q psy16960 30 GSPADKSD--LEIGDEILEVNGKTFKDNC 56 (69)
Q Consensus 30 gspA~~aG--Lk~GD~Il~Vng~~i~~~~ 56 (69)
.||-.+.| +++||.|++|||+++..-.
T Consensus 30 ~sPL~~pGv~v~~GD~I~aInG~~v~~~~ 58 (88)
T PF14685_consen 30 RSPLAQPGVDVREGDYILAINGQPVTADA 58 (88)
T ss_dssp B-GGGGGS----TT-EEEEETTEE-BTTB
T ss_pred cCCccCCCCCCCCCCEEEEECCEECCCCC
Confidence 48888887 5599999999999999776
No 49
>KOG0606|consensus
Probab=96.63 E-value=0.0015 Score=54.44 Aligned_cols=39 Identities=36% Similarity=0.448 Sum_probs=36.4
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
+.+|+||..+||+++|.|+.|||+++.+.. |.++++++-
T Consensus 665 v~egsPA~~agls~~DlIthvnge~v~gl~-H~ev~~Lll 703 (1205)
T KOG0606|consen 665 VEEGSPAFEAGLSAGDLITHVNGEPVHGLV-HTEVMELLL 703 (1205)
T ss_pred ecCCCCccccCCCccceeEeccCcccchhh-HHHHHHHHH
Confidence 468999999999999999999999999999 999999874
No 50
>KOG1320|consensus
Probab=96.61 E-value=0.002 Score=49.37 Aligned_cols=38 Identities=32% Similarity=0.417 Sum_probs=33.1
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
+.+|+++..++++.||+|++|||+++.+.. ++..+|+.
T Consensus 405 Vlp~~~~~~~~~~~g~~V~~vng~~V~n~~---~l~~~i~~ 442 (473)
T KOG1320|consen 405 VLPGSINGGYGLKPGDQVVKVNGKPVKNLK---HLYELIEE 442 (473)
T ss_pred eccCCCcccccccCCCEEEEECCEEeechH---HHHHHHHh
Confidence 358999999999999999999999999888 66666654
No 51
>KOG3605|consensus
Probab=96.59 E-value=0.0056 Score=49.11 Aligned_cols=39 Identities=31% Similarity=0.527 Sum_probs=35.1
Q ss_pred ecCChHhhcC-CCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 28 LYGSPADKSD-LEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 28 ~~gspA~~aG-Lk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
+.++||++.| |-.||+|++|||.+.-+.. +..-..+|+.
T Consensus 681 m~~GpAarsgkLnIGDQiiaING~SLVGLP-LstcQs~Ik~ 720 (829)
T KOG3605|consen 681 MHGGPAARSGKLNIGDQIMSINGTSLVGLP-LSTCQSIIKG 720 (829)
T ss_pred ccCChhhhcCCccccceeEeecCceecccc-HHHHHHHHhc
Confidence 4799999998 9999999999999999998 8888888765
No 52
>KOG3605|consensus
Probab=96.55 E-value=0.0023 Score=51.17 Aligned_cols=38 Identities=24% Similarity=0.571 Sum_probs=35.6
Q ss_pred ecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 28 LYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
..|+=|++.|+++|-+|++|||++|---. |+.|+++|.
T Consensus 764 lRGGIAERGGVRVGHRIIEINgQSVVA~p-HekIV~lLs 801 (829)
T KOG3605|consen 764 LRGGIAERGGVRVGHRIIEINGQSVVATP-HEKIVQLLS 801 (829)
T ss_pred hcccchhccCceeeeeEEEECCceEEecc-HHHHHHHHH
Confidence 47999999999999999999999999999 999999874
No 53
>PRK09681 putative type II secretion protein GspC; Provisional
Probab=96.52 E-value=0.0029 Score=45.62 Aligned_cols=39 Identities=21% Similarity=0.307 Sum_probs=27.7
Q ss_pred EecCChH---hhcCCCCCCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 27 KLYGSPA---DKSDLEIGDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 27 v~~gspA---~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
+.+|..+ .++|||+||.+++|||.++.+.++..++.+.|
T Consensus 211 l~Pgkd~~lF~~~GLq~GDva~sING~dL~D~~qa~~l~~~L 252 (276)
T PRK09681 211 VKPGADRSLFDASGFKEGDIAIALNQQDFTDPRAMIALMRQL 252 (276)
T ss_pred ECCCCcHHHHHHcCCCCCCEEEEeCCeeCCCHHHHHHHHHHh
Confidence 3455433 47799999999999999999776333444443
No 54
>KOG3549|consensus
Probab=96.50 E-value=0.003 Score=47.83 Aligned_cols=57 Identities=26% Similarity=0.385 Sum_probs=45.8
Q ss_pred ccCCeEEEEEEcCCCeE------EecCChHhhcC-CCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 10 DLKGYCIIIAETPDGKV------KLYGSPADKSD-LEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 10 ~~~g~~i~l~~~~~~~i------v~~gspA~~aG-Lk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
+..|+|+-+.......+ +...-+|+..| |-.||-|++|||..+..-. |||++++++.
T Consensus 64 ~vGGlGLSIKGGaEHn~PvviSkI~kdQaAd~tG~LFvGDAilqvNGi~v~~c~-HeevV~iLRN 127 (505)
T KOG3549|consen 64 KVGGLGLSIKGGAEHNLPVVISKIYKDQAADITGQLFVGDAILQVNGIYVTACP-HEEVVNILRN 127 (505)
T ss_pred ecCcceeeeccccccCccEEeehhhhhhhhhhcCceEeeeeeEEeccEEeecCC-hHHHHHHHHh
Confidence 36788888876655432 23577888887 8899999999999999999 9999999864
No 55
>KOG3606|consensus
Probab=96.41 E-value=0.0051 Score=45.19 Aligned_cols=39 Identities=28% Similarity=0.446 Sum_probs=35.3
Q ss_pred ecCChHhhcC-CCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 28 LYGSPADKSD-LEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 28 ~~gspA~~aG-Lk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
++|+-|+.-| |.++|+|++|||.++.+.+ ++++...|-+
T Consensus 202 VpGGLAeSTGLLaVnDEVlEVNGIEVaGKT-LDQVTDMMvA 241 (358)
T KOG3606|consen 202 VPGGLAESTGLLAVNDEVLEVNGIEVAGKT-LDQVTDMMVA 241 (358)
T ss_pred cCCccccccceeeecceeEEEcCEEecccc-HHHHHHHHhh
Confidence 5899999999 7899999999999999999 9999887743
No 56
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=96.29 E-value=0.0058 Score=43.68 Aligned_cols=30 Identities=27% Similarity=0.255 Sum_probs=28.2
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCC
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNC 56 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~ 56 (69)
+..+++|+.+||++||+|+++|+.++.+|+
T Consensus 136 v~~~s~a~~a~l~~Gd~iv~~~~~~i~~~~ 165 (375)
T COG0750 136 VAPKSAAALAGLRPGDRIVAVDGEKVASWD 165 (375)
T ss_pred cCCCCHHHHcCCCCCCEEEeECCEEccCHH
Confidence 467899999999999999999999999998
No 57
>KOG3571|consensus
Probab=96.16 E-value=0.0048 Score=48.24 Aligned_cols=40 Identities=23% Similarity=0.449 Sum_probs=34.1
Q ss_pred EecCChHhhcC-CCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 27 KLYGSPADKSD-LEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 27 v~~gspA~~aG-Lk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
+++|++-+.-| +.+||.|+.||..++++++ .++++..|++
T Consensus 284 ImkgGAVA~DGRIe~GDMiLQVNevsFENmS-Nd~AVrvLRE 324 (626)
T KOG3571|consen 284 IMKGGAVALDGRIEPGDMILQVNEVSFENMS-NDQAVRVLRE 324 (626)
T ss_pred eccCceeeccCccCccceEEEeeecchhhcC-chHHHHHHHH
Confidence 46777666665 9999999999999999999 9999988863
No 58
>KOG3580|consensus
Probab=96.01 E-value=0.0058 Score=49.07 Aligned_cols=38 Identities=26% Similarity=0.405 Sum_probs=32.0
Q ss_pred CChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcCC
Q psy16960 30 GSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 30 gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~~ 68 (69)
|=+|...+|+.||.|++|||...++++ +.+..++|..+
T Consensus 230 gLAardgnlqEGDiiLkINGtvteNmS-LtDar~LIEkS 267 (1027)
T KOG3580|consen 230 GLAARDGNLQEGDIILKINGTVTENMS-LTDARKLIEKS 267 (1027)
T ss_pred chhhccCCcccccEEEEECcEeecccc-chhHHHHHHhc
Confidence 444445579999999999999999999 99999998654
No 59
>KOG1738|consensus
Probab=95.39 E-value=0.029 Score=44.48 Aligned_cols=57 Identities=26% Similarity=0.359 Sum_probs=46.3
Q ss_pred ccCCeEEEEEEcCCCeE----EecCChHhhcC-CCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 10 DLKGYCIIIAETPDGKV----KLYGSPADKSD-LEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 10 ~~~g~~i~l~~~~~~~i----v~~gspA~~aG-Lk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
+-.|-|+++...-+|.. +.+++||.... +..||+|+.||++.+.+|+ +.-+++.++.
T Consensus 211 p~eglg~~I~Ssydg~h~~s~~~e~Spad~~~kI~dgdEv~qiN~qtvVgwq-lk~vV~sL~~ 272 (638)
T KOG1738|consen 211 PSEGLGLYIDSSYDGPHVTSKIFEQSPADYRQKILDGDEVLQINEQTVVGWQ-LKVVVSSLRE 272 (638)
T ss_pred cccCCceEEeeecCCceeccccccCChHHHhhcccCccceeeecccccccch-hHhHHhhccc
Confidence 34567777777777653 35799999875 9999999999999999999 9999887754
No 60
>COG3480 SdrC Predicted secreted protein containing a PDZ domain [Signal transduction mechanisms]
Probab=94.21 E-value=0.069 Score=39.68 Aligned_cols=35 Identities=34% Similarity=0.582 Sum_probs=28.4
Q ss_pred ecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 28 LYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
.+++|+... |+.||.|++|||+++.+.+ ++..+++
T Consensus 138 ~~~~~~~gk-l~~gD~i~avdg~~f~s~~---e~i~~v~ 172 (342)
T COG3480 138 IDNSPFKGK-LEAGDTIIAVDGEPFTSSD---ELIDYVS 172 (342)
T ss_pred cCCcchhce-eccCCeEEeeCCeecCCHH---HHHHHHh
Confidence 456777664 9999999999999999887 7766664
No 61
>COG3031 PulC Type II secretory pathway, component PulC [Intracellular trafficking and secretion]
Probab=93.43 E-value=0.12 Score=37.34 Aligned_cols=35 Identities=26% Similarity=0.309 Sum_probs=28.3
Q ss_pred cCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 29 YGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
+++.=++.|||.||.-+++|+.++.+-+ ++.++++
T Consensus 216 d~slF~~sglq~GDIavaiNnldltdp~---~m~~llq 250 (275)
T COG3031 216 DGSLFYKSGLQRGDIAVAINNLDLTDPE---DMFRLLQ 250 (275)
T ss_pred CcchhhhhcCCCcceEEEecCcccCCHH---HHHHHHH
Confidence 3566778899999999999999998766 6666554
No 62
>KOG2921|consensus
Probab=91.68 E-value=0.15 Score=39.19 Aligned_cols=47 Identities=23% Similarity=0.345 Sum_probs=33.6
Q ss_pred CCceEec--cCCeEEEEEEcCCCeEEecCChHh-hcCCCCCCEEEEECCEEeCCCC
Q psy16960 4 SPSHMID--LKGYCIIIAETPDGKVKLYGSPAD-KSDLEIGDEILEVNGKTFKDNC 56 (69)
Q Consensus 4 ~~~~~~~--~~g~~i~l~~~~~~~iv~~gspA~-~aGLk~GD~Il~Vng~~i~~~~ 56 (69)
.|=-|-+ ..|+++.+.+... -||+. .-||.+||+|.++||-++++-+
T Consensus 208 lpViLsPfya~g~gV~Vtev~~------~Spl~gprGL~vgdvitsldgcpV~~v~ 257 (484)
T KOG2921|consen 208 LPVILSPFYAHGEGVTVTEVPS------VSPLFGPRGLSVGDVITSLDGCPVHKVS 257 (484)
T ss_pred hhHhhchhhhcCceEEEEeccc------cCCCcCcccCCccceEEecCCcccCCHH
Confidence 3444455 6788888877532 24443 2299999999999999998766
No 63
>KOG1421|consensus
Probab=88.87 E-value=0.28 Score=40.10 Aligned_cols=32 Identities=38% Similarity=0.479 Sum_probs=26.3
Q ss_pred ecCChHhhcCCCCCCEEEEECCEEeCCCCChHH
Q psy16960 28 LYGSPADKSDLEIGDEILEVNGKTFKDNCNHNE 60 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~e 60 (69)
.+++||++. |++||.+++||+.-+.++..+++
T Consensus 311 L~~gpa~k~-Le~GDillavN~t~l~df~~l~~ 342 (955)
T KOG1421|consen 311 LPEGPAEKK-LEPGDILLAVNSTCLNDFEALEQ 342 (955)
T ss_pred ccCCchhhc-cCCCcEEEEEcceehHHHHHHHH
Confidence 579999997 99999999999888876663333
No 64
>PF11874 DUF3394: Domain of unknown function (DUF3394); InterPro: IPR021814 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with PF06808 from PFAM.
Probab=88.64 E-value=0.68 Score=31.70 Aligned_cols=36 Identities=28% Similarity=0.418 Sum_probs=26.4
Q ss_pred CeEEEEEEcCCCeE---EecCChHhhcCCCCCCEEEEEC
Q psy16960 13 GYCIIIAETPDGKV---KLYGSPADKSDLEIGDEILEVN 48 (69)
Q Consensus 13 g~~i~l~~~~~~~i---v~~gspA~~aGLk~GD~Il~Vn 48 (69)
..|+.+....+..+ +..||||+++|+.-|++|++|-
T Consensus 112 ~~GL~l~~e~~~~~Vd~v~fgS~A~~~g~d~d~~I~~v~ 150 (183)
T PF11874_consen 112 AAGLTLMEEGGKVIVDEVEFGSPAEKAGIDFDWEITEVE 150 (183)
T ss_pred hCCCEEEeeCCEEEEEecCCCCHHHHcCCCCCcEEEEEE
Confidence 34677755443332 3479999999999999999874
No 65
>KOG3938|consensus
Probab=88.16 E-value=0.36 Score=35.54 Aligned_cols=40 Identities=28% Similarity=0.416 Sum_probs=33.9
Q ss_pred ecCChHhhc-CCCCCCEEEEECCEEeCCCCChHHHHHhhcCC
Q psy16960 28 LYGSPADKS-DLEIGDEILEVNGKTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 28 ~~gspA~~a-GLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~~ 68 (69)
-+||--.+. -+++||.|.+|||+++-+|. |-++..+++..
T Consensus 157 kegsvidri~~i~VGd~IEaiNge~ivG~R-HYeVArmLKel 197 (334)
T KOG3938|consen 157 KEGSVIDRIEAICVGDHIEAINGESIVGKR-HYEVARMLKEL 197 (334)
T ss_pred cCCchhhhhhheeHHhHHHhhcCccccchh-HHHHHHHHHhc
Confidence 467766655 48999999999999999999 99999988753
No 66
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=85.16 E-value=0.82 Score=27.33 Aligned_cols=36 Identities=19% Similarity=0.223 Sum_probs=22.9
Q ss_pred cCCeEEEEEEcC-----CCeEEecCChHhhcCCCCCCEEEE
Q psy16960 11 LKGYCIIIAETP-----DGKVKLYGSPADKSDLEIGDEILE 46 (69)
Q Consensus 11 ~~g~~i~l~~~~-----~~~iv~~gspA~~aGLk~GD~Il~ 46 (69)
-.||||.-.... ..-+.++.+...+-||+.||.|.-
T Consensus 11 ~dGyGFLR~~~~~y~~~~~DvYVs~~qIrrf~LR~GD~V~G 51 (78)
T PF07497_consen 11 PDGYGFLRSPDNNYLPSPDDVYVSPSQIRRFGLRTGDLVEG 51 (78)
T ss_dssp TTS-EEEE-GGGTTS-STTSEEE-CCCCCCTT--TTEEEEE
T ss_pred CCCcEEeECCCcCCCCCCCCEEECHHHHHHcCCCCCCEEEE
Confidence 479999987621 233667778888999999999874
No 67
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=84.01 E-value=1.6 Score=25.38 Aligned_cols=37 Identities=14% Similarity=0.238 Sum_probs=26.8
Q ss_pred cCCeEEEEEEcC-----CCeEEecCChHhhcCCCCCCEEEEE
Q psy16960 11 LKGYCIIIAETP-----DGKVKLYGSPADKSDLEIGDEILEV 47 (69)
Q Consensus 11 ~~g~~i~l~~~~-----~~~iv~~gspA~~aGLk~GD~Il~V 47 (69)
-.||||...... .+-+.++.+.-.+-||+.||.|.-.
T Consensus 9 ~~g~GFLR~~~~~y~~~~~DvyVs~~~Irr~~LR~GD~V~G~ 50 (68)
T cd04459 9 PDGFGFLRSSGYNYLPGPDDIYVSPSQIRRFNLRTGDTVVGQ 50 (68)
T ss_pred CCCceEEecCCcCCCCCCCCEEECHHHHHHhCCCCCCEEEEE
Confidence 458998886632 1235567777888999999999863
No 68
>KOG4407|consensus
Probab=82.07 E-value=0.91 Score=39.61 Aligned_cols=40 Identities=23% Similarity=0.392 Sum_probs=36.7
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
|.+++||.-+.||-||+++.||.+++.... ..+++..|++
T Consensus 150 V~~n~~~~~a~LQ~~~~V~~v~~q~~A~i~-~s~~~S~~~q 189 (1973)
T KOG4407|consen 150 VQANGPAHYANLQTGDRVLMVNNQPIAGIA-YSTIVSMIKQ 189 (1973)
T ss_pred hccCChhHHHhhhccceeEEeecCcccchh-hhhhhhhhcc
Confidence 457999999999999999999999999998 9999988875
No 69
>KOG3834|consensus
Probab=81.77 E-value=3.1 Score=32.21 Aligned_cols=30 Identities=33% Similarity=0.364 Sum_probs=25.2
Q ss_pred EecCChHhhcCCCC-CCEEEEECCEEeCCCC
Q psy16960 27 KLYGSPADKSDLEI-GDEILEVNGKTFKDNC 56 (69)
Q Consensus 27 v~~gspA~~aGLk~-GD~Il~Vng~~i~~~~ 56 (69)
+.++|||++|||.+ =|-|++|||..++...
T Consensus 22 VqedSpa~~aglepffdFIvSI~g~rL~~dn 52 (462)
T KOG3834|consen 22 VQEDSPAHKAGLEPFFDFIVSINGIRLNKDN 52 (462)
T ss_pred eecCChHHhcCcchhhhhhheeCcccccCch
Confidence 46789999999887 5788999999998544
No 70
>PRK03760 hypothetical protein; Provisional
Probab=77.15 E-value=5.2 Score=25.22 Aligned_cols=18 Identities=28% Similarity=0.172 Sum_probs=15.2
Q ss_pred ecCChHhhcCCCCCCEEE
Q psy16960 28 LYGSPADKSDLEIGDEIL 45 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il 45 (69)
.+++.+++.|+++||+|.
T Consensus 96 l~aG~~~~~gi~~Gd~v~ 113 (117)
T PRK03760 96 GPVGKIRVLKVEVGDEIE 113 (117)
T ss_pred eCCChHHHcCCCCCCEEE
Confidence 467888899999999984
No 71
>COG5233 GRH1 Peripheral Golgi membrane protein [Intracellular trafficking and secretion]
Probab=72.38 E-value=2.4 Score=32.03 Aligned_cols=27 Identities=33% Similarity=0.518 Sum_probs=23.6
Q ss_pred EecCChHhhcCCCCCCEEEEECCEEeC
Q psy16960 27 KLYGSPADKSDLEIGDEILEVNGKTFK 53 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il~Vng~~i~ 53 (69)
+.+.+||+++|.-.||.|+-+|+.++.
T Consensus 70 v~~~~~~e~~~~~~~dyilg~n~Dp~~ 96 (417)
T COG5233 70 VNPESPAEKAGMVVGDYILGINEDPLR 96 (417)
T ss_pred ccccChhHhhccccceeEEeecCCcHH
Confidence 457899999999999999999977754
No 72
>KOG1421|consensus
Probab=69.12 E-value=4.4 Score=33.51 Aligned_cols=34 Identities=29% Similarity=0.321 Sum_probs=29.2
Q ss_pred cCChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 29 YGSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
.||||.+ +|++---|++|||+.+.+++ +....++
T Consensus 871 ~gspalq-~l~aa~fitavng~~t~~ld---df~~~~~ 904 (955)
T KOG1421|consen 871 YGSPALQ-MLRAAHFITAVNGHDTNTLD---DFYHMLL 904 (955)
T ss_pred cCChhHh-hcchheeEEEecccccCcHH---HHHHHHh
Confidence 6899999 99999999999999998777 6666553
No 73
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=68.94 E-value=10 Score=22.44 Aligned_cols=34 Identities=9% Similarity=0.141 Sum_probs=26.4
Q ss_pred EEEEEEcCCCeEEecCChHhhcCCCCCCEEEEEC
Q psy16960 15 CIIIAETPDGKVKLYGSPADKSDLEIGDEILEVN 48 (69)
Q Consensus 15 ~i~l~~~~~~~iv~~gspA~~aGLk~GD~Il~Vn 48 (69)
.++..-...+++++|-.-.++-||+.||.+.-++
T Consensus 5 ~~~~kV~~~GqIvIPkeiR~~lgi~~Gd~lei~~ 38 (89)
T COG2002 5 MEVVKVDRKGQIVIPKEIREALGIKEGDVLEIIV 38 (89)
T ss_pred eeEEEECcCceEEecHHHHHHhCCCCCCEEEEEE
Confidence 4455555677898987788888999999998655
No 74
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=65.59 E-value=15 Score=19.13 Aligned_cols=33 Identities=27% Similarity=0.377 Sum_probs=20.3
Q ss_pred CCeEEEEEEcCCCeEEecCChHh----hcCCCCCCEEEE
Q psy16960 12 KGYCIIIAETPDGKVKLYGSPAD----KSDLEIGDEILE 46 (69)
Q Consensus 12 ~g~~i~l~~~~~~~iv~~gspA~----~aGLk~GD~Il~ 46 (69)
+|||++........+.++ +.. ..+++.||+|+.
T Consensus 9 ~g~gfv~~~~~~~~i~v~--~~~~~~~~~~~~~Gd~V~~ 45 (64)
T smart00357 9 KGFGFIRPDDGGKDVFVH--PSQIQGGLKSLREGDEVEF 45 (64)
T ss_pred CCeeEEecCCCCccEEEE--hHHhhcCCCcCCCCCEEEE
Confidence 688888764332345443 222 456899999974
No 75
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=64.66 E-value=7 Score=20.38 Aligned_cols=25 Identities=28% Similarity=0.345 Sum_probs=18.3
Q ss_pred CCCeEEecCChHhhcCCCCCCEEEE
Q psy16960 22 PDGKVKLYGSPADKSDLEIGDEILE 46 (69)
Q Consensus 22 ~~~~iv~~gspA~~aGLk~GD~Il~ 46 (69)
+...++.|-.-+.+.||++||.|.-
T Consensus 5 ~s~~v~iPk~~~~~l~l~~Gd~v~i 29 (47)
T PF04014_consen 5 NSGQVTIPKEIREKLGLKPGDEVEI 29 (47)
T ss_dssp TCSEEEE-HHHHHHTTSSTTTEEEE
T ss_pred CCceEECCHHHHHHcCCCCCCEEEE
Confidence 3445667767778889999999873
No 76
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=64.12 E-value=17 Score=20.53 Aligned_cols=42 Identities=21% Similarity=0.252 Sum_probs=23.4
Q ss_pred CceEec-cCCeEEEEEEcCCCeEEecCChHhh---cCCCCCCEEEE
Q psy16960 5 PSHMID-LKGYCIIIAETPDGKVKLYGSPADK---SDLEIGDEILE 46 (69)
Q Consensus 5 ~~~~~~-~~g~~i~l~~~~~~~iv~~gspA~~---aGLk~GD~Il~ 46 (69)
-+-..+ -+|||++........+..-=+.-.. ..|+.||+|.-
T Consensus 5 ~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~l~~G~~V~f 50 (68)
T TIGR02381 5 IVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQF 50 (68)
T ss_pred EEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCCCCCCCEEEE
Confidence 333444 7999999865433334222122222 24899998863
No 77
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=60.64 E-value=22 Score=20.59 Aligned_cols=41 Identities=17% Similarity=0.202 Sum_probs=22.1
Q ss_pred CceEec-cCCeEEEEEEcCCCeEEecCChHh---hcCCCCCCEEE
Q psy16960 5 PSHMID-LKGYCIIIAETPDGKVKLYGSPAD---KSDLEIGDEIL 45 (69)
Q Consensus 5 ~~~~~~-~~g~~i~l~~~~~~~iv~~gspA~---~aGLk~GD~Il 45 (69)
-+-..+ -+||||+........|..-=+.-. ...|+.||.|.
T Consensus 5 ~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~l~~G~~V~ 49 (74)
T PRK09937 5 TVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQ 49 (74)
T ss_pred EEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCCCCCCCEEE
Confidence 334444 799999975433233321111111 13599999886
No 78
>PRK14998 cold shock-like protein CspD; Provisional
Probab=60.48 E-value=21 Score=20.62 Aligned_cols=44 Identities=18% Similarity=0.207 Sum_probs=23.6
Q ss_pred CCCCceEec-cCCeEEEEEEcCCCeEEecCChHh---hcCCCCCCEEE
Q psy16960 2 STSPSHMID-LKGYCIIIAETPDGKVKLYGSPAD---KSDLEIGDEIL 45 (69)
Q Consensus 2 ~~~~~~~~~-~~g~~i~l~~~~~~~iv~~gspA~---~aGLk~GD~Il 45 (69)
.+.-+-..+ -+||||+........|..-=+.-+ ...|+.|+.+.
T Consensus 2 ~~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~l~~G~~V~ 49 (73)
T PRK14998 2 ETGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVR 49 (73)
T ss_pred CCeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCCCCCCCEEE
Confidence 333344445 799999885543333321111111 13499999876
No 79
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=59.51 E-value=12 Score=18.46 Aligned_cols=27 Identities=19% Similarity=0.302 Sum_probs=21.8
Q ss_pred cCCCeEEecCChHhhcCCCCCCEEEEE
Q psy16960 21 TPDGKVKLYGSPADKSDLEIGDEILEV 47 (69)
Q Consensus 21 ~~~~~iv~~gspA~~aGLk~GD~Il~V 47 (69)
..++++..+-.-.+..+++.||.+.-.
T Consensus 4 ~~kgri~iP~~~r~~l~~~~gd~~~i~ 30 (43)
T TIGR01439 4 DKKGQIVIPKEIREKLGLKEGDRLEVI 30 (43)
T ss_pred CcCCeEEecHHHHHHcCcCCCCEEEEE
Confidence 345678888888889999999998755
No 80
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=59.21 E-value=13 Score=25.02 Aligned_cols=35 Identities=14% Similarity=0.063 Sum_probs=29.2
Q ss_pred eEEEEEEcCCCeEEecCChHhhcCCCCCCEEE-EEC
Q psy16960 14 YCIIIAETPDGKVKLYGSPADKSDLEIGDEIL-EVN 48 (69)
Q Consensus 14 ~~i~l~~~~~~~iv~~gspA~~aGLk~GD~Il-~Vn 48 (69)
.|++......++|+.|-.-.++.||+.||.+. .++
T Consensus 3 ~g~v~~id~~Gri~iP~~iR~~l~i~~gd~~~~~~~ 38 (180)
T TIGR02851 3 TGIVRRIDDLGRVVIPKEIRRTLRIREGDPLEIFTD 38 (180)
T ss_pred cceEEEECCCCcEEEeHHHHHHcCCCCCCeEEEEEe
Confidence 47777778889999998888899999999995 455
No 81
>PRK10943 cold shock-like protein CspC; Provisional
Probab=55.22 E-value=20 Score=20.35 Aligned_cols=35 Identities=20% Similarity=0.191 Sum_probs=20.5
Q ss_pred cCCeEEEEEEcCCCeEEecCChHhh---cCCCCCCEEE
Q psy16960 11 LKGYCIIIAETPDGKVKLYGSPADK---SDLEIGDEIL 45 (69)
Q Consensus 11 ~~g~~i~l~~~~~~~iv~~gspA~~---aGLk~GD~Il 45 (69)
.+||||+........+..-=+.-+. ..|+.||.|.
T Consensus 14 ~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~ 51 (69)
T PRK10943 14 SKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVE 51 (69)
T ss_pred CCCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEE
Confidence 6899998855433334222122222 2489999886
No 82
>KOG3834|consensus
Probab=54.24 E-value=9.4 Score=29.65 Aligned_cols=36 Identities=22% Similarity=0.269 Sum_probs=25.2
Q ss_pred EecCChHhhcCCC-CCCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 27 KLYGSPADKSDLE-IGDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 27 v~~gspA~~aGLk-~GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
|.++|||+.|||+ -+|.|+-+-..-... .+|+..+|
T Consensus 116 V~p~SPaalAgl~~~~DYivG~~~~~~~~---~eDl~~lI 152 (462)
T KOG3834|consen 116 VEPNSPAALAGLRPYTDYIVGIWDAVMHE---EEDLFTLI 152 (462)
T ss_pred cCCCCHHHhcccccccceEecchhhhccc---hHHHHHHH
Confidence 4579999999999 899999883233332 33565555
No 83
>PF06838 Met_gamma_lyase: Methionine gamma-lyase ; InterPro: IPR009651 This family represents the aluminium resistance protein, which confers resistance to aluminium in bacteria [].; PDB: 3JZL_A 3I16_C 3GWP_A 3FD0_B 3HT4_F.
Probab=53.91 E-value=6 Score=30.23 Aligned_cols=27 Identities=41% Similarity=0.500 Sum_probs=16.7
Q ss_pred HhhcCCCCCCEEEEECCEEeCCCCChHHHH
Q psy16960 33 ADKSDLEIGDEILEVNGKTFKDNCNHNEVI 62 (69)
Q Consensus 33 A~~aGLk~GD~Il~Vng~~i~~~~~~~ev~ 62 (69)
|-.+-|++||+++++-|+|-++.+ +++
T Consensus 88 ~Lfg~LrpGD~ll~~tG~PYDTL~---~VI 114 (403)
T PF06838_consen 88 ALFGVLRPGDELLSITGKPYDTLE---EVI 114 (403)
T ss_dssp HHHHH--TT-EEEESSSS--CCHH---HHH
T ss_pred HHHhcCCCCCeEEEcCCCchhhHH---HHh
Confidence 334459999999999999988766 665
No 84
>PRK08577 hypothetical protein; Provisional
Probab=52.34 E-value=24 Score=22.11 Aligned_cols=31 Identities=10% Similarity=0.126 Sum_probs=24.9
Q ss_pred EcCCCeEEecCChHhhcCCCCCCEEEE-ECCE
Q psy16960 20 ETPDGKVKLYGSPADKSDLEIGDEILE-VNGK 50 (69)
Q Consensus 20 ~~~~~~iv~~gspA~~aGLk~GD~Il~-Vng~ 50 (69)
-...++++.|-.-.++.||++||.+.- +++.
T Consensus 9 ~~~~g~i~ip~~~r~~l~~~~g~~~~~~~~~~ 40 (136)
T PRK08577 9 VDSKGRITIPLEIREALGIREGMYVLLIADTD 40 (136)
T ss_pred ECcCCeEEecHHHHHHcCcCCCCEEEEEEECC
Confidence 456788999988999999999999964 4543
No 85
>COG0207 ThyA Thymidylate synthase [Nucleotide transport and metabolism]
Probab=51.32 E-value=19 Score=26.13 Aligned_cols=37 Identities=16% Similarity=0.228 Sum_probs=31.6
Q ss_pred CChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 30 GSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 30 gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
---|+..||++|+.+.-+++--|..-. ++.+..++++
T Consensus 190 ~mvA~~~Gle~G~f~h~~~daHIY~nh-~e~~~~ql~R 226 (268)
T COG0207 190 HMVAQVTGLEPGEFVHTIGDAHIYDNH-FDQAKEQLKR 226 (268)
T ss_pred HHHHHHhCCcceEEEEEeeeeEEEhhh-HHHHHHHhcc
Confidence 467899999999999999999999777 8888877655
No 86
>PF04887 Pox_M2: Poxvirus M2 protein; InterPro: IPR006971 This family includes M2 protein of unknown function from variola virus.
Probab=49.82 E-value=18 Score=25.21 Aligned_cols=42 Identities=19% Similarity=0.191 Sum_probs=25.6
Q ss_pred CCCceEec----------cCCeEEEEEEcCCCeEEecCChHhhcCCCCCCEEE
Q psy16960 3 TSPSHMID----------LKGYCIIIAETPDGKVKLYGSPADKSDLEIGDEIL 45 (69)
Q Consensus 3 ~~~~~~~~----------~~g~~i~l~~~~~~~iv~~gspA~~aGLk~GD~Il 45 (69)
+.-|||.. +.|||+.+.....+.+.. --.|++.|+-.++.|.
T Consensus 27 ~~EC~~~~~~~~~~s~i~lTGYGL~I~m~it~~~dq-r~VaaaeG~~n~Ntl~ 78 (197)
T PF04887_consen 27 TGECHMKIIYNDHNSTINLTGYGLNINMEITNEIDQ-RFVAAAEGVGNNNTLS 78 (197)
T ss_pred cceEEEEEeecccccceeeeeccEEEEEEEccccch-hheehhhccccCceEE
Confidence 45699987 889999998765543211 1234444666666553
No 87
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=48.72 E-value=19 Score=23.28 Aligned_cols=18 Identities=17% Similarity=0.202 Sum_probs=14.6
Q ss_pred cCChHhhcCCCCCCEEEE
Q psy16960 29 YGSPADKSDLEIGDEILE 46 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~ 46 (69)
+.+-+.+.|+++||++.-
T Consensus 102 ~~G~~~~~~i~vGd~v~~ 119 (126)
T COG1430 102 PAGWAARLGIKVGDRVEF 119 (126)
T ss_pred cCCchhhcCCccCCEEEe
Confidence 457778889999999864
No 88
>PRK09890 cold shock protein CspG; Provisional
Probab=48.36 E-value=27 Score=19.87 Aligned_cols=36 Identities=14% Similarity=0.113 Sum_probs=20.3
Q ss_pred cCCeEEEEEEcCCCeEEecCChHhh---cCCCCCCEEEE
Q psy16960 11 LKGYCIIIAETPDGKVKLYGSPADK---SDLEIGDEILE 46 (69)
Q Consensus 11 ~~g~~i~l~~~~~~~iv~~gspA~~---aGLk~GD~Il~ 46 (69)
.+||||+....-...+..-=+.-.. ..|++||.+.-
T Consensus 15 ~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f 53 (70)
T PRK09890 15 DKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEF 53 (70)
T ss_pred CCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEE
Confidence 6899998865433334221111111 24899998864
No 89
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=47.53 E-value=26 Score=19.82 Aligned_cols=35 Identities=20% Similarity=0.257 Sum_probs=19.4
Q ss_pred cCCeEEEEEEcCCCeEEecCChHhh---cCCCCCCEEE
Q psy16960 11 LKGYCIIIAETPDGKVKLYGSPADK---SDLEIGDEIL 45 (69)
Q Consensus 11 ~~g~~i~l~~~~~~~iv~~gspA~~---aGLk~GD~Il 45 (69)
.+||||+........+..-=+.-.. ..|+.||.+.
T Consensus 15 ~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~ 52 (70)
T PRK10354 15 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVS 52 (70)
T ss_pred CCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEE
Confidence 6999998744332233221111111 3489999886
No 90
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=46.83 E-value=20 Score=19.50 Aligned_cols=39 Identities=23% Similarity=0.244 Sum_probs=21.1
Q ss_pred eEeccCCeEEEEEEcCCCeEEecCChHh---hcCCCCCCEEE
Q psy16960 7 HMIDLKGYCIIIAETPDGKVKLYGSPAD---KSDLEIGDEIL 45 (69)
Q Consensus 7 ~~~~~~g~~i~l~~~~~~~iv~~gspA~---~aGLk~GD~Il 45 (69)
.+.+-+|||++.....+..+...-+.-. -.-|+.||+|.
T Consensus 7 ~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~ 48 (66)
T PF00313_consen 7 WFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVE 48 (66)
T ss_dssp EEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEE
T ss_pred EEECCCCceEEEEcccceeEEeccccccccccccCCCCCEEE
Confidence 3445789999997665544522111111 23489999985
No 91
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=46.39 E-value=35 Score=19.34 Aligned_cols=36 Identities=22% Similarity=0.190 Sum_probs=20.0
Q ss_pred cCCeEEEEEEcCCCeEEecCChHhh---cCCCCCCEEEE
Q psy16960 11 LKGYCIIIAETPDGKVKLYGSPADK---SDLEIGDEILE 46 (69)
Q Consensus 11 ~~g~~i~l~~~~~~~iv~~gspA~~---aGLk~GD~Il~ 46 (69)
.+||||+........+..-=+.-.. .-|+.||.+.-
T Consensus 14 ~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f 52 (69)
T PRK09507 14 SKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEF 52 (69)
T ss_pred CCCcEEEecCCCCeeEEEEeecccccCCCCCCCCCEEEE
Confidence 6899998754433234221111112 24899998863
No 92
>PRK15464 cold shock-like protein CspH; Provisional
Probab=44.17 E-value=39 Score=19.37 Aligned_cols=35 Identities=23% Similarity=0.133 Sum_probs=19.9
Q ss_pred cCCeEEEEEEcCCCeEEecCCh---HhhcCCCCCCEEE
Q psy16960 11 LKGYCIIIAETPDGKVKLYGSP---ADKSDLEIGDEIL 45 (69)
Q Consensus 11 ~~g~~i~l~~~~~~~iv~~gsp---A~~aGLk~GD~Il 45 (69)
-+||||+........+.+-=+. +....|++||.|.
T Consensus 15 ~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~ 52 (70)
T PRK15464 15 KSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVE 52 (70)
T ss_pred CCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEE
Confidence 7899998755433333221111 1123599999886
No 93
>COG0260 PepB Leucyl aminopeptidase [Amino acid transport and metabolism]
Probab=43.28 E-value=16 Score=28.49 Aligned_cols=28 Identities=29% Similarity=0.361 Sum_probs=22.1
Q ss_pred ecCChHhhcCCCCCCEEEEECCEEeCCCC
Q psy16960 28 LYGSPADKSDLEIGDEILEVNGKTFKDNC 56 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~Vng~~i~~~~ 56 (69)
.++.|.-.| .|+||+|..-||+.|+=.+
T Consensus 306 ~ENm~~g~A-~rPGDVits~~GkTVEV~N 333 (485)
T COG0260 306 VENMPSGNA-YRPGDVITSMNGKTVEVLN 333 (485)
T ss_pred eccCCCCCC-CCCCCeEEecCCcEEEEcc
Confidence 356777665 8999999999999986443
No 94
>PRK09974 putative regulator PrlF; Provisional
Probab=42.89 E-value=31 Score=21.92 Aligned_cols=29 Identities=17% Similarity=0.079 Sum_probs=23.0
Q ss_pred EEcCCCeEEecCChHhhcCCCCCCEEEEE
Q psy16960 19 AETPDGKVKLYGSPADKSDLEIGDEILEV 47 (69)
Q Consensus 19 ~~~~~~~iv~~gspA~~aGLk~GD~Il~V 47 (69)
..+..+++++|-.-.++-||++||+|.-.
T Consensus 13 tvTsKGQvTIPk~IR~~Lgl~~GdkI~f~ 41 (111)
T PRK09974 13 KLTDRGQTTVPAPVRKALKLKKRDSIHYE 41 (111)
T ss_pred EEecCCCEeccHHHHHHcCCCCCCEEEEE
Confidence 34456778888788888899999999863
No 95
>COG4100 Cystathionine beta-lyase family protein involved in aluminum resistance [Inorganic ion transport and metabolism]
Probab=42.51 E-value=14 Score=28.11 Aligned_cols=23 Identities=39% Similarity=0.551 Sum_probs=19.2
Q ss_pred CCCCCCEEEEECCEEeCCCCChHHHH
Q psy16960 37 DLEIGDEILEVNGKTFKDNCNHNEVI 62 (69)
Q Consensus 37 GLk~GD~Il~Vng~~i~~~~~~~ev~ 62 (69)
-||+||+++.|-|.|.++.. |++
T Consensus 103 ~LRpgDell~i~G~PYDTLe---evI 125 (416)
T COG4100 103 ILRPGDELLYITGSPYDTLE---EVI 125 (416)
T ss_pred ccCCCCeEEEecCCcchhHH---HHh
Confidence 49999999999999987655 654
No 96
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=42.36 E-value=26 Score=20.83 Aligned_cols=19 Identities=21% Similarity=0.216 Sum_probs=15.1
Q ss_pred ChHhhcCCCCCCEEEEECC
Q psy16960 31 SPADKSDLEIGDEILEVNG 49 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vng 49 (69)
.-|++.||+.||.|.-.|+
T Consensus 42 ~dA~~lgi~~Gd~V~v~~~ 60 (122)
T cd02791 42 EDAARLGLKEGDLVRVTSR 60 (122)
T ss_pred HHHHHcCCCCCCEEEEEcC
Confidence 4577889999999976663
No 97
>PRK15463 cold shock-like protein CspF; Provisional
Probab=40.80 E-value=60 Score=18.50 Aligned_cols=36 Identities=17% Similarity=0.126 Sum_probs=20.2
Q ss_pred cCCeEEEEEEcCCCeEEecCChHh---hcCCCCCCEEEE
Q psy16960 11 LKGYCIIIAETPDGKVKLYGSPAD---KSDLEIGDEILE 46 (69)
Q Consensus 11 ~~g~~i~l~~~~~~~iv~~gspA~---~aGLk~GD~Il~ 46 (69)
-+||||+.-......|.+-=+.-. ...|++||.|.-
T Consensus 15 ~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f 53 (70)
T PRK15463 15 KSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEF 53 (70)
T ss_pred CCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEE
Confidence 689999875543333422111111 225999998863
No 98
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=40.76 E-value=18 Score=22.83 Aligned_cols=20 Identities=30% Similarity=0.519 Sum_probs=11.9
Q ss_pred hHhhc-CCCCCCEEEEECCEE
Q psy16960 32 PADKS-DLEIGDEILEVNGKT 51 (69)
Q Consensus 32 pA~~a-GLk~GD~Il~Vng~~ 51 (69)
-+-+| -|++||+|+.-+|..
T Consensus 70 gWv~A~~L~~GD~L~~~~G~~ 90 (130)
T PF07591_consen 70 GWVEAEDLKVGDRLLTADGSW 90 (130)
T ss_dssp --EEGGG--TTSEEEEE-SSE
T ss_pred hhhhHhhCCCCCEEEcCCCCE
Confidence 34444 599999999999875
No 99
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=39.96 E-value=21 Score=20.47 Aligned_cols=13 Identities=23% Similarity=0.358 Sum_probs=7.6
Q ss_pred HhhcCCCCCCEEE
Q psy16960 33 ADKSDLEIGDEIL 45 (69)
Q Consensus 33 A~~aGLk~GD~Il 45 (69)
+...+|+.||.++
T Consensus 69 v~~n~L~~GD~~~ 81 (100)
T PF02362_consen 69 VRDNGLKEGDVCV 81 (100)
T ss_dssp HHHCT--TT-EEE
T ss_pred HHHcCCCCCCEEE
Confidence 4456899999987
No 100
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=39.81 E-value=21 Score=21.21 Aligned_cols=16 Identities=31% Similarity=0.609 Sum_probs=12.9
Q ss_pred hcCCCCCCEEEEECCE
Q psy16960 35 KSDLEIGDEILEVNGK 50 (69)
Q Consensus 35 ~aGLk~GD~Il~Vng~ 50 (69)
.+.|++||+|+-..|.
T Consensus 35 ~~~L~~Gd~VvT~gGi 50 (84)
T TIGR00739 35 IESLKKGDKVLTIGGI 50 (84)
T ss_pred HHhCCCCCEEEECCCe
Confidence 4579999999887763
No 101
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=39.75 E-value=22 Score=21.75 Aligned_cols=18 Identities=22% Similarity=0.337 Sum_probs=11.7
Q ss_pred ecCChHhhcCCCCCCEEE
Q psy16960 28 LYGSPADKSDLEIGDEIL 45 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il 45 (69)
.+.+.+++.||++||+|.
T Consensus 88 ~~aG~~~~~~i~~Gd~v~ 105 (108)
T PF02643_consen 88 LPAGWFEKLGIKVGDRVR 105 (108)
T ss_dssp EETTHHHHHT--TT-EEE
T ss_pred cCCCchhhcCCCCCCEEE
Confidence 356778888999999984
No 102
>PRK13821 thyA thymidylate synthase; Provisional
Probab=39.69 E-value=31 Score=25.60 Aligned_cols=38 Identities=3% Similarity=-0.121 Sum_probs=32.3
Q ss_pred CChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcCC
Q psy16960 30 GSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 30 gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~~ 68 (69)
---|+..||++|+.+-.+++.-|..-. .+.+-++|++.
T Consensus 234 ~miA~~~gl~~G~~ih~igdaHIY~nh-i~~v~eqL~R~ 271 (323)
T PRK13821 234 SLVGRLTGYTPRWFTYFIGDAHIYENQ-LDMLQEQLTRE 271 (323)
T ss_pred HHHHHHhCCEeeeEEEEEEEEEEeHhH-HHHHHHHhcCC
Confidence 356888899999999999999999877 88888887654
No 103
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=39.67 E-value=23 Score=20.68 Aligned_cols=18 Identities=22% Similarity=0.167 Sum_probs=12.2
Q ss_pred ChHhhcCCCCCCEEEEEC
Q psy16960 31 SPADKSDLEIGDEILEVN 48 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vn 48 (69)
.-|++.||+.||.|.-.+
T Consensus 37 ~dA~~~Gi~~Gd~V~v~s 54 (110)
T PF01568_consen 37 EDAAKLGIKDGDWVRVSS 54 (110)
T ss_dssp HHHHHCT--TTCEEEEEE
T ss_pred HHHHHhcCcCCCEEEEEe
Confidence 457777999999997654
No 104
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=39.43 E-value=35 Score=20.01 Aligned_cols=19 Identities=16% Similarity=0.249 Sum_probs=15.0
Q ss_pred ChHhhcCCCCCCEEEEECC
Q psy16960 31 SPADKSDLEIGDEILEVNG 49 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vng 49 (69)
.-|++-||+.||.|.-.+.
T Consensus 42 ~dA~~lgi~~Gd~V~v~~~ 60 (116)
T cd02790 42 EDAKRLGIEDGEKVRVSSR 60 (116)
T ss_pred HHHHHcCCCCCCEEEEEcC
Confidence 4477779999999987664
No 105
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=39.41 E-value=20 Score=22.70 Aligned_cols=16 Identities=25% Similarity=0.596 Sum_probs=12.9
Q ss_pred hcCCCCCCEEEEECCE
Q psy16960 35 KSDLEIGDEILEVNGK 50 (69)
Q Consensus 35 ~aGLk~GD~Il~Vng~ 50 (69)
.+.|++||+|+-+.|.
T Consensus 34 ~~sLk~GD~VvT~GGi 49 (113)
T PRK06531 34 LNAIQKGDEVVTIGGL 49 (113)
T ss_pred HHhcCCCCEEEECCCc
Confidence 4589999999987763
No 106
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=39.37 E-value=20 Score=22.23 Aligned_cols=17 Identities=35% Similarity=0.430 Sum_probs=12.9
Q ss_pred hhcCCCCCCEEEEECCE
Q psy16960 34 DKSDLEIGDEILEVNGK 50 (69)
Q Consensus 34 ~~aGLk~GD~Il~Vng~ 50 (69)
-.+.|++||+|+-+.|.
T Consensus 49 ~~~~Lk~Gd~VvT~gGi 65 (106)
T PRK05585 49 MLSSLAKGDEVVTNGGI 65 (106)
T ss_pred HHHhcCCCCEEEECCCe
Confidence 35589999999776653
No 107
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=39.32 E-value=35 Score=20.07 Aligned_cols=19 Identities=16% Similarity=0.158 Sum_probs=15.1
Q ss_pred ChHhhcCCCCCCEEEEECC
Q psy16960 31 SPADKSDLEIGDEILEVNG 49 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vng 49 (69)
.-|++-||+.||.|.--|+
T Consensus 42 ~dA~~lgi~~Gd~V~v~~~ 60 (120)
T cd00508 42 EDAARLGIKDGDLVRVSSR 60 (120)
T ss_pred HHHHHcCCCCCCEEEEEeC
Confidence 4577789999999986663
No 108
>TIGR02876 spore_yqfD sporulation protein YqfD. YqfD is part of the sigma-E regulon in the sporulation program of endospore-forming Gram-positive bacteria. Mutation results in a sporulation defect in Bacillus subtilis. Members are found in all currently known endospore-forming bacteria, including the genera Bacillus, Symbiobacterium, Carboxydothermus, Clostridium, and Thermoanaerobacter.
Probab=38.73 E-value=44 Score=24.86 Aligned_cols=37 Identities=19% Similarity=0.355 Sum_probs=23.0
Q ss_pred CCCceEec-cCCeEEEEEEcCCCeEEecCChHhhcC--CCCCCEEEE
Q psy16960 3 TSPSHMID-LKGYCIIIAETPDGKVKLYGSPADKSD--LEIGDEILE 46 (69)
Q Consensus 3 ~~~~~~~~-~~g~~i~l~~~~~~~iv~~gspA~~aG--Lk~GD~Il~ 46 (69)
.+|||++- -+|....+. +..|.|.-+.| .++||.+++
T Consensus 184 ~~P~~lVA~kdGvI~~i~-------v~~G~p~Vk~GD~VkkGqvLIs 223 (382)
T TIGR02876 184 AEPRNIVAKKDGVIKRVY-------VTSGEPVVKKGDVVKKGDLLIS 223 (382)
T ss_pred CCCccEEECCCCEEEEEE-------EcCCeEEEccCCEEcCCCEEEE
Confidence 46888765 444433332 24566666665 888998885
No 109
>PRK00913 multifunctional aminopeptidase A; Provisional
Probab=38.10 E-value=21 Score=27.67 Aligned_cols=27 Identities=22% Similarity=0.316 Sum_probs=22.2
Q ss_pred ecCChHhhcCCCCCCEEEEECCEEeCCC
Q psy16960 28 LYGSPADKSDLEIGDEILEVNGKTFKDN 55 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~Vng~~i~~~ 55 (69)
.++.|...| .++||+|..-||+.|+-.
T Consensus 307 ~ENm~~~~A-~rPgDVi~~~~GkTVEV~ 333 (483)
T PRK00913 307 CENMPSGNA-YRPGDVLTSMSGKTIEVL 333 (483)
T ss_pred eccCCCCCC-CCCCCEEEECCCcEEEee
Confidence 367777776 999999999999998643
No 110
>PF06898 YqfD: Putative stage IV sporulation protein YqfD; InterPro: IPR010690 This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis (P54469 from SWISSPROT) is known to be essential for efficient sporulation although its exact function is unknown [].
Probab=37.86 E-value=46 Score=24.68 Aligned_cols=37 Identities=22% Similarity=0.383 Sum_probs=22.9
Q ss_pred CCCceEec-cCCeEEEEEEcCCCeEEecCChHhhcC--CCCCCEEEE
Q psy16960 3 TSPSHMID-LKGYCIIIAETPDGKVKLYGSPADKSD--LEIGDEILE 46 (69)
Q Consensus 3 ~~~~~~~~-~~g~~i~l~~~~~~~iv~~gspA~~aG--Lk~GD~Il~ 46 (69)
.+|||++- -+|....+. +..|.|.-+.| .++||.+++
T Consensus 187 ~~p~~lVA~kdGvI~~i~-------v~~G~p~Vk~Gd~VkkGdvLIS 226 (385)
T PF06898_consen 187 EEPCNLVAKKDGVITSII-------VRSGTPLVKVGDTVKKGDVLIS 226 (385)
T ss_pred CCCcceEECCCCEEEEEE-------ecCCeEEecCCCEECCCCEEEe
Confidence 46777764 444333321 24567777666 889999885
No 111
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=36.99 E-value=29 Score=21.87 Aligned_cols=20 Identities=30% Similarity=0.446 Sum_probs=16.0
Q ss_pred ecCChHhhcCCCCCCEEEEE
Q psy16960 28 LYGSPADKSDLEIGDEILEV 47 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~V 47 (69)
+..+.|...-|++||.+++-
T Consensus 46 I~~~~~~~~~L~~GD~VLA~ 65 (124)
T PF15057_consen 46 IALSDAMRHSLQVGDKVLAP 65 (124)
T ss_pred EEccCcccCcCCCCCEEEEe
Confidence 35566667789999999986
No 112
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=36.46 E-value=42 Score=19.91 Aligned_cols=18 Identities=17% Similarity=0.224 Sum_probs=14.1
Q ss_pred ChHhhcCCCCCCEEEEEC
Q psy16960 31 SPADKSDLEIGDEILEVN 48 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vn 48 (69)
.-|++-||+.||.|.-.+
T Consensus 42 ~dA~~lgi~~Gd~V~v~s 59 (122)
T cd02792 42 ELAAERGIKNGDMVWVSS 59 (122)
T ss_pred HHHHHcCCCCCCEEEEEc
Confidence 357777999999997555
No 113
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=36.35 E-value=38 Score=25.97 Aligned_cols=36 Identities=17% Similarity=0.260 Sum_probs=25.0
Q ss_pred cCCeEEEEEEcC-----CCeEEecCChHhhcCCCCCCEEEE
Q psy16960 11 LKGYCIIIAETP-----DGKVKLYGSPADKSDLEIGDEILE 46 (69)
Q Consensus 11 ~~g~~i~l~~~~-----~~~iv~~gspA~~aGLk~GD~Il~ 46 (69)
..||||.-.... ++-+.++-+.-.+-+|+.||.|.-
T Consensus 59 ~~g~gflr~~~~~~~~~~~d~yvs~~~i~~~~lr~gd~v~g 99 (415)
T TIGR00767 59 PDGFGFLRSPDSSYLPGPDDIYVSPSQIRRFNLRTGDTIEG 99 (415)
T ss_pred CCCCeEEeCCCcCCCCCCCCeeeCHHHHHhcCCCCCCEEEE
Confidence 468999886421 123455566777889999999985
No 114
>cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=36.35 E-value=33 Score=20.36 Aligned_cols=20 Identities=15% Similarity=0.135 Sum_probs=15.3
Q ss_pred ChHhhcCCCCCCEEEEECCE
Q psy16960 31 SPADKSDLEIGDEILEVNGK 50 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vng~ 50 (69)
.-|++-||+.||.|.-.|..
T Consensus 38 ~dA~~lgI~dGd~V~v~s~~ 57 (112)
T cd02787 38 DDIARLGLKAGDRVDLESAF 57 (112)
T ss_pred HHHHHhCCCCCCEEEEEecC
Confidence 44677799999999876643
No 115
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=35.91 E-value=39 Score=19.98 Aligned_cols=19 Identities=21% Similarity=0.261 Sum_probs=14.3
Q ss_pred CChHhhcCCCCCCEEEEEC
Q psy16960 30 GSPADKSDLEIGDEILEVN 48 (69)
Q Consensus 30 gspA~~aGLk~GD~Il~Vn 48 (69)
-.-|++-||+.||.|.-.+
T Consensus 37 p~dA~~lgi~~Gd~V~v~s 55 (116)
T cd02786 37 PADAAARGIADGDLVVVFN 55 (116)
T ss_pred HHHHHHcCCCCCCEEEEEc
Confidence 3557778999999986544
No 116
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.37 E-value=30 Score=22.02 Aligned_cols=16 Identities=19% Similarity=0.378 Sum_probs=12.5
Q ss_pred hHhhcCCCCCCEEEEE
Q psy16960 32 PADKSDLEIGDEILEV 47 (69)
Q Consensus 32 pA~~aGLk~GD~Il~V 47 (69)
-+.+.++++||.|+-=
T Consensus 28 d~krr~ik~GD~IiF~ 43 (111)
T COG4043 28 DPKRRQIKPGDKIIFN 43 (111)
T ss_pred CHhhcCCCCCCEEEEc
Confidence 3566789999999854
No 117
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=35.27 E-value=26 Score=22.08 Aligned_cols=16 Identities=25% Similarity=0.472 Sum_probs=12.9
Q ss_pred hcCCCCCCEEEEECCE
Q psy16960 35 KSDLEIGDEILEVNGK 50 (69)
Q Consensus 35 ~aGLk~GD~Il~Vng~ 50 (69)
.+.|++||+|+-+.|.
T Consensus 36 ~~~Lk~GD~VvT~gGi 51 (109)
T PRK05886 36 HESLQPGDRVHTTSGL 51 (109)
T ss_pred HHhcCCCCEEEECCCe
Confidence 3689999999887764
No 118
>PF00817 IMS: impB/mucB/samB family; InterPro: IPR001126 In Escherichia coli, UV and many chemicals appear to cause mutagenesis by a process of translesion synthesis that requires DNA polymerase III and the SOS-regulated proteins UmuD, UmuC and RecA. This machinery allows the replication to continue through DNA lesion, and therefore avoid lethal interruption of DNA replication after DNA damage []. UmuC is a well conserved protein in prokaryotes, with a homologue in yeast species. Proteins currently known to belong to this family are listed below: E. coli MucB protein. Plasmid-born analogue of the UmuC protein. Saccharomyces cerevisiae (Baker's yeast) Rev1 protein. Homologue of UmuC also required for normal induction of mutations by physical and chemical agents. Salmonella typhimurium ImpB protein. Plasmid-born analogue of the UmuC protein. Bacterial UmuC protein. E. coli DNA-damage-inducible protein P (DinP). S. typhimurium SamB homologue of UmuC plasmid associated. ; GO: 0003684 damaged DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006281 DNA repair; PDB: 3BJY_A 2AQ4_A 3OSP_A 4DL7_A 4DL6_A 3TQ1_A 3MR2_A 4EEY_A 3MR3_A 4DL4_A ....
Probab=35.07 E-value=54 Score=20.51 Aligned_cols=33 Identities=15% Similarity=0.229 Sum_probs=21.9
Q ss_pred CCeEEEEEEcCC--CeEEecCChHhhcCCCCCCEE
Q psy16960 12 KGYCIIIAETPD--GKVKLYGSPADKSDLEIGDEI 44 (69)
Q Consensus 12 ~g~~i~l~~~~~--~~iv~~gspA~~aGLk~GD~I 44 (69)
.+.-+++..... +.|+..+.+|.+.|++.|..+
T Consensus 19 ~~~PvaV~~~~~~~~~V~a~n~~Ar~~GV~~Gm~~ 53 (149)
T PF00817_consen 19 RGRPVAVVSGQGNRGRVIAANYEARAAGVRPGMPL 53 (149)
T ss_dssp TTSSEEEEECTSSTCEEEEE-HHHHTTTSTTTSBH
T ss_pred cCCCEEEEecccccchhhhhHHHHHhhccccchhh
Confidence 444455555544 556778889999999998653
No 119
>cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=35.05 E-value=48 Score=18.75 Aligned_cols=21 Identities=14% Similarity=0.093 Sum_probs=15.6
Q ss_pred ecCChHhhcCCCCCCEEEEEC
Q psy16960 28 LYGSPADKSDLEIGDEILEVN 48 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~Vn 48 (69)
+.-.-|++-||+.||.+.-.+
T Consensus 27 ~~~~da~~lgl~~Gd~v~v~~ 47 (101)
T cd02775 27 INPEDAAALGIKDGDLVRVES 47 (101)
T ss_pred ECHHHHHHcCCCCCCEEEEEc
Confidence 333557788999999987555
No 120
>cd00433 Peptidase_M17 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and play a key role in protein degradation and in the metabolism of biologically active peptides. They do not contain HEXXH motif (which is used as one of the signature patterns to group the peptidase families) in the metal-binding site. The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase. The enzyme is a hexamer, with the catalytic domains clustered around the three-fold axis, and the two trimers related to one another by a two-fold rotation. The N-terminal domain is structurally similar to the ADP-ribose binding Macro domain. This family includes proteins from bacteria, archaea, animals and plants.
Probab=34.98 E-value=25 Score=27.06 Aligned_cols=27 Identities=22% Similarity=0.143 Sum_probs=21.8
Q ss_pred ecCChHhhcCCCCCCEEEEECCEEeCCC
Q psy16960 28 LYGSPADKSDLEIGDEILEVNGKTFKDN 55 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~Vng~~i~~~ 55 (69)
.++.+...+ .++||+|..-||+.|+-.
T Consensus 293 ~EN~is~~A-~rPgDVi~s~~GkTVEI~ 319 (468)
T cd00433 293 AENMISGNA-YRPGDVITSRSGKTVEIL 319 (468)
T ss_pred eecCCCCCC-CCCCCEeEeCCCcEEEEe
Confidence 367777776 899999999999998643
No 121
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=34.43 E-value=81 Score=20.11 Aligned_cols=19 Identities=16% Similarity=0.260 Sum_probs=13.1
Q ss_pred cCChHhhcCCCCCCEEEEEC
Q psy16960 29 YGSPADKSDLEIGDEILEVN 48 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~Vn 48 (69)
.+++|++- .++||+|+=..
T Consensus 70 lNGAAAr~-~~~GD~vII~s 88 (111)
T cd06919 70 LNGAAARL-GQPGDRVIIMA 88 (111)
T ss_pred eCCHHHhc-CCCCCEEEEEE
Confidence 45666664 79999998543
No 122
>TIGR03284 thym_sym thymidylate synthase. Members of this protein family are thymidylate synthase, an enzyme that produces dTMP from dUMP. In prokaryotes, its gene usually is found close to that for dihydrofolate reductase, and in some systems the two enzymes are found as a fusion protein. This model excludes a set of related proteins (TIGR03283) that appears to replace this family in archaeal methanogens, where tetrahydrofolate is replaced by tetrahydromethanopterin.
Probab=34.34 E-value=39 Score=24.80 Aligned_cols=38 Identities=13% Similarity=0.201 Sum_probs=32.0
Q ss_pred CChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcCC
Q psy16960 30 GSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 30 gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~~ 68 (69)
---|+..||++|+.+-.+++.-|..-. ++.+-++|.+.
T Consensus 218 ~mvA~~~Gl~~G~~~h~igdaHIY~nh-i~~v~~qL~R~ 255 (296)
T TIGR03284 218 HMIAQETGLEVGEFVHTLGDAHLYSNH-LEQAKLQLTRE 255 (296)
T ss_pred HHHHHHhCCEeEEEEEEEEEEEEehhH-HHHHHHHhcCC
Confidence 356888999999999999999999877 88888877653
No 123
>KOG0792|consensus
Probab=34.14 E-value=29 Score=29.84 Aligned_cols=39 Identities=31% Similarity=0.590 Sum_probs=32.4
Q ss_pred cCChHhhcC--CCCCCEEEEECCEEeCCCCChHHHHHhhcCC
Q psy16960 29 YGSPADKSD--LEIGDEILEVNGKTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 29 ~gspA~~aG--Lk~GD~Il~Vng~~i~~~~~~~ev~~~i~~~ 68 (69)
++++|.... +-.||+++.|||..+.... ++.++.+|+.+
T Consensus 757 p~s~~d~~~P~~~e~dq~~~ingr~~~~~~-~~~~vs~irs~ 797 (1144)
T KOG0792|consen 757 PESTADDCTPRLNEGDQVTSINGRDVSESE-HDQVVSLIRSP 797 (1144)
T ss_pred CCCCccccccCCCcccceeeeccccccccc-ccchHHHHhhh
Confidence 566776653 8899999999999999998 99999888643
No 124
>PRK12608 transcription termination factor Rho; Provisional
Probab=34.08 E-value=43 Score=25.37 Aligned_cols=36 Identities=14% Similarity=0.158 Sum_probs=25.2
Q ss_pred cCCeEEEEEEcC-----CCeEEecCChHhhcCCCCCCEEEE
Q psy16960 11 LKGYCIIIAETP-----DGKVKLYGSPADKSDLEIGDEILE 46 (69)
Q Consensus 11 ~~g~~i~l~~~~-----~~~iv~~gspA~~aGLk~GD~Il~ 46 (69)
.+||||.-.... +.-+.++-+.-.+.||+.||.|..
T Consensus 27 ~~g~gflr~~~~~~~~~~~d~yv~~~~i~~~~l~~Gd~V~~ 67 (380)
T PRK12608 27 GDGFGFLRSARRNYLPSPDDVFVPPALIRRFNLRTGDVVEG 67 (380)
T ss_pred CCCceEeecCccCCCCCCCCeeeCHHHHHHhCCCCCCEEEe
Confidence 468999886421 122456667777889999999876
No 125
>PF01887 SAM_adeno_trans: S-adenosyl-l-methionine hydroxide adenosyltransferase; InterPro: IPR002747 The S-adenosyl-L-methionine (SAM) hydroxide adenosyltransferase family groups several fluorinase and chlorinase enzymes whose common feature is that they mediate nucleophilic reactions of their respective halide ions to the C-5' carbon of SAM []. These enzymes utilise a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. Structural studies indicate that the protein is a homotrimer, with each monomer being composed of N- and C-terminal domains [, ]. The N-terminal domain has a central seven-stranded beta-sheet, which combines parallel and antiparallel strands sandwiched between alpha helices. The C-terminal domain forms a beta-barrel with a greek-key topology. SAM is bound at the interface between the C-terminal domain of one monomer and the N-terminal domain of the neighbouring monomer, with a total of three molecules bound by the trimer.; PDB: 2CW5_C 1WU8_C 2WR8_A 2Q6O_B 2Q6L_A 2Q6K_A 2Q6I_A 2V7T_B 2C4U_F 1RQP_C ....
Probab=33.88 E-value=65 Score=22.81 Aligned_cols=19 Identities=32% Similarity=0.333 Sum_probs=13.1
Q ss_pred EecCChHhhcCCCCCCEEE
Q psy16960 27 KLYGSPADKSDLEIGDEIL 45 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il 45 (69)
+..|++|+.-||+.||.|.
T Consensus 239 vn~G~Aa~~lgl~~Gd~V~ 257 (258)
T PF01887_consen 239 VNQGSAAELLGLKPGDRVR 257 (258)
T ss_dssp ETTB-HHHHHT--TTSEEE
T ss_pred EeCcCHHHHcCCCCCCEEE
Confidence 3468999999999999984
No 126
>cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=33.18 E-value=52 Score=19.72 Aligned_cols=19 Identities=11% Similarity=0.004 Sum_probs=14.8
Q ss_pred ChHhhcCCCCCCEEEEECC
Q psy16960 31 SPADKSDLEIGDEILEVNG 49 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vng 49 (69)
.-|++.||+.||.|.-.|.
T Consensus 38 ~dA~~lgi~~Gd~V~v~~~ 56 (106)
T cd02789 38 EDYKLLGKPEGDKVKVTSE 56 (106)
T ss_pred HHHHHcCCCCCCEEEEEcC
Confidence 3477889999999876553
No 127
>PF00883 Peptidase_M17: Cytosol aminopeptidase family, catalytic domain; InterPro: IPR000819 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF), the type example being leucyl aminopeptidase from Bos taurus (Bovine). Aminopeptidases are exopeptidases involved in the processing and regular turnover of intracellular proteins, although their precise role in cellular metabolism is unclear [, ]. Leucine aminopeptidases cleave leucine residues from the N-terminal of polypeptide chains, but substantial rates are evident for all amino acids []. The enzymes exist as homo-hexamers, comprising 2 trimers stacked on top of one another []. Each monomer binds 2 zinc ions and folds into 2 alpha/beta-type quasi-spherical globular domains, producing a comma-like shape []. The N-terminal 150 residues form a 5-stranded beta-sheet with 4 parallel and 1 anti-parallel strand sandwiched between 4 alpha-helices []. An alpha-helix extends into the C-terminal domain, which comprises a central 8-stranded saddle-shaped beta-sheet sandwiched between groups of helices, forming the monomer hydrophobic core []. A 3-stranded beta-sheet resides on the surface of the monomer, where it interacts with other members of the hexamer []. The 2 zinc ions and the active site are entirely located in the C-terminal catalytic domain [].; GO: 0004177 aminopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 3KZW_L 3KQX_C 3KQZ_L 3KR4_I 3KR5_J 3T8W_C 3H8F_D 3H8G_A 3H8E_B 3IJ3_A ....
Probab=33.10 E-value=18 Score=26.63 Aligned_cols=27 Identities=26% Similarity=0.265 Sum_probs=18.3
Q ss_pred ecCChHhhcCCCCCCEEEEECCEEeCCC
Q psy16960 28 LYGSPADKSDLEIGDEILEVNGKTFKDN 55 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il~Vng~~i~~~ 55 (69)
.++.|...+ .++||+|.+-||+.|+=.
T Consensus 138 ~EN~i~~~a-~~pgDVi~s~~GkTVEI~ 164 (311)
T PF00883_consen 138 AENMISGNA-YRPGDVITSMNGKTVEIG 164 (311)
T ss_dssp EEE--STTS-TTTTEEEE-TTS-EEEES
T ss_pred ccccCCCCC-CCCCCEEEeCCCCEEEEE
Confidence 466777766 999999999999997543
No 128
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=32.60 E-value=47 Score=25.56 Aligned_cols=36 Identities=14% Similarity=0.278 Sum_probs=25.1
Q ss_pred cCCeEEEEEEcCC-----CeEEecCChHhhcCCCCCCEEEE
Q psy16960 11 LKGYCIIIAETPD-----GKVKLYGSPADKSDLEIGDEILE 46 (69)
Q Consensus 11 ~~g~~i~l~~~~~-----~~iv~~gspA~~aGLk~GD~Il~ 46 (69)
.+||||.-....+ +-+.++.+.-.+-+|+.||.|.-
T Consensus 59 ~~g~gflr~~~~~y~~~~~d~yvs~~~ir~~~lr~gd~v~g 99 (416)
T PRK09376 59 PDGFGFLRSPDANYLPGPDDIYVSPSQIRRFNLRTGDTVEG 99 (416)
T ss_pred CCCCeEEeCCCcCCCCCCCCeeeCHHHHHhcCCCCCCEEEE
Confidence 3689998863221 23556667777889999999874
No 129
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=32.51 E-value=88 Score=20.36 Aligned_cols=19 Identities=16% Similarity=0.401 Sum_probs=13.4
Q ss_pred cCChHhhcCCCCCCEEEEEC
Q psy16960 29 YGSPADKSDLEIGDEILEVN 48 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~Vn 48 (69)
-+++|++- .++||+|+=..
T Consensus 71 lNGAAArl-~~~GD~VII~s 89 (126)
T TIGR00223 71 VNGAAARC-VSVGDIVIIAS 89 (126)
T ss_pred eCCHHHhc-CCCCCEEEEEE
Confidence 35666664 79999998653
No 130
>cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin.
Probab=32.49 E-value=46 Score=19.95 Aligned_cols=21 Identities=24% Similarity=0.232 Sum_probs=16.0
Q ss_pred cCChHhhcCCCCCCEEEEECC
Q psy16960 29 YGSPADKSDLEIGDEILEVNG 49 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~Vng 49 (69)
.-.-|++-||+.||.|.-.|.
T Consensus 38 n~~dA~~lgi~~Gd~V~v~s~ 58 (115)
T cd02779 38 NPEDAKREGLKNGDLVEVYND 58 (115)
T ss_pred CHHHHHHcCCCCCCEEEEEeC
Confidence 335677889999999986663
No 131
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=32.20 E-value=1e+02 Score=19.06 Aligned_cols=27 Identities=22% Similarity=0.219 Sum_probs=22.2
Q ss_pred CCCeEEecCChHhhcCCCCCCEEEEEC
Q psy16960 22 PDGKVKLYGSPADKSDLEIGDEILEVN 48 (69)
Q Consensus 22 ~~~~iv~~gspA~~aGLk~GD~Il~Vn 48 (69)
.++.....++|....||-.||.|....
T Consensus 10 ~~~~y~l~n~Pf~a~glA~gDvV~~~~ 36 (117)
T PF14085_consen 10 GDDTYRLDNIPFFAYGLALGDVVRAEP 36 (117)
T ss_pred CCCEEEEEecccccCCCCCCCEEEEEe
Confidence 345667889999999999999998654
No 132
>cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=31.83 E-value=48 Score=19.91 Aligned_cols=18 Identities=28% Similarity=0.368 Sum_probs=14.4
Q ss_pred ChHhhcCCCCCCEEEEEC
Q psy16960 31 SPADKSDLEIGDEILEVN 48 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vn 48 (69)
.-|++.||+.||.|.-.+
T Consensus 37 ~~A~~~gi~~Gd~V~v~s 54 (121)
T cd02794 37 LDAAARGIKDGDRVLVFN 54 (121)
T ss_pred HHHHHcCCCCCCEEEEEc
Confidence 457788999999997555
No 133
>cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=31.67 E-value=56 Score=19.69 Aligned_cols=18 Identities=22% Similarity=0.163 Sum_probs=14.2
Q ss_pred ChHhhcCCCCCCEEEEEC
Q psy16960 31 SPADKSDLEIGDEILEVN 48 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vn 48 (69)
.-|++-||+.||.|.-.|
T Consensus 40 ~dA~~~gi~~Gd~V~v~s 57 (130)
T cd02781 40 ETAAKLGIADGDWVWVET 57 (130)
T ss_pred HHHHHcCCCCCCEEEEEC
Confidence 457778999999997555
No 134
>KOG1753|consensus
Probab=31.57 E-value=46 Score=22.11 Aligned_cols=35 Identities=11% Similarity=0.179 Sum_probs=25.5
Q ss_pred ChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 31 SPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
.+.+-+.-+.|+=+++|||.|++-.+ .+-+.-.+.
T Consensus 17 ~AtAva~ck~G~glikvNg~ple~ie-~~~L~~Kl~ 51 (145)
T KOG1753|consen 17 TATAVAHCKHGSGLIKVNGRPLELIE-PEILRYKLL 51 (145)
T ss_pred ceEEEEEeecCceEEEECCcchHhcc-HHHHHHHHh
Confidence 34445567999999999999998777 655554443
No 135
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=31.26 E-value=34 Score=21.12 Aligned_cols=15 Identities=33% Similarity=0.716 Sum_probs=12.5
Q ss_pred cCCCCCCEEEEECCE
Q psy16960 36 SDLEIGDEILEVNGK 50 (69)
Q Consensus 36 aGLk~GD~Il~Vng~ 50 (69)
..|+.||+|+-+.|.
T Consensus 42 ~sL~kGD~VvT~gGi 56 (97)
T COG1862 42 NSLKKGDEVVTIGGI 56 (97)
T ss_pred HhccCCCEEEEcCCe
Confidence 469999999988865
No 136
>PRK05015 aminopeptidase B; Provisional
Probab=31.17 E-value=32 Score=26.50 Aligned_cols=27 Identities=26% Similarity=0.239 Sum_probs=21.3
Q ss_pred cCChHhhcCCCCCCEEEEECCEEeCCCC
Q psy16960 29 YGSPADKSDLEIGDEILEVNGKTFKDNC 56 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~Vng~~i~~~~ 56 (69)
++.+...+ .|+||+|..-||+.|+-.+
T Consensus 245 ENmisg~A-~kpgDVIt~~nGkTVEI~N 271 (424)
T PRK05015 245 ENLISGNA-FKLGDIITYRNGKTVEVMN 271 (424)
T ss_pred ccCCCCCC-CCCCCEEEecCCcEEeeec
Confidence 56666665 8999999999999986443
No 137
>PRK00956 thyA thymidylate synthase; Provisional
Probab=31.09 E-value=46 Score=22.77 Aligned_cols=35 Identities=11% Similarity=0.061 Sum_probs=29.3
Q ss_pred ChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 31 SPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
--|++.|++.|..+.-+++--|..-. .+.+-++|+
T Consensus 173 ~iA~~~gl~~G~~~~~~~~~HIY~~~-~~~v~~~l~ 207 (208)
T PRK00956 173 YVAEKVGVELGTYTHHSVSAHIYERD-WDYLEKIFK 207 (208)
T ss_pred HHHHHhCCcceEEEEEEEEEEEeHHH-HHHHHHHhc
Confidence 45788899999999999999998766 777777665
No 138
>cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom
Probab=30.87 E-value=53 Score=19.90 Aligned_cols=20 Identities=20% Similarity=0.152 Sum_probs=15.5
Q ss_pred CChHhhcCCCCCCEEEEECC
Q psy16960 30 GSPADKSDLEIGDEILEVNG 49 (69)
Q Consensus 30 gspA~~aGLk~GD~Il~Vng 49 (69)
-.-|++.||+.||.|.-.+.
T Consensus 40 p~dA~~lgi~~Gd~V~v~s~ 59 (127)
T cd02777 40 PLDAAARGIKDGDIVRVFND 59 (127)
T ss_pred HHHHHHcCCCCCCEEEEEcC
Confidence 35577889999999976663
No 139
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=30.68 E-value=49 Score=19.97 Aligned_cols=18 Identities=22% Similarity=0.174 Sum_probs=14.2
Q ss_pred ChHhhcCCCCCCEEEEEC
Q psy16960 31 SPADKSDLEIGDEILEVN 48 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vn 48 (69)
.-|++.||+.||.|.-.+
T Consensus 39 ~dA~~~gi~~Gd~V~v~s 56 (124)
T cd02785 39 IDAAARGIAHGDLVEVYN 56 (124)
T ss_pred HHHHHcCCCCCCEEEEEe
Confidence 457788999999986555
No 140
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=30.59 E-value=94 Score=16.66 Aligned_cols=37 Identities=27% Similarity=0.268 Sum_probs=21.5
Q ss_pred ccCCeEEEEEEcCCCeEEecCChHh---hcCCCCCCEEEE
Q psy16960 10 DLKGYCIIIAETPDGKVKLYGSPAD---KSDLEIGDEILE 46 (69)
Q Consensus 10 ~~~g~~i~l~~~~~~~iv~~gspA~---~aGLk~GD~Il~ 46 (69)
+.+|||++........+...-+.-. ..-|++||.+.-
T Consensus 10 ~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f 49 (65)
T cd04458 10 DEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEF 49 (65)
T ss_pred CCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEE
Confidence 3689999987653434422111111 235899998863
No 141
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=30.26 E-value=1e+02 Score=20.07 Aligned_cols=19 Identities=16% Similarity=0.386 Sum_probs=13.1
Q ss_pred cCChHhhcCCCCCCEEEEEC
Q psy16960 29 YGSPADKSDLEIGDEILEVN 48 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~Vn 48 (69)
-+++|++- .++||+|+=..
T Consensus 71 lNGAAAr~-~~~GD~vII~a 89 (126)
T PRK05449 71 LNGAAARL-VQVGDLVIIAA 89 (126)
T ss_pred eCCHHHhc-CCCCCEEEEEE
Confidence 35566654 69999998543
No 142
>cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=30.09 E-value=55 Score=20.04 Aligned_cols=19 Identities=21% Similarity=0.223 Sum_probs=15.0
Q ss_pred ChHhhcCCCCCCEEEEECC
Q psy16960 31 SPADKSDLEIGDEILEVNG 49 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vng 49 (69)
.-|++.||+.||.|.-.|.
T Consensus 40 ~dA~~~gi~~Gd~V~v~s~ 58 (129)
T cd02793 40 ADAAARGIADGDIVRVFND 58 (129)
T ss_pred HHHHHcCCCCCCEEEEEcC
Confidence 4477889999999976663
No 143
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=29.61 E-value=45 Score=18.96 Aligned_cols=17 Identities=18% Similarity=0.227 Sum_probs=12.1
Q ss_pred HhhcCCCCCCEEEEECCE
Q psy16960 33 ADKSDLEIGDEILEVNGK 50 (69)
Q Consensus 33 A~~aGLk~GD~Il~Vng~ 50 (69)
-.++|.+.||.|. |.+.
T Consensus 49 L~~~G~~~GD~V~-Ig~~ 65 (69)
T TIGR03595 49 LRKAGAKDGDTVR-IGDF 65 (69)
T ss_pred HHHcCCCCCCEEE-EccE
Confidence 3678999999874 4443
No 144
>KOG0820|consensus
Probab=29.20 E-value=48 Score=24.68 Aligned_cols=19 Identities=37% Similarity=0.497 Sum_probs=16.8
Q ss_pred CChHhhcCCCCCCEEEEEC
Q psy16960 30 GSPADKSDLEIGDEILEVN 48 (69)
Q Consensus 30 gspA~~aGLk~GD~Il~Vn 48 (69)
.+-.++|.+|++|.+++|+
T Consensus 48 ~~I~~ka~~k~tD~VLEvG 66 (315)
T KOG0820|consen 48 DQIVEKADLKPTDVVLEVG 66 (315)
T ss_pred HHHHhccCCCCCCEEEEeC
Confidence 4667889999999999999
No 145
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=28.78 E-value=17 Score=21.46 Aligned_cols=26 Identities=15% Similarity=0.114 Sum_probs=18.0
Q ss_pred ChHhhcCCCCCCEEEEECCEEeCCCC
Q psy16960 31 SPADKSDLEIGDEILEVNGKTFKDNC 56 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vng~~i~~~~ 56 (69)
.-+++.|+.+.|..+.+...+-++|+
T Consensus 55 ~L~~~~gi~p~Dv~I~l~e~~~edWS 80 (82)
T PF14552_consen 55 RLAEKLGIRPEDVMIVLVENPREDWS 80 (82)
T ss_dssp HHHHHH---GGGEEEEEEEE-GGGEE
T ss_pred HHHHHcCCCHHHEEEEEEECCcccCC
Confidence 44567899999999999988888886
No 146
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=28.56 E-value=21 Score=20.97 Aligned_cols=16 Identities=31% Similarity=0.621 Sum_probs=1.0
Q ss_pred hcCCCCCCEEEEECCE
Q psy16960 35 KSDLEIGDEILEVNGK 50 (69)
Q Consensus 35 ~aGLk~GD~Il~Vng~ 50 (69)
.+.|++||+|+-..|.
T Consensus 34 ~~~Lk~Gd~VvT~gGi 49 (82)
T PF02699_consen 34 LASLKPGDEVVTIGGI 49 (82)
T ss_dssp GG--------------
T ss_pred HHcCCCCCEEEECCcE
Confidence 4579999999987764
No 147
>COG3127 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=28.38 E-value=51 Score=27.53 Aligned_cols=26 Identities=23% Similarity=0.410 Sum_probs=21.0
Q ss_pred ecCChHhhcCCCCCCEEE-EECCEEeC
Q psy16960 28 LYGSPADKSDLEIGDEIL-EVNGKTFK 53 (69)
Q Consensus 28 ~~gspA~~aGLk~GD~Il-~Vng~~i~ 53 (69)
++..-|++.|||-||.++ .|+|+++.
T Consensus 601 ~e~~~A~~LglKLGDtvTf~v~gq~i~ 627 (829)
T COG3127 601 MEEGEAKRLGLKLGDTVTFMVLGQNIT 627 (829)
T ss_pred hhHhHHHHhCCccCCEEEEEeccceEE
Confidence 345667888999999998 79998864
No 148
>TIGR02828 putative membrane fusion protein. Members of this family show similarity to the members of TIGR00999, the membrane fusion protein (MFP) cluster 2 family, which is linked to RND transport systems.
Probab=28.38 E-value=36 Score=21.93 Aligned_cols=13 Identities=15% Similarity=-0.117 Sum_probs=10.6
Q ss_pred hhcCCCCCCEEEE
Q psy16960 34 DKSDLEIGDEILE 46 (69)
Q Consensus 34 ~~aGLk~GD~Il~ 46 (69)
.-.||++||+|+.
T Consensus 174 ~i~GL~~GD~Vv~ 186 (188)
T TIGR02828 174 AVEGDKPPDAQLL 186 (188)
T ss_pred EEecCCCCCEEEe
Confidence 4469999999974
No 149
>PF02353 CMAS: Mycolic acid cyclopropane synthetase; InterPro: IPR003333 This entry represents mycolic acid cyclopropane synthases and related enzymes, including CmaA1, CmaA2 (cyclopropane mycolic acid synthase A1 and A2) and MmaA1-4 (methoxymycolic acid synthase A1-4). All are thought to be S-adenosyl-L-methionine (SAM) utilising methyltransferases []. Mycolic acid cyclopropane synthase or cyclopropane-fatty-acyl-phospholipid synthase (CFA synthase) 2.1.1.79 from EC catalyses the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid -> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid. The major mycolic acid produced by Mycobacterium tuberculosis contains two cis-cyclopropanes in the meromycolate chain. Cyclopropanation may contribute to the structural integrity of the cell wall complex [].; GO: 0008610 lipid biosynthetic process; PDB: 3HA5_A 2FK8_A 3HA7_A 3HA3_A 2FK7_A 1KPG_D 1KP9_B 1KPH_D 3VC2_E 3VC1_D ....
Probab=28.15 E-value=44 Score=23.60 Aligned_cols=18 Identities=28% Similarity=0.512 Sum_probs=12.6
Q ss_pred ChHhhcCCCCCCEEEEEC
Q psy16960 31 SPADKSDLEIGDEILEVN 48 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vn 48 (69)
--+++++|++|++|+.|.
T Consensus 53 ~~~~~~~l~~G~~vLDiG 70 (273)
T PF02353_consen 53 LLCEKLGLKPGDRVLDIG 70 (273)
T ss_dssp HHHTTTT--TT-EEEEES
T ss_pred HHHHHhCCCCCCEEEEeC
Confidence 346788999999999998
No 150
>PRK01827 thyA thymidylate synthase; Reviewed
Probab=27.99 E-value=56 Score=23.41 Aligned_cols=36 Identities=11% Similarity=0.222 Sum_probs=30.3
Q ss_pred ChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcC
Q psy16960 31 SPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHD 67 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~ 67 (69)
--|+..||++|+.+..+++--|.... .+.+-+++.+
T Consensus 187 ~vA~~~gl~~G~~~h~~g~~HIY~~h-~~~~~~ql~r 222 (264)
T PRK01827 187 MIAQQTGLKVGEFVHTIGDAHIYSNH-LEQAREQLSR 222 (264)
T ss_pred HHHHHcCCeeEEEEEEEeeEEEEhhH-hhHHHHHhcC
Confidence 56788899999999999999998776 7777777755
No 151
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=26.63 E-value=43 Score=19.01 Aligned_cols=14 Identities=21% Similarity=0.302 Sum_probs=7.8
Q ss_pred hHhhcCCCCCCEEE
Q psy16960 32 PADKSDLEIGDEIL 45 (69)
Q Consensus 32 pA~~aGLk~GD~Il 45 (69)
.-.++|.+.||.|.
T Consensus 48 ~L~~~G~~~GD~V~ 61 (69)
T PF09269_consen 48 ALRKAGAKEGDTVR 61 (69)
T ss_dssp HHHTTT--TT-EEE
T ss_pred HHHHcCCCCCCEEE
Confidence 34578999999874
No 152
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=26.54 E-value=73 Score=18.92 Aligned_cols=18 Identities=17% Similarity=0.248 Sum_probs=13.8
Q ss_pred ChHhhcCCCCCCEEEEEC
Q psy16960 31 SPADKSDLEIGDEILEVN 48 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vn 48 (69)
.-|++-||+.||.|.-.+
T Consensus 37 ~dA~~~gi~~Gd~V~v~s 54 (123)
T cd02778 37 ETAARLGIKDGDRVEVSS 54 (123)
T ss_pred HHHHHcCCCCCCEEEEEe
Confidence 456777999999987544
No 153
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A ....
Probab=26.37 E-value=78 Score=20.32 Aligned_cols=17 Identities=18% Similarity=0.528 Sum_probs=9.9
Q ss_pred CChHhhcCCCCCCEEEEE
Q psy16960 30 GSPADKSDLEIGDEILEV 47 (69)
Q Consensus 30 gspA~~aGLk~GD~Il~V 47 (69)
+++|++- .++||+|+=+
T Consensus 72 NGaAArl-~~~GD~vII~ 88 (116)
T PF02261_consen 72 NGAAARL-VQVGDRVIIM 88 (116)
T ss_dssp EGGGGGC-S-TT-EEEEE
T ss_pred CCHHHhc-cCCCCEEEEE
Confidence 4555554 6999998854
No 154
>COG1912 Uncharacterized conserved protein [Function unknown]
Probab=26.23 E-value=65 Score=23.49 Aligned_cols=19 Identities=42% Similarity=0.473 Sum_probs=16.6
Q ss_pred EecCChHhhcCCCCCCEEE
Q psy16960 27 KLYGSPADKSDLEIGDEIL 45 (69)
Q Consensus 27 v~~gspA~~aGLk~GD~Il 45 (69)
+..|++|++-|++.||.|.
T Consensus 246 Vn~Gsaa~~l~v~~gd~i~ 264 (268)
T COG1912 246 VNMGSAAEKLGVKEGDEIE 264 (268)
T ss_pred EecCCHHHHhCCCCCCeEE
Confidence 3579999999999999985
No 155
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=26.12 E-value=59 Score=19.41 Aligned_cols=19 Identities=32% Similarity=0.349 Sum_probs=13.3
Q ss_pred CChHhhc-CCCCCCEEEEEC
Q psy16960 30 GSPADKS-DLEIGDEILEVN 48 (69)
Q Consensus 30 gspA~~a-GLk~GD~Il~Vn 48 (69)
.-|+.+. |+++||.|-=+.
T Consensus 43 ~DPv~r~~g~k~GdVvkI~R 62 (79)
T PRK09570 43 SDPVVKAIGAKPGDVIKIVR 62 (79)
T ss_pred cChhhhhcCCCCCCEEEEEE
Confidence 4455555 999999886544
No 156
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=26.09 E-value=65 Score=19.45 Aligned_cols=18 Identities=28% Similarity=0.326 Sum_probs=12.8
Q ss_pred CCh-HhhcCCCCCCEEEEE
Q psy16960 30 GSP-ADKSDLEIGDEILEV 47 (69)
Q Consensus 30 gsp-A~~aGLk~GD~Il~V 47 (69)
.-| |...|.+.||.|-=|
T Consensus 46 ~DPva~~lgak~GdvVkIv 64 (80)
T COG2012 46 SDPVAKALGAKPGDVVKIV 64 (80)
T ss_pred cChhHHHccCCCCcEEEEE
Confidence 455 667799999965444
No 157
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=25.81 E-value=73 Score=18.57 Aligned_cols=18 Identities=22% Similarity=0.082 Sum_probs=13.6
Q ss_pred ChHhhcCCCCCCEEEEEC
Q psy16960 31 SPADKSDLEIGDEILEVN 48 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vn 48 (69)
.-|++-||+.||.|.-.+
T Consensus 36 ~dA~~lGi~~Gd~V~v~s 53 (96)
T cd02788 36 ADAARLGLADGDLVEFSL 53 (96)
T ss_pred HHHHHcCCCCCCEEEEEE
Confidence 347777999999986444
No 158
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=25.33 E-value=1.2e+02 Score=22.95 Aligned_cols=49 Identities=22% Similarity=0.312 Sum_probs=31.7
Q ss_pred CceEec--cCCeEEEEEEcCCCeE--Ee-cCChHhhcCCCCCCEEEEECCEEeC
Q psy16960 5 PSHMID--LKGYCIIIAETPDGKV--KL-YGSPADKSDLEIGDEILEVNGKTFK 53 (69)
Q Consensus 5 ~~~~~~--~~g~~i~l~~~~~~~i--v~-~gspA~~aGLk~GD~Il~Vng~~i~ 53 (69)
|-.++. |.|..+.....+-..| +. .|.|-.-+.|++||.++---...-.
T Consensus 310 Pl~lIeAey~g~~i~tiLQNAETIkLv~~dG~pvSV~eLk~GD~vlv~~ee~aR 363 (376)
T COG1465 310 PLMLIEAEYEGVEISTILQNAETIKLVNPDGEPVSVAELKPGDEVLVYLEEKAR 363 (376)
T ss_pred ceEEEEEEecCcEEEEEeccceeEEEEcCCCcEeeeEecCCCCEEEEEehhccc
Confidence 334444 6676666555544444 33 5788889999999999976544433
No 159
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=25.29 E-value=1.3e+02 Score=16.38 Aligned_cols=38 Identities=21% Similarity=0.333 Sum_probs=19.9
Q ss_pred EeccCCeEEEEEEcCCCeEEecCChHhhcCCCCCCEEEE
Q psy16960 8 MIDLKGYCIIIAETPDGKVKLYGSPADKSDLEIGDEILE 46 (69)
Q Consensus 8 ~~~~~g~~i~l~~~~~~~iv~~gspA~~aGLk~GD~Il~ 46 (69)
.++.+.+|.+|.....+.+..+.+-.. ..++.||.|.-
T Consensus 9 V~~~~~~g~fL~~~~~~~vlLp~~e~~-~~~~~Gd~v~V 46 (61)
T PF13509_consen 9 VVDKNEFGYFLDDGEGKEVLLPKSEVP-EPLKVGDEVEV 46 (61)
T ss_dssp EEEE-SSEEEEEETT-EEEEEEGGG-------TTSEEEE
T ss_pred EEEEeCCEEEEECCCCCEEEechHHcC-CCCCCCCEEEE
Confidence 455777888886555455555544332 45999999874
No 160
>KOG3369|consensus
Probab=25.00 E-value=38 Score=23.55 Aligned_cols=25 Identities=20% Similarity=0.372 Sum_probs=20.8
Q ss_pred hHhhcCCCCCCEEEEECCEEeCCCC
Q psy16960 32 PADKSDLEIGDEILEVNGKTFKDNC 56 (69)
Q Consensus 32 pA~~aGLk~GD~Il~Vng~~i~~~~ 56 (69)
-+.+-|++.|-.+.+|||.++.+..
T Consensus 46 f~~kdgik~~~~~~~vNg~~v~g~~ 70 (199)
T KOG3369|consen 46 FGSKDGIKVGHLVQAVNGENVNGYI 70 (199)
T ss_pred eecccccchhheeeeecccccccce
Confidence 3567799999999999999987654
No 161
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=24.93 E-value=1.3e+02 Score=16.22 Aligned_cols=34 Identities=21% Similarity=0.410 Sum_probs=18.9
Q ss_pred cCCeEEEEEEcCCCeEEecCChHhhcCCCCCCEEEE
Q psy16960 11 LKGYCIIIAETPDGKVKLYGSPADKSDLEIGDEILE 46 (69)
Q Consensus 11 ~~g~~i~l~~~~~~~iv~~gspA~~aGLk~GD~Il~ 46 (69)
-+||||+.......-|.+ ++.+-.+-..||+++.
T Consensus 7 ~~GfGFv~~~~~~~DifI--p~~~l~~A~~gD~V~v 40 (58)
T PF08206_consen 7 PKGFGFVIPDDGGEDIFI--PPRNLNGAMDGDKVLV 40 (58)
T ss_dssp SSS-EEEEECT-TEEEEE---HHHHTTS-TT-EEEE
T ss_pred cCCCEEEEECCCCCCEEE--CHHHHCCCCCCCEEEE
Confidence 589999996652323433 3455557788998875
No 162
>PF12700 HlyD_2: HlyD family secretion protein; PDB: 3LNN_B 4DK0_A 4DK1_C 3FPP_B 2K32_A 2K33_A 3OW7_B 3OOC_A 3T53_B 4DNT_C ....
Probab=24.87 E-value=1.1e+02 Score=20.86 Aligned_cols=11 Identities=36% Similarity=0.610 Sum_probs=8.6
Q ss_pred hcCCCCCCEEE
Q psy16960 35 KSDLEIGDEIL 45 (69)
Q Consensus 35 ~aGLk~GD~Il 45 (69)
..||+.||+|+
T Consensus 317 ~~GL~~gd~Vv 327 (328)
T PF12700_consen 317 ISGLKEGDKVV 327 (328)
T ss_dssp SSSSSTT-EEE
T ss_pred cCCCCCCCEEE
Confidence 47999999986
No 163
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=24.54 E-value=48 Score=22.94 Aligned_cols=19 Identities=47% Similarity=0.781 Sum_probs=10.8
Q ss_pred CChHhhcCCCCCCEEEEEC
Q psy16960 30 GSPADKSDLEIGDEILEVN 48 (69)
Q Consensus 30 gspA~~aGLk~GD~Il~Vn 48 (69)
|+.-.-..|++||+|++++
T Consensus 24 G~~k~m~~L~iGD~Vla~d 42 (217)
T PF01079_consen 24 GGRKRMSDLKIGDRVLAVD 42 (217)
T ss_dssp S-EEEGGG--TT-EEEEE-
T ss_pred CCEeEHHHCCCCCEEEEec
Confidence 4455555799999999998
No 164
>PTZ00412 leucyl aminopeptidase; Provisional
Probab=24.27 E-value=46 Score=26.65 Aligned_cols=26 Identities=15% Similarity=-0.004 Sum_probs=20.3
Q ss_pred cCChHhhcCCCCCCEEEEECCEEeCCC
Q psy16960 29 YGSPADKSDLEIGDEILEVNGKTFKDN 55 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~Vng~~i~~~ 55 (69)
++.|.-.+ .++||+|..-||+.|+-.
T Consensus 353 ENm~sg~A-~rPGDVits~nGkTVEV~ 378 (569)
T PTZ00412 353 ENAIGPES-YHPSSIITSRKGLTVEVL 378 (569)
T ss_pred hcCCCCCC-CCCCCEeEecCCCEEeec
Confidence 45666555 899999999999997543
No 165
>PRK13669 hypothetical protein; Provisional
Probab=24.23 E-value=88 Score=18.68 Aligned_cols=32 Identities=16% Similarity=0.186 Sum_probs=24.9
Q ss_pred hhcCCCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 34 DKSDLEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 34 ~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
...|+-.-.-..-|||+.|...+ -+++++.|.
T Consensus 38 s~CG~C~~~~FAlVng~~V~a~t-~eeL~~kI~ 69 (78)
T PRK13669 38 GYCGICSEGLFALVNGEVVEGET-PEELVENIY 69 (78)
T ss_pred hhCcCcccCceEEECCeEeecCC-HHHHHHHHH
Confidence 34466666667789999999998 899888774
No 166
>cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=24.09 E-value=88 Score=18.86 Aligned_cols=18 Identities=22% Similarity=0.226 Sum_probs=14.0
Q ss_pred ChHhhcCCCCCCEEEEEC
Q psy16960 31 SPADKSDLEIGDEILEVN 48 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vn 48 (69)
.-|++.||+.||.|.-.+
T Consensus 40 ~dA~~~gi~~Gd~V~v~s 57 (129)
T cd02782 40 DDAAALGLADGDKVRVTS 57 (129)
T ss_pred HHHHHcCCCCCCEEEEEc
Confidence 457777999999987555
No 167
>COG1158 Rho Transcription termination factor [Transcription]
Probab=23.69 E-value=76 Score=24.46 Aligned_cols=36 Identities=14% Similarity=0.267 Sum_probs=23.9
Q ss_pred cCCeEEEEEEcCC-----CeEEecCChHhhcCCCCCCEEEE
Q psy16960 11 LKGYCIIIAETPD-----GKVKLYGSPADKSDLEIGDEILE 46 (69)
Q Consensus 11 ~~g~~i~l~~~~~-----~~iv~~gspA~~aGLk~GD~Il~ 46 (69)
..||||.-....+ +-|.+.-|.-.+-+|+.||.|.-
T Consensus 62 ~dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf~LrtGD~v~G 102 (422)
T COG1158 62 PDGFGFLRSADSSYLPGPDDIYVSPSQIRRFNLRTGDTVEG 102 (422)
T ss_pred cCCcceeecCccccCCCCCceEECHHHHhhccCccCCEEee
Confidence 3789988755421 22445556666789999999873
No 168
>PF05708 DUF830: Orthopoxvirus protein of unknown function (DUF830); PDB: 2IF6_B 3KW0_C.
Probab=23.51 E-value=43 Score=20.86 Aligned_cols=12 Identities=42% Similarity=0.526 Sum_probs=6.7
Q ss_pred CCCCCEEEEECC
Q psy16960 38 LEIGDEILEVNG 49 (69)
Q Consensus 38 Lk~GD~Il~Vng 49 (69)
||+||+|+.-..
T Consensus 2 l~~GDIil~~~~ 13 (158)
T PF05708_consen 2 LQTGDIILTRGK 13 (158)
T ss_dssp --TT-EEEEEE-
T ss_pred CCCeeEEEEECC
Confidence 789999997653
No 169
>PF13624 SurA_N_3: SurA N-terminal domain; PDB: 3NRK_A.
Probab=23.49 E-value=55 Score=20.23 Aligned_cols=28 Identities=14% Similarity=0.201 Sum_probs=16.1
Q ss_pred hcCCCCCCEEEEECCEEeCCCCChHHHHH
Q psy16960 35 KSDLEIGDEILEVNGKTFKDNCNHNEVIT 63 (69)
Q Consensus 35 ~aGLk~GD~Il~Vng~~i~~~~~~~ev~~ 63 (69)
.++...++.+..|||.+|...+ +++-..
T Consensus 33 ~~~~~~~~~vA~V~g~~It~~e-~~~~~~ 60 (154)
T PF13624_consen 33 GSGSSNNNVVAKVNGEKITKSE-LDRRVQ 60 (154)
T ss_dssp --------EEEEETTEEEEHHH-HHHHHH
T ss_pred hccCCCCCEEEEECCEEeCHHH-HHHHHH
Confidence 3333778899999999998776 665544
No 170
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=23.48 E-value=1.6e+02 Score=16.90 Aligned_cols=12 Identities=25% Similarity=0.476 Sum_probs=9.9
Q ss_pred hcCCCCCCEEEE
Q psy16960 35 KSDLEIGDEILE 46 (69)
Q Consensus 35 ~aGLk~GD~Il~ 46 (69)
.+.+++||+|.-
T Consensus 42 ~~~~~~Gd~V~v 53 (78)
T cd04486 42 GADVAVGDLVRV 53 (78)
T ss_pred CCCCCCCCEEEE
Confidence 678999999864
No 171
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=23.32 E-value=68 Score=18.32 Aligned_cols=20 Identities=25% Similarity=0.298 Sum_probs=15.8
Q ss_pred EEecCChHhhcCCCCCCEEE
Q psy16960 26 VKLYGSPADKSDLEIGDEIL 45 (69)
Q Consensus 26 iv~~gspA~~aGLk~GD~Il 45 (69)
++.|-.-.++.||+.||.|.
T Consensus 12 vtIPk~i~~~lgl~~Gd~v~ 31 (74)
T TIGR02609 12 VTLPKEVLESLGLKEGDTLY 31 (74)
T ss_pred EEECHHHHHHcCcCCCCEEE
Confidence 45566677888999999985
No 172
>cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins.
Probab=23.28 E-value=78 Score=19.66 Aligned_cols=18 Identities=28% Similarity=0.387 Sum_probs=14.1
Q ss_pred ChHhhcCCCCCCEEEEEC
Q psy16960 31 SPADKSDLEIGDEILEVN 48 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vn 48 (69)
.-|++-||+.||.|.-.+
T Consensus 37 ~dA~~lgI~~Gd~V~v~s 54 (143)
T cd02780 37 EDAAKLGIKTGDRVRVVT 54 (143)
T ss_pred HHHHHcCCCCCCEEEEEe
Confidence 457777999999997544
No 173
>COG4273 Uncharacterized conserved protein [Function unknown]
Probab=23.15 E-value=42 Score=22.11 Aligned_cols=25 Identities=28% Similarity=0.436 Sum_probs=19.8
Q ss_pred cCChHhhcCCCCCCEEEEECCEEeC
Q psy16960 29 YGSPADKSDLEIGDEILEVNGKTFK 53 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~Vng~~i~ 53 (69)
-|.|+...-=+.|++|+++||-+..
T Consensus 55 ~gv~~l~~~arsgrrIlalDGCp~~ 79 (135)
T COG4273 55 AGVPALVDAARSGRRILALDGCPLR 79 (135)
T ss_pred CCcHHHHHHhhcCCceEEecCChHH
Confidence 4677776667899999999998753
No 174
>cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=23.12 E-value=87 Score=20.05 Aligned_cols=19 Identities=16% Similarity=0.132 Sum_probs=15.1
Q ss_pred CChHhhcCCCCCCEEEEEC
Q psy16960 30 GSPADKSDLEIGDEILEVN 48 (69)
Q Consensus 30 gspA~~aGLk~GD~Il~Vn 48 (69)
-.-|++.||+.||.|.-.+
T Consensus 38 p~dA~~~GI~dGd~V~v~s 56 (156)
T cd02783 38 PKTAKELGIKDGDWVWVES 56 (156)
T ss_pred HHHHHHcCCCCCCEEEEEc
Confidence 3567777999999998666
No 175
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=23.12 E-value=66 Score=20.10 Aligned_cols=23 Identities=35% Similarity=0.663 Sum_probs=16.9
Q ss_pred CCeEEecCChHhhc-CCCCCCEEE
Q psy16960 23 DGKVKLYGSPADKS-DLEIGDEIL 45 (69)
Q Consensus 23 ~~~iv~~gspA~~a-GLk~GD~Il 45 (69)
.++|.+.|.+|..+ -++.||+|.
T Consensus 33 ~GrV~vNG~~aKpS~~VK~GD~l~ 56 (100)
T COG1188 33 GGRVKVNGQRAKPSKEVKVGDILT 56 (100)
T ss_pred CCeEEECCEEcccccccCCCCEEE
Confidence 35666777777655 499999986
No 176
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=22.84 E-value=63 Score=18.98 Aligned_cols=19 Identities=16% Similarity=0.186 Sum_probs=11.0
Q ss_pred cCChHh-hcCCCCCCEEEEE
Q psy16960 29 YGSPAD-KSDLEIGDEILEV 47 (69)
Q Consensus 29 ~gspA~-~aGLk~GD~Il~V 47 (69)
..-|.. ..|+++||.|-=+
T Consensus 39 ~~DPv~r~~g~k~GdVvkI~ 58 (74)
T PF01191_consen 39 SSDPVARYLGAKPGDVVKII 58 (74)
T ss_dssp TTSHHHHHTT--TTSEEEEE
T ss_pred ccChhhhhcCCCCCCEEEEE
Confidence 344555 4599999987544
No 177
>PF09298 FAA_hydrolase_N: Fumarylacetoacetase N-terminal; InterPro: IPR015377 Fumarylacetoacetase (3.7.1.2 from EC; also known as fumarylacetoacetate hydrolase or FAH) catalyses the hydrolytic cleavage of a carbon-carbon bond in fumarylacetoacetate to yield fumarate and acetoacetate as the final step in phenylalanine and tyrosine degradation []. This is an essential metabolic function in humans, the lack of FAH causing type I tyrosinaemia, which is associated with liver and kidney abnormalities and neurological disorders [, ]. The enzyme mechanism involves a catalytic metal ion, a Glu/His catalytic dyad, and a charged oxyanion hole []. FAH folds into two domains: an N-terminal domain SH3-like beta-barrel, and a C-terminal with an unusual fold consisting of three layers of beta-sheet structures []. This entry represents the N-terminal domain of fumarylacetoacetase.; GO: 0004334 fumarylacetoacetase activity, 0009072 aromatic amino acid family metabolic process; PDB: 1QCN_B 1QCO_B 2HZY_A 1QQJ_B 1HYO_A.
Probab=22.59 E-value=25 Score=21.73 Aligned_cols=16 Identities=31% Similarity=0.810 Sum_probs=11.3
Q ss_pred ChHhhcCCCCCCEEEE
Q psy16960 31 SPADKSDLEIGDEILE 46 (69)
Q Consensus 31 spA~~aGLk~GD~Il~ 46 (69)
++..+.|...||.|+-
T Consensus 13 ~~~pR~gvaIGd~VlD 28 (107)
T PF09298_consen 13 DPSPRVGVAIGDQVLD 28 (107)
T ss_dssp EESEEEEEEETTEEEE
T ss_pred CCCCeeEEEECCEEEe
Confidence 4556678888888874
No 178
>PF14172 DUF4309: Domain of unknown function (DUF4309)
Probab=22.51 E-value=1e+02 Score=19.80 Aligned_cols=33 Identities=21% Similarity=0.339 Sum_probs=25.8
Q ss_pred hcCCCCCCEEEEEC--CEEeCCCCChHHHHHhhcCC
Q psy16960 35 KSDLEIGDEILEVN--GKTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 35 ~aGLk~GD~Il~Vn--g~~i~~~~~~~ev~~~i~~~ 68 (69)
.-|.-.|++|.+|. +..++..+ ++++.+.+..|
T Consensus 58 ~fg~nk~~~i~eIrs~d~~l~~it-l~~vk~~LG~P 92 (134)
T PF14172_consen 58 VFGYNKGDQIFEIRSFDPNLKSIT-LSDVKKVLGKP 92 (134)
T ss_pred EEEECCCCeEEEEEEcCccccccC-HHHHHHHhCCC
Confidence 33667899999888 55688888 88998888766
No 179
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=22.48 E-value=58 Score=19.65 Aligned_cols=13 Identities=31% Similarity=0.708 Sum_probs=10.3
Q ss_pred hcCCCCCCEEEEE
Q psy16960 35 KSDLEIGDEILEV 47 (69)
Q Consensus 35 ~aGLk~GD~Il~V 47 (69)
.-+|++||.++-+
T Consensus 74 ~~~Lk~GD~V~ll 86 (100)
T PF10844_consen 74 TDGLKVGDKVLLL 86 (100)
T ss_pred ecCCcCCCEEEEE
Confidence 3489999998854
No 180
>PF08121 Toxin_33: Waglerin family; InterPro: IPR012637 This family consists of the lethal peptides (waglerins) that are found in the venom of Trimeresurus wagleri (Wagler's pit viper) (Tropidolaemus wagleri). Waglerins are 22-24 residue lethal peptides and are competitive antagonist of the muscle nicotinic receptor (nAChR). Waglerin-1 possesses a distinctive selectivity for the alpha-epsilon interface binding site of the mouse nAChR [].; GO: 0030550 acetylcholine receptor inhibitor activity, 0005576 extracellular region
Probab=22.06 E-value=31 Score=15.76 Aligned_cols=7 Identities=43% Similarity=0.819 Sum_probs=5.3
Q ss_pred CCceEec
Q psy16960 4 SPSHMID 10 (69)
Q Consensus 4 ~~~~~~~ 10 (69)
.|||.++
T Consensus 11 ppchyip 17 (22)
T PF08121_consen 11 PPCHYIP 17 (22)
T ss_pred CCccccC
Confidence 5788876
No 181
>PF13403 Hint_2: Hint domain
Probab=21.70 E-value=88 Score=20.09 Aligned_cols=25 Identities=28% Similarity=0.482 Sum_probs=16.8
Q ss_pred EEecCChHhhcCCCCCCEEEEECCE
Q psy16960 26 VKLYGSPADKSDLEIGDEILEVNGK 50 (69)
Q Consensus 26 iv~~gspA~~aGLk~GD~Il~Vng~ 50 (69)
|-.+.++-.--.|++||+++.-+|.
T Consensus 9 I~T~~G~~~Ve~L~~GD~V~T~dgg 33 (147)
T PF13403_consen 9 IETPDGPRPVEDLRPGDRVLTRDGG 33 (147)
T ss_pred EecCCcCeEeeccCCCCEEEecCCC
Confidence 3334444444579999999998643
No 182
>PTZ00164 bifunctional dihydrofolate reductase-thymidylate synthase; Provisional
Probab=21.69 E-value=1e+02 Score=24.13 Aligned_cols=38 Identities=11% Similarity=0.052 Sum_probs=32.1
Q ss_pred CChHhhcCCCCCCEEEEECCEEeCCCCChHHHHHhhcCC
Q psy16960 30 GSPADKSDLEIGDEILEVNGKTFKDNCNHNEVITHIHDP 68 (69)
Q Consensus 30 gspA~~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i~~~ 68 (69)
---|+..||++|+.+-.+++.-|..-. ++.+-+++.+.
T Consensus 436 ~~iA~~~gl~~G~~~h~~g~~HIY~~h-~~~~~~ql~r~ 473 (514)
T PTZ00164 436 HMIAQVCGLRPGEFVHFLGDAHVYSNH-VDALKEQLERV 473 (514)
T ss_pred HHHHHHhCCEeeEEEEEeccceeehhh-HHHHHHHhcCC
Confidence 356888899999999999999999877 88888877653
No 183
>PRK12678 transcription termination factor Rho; Provisional
Probab=21.45 E-value=97 Score=25.37 Aligned_cols=36 Identities=19% Similarity=0.267 Sum_probs=24.9
Q ss_pred cCCeEEEEEEcC---CCeEEecCChHhhcCCCCCCEEEE
Q psy16960 11 LKGYCIIIAETP---DGKVKLYGSPADKSDLEIGDEILE 46 (69)
Q Consensus 11 ~~g~~i~l~~~~---~~~iv~~gspA~~aGLk~GD~Il~ 46 (69)
+.||+|+-.... .+-|.+.-+.-.+.||+.||.|.-
T Consensus 303 ~dg~gFlR~~~y~~~~~Dvyvs~~qirr~~Lr~Gd~v~G 341 (672)
T PRK12678 303 LDNYAFVRTSGYLPGPNDVYVSMNQVRKNGLRKGDAVTG 341 (672)
T ss_pred cCCeeEeeCCCCCCCCCCeeeCHHHHHHcCCCCCCEEEE
Confidence 468888875421 122455566677889999999985
No 184
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=21.38 E-value=1.6e+02 Score=19.17 Aligned_cols=19 Identities=16% Similarity=0.433 Sum_probs=13.8
Q ss_pred cCChHhhcCCCCCCEEEEEC
Q psy16960 29 YGSPADKSDLEIGDEILEVN 48 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~Vn 48 (69)
.+++|++- .++||+++=..
T Consensus 70 lNGAAArl-~~~GD~VII~s 88 (126)
T COG0853 70 LNGAAARL-VQVGDLVIIMS 88 (126)
T ss_pred echHHHhh-CCCCCEEEEEE
Confidence 45666665 79999988654
No 185
>cd02776 MopB_CT_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. This CD (MopB_CT_Nitrate-R-NarG-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=21.15 E-value=94 Score=19.71 Aligned_cols=18 Identities=17% Similarity=0.077 Sum_probs=14.2
Q ss_pred ChHhhcCCCCCCEEEEEC
Q psy16960 31 SPADKSDLEIGDEILEVN 48 (69)
Q Consensus 31 spA~~aGLk~GD~Il~Vn 48 (69)
.-|++-||+.||.|.-.|
T Consensus 38 ~dA~~lgI~dGd~V~v~~ 55 (141)
T cd02776 38 KDAAELGIKDNDWVEVFN 55 (141)
T ss_pred HHHHHcCCCCCCEEEEEe
Confidence 447788999999987655
No 186
>PF01119 DNA_mis_repair: DNA mismatch repair protein, C-terminal domain; InterPro: IPR013507 This entry represents the C-terminal domain of DNA mismatch repair proteins, such as MutL. This domain functions in promoting dimerisation []. The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1B62_A 1NHJ_A 1BKN_B 1NHH_A 1B63_A 1NHI_A 3NA3_A 1EA6_A 1H7U_A 1H7S_B ....
Probab=21.05 E-value=1.4e+02 Score=17.99 Aligned_cols=24 Identities=17% Similarity=0.354 Sum_probs=17.0
Q ss_pred CCCCEEEEECCEEeCCCCChHHHHH
Q psy16960 39 EIGDEILEVNGKTFKDNCNHNEVIT 63 (69)
Q Consensus 39 k~GD~Il~Vng~~i~~~~~~~ev~~ 63 (69)
....+.+-|||++|.... +..++.
T Consensus 38 ~~~~q~ifVN~R~V~~~~-l~~~I~ 61 (119)
T PF01119_consen 38 SRDRQFIFVNGRPVENKA-LSKAIN 61 (119)
T ss_dssp SCTCEEEEETTEEE--HH-HHHHHH
T ss_pred CCCcEEEEeCCCeEeChH-HHHHHH
Confidence 357899999999999876 665554
No 187
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=20.86 E-value=1.5e+02 Score=15.56 Aligned_cols=18 Identities=28% Similarity=0.409 Sum_probs=11.5
Q ss_pred cCChHhhcCCCCCCEEEE
Q psy16960 29 YGSPADKSDLEIGDEILE 46 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~ 46 (69)
....+++-+|++||.+..
T Consensus 38 t~~~~~~L~L~~G~~V~~ 55 (64)
T PF03459_consen 38 TPESAEELGLKPGDEVYA 55 (64)
T ss_dssp EHHHHHHCT-STT-EEEE
T ss_pred cHHHHHHcCCCCCCEEEE
Confidence 445566668999999974
No 188
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=20.64 E-value=1.8e+02 Score=17.11 Aligned_cols=12 Identities=33% Similarity=0.457 Sum_probs=9.5
Q ss_pred hhcCCCCCCEEE
Q psy16960 34 DKSDLEIGDEIL 45 (69)
Q Consensus 34 ~~aGLk~GD~Il 45 (69)
.+-||++||+..
T Consensus 49 ~~m~L~PGdEFe 60 (71)
T PF14250_consen 49 KQMGLKPGDEFE 60 (71)
T ss_pred HHhCCCCCCEEE
Confidence 355999999975
No 189
>PRK00474 rps9p 30S ribosomal protein S9P; Reviewed
Probab=20.47 E-value=40 Score=21.89 Aligned_cols=30 Identities=13% Similarity=0.154 Sum_probs=21.1
Q ss_pred hcCCCCCCEEEEECCEEeCCCCChHHHHHhh
Q psy16960 35 KSDLEIGDEILEVNGKTFKDNCNHNEVITHI 65 (69)
Q Consensus 35 ~aGLk~GD~Il~Vng~~i~~~~~~~ev~~~i 65 (69)
.+-|++|.=.+.|||++++.+. .+.....+
T Consensus 17 ~v~l~~G~G~i~VNg~~~~~y~-~~~~r~~i 46 (134)
T PRK00474 17 RATIREGKGRVRINGVPLELIE-PELARLKI 46 (134)
T ss_pred EEEEEcCceEEEECCEeHHHHC-CHHHHHHH
Confidence 3347788888999999988776 54444333
No 190
>KOG2597|consensus
Probab=20.27 E-value=66 Score=25.46 Aligned_cols=24 Identities=33% Similarity=0.404 Sum_probs=20.4
Q ss_pred cCChHhhcCCCCCCEEEEECCEEeC
Q psy16960 29 YGSPADKSDLEIGDEILEVNGKTFK 53 (69)
Q Consensus 29 ~gspA~~aGLk~GD~Il~Vng~~i~ 53 (69)
+++|.-.| -|+||.|..-||+.|+
T Consensus 329 ENm~sg~A-~kpgDVit~~nGKtve 352 (513)
T KOG2597|consen 329 ENMPSGNA-TKPGDVITLRNGKTVE 352 (513)
T ss_pred ccCCCccC-CCCCcEEEecCCcEEE
Confidence 67777775 8999999999999875
No 191
>COG1582 FlgEa Uncharacterized protein, possibly involved in motility [Cell motility and secretion]
Probab=20.02 E-value=1.6e+02 Score=17.14 Aligned_cols=29 Identities=28% Similarity=0.243 Sum_probs=22.4
Q ss_pred CCCCCEEEEECCEEeCCCCChHHHHHhhc
Q psy16960 38 LEIGDEILEVNGKTFKDNCNHNEVITHIH 66 (69)
Q Consensus 38 Lk~GD~Il~Vng~~i~~~~~~~ev~~~i~ 66 (69)
--+.-.|.-+||++.--.++.+++++.|.
T Consensus 24 ~~PDttItLinGkkyvVkEsveEVi~kI~ 52 (67)
T COG1582 24 AFPDTTITLINGKKYVVKESVEEVINKII 52 (67)
T ss_pred ccCCcEEEEEcCcEEEEcccHHHHHHHHH
Confidence 34667889999999776666888888763
No 192
>COG2230 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]
Probab=20.02 E-value=97 Score=22.52 Aligned_cols=17 Identities=24% Similarity=0.378 Sum_probs=14.8
Q ss_pred hHhhcCCCCCCEEEEEC
Q psy16960 32 PADKSDLEIGDEILEVN 48 (69)
Q Consensus 32 pA~~aGLk~GD~Il~Vn 48 (69)
-+++.+|++|+.++.|.
T Consensus 64 ~~~kl~L~~G~~lLDiG 80 (283)
T COG2230 64 ILEKLGLKPGMTLLDIG 80 (283)
T ss_pred HHHhcCCCCCCEEEEeC
Confidence 45678999999999998
No 193
>PF01959 DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); InterPro: IPR002812 3-Dehydroquinate synthase (4.2.3.4 from EC) is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid []. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process
Probab=20.01 E-value=2.1e+02 Score=21.59 Aligned_cols=37 Identities=24% Similarity=0.311 Sum_probs=23.0
Q ss_pred cCCeEEEEEEcCCCeE--Eec-CChHhhcCCCCCCEEEEE
Q psy16960 11 LKGYCIIIAETPDGKV--KLY-GSPADKSDLEIGDEILEV 47 (69)
Q Consensus 11 ~~g~~i~l~~~~~~~i--v~~-gspA~~aGLk~GD~Il~V 47 (69)
.+|-.+.+...+...| +-+ |.|-.-..||+||+|+--
T Consensus 296 ~~g~~~svilQnaetIRlv~p~G~~vsVt~Lk~GD~vL~~ 335 (354)
T PF01959_consen 296 ADGKRISVILQNAETIRLVGPDGEPVSVTELKPGDEVLVY 335 (354)
T ss_pred eCCeEEEEEEecCcEEEEECCCCCEeeeeecCCCCEEEEE
Confidence 4555555544444444 333 556667789999999853
Done!