Query 023901
Match_columns 275
No_of_seqs 20 out of 22
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 07:28:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023901.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023901hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0154 RNA-binding protein RB 98.5 7E-09 1.5E-13 100.1 -3.7 206 66-272 235-442 (573)
2 KOG4509 Uncharacterized conser 88.7 0.86 1.9E-05 42.1 5.2 80 117-196 40-120 (247)
3 TIGR02395 rpoN_sigma RNA polym 86.5 2.4 5.1E-05 41.3 7.1 89 148-236 300-418 (429)
4 PF04552 Sigma54_DBD: Sigma-54 85.3 0.58 1.2E-05 40.3 2.1 88 148-235 31-147 (160)
5 PF14297 DUF4373: Domain of un 84.5 4.9 0.00011 30.4 6.6 70 156-226 1-70 (87)
6 PRK05932 RNA polymerase factor 81.3 3.8 8.3E-05 40.2 6.2 89 148-236 325-442 (455)
7 PLN02777 photosystem I P subun 81.1 1.2 2.7E-05 39.6 2.5 27 1-27 1-41 (167)
8 COG1508 RpoN DNA-directed RNA 77.7 7.1 0.00015 39.1 6.8 100 137-236 300-430 (444)
9 PRK12469 RNA polymerase factor 75.0 8.1 0.00018 38.7 6.4 89 148-236 351-468 (481)
10 PF03874 RNA_pol_Rpb4: RNA pol 73.0 11 0.00023 29.5 5.5 57 171-227 27-84 (117)
11 smart00657 RPOL4c DNA-directed 72.9 10 0.00022 30.6 5.4 45 180-224 34-79 (118)
12 PF06570 DUF1129: Protein of u 71.2 5.6 0.00012 34.4 3.8 49 198-247 6-56 (206)
13 PRK00440 rfc replication facto 68.4 28 0.00061 30.1 7.5 58 146-206 163-223 (319)
14 smart00422 HTH_MERR helix_turn 67.2 27 0.00058 24.2 5.9 54 169-224 3-68 (70)
15 cd04780 HTH_MerR-like_sg5 Heli 66.9 19 0.00042 28.0 5.7 56 169-225 3-70 (95)
16 PRK12402 replication factor C 65.8 30 0.00065 30.3 7.2 102 147-253 187-292 (337)
17 KOG2499 Beta-N-acetylhexosamin 64.8 6.9 0.00015 40.2 3.5 51 142-192 306-373 (542)
18 TIGR01856 hisJ_fam histidinol 62.0 36 0.00077 30.0 7.0 82 165-246 121-210 (253)
19 TIGR00865 bcl-2 Apoptosis regu 61.1 13 0.00028 33.6 4.3 63 178-240 3-88 (213)
20 PF06798 PrkA: PrkA serine pro 60.6 45 0.00098 30.7 7.7 79 165-251 149-250 (254)
21 PF02847 MA3: MA3 domain; Int 60.0 10 0.00022 28.7 2.9 78 151-230 7-85 (113)
22 PF01402 RHH_1: Ribbon-helix-h 59.0 19 0.00042 23.0 3.7 28 166-193 11-38 (39)
23 COG2137 OraA Uncharacterized p 58.7 23 0.0005 31.2 5.2 70 182-254 34-104 (174)
24 KOG2351 RNA polymerase II, fou 57.5 26 0.00056 30.6 5.2 36 179-214 49-85 (134)
25 TIGR01359 UMP_CMP_kin_fam UMP- 56.6 32 0.00069 27.6 5.4 52 169-226 16-70 (183)
26 PHA01748 hypothetical protein 56.5 12 0.00026 27.5 2.7 29 168-196 16-44 (60)
27 cd01104 HTH_MlrA-CarA Helix-Tu 56.4 45 0.00098 23.1 5.5 54 169-223 3-67 (68)
28 KOG2629 Peroxisomal membrane a 55.5 86 0.0019 30.5 8.8 56 100-158 77-132 (300)
29 cd04764 HTH_MlrA-like_sg1 Heli 54.8 39 0.00085 23.7 5.0 54 169-224 3-67 (67)
30 PF07568 HisKA_2: Histidine ki 54.0 22 0.00047 26.6 3.8 33 198-231 9-41 (76)
31 TIGR01128 holA DNA polymerase 53.5 51 0.0011 28.5 6.5 65 146-211 113-180 (302)
32 smart00352 POU Found in Pit-Oc 53.0 16 0.00035 28.8 3.1 24 201-224 12-35 (75)
33 PF11166 DUF2951: Protein of u 53.0 12 0.00026 31.2 2.4 22 107-129 74-95 (98)
34 PRK06585 holA DNA polymerase I 53.0 55 0.0012 29.5 6.8 61 146-206 144-207 (343)
35 smart00544 MA3 Domain in DAP-5 52.5 52 0.0011 25.0 5.7 77 151-229 7-84 (113)
36 smart00265 BH4 BH4 Bcl-2 homol 51.8 16 0.00034 24.1 2.3 23 177-199 2-24 (27)
37 PF10746 Phage_holin_6: Phage 50.9 12 0.00027 29.1 2.1 47 86-132 3-60 (66)
38 PF08542 Rep_fac_C: Replicatio 50.8 46 0.00099 24.3 5.0 56 149-206 7-62 (89)
39 smart00845 GatB_Yqey GatB doma 50.2 38 0.00083 27.9 5.0 31 196-226 38-68 (147)
40 PF07766 LETM1: LETM1-like pro 50.0 39 0.00086 30.8 5.5 38 204-252 210-247 (268)
41 COG4174 ABC-type uncharacteriz 49.6 22 0.00048 34.9 4.0 51 159-209 75-131 (364)
42 PRK05574 holA DNA polymerase I 49.2 65 0.0014 28.4 6.6 63 146-209 148-213 (340)
43 cd00592 HTH_MerR-like Helix-Tu 48.5 75 0.0016 23.9 6.0 54 169-224 3-67 (100)
44 PRK07452 DNA polymerase III su 48.2 70 0.0015 28.5 6.7 60 148-207 134-197 (326)
45 PRK03987 translation initiatio 47.6 67 0.0015 29.6 6.6 85 166-251 101-192 (262)
46 PF00046 Homeobox: Homeobox do 47.4 34 0.00073 23.2 3.6 41 142-183 4-44 (57)
47 KOG0488 Transcription factor B 46.0 22 0.00048 33.6 3.4 48 160-225 175-222 (309)
48 KOG2286 Exocyst complex subuni 44.3 40 0.00087 35.5 5.2 67 148-236 513-582 (667)
49 PRK00117 recX recombination re 44.3 54 0.0012 26.7 5.0 37 190-226 33-70 (157)
50 PF02885 Glycos_trans_3N: Glyc 44.1 62 0.0013 23.4 4.8 52 169-222 6-57 (66)
51 PF13560 HTH_31: Helix-turn-he 44.0 68 0.0015 22.4 4.8 53 168-221 5-63 (64)
52 PF02631 RecX: RecX family; I 43.9 29 0.00064 27.2 3.3 38 184-224 30-67 (121)
53 PF01381 HTH_3: Helix-turn-hel 43.7 18 0.0004 24.0 1.9 28 206-234 2-29 (55)
54 PF02797 Chal_sti_synt_C: Chal 42.7 18 0.00039 30.6 2.0 34 198-236 66-99 (151)
55 PF04510 DUF577: Family of unk 42.5 63 0.0014 29.1 5.5 85 92-194 89-174 (174)
56 COG4915 XpaC 5-bromo-4-chloroi 41.7 72 0.0016 29.5 5.8 53 171-232 58-115 (204)
57 TIGR01360 aden_kin_iso1 adenyl 41.6 1.8E+02 0.0039 23.1 7.6 73 162-240 13-88 (188)
58 PRK06266 transcription initiat 40.9 42 0.00092 29.2 4.1 43 178-223 4-46 (178)
59 cd00056 ENDO3c endonuclease II 40.5 86 0.0019 25.1 5.6 63 161-239 14-76 (158)
60 PF08069 Ribosomal_S13_N: Ribo 40.4 28 0.00062 26.4 2.6 28 197-225 28-56 (60)
61 TIGR00270 conserved hypothetic 40.3 57 0.0012 28.0 4.7 80 131-219 48-128 (154)
62 PRK09392 ftrB transcriptional 40.3 1.5E+02 0.0032 24.9 7.1 102 134-245 107-218 (236)
63 PF02417 Chromate_transp: Chro 40.0 30 0.00065 29.0 3.0 63 69-134 29-102 (169)
64 PF02180 BH4: Bcl-2 homology r 39.8 14 0.0003 24.4 0.8 23 178-200 3-25 (27)
65 PF00428 Ribosomal_60s: 60s Ac 39.1 2.9 6.3E-05 32.1 -3.0 7 69-75 77-83 (88)
66 PF11836 DUF3356: Protein of u 38.9 82 0.0018 25.3 5.1 39 164-207 18-57 (101)
67 PF06281 DUF1035: Protein of u 38.2 28 0.00061 27.7 2.3 44 89-132 24-70 (73)
68 COG2059 ChrA Chromate transpor 38.0 35 0.00077 30.5 3.2 28 68-99 33-61 (195)
69 PRK02998 prsA peptidylprolyl i 38.0 77 0.0017 28.7 5.4 52 211-263 66-118 (283)
70 cd04765 HTH_MlrA-like_sg2 Heli 37.9 1.2E+02 0.0027 23.7 5.9 31 195-225 37-70 (99)
71 COG2704 DcuB Anaerobic C4-dica 37.8 27 0.00059 35.2 2.7 39 68-124 311-349 (436)
72 PRK10072 putative transcriptio 37.8 26 0.00057 28.0 2.2 33 201-234 34-66 (96)
73 PF10112 Halogen_Hydrol: 5-bro 37.5 1.2E+02 0.0026 25.9 6.3 53 172-232 59-115 (199)
74 PHA00739 V3 structural protein 37.2 27 0.00058 28.8 2.2 35 89-123 43-80 (92)
75 PHA01976 helix-turn-helix prot 37.2 24 0.00053 24.4 1.7 29 204-233 6-34 (67)
76 PRK06645 DNA polymerase III su 37.2 1.8E+02 0.0039 29.3 8.3 61 146-206 189-253 (507)
77 PRK14137 recX recombination re 37.2 45 0.00097 29.6 3.7 65 188-258 60-125 (195)
78 PF15176 LRR19-TM: Leucine-ric 36.9 42 0.00092 28.1 3.3 48 95-142 6-57 (102)
79 PF09840 DUF2067: Uncharacteri 36.9 69 0.0015 28.5 4.8 67 176-257 71-149 (190)
80 KOG4718 Non-SMC (structural ma 36.3 74 0.0016 30.0 5.1 57 171-227 86-147 (235)
81 PRK07668 hypothetical protein; 36.1 53 0.0011 30.7 4.1 45 198-243 6-53 (254)
82 PF12324 HTH_15: Helix-turn-he 36.0 63 0.0014 25.7 4.0 54 179-238 21-74 (77)
83 PRK04195 replication factor C 36.0 2E+02 0.0044 27.8 8.2 55 167-224 350-404 (482)
84 TIGR01167 LPXTG_anchor LPXTG-m 35.8 47 0.001 20.8 2.7 21 99-119 3-23 (34)
85 PRK14530 adenylate kinase; Pro 35.3 1.3E+02 0.0027 25.5 6.0 63 162-226 13-78 (215)
86 cd00086 homeodomain Homeodomai 34.2 82 0.0018 20.8 3.9 38 145-183 7-44 (59)
87 KOG1577 Aldo/keto reductase fa 34.2 1.2E+02 0.0025 29.3 6.1 64 162-229 218-288 (300)
88 PHA02591 hypothetical protein; 33.7 35 0.00076 27.7 2.3 36 198-234 44-79 (83)
89 cd04770 HTH_HMRTR Helix-Turn-H 33.2 2.3E+02 0.0049 22.3 6.8 13 212-224 56-68 (123)
90 COG4860 Uncharacterized protei 32.6 76 0.0017 28.6 4.4 40 202-242 96-135 (170)
91 cd04765 HTH_MlrA-like_sg2 Heli 32.2 60 0.0013 25.4 3.3 54 178-231 39-93 (99)
92 COG2761 FrnE Predicted dithiol 31.9 72 0.0015 29.5 4.2 40 145-184 119-158 (225)
93 PTZ00072 40S ribosomal protein 31.8 57 0.0012 28.9 3.4 31 196-226 24-54 (148)
94 KOG1869 Splicing coactivator S 31.8 87 0.0019 31.7 5.1 52 169-220 73-145 (425)
95 cd04784 HTH_CadR-PbrR Helix-Tu 31.8 2.3E+02 0.005 22.6 6.7 9 175-183 55-63 (127)
96 PRK03892 ribonuclease P protei 31.7 1.1E+02 0.0023 28.6 5.3 65 169-233 137-215 (216)
97 PF13934 ELYS: Nuclear pore co 31.5 2.9E+02 0.0064 24.5 7.9 105 92-218 97-204 (226)
98 PRK11448 hsdR type I restricti 31.4 2E+02 0.0043 31.9 8.0 104 142-252 967-1093(1123)
99 PF10389 CoatB: Bacteriophage 31.4 51 0.0011 24.0 2.6 24 109-132 22-45 (46)
100 PRK08561 rps15p 30S ribosomal 31.3 71 0.0015 28.2 3.9 31 196-226 27-57 (151)
101 PF06595 BDV_P24: Borna diseas 31.1 38 0.00083 31.0 2.3 80 131-233 25-107 (201)
102 PHA02902 putative IMV membrane 31.0 52 0.0011 26.0 2.8 54 109-174 8-64 (70)
103 PF08006 DUF1700: Protein of u 31.0 56 0.0012 27.4 3.2 29 207-235 34-65 (181)
104 PF13443 HTH_26: Cro/C1-type H 30.9 1.4E+02 0.0031 20.3 4.7 44 170-219 14-57 (63)
105 PRK14135 recX recombination re 30.5 2.3E+02 0.005 25.0 7.1 45 186-235 126-170 (263)
106 PRK09726 antitoxin HipB; Provi 30.5 65 0.0014 24.3 3.2 38 195-233 6-44 (88)
107 cd08315 Death_TRAILR_DR4_DR5 D 30.5 1.4E+02 0.003 23.6 5.2 72 151-227 4-78 (96)
108 PRK14532 adenylate kinase; Pro 30.2 1.8E+02 0.004 23.6 6.0 70 164-240 12-84 (188)
109 TIGR00694 thiM hydroxyethylthi 29.7 2E+02 0.0044 25.5 6.6 63 197-260 38-104 (249)
110 COG4858 Uncharacterized membra 29.6 91 0.002 29.2 4.5 23 211-233 33-55 (226)
111 PF09524 Phg_2220_C: Conserved 29.6 1.4E+02 0.0031 23.3 4.9 55 169-224 2-59 (74)
112 PF00248 Aldo_ket_red: Aldo/ke 29.2 96 0.0021 26.6 4.4 54 165-222 217-278 (283)
113 PF11169 DUF2956: Protein of u 29.2 51 0.0011 27.7 2.6 22 96-118 75-96 (103)
114 cd07321 Extradiol_Dioxygenase_ 29.2 42 0.00091 25.7 2.0 54 185-238 6-59 (77)
115 PRK13344 spxA transcriptional 29.2 1.8E+02 0.0039 23.9 5.8 39 148-186 11-59 (132)
116 PRK06361 hypothetical protein; 29.2 75 0.0016 26.8 3.7 40 196-235 173-212 (212)
117 PF09279 EF-hand_like: Phospho 29.1 72 0.0016 23.2 3.1 62 181-251 3-65 (83)
118 PF13154 DUF3991: Protein of u 29.0 33 0.00072 25.5 1.4 19 189-207 1-19 (77)
119 PF05598 DUF772: Transposase d 28.5 79 0.0017 22.6 3.2 32 196-227 4-36 (77)
120 cd01310 TatD_DNAse TatD like p 28.3 94 0.002 25.7 4.0 32 200-231 218-250 (251)
121 PF10771 DUF2582: Protein of u 28.3 71 0.0015 24.3 3.0 35 187-227 12-47 (65)
122 PF02936 COX4: Cytochrome c ox 28.3 41 0.0009 28.6 2.0 62 69-136 36-102 (142)
123 cd01108 HTH_CueR Helix-Turn-He 28.3 3E+02 0.0066 22.1 6.8 9 175-183 55-63 (127)
124 PF04695 Pex14_N: Peroxisomal 28.1 1.7E+02 0.0037 24.2 5.5 50 180-230 2-51 (136)
125 PF12335 SBF2: Myotubularin pr 28.0 46 0.001 30.4 2.4 69 166-236 47-121 (225)
126 COG2212 MnhF Multisubunit Na+/ 27.8 60 0.0013 26.3 2.7 39 106-148 3-41 (89)
127 PRK00118 putative DNA-binding 27.7 44 0.00094 27.3 1.9 69 199-267 19-89 (104)
128 PF12446 DUF3682: Protein of u 27.6 30 0.00066 30.1 1.0 15 61-75 93-107 (133)
129 PRK14955 DNA polymerase III su 27.6 4.5E+02 0.0098 24.9 8.8 61 146-206 188-254 (397)
130 PRK14970 DNA polymerase III su 27.4 3.7E+02 0.0081 24.6 8.0 58 147-206 170-230 (367)
131 PRK00117 recX recombination re 27.4 3.4E+02 0.0074 22.1 9.7 117 130-267 23-145 (157)
132 PRK14954 DNA polymerase III su 27.2 3.8E+02 0.0082 27.8 8.8 60 147-206 189-254 (620)
133 TIGR03880 KaiC_arch_3 KaiC dom 27.2 3.3E+02 0.0072 22.9 7.2 58 182-240 93-150 (224)
134 PRK09111 DNA polymerase III su 27.0 2.9E+02 0.0064 28.4 8.0 60 146-207 193-255 (598)
135 PHA03211 serine/threonine kina 27.0 28 0.0006 33.6 0.8 35 66-100 94-128 (461)
136 PRK00024 hypothetical protein; 27.0 92 0.002 27.9 4.0 27 210-236 20-56 (224)
137 PRK11677 hypothetical protein; 26.9 65 0.0014 27.5 2.9 22 106-127 1-22 (134)
138 cd04411 Ribosomal_P1_P2_L12p R 26.9 24 0.00051 28.8 0.3 9 69-77 94-102 (105)
139 TIGR02384 RelB_DinJ addiction 26.9 2.2E+02 0.0049 22.0 5.6 30 168-197 16-45 (83)
140 PF13744 HTH_37: Helix-turn-he 26.9 70 0.0015 23.8 2.8 23 202-224 20-42 (80)
141 KOG2510 SWI-SNF chromatin-remo 26.8 46 0.00099 34.5 2.3 74 101-206 310-384 (532)
142 cd08801 Death_UNC5D Death doma 26.3 1.6E+02 0.0035 24.7 4.9 67 149-228 9-75 (98)
143 cd04785 HTH_CadR-PbrR-like Hel 26.0 3.3E+02 0.0072 21.8 6.7 12 212-223 56-67 (126)
144 PF02631 RecX: RecX family; I 26.0 1.3E+02 0.0027 23.6 4.2 42 185-234 45-86 (121)
145 PF08708 PriCT_1: Primase C te 26.0 1.9E+02 0.0041 20.8 4.8 22 211-232 50-71 (71)
146 COG3082 Uncharacterized protei 25.9 46 0.001 26.6 1.7 51 211-262 4-64 (74)
147 PF12651 RHH_3: Ribbon-helix-h 25.9 1.1E+02 0.0023 21.2 3.3 28 167-194 15-42 (44)
148 TIGR00017 cmk cytidylate kinas 25.8 3.1E+02 0.0068 24.0 7.0 81 163-245 13-131 (217)
149 PRK13890 conjugal transfer pro 25.7 3E+02 0.0066 22.3 6.5 49 169-219 10-64 (120)
150 PRK00236 xerC site-specific ty 25.6 3.8E+02 0.0082 22.0 8.2 29 197-225 53-81 (297)
151 PF01026 TatD_DNase: TatD rela 25.6 1.1E+02 0.0023 26.9 4.1 35 198-232 220-255 (255)
152 COG0599 Uncharacterized homolo 25.3 56 0.0012 26.1 2.1 21 206-226 75-97 (124)
153 PRK14038 ADP-dependent glucoki 25.3 99 0.0021 31.3 4.3 102 131-232 188-313 (453)
154 COG5590 Uncharacterized conser 24.9 2.9E+02 0.0062 26.2 6.9 52 145-198 28-95 (229)
155 PF03619 Solute_trans_a: Organ 24.9 87 0.0019 28.2 3.5 33 108-140 3-38 (274)
156 PF08461 HTH_12: Ribonuclease 24.8 1.6E+02 0.0036 21.7 4.4 36 156-191 6-42 (66)
157 PRK11172 dkgB 2,5-diketo-D-glu 24.8 2.4E+02 0.0053 24.8 6.2 58 165-227 188-251 (267)
158 TIGR00044 pyridoxal phosphate 24.7 1.7E+02 0.0037 25.6 5.2 106 150-262 40-150 (229)
159 cd04773 HTH_TioE_rpt2 Second H 24.7 3.4E+02 0.0074 21.3 6.4 55 170-225 4-69 (108)
160 PRK00430 fis global DNA-bindin 24.6 2.7E+02 0.0058 22.1 5.8 52 148-206 27-78 (95)
161 TIGR02044 CueR Cu(I)-responsiv 24.6 3.7E+02 0.0079 21.5 6.7 12 212-223 56-67 (127)
162 smart00229 RasGEFN Guanine nuc 24.5 3.3E+02 0.0072 21.0 7.2 95 118-229 25-125 (127)
163 PRK08123 histidinol-phosphatas 24.5 1.2E+02 0.0027 27.0 4.4 69 178-246 145-222 (270)
164 KOG0774 Transcription factor P 24.4 91 0.002 30.5 3.7 82 130-216 183-270 (334)
165 PRK10026 arsenate reductase; P 24.3 1E+02 0.0023 26.2 3.7 81 162-243 37-137 (141)
166 PRK13848 conjugal transfer pro 24.1 91 0.002 26.1 3.1 31 206-236 33-66 (98)
167 TIGR02047 CadR-PbrR Cd(II)/Pb( 24.0 3.9E+02 0.0084 21.6 6.8 9 175-183 55-63 (127)
168 PRK13749 transcriptional regul 23.8 1.2E+02 0.0026 25.2 3.8 56 169-225 6-72 (121)
169 TIGR01884 cas_HTH CRISPR locus 23.7 2.7E+02 0.0059 23.8 6.1 80 176-262 6-110 (203)
170 smart00422 HTH_MERR helix_turn 23.7 1.3E+02 0.0029 20.7 3.5 32 177-208 38-69 (70)
171 KOG0480 DNA replication licens 23.6 2.2E+02 0.0048 30.9 6.5 79 174-253 554-678 (764)
172 PF01823 MACPF: MAC/Perforin d 23.5 34 0.00074 27.9 0.6 37 197-240 45-81 (212)
173 cd07922 CarBa CarBa is the A s 23.4 72 0.0016 25.3 2.3 45 185-229 7-51 (81)
174 PRK11565 dkgA 2,5-diketo-D-glu 23.3 2.6E+02 0.0056 24.9 6.1 55 164-222 197-257 (275)
175 PRK14958 DNA polymerase III su 23.3 4E+02 0.0087 26.7 8.0 75 146-227 180-257 (509)
176 PF14163 SieB: Superinfection 23.1 1.7E+02 0.0037 24.1 4.6 12 196-207 101-112 (151)
177 PRK13765 ATP-dependent proteas 22.8 2E+02 0.0043 29.9 6.0 59 179-238 315-387 (637)
178 PRK09459 pspG phage shock prot 22.7 51 0.0011 26.4 1.4 17 123-139 58-74 (76)
179 PLN02196 abscisic acid 8'-hydr 22.5 3.5E+02 0.0076 25.4 7.0 67 92-162 30-99 (463)
180 PRK14951 DNA polymerase III su 22.5 4.5E+02 0.0097 27.4 8.3 59 146-206 185-246 (618)
181 PF08519 RFC1: Replication fac 22.5 39 0.00085 28.8 0.8 48 179-227 77-129 (155)
182 cd04776 HTH_GnyR Helix-Turn-He 22.4 3.4E+02 0.0075 21.7 6.1 12 212-223 54-65 (118)
183 PF02954 HTH_8: Bacterial regu 22.4 1E+02 0.0023 20.5 2.7 28 179-206 1-28 (42)
184 PF07261 DnaB_2: Replication i 22.4 84 0.0018 22.2 2.4 58 169-226 2-60 (77)
185 PRK00283 xerD site-specific ty 22.3 4.6E+02 0.01 21.8 8.2 44 183-226 33-80 (299)
186 PRK01326 prsA foldase protein 22.3 1.4E+02 0.003 27.6 4.3 61 201-262 61-121 (310)
187 cd03022 DsbA_HCCA_Iso DsbA fam 22.3 1.8E+02 0.0038 23.3 4.5 37 147-183 104-140 (192)
188 PF13411 MerR_1: MerR HTH fami 22.2 74 0.0016 22.1 2.0 55 169-225 3-68 (69)
189 PRK08456 flagellar motor prote 22.2 4.8E+02 0.01 23.8 7.7 54 148-207 76-129 (257)
190 PF01323 DSBA: DSBA-like thior 22.0 2.2E+02 0.0047 22.8 4.9 38 148-185 105-142 (193)
191 PF00406 ADK: Adenylate kinase 22.0 3.1E+02 0.0067 21.7 5.7 82 166-261 10-94 (151)
192 PTZ00373 60S Acidic ribosomal 21.9 33 0.00071 28.6 0.2 9 69-77 100-108 (112)
193 PF02459 Adeno_terminal: Adeno 21.8 34 0.00073 35.5 0.3 14 120-133 360-373 (548)
194 PF11377 DUF3180: Protein of u 21.8 59 0.0013 27.3 1.7 38 104-143 27-64 (138)
195 PLN00138 large subunit ribosom 21.6 33 0.0007 28.5 0.1 12 66-77 98-109 (113)
196 PRK00440 rfc replication facto 21.4 2.5E+02 0.0055 24.3 5.5 37 169-206 250-286 (319)
197 PF07308 DUF1456: Protein of u 21.4 91 0.002 23.7 2.5 39 182-225 3-41 (68)
198 PTZ00240 60S ribosomal protein 21.3 26 0.00055 33.7 -0.6 11 66-76 308-318 (323)
199 PRK13477 bifunctional pantoate 21.3 2.6E+02 0.0057 28.4 6.4 82 159-242 291-411 (512)
200 cd03025 DsbA_FrnE_like DsbA fa 21.3 1.8E+02 0.0038 23.4 4.3 36 149-184 107-143 (193)
201 cd08315 Death_TRAILR_DR4_DR5 D 21.3 83 0.0018 24.9 2.3 41 180-225 2-42 (96)
202 PRK01905 DNA-binding protein F 21.2 2.8E+02 0.006 20.8 5.0 53 148-207 9-61 (77)
203 TIGR03290 CoB_CoM_SS_C CoB--Co 21.1 2.1E+02 0.0045 23.4 4.7 47 160-216 96-142 (144)
204 PRK12657 putative monovalent c 21.1 83 0.0018 25.6 2.4 42 106-151 6-47 (100)
205 PF04472 DUF552: Protein of un 21.0 1.3E+02 0.0029 22.1 3.3 33 217-254 10-42 (73)
206 PF03147 FDX-ACB: Ferredoxin-f 21.0 93 0.002 23.7 2.5 25 213-237 68-92 (94)
207 PF00286 Flexi_CP: Viral coat 21.0 2.7E+02 0.0058 24.1 5.5 64 198-261 6-71 (140)
208 PF00690 Cation_ATPase_N: Cati 20.9 66 0.0014 22.9 1.6 33 198-238 5-37 (69)
209 PF12385 Peptidase_C70: Papain 20.8 66 0.0014 28.9 1.9 41 200-240 74-114 (166)
210 PF02410 Oligomerisation: Olig 20.5 89 0.0019 24.4 2.4 37 211-247 35-71 (100)
211 PTZ00135 60S acidic ribosomal 20.3 28 0.00061 32.9 -0.5 10 66-75 295-304 (310)
212 PRK14136 recX recombination re 20.2 1.3E+02 0.0027 29.3 3.7 72 176-256 175-247 (309)
213 cd04774 HTH_YfmP Helix-Turn-He 20.2 2.9E+02 0.0062 21.5 5.1 16 195-210 56-71 (96)
214 PF04733 Coatomer_E: Coatomer 20.0 6.9E+02 0.015 23.0 8.5 89 138-226 155-262 (290)
No 1
>KOG0154 consensus RNA-binding protein RBM5 and related proteins, contain G-patch and RRM domains [General function prediction only]
Probab=98.49 E-value=7e-09 Score=100.12 Aligned_cols=206 Identities=16% Similarity=0.066 Sum_probs=183.6
Q ss_pred hhHHHHHhcchhhHHhhhhhhhhccccccccCCCCCCCCCchhHHHHHHHhhhhHhhhhhhhhhhhcCChhhhhhhhhcc
Q 023901 66 EVEVEVEEELPWIQEKALDLVEFTGSVTQAIPGPRVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNK 145 (275)
Q Consensus 66 ~~e~e~e~e~~wiqekaldlveftg~v~qaiPgPrvg~s~lPwiLAlPLAylGiTFviA~vRTvrK~tSPraKRkR~VnK 145 (275)
+.++..++..+|+++++.+-++|+....|.+.+++...+-++|-++-.+++.|.+.+..++....+....+.+.+....=
T Consensus 235 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~l~~d~~~s~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~i~q~~~~~~~~~ 314 (573)
T KOG0154|consen 235 ETDEYYEDPETSVYYDTDSGLYFNDASSQYLYGDDEQSDYFYAKLSPSLPEFGVPNALQKKKKKEKPKIAQVKTKDMEKW 314 (573)
T ss_pred cccCceecCCccceeeccccceeccccccccccCCCcceeeecccccccccccccHHHhhhcccccccchhhhhhhHHhh
Confidence 55566778899999999999999999999999999999999999999999999999999999999999999999988888
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhc--CCCcHHHHHHH
Q 023901 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKAS--MLDDSQVAEIL 223 (275)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as--~L~d~evaeiL 223 (275)
++++++..|+|.-... ..+.....++....|.....|-.+|..|..+|+.++|+.+...+|.+... ++.+..++..-
T Consensus 315 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 393 (573)
T KOG0154|consen 315 AKYLSKEKDSYLLSST-PAHEGVHTGVNTSKGAEPGPVKKEKKLYKKKEKFVNPELSKRGSHVSPSKNLKLIDVSTGLSD 393 (573)
T ss_pred hhhhhccccccccccc-ccceecccccccccccCchhhhhhccccccchhccCccccccccccCccccccccccccCCCc
Confidence 8999988888765544 47888899999999999999999999999999999999999999998863 56666666666
Q ss_pred HHHHHhhhhhcCCeeeeccccchhhhhhHHHHHHHHHhhhhhccCcccc
Q 023901 224 NEISRRFVREKGPVVMNMSGYSEKGFKRKLAVQALFGKVFYLSEVNNET 272 (275)
Q Consensus 224 ~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a~~aLF~K~~yLsEl~ef~ 272 (275)
++.....-++++.....+.++.+.+|..+.+++.-|....+..|..+++
T Consensus 394 ~~~~~~~~~~~~~~~~~~~~l~r~~~~~~~~~~~~~~~s~~h~~n~~~~ 442 (573)
T KOG0154|consen 394 SELEQEKSLKLVDKLKLMCLLCRRQFPSKGSLQKHLTPSDLHKENLDKH 442 (573)
T ss_pred hHhhhhhhhhccccchhhhhhhhccCCchHHHhhhcccccchhhhHHhh
Confidence 6666666668888889999999999999999999999999999988765
No 2
>KOG4509 consensus Uncharacterized conserved protein [Function unknown]
Probab=88.70 E-value=0.86 Score=42.11 Aligned_cols=80 Identities=16% Similarity=0.178 Sum_probs=63.8
Q ss_pred hhhHhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCC-chHHHHHHHHhCCChHHHHHHHHHHHhcCC
Q 023901 117 VGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVN-PPALKGLVQKTGFSMEDVLRKYIRYALNEK 195 (275)
Q Consensus 117 lGiTFviA~vRTvrK~tSPraKRkR~VnKNa~LvkSLdeyfp~gRda~~-~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr 195 (275)
=||-++.-..|+.+-=|.-|-|=+--+.+-..-++.|.+|+.+..+... ..-.|--++.||||-+-||++|+.=.|+|-
T Consensus 40 eGIdLi~e~lk~~~ldna~R~~i~~k~s~Ym~ka~diekYLdqekEdgk~~eQ~KI~~NaTG~SY~~iF~e~~dd~l~~V 119 (247)
T KOG4509|consen 40 EGIDLIAEALKGMKLDNADRCKIMAKFSDYMDKAADIEKYLDQEKEDGKTHEQIKIAANATGFSYARIFGECCDDRLREV 119 (247)
T ss_pred hhHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhccCcccHHHHHHHHHhhhhhee
Confidence 4888888888887766666666666677777778889999997776655 666777789999999999999999888875
Q ss_pred C
Q 023901 196 P 196 (275)
Q Consensus 196 ~ 196 (275)
-
T Consensus 120 ~ 120 (247)
T KOG4509|consen 120 H 120 (247)
T ss_pred e
Confidence 3
No 3
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=86.53 E-value=2.4 Score=41.26 Aligned_cols=89 Identities=26% Similarity=0.465 Sum_probs=70.0
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH----HHH---------HHHhcC--------CCCChHHHHHHH
Q 023901 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYI---------RYALNE--------KPFNPDLVVNLI 206 (275)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~R----KYi---------rY~LnE--------r~F~~d~VaDLi 206 (275)
.||+.=.+||..|..++.+=.||.+..++|.+-.-|=| ||+ +|.... ...+.+.|-+.|
T Consensus 300 ~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~~~~~~g~~~S~~~Ik~~I 379 (429)
T TIGR02395 300 AIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSRGVQTDSGEGEVSSTAIKALI 379 (429)
T ss_pred HHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCCccCCCCCCCccCHHHHHHHH
Confidence 45666678999999999999999999999999998887 774 566643 236777776665
Q ss_pred HH-----HhhcCCCcHHHHHHHHH----HHHhhhhhcCC
Q 023901 207 QL-----RKASMLDDSQVAEILNE----ISRRFVREKGP 236 (275)
Q Consensus 207 ~L-----r~as~L~d~evaeiL~E----~s~Ri~~~~G~ 236 (275)
+- -+.--|||.+++++|.+ ||||-|-||=.
T Consensus 380 ~~lI~~E~~~~PlSD~~I~~~L~~~Gi~IaRRTVaKYRe 418 (429)
T TIGR02395 380 KELIAAEDKRKPLSDQKIAELLKEKGIKIARRTVAKYRE 418 (429)
T ss_pred HHHHHhcCCCCCCCHHHHHHHHHhcCCCeehHHHHHHHH
Confidence 52 23456999999999985 79999999943
No 4
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=85.26 E-value=0.58 Score=40.25 Aligned_cols=88 Identities=27% Similarity=0.454 Sum_probs=20.7
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH----HHHHH---------HhcCC-------CCChHHHHHHH-
Q 023901 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYIRY---------ALNEK-------PFNPDLVVNLI- 206 (275)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~R----KYirY---------~LnEr-------~F~~d~VaDLi- 206 (275)
+||+.=.+||..|...+.+=-++.+...+|++..-|=| ||+.. .+.-. .++.+.|-+.|
T Consensus 31 ~iv~~Q~~ff~~g~~~l~PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~ 110 (160)
T PF04552_consen 31 AIVERQKDFFLGGPGALKPLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIK 110 (160)
T ss_dssp ------------------------------------------------------S-----SS--SS-SS---TTH-HHHH
T ss_pred HHHHHHHHHHhcCcccCcCCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHH
Confidence 56777788999998899999999999999999988877 88753 22211 13344454433
Q ss_pred ---HH-HhhcCCCcHHHHHHHH----HHHHhhhhhcC
Q 023901 207 ---QL-RKASMLDDSQVAEILN----EISRRFVREKG 235 (275)
Q Consensus 207 ---~L-r~as~L~d~evaeiL~----E~s~Ri~~~~G 235 (275)
+= -+.-.|||++++++|+ .+|||-|-||=
T Consensus 111 ~lI~~Ed~~~PlSD~~i~~~L~~~gi~isRRTVaKYR 147 (160)
T PF04552_consen 111 ELIEEEDKKKPLSDQEIAELLKEEGIKISRRTVAKYR 147 (160)
T ss_dssp HHHTTS-TTS---HHHHHHHHTTTTS---HHHHHHHH
T ss_pred HHHHhcCCCCCCCHHHHHHHHHHcCCCccHHHHHHHH
Confidence 32 2346899999999997 58999999984
No 5
>PF14297 DUF4373: Domain of unknown function (DUF4373)
Probab=84.49 E-value=4.9 Score=30.40 Aligned_cols=70 Identities=17% Similarity=0.238 Sum_probs=55.4
Q ss_pred HHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023901 156 LFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (275)
Q Consensus 156 yfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (275)
|||-.-++++-..++.|+++.|-...-|+-+=|.++-.+.-+-...= ++..+-.-.+.+.+.|.+|++|.
T Consensus 1 YFp~dv~~~~D~ki~~l~~~~G~~G~~~y~~ll~~iy~~~~y~~~~~-~~~~~a~~~~~~~~~v~~II~~~ 70 (87)
T PF14297_consen 1 YFPLDVDFFSDPKIRRLMAEYGCEGYGIYWYLLEYIYKQGGYYLWWD-KLFLIARKLGVSEEYVEEIINEY 70 (87)
T ss_pred CcccccccccCHHHHHHHHHcCCchHHHHHHHHHHHHcCCCeEeeHH-HHHHHHHHHCcCHHHHHHHHHHh
Confidence 68888899999999999999999999999998888887776632211 14444455699999999999944
No 6
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=81.29 E-value=3.8 Score=40.19 Aligned_cols=89 Identities=26% Similarity=0.487 Sum_probs=68.0
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH----HHH---------HHHhcCC-------CCChHHHHHHHH
Q 023901 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYI---------RYALNEK-------PFNPDLVVNLIQ 207 (275)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~R----KYi---------rY~LnEr-------~F~~d~VaDLi~ 207 (275)
.||+.=.+||..|..++.+=.||.+..++|+.-.-|=| ||+ +|..... ..+.+.|-+.|+
T Consensus 325 ~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~~~~~g~~~S~~~Ik~~Ik 404 (455)
T PRK05932 325 CIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATTNKYMATPRGIFELKYFFSSAVSTDGGGEASSTAIRALIK 404 (455)
T ss_pred HHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhcCceeecCCceEEHHHhcccccCCCCCccccHHHHHHHHH
Confidence 35555678999999999999999999999999998887 774 5655422 245556665554
Q ss_pred H-----HhhcCCCcHHHHHHHHH----HHHhhhhhcCC
Q 023901 208 L-----RKASMLDDSQVAEILNE----ISRRFVREKGP 236 (275)
Q Consensus 208 L-----r~as~L~d~evaeiL~E----~s~Ri~~~~G~ 236 (275)
- =+.--|||.+++++|.+ ||||-|-||=.
T Consensus 405 ~lI~~Ed~~~PlSD~~I~~~L~~~Gi~IaRRTVaKYRe 442 (455)
T PRK05932 405 KLIAAENPKKPLSDSKIAELLKEQGIDVARRTVAKYRE 442 (455)
T ss_pred HHHHhcCCCCCCCHHHHHHHHHHcCCCeehHHHHHHHH
Confidence 2 12346999999999986 89999999954
No 7
>PLN02777 photosystem I P subunit (PSI-P)
Probab=81.12 E-value=1.2 Score=39.60 Aligned_cols=27 Identities=44% Similarity=0.699 Sum_probs=16.3
Q ss_pred Cccccccccccc--------------cccCCCCCCCCCCCC
Q 023901 1 MASLATSSFSSL--------------QFLPRPKIPQPPFSS 27 (275)
Q Consensus 1 ~~~~~~~~~~~~--------------q~~~~p~~p~~~~s~ 27 (275)
|+.|.++|++|+ |.+.-|.+|||+-.+
T Consensus 1 ~~~l~~~~~~~~~~~~~~~~~~a~~~~~~~lp~lppp~~~~ 41 (167)
T PLN02777 1 MTPLSISSSSTLIDSKAPRSSAAASPQCVSLPTLPPPPVQS 41 (167)
T ss_pred CCccccccccccccCCCCCcCcccCCccccCCCCCCCCccc
Confidence 677777766653 555556666554443
No 8
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=77.72 E-value=7.1 Score=39.10 Aligned_cols=100 Identities=26% Similarity=0.440 Sum_probs=78.7
Q ss_pred hhhhhhhcch-hhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH----HHH---------HHH----hcCC---
Q 023901 137 FKRKKLVNKN-AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYI---------RYA----LNEK--- 195 (275)
Q Consensus 137 aKRkR~VnKN-a~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~R----KYi---------rY~----LnEr--- 195 (275)
.+|++++=|= .++|+-=++||..|..++.+=+||.+..+.|..-.-|-| ||+ +|. +...
T Consensus 300 ~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i~s~~gg 379 (444)
T COG1508 300 EQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGG 379 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhccCCCCC
Confidence 3455555443 367788889999999999999999999999999999988 775 443 3344
Q ss_pred -CCChHHHHHHHH-----HHhhcCCCcHHHHHHHHH----HHHhhhhhcCC
Q 023901 196 -PFNPDLVVNLIQ-----LRKASMLDDSQVAEILNE----ISRRFVREKGP 236 (275)
Q Consensus 196 -~F~~d~VaDLi~-----Lr~as~L~d~evaeiL~E----~s~Ri~~~~G~ 236 (275)
..+-+.|-++|+ =++..-|||+.++++|-| +|||-|-||=-
T Consensus 380 ~~~S~~~Ik~~Ik~lI~~E~~~~pLSD~kIa~lLkekGi~iARRTVAKYRe 430 (444)
T COG1508 380 EASSTEAIKALIKKLIEAEDKKKPLSDSKIAELLKEKGIDVARRTVAKYRE 430 (444)
T ss_pred ccccHHHHHHHHHHHHhhccCCCCCCHHHHHHHHHHcCCchhHHhHHHHHH
Confidence 577878877764 245568999999999997 79999999954
No 9
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=74.99 E-value=8.1 Score=38.65 Aligned_cols=89 Identities=25% Similarity=0.382 Sum_probs=68.9
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH----HHH---------HHHhcCC-------CCChHHHHHHHH
Q 023901 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYI---------RYALNEK-------PFNPDLVVNLIQ 207 (275)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~R----KYi---------rY~LnEr-------~F~~d~VaDLi~ 207 (275)
.+|+.=.+||..|..++.+=.||.+..+.|..-.-|=| ||+ +|...-. ....+.|-++|+
T Consensus 351 ~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g~~~Ss~~Ik~~Ik 430 (481)
T PRK12469 351 CIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGGGECSAAAVRALIK 430 (481)
T ss_pred HHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCCccccHHHHHHHHH
Confidence 35555679999999999999999999999999988877 774 5666422 245556666554
Q ss_pred H-----HhhcCCCcHHHHHHHHH----HHHhhhhhcCC
Q 023901 208 L-----RKASMLDDSQVAEILNE----ISRRFVREKGP 236 (275)
Q Consensus 208 L-----r~as~L~d~evaeiL~E----~s~Ri~~~~G~ 236 (275)
- -+.--|||.+++++|++ ||||-|-||=.
T Consensus 431 ~lI~~Ed~~kPLSD~~I~~~L~~~GI~IARRTVAKYRe 468 (481)
T PRK12469 431 EMIAAEQAGDPLSDVALAEMLAGRGVLIARRTVAKYRE 468 (481)
T ss_pred HHHHhcCCCCCCCHHHHHHHHHhcCCCeechhHHHHHH
Confidence 3 22356999999999986 89999999955
No 10
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=73.03 E-value=11 Score=29.47 Aligned_cols=57 Identities=16% Similarity=0.166 Sum_probs=39.4
Q ss_pred HHHHHhCCChHHHHHHHHHHHhcCCCCC-hHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 023901 171 GLVQKTGFSMEDVLRKYIRYALNEKPFN-PDLVVNLIQLRKASMLDDSQVAEILNEIS 227 (275)
Q Consensus 171 ~L~~KTGFs~~Ei~RKYirY~LnEr~F~-~d~VaDLi~Lr~as~L~d~evaeiL~E~s 227 (275)
.........+..+++|-+.|+-+=..+. ++.+..++..=+..||++.|+..|+|-.=
T Consensus 27 ~~~~~~~~~~~~~~~~~~~Yl~~~~~~~~~e~~~~l~~~L~~~~L~~~E~~qi~Nl~P 84 (117)
T PF03874_consen 27 KNKEDPPENLNTIQYKTLEYLEKFSKFQNPESIKELREELKKFGLTEFEILQIINLRP 84 (117)
T ss_dssp HHHHHCSSCHCHHHHHHHHHHHHH-SSSSHHHHHHHHHHHTTSTS-HHHHHHHHHH--
T ss_pred ccccccccchHHHHHHHHHHHHccccCCCHHHHHHHHHHHhcccCCHHHHHHHhcCCC
Confidence 4455666777778888888877766666 77777777777777788888888877543
No 11
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=72.93 E-value=10 Score=30.61 Aligned_cols=45 Identities=24% Similarity=0.392 Sum_probs=28.1
Q ss_pred hHHHHHHHHHHHhcCCCC-ChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 023901 180 MEDVLRKYIRYALNEKPF-NPDLVVNLIQLRKASMLDDSQVAEILN 224 (275)
Q Consensus 180 ~~Ei~RKYirY~LnEr~F-~~d~VaDLi~Lr~as~L~d~evaeiL~ 224 (275)
..+|++|.+.|+-+=..| |++.+..+..+=+..+|++.|++-|.|
T Consensus 34 l~~v~~~tl~Yl~~~~~~~~~e~i~~~~~~L~~~~L~k~E~~~i~N 79 (118)
T smart00657 34 LSTVMKKTLKYLSKFARFKNREIVRAVRTLLKSKKLHKFEIAQLGN 79 (118)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhC
Confidence 345677777776544444 667777666655556777666665555
No 12
>PF06570 DUF1129: Protein of unknown function (DUF1129); InterPro: IPR009214 There are currently no experimental data for members of this group or their homologues. However, these proteins contain predicted integral membrane proteins (with several transmembrane segments).
Probab=71.21 E-value=5.6 Score=34.37 Aligned_cols=49 Identities=22% Similarity=0.444 Sum_probs=39.9
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhh--hcCCeeeeccccchh
Q 023901 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVR--EKGPVVMNMSGYSEK 247 (275)
Q Consensus 198 ~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~--~~G~vmmn~~G~Te~ 247 (275)
|+|.+.|+-+-=++.+++|+|+.|+|+|+-..+.+ +.|.--.|+=| |.+
T Consensus 6 N~~y~~~l~~~L~~~~~~e~~~e~~L~eil~~LleaQk~G~tA~~lfG-~P~ 56 (206)
T PF06570_consen 6 NQEYIFDLRKYLRSSGVSEEEIEELLEEILPHLLEAQKKGKTARQLFG-DPK 56 (206)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhCCCcHHHHcC-CHH
Confidence 67788887654488999999999999999999986 67777777777 654
No 13
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=68.38 E-value=28 Score=30.10 Aligned_cols=58 Identities=14% Similarity=0.163 Sum_probs=44.0
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhcCCCCChHHHHHHH
Q 023901 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLI 206 (275)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei---~RKYirY~LnEr~F~~d~VaDLi 206 (275)
...+.+-|..++.+.+-.++.+++..|...+|-++-.+ ++++..| .++-|.+.|.+++
T Consensus 163 ~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~---~~~it~~~v~~~~ 223 (319)
T PRK00440 163 KEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAAT---GKEVTEEAVYKIT 223 (319)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc---CCCCCHHHHHHHh
Confidence 34567778888888777799999999999999887765 4555443 4678888887665
No 14
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=67.18 E-value=27 Score=24.20 Aligned_cols=54 Identities=20% Similarity=0.328 Sum_probs=37.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhc---------CCCCChHHHHHH---HHHHhhcCCCcHHHHHHHH
Q 023901 169 LKGLVQKTGFSMEDVLRKYIRYALN---------EKPFNPDLVVNL---IQLRKASMLDDSQVAEILN 224 (275)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~Ln---------Er~F~~d~VaDL---i~Lr~as~L~d~evaeiL~ 224 (275)
++++.+++|-+.. -+|+|.+.-+- .+.|+++.|..+ ..||. .|++.++|+.+|+
T Consensus 3 ~~eva~~~gvs~~-tlr~~~~~gli~~~~~~~~g~r~y~~~dl~~l~~i~~lr~-~g~~~~~i~~~l~ 68 (70)
T smart00422 3 IGEVAKLAGVSVR-TLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKE-LGFSLEEIKELLE 68 (70)
T ss_pred HHHHHHHHCcCHH-HHHHHHHCCCCCCCccCCCCCEecCHHHHHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 4567788887764 45677665442 145888777654 55666 8999999998875
No 15
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=66.93 E-value=19 Score=28.00 Aligned_cols=56 Identities=27% Similarity=0.450 Sum_probs=43.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHh---------cCCCCChHHHHHHHH---HHhhcCCCcHHHHHHHHH
Q 023901 169 LKGLVQKTGFSMEDVLRKYIRYAL---------NEKPFNPDLVVNLIQ---LRKASMLDDSQVAEILNE 225 (275)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~L---------nEr~F~~d~VaDLi~---Lr~as~L~d~evaeiL~E 225 (275)
+.++..+||-+.. -+|-|.+.-| +.+-|+++.|..|-. ||+.+|++=+||+++|+.
T Consensus 3 I~eva~~~gvs~~-tlR~Ye~~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 3 MSELSKRSGVSVA-TIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHHHCcCHH-HHHHHHHCCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4678899999876 5677777655 346799999988765 555689999999999986
No 16
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=65.81 E-value=30 Score=30.28 Aligned_cols=102 Identities=10% Similarity=0.113 Sum_probs=64.4
Q ss_pred hhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCC-cHHHHHHHHH
Q 023901 147 AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLD-DSQVAEILNE 225 (275)
Q Consensus 147 a~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~-d~evaeiL~E 225 (275)
..+++-|.+.+.+.+-.++..+++.|...+|-++.+++.---.|+...+..|.+.|.+++.- .+ ++.|-++++.
T Consensus 187 ~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~~~~~It~~~v~~~~~~-----~~~~~~i~~l~~a 261 (337)
T PRK12402 187 DELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAGEITMEAAYEALGD-----VGTDEVIESLLDA 261 (337)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCCHHHHHHHhCC-----CCCHHHHHHHHHH
Confidence 45677888888888878999999999999999999987544445555567787777654321 12 4566666665
Q ss_pred HHHhhhhhcCCeeee---ccccchhhhhhHH
Q 023901 226 ISRRFVREKGPVVMN---MSGYSEKGFKRKL 253 (275)
Q Consensus 226 ~s~Ri~~~~G~vmmn---~~G~Te~G~kRK~ 253 (275)
++.+=+++-=.++.+ -.|++.+.+-+.+
T Consensus 262 i~~~~~~~a~~~l~~l~~~~g~~~~~i~~~l 292 (337)
T PRK12402 262 AEAGDFTDARKTLDDLLIDEGLSGGEVLEEL 292 (337)
T ss_pred HHcCCHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 543211111111222 2566666555554
No 17
>KOG2499 consensus Beta-N-acetylhexosaminidase [Carbohydrate transport and metabolism]
Probab=64.81 E-value=6.9 Score=40.20 Aligned_cols=51 Identities=35% Similarity=0.670 Sum_probs=42.5
Q ss_pred hhcchhhHHhhH---------HHHHhcCCCCCC------chHHHHHHHHhCCChHH--HHHHHHHHHh
Q 023901 142 LVNKNAMVCKTI---------DELFQKGGDAVN------PPALKGLVQKTGFSMED--VLRKYIRYAL 192 (275)
Q Consensus 142 ~VnKNa~LvkSL---------deyfp~gRda~~------~gvLk~L~~KTGFs~~E--i~RKYirY~L 192 (275)
+.|++-.+++.+ |+||+-|+|+++ .+.+|+.|+|-||..++ ..|.|+.+++
T Consensus 306 ~~n~tydvls~i~~dv~evFp~~~~HlGGDEV~~~CW~s~~~Iq~fM~~kGfg~~~~~~~~~~~~~~~ 373 (542)
T KOG2499|consen 306 TNNHTYDVLSEIFEDVSEVFPDEFFHLGGDEVSTPCWKSNPEIQDFMRKKGFGLDTKSLERLYIQFLL 373 (542)
T ss_pred CchhHHHHHHHHHHHHHHhCcHHHeecCCceeecccccCChHHHHHHHhCCCCchHHHHHHHHHHHHH
Confidence 456666666655 789999999997 46899999999999998 8999998875
No 18
>TIGR01856 hisJ_fam histidinol phosphate phosphatase HisJ family. This model represents the histidinol phosphate phosphatase HisJ of Bacillus subtilis, and related proteins from a number of species within a larger family of phosphatases in the PHP hydrolase family. HisJ catalyzes the penultimate step of histidine biosynthesis but shows no homology to the functionally equivalent sequence in E. coli, a domain of the bifunctional HisB protein. Note, however, that many species have two members and that Clostridium perfringens, predicted not to make histidine, has five members of this family; this family is designated subfamily rather than equivalog to indicate that members may not all act as HisJ.
Probab=61.99 E-value=36 Score=30.00 Aligned_cols=82 Identities=17% Similarity=0.195 Sum_probs=50.7
Q ss_pred CchHHHHHHHHhCCChHHHHHHHHHHH--hcCCCCChHHHHHHHHHHhhcCC------CcHHHHHHHHHHHHhhhhhcCC
Q 023901 165 NPPALKGLVQKTGFSMEDVLRKYIRYA--LNEKPFNPDLVVNLIQLRKASML------DDSQVAEILNEISRRFVREKGP 236 (275)
Q Consensus 165 ~~gvLk~L~~KTGFs~~Ei~RKYirY~--LnEr~F~~d~VaDLi~Lr~as~L------~d~evaeiL~E~s~Ri~~~~G~ 236 (275)
+.+.+.....+.|-+.+++++.|.... +-+.-|++|.++-+=-.|+-... ++..+-+.+.++.+.+-+.-..
T Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~i~~~~~~dvlgH~Dli~~~~~~~~~~~~~~~~~~~~~~~il~~~~~~g~~ 200 (253)
T TIGR01856 121 DAEEFNEGLVSFYGNLEQAQRDYFESVYDSIQALFKPLVIGHIDLVQKFGPLFTDVSSFSDEVYELLQRILKLVASQGKA 200 (253)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCcccHhHHHHhCccccccccccHHHHHHHHHHHHHHHHcCCE
Confidence 344555544566778999999998773 34556678888743222322222 4455666776666666555445
Q ss_pred eeeeccccch
Q 023901 237 VVMNMSGYSE 246 (275)
Q Consensus 237 vmmn~~G~Te 246 (275)
+=+|++|+..
T Consensus 201 lEiNt~g~r~ 210 (253)
T TIGR01856 201 LEFNTSGLRK 210 (253)
T ss_pred EEEEcHhhcC
Confidence 5589998754
No 19
>TIGR00865 bcl-2 Apoptosis regulator. in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC.
Probab=61.08 E-value=13 Score=33.64 Aligned_cols=63 Identities=21% Similarity=0.187 Sum_probs=44.3
Q ss_pred CChHHHHHHHHHHHhcCCCCChHHHHHH-----------HHHHhh------------cCCCcHHHHHHHHHHHHhhhhhc
Q 023901 178 FSMEDVLRKYIRYALNEKPFNPDLVVNL-----------IQLRKA------------SMLDDSQVAEILNEISRRFVREK 234 (275)
Q Consensus 178 Fs~~Ei~RKYirY~LnEr~F~~d~VaDL-----------i~Lr~a------------s~L~d~evaeiL~E~s~Ri~~~~ 234 (275)
.|.-|++-|||-|.|.-+.+.++.-+++ ++=|.. .+-..+++++.|+.++.-+=++|
T Consensus 3 ~~~r~~v~~~~~yklsq~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ps~v~~~Lr~igdEle~~~ 82 (213)
T TIGR00865 3 GSNRELVMKFISYKLSQRGGSWTAGEQIMKNGAPLLHGFIQHRAGPMTGETPSEGPPQDPPPSAVHQALRRAGDEFERRY 82 (213)
T ss_pred CchHHHHHHHHHHhhcccCCCCcchhhHHhhhhhhhccccccccccccccccccCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 4567999999999999999887654432 221211 22445679999999999888877
Q ss_pred CCeeee
Q 023901 235 GPVVMN 240 (275)
Q Consensus 235 G~vmmn 240 (275)
-...-|
T Consensus 83 ~~~f~~ 88 (213)
T TIGR00865 83 RRAFSD 88 (213)
T ss_pred HHHHHH
Confidence 655433
No 20
>PF06798 PrkA: PrkA serine protein kinase C-terminal domain; InterPro: IPR010650 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry is found at the C terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length. PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.
Probab=60.55 E-value=45 Score=30.67 Aligned_cols=79 Identities=19% Similarity=0.354 Sum_probs=54.0
Q ss_pred CchHHHHHHHHhCCCh-------HHHHHHHHHHHhcCCCCChH---------------HHHHHHHHHh-hcCCCcHHHHH
Q 023901 165 NPPALKGLVQKTGFSM-------EDVLRKYIRYALNEKPFNPD---------------LVVNLIQLRK-ASMLDDSQVAE 221 (275)
Q Consensus 165 ~~gvLk~L~~KTGFs~-------~Ei~RKYirY~LnEr~F~~d---------------~VaDLi~Lr~-as~L~d~evae 221 (275)
+..-|+.++.+-|.+- .||...|-+++-+-+.|+.+ .|.|++.+=. .+.-.|.+..+
T Consensus 149 dE~~mrsIEe~igi~~~~~~~FR~ei~~~~~~~~~~g~~~~~~~~e~Lr~~iEkkL~~d~~~~~~~~t~~~k~~d~e~~~ 228 (254)
T PF06798_consen 149 DERFMRSIEERIGISEEAKKDFRREIIKYISALAREGKKFDYTSYERLREAIEKKLFSDVKDLIKIITESSKTPDKEQQR 228 (254)
T ss_pred cHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHcCCCCCChhhhHHHHHHHHHHHHHHHHHHHHhcchhccCCCHHHHH
Confidence 3556778887777765 46776674555556788876 3555555444 44456888888
Q ss_pred HHHHHHHhhhhhcCCeeeeccccchhhhhh
Q 023901 222 ILNEISRRFVREKGPVVMNMSGYSEKGFKR 251 (275)
Q Consensus 222 iL~E~s~Ri~~~~G~vmmn~~G~Te~G~kR 251 (275)
-.++.-.|+.++| |||+.|.+.
T Consensus 229 ~~~~~i~rL~~~~--------GY~~~~A~~ 250 (254)
T PF06798_consen 229 KIDEVIERLIKKY--------GYCEACARE 250 (254)
T ss_pred HHHHHHHHHHHcC--------CCCHHHHHH
Confidence 8889999988887 478777653
No 21
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=60.04 E-value=10 Score=28.69 Aligned_cols=78 Identities=21% Similarity=0.255 Sum_probs=53.5
Q ss_pred hhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcC-CCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 023901 151 KTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNE-KPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRR 229 (275)
Q Consensus 151 kSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnE-r~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~R 229 (275)
..|++||-++...--...+++|..+ .-..+|++.=|..+|.+ +.+++-...=|-+|-+.--++.+++.+.+.+.-+.
T Consensus 7 ~~l~ey~~~~d~~ea~~~l~el~~~--~~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~ 84 (113)
T PF02847_consen 7 SILMEYFSSGDVDEAVECLKELKLP--SQHHEVVKVILECALEEKKSYREYYSKLLSHLCKRKLISKEQFQEGFEDLLES 84 (113)
T ss_dssp HHHHHHHHHT-HHHHHHHHHHTT-G--GGHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCHHHHHHHHHHhCCC--ccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhH
Confidence 4678899886443335555555444 66789999999999999 44444444444568888889999999998876554
Q ss_pred h
Q 023901 230 F 230 (275)
Q Consensus 230 i 230 (275)
+
T Consensus 85 l 85 (113)
T PF02847_consen 85 L 85 (113)
T ss_dssp H
T ss_pred h
Confidence 4
No 22
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=58.99 E-value=19 Score=23.01 Aligned_cols=28 Identities=29% Similarity=0.344 Sum_probs=24.0
Q ss_pred chHHHHHHHHhCCChHHHHHHHHHHHhc
Q 023901 166 PPALKGLVQKTGFSMEDVLRKYIRYALN 193 (275)
Q Consensus 166 ~gvLk~L~~KTGFs~~Ei~RKYirY~Ln 193 (275)
...|+.+..+.|-|..+++|..|+..++
T Consensus 11 ~~~l~~~a~~~g~s~s~~ir~ai~~~l~ 38 (39)
T PF01402_consen 11 YERLDELAKELGRSRSELIREAIREYLE 38 (39)
T ss_dssp HHHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHHHHh
Confidence 3467899999999999999999988764
No 23
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=58.68 E-value=23 Score=31.15 Aligned_cols=70 Identities=27% Similarity=0.443 Sum_probs=50.1
Q ss_pred HHHHHHHHHHhcCCCCChHHHHHHHHHHhhc-CCCcHHHHHHHHHHHHhhhhhcCCeeeeccccchhhhhhHHH
Q 023901 182 DVLRKYIRYALNEKPFNPDLVVNLIQLRKAS-MLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRKLA 254 (275)
Q Consensus 182 Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as-~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a 254 (275)
+-.+|=||-.|.++.|+++.|+++|+-=... -|+|.+.||.. +..|+-+-|||..+- ..+-++|+-+-+.
T Consensus 34 ~rse~ELr~kL~k~~~~~~~Ie~Vi~~l~~~~~ldD~~fAe~~--i~~r~~~g~G~~rl~-qeL~qkGi~~~~I 104 (174)
T COG2137 34 DRSEKELRRKLAKKEFSEEIIEEVIDRLAEEGYLDDTRFAEAY--IRSRSRKGKGPARLK-QELKQKGIDDEII 104 (174)
T ss_pred HHHHHHHHHHHHhccCCHHHHHHHHHHHHHcCcccHHHHHHHH--HHHHHhcccChHHHH-HHHHHcCCCHHHH
Confidence 5566777888999999999999999855554 47999999975 345555559998763 3344555444433
No 24
>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]
Probab=57.48 E-value=26 Score=30.58 Aligned_cols=36 Identities=25% Similarity=0.325 Sum_probs=26.2
Q ss_pred ChHHHHHHHHHHHhcCCCC-ChHHHHHHHHHHhhcCC
Q 023901 179 SMEDVLRKYIRYALNEKPF-NPDLVVNLIQLRKASML 214 (275)
Q Consensus 179 s~~Ei~RKYirY~LnEr~F-~~d~VaDLi~Lr~as~L 214 (275)
.+.|||+|-+.|+=+=-.| |+++|.++.++=...||
T Consensus 49 ~~s~Vf~kTl~Y~~~FsRfKn~etv~avr~iLs~~~l 85 (134)
T KOG2351|consen 49 EMSDVFKKTLQYLDRFSRFKNRETVRAVRTILSGKGL 85 (134)
T ss_pred hHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHhhCCc
Confidence 4778999988888664444 78888888777665554
No 25
>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family. This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.
Probab=56.63 E-value=32 Score=27.64 Aligned_cols=52 Identities=23% Similarity=0.424 Sum_probs=34.3
Q ss_pred HHHHHHHhCC---ChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023901 169 LKGLVQKTGF---SMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (275)
Q Consensus 169 Lk~L~~KTGF---s~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (275)
-+.|.++.|| |+.|++|++++ +..-....+.+++ ..+.-.+|+-+.+.|.+.
T Consensus 16 a~~la~~~~~~~is~~d~lr~~~~----~~~~~~~~~~~~~--~~g~~~~~~~~~~ll~~~ 70 (183)
T TIGR01359 16 CAKIVENFGFTHLSAGDLLRAEIK----SGSENGELIESMI--KNGKIVPSEVTVKLLKNA 70 (183)
T ss_pred HHHHHHHcCCeEEECChHHHHHHh----cCChHHHHHHHHH--HCCCcCCHHHHHHHHHHH
Confidence 3788999998 68899999987 2222233455553 455666776666666654
No 26
>PHA01748 hypothetical protein
Probab=56.49 E-value=12 Score=27.45 Aligned_cols=29 Identities=21% Similarity=0.329 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhcCCC
Q 023901 168 ALKGLVQKTGFSMEDVLRKYIRYALNEKP 196 (275)
Q Consensus 168 vLk~L~~KTGFs~~Ei~RKYirY~LnEr~ 196 (275)
.|..+.++.|++..|++|+.|+..+.|+.
T Consensus 16 eld~~a~~~g~~RSE~Ir~Ai~~~~~~~~ 44 (60)
T PHA01748 16 LLDRYAIKHGLNRSEAIRKAIEKMVKDEL 44 (60)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 34567788999999999999998886643
No 27
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=56.42 E-value=45 Score=23.07 Aligned_cols=54 Identities=26% Similarity=0.395 Sum_probs=35.9
Q ss_pred HHHHHHHhCCChHHHHHHHHH-HHhc-----C---CCCChHHHHHHHHHHh--hcCCCcHHHHHHH
Q 023901 169 LKGLVQKTGFSMEDVLRKYIR-YALN-----E---KPFNPDLVVNLIQLRK--ASMLDDSQVAEIL 223 (275)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYir-Y~Ln-----E---r~F~~d~VaDLi~Lr~--as~L~d~evaeiL 223 (275)
++++.+.+|.+.. .+|+|.. +-+. + +.|+++.|.-|..++. ..|++-+|+++.|
T Consensus 3 ~~eva~~~gvs~~-tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 3 IGAVARLTGVSPD-TLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred HHHHHHHHCcCHH-HHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 4567788887654 5677775 4331 1 5788887766544332 3899999998876
No 28
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=55.54 E-value=86 Score=30.50 Aligned_cols=56 Identities=16% Similarity=0.223 Sum_probs=36.6
Q ss_pred CCCCCCchhHHHHHHHhhhhHhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHh
Q 023901 100 RVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQ 158 (275)
Q Consensus 100 rvg~s~lPwiLAlPLAylGiTFviA~vRTvrK~tSPraKRkR~VnKNa~LvkSLdeyfp 158 (275)
-.+.++.=|.+++.+.+.| |++++|+.||+|=-|..--... +|=...-+.||+.|-
T Consensus 77 ~~~~~rwrdy~vmAvi~aG--i~y~~y~~~K~YV~P~~l~~~~-~k~e~~k~~Ld~~~~ 132 (300)
T KOG2629|consen 77 QNVLRRWRDYFVMAVILAG--IAYAAYRFVKSYVLPRFLGESK-DKLEADKRQLDDQFD 132 (300)
T ss_pred ccchhhHHHHHHHHHHHhh--HHHHHHHHHHHHHHHHhhCccc-hhHHHHHHHHHHHHH
Confidence 3455667788888888888 8999999999998775322111 022344455666554
No 29
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=54.78 E-value=39 Score=23.73 Aligned_cols=54 Identities=24% Similarity=0.364 Sum_probs=35.9
Q ss_pred HHHHHHHhCCChHHHHHHHHH-HHh-------cCCCCChHHHHHHHH---HHhhcCCCcHHHHHHHH
Q 023901 169 LKGLVQKTGFSMEDVLRKYIR-YAL-------NEKPFNPDLVVNLIQ---LRKASMLDDSQVAEILN 224 (275)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYir-Y~L-------nEr~F~~d~VaDLi~---Lr~as~L~d~evaeiL~ 224 (275)
+.++.+.+|-+.. -+|.|-. +.+ +-|-|+++.|..|.. ||. .|++=+||+++||
T Consensus 3 i~evA~~~gvs~~-tlR~~~~~g~l~~~~~~~g~R~y~~~~l~~l~~i~~l~~-~g~~l~~i~~~l~ 67 (67)
T cd04764 3 IKEVSEIIGVKPH-TLRYYEKEFNLYIPRTENGRRYYTDEDIELLKKIKTLLE-KGLSIKEIKEILN 67 (67)
T ss_pred HHHHHHHHCcCHH-HHHHHHHhcCCCCCCCCCCceeeCHHHHHHHHHHHHHHH-CCCCHHHHHHHhC
Confidence 3456667777665 4566654 223 335688888876654 455 8999999999885
No 30
>PF07568 HisKA_2: Histidine kinase; InterPro: IPR011495 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This is the dimerisation and phosphoacceptor domain of a subfamily of histidine kinases. It shares sequence similarity with IPR003661 from INTERPRO and IPR011102 from INTERPRO. It is usually found adjacent to a C-terminal ATPase domain (IPR003594 from INTERPRO). This domain is found in a wide range of bacteria and also several archaea.
Probab=53.96 E-value=22 Score=26.59 Aligned_cols=33 Identities=24% Similarity=0.443 Sum_probs=27.4
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhh
Q 023901 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFV 231 (275)
Q Consensus 198 ~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~ 231 (275)
|.-.|..||.|. +....|.++.++|.+...||.
T Consensus 9 nLq~i~sll~lq-~~~~~~~e~~~~L~~~~~RI~ 41 (76)
T PF07568_consen 9 NLQIISSLLRLQ-ARRSEDPEAREALEDAQNRIQ 41 (76)
T ss_pred HHHHHHHHHHHH-HhcCCCHHHHHHHHHHHHHHH
Confidence 456788999998 456799999999999999873
No 31
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=53.53 E-value=51 Score=28.46 Aligned_cols=65 Identities=17% Similarity=0.151 Sum_probs=53.6
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhcCCCCChHHHHHHHHHHhh
Q 023901 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLIQLRKA 211 (275)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei---~RKYirY~LnEr~F~~d~VaDLi~Lr~a 211 (275)
...+.+-|.++|.+.+-.+++.+++.|...+|.++..+ +.|-.-|+-++ +.|.+.|.+++.-...
T Consensus 113 ~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~-~It~e~I~~~~~~~~~ 180 (302)
T TIGR01128 113 EQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDG-KITLEDVEEAVSDSAR 180 (302)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCC-CCCHHHHHHHHhhhhc
Confidence 34566778999999999999999999999999998866 78888887666 7899999888765443
No 32
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=53.03 E-value=16 Score=28.77 Aligned_cols=24 Identities=17% Similarity=0.106 Sum_probs=21.0
Q ss_pred HHHHHHHHHhhcCCCcHHHHHHHH
Q 023901 201 LVVNLIQLRKASMLDDSQVAEILN 224 (275)
Q Consensus 201 ~VaDLi~Lr~as~L~d~evaeiL~ 224 (275)
+...+.+.|+.+|||-.|||+.++
T Consensus 12 ~~~~lk~~R~~lGLTQ~dvA~~lg 35 (75)
T smart00352 12 FAKTFKQRRIKLGFTQADVGLALG 35 (75)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhc
Confidence 456688999999999999999876
No 33
>PF11166 DUF2951: Protein of unknown function (DUF2951); InterPro: IPR021337 This family of proteins has no known function. It has a highly conserved sequence.
Probab=53.01 E-value=12 Score=31.16 Aligned_cols=22 Identities=36% Similarity=0.732 Sum_probs=18.9
Q ss_pred hhHHHHHHHhhhhHhhhhhhhhh
Q 023901 107 PWILAVPLAYVGVSFVIAFVKTV 129 (275)
Q Consensus 107 PwiLAlPLAylGiTFviA~vRTv 129 (275)
-|||.+--..+| ||+||+.||+
T Consensus 74 mwilGlvgTi~g-sliia~lr~~ 95 (98)
T PF11166_consen 74 MWILGLVGTIFG-SLIIALLRTI 95 (98)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHH
Confidence 388888777888 9999999996
No 34
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=53.01 E-value=55 Score=29.52 Aligned_cols=61 Identities=21% Similarity=0.212 Sum_probs=52.2
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhcCCCCChHHHHHHH
Q 023901 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLI 206 (275)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei---~RKYirY~LnEr~F~~d~VaDLi 206 (275)
...+.+-|.+.+.+.+-.+++.+++.|...+|-++..+ +.|-.-|+-..+.-|.+.|.+++
T Consensus 144 ~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv 207 (343)
T PRK06585 144 ERDLARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVV 207 (343)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHh
Confidence 56678889999999999999999999999999988665 67888887766788888887765
No 35
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=52.46 E-value=52 Score=25.01 Aligned_cols=77 Identities=19% Similarity=0.215 Sum_probs=56.0
Q ss_pred hhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCC-CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 023901 151 KTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEK-PFNPDLVVNLIQLRKASMLDDSQVAEILNEISRR 229 (275)
Q Consensus 151 kSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr-~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~R 229 (275)
..|++||..+.-.--...|++|..+ .-..|+++.-|..+|.|+ .+++-...=|-+|.+.--++.+++.+.+.++-..
T Consensus 7 ~~l~ey~~~~D~~ea~~~l~~L~~~--~~~~~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~ 84 (113)
T smart00544 7 LIIEEYLSSGDTDEAVHCLLELKLP--EQHHEVVKVLLTCALEEKRTYREMYSVLLSRLCQANVISTKQFEKGFWRLLED 84 (113)
T ss_pred HHHHHHHHcCCHHHHHHHHHHhCCC--cchHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhh
Confidence 3788999776443335555666545 357899999999999996 5666666666678888889999999888764433
No 36
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=51.83 E-value=16 Score=24.14 Aligned_cols=23 Identities=13% Similarity=0.427 Sum_probs=19.5
Q ss_pred CCChHHHHHHHHHHHhcCCCCCh
Q 023901 177 GFSMEDVLRKYIRYALNEKPFNP 199 (275)
Q Consensus 177 GFs~~Ei~RKYirY~LnEr~F~~ 199 (275)
+++..|++-+||.|.|..+-+..
T Consensus 2 ~~~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 2 RLDNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred CcchHHHHHHHHHHHHhhcCCCC
Confidence 67889999999999998876543
No 37
>PF10746 Phage_holin_6: Phage holin family 6; InterPro: IPR019682 This entry represents a protein conserved in Caudovirales (known as tailed bacteriophages). Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis.
Probab=50.90 E-value=12 Score=29.11 Aligned_cols=47 Identities=26% Similarity=0.456 Sum_probs=37.1
Q ss_pred hhhccccccccC---CC------CC--CCCCchhHHHHHHHhhhhHhhhhhhhhhhhc
Q 023901 86 VEFTGSVTQAIP---GP------RV--GQSKLPWILAVPLAYVGVSFVIAFVKTVKKF 132 (275)
Q Consensus 86 veftg~v~qaiP---gP------rv--g~s~lPwiLAlPLAylGiTFviA~vRTvrK~ 132 (275)
+.|+-.|.||.| ++ |. |-|---|..+.-++|.-+-...-+|++++|+
T Consensus 3 ~df~n~vvkaaPi~~~a~A~~~a~~f~GLslneWfyiati~YtvlQig~~v~k~v~~~ 60 (66)
T PF10746_consen 3 LDFNNEVVKAAPIVGTAGADVVARYFWGLSLNEWFYIATIAYTVLQIGYLVWKKVRDW 60 (66)
T ss_pred cccccchheecCCccchhHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 357888899999 33 44 6666679999999998888888888888775
No 38
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=50.83 E-value=46 Score=24.34 Aligned_cols=56 Identities=18% Similarity=0.230 Sum_probs=34.7
Q ss_pred HHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHH
Q 023901 149 VCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLI 206 (275)
Q Consensus 149 LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi 206 (275)
.++.|=+...++.=.--...+.+|... ||+..+|++.-.++.++- .+++.....++
T Consensus 7 ~i~~i~~~~~~~~~~~~~~~~~~l~~~-G~s~~~Il~~l~~~l~~~-~~~~~~k~~i~ 62 (89)
T PF08542_consen 7 VIEEILESCLNGDFKEARKKLYELLVE-GYSASDILKQLHEVLVES-DIPDSQKAEIL 62 (89)
T ss_dssp HHHHHHHHHHHTCHHHHHHHHHHHHHT-T--HHHHHHHHHHHHHTS-TSSHHHHHHHH
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHHh-hccHHHHHHHH
Confidence 344444444444222225667788888 999999999999998887 66665555443
No 39
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=50.19 E-value=38 Score=27.88 Aligned_cols=31 Identities=23% Similarity=0.540 Sum_probs=15.3
Q ss_pred CCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023901 196 PFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (275)
Q Consensus 196 ~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (275)
+++|+.+++|+.|=..=.+|.+.+.++|.+.
T Consensus 38 ~i~~~~l~~li~lv~~g~It~~~ak~vl~~~ 68 (147)
T smart00845 38 PITPEHLAELLKLIEDGTISGKIAKEVLEEL 68 (147)
T ss_pred CCCHHHHHHHHHHHHcCCCcHHHHHHHHHHH
Confidence 3445555555555444445555555544443
No 40
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=50.01 E-value=39 Score=30.78 Aligned_cols=38 Identities=18% Similarity=0.309 Sum_probs=20.6
Q ss_pred HHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCeeeeccccchhhhhhH
Q 023901 204 NLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRK 252 (275)
Q Consensus 204 DLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK 252 (275)
.+|.--....||++|+.++..+++ ||..|+|..-+++.
T Consensus 210 ~~i~~eGv~~Ls~~EL~~Ac~~RG-----------l~~~~~s~~~lr~~ 247 (268)
T PF07766_consen 210 RLIKREGVDSLSEEELQDACYERG-----------LRSTGLSEEELREW 247 (268)
T ss_dssp HHHHHH-GGGS-HHHHHHHHHHTT--------------TT--HHHHHHH
T ss_pred HHHHHhccccCCHHHHHHHHHHhC-----------CCcCCCCHHHHHHH
Confidence 334333456788999999988887 56667776554443
No 41
>COG4174 ABC-type uncharacterized transport system, permease component [General function prediction only]
Probab=49.61 E-value=22 Score=34.87 Aligned_cols=51 Identities=24% Similarity=0.492 Sum_probs=44.3
Q ss_pred cCCCCCCchHHHHHHHHhCCCh------HHHHHHHHHHHhcCCCCChHHHHHHHHHH
Q 023901 159 KGGDAVNPPALKGLVQKTGFSM------EDVLRKYIRYALNEKPFNPDLVVNLIQLR 209 (275)
Q Consensus 159 ~gRda~~~gvLk~L~~KTGFs~------~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr 209 (275)
.|...+++..+++|++..||+- -..+-+|+|+-.-|.-|-..-|-|||.=|
T Consensus 75 rg~~GlDpe~i~~i~~~~GFDKp~~eR~~~Ml~~y~rfDfGeS~fr~~~VidLI~ek 131 (364)
T COG4174 75 RGAQGLDPELIAEIEKQYGFDKPPLERYFLMLWDYARFDFGESFFRDASVIDLIKEK 131 (364)
T ss_pred ccccCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhccccHHhhcCChHHHHHHHh
Confidence 3566789999999999999995 35678999999999999999999999755
No 42
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=49.23 E-value=65 Score=28.43 Aligned_cols=63 Identities=14% Similarity=0.116 Sum_probs=51.3
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHhcCCCCChHHHHHHHHHH
Q 023901 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYALNEKPFNPDLVVNLIQLR 209 (275)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~R---KYirY~LnEr~F~~d~VaDLi~Lr 209 (275)
...+.+-|.++|.+.+-.+++.+++.|...+|-++..+-. |..-|+-+.+ .|.+.|..++.-.
T Consensus 148 ~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~~ 213 (340)
T PRK05574 148 EAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPDS 213 (340)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhhh
Confidence 4457788999999999999999999999999999887654 7777765544 8999998776543
No 43
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=48.47 E-value=75 Score=23.86 Aligned_cols=54 Identities=22% Similarity=0.332 Sum_probs=36.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHh--------cCCCCChHHHHHHH---HHHhhcCCCcHHHHHHHH
Q 023901 169 LKGLVQKTGFSMEDVLRKYIRYAL--------NEKPFNPDLVVNLI---QLRKASMLDDSQVAEILN 224 (275)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~L--------nEr~F~~d~VaDLi---~Lr~as~L~d~evaeiL~ 224 (275)
++++..++|-+.. -+|.|.+.-+ +.+-|+++.|..+- .||. .|++-.+|+.+|.
T Consensus 3 ~~eva~~~gi~~~-tlr~~~~~Gll~~~~~~~g~r~y~~~dv~~l~~i~~l~~-~g~~~~~i~~~l~ 67 (100)
T cd00592 3 IGEVAKLLGVSVR-TLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRE-LGLSLKEIRELLD 67 (100)
T ss_pred HHHHHHHHCcCHH-HHHHHHHCCCcCCCcCCCCCcccCHHHHHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 3566777777654 4466766544 44568887776654 4555 8999999988885
No 44
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=48.16 E-value=70 Score=28.54 Aligned_cols=60 Identities=23% Similarity=0.295 Sum_probs=51.6
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHh-cCCCCChHHHHHHHH
Q 023901 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYAL-NEKPFNPDLVVNLIQ 207 (275)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei---~RKYirY~L-nEr~F~~d~VaDLi~ 207 (275)
.+.+-|.+.+.+.+-.++..+++.|...+|.++..+ +.|-+-|+. ..+.-|++.|..++.
T Consensus 134 ~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~ 197 (326)
T PRK07452 134 GLKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVS 197 (326)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhc
Confidence 377888999999999999999999999999999888 678777764 466789999998875
No 45
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=47.55 E-value=67 Score=29.63 Aligned_cols=85 Identities=16% Similarity=0.030 Sum_probs=51.0
Q ss_pred chHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHH----HHhhcCCCcHHHHHHHHHHHHhhhh-hcCC--ee
Q 023901 166 PPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQ----LRKASMLDDSQVAEILNEISRRFVR-EKGP--VV 238 (275)
Q Consensus 166 ~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~----Lr~as~L~d~evaeiL~E~s~Ri~~-~~G~--vm 238 (275)
..-|+-..+++|.+.+|..++.-|.+.++-.=--|+..+.+. .=..++++ +++++.|.++++|=++ ..=. -.
T Consensus 101 ~~il~~~a~~~~~~~e~~~~~~~~~l~~~yg~~y~af~~~~~~~~~~l~~~~~~-~~~~~~l~~~~~~~~~~~~vki~~~ 179 (262)
T PRK03987 101 DKWLELAAEKLGKSLEEAWEEVGYKLEDEFGDLYDAFEEAAIEGEEALDDLGVP-EEWADALVEIARENIEVPKVKISGY 179 (262)
T ss_pred hhHHHHHHHHcCCCHHHHHHHHHHHHHHHhCcHHHHHHHHHhcChhhhccCCCC-HHHHHHHHHHHHHhCCCCcEEEEEE
Confidence 467889999999999999999999887772211112222111 12233455 5666666666665332 2211 23
Q ss_pred eeccccchhhhhh
Q 023901 239 MNMSGYSEKGFKR 251 (275)
Q Consensus 239 mn~~G~Te~G~kR 251 (275)
+++.-++-.|+++
T Consensus 180 ie~~~~~~dGi~~ 192 (262)
T PRK03987 180 VDLTSPEPDGVEI 192 (262)
T ss_pred EEEEeCCCChHHH
Confidence 5666677788875
No 46
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=47.44 E-value=34 Score=23.17 Aligned_cols=41 Identities=17% Similarity=0.206 Sum_probs=32.6
Q ss_pred hhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH
Q 023901 142 LVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV 183 (275)
Q Consensus 142 ~VnKNa~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei 183 (275)
...-+..-++-|.++|.. ..-.+......|..++|-+...|
T Consensus 4 r~~~t~~q~~~L~~~f~~-~~~p~~~~~~~la~~l~l~~~~V 44 (57)
T PF00046_consen 4 RTRFTKEQLKVLEEYFQE-NPYPSKEEREELAKELGLTERQV 44 (57)
T ss_dssp SSSSSHHHHHHHHHHHHH-SSSCHHHHHHHHHHHHTSSHHHH
T ss_pred CCCCCHHHHHHHHHHHHH-hcccccccccccccccccccccc
Confidence 344567778889999998 55577888999999999998888
No 47
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=46.01 E-value=22 Score=33.57 Aligned_cols=48 Identities=25% Similarity=0.279 Sum_probs=38.1
Q ss_pred CCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 023901 160 GGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNE 225 (275)
Q Consensus 160 gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E 225 (275)
-|.+++.--|++|++..- .-||| .|+|=+.|=..+||||.||+---.-
T Consensus 175 sRTaFT~~Ql~~LEkrF~------~QKYL------------S~~DR~~LA~~LgLTdaQVKtWfQN 222 (309)
T KOG0488|consen 175 SRTAFSDHQLFELEKRFE------KQKYL------------SVADRIELAASLGLTDAQVKTWFQN 222 (309)
T ss_pred chhhhhHHHHHHHHHHHH------Hhhcc------------cHHHHHHHHHHcCCchhhHHHHHhh
Confidence 456777777888888763 46887 5889999999999999999876544
No 48
>KOG2286 consensus Exocyst complex subunit SEC6 [Intracellular trafficking, secretion, and vesicular transport]
Probab=44.30 E-value=40 Score=35.51 Aligned_cols=67 Identities=13% Similarity=0.262 Sum_probs=46.1
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHH---
Q 023901 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILN--- 224 (275)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~--- 224 (275)
-+|.++|+||+-=..-+... +..+.... +.+++-+|||-++++|.++. +.+|-+.
T Consensus 513 ~Iv~T~~dy~~D~~~~~~~~-f~~fi~e~---~~~~v~~Yl~~l~~kr~~~~------------------~~~~~i~~d~ 570 (667)
T KOG2286|consen 513 NIVATLDDYLPDFKELMGEY-FVRFIEEA---SLELVIEYLRALSKKRASIQ------------------ELIEKIKSDA 570 (667)
T ss_pred HHHHHHHHHHHHHHHHhhhH-HHHHHHHH---HHHHHHHHHHHHHhhhhhHH------------------HHHHHHHhhH
Confidence 48999999998655544444 43333332 46889999999999999822 2222222
Q ss_pred HHHHhhhhhcCC
Q 023901 225 EISRRFVREKGP 236 (275)
Q Consensus 225 E~s~Ri~~~~G~ 236 (275)
|+..++|++||.
T Consensus 571 ~~~~~~f~~~~~ 582 (667)
T KOG2286|consen 571 ETLYHFFRKYGS 582 (667)
T ss_pred HHHHHHHHHhCc
Confidence 566789999998
No 49
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=44.26 E-value=54 Score=26.75 Aligned_cols=37 Identities=24% Similarity=0.314 Sum_probs=21.9
Q ss_pred HHhcCCCCChHHHHHHHHHHhhcC-CCcHHHHHHHHHH
Q 023901 190 YALNEKPFNPDLVVNLIQLRKASM-LDDSQVAEILNEI 226 (275)
Q Consensus 190 Y~LnEr~F~~d~VaDLi~Lr~as~-L~d~evaeiL~E~ 226 (275)
-.|.++-|+++.+++.|+-=+..| |+|...|+..-..
T Consensus 33 ~kL~~kg~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~ 70 (157)
T PRK00117 33 RKLAAKGFSEEVIEAVLDRLKEEGLLDDERFAESFVRS 70 (157)
T ss_pred HHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence 345566777777777666444555 5666666654433
No 50
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=44.11 E-value=62 Score=23.40 Aligned_cols=52 Identities=13% Similarity=0.155 Sum_probs=19.7
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHH
Q 023901 169 LKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEI 222 (275)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaei 222 (275)
|+.|.+....|.+|+ +.-++..++. ..++..++.++..=+.-|.|.+|++..
T Consensus 6 l~~l~~g~~Ls~~e~-~~~~~~i~~g-~~s~~qiaAfL~al~~kget~~Eiag~ 57 (66)
T PF02885_consen 6 LKKLRDGEDLSREEA-KAAFDAILDG-EVSDAQIAAFLMALRMKGETPEEIAGF 57 (66)
T ss_dssp HHHHHTT----HHHH-HHHHHHHHTT-SS-HHHHHHHHHHHHHH---HHHHHHH
T ss_pred HHHHHcCCCCCHHHH-HHHHHHHHcC-CCCHHHHHHHHHHHHHhCcCHHHHHHH
Confidence 334444444444443 2223333332 445555555554444555666665543
No 51
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=43.99 E-value=68 Score=22.39 Aligned_cols=53 Identities=19% Similarity=0.197 Sum_probs=34.5
Q ss_pred HHHHHHHHhCCChHHHHH------HHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHH
Q 023901 168 ALKGLVQKTGFSMEDVLR------KYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAE 221 (275)
Q Consensus 168 vLk~L~~KTGFs~~Ei~R------KYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evae 221 (275)
.|+.+..+.|+|..++-+ .||+..-+-+...| ....+.+|=.++|++++++++
T Consensus 5 ~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p-~~~~l~~l~~~l~~~~~~~~~ 63 (64)
T PF13560_consen 5 RLRRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRP-SPDTLQRLARALGVPPDERAE 63 (64)
T ss_dssp HHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS--BHHHHHHHHHHTT--HHHHHC
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCC-CHHHHHHHHHHHCcCHHHHcc
Confidence 466777777777777654 58888888877644 234566677789999888764
No 52
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=43.94 E-value=29 Score=27.17 Aligned_cols=38 Identities=21% Similarity=0.342 Sum_probs=18.1
Q ss_pred HHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 023901 184 LRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILN 224 (275)
Q Consensus 184 ~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~ 224 (275)
.+.|++..++-+...|-.+..=+.-| |++++.|.++|.
T Consensus 30 a~~~v~~~~~~~~~G~~~I~~~L~~k---Gi~~~~i~~~l~ 67 (121)
T PF02631_consen 30 AESYVRSRLRRKGKGPRRIRQKLKQK---GIDREIIEEALE 67 (121)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHT---T--HHHHHHHHT
T ss_pred HHHHHHHhcccccccHHHHHHHHHHH---CCChHHHHHHHH
Confidence 34556666655555555554433222 566666666665
No 53
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=43.73 E-value=18 Score=24.02 Aligned_cols=28 Identities=36% Similarity=0.419 Sum_probs=20.3
Q ss_pred HHHHhhcCCCcHHHHHHHHHHHHhhhhhc
Q 023901 206 IQLRKASMLDDSQVAEILNEISRRFVREK 234 (275)
Q Consensus 206 i~Lr~as~L~d~evaeiL~E~s~Ri~~~~ 234 (275)
-++|+..|+|-.|+|+.++ +++..+.+|
T Consensus 2 k~~r~~~gls~~~la~~~g-is~~~i~~~ 29 (55)
T PF01381_consen 2 KELRKEKGLSQKELAEKLG-ISRSTISRI 29 (55)
T ss_dssp HHHHHHTTS-HHHHHHHHT-S-HHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHhC-CCcchhHHH
Confidence 3678899999999999987 776666654
No 54
>PF02797 Chal_sti_synt_C: Chalcone and stilbene synthases, C-terminal domain; InterPro: IPR012328 Synonym(s): Chalcone synthase, Flavonone synthase, 6'-deoxychalcone synthase Naringenin-chalcone synthases (2.3.1.74 from EC) and stilbene synthases (STS) (formerly known as resveratrol synthases) are related plant enzymes. CHS is an important enzyme in flavanoid biosynthesis and STS is a key enzyme in stilbene-type phyloalexin biosynthesis. Both enzymes catalyze the addition of three molecules of malonyl-CoA to a starter CoA ester (a typical example is 4-coumaroyl-CoA), producing either a chalcone (with CHS) or stilbene (with STS) []. These enzymes have a conserved cysteine residue, located in the central section of the protein sequence, which is essential for the catalytic activity of both enzymes and probably represents the binding site for the 4-coumaryl-CoA group []. This domain of chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase. The differences in activity are accounted for by differences in the N-terminal domain. ; GO: 0016746 transferase activity, transferring acyl groups; PDB: 3OV2_A 3OV3_B 1Z1F_A 1Z1E_A 3ALE_C 3OIT_A 2H84_A 1TEE_D 1TED_A 2P0U_A ....
Probab=42.73 E-value=18 Score=30.64 Aligned_cols=34 Identities=29% Similarity=0.270 Sum_probs=23.7
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCC
Q 023901 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGP 236 (275)
Q Consensus 198 ~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~ 236 (275)
-|+=-+=|-++.++++|+++++ +-|+.++++|||
T Consensus 66 HPGG~~ILd~v~~~L~L~~~~l-----~~Sr~vLr~yGN 99 (151)
T PF02797_consen 66 HPGGRKILDAVEEALGLSPEQL-----RASREVLREYGN 99 (151)
T ss_dssp E-SSHHHHHHHHHHHTS-GGGG-----HHHHHHHHHH-B
T ss_pred cCChHHHHHHHHHHcCCCHHHH-----HHHHHHHHhcCC
Confidence 3444445667889999999986 468999999996
No 55
>PF04510 DUF577: Family of unknown function (DUF577); InterPro: IPR007598 This is a family of Arabidopsis thaliana (Mouse-ear cress) proteins. Many of these members contain a repeated region.
Probab=42.54 E-value=63 Score=29.05 Aligned_cols=85 Identities=21% Similarity=0.302 Sum_probs=52.1
Q ss_pred cccccCCCCCCCCCchhHHHHHHHhhhhHhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCC-CCCchHHH
Q 023901 92 VTQAIPGPRVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGD-AVNPPALK 170 (275)
Q Consensus 92 v~qaiPgPrvg~s~lPwiLAlPLAylGiTFviA~vRTvrK~tSPraKRkR~VnKNa~LvkSLdeyfp~gRd-a~~~gvLk 170 (275)
+.|..=.|+- ...==|+||+--||-. .|-+.-+ .+....-+.++++ +++|+.|+..+|.+ ++--.+|+
T Consensus 89 ~~~~L~~p~~-~d~~~W~LAl~~a~~~---~Iql~e~----~~~~~~vk~L~~~---mv~Sv~elV~~g~E~~~l~rgl~ 157 (174)
T PF04510_consen 89 ISKVLLPPEE-VDVEDWVLALTGAVCM---AIQLLES----SMRVDLVKELLPK---MVKSVKELVERGMEVGFLRRGLR 157 (174)
T ss_pred HHHHcCCchh-ccHHHHHHHHHHHHHH---HHHHhcc----ccHHHHHHHHHHH---HHHHHHHHHHcccHHHHHHHHHH
Confidence 4455556654 2223499998665542 1222221 2223444556665 89999999999999 76677777
Q ss_pred HHHHHhCCChHHHHHHHHHHHhcC
Q 023901 171 GLVQKTGFSMEDVLRKYIRYALNE 194 (275)
Q Consensus 171 ~L~~KTGFs~~Ei~RKYirY~LnE 194 (275)
.++.. |-|.+-||.-||
T Consensus 158 ~~e~~-------v~~~~~~y~~~~ 174 (174)
T PF04510_consen 158 DFESF-------VSRQMNWYKTSE 174 (174)
T ss_pred HHHHH-------HHHHHHHhhccC
Confidence 76653 446677776554
No 56
>COG4915 XpaC 5-bromo-4-chloroindolyl phosphate hydrolysis protein [General function prediction only]
Probab=41.70 E-value=72 Score=29.53 Aligned_cols=53 Identities=32% Similarity=0.417 Sum_probs=40.7
Q ss_pred HHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCc-----HHHHHHHHHHHHhhhh
Q 023901 171 GLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDD-----SQVAEILNEISRRFVR 232 (275)
Q Consensus 171 ~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d-----~evaeiL~E~s~Ri~~ 232 (275)
+-..++|-+-.|+ ||||=-|+| +=..++.|+|++-=.+ .|+.++| ++++|||.
T Consensus 58 ~~l~e~gLT~kdy--kyiR~nLee------arqki~~l~K~l~q~kslq~f~q~n~~l-~iskriy~ 115 (204)
T COG4915 58 ERLHEAGLTDKDY--KYIRENLEE------ARQKIKRLEKLLKQEKSLQVFEQVNGGL-EISKRIYK 115 (204)
T ss_pred HHHHHccCccchH--HHHHHhHHH------HHHHHHHHHHHHHhhhHHHHHHHHhhHH-HHHHHHHH
Confidence 4457889999887 899999986 5577888888876554 4677766 68999974
No 57
>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily. Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.
Probab=41.57 E-value=1.8e+02 Score=23.13 Aligned_cols=73 Identities=12% Similarity=0.222 Sum_probs=43.8
Q ss_pred CCCCchHHHHHHHHhCCC---hHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCee
Q 023901 162 DAVNPPALKGLVQKTGFS---MEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVV 238 (275)
Q Consensus 162 da~~~gvLk~L~~KTGFs---~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vm 238 (275)
.+...-..+.|..+.||. +.+|+|+++. .+.+. -..+.++++ ....+.+..+.+.|.+.......+.+.++
T Consensus 13 GsGKsTl~~~l~~~~g~~~~~~g~~~~~~~~---~~~~~-~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~~~i 86 (188)
T TIGR01360 13 GSGKGTQCEKIVEKYGFTHLSTGDLLRAEVA---SGSER-GKQLQAIME--SGDLVPLDTVLDLLKDAMVAALGTSKGFL 86 (188)
T ss_pred CCCHHHHHHHHHHHhCCcEEeHHHHHHHHHh---cCCHH-HHHHHHHHH--CCCCCCHHHHHHHHHHHHHcccCcCCeEE
Confidence 344455667888777764 7788988753 12221 123444432 34455667777777776665555666678
Q ss_pred ee
Q 023901 239 MN 240 (275)
Q Consensus 239 mn 240 (275)
+|
T Consensus 87 ~d 88 (188)
T TIGR01360 87 ID 88 (188)
T ss_pred Ee
Confidence 87
No 58
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=40.89 E-value=42 Score=29.20 Aligned_cols=43 Identities=16% Similarity=0.145 Sum_probs=30.6
Q ss_pred CChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHH
Q 023901 178 FSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEIL 223 (275)
Q Consensus 178 Fs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL 223 (275)
...+.++++||+..... +...+.=|-+|..-.-+||+|+|+.|
T Consensus 4 ~~~~~~v~~~l~~~~~~---~~~~~~Vl~~L~~~g~~tdeeLA~~L 46 (178)
T PRK06266 4 MLNNPLVQKVLFEIMEG---DEEGFEVLKALIKKGEVTDEEIAEQT 46 (178)
T ss_pred hhcCHHHHHHHHHHhcC---CccHhHHHHHHHHcCCcCHHHHHHHH
Confidence 44567899999998874 32333334456665679999999987
No 59
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=40.55 E-value=86 Score=25.12 Aligned_cols=63 Identities=22% Similarity=0.241 Sum_probs=41.7
Q ss_pred CCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCeee
Q 023901 161 GDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVM 239 (275)
Q Consensus 161 Rda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmm 239 (275)
..+.-..+++.|.++.|.|.++|.+ -++ +||-.+-..+| ...-++.|.++++.+.++|+....
T Consensus 14 s~~~a~~~~~~l~~~~gpt~~~l~~-----------~~~---~~l~~~~~~~G--~~~kA~~i~~~a~~~~~~~~~~~~ 76 (158)
T cd00056 14 TDKAVNKAYERLFERYGPTPEALAA-----------ADE---EELRELIRSLG--YRRKAKYLKELARAIVEGFGGLVL 76 (158)
T ss_pred cHHHHHHHHHHHHHHhCCCHHHHHC-----------CCH---HHHHHHHHhcC--hHHHHHHHHHHHHHHHHHcCCccC
Confidence 3333455666777777744444432 122 45556666667 567899999999999999998763
No 60
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=40.40 E-value=28 Score=26.41 Aligned_cols=28 Identities=39% Similarity=0.554 Sum_probs=22.1
Q ss_pred CChHHHHHHHH-HHhhcCCCcHHHHHHHHH
Q 023901 197 FNPDLVVNLIQ-LRKASMLDDSQVAEILNE 225 (275)
Q Consensus 197 F~~d~VaDLi~-Lr~as~L~d~evaeiL~E 225 (275)
.++|.|.|+|- |.| -|++.+||.-||+|
T Consensus 28 ~~~~eVe~~I~klak-kG~tpSqIG~iLRD 56 (60)
T PF08069_consen 28 YSPEEVEELIVKLAK-KGLTPSQIGVILRD 56 (60)
T ss_dssp S-HHHHHHHHHHHCC-TTHCHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHH-cCCCHHHhhhhhhh
Confidence 57788888764 444 89999999999997
No 61
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=40.31 E-value=57 Score=27.96 Aligned_cols=80 Identities=11% Similarity=0.120 Sum_probs=50.6
Q ss_pred hcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhc-CCCCChHHHHHHHHHH
Q 023901 131 KFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALN-EKPFNPDLVVNLIQLR 209 (275)
Q Consensus 131 K~tSPraKRkR~VnKNa~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~Ln-Er~F~~d~VaDLi~Lr 209 (275)
+.+.++.+|++..+....|++.+++.+..-|.+..-. .++|.++.|.+ +.||.-.-| +..-+.+ .+.+|=
T Consensus 48 ~~~~~~~~~~~~~d~~~~l~~~~g~~Ir~~Re~~glS-qeeLA~~lgvs-----~s~IsriE~G~~~Ps~~---~l~kLa 118 (154)
T TIGR00270 48 GARKPVKRKRRKIDTTEELVEDYGIIIRREREKRGWS-QEQLAKKIQEK-----ESLIKKIENAEIEPEPK---VVEKLE 118 (154)
T ss_pred cCCCCCCCCCCccchHHHHHHHHHHHHHHHHHHcCCC-HHHHHHHhCCC-----HHHHHHHHCCCCCCCHH---HHHHHH
Confidence 3444555555566667778888888877777765543 56777777776 456655555 3444444 456666
Q ss_pred hhcCCCcHHH
Q 023901 210 KASMLDDSQV 219 (275)
Q Consensus 210 ~as~L~d~ev 219 (275)
+++|.+-.+.
T Consensus 119 ~~Lgvsl~el 128 (154)
T TIGR00270 119 KLLKIKLREQ 128 (154)
T ss_pred HHhCCCHHHH
Confidence 7888876663
No 62
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=40.26 E-value=1.5e+02 Score=24.93 Aligned_cols=102 Identities=10% Similarity=0.156 Sum_probs=60.5
Q ss_pred ChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCC--------CCChHHHHHH
Q 023901 134 SPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEK--------PFNPDLVVNL 205 (275)
Q Consensus 134 SPraKRkR~VnKNa~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr--------~F~~d~VaDL 205 (275)
=|+..=.+.+.+|..+..-+-..+.+. .....+.+.+-...+..+=+..||.+..+.. +++...+|++
T Consensus 107 i~~~~~~~l~~~~p~l~~~~~~~l~~~----~~~~~~~~~~~~~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~ 182 (236)
T PRK09392 107 IPAELVREAMSEDPGFMRAVVFELAGC----YRGLVKSLKNQKLRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASY 182 (236)
T ss_pred EeHHHHHHHHHHCHHHHHHHHHHHHHH----HHHHHHHHHHhhcCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHH
Confidence 355555666777777766655554322 1223344445556677776666666544321 3455667777
Q ss_pred HHHHhhcCCCcHHHHHHHHHHHHhhhh-hcCCe-eeeccccc
Q 023901 206 IQLRKASMLDDSQVAEILNEISRRFVR-EKGPV-VMNMSGYS 245 (275)
Q Consensus 206 i~Lr~as~L~d~evaeiL~E~s~Ri~~-~~G~v-mmn~~G~T 245 (275)
+ |++.+-|..+|++..++=+. ++|.| +.|.+|+.
T Consensus 183 l------G~tretvsR~l~~L~~~gl~~~~~~i~I~d~~~L~ 218 (236)
T PRK09392 183 L------GMTPENLSRAFAALASHGVHVDGSAVTITDPAGLA 218 (236)
T ss_pred h------CCChhHHHHHHHHHHhCCeEeeCCEEEEcCHHHHH
Confidence 6 88889999999886554332 23455 45777664
No 63
>PF02417 Chromate_transp: Chromate transporter; InterPro: IPR003370 This entry represents chromate transporters (CHR) [, ]. These proteins reduce chromate accumulation and are essential for chromate resistance. They are composed of one or two copies of this region. The short-chain CHR proteins form heterodimer transporters which efflux chromate ions from the cytoplasm, while the long chain CHR proteins appear to have arisen from a gene fusion event of two short chain transporters[].; GO: 0015109 chromate transmembrane transporter activity, 0015703 chromate transport
Probab=39.97 E-value=30 Score=28.95 Aligned_cols=63 Identities=21% Similarity=0.388 Sum_probs=35.9
Q ss_pred HHHHhcchhhHHhhhhhhhhccccccccCCCC-------CCCCCchhHHHHHHH----hhhhHhhhhhhhhhhhcCC
Q 023901 69 VEVEEELPWIQEKALDLVEFTGSVTQAIPGPR-------VGQSKLPWILAVPLA----YVGVSFVIAFVKTVKKFNS 134 (275)
Q Consensus 69 ~e~e~e~~wiqekaldlveftg~v~qaiPgPr-------vg~s~lPwiLAlPLA----ylGiTFviA~vRTvrK~tS 134 (275)
+|.-++..||-|+-. .|.- .+.|..|||- +|-.--.|++|+-.. .=+..+++.+...++++.+
T Consensus 29 ~~~V~~~~wlt~~~f--~~~~-al~q~~PGP~~~n~a~~iG~~~~G~~Gai~a~~~~~lP~~l~~~~~~~~~~~~~~ 102 (169)
T PF02417_consen 29 REFVERRGWLTEEEF--LEGL-ALAQALPGPIAINLATFIGYRLAGFLGAIVATIGFILPSFLLILLLSPLYSRFRE 102 (169)
T ss_pred HHHhHccCCCCHHHH--HHHH-HHHHcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 344456788876532 2221 4789999994 344445666665432 1123345566677777764
No 64
>PF02180 BH4: Bcl-2 homology region 4; InterPro: IPR003093 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 1AF3_A 2PON_B 1YSN_A 3PL7_B 3R85_A 2O2N_A 2P1L_C 1R2G_A 2O1Y_A 1BXL_A ....
Probab=39.82 E-value=14 Score=24.44 Aligned_cols=23 Identities=17% Similarity=0.556 Sum_probs=18.9
Q ss_pred CChHHHHHHHHHHHhcCCCCChH
Q 023901 178 FSMEDVLRKYIRYALNEKPFNPD 200 (275)
Q Consensus 178 Fs~~Ei~RKYirY~LnEr~F~~d 200 (275)
++..|++-+||.|.|..|-+..+
T Consensus 3 ~~nR~lV~~yi~yKLsQrgy~w~ 25 (27)
T PF02180_consen 3 YDNRELVEDYISYKLSQRGYVWE 25 (27)
T ss_dssp HHHHHHHHHHHHHHHHHTTSTST
T ss_pred ccHHHHHHHHHHHHhhhcCCCCC
Confidence 56789999999999998876543
No 65
>PF00428 Ribosomal_60s: 60s Acidic ribosomal protein; InterPro: IPR001813 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The 60S acidic ribosomal protein plays an important role in the elongation step of protein synthesis. This family includes archaebacterial L12, eukaryotic P0, P1 and P2 []. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Alt a 6, Alt a 12, Cla h 3, Cla h 4 and Cla h 12.; GO: 0003735 structural constituent of ribosome, 0006414 translational elongation, 0005622 intracellular, 0005840 ribosome; PDB: 3A1Y_C 3N2D_B 2LBF_A 3IZS_t 3IZR_t 1S4J_A 2JDL_C 2W1O_B 1S4H_A 2ZKR_g.
Probab=39.07 E-value=2.9 Score=32.14 Aligned_cols=7 Identities=14% Similarity=0.511 Sum_probs=2.6
Q ss_pred HHHHhcc
Q 023901 69 VEVEEEL 75 (275)
Q Consensus 69 ~e~e~e~ 75 (275)
||+|++|
T Consensus 77 EEed~dm 83 (88)
T PF00428_consen 77 EEEDDDM 83 (88)
T ss_dssp SS-SSSS
T ss_pred ccccccc
Confidence 3444444
No 66
>PF11836 DUF3356: Protein of unknown function (DUF3356); InterPro: IPR021791 This entry consists of bacterial and phage proteins whose function is not currently known. Many of the bacterial sequences are found within known or suspected prophages or gene transfer agents (GTA). Gene transfer agents are related to bacteriophages, but are distinguished by cellular regulatory mechanisms that strongly suggest they are more than just defective prophages [, ].
Probab=38.87 E-value=82 Score=25.27 Aligned_cols=39 Identities=18% Similarity=0.232 Sum_probs=33.6
Q ss_pred CCchHHHHHHHHhCC-ChHHHHHHHHHHHhcCCCCChHHHHHHHH
Q 023901 164 VNPPALKGLVQKTGF-SMEDVLRKYIRYALNEKPFNPDLVVNLIQ 207 (275)
Q Consensus 164 ~~~gvLk~L~~KTGF-s~~Ei~RKYirY~LnEr~F~~d~VaDLi~ 207 (275)
++.++|.+|+.++|= +..+++.+ ++...|.-+.|..+|.
T Consensus 18 LtlgaLaeLE~~~g~~~l~aL~~R-----f~~g~~s~~Dv~~vi~ 57 (101)
T PF11836_consen 18 LTLGALAELEAALGAGGLFALVER-----FETGRFSARDVRAVIR 57 (101)
T ss_pred CCHHHHHHHHHHcCCCCHHHHHHH-----HhcCCCCHHHHHHHHH
Confidence 568999999999999 89999887 6778898888888875
No 67
>PF06281 DUF1035: Protein of unknown function (DUF1035); InterPro: IPR009379 Sulfolobus virus-like particle SSV1 and its fusellovirus homologues can be found in many acidic (pH less than 4.0) hot springs (greater than 70 degrees C) around the world. SSV1 contains a 15.5-kb double-stranded DNA genome that encodes 34 proteins with greater than 50 amino acids []. A site-specific integrase and a DnaA-like protein have been previously identified by sequence homology, and three structural proteins have been isolated from purified virus and identified by N-terminal sequencing (VP1, VP2, and VP3).; GO: 0005198 structural molecule activity, 0016021 integral to membrane
Probab=38.21 E-value=28 Score=27.67 Aligned_cols=44 Identities=32% Similarity=0.489 Sum_probs=31.2
Q ss_pred cccccc--ccCCC-CCCCCCchhHHHHHHHhhhhHhhhhhhhhhhhc
Q 023901 89 TGSVTQ--AIPGP-RVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKF 132 (275)
Q Consensus 89 tg~v~q--aiPgP-rvg~s~lPwiLAlPLAylGiTFviA~vRTvrK~ 132 (275)
.|+++| -++.| -||+|..|..--+|++|+=+..+.-.|-.+|-|
T Consensus 24 sgt~t~ssfv~nP~yvGSsnA~iv~LVplFylLvlIiVPAvi~Yk~y 70 (73)
T PF06281_consen 24 SGTVTTSSFVSNPQYVGSSNATIVSLVPLFYLLVLIIVPAVIAYKIY 70 (73)
T ss_pred ecceeeccccCCcceecCCCccHHHHHHHHHHHHHHHhhhheeeeee
Confidence 477766 46888 688889999999999998765554444333333
No 68
>COG2059 ChrA Chromate transport protein ChrA [Inorganic ion transport and metabolism]
Probab=38.01 E-value=35 Score=30.49 Aligned_cols=28 Identities=39% Similarity=0.732 Sum_probs=19.2
Q ss_pred HHHHHhcchhhHHh-hhhhhhhccccccccCCC
Q 023901 68 EVEVEEELPWIQEK-ALDLVEFTGSVTQAIPGP 99 (275)
Q Consensus 68 e~e~e~e~~wiqek-aldlveftg~v~qaiPgP 99 (275)
++|.-++-.||-|+ =.|++ ...|.+|||
T Consensus 33 ~~e~V~~r~Wis~~ef~~~l----aisq~lPGP 61 (195)
T COG2059 33 RREVVERRKWISEEEFADAL----AISQLLPGP 61 (195)
T ss_pred HHHHHHhccCCCHHHHHHHH----HHHhcCCCH
Confidence 45555666999665 34454 357999999
No 69
>PRK02998 prsA peptidylprolyl isomerase; Reviewed
Probab=38.00 E-value=77 Score=28.75 Aligned_cols=52 Identities=15% Similarity=0.253 Sum_probs=38.8
Q ss_pred hcCCCcHHHHHHHHHHHHhhhhhcCCeeeecccc-chhhhhhHHHHHHHHHhhh
Q 023901 211 ASMLDDSQVAEILNEISRRFVREKGPVVMNMSGY-SEKGFKRKLAVQALFGKVF 263 (275)
Q Consensus 211 as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~-Te~G~kRK~a~~aLF~K~~ 263 (275)
....||+||.+.++++.++.-..+... +.-.|+ ++..+++.+--+-+..++.
T Consensus 66 ~i~vsd~ev~~~i~~~~~~~~~~f~~~-L~~~G~~~~~~~r~~i~~~l~~~~~~ 118 (283)
T PRK02998 66 KYKVSDEEAKKQVEEAKDKMGDNFKST-LEQVGLKNEDELKEKMKPEIAFEKAI 118 (283)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHcCCCcHHHHHHHHHHHHHHHHHh
Confidence 357799999999999988764445433 455688 4788988888887777765
No 70
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=37.87 E-value=1.2e+02 Score=23.69 Aligned_cols=31 Identities=16% Similarity=0.216 Sum_probs=19.3
Q ss_pred CCCChHHHHHHHHHHh---hcCCCcHHHHHHHHH
Q 023901 195 KPFNPDLVVNLIQLRK---ASMLDDSQVAEILNE 225 (275)
Q Consensus 195 r~F~~d~VaDLi~Lr~---as~L~d~evaeiL~E 225 (275)
|-|+++.|..|..++. ..|++=++|+++|++
T Consensus 37 R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~ 70 (99)
T cd04765 37 RYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKE 70 (99)
T ss_pred eeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 3466666666655553 467777777766664
No 71
>COG2704 DcuB Anaerobic C4-dicarboxylate transporter [General function prediction only]
Probab=37.80 E-value=27 Score=35.20 Aligned_cols=39 Identities=33% Similarity=0.551 Sum_probs=31.3
Q ss_pred HHHHHhcchhhHHhhhhhhhhccccccccCCCCCCCCCchhHHHHHHHhhhhHhhhh
Q 023901 68 EVEVEEELPWIQEKALDLVEFTGSVTQAIPGPRVGQSKLPWILAVPLAYVGVSFVIA 124 (275)
Q Consensus 68 e~e~e~e~~wiqekaldlveftg~v~qaiPgPrvg~s~lPwiLAlPLAylGiTFviA 124 (275)
+-=+...++||++-+.|||+ .-||++|+.+++++ -++.+
T Consensus 311 dTf~~~h~~~iK~~~~~lv~-----------------~~PW~~AvalF~vS-~lv~S 349 (436)
T COG2704 311 DTFVSAHIDEIKAVAGELVQ-----------------TYPWLLAVALFFVS-ALVNS 349 (436)
T ss_pred HHHHHhhHHHHHHHHHHHHH-----------------cCcHHHHHHHHHHH-HHHhh
Confidence 44566789999999999986 35999999999988 55543
No 72
>PRK10072 putative transcriptional regulator; Provisional
Probab=37.76 E-value=26 Score=28.03 Aligned_cols=33 Identities=30% Similarity=0.348 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhc
Q 023901 201 LVVNLIQLRKASMLDDSQVAEILNEISRRFVREK 234 (275)
Q Consensus 201 ~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~ 234 (275)
...|+-+||+..|+|..|+|+.|. ++.+-|.+|
T Consensus 34 ~~~eik~LR~~~glTQ~elA~~lG-vS~~TVs~W 66 (96)
T PRK10072 34 SFTEFEQLRKGTGLKIDDFARVLG-VSVAMVKEW 66 (96)
T ss_pred ChHHHHHHHHHcCCCHHHHHHHhC-CCHHHHHHH
Confidence 345677778888888888888777 666666655
No 73
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=37.49 E-value=1.2e+02 Score=25.87 Aligned_cols=53 Identities=26% Similarity=0.475 Sum_probs=33.5
Q ss_pred HHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcC-CCcHHHHHH---HHHHHHhhhh
Q 023901 172 LVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASM-LDDSQVAEI---LNEISRRFVR 232 (275)
Q Consensus 172 L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~-L~d~evaei---L~E~s~Ri~~ 232 (275)
..++.|.+..|+ +|++=.|+| +-.++-+|+++.- ..|.++.+- +.+++++||+
T Consensus 59 ~~~~~gls~~e~--~~~~~~l~e------a~~~i~~i~~~~~~i~~~~~~~~~~~~~~~~~~I~~ 115 (199)
T PF10112_consen 59 FLKEAGLSDREY--EYIREILEE------AKEKIRRIEKAIKRIRDLEMIEKVSRIEKIARRIFK 115 (199)
T ss_pred HhhhcCCChhHH--HHHHHHHHH------HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence 456778888886 678777775 4466666666543 444454444 4556777765
No 74
>PHA00739 V3 structural protein VP3
Probab=37.24 E-value=27 Score=28.78 Aligned_cols=35 Identities=34% Similarity=0.609 Sum_probs=27.4
Q ss_pred ccccccc--cCCC-CCCCCCchhHHHHHHHhhhhHhhh
Q 023901 89 TGSVTQA--IPGP-RVGQSKLPWILAVPLAYVGVSFVI 123 (275)
Q Consensus 89 tg~v~qa--iPgP-rvg~s~lPwiLAlPLAylGiTFvi 123 (275)
+|++||. +|.| -||+|..|..--+|++|+=+-.+.
T Consensus 43 sgt~ttssfv~np~Yvgssnat~~sLVPlFYllVlIiV 80 (92)
T PHA00739 43 SGTVTTSSFVSNPQYVGSSNATLVSLVPLFYLLVLIIV 80 (92)
T ss_pred eeeEEeeccccCcceecCCCCchHhHHHHHHHHHHHHh
Confidence 5666654 5888 599999999999999998754443
No 75
>PHA01976 helix-turn-helix protein
Probab=37.20 E-value=24 Score=24.44 Aligned_cols=29 Identities=14% Similarity=0.312 Sum_probs=20.6
Q ss_pred HHHHHHhhcCCCcHHHHHHHHHHHHhhhhh
Q 023901 204 NLIQLRKASMLDDSQVAEILNEISRRFVRE 233 (275)
Q Consensus 204 DLi~Lr~as~L~d~evaeiL~E~s~Ri~~~ 233 (275)
-|.++|+..|||-.|+|+.+. +++.-+.+
T Consensus 6 rl~~~R~~~glt~~~lA~~~g-vs~~~v~~ 34 (67)
T PHA01976 6 QLIKARNARAWSAPELSRRAG-VRHSLIYD 34 (67)
T ss_pred HHHHHHHHcCCCHHHHHHHhC-CCHHHHHH
Confidence 466788888888888888876 44444443
No 76
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=37.19 E-value=1.8e+02 Score=29.34 Aligned_cols=61 Identities=13% Similarity=0.187 Sum_probs=48.0
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhc-CCCCChHHHHHHH
Q 023901 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALN-EKPFNPDLVVNLI 206 (275)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei---~RKYirY~Ln-Er~F~~d~VaDLi 206 (275)
...+.+.|...+.+.+-.++..++..|.+.++-|+-++ +.|.+-|.-. .+.-+.+.|.+++
T Consensus 189 ~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~GslR~al~~Ldkai~~~~~~~~~It~~~V~~ll 253 (507)
T PRK06645 189 FEEIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSILDQAASMSAKSDNIISPQVINQML 253 (507)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhhccCCCCcCHHHHHHHH
Confidence 45678888888888888899999999999999998877 5677777653 3357777776664
No 77
>PRK14137 recX recombination regulator RecX; Provisional
Probab=37.17 E-value=45 Score=29.58 Aligned_cols=65 Identities=23% Similarity=0.355 Sum_probs=43.9
Q ss_pred HHHHhcCCCCChHHHHHHHH-HHhhcCCCcHHHHHHHHHHHHhhhhhcCCeeeeccccchhhhhhHHHHHHH
Q 023901 188 IRYALNEKPFNPDLVVNLIQ-LRKASMLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRKLAVQAL 258 (275)
Q Consensus 188 irY~LnEr~F~~d~VaDLi~-Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a~~aL 258 (275)
|+-.|.++.|+++.|+.+|+ |+.-=-|+|...|+..+ .-+.|||..+ ..-+.++|+...+.-++|
T Consensus 60 Lr~KL~~kg~~~e~Ie~vI~rL~e~gyLDD~rfAe~~~-----~~k~~Gp~rI-~~eL~qKGI~~~lI~~al 125 (195)
T PRK14137 60 LRAKLERRSEDEALVTEVLERVQELGYQDDAQVARAEN-----SRRGVGALRV-RQTLRRRGVEETLIEETL 125 (195)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHH-----HhcCchHHHH-HHHHHHcCCCHHHHHHHH
Confidence 33356778999999999886 55555579999998742 1256888555 334567777766655444
No 78
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=36.87 E-value=42 Score=28.09 Aligned_cols=48 Identities=25% Similarity=0.382 Sum_probs=36.4
Q ss_pred ccCCCCCCCCCchhHHHHHHHhhhhHhhhhhh---hhhhh-cCChhhhhhhh
Q 023901 95 AIPGPRVGQSKLPWILAVPLAYVGVSFVIAFV---KTVKK-FNSPKFKRKKL 142 (275)
Q Consensus 95 aiPgPrvg~s~lPwiLAlPLAylGiTFviA~v---RTvrK-~tSPraKRkR~ 142 (275)
-.|+|.-|+-+.|.+..+-++-+.++++|++. .+++| +.|=|++|-..
T Consensus 6 ~~~~~~~~g~sW~~LVGVv~~al~~SlLIalaaKC~~~~k~~~SY~H~rL~e 57 (102)
T PF15176_consen 6 NAPGPGEGGRSWPFLVGVVVTALVTSLLIALAAKCPVWYKYLASYRHHRLPE 57 (102)
T ss_pred cCCCCCCCCcccHhHHHHHHHHHHHHHHHHHHHHhHHHHHHHhccccccCCc
Confidence 46899999999999999999999999999864 23333 45666665443
No 79
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=36.85 E-value=69 Score=28.51 Aligned_cols=67 Identities=24% Similarity=0.337 Sum_probs=42.0
Q ss_pred hCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhh----------cCCCcHHHHHHHHHHHHhhhhhcCCeeeecccc-
Q 023901 176 TGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKA----------SMLDDSQVAEILNEISRRFVREKGPVVMNMSGY- 244 (275)
Q Consensus 176 TGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~a----------s~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~- 244 (275)
..|+.++|||+ -+++|+||.+.|.+.++.- +.++=+++-+++++++ +-|- .++++
T Consensus 71 ~~y~l~~i~r~------a~~~vp~d~L~~~L~~~G~~ae~~~~~i~T~a~~eev~~l~~~Ls----e~~~----e~~~~~ 136 (190)
T PF09840_consen 71 YRYSLDDIFRE------AGYPVPPDLLVDALKLLGYKAEYREDVIKTDAPLEEVVELAERLS----EIYK----ELRFQP 136 (190)
T ss_pred eEEcHHHHHHH------cCCCCCHHHHHHHHHhCCCeeEEeCCeEEecCCHHHHHHHHHHHH----HHHH----HHhcCc
Confidence 45788899885 4599999999999998642 2333444444444444 4332 45555
Q ss_pred -chhhhhhHHHHHH
Q 023901 245 -SEKGFKRKLAVQA 257 (275)
Q Consensus 245 -Te~G~kRK~a~~a 257 (275)
|.+ .||=+++-+
T Consensus 137 ~~~~-aK~vi~~~s 149 (190)
T PF09840_consen 137 LGTK-AKRVIAAVS 149 (190)
T ss_pred cCHH-HHHHHHHHH
Confidence 666 555554433
No 80
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=36.26 E-value=74 Score=30.02 Aligned_cols=57 Identities=18% Similarity=0.312 Sum_probs=46.0
Q ss_pred HHHHHhCCChHHH--HHHHHHHHhcCC---CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 023901 171 GLVQKTGFSMEDV--LRKYIRYALNEK---PFNPDLVVNLIQLRKASMLDDSQVAEILNEIS 227 (275)
Q Consensus 171 ~L~~KTGFs~~Ei--~RKYirY~LnEr---~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s 227 (275)
.=++.|||...|| |||-|...+-++ ...-++..|++-+++.-+|..+++.+.|..--
T Consensus 86 ~SkmaT~f~~nEielfrkalE~im~sed~~~asst~~~~~vlq~k~k~L~ks~iE~lLqkf~ 147 (235)
T KOG4718|consen 86 DSKMATGFTANEIELFRKALEKIMSSEDCHIASSTAYNDIVLQAKSKPLKKSRIEELLQKFI 147 (235)
T ss_pred hHHhcCCCCHHHHHHHHHHHHHHHhhhHhhhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence 4578999999975 999998888772 22346788999999999999999999987543
No 81
>PRK07668 hypothetical protein; Validated
Probab=36.07 E-value=53 Score=30.68 Aligned_cols=45 Identities=13% Similarity=0.327 Sum_probs=33.1
Q ss_pred ChHHHHHH-HHHHhhcCCCcHHHHHHHHHHHHhhhh--hcCCeeeeccc
Q 023901 198 NPDLVVNL-IQLRKASMLDDSQVAEILNEISRRFVR--EKGPVVMNMSG 243 (275)
Q Consensus 198 ~~d~VaDL-i~Lr~as~L~d~evaeiL~E~s~Ri~~--~~G~vmmn~~G 243 (275)
|+|.+.|| .+| .+.|++|+|+.|+|+|+-..+.+ +.|-=.-|+-|
T Consensus 6 Neefl~~L~~yL-~~~glseeeieeiL~Ei~~hLlEgQk~GkTA~~IfG 53 (254)
T PRK07668 6 GRKFLDDTRVYL-IAKGIKEEDIESFLEDAELHLIEGEKDGKTVEDIFG 53 (254)
T ss_pred HHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHHHHHcCCcHHHHhC
Confidence 56778888 456 45689999999999999998885 34444444444
No 82
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=36.05 E-value=63 Score=25.69 Aligned_cols=54 Identities=17% Similarity=0.223 Sum_probs=40.8
Q ss_pred ChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCee
Q 023901 179 SMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVV 238 (275)
Q Consensus 179 s~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vm 238 (275)
....+||--+|.+-.=+|-+.+.+| .|+|.+.+||+.+|....---|++-|.||
T Consensus 21 ~~~~L~r~LLr~LA~G~PVt~~~LA------~a~g~~~e~v~~~L~~~p~tEyD~~GrIV 74 (77)
T PF12324_consen 21 GFAWLLRPLLRLLAKGQPVTVEQLA------AALGWPVEEVRAALAAMPDTEYDDQGRIV 74 (77)
T ss_dssp THHHHHHHHHHHHTTTS-B-HHHHH------HHHT--HHHHHHHHHH-TTSEEETTSEEE
T ss_pred ccHHHHHHHHHHHHcCCCcCHHHHH------HHHCCCHHHHHHHHHhCCCceEcCCCCee
Confidence 4677899999998888888776655 58999999999999998877788888876
No 83
>PRK04195 replication factor C large subunit; Provisional
Probab=35.96 E-value=2e+02 Score=27.84 Aligned_cols=55 Identities=15% Similarity=0.052 Sum_probs=40.6
Q ss_pred hHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 023901 167 PALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILN 224 (275)
Q Consensus 167 gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~ 224 (275)
..+..|..+++-|...+-.-|+.|+.-=-.=| ...-++|-..++||++||.-++.
T Consensus 350 ~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~ 404 (482)
T PRK04195 350 SIAKKIAEKLHTSKRKVRREVLPFLSIIFKHN---PELAARLAAFLELTEEEIEFLTG 404 (482)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC---HHHHHHHHHHcCCCHHHHHHHhC
Confidence 34568999999999999998888764211112 45566777899999999987764
No 84
>TIGR01167 LPXTG_anchor LPXTG-motif cell wall anchor domain. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region.
Probab=35.81 E-value=47 Score=20.81 Aligned_cols=21 Identities=29% Similarity=0.559 Sum_probs=16.8
Q ss_pred CCCCCCCchhHHHHHHHhhhh
Q 023901 99 PRVGQSKLPWILAVPLAYVGV 119 (275)
Q Consensus 99 Prvg~s~lPwiLAlPLAylGi 119 (275)
|.-|+....|+..+.++.+++
T Consensus 3 P~TG~~~~~~~~~~G~~l~~~ 23 (34)
T TIGR01167 3 PKTGESGNSLLLLLGLLLLGL 23 (34)
T ss_pred CCCCCcccHHHHHHHHHHHHH
Confidence 677888889998888866664
No 85
>PRK14530 adenylate kinase; Provisional
Probab=35.26 E-value=1.3e+02 Score=25.49 Aligned_cols=63 Identities=19% Similarity=0.241 Sum_probs=39.4
Q ss_pred CCCCchHHHHHHHHhCC---ChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023901 162 DAVNPPALKGLVQKTGF---SMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (275)
Q Consensus 162 da~~~gvLk~L~~KTGF---s~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (275)
.+...-.-+.|.++.|| ++.+++|+++..-.++..-.-+...+. ++.+....|+.+.++|.+.
T Consensus 13 GsGKsT~~~~La~~~~~~~i~~g~~lr~~~~~~~~~~~~~~~~~~~~--~~~g~~~~d~~~~~~l~~~ 78 (215)
T PRK14530 13 GAGKGTQSSNLAEEFGVEHVTTGDALRANKQMDISDMDTEYDTPGEY--MDAGELVPDAVVNEIVEEA 78 (215)
T ss_pred CCCHHHHHHHHHHHhCCeEEeccHHHHHhccCCcccccchHHHHHHH--HHcCCCCCHHHHHHHHHHH
Confidence 34445567889999999 999999998744333332222333442 3455556776666666554
No 86
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=34.25 E-value=82 Score=20.83 Aligned_cols=38 Identities=13% Similarity=0.179 Sum_probs=23.4
Q ss_pred chhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH
Q 023901 145 KNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV 183 (275)
Q Consensus 145 KNa~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei 183 (275)
....-..-|.++|..+. -.+...+..|...+|-+...|
T Consensus 7 ~~~~~~~~Le~~f~~~~-~P~~~~~~~la~~~~l~~~qV 44 (59)
T cd00086 7 FTPEQLEELEKEFEKNP-YPSREEREELAKELGLTERQV 44 (59)
T ss_pred CCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHCcCHHHH
Confidence 33444556667776643 456666777777777666555
No 87
>KOG1577 consensus Aldo/keto reductase family proteins [General function prediction only]
Probab=34.23 E-value=1.2e+02 Score=29.29 Aligned_cols=64 Identities=22% Similarity=0.358 Sum_probs=52.8
Q ss_pred CCCCchHHHHHHHHhCCChHHHHHHHHHHHhcC------CCCChHHHHHHHHHHhhcCCCcHHHHHHH-HHHHHh
Q 023901 162 DAVNPPALKGLVQKTGFSMEDVLRKYIRYALNE------KPFNPDLVVNLIQLRKASMLDDSQVAEIL-NEISRR 229 (275)
Q Consensus 162 da~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnE------r~F~~d~VaDLi~Lr~as~L~d~evaeiL-~E~s~R 229 (275)
+-+..+.++.|.+|.|=|-..|+ |||++.- |-+||+-+.+=++.-. ..||++|++.+- ...-.|
T Consensus 218 ~ll~~~~l~~iA~K~~kt~aQIl---Lrw~~q~g~~vipKS~~~~Ri~eN~~vfd-f~Lt~ed~~~i~~~~~~~r 288 (300)
T KOG1577|consen 218 DLLEDPVLKEIAKKYNKTPAQIL---LRWALQRGVSVIPKSSNPERIKENFKVFD-FELTEEDMKKLDSLNSNER 288 (300)
T ss_pred ccccCHHHHHHHHHhCCCHHHHH---HHHHHhCCcEEEeccCCHHHHHHHHhhcc-ccCCHHHHHHHhhccccce
Confidence 44778999999999999999998 7888876 6899999888888655 889999999987 333343
No 88
>PHA02591 hypothetical protein; Provisional
Probab=33.66 E-value=35 Score=27.74 Aligned_cols=36 Identities=19% Similarity=0.230 Sum_probs=27.1
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhc
Q 023901 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREK 234 (275)
Q Consensus 198 ~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~ 234 (275)
+.|.+..|.+-=...|+|-++||+.|. ++++.|++|
T Consensus 44 ~~dd~~~vA~eL~eqGlSqeqIA~~LG-VsqetVrKY 79 (83)
T PHA02591 44 SEDDLISVTHELARKGFTVEKIASLLG-VSVRKVRRY 79 (83)
T ss_pred ccchHHHHHHHHHHcCCCHHHHHHHhC-CCHHHHHHH
Confidence 456666777766788999999999874 667777766
No 89
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=33.17 E-value=2.3e+02 Score=22.25 Aligned_cols=13 Identities=15% Similarity=0.245 Sum_probs=5.8
Q ss_pred cCCCcHHHHHHHH
Q 023901 212 SMLDDSQVAEILN 224 (275)
Q Consensus 212 s~L~d~evaeiL~ 224 (275)
+|++=+||+++|+
T Consensus 56 ~G~sl~eI~~~l~ 68 (123)
T cd04770 56 LGFSLAEIRELLS 68 (123)
T ss_pred CCCCHHHHHHHHH
Confidence 3444444444443
No 90
>COG4860 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.63 E-value=76 Score=28.58 Aligned_cols=40 Identities=23% Similarity=0.424 Sum_probs=31.0
Q ss_pred HHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCeeeecc
Q 023901 202 VVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMNMS 242 (275)
Q Consensus 202 VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~ 242 (275)
+.||-..=-|.-|+|+||.|...|+ .+++++=+++|.|+.
T Consensus 96 l~dL~dii~~~f~sdeev~ey~~ei-~~l~e~g~ts~~~vt 135 (170)
T COG4860 96 LSDLADIIYAAFLSDEEVKEYEDEI-KALMEEGNTSFLDVT 135 (170)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHH-HHHHHcCCceEeehh
Confidence 3444444456779999999999998 567888899998865
No 91
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=32.22 E-value=60 Score=25.44 Aligned_cols=54 Identities=19% Similarity=0.230 Sum_probs=41.1
Q ss_pred CChHHHHHH-HHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhh
Q 023901 178 FSMEDVLRK-YIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFV 231 (275)
Q Consensus 178 Fs~~Ei~RK-YirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~ 231 (275)
|+.+||.+= .|+.+|++.-|+.+.+..++..........+++-..|+++-.-+.
T Consensus 39 Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 93 (99)
T cd04765 39 YRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDGAAAIREEEAEERLPSIRAELL 93 (99)
T ss_pred eCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhccccccchhhHHHHHHHHHHHHH
Confidence 777777653 466677888999999999998877777777788888877755443
No 92
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=31.87 E-value=72 Score=29.50 Aligned_cols=40 Identities=13% Similarity=0.346 Sum_probs=36.1
Q ss_pred chhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHH
Q 023901 145 KNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVL 184 (275)
Q Consensus 145 KNa~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~ 184 (275)
.+.++-+--..||..|++=.+..+|-.|....|.+.+|+-
T Consensus 119 ~~~~~~~lf~AyF~eg~nI~D~dVL~diA~~~GLD~~~~~ 158 (225)
T COG2761 119 QDRFLEALFEAYFEEGRNIGDEDVLADIAEEVGLDREEFK 158 (225)
T ss_pred HHHHHHHHHHHHhccCCCCCcHHHHHHHHHHhCCCHHHHH
Confidence 4778888889999999999999999999999999998864
No 93
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=31.82 E-value=57 Score=28.85 Aligned_cols=31 Identities=23% Similarity=0.160 Sum_probs=26.0
Q ss_pred CCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023901 196 PFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (275)
Q Consensus 196 ~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (275)
..++|.|.|+|-==.--|++.+||+-+|++.
T Consensus 24 ~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~ 54 (148)
T PTZ00072 24 KLSSSEVEDQICKLAKKGLTPSQIGVILRDS 54 (148)
T ss_pred cCCHHHHHHHHHHHHHCCCCHhHhhhhhhhc
Confidence 4688889888866666799999999999975
No 94
>KOG1869 consensus Splicing coactivator SRm160/300, subunit SRm300 [RNA processing and modification]
Probab=31.80 E-value=87 Score=31.72 Aligned_cols=52 Identities=23% Similarity=0.095 Sum_probs=37.7
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhcCCCCCh---------------------HHHHHHHHHHhhcCCCcHHHH
Q 023901 169 LKGLVQKTGFSMEDVLRKYIRYALNEKPFNP---------------------DLVVNLIQLRKASMLDDSQVA 220 (275)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~---------------------d~VaDLi~Lr~as~L~d~eva 220 (275)
|+.+...-|++-.||.+|---|-+|+-.=++ -.+..+.|+|.|+||.|.+|.
T Consensus 73 ~ee~lleqg~seeei~~k~~e~rknl~~~a~~~nE~~~~qe~S~teThqlara~eeq~e~~raAlgL~e~qv~ 145 (425)
T KOG1869|consen 73 LEESLLEQGLSEEEILSKVQEDRKNLLLRAKLTNEEQEDQEMSSTETHQLARATEEQHEHERAALGLKELQVQ 145 (425)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhHHhhccCCccccccchhhhhhhHHHHHHHHHHHHHHHHHhCcchhhcc
Confidence 4455666799999999987777655432222 246678999999999999874
No 95
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=31.78 E-value=2.3e+02 Score=22.57 Aligned_cols=9 Identities=11% Similarity=0.519 Sum_probs=4.4
Q ss_pred HhCCChHHH
Q 023901 175 KTGFSMEDV 183 (275)
Q Consensus 175 KTGFs~~Ei 183 (275)
+.||+..||
T Consensus 55 ~~G~sL~eI 63 (127)
T cd04784 55 SLDMSLDEI 63 (127)
T ss_pred HcCCCHHHH
Confidence 445555553
No 96
>PRK03892 ribonuclease P protein component 3; Provisional
Probab=31.70 E-value=1.1e+02 Score=28.55 Aligned_cols=65 Identities=14% Similarity=0.133 Sum_probs=50.8
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhcCCC--------------CChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhh
Q 023901 169 LKGLVQKTGFSMEDVLRKYIRYALNEKP--------------FNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVRE 233 (275)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~LnEr~--------------F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~ 233 (275)
|+.|-+..|+...-+++.|-...-=-++ |+.-..-||++|=...|++.+|+.+.|.+..+.|.++
T Consensus 137 L~plL~~~G~~Rar~L~~~r~~l~L~rKYd~P~VISS~A~s~~~lRsPRdl~aL~~~iGme~~ea~~~Ls~~p~~i~~~ 215 (216)
T PRK03892 137 LSPLLRANPYERANILRFMMKAWQLVNKYKVPRFITSSAESKWEVRGPRDLMSLGINIGMEIPQAKASLSFYPRIILKR 215 (216)
T ss_pred cHHHHhhCchhHHHHHHHHHHHHHHHHHcCCCEEEecCcchhccCCCHHHHHHHHHHhCCCHHHHHHHHHHhHHHHhhc
Confidence 4455667888888888777665443344 4556778999999999999999999999999888764
No 97
>PF13934 ELYS: Nuclear pore complex assembly
Probab=31.45 E-value=2.9e+02 Score=24.54 Aligned_cols=105 Identities=14% Similarity=0.141 Sum_probs=66.4
Q ss_pred cccccCCCCCCCCCchhHHHHHHHhhhhHhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHH
Q 023901 92 VTQAIPGPRVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKG 171 (275)
Q Consensus 92 v~qaiPgPrvg~s~lPwiLAlPLAylGiTFviA~vRTvrK~tSPraKRkR~VnKNa~LvkSLdeyfp~gRda~~~gvLk~ 171 (275)
+..-++.|++.+.--+||+.+=+..-.-..+++++|+++-.-+....-. .=..+.-+.++-|=|.
T Consensus 97 A~~~L~~ps~~~~~~~~Il~~L~~~~~~~lAL~y~~~~~p~l~s~~~~~--~~~~~La~~~v~EAf~------------- 161 (226)
T PF13934_consen 97 ALELLSHPSLIPWFPDKILQALLRRGDPKLALRYLRAVGPPLSSPEALT--LYFVALANGLVTEAFS------------- 161 (226)
T ss_pred HHHHhCCCCCCcccHHHHHHHHHHCCChhHHHHHHHhcCCCCCCHHHHH--HHHHHHHcCCHHHHHH-------------
Confidence 3445689988877777999998888888999999999877655441111 0011122222333222
Q ss_pred HHHHhCCCh---HHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHH
Q 023901 172 LVQKTGFSM---EDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQ 218 (275)
Q Consensus 172 L~~KTGFs~---~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~e 218 (275)
-...|.. .+.+.+-+.+.+++.+ ..+.+.+|+.| -|+++|
T Consensus 162 --~~R~~~~~~~~~l~e~l~~~~~~~~~-~~~~~~~Ll~L----Pl~~~E 204 (226)
T PF13934_consen 162 --FQRSYPDELRRRLFEQLLEHCLEECA-RSGRLDELLSL----PLDEEE 204 (226)
T ss_pred --HHHhCchhhhHHHHHHHHHHHHHHhh-hhhHHHHHHhC----CCChHH
Confidence 2222322 4588999999998887 56777777764 455554
No 98
>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional
Probab=31.42 E-value=2e+02 Score=31.93 Aligned_cols=104 Identities=21% Similarity=0.364 Sum_probs=65.5
Q ss_pred hhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHH---hCCChHHHHHHHHHHHhcCCCCChHHHHHHHH-HHhhcCCC--
Q 023901 142 LVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQK---TGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQ-LRKASMLD-- 215 (275)
Q Consensus 142 ~VnKNa~LvkSLdeyfp~gRda~~~gvLk~L~~K---TGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~-Lr~as~L~-- 215 (275)
.|..|..=..-|..+..++ ..++...|++|+.+ -||+-+.+-+-|= ... |.|..||+|. .|.|.|++
T Consensus 967 ~i~~~~~~i~al~~~~~~p-~~lt~~~l~~l~~~l~~~~~~~~~l~~a~~-----~~~-~~~~~a~ii~~iR~~~~~~~l 1039 (1123)
T PRK11448 967 FVRENINQIPALQVVVNRP-RDLTRKELKELRLLLDQQGFSEASLRSAWK-----ETK-NEDIAASIIGFIRQAALGDAL 1039 (1123)
T ss_pred HHHhcccccHHHHHHHhCC-ccCCHHHHHHHHHHhhhCCCCHHHHHHHHH-----hch-hhhHHHHHHHHHHHHhcCCcC
Confidence 3444444445555555555 44888888888733 4888776655543 222 8888999996 59999998
Q ss_pred ---cHHHHHHHHHHHH------------hhhhhc--CCeeeeccccchhhhhhH
Q 023901 216 ---DSQVAEILNEISR------------RFVREK--GPVVMNMSGYSEKGFKRK 252 (275)
Q Consensus 216 ---d~evaeiL~E~s~------------Ri~~~~--G~vmmn~~G~Te~G~kRK 252 (275)
++-|..+++.+-. +..+++ ...++|.+-+...-|+++
T Consensus 1040 ~~~~~~v~~a~~~~~~~~~~t~~Q~~wl~~i~~~~~~~~~~~~~~~~~~pf~~~ 1093 (1123)
T PRK11448 1040 VPFEERVDHAMQKIYAERDWTPVQRKWLERIAKQLKEEVVLDRDAFDTGPFKRR 1093 (1123)
T ss_pred CCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhheeecHHHhccCccccc
Confidence 6778777766211 122333 567777776665545443
No 99
>PF10389 CoatB: Bacteriophage coat protein B ; InterPro: IPR008020 The major coat protein in the capsid of filamentous bacteriophage forms a helical assembly of about 7000 identical protomers, with each protomer comprised of 46 amino acids, after the cleavage of the signal peptide. Each protomer forms a slightly curved helix that combines to form a tubular structure that encapsulates the viral DNA [].; PDB: 2IFO_A.
Probab=31.38 E-value=51 Score=24.04 Aligned_cols=24 Identities=29% Similarity=0.278 Sum_probs=21.2
Q ss_pred HHHHHHHhhhhHhhhhhhhhhhhc
Q 023901 109 ILAVPLAYVGVSFVIAFVKTVKKF 132 (275)
Q Consensus 109 iLAlPLAylGiTFviA~vRTvrK~ 132 (275)
+.++..+.||+...|+.||-+||.
T Consensus 22 i~~ig~avL~v~V~i~v~kwiRra 45 (46)
T PF10389_consen 22 IATIGGAVLGVIVGIAVYKWIRRA 45 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Confidence 577888999999999999999873
No 100
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=31.29 E-value=71 Score=28.22 Aligned_cols=31 Identities=16% Similarity=0.243 Sum_probs=26.4
Q ss_pred CCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023901 196 PFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (275)
Q Consensus 196 ~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (275)
.+++|.|.++|-==.--|++.+||+-+|++.
T Consensus 27 ~~~~eeve~~I~~lakkG~~pSqIG~~LRD~ 57 (151)
T PRK08561 27 DYSPEEIEELVVELAKQGYSPSMIGIILRDQ 57 (151)
T ss_pred cCCHHHHHHHHHHHHHCCCCHHHhhhhHhhc
Confidence 4788999988876666799999999999985
No 101
>PF06595 BDV_P24: Borna disease virus P24 protein; InterPro: IPR009517 Borna disease virus (BDV) is a non-cytolytic, neurotropic RNA virus that has a broad host range in warm-blooded animals. BDV is an enveloped virus, non-segmented, negative-stranded RNA genome and has an organisation characteristic of a member of Bornaviridae in the order of Mononegavirale. This family consists of several BDV P24 (phosphoprotein 24) proteins. They are essential components of the RNA polymerase transcription and replication complex. P24 is encoded by open reading frame II (ORF-II) and undergoes high rates of mutation in humans. They bind amphoterin-HMGB1, a multifunctional protein, directly may cause deleterious effects in cellular functions by its interference with HMGB1 []. Horse and human P24 have no species-specific amino acid residues, suggesting that the two viruses related [, ]. Numerous interactions of the immune system with the central nervous system have been described. Mood and psychotic disorders, such as severe depression and schizophrenia, are both heterogeneous disorders regarding clinical symptomatology, the acuity of symptoms, the clinical course and the treatment response []. BDV p24 RNA has been detected in the peripheral blood mononuclear cells (PBMCs) of psychiatric patients with such conditions []. Some studies find a significant difference in the prevalence of BDV p24 RNA in patients with mood disorders and schizophrenia [], whilst others find no difference between patients and control groups []. Consequently, debate about the role of BDV in psychiatric diseases remains alive.
Probab=31.08 E-value=38 Score=30.96 Aligned_cols=80 Identities=21% Similarity=0.484 Sum_probs=48.1
Q ss_pred hcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhC---CChHHHHHHHHHHHhcCCCCChHHHHHHHH
Q 023901 131 KFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTG---FSMEDVLRKYIRYALNEKPFNPDLVVNLIQ 207 (275)
Q Consensus 131 K~tSPraKRkR~VnKNa~LvkSLdeyfp~gRda~~~gvLk~L~~KTG---Fs~~Ei~RKYirY~LnEr~F~~d~VaDLi~ 207 (275)
++.|| |+|.|.+|+.- -..++++.+-+. |++.+-.=.++|| .|.+|++++.+--
T Consensus 25 RSrSP---Rrrri~~~aLt-~pVe~Ll~~~kk--nPsmisD~~~~TGREqLSndeLikqLvtE----------------- 81 (201)
T PF06595_consen 25 RSRSP---RRRRIPRDALT-QPVEQLLKQLKK--NPSMISDPDQRTGREQLSNDELIKQLVTE----------------- 81 (201)
T ss_pred hcCCC---CcccCChHhhc-chHHHHHHHHhc--CCccccCCcccchHHhhchHHHHHHHHHH-----------------
Confidence 46778 33449998753 344444433221 3444444456676 4666766664432
Q ss_pred HHhhcCCCcHHHHHHHHHHHHhhhhh
Q 023901 208 LRKASMLDDSQVAEILNEISRRFVRE 233 (275)
Q Consensus 208 Lr~as~L~d~evaeiL~E~s~Ri~~~ 233 (275)
|-.-++.+-+.+...|.+++.||...
T Consensus 82 lae~~mieaE~l~~~L~~i~~r~e~g 107 (201)
T PF06595_consen 82 LAENSMIEAEGLKGSLDDIAQRMESG 107 (201)
T ss_pred HhhccchhHHHhhccHHHHHHHHHHh
Confidence 23456777788888899999998643
No 102
>PHA02902 putative IMV membrane protein; Provisional
Probab=31.05 E-value=52 Score=26.02 Aligned_cols=54 Identities=24% Similarity=0.353 Sum_probs=32.4
Q ss_pred HHHHHHHhhhhHhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcC---CCCCCchHHHHHHH
Q 023901 109 ILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKG---GDAVNPPALKGLVQ 174 (275)
Q Consensus 109 iLAlPLAylGiTFviA~vRTvrK~tSPraKRkR~VnKNa~LvkSLdeyfp~g---Rda~~~gvLk~L~~ 174 (275)
|+|+-++.+- -++||.||-+|--.||+.+-++. ++++++. +|.+.++-+|.|-+
T Consensus 8 i~~v~v~Ivc-lliya~YrR~kci~sP~~~d~~~-----------~~~l~~d~~F~D~lTpDQirAlHr 64 (70)
T PHA02902 8 ILAVIVIIFC-LLIYAAYKRYKCIPSPDDRDERF-----------GDTLEDDPLFKDSLTPDQIKALHR 64 (70)
T ss_pred HHHHHHHHHH-HHHHHHHHHhcCCCCCCCccccc-----------cccCCCCchhhccCCHHHHHHHHH
Confidence 5566555555 45666666655558888776653 4444443 46666666666543
No 103
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=31.04 E-value=56 Score=27.43 Aligned_cols=29 Identities=17% Similarity=0.200 Sum_probs=22.8
Q ss_pred HHHhhcCCCcHHHHHHH---HHHHHhhhhhcC
Q 023901 207 QLRKASMLDDSQVAEIL---NEISRRFVREKG 235 (275)
Q Consensus 207 ~Lr~as~L~d~evaeiL---~E~s~Ri~~~~G 235 (275)
.-+..-|.|++|+-+-| +|+|+.+..+|+
T Consensus 34 ~d~~~~G~sEeeii~~LG~P~~iA~~i~~~~~ 65 (181)
T PF08006_consen 34 DDAGEEGKSEEEIIAELGSPKEIAREILAEYS 65 (181)
T ss_pred HHhhhCCCCHHHHHHHcCCHHHHHHHHHHhhh
Confidence 34556788888888887 788999988876
No 104
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=30.89 E-value=1.4e+02 Score=20.28 Aligned_cols=44 Identities=30% Similarity=0.305 Sum_probs=20.1
Q ss_pred HHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHH
Q 023901 170 KGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQV 219 (275)
Q Consensus 170 k~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~ev 219 (275)
+.|.+++|.+.. .+.-.++.+.- .=-+..|.+|=++++.+-+|+
T Consensus 14 ~~La~~~gis~~-----tl~~~~~~~~~-~~~~~~l~~ia~~l~~~~~el 57 (63)
T PF13443_consen 14 KDLARKTGISRS-----TLSRILNGKPS-NPSLDTLEKIAKALNCSPEEL 57 (63)
T ss_dssp HHHHHHHT--HH-----HHHHHHTTT------HHHHHHHHHHHT--HHHC
T ss_pred HHHHHHHCcCHH-----HHHHHHhcccc-cccHHHHHHHHHHcCCCHHHH
Confidence 345555555543 44445565522 223356667777888775553
No 105
>PRK14135 recX recombination regulator RecX; Provisional
Probab=30.54 E-value=2.3e+02 Score=24.99 Aligned_cols=45 Identities=9% Similarity=0.289 Sum_probs=27.3
Q ss_pred HHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcC
Q 023901 186 KYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKG 235 (275)
Q Consensus 186 KYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G 235 (275)
.-|++.|..+.|+++.+.+.+.- +++.+--+.++..+++.++.+.
T Consensus 126 ~~I~~kL~~kGi~~~~Ie~~l~~-----l~~~~~~d~a~~~~~k~~~~~~ 170 (263)
T PRK14135 126 RVIKQKLLQKGIEDEIIEEALSE-----YTEEDQIEVAQKLAEKLLKKYQ 170 (263)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHh-----CChhhHHHHHHHHHHHHHHHhc
Confidence 34566777788888888877752 3443333444555666666554
No 106
>PRK09726 antitoxin HipB; Provisional
Probab=30.53 E-value=65 Score=24.26 Aligned_cols=38 Identities=16% Similarity=0.315 Sum_probs=27.6
Q ss_pred CCCChHHHH-HHHHHHhhcCCCcHHHHHHHHHHHHhhhhh
Q 023901 195 KPFNPDLVV-NLIQLRKASMLDDSQVAEILNEISRRFVRE 233 (275)
Q Consensus 195 r~F~~d~Va-DLi~Lr~as~L~d~evaeiL~E~s~Ri~~~ 233 (275)
..+++..+. -|-.+|+..|+|.+|+|+.+. +++.-+.+
T Consensus 6 ~~~~~~~l~~~lk~~R~~~gltq~elA~~~g-vs~~tis~ 44 (88)
T PRK09726 6 KIYSPTQLANAMKLVRQQNGWTQSELAKKIG-IKQATISN 44 (88)
T ss_pred cccCHHHHHHHHHHHHHHcCCCHHHHHHHHC-cCHHHHHH
Confidence 566777765 455789999999999999887 55555444
No 107
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=30.52 E-value=1.4e+02 Score=23.63 Aligned_cols=72 Identities=11% Similarity=0.152 Sum_probs=37.6
Q ss_pred hhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHH---HhhcCCCcHHHHHHHHHHH
Q 023901 151 KTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQL---RKASMLDDSQVAEILNEIS 227 (275)
Q Consensus 151 kSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~L---r~as~L~d~evaeiL~E~s 227 (275)
+.|..+|+.--+.+.....+.|.++-|+|-.||-+-=. +.+=|.|.+-.++.. |.+.+=|-..+.++|+.+.
T Consensus 4 ~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~~i~~-----~~~~~~eq~~qmL~~W~~~~G~~At~~~L~~aL~~~~ 78 (96)
T cd08315 4 ETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEIDVAKA-----NERVTREQLYQMLLTWVNKTGRKASVNTLLDALEAIG 78 (96)
T ss_pred hHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHHHHHH-----HCCCCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHcc
Confidence 45666666666666666666777777777766654211 112234555544432 3333334444555555543
No 108
>PRK14532 adenylate kinase; Provisional
Probab=30.18 E-value=1.8e+02 Score=23.62 Aligned_cols=70 Identities=20% Similarity=0.309 Sum_probs=39.1
Q ss_pred CCchHHHHHHHHhCC---ChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCeeee
Q 023901 164 VNPPALKGLVQKTGF---SMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMN 240 (275)
Q Consensus 164 ~~~gvLk~L~~KTGF---s~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn 240 (275)
...-.-+.|.++.|| |+.|++|+.++- +-+.. ..+.+.++ ++-...|+-+.+++.+.-..+- ..|.+++|
T Consensus 12 GKsT~a~~la~~~g~~~is~~d~lr~~~~~---~~~~~-~~~~~~~~--~g~~~~~~~~~~~~~~~~~~~~-~~~g~vld 84 (188)
T PRK14532 12 GKGTQAKRLVEERGMVQLSTGDMLRAAIAS---GSELG-QRVKGIMD--RGELVSDEIVIALIEERLPEAE-AAGGAIFD 84 (188)
T ss_pred CHHHHHHHHHHHcCCeEEeCcHHHHHHHHc---CCHHH-HHHHHHHH--CCCccCHHHHHHHHHHHHhCcC-ccCcEEEe
Confidence 334455678888887 556899998741 11111 12444444 3444567667776666554442 33446666
No 109
>TIGR00694 thiM hydroxyethylthiazole kinase. This model represents the hydoxyethylthiazole kinase, ThiM, of a number of bacteria, and C-terminal domains of bifunctional thiamine biosynthesis proteins of Saccharomyces cerevisiae and Schizosaccharomyces pombe, in which the N-terminal domain corresponds to the bacterial thiamine-phosphate pyrophosphorylase (EC 2.5.1.3), ThiE.
Probab=29.74 E-value=2e+02 Score=25.46 Aligned_cols=63 Identities=17% Similarity=0.153 Sum_probs=42.2
Q ss_pred CChHHHHHHHHHHhh----cCCCcHHHHHHHHHHHHhhhhhcCCeeeeccccchhhhhhHHHHHHHHH
Q 023901 197 FNPDLVVNLIQLRKA----SMLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRKLAVQALFG 260 (275)
Q Consensus 197 F~~d~VaDLi~Lr~a----s~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a~~aLF~ 260 (275)
-+++.|.|++..-.| .|+-.++..+.+....+..-+..-|||+|--|..-+|... .....|+.
T Consensus 38 ~~~~e~~~~~~~~~al~ik~G~l~~~~~~~i~~~~~~~~~~~~pvVlDPV~~~~s~~r~-~~~~~Ll~ 104 (249)
T TIGR00694 38 EAEEEVAELAKIAGALVINIGTLDKESIEAMIAAGKSANELGVPVVLDPVGVGATKFRT-ETALELLS 104 (249)
T ss_pred CCHHHHHHHHHHcCceEEeCCCCCHHHHHHHHHHHHHHHhcCCCEEEcccccccchhHH-HHHHHHHh
Confidence 367788888755444 3544557788887777655444568999999999998744 33344443
No 110
>COG4858 Uncharacterized membrane-bound protein conserved in bacteria [Function unknown]
Probab=29.64 E-value=91 Score=29.20 Aligned_cols=23 Identities=22% Similarity=0.336 Sum_probs=20.6
Q ss_pred hcCCCcHHHHHHHHHHHHhhhhh
Q 023901 211 ASMLDDSQVAEILNEISRRFVRE 233 (275)
Q Consensus 211 as~L~d~evaeiL~E~s~Ri~~~ 233 (275)
.-|-||+|+.+||+|+-..|.++
T Consensus 33 ~~gksdeeik~Il~e~ipqIlee 55 (226)
T COG4858 33 GDGKSDEEIKIILEEMIPQILEE 55 (226)
T ss_pred hcCCCHHHHHHHHHHHHHHHHHh
Confidence 46899999999999999999874
No 111
>PF09524 Phg_2220_C: Conserved phage C-terminus (Phg_2220_C); InterPro: IPR011741 This entry is represented by the C-terminal domain of Bacteriophage r1t, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Probab=29.62 E-value=1.4e+02 Score=23.30 Aligned_cols=55 Identities=25% Similarity=0.341 Sum_probs=45.0
Q ss_pred HHHHHHHhC--CC-hHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 023901 169 LKGLVQKTG--FS-MEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILN 224 (275)
Q Consensus 169 Lk~L~~KTG--Fs-~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~ 224 (275)
+.-|-+||| |. ..+--+++|+=-|+| -|+.|..--+|..+.+-=+.|.++..-||
T Consensus 2 I~yLN~~tg~~f~~~~~~~~~~I~aRl~e-G~t~edf~~VID~k~~~W~~~~~m~~YLR 59 (74)
T PF09524_consen 2 IDYLNKKTGKKFKSNTKSTKKLIKARLNE-GYTLEDFKKVIDNKVAEWKGDPKMEKYLR 59 (74)
T ss_pred HHHHHHHhcCccCCCcHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHCCCHHHHHhcC
Confidence 344556666 66 678889999999999 89999999999999998888888877665
No 112
>PF00248 Aldo_ket_red: Aldo/keto reductase family; InterPro: IPR023210 The aldo-keto reductase family includes a number of related monomeric NADPH-dependent oxidoreductases, such as aldehyde reductase, aldose reductase, prostaglandin F synthase, xylose reductase, rho crystallin, and many others []. All possess a similar structure, with a beta-alpha-beta fold characteristic of nucleotide binding proteins []. The fold comprises a parallel beta-8/alpha-8-barrel, which contains a novel NADP-binding motif. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the beta sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones []. Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases []. Some proteins of this entry contain a K+ ion channel beta chain regulatory domain; these are reported to have oxidoreductase activity []. This entry represents the NADP-dependent oxidoreductase domain found in these proteins.; PDB: 1C9W_A 4F40_B 1VBJ_A 1XGD_A 1X97_A 2ACS_A 1EF3_A 2ACU_A 1PWM_A 2NVD_A ....
Probab=29.22 E-value=96 Score=26.61 Aligned_cols=54 Identities=22% Similarity=0.347 Sum_probs=40.2
Q ss_pred CchHHHHHHHHhCCChHHHHHHHHHHHhcCC--------CCChHHHHHHHHHHhhcCCCcHHHHHH
Q 023901 165 NPPALKGLVQKTGFSMEDVLRKYIRYALNEK--------PFNPDLVVNLIQLRKASMLDDSQVAEI 222 (275)
Q Consensus 165 ~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr--------~F~~d~VaDLi~Lr~as~L~d~evaei 222 (275)
....++.+..+.|.+..++. |+|+|... .-+++-|.+.++--.. -||++|+++|
T Consensus 217 ~~~~l~~~a~~~g~s~~q~a---l~~~l~~~~~~~~i~g~~~~~~l~en~~a~~~-~L~~~~~~~i 278 (283)
T PF00248_consen 217 LADALRELAEEHGVSPAQLA---LRWVLSHPGVASVIVGASSPEHLEENLAALDF-PLTEEELAEI 278 (283)
T ss_dssp GHHHHHHHHHHHTSSHHHHH---HHHHHTSHTTEEEEEB-SSHHHHHHHHGGSSS-G--HHHHHHH
T ss_pred hhhhhhhhhhhcccccchhh---hhhhhhccccccccCCCCCHHHHHHHHHHhCC-CCCHHHHHHH
Confidence 35689999999999999987 67777532 3578888888876644 8999999876
No 113
>PF11169 DUF2956: Protein of unknown function (DUF2956); InterPro: IPR021339 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=29.19 E-value=51 Score=27.69 Aligned_cols=22 Identities=32% Similarity=0.578 Sum_probs=15.8
Q ss_pred cCCCCCCCCCchhHHHHHHHhhh
Q 023901 96 IPGPRVGQSKLPWILAVPLAYVG 118 (275)
Q Consensus 96 iPgPrvg~s~lPwiLAlPLAylG 118 (275)
...+...++.|||+| |-|-.+|
T Consensus 75 ~~~~~~~~~~LPW~L-L~lSW~g 96 (103)
T PF11169_consen 75 EISSQSRSSWLPWGL-LVLSWIG 96 (103)
T ss_pred cccccccccchhHHH-HHHHHHH
Confidence 345677889999996 4566666
No 114
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=29.19 E-value=42 Score=25.70 Aligned_cols=54 Identities=9% Similarity=-0.034 Sum_probs=42.5
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCee
Q 023901 185 RKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVV 238 (275)
Q Consensus 185 RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vm 238 (275)
.+-++..+++..+-..+.+|=-++=...|||++|...++.---.+++.-=|+.+
T Consensus 6 ~~~~~~~~~~~~~re~f~~dp~a~~~~~~Lt~eE~~al~~rD~~~L~~lG~~~~ 59 (77)
T cd07321 6 EKLLEQLLVKPEVKERFKADPEAVLAEYGLTPEEKAALLARDVGALYVLGVNPM 59 (77)
T ss_pred HHHHHHHhcCHHHHHHHHhCHHHHHHHcCCCHHHHHHHHcCCHHHHHHcCCCHH
Confidence 677888888887878888888888888999999999888776667666555443
No 115
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=29.18 E-value=1.8e+02 Score=23.90 Aligned_cols=39 Identities=13% Similarity=0.306 Sum_probs=28.8
Q ss_pred hHHhhHHHHHhcCC----------CCCCchHHHHHHHHhCCChHHHHHH
Q 023901 148 MVCKTIDELFQKGG----------DAVNPPALKGLVQKTGFSMEDVLRK 186 (275)
Q Consensus 148 ~LvkSLdeyfp~gR----------da~~~gvLk~L~~KTGFs~~Ei~RK 186 (275)
.-|+-..++|.+.+ +..+...|+.+..++|.+.++++++
T Consensus 11 ~~crkA~~~L~~~~i~~~~~d~~~~~~s~~eL~~~l~~~~~~~~~lin~ 59 (132)
T PRK13344 11 TSCKKAKTWLNAHQLSYKEQNLGKEPLTKEEILAILTKTENGIESIVSS 59 (132)
T ss_pred HHHHHHHHHHHHcCCCeEEEECCCCCCCHHHHHHHHHHhCCCHHHhhcc
Confidence 33444555555443 5677889999999999999999986
No 116
>PRK06361 hypothetical protein; Provisional
Probab=29.17 E-value=75 Score=26.80 Aligned_cols=40 Identities=13% Similarity=0.144 Sum_probs=33.9
Q ss_pred CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcC
Q 023901 196 PFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKG 235 (275)
Q Consensus 196 ~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G 235 (275)
+-+.+....+.++.+-.|++++||-.++.+.-+|+.+.-|
T Consensus 173 ~~d~~~~~~~~~i~~~~gl~~~~v~~~~~~~~~~~~~~~~ 212 (212)
T PRK06361 173 PSDLITYEFARKVALGAGLTEKELEEALENNPKLLLKRLG 212 (212)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhHHHHHHhcC
Confidence 4455667788999999999999999999999999887654
No 117
>PF09279 EF-hand_like: Phosphoinositide-specific phospholipase C, efhand-like; InterPro: IPR015359 This domain is predominantly found in the enzyme phosphoinositol-specific phospholipase C. It adopts a structure consisting of a core of four alpha helices, in an EF like fold, and is required for functioning of the enzyme []. ; PDB: 3OHM_B 3QR0_A 2ZKM_X 2FJU_B 3QR1_D 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B ....
Probab=29.09 E-value=72 Score=23.24 Aligned_cols=62 Identities=19% Similarity=0.407 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHhcCCCCChHHHHHHHHHHh-hcCCCcHHHHHHHHHHHHhhhhhcCCeeeeccccchhhhhh
Q 023901 181 EDVLRKYIRYALNEKPFNPDLVVNLIQLRK-ASMLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKR 251 (275)
Q Consensus 181 ~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~-as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kR 251 (275)
.+||++|-. +....+.+...+-+.=.. -..+|++++.++++.-.... +.. +-.+||..||-+
T Consensus 3 ~~if~~ys~---~~~~mt~~~f~~FL~~eQ~~~~~~~~~~~~li~~~~~~~-~~~-----~~~~lt~~gF~~ 65 (83)
T PF09279_consen 3 EEIFRKYSS---DKEYMTAEEFRRFLREEQGEPRLTDEQAKELIEKFEPDE-RNR-----QKGQLTLEGFTR 65 (83)
T ss_dssp HHHHHHHCT---TSSSEEHHHHHHHHHHTSS-TTSSHHHHHHHHHHHHHHH-HHH-----CTTEEEHHHHHH
T ss_pred HHHHHHHhC---CCCcCCHHHHHHHHHHHhccccCcHHHHHHHHHHHccch-hhc-----ccCCcCHHHHHH
Confidence 455666522 455556555555543222 22457777777776532221 101 115667777654
No 118
>PF13154 DUF3991: Protein of unknown function (DUF3991)
Probab=28.95 E-value=33 Score=25.49 Aligned_cols=19 Identities=26% Similarity=0.588 Sum_probs=17.6
Q ss_pred HHHhcCCCCChHHHHHHHH
Q 023901 189 RYALNEKPFNPDLVVNLIQ 207 (275)
Q Consensus 189 rY~LnEr~F~~d~VaDLi~ 207 (275)
+|+.+||..+++.|..++.
T Consensus 1 ~YL~~~RgI~~~~v~~~~~ 19 (77)
T PF13154_consen 1 AYLTEERGIDPEIVDAFIN 19 (77)
T ss_pred CchhhhcCcCHHHHHHHHH
Confidence 4899999999999999987
No 119
>PF05598 DUF772: Transposase domain (DUF772); InterPro: IPR008490 This presumed domain is found at the N terminus of transposase insH and other related transposases.
Probab=28.51 E-value=79 Score=22.61 Aligned_cols=32 Identities=19% Similarity=0.332 Sum_probs=27.8
Q ss_pred CCChHHHHHHHHHHhhcCC-CcHHHHHHHHHHH
Q 023901 196 PFNPDLVVNLIQLRKASML-DDSQVAEILNEIS 227 (275)
Q Consensus 196 ~F~~d~VaDLi~Lr~as~L-~d~evaeiL~E~s 227 (275)
+++|....-++=++...|+ ||.++.|.+++--
T Consensus 4 ~~~~~~ml~~ll~~~~~~~~S~r~l~~~l~~~~ 36 (77)
T PF05598_consen 4 AYPPRMMLKALLLKYLFGLRSDRELEERLRDNL 36 (77)
T ss_pred CCCHHHHHHHHHHHHHHhcchHHHHHhhHhhhh
Confidence 6888889889999999999 9999999988753
No 120
>cd01310 TatD_DNAse TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity.
Probab=28.35 E-value=94 Score=25.75 Aligned_cols=32 Identities=19% Similarity=0.309 Sum_probs=25.2
Q ss_pred HHHHHHHH-HHhhcCCCcHHHHHHHHHHHHhhh
Q 023901 200 DLVVNLIQ-LRKASMLDDSQVAEILNEISRRFV 231 (275)
Q Consensus 200 d~VaDLi~-Lr~as~L~d~evaeiL~E~s~Ri~ 231 (275)
..+..++. |....||+++++..++.+-++|++
T Consensus 218 ~~~~~~~~~la~~~gl~~e~~~~~~~~N~~~ll 250 (251)
T cd01310 218 AYVKHVAEKIAELKGISVEEVAEVTTENAKRLF 250 (251)
T ss_pred hhHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 34444444 556799999999999999999986
No 121
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=28.28 E-value=71 Score=24.29 Aligned_cols=35 Identities=26% Similarity=0.327 Sum_probs=19.2
Q ss_pred HHHHHhcC-CCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 023901 187 YIRYALNE-KPFNPDLVVNLIQLRKASMLDDSQVAEILNEIS 227 (275)
Q Consensus 187 YirY~LnE-r~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s 227 (275)
.||-+|+| +..+ +-.|+++++|+|.++.-+|-=.+
T Consensus 12 ~Vw~~L~~~~~~s------~~el~k~~~l~~~~~~~AiGWLa 47 (65)
T PF10771_consen 12 KVWQLLNENGEWS------VSELKKATGLSDKEVYLAIGWLA 47 (65)
T ss_dssp HHHHHHCCSSSEE------HHHHHHHCT-SCHHHHHHHHHHH
T ss_pred HHHHHHhhCCCcC------HHHHHHHhCcCHHHHHHHHHHHh
Confidence 35667777 3332 22345777777777776654333
No 122
>PF02936 COX4: Cytochrome c oxidase subunit IV; InterPro: IPR004203 Cytochrome c oxidase, a 13 sub-unit complex (1.9.3.1 from EC) is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit IV. The Dictyostelium discoideum (Slime mould) member of this family is called COX VI. The Saccharomyces cerevisiae protein YGX6_YEAST appears to be the yeast COX IV subunit.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3ABK_Q 3AG1_Q 3ASN_Q 1OCZ_D 2EIN_Q 2OCC_D 2YBB_O 3AG3_D 1OCO_Q 1V55_Q ....
Probab=28.27 E-value=41 Score=28.57 Aligned_cols=62 Identities=21% Similarity=0.381 Sum_probs=32.5
Q ss_pred HHHHhcchhh----HH-hhhhhhhhccccccccCCCCCCCCCchhHHHHHHHhhhhHhhhhhhhhhhhcCChh
Q 023901 69 VEVEEELPWI----QE-KALDLVEFTGSVTQAIPGPRVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPK 136 (275)
Q Consensus 69 ~e~e~e~~wi----qe-kaldlveftg~v~qaiPgPrvg~s~lPwiLAlPLAylGiTFviA~vRTvrK~tSPr 136 (275)
-.+-++-+|= +| ||+=-+-|- =.|||....+-.|-..+...+++++|.+.++=.+|.|-.|-
T Consensus 36 LkeKekg~Wk~LS~eEKkalY~isFg------~~g~r~~~~~gewk~v~~~~~~~i~~s~~l~~~~r~~~~~~ 102 (142)
T PF02936_consen 36 LKEKEKGDWKKLSLEEKKALYRISFG------QTGPRMKAPTGEWKKVFGGVFIFIGFSVLLFIWQRSYVYPP 102 (142)
T ss_dssp HHHHTTS-GGGS-HHHHHHHHHHH-S------S-HHHHT---SHHHHHHHHHHHHHHHHHHHHHHHHHHT---
T ss_pred HHHHHhCCHhhCCHHHHHHHHHhhhc------CcccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 3444666773 33 344444442 25778777777787777777777666666666777776554
No 123
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=28.27 E-value=3e+02 Score=22.07 Aligned_cols=9 Identities=44% Similarity=1.007 Sum_probs=4.2
Q ss_pred HhCCChHHH
Q 023901 175 KTGFSMEDV 183 (275)
Q Consensus 175 KTGFs~~Ei 183 (275)
+.||+..||
T Consensus 55 ~~G~sL~eI 63 (127)
T cd01108 55 DLGFSLEEI 63 (127)
T ss_pred HcCCCHHHH
Confidence 344444443
No 124
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=28.06 E-value=1.7e+02 Score=24.23 Aligned_cols=50 Identities=16% Similarity=0.250 Sum_probs=31.3
Q ss_pred hHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhh
Q 023901 180 MEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRF 230 (275)
Q Consensus 180 ~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri 230 (275)
.+|++..=++|+-+.+-=+-- .+.=++.=+.=|||++||.|+|.+....-
T Consensus 2 Re~li~~A~~FL~~p~V~~sp-~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 2 REDLIEQAVKFLQDPKVRNSP-LEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHHHCTTTCCCS--HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHHHhCCcccccCC-HHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 456666777777776654443 45555555666999999999998865443
No 125
>PF12335 SBF2: Myotubularin protein ; InterPro: IPR022096 This domain family is found in eukaryotes, and is approximately 220 amino acids in length. The family is found in association with PF02141 from PFAM, PF03456 from PFAM, PF03455 from PFAM. This family is the middle region of SBF2, a member of the myotubularin family. Myotubularin-related proteins have been suggested to work in phosphoinositide-mediated signalling events that may also convey control of myelination. Mutations of SBF2 are implicated in Charcot-Marie-Tooth disease.
Probab=27.95 E-value=46 Score=30.41 Aligned_cols=69 Identities=28% Similarity=0.421 Sum_probs=50.0
Q ss_pred chHHHHHHHHhCCC-hHHHHHHHHHH---HhcCCCCChHHHHHHH--HHHhhcCCCcHHHHHHHHHHHHhhhhhcCC
Q 023901 166 PPALKGLVQKTGFS-MEDVLRKYIRY---ALNEKPFNPDLVVNLI--QLRKASMLDDSQVAEILNEISRRFVREKGP 236 (275)
Q Consensus 166 ~gvLk~L~~KTGFs-~~Ei~RKYirY---~LnEr~F~~d~VaDLi--~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~ 236 (275)
+.+++.|+.+.|=. ..+.+.+|+.= .|++.+|+ .|++|| +|...++.+|--+|.+|...+..+|++-++
T Consensus 47 ~av~~~lk~~~aR~~~~~~L~~~~~~~k~~L~~~qF~--~lv~lin~aLq~~s~~dd~~~Aa~LL~ls~~fyrkl~~ 121 (225)
T PF12335_consen 47 PAVLRALKSRSARQAFCRELSKHVKSNKAVLDDQQFD--YLVRLINCALQDCSESDDYGIAAALLPLSTAFYRKLSN 121 (225)
T ss_pred HHHHHHHccchHHHHHHHHHHHHHhcCCccCCHHHHH--HHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHcCc
Confidence 45566666555422 23455565532 36777775 788887 689999999999999999999999998644
No 126
>COG2212 MnhF Multisubunit Na+/H+ antiporter, MnhF subunit [Inorganic ion transport and metabolism]
Probab=27.84 E-value=60 Score=26.26 Aligned_cols=39 Identities=18% Similarity=0.473 Sum_probs=30.1
Q ss_pred chhHHHHHHHhhhhHhhhhhhhhhhhcCChhhhhhhhhcchhh
Q 023901 106 LPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAM 148 (275)
Q Consensus 106 lPwiLAlPLAylGiTFviA~vRTvrK~tSPraKRkR~VnKNa~ 148 (275)
+.|++-+.+..+++++.+++||+++-=|.| .|.|.-|..
T Consensus 3 ~~~~~~ial~i~~la~~l~~yRvi~GPt~~----DRvvalD~l 41 (89)
T COG2212 3 LEIMLLIALIILGLALLLALYRVIRGPTLP----DRVVALDTL 41 (89)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCcc----chhhhHhHH
Confidence 578999999999999999999997765554 456555443
No 127
>PRK00118 putative DNA-binding protein; Validated
Probab=27.75 E-value=44 Score=27.30 Aligned_cols=69 Identities=17% Similarity=0.199 Sum_probs=40.3
Q ss_pred hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCeeeecccc--chhhhhhHHHHHHHHHhhhhhcc
Q 023901 199 PDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMNMSGY--SEKGFKRKLAVQALFGKVFYLSE 267 (275)
Q Consensus 199 ~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~--Te~G~kRK~a~~aLF~K~~yLsE 267 (275)
++--.+++.|+-..|+|..|||++++-.-..|++...-..-++.-+ -..+++|-+.-+++|.++.|+-|
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNELFDKIAYLKE 89 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHH
Confidence 3345667777777788888888776532222222211111111110 12367888888999999998865
No 128
>PF12446 DUF3682: Protein of unknown function (DUF3682); InterPro: IPR022152 This domain family is found in eukaryotes, and is typically between 125 and 136 amino acids in length.
Probab=27.61 E-value=30 Score=30.12 Aligned_cols=15 Identities=40% Similarity=0.399 Sum_probs=7.8
Q ss_pred hhhhhhhHHHHHhcc
Q 023901 61 KKKAEEVEVEVEEEL 75 (275)
Q Consensus 61 ~~~~~~~e~e~e~e~ 75 (275)
-+++||+|||+|.|+
T Consensus 93 h~rqEeeEEeEe~Ek 107 (133)
T PF12446_consen 93 HTRQEEEEEEEENEK 107 (133)
T ss_pred ccchhhhhhhhhhhh
Confidence 344555545555554
No 129
>PRK14955 DNA polymerase III subunits gamma and tau; Provisional
Probab=27.58 E-value=4.5e+02 Score=24.90 Aligned_cols=61 Identities=21% Similarity=0.282 Sum_probs=45.9
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHhc---CCCCChHHHHHHH
Q 023901 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYALN---EKPFNPDLVVNLI 206 (275)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~R---KYirY~Ln---Er~F~~d~VaDLi 206 (275)
...+.+.|.+.+.+.+-.++..++..|...+|-++..+.+ |=+.|+.. .+.-+.+.|.+++
T Consensus 188 ~~ei~~~l~~~~~~~g~~i~~~al~~l~~~s~g~lr~a~~~L~kl~~~~~~~~~~~~It~~~v~~~v 254 (397)
T PRK14955 188 LEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDAQSILDQVIAFSVESEGEGSIRYDKVAELL 254 (397)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccccCCCCccCHHHHHHHH
Confidence 4466777888888888889999999999999999987765 54556531 3466777777665
No 130
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=27.43 E-value=3.7e+02 Score=24.57 Aligned_cols=58 Identities=14% Similarity=0.188 Sum_probs=43.7
Q ss_pred hhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhcCCCCChHHHHHHH
Q 023901 147 AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLI 206 (275)
Q Consensus 147 a~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei---~RKYirY~LnEr~F~~d~VaDLi 206 (275)
..+++-|.+.+.+.+-.++..++..|...+|-|+..+ +.|..-|+-.+ -+.+.|.+++
T Consensus 170 ~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~gdlr~~~~~lekl~~y~~~~--it~~~v~~~~ 230 (367)
T PRK14970 170 KDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFDRVVTFCGKN--ITRQAVTENL 230 (367)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCC--CCHHHHHHHh
Confidence 5677778888888887899999999999999988755 56666665433 6666666554
No 131
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=27.37 E-value=3.4e+02 Score=22.09 Aligned_cols=117 Identities=18% Similarity=0.232 Sum_probs=66.8
Q ss_pred hhcCChhhhhhhhhcc--hhhHHhhHHHHHhcCCCCCC-chHHHHHH---HHhCCChHHHHHHHHHHHhcCCCCChHHHH
Q 023901 130 KKFNSPKFKRKKLVNK--NAMVCKTIDELFQKGGDAVN-PPALKGLV---QKTGFSMEDVLRKYIRYALNEKPFNPDLVV 203 (275)
Q Consensus 130 rK~tSPraKRkR~VnK--Na~LvkSLdeyfp~gRda~~-~gvLk~L~---~KTGFs~~Ei~RKYirY~LnEr~F~~d~Va 203 (275)
++..|-+-=|.++..| +..+++..=+.|...+- +| ..--+... ...|++ +..|++.|..+-|+.+.+.
T Consensus 23 ~r~~s~~el~~kL~~kg~~~~~i~~vl~~l~~~~~-ldD~~~a~~~~~~~~~~~~g-----~~~I~~~L~~kGi~~~~I~ 96 (157)
T PRK00117 23 RREHSRAELRRKLAAKGFSEEVIEAVLDRLKEEGL-LDDERFAESFVRSRARKGYG-----PRRIRQELRQKGVDREIIE 96 (157)
T ss_pred cchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhCCch-----HHHHHHHHHHcCCCHHHHH
Confidence 4445555555556555 55666666555554332 33 11111111 123333 7789999999999999999
Q ss_pred HHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCeeeeccccchhhhhhHHHHHHHHHhhhhhcc
Q 023901 204 NLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRKLAVQALFGKVFYLSE 267 (275)
Q Consensus 204 DLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a~~aLF~K~~yLsE 267 (275)
+.+.-- . .|++ |++.+.+++.++++- +... ..+.-..+.|++|=|-.+.
T Consensus 97 ~~l~~~---~-~d~~--e~a~~~~~k~~~~~~-------~~~~--~~k~Ki~~~L~rkGF~~~~ 145 (157)
T PRK00117 97 EALAEL---D-IDWE--ELARELARKKFRRPL-------PDDA--KEKAKLVRFLARRGFSMDV 145 (157)
T ss_pred HHHHHc---C-ccHH--HHHHHHHHHHcCCCC-------CCCH--HHHHHHHHHHHHCCCCHHH
Confidence 988742 2 3333 677777777666542 2232 2333456777777665543
No 132
>PRK14954 DNA polymerase III subunits gamma and tau; Provisional
Probab=27.20 E-value=3.8e+02 Score=27.85 Aligned_cols=60 Identities=20% Similarity=0.264 Sum_probs=44.7
Q ss_pred hhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHh---cCCCCChHHHHHHH
Q 023901 147 AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYAL---NEKPFNPDLVVNLI 206 (275)
Q Consensus 147 a~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~R---KYirY~L---nEr~F~~d~VaDLi 206 (275)
..+.+-|.+.+.+.+-.++..++..|...+|-++..+++ |=+-|.. ..+.-+.+.|.+++
T Consensus 189 ~ei~~~L~~i~~~egi~I~~eal~~La~~s~Gdlr~al~eLeKL~~y~~~~~~~~~It~~~V~~lv 254 (620)
T PRK14954 189 DEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDAQSILDQVIAFSVGSEAEKVIAYQGVAELL 254 (620)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhccccccCCccCHHHHHHHH
Confidence 456667777777777789999999999999999987765 5556763 24556777776654
No 133
>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family. This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.
Probab=27.16 E-value=3.3e+02 Score=22.93 Aligned_cols=58 Identities=9% Similarity=0.050 Sum_probs=38.1
Q ss_pred HHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCeeee
Q 023901 182 DVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMN 240 (275)
Q Consensus 182 Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn 240 (275)
+-++++++..++|.+++-=.++.+-.|+... -++.+..+.+.++.+.+-+...|+++=
T Consensus 93 ~~l~~~~~~~i~~~~~~~vVIDsls~l~~~~-~~~~~~r~~l~~l~~~lk~~~~tvll~ 150 (224)
T TIGR03880 93 NRIKNELPILIKELGASRVVIDPISLLETLF-DDDAERRTELFRFYSSLRETGVTTILT 150 (224)
T ss_pred HHHHHHHHHHHHHhCCCEEEEcChHHHhhhc-CCHHHHHHHHHHHHHHHHhCCCEEEEE
Confidence 3466788888888887755566666664333 245666777777877775555556543
No 134
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=27.02 E-value=2.9e+02 Score=28.41 Aligned_cols=60 Identities=17% Similarity=0.198 Sum_probs=48.9
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH---HHHHHHHHhcCCCCChHHHHHHHH
Q 023901 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLIQ 207 (275)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei---~RKYirY~LnEr~F~~d~VaDLi~ 207 (275)
...+.+-|.+.+.+.+-.++..+++.|.+.+|-++-++ +.|.+-|. .+..|.+.|.+++.
T Consensus 193 ~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~g--~g~It~e~V~~llg 255 (598)
T PRK09111 193 ADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLLDQAIAHG--AGEVTAEAVRDMLG 255 (598)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhc--CCCcCHHHHHHHhC
Confidence 45778888899998998999999999999999998776 45778774 45688888887653
No 135
>PHA03211 serine/threonine kinase US3; Provisional
Probab=27.00 E-value=28 Score=33.59 Aligned_cols=35 Identities=14% Similarity=0.159 Sum_probs=20.7
Q ss_pred hhHHHHHhcchhhHHhhhhhhhhccccccccCCCC
Q 023901 66 EVEVEVEEELPWIQEKALDLVEFTGSVTQAIPGPR 100 (275)
Q Consensus 66 ~~e~e~e~e~~wiqekaldlveftg~v~qaiPgPr 100 (275)
+.++..+.+..|-.+.+.|.-.-.+.+...+|.|.
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 128 (461)
T PHA03211 94 DDDDDAPDDVAYPDEYAEDDFLPGDGAPDHDPAPC 128 (461)
T ss_pred cCCCCCccccCCCCCCCCcceecCCCCCCCCCCCC
Confidence 33344455566777777766665566666666553
No 136
>PRK00024 hypothetical protein; Reviewed
Probab=26.99 E-value=92 Score=27.92 Aligned_cols=27 Identities=26% Similarity=0.500 Sum_probs=19.2
Q ss_pred hhcCCCcHHHHHHHH----------HHHHhhhhhcCC
Q 023901 210 KASMLDDSQVAEILN----------EISRRFVREKGP 236 (275)
Q Consensus 210 ~as~L~d~evaeiL~----------E~s~Ri~~~~G~ 236 (275)
.+..|+|.|+-++|. ++|+++.++||.
T Consensus 20 G~~~Lsd~ELLa~lL~~g~~~~~~~~LA~~LL~~fgs 56 (224)
T PRK00024 20 GAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGS 56 (224)
T ss_pred CcccCCHHHHHHHHHcCCCCCCCHHHHHHHHHHHcCC
Confidence 455677777776654 678888888885
No 137
>PRK11677 hypothetical protein; Provisional
Probab=26.92 E-value=65 Score=27.52 Aligned_cols=22 Identities=18% Similarity=0.298 Sum_probs=15.8
Q ss_pred chhHHHHHHHhhhhHhhhhhhh
Q 023901 106 LPWILAVPLAYVGVSFVIAFVK 127 (275)
Q Consensus 106 lPwiLAlPLAylGiTFviA~vR 127 (275)
|+|++|+-.+-+|+.+.+.+.|
T Consensus 1 M~W~~a~i~livG~iiG~~~~R 22 (134)
T PRK11677 1 MTWEYALIGLVVGIIIGAVAMR 22 (134)
T ss_pred CcHHHHHHHHHHHHHHHHHHHh
Confidence 5799999888888555555544
No 138
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=26.89 E-value=24 Score=28.81 Aligned_cols=9 Identities=22% Similarity=0.475 Sum_probs=4.9
Q ss_pred HHHHhcchh
Q 023901 69 VEVEEELPW 77 (275)
Q Consensus 69 ~e~e~e~~w 77 (275)
||+|++|.|
T Consensus 94 eE~dddmgf 102 (105)
T cd04411 94 EEEDEDFGF 102 (105)
T ss_pred cccccccCc
Confidence 444556765
No 139
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=26.87 E-value=2.2e+02 Score=21.98 Aligned_cols=30 Identities=10% Similarity=0.361 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhcCCCC
Q 023901 168 ALKGLVQKTGFSMEDVLRKYIRYALNEKPF 197 (275)
Q Consensus 168 vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F 197 (275)
....+-.+.|.++.+.+|-+++|..+++.+
T Consensus 16 ~a~~i~~~lGl~~s~ai~~fl~qvv~~~~l 45 (83)
T TIGR02384 16 EAYAVFEELGLTPSTAIRMFLKQVIREQGL 45 (83)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 445566889999999999999999999864
No 140
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=26.87 E-value=70 Score=23.79 Aligned_cols=23 Identities=26% Similarity=0.395 Sum_probs=12.9
Q ss_pred HHHHHHHHhhcCCCcHHHHHHHH
Q 023901 202 VVNLIQLRKASMLDDSQVAEILN 224 (275)
Q Consensus 202 VaDLi~Lr~as~L~d~evaeiL~ 224 (275)
+.-+.+++++.|||..|+|+.|.
T Consensus 20 ~~~i~~~~~~~~ltQ~e~A~~lg 42 (80)
T PF13744_consen 20 MAAIRELREERGLTQAELAERLG 42 (80)
T ss_dssp HHHHHHHHHCCT--HHHHHHHHT
T ss_pred HHHHHHHHHHcCCCHHHHHHHHC
Confidence 34466666666666666666653
No 141
>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics]
Probab=26.77 E-value=46 Score=34.47 Aligned_cols=74 Identities=23% Similarity=0.240 Sum_probs=45.9
Q ss_pred CCCCCchhHHHHHHHhhhhHhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCCh
Q 023901 101 VGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSM 180 (275)
Q Consensus 101 vg~s~lPwiLAlPLAylGiTFviA~vRTvrK~tSPraKRkR~VnKNa~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~ 180 (275)
-+-+.+|.+.|-||-+++ ..+.++++. -+ -+||||+ .++|-+.+ ......
T Consensus 310 Sp~t~~p~~gakPldl~r-lYvsvke~g--g~--------~~v~knk------rd~a~~lg-ssaa~~------------ 359 (532)
T KOG2510|consen 310 SPMTNLPAVGAKPLDLYR-LYVSVKEIG--GL--------TQVNKNK------RDLATNLG-SSAASS------------ 359 (532)
T ss_pred CcccccccccccchhHHH-HHHHHHHhc--cc--------eeeccch------hhhhhccc-hHHHHH------------
Confidence 466789999999999998 455444443 22 2577777 56666655 122222
Q ss_pred HHHHHHHHHHHhc-CCCCChHHHHHHH
Q 023901 181 EDVLRKYIRYALN-EKPFNPDLVVNLI 206 (275)
Q Consensus 181 ~Ei~RKYirY~Ln-Er~F~~d~VaDLi 206 (275)
...-||||+++ |-.|+-+.-.|+.
T Consensus 360 --l~k~y~~~lf~fec~f~Rg~e~p~~ 384 (532)
T KOG2510|consen 360 --LKKQYIQYLFAFECKFERGEEPPPD 384 (532)
T ss_pred --HHHHHHHHHHhhceeeeccCCCCHH
Confidence 23459999996 5566655555553
No 142
>cd08801 Death_UNC5D Death domain found in Uncoordinated-5D. Death Domain (DD) found in Uncoordinated-5D (UNC5D). UNC5D is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=26.29 E-value=1.6e+02 Score=24.66 Aligned_cols=67 Identities=27% Similarity=0.349 Sum_probs=43.5
Q ss_pred HHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 023901 149 VCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISR 228 (275)
Q Consensus 149 LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~ 228 (275)
||.+||.=-.+|+| -|.|.+|-+.+. ||-|.-+- +=--+.+-||-.-|.-.+=+=++++-+|.|++|
T Consensus 9 lC~~LD~p~~kg~D------WR~LA~kL~iDR------yl~yFatk-~SPT~viLdLWEa~~~~~g~L~~La~aleeiGr 75 (98)
T cd08801 9 ICATFDTPNAKGKD------WQMLAQKNSIDR------NLSYFATQ-SSPSAVILSLWEARHQHDGDLDSLACALEEIGR 75 (98)
T ss_pred HHHHcCCCCCCCcc------HHHHHHHhcchh------HHHHHhcC-CChHHHHHHHHHHhcCCCCCHHHHHHHHHHhCc
Confidence 68999887777776 899999999763 99997654 222234444444444333344556667777665
No 143
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=26.02 E-value=3.3e+02 Score=21.82 Aligned_cols=12 Identities=8% Similarity=0.116 Sum_probs=5.1
Q ss_pred cCCCcHHHHHHH
Q 023901 212 SMLDDSQVAEIL 223 (275)
Q Consensus 212 s~L~d~evaeiL 223 (275)
+|++=+||+++|
T Consensus 56 ~G~sL~eI~~~l 67 (126)
T cd04785 56 LGFSLEEIRALL 67 (126)
T ss_pred CCCCHHHHHHHH
Confidence 344444444443
No 144
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=26.00 E-value=1.3e+02 Score=23.64 Aligned_cols=42 Identities=17% Similarity=0.305 Sum_probs=29.6
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhc
Q 023901 185 RKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREK 234 (275)
Q Consensus 185 RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~ 234 (275)
+++|+..|..+-.+++.+++.+. ..++.+. +.+.+++-++.+
T Consensus 45 ~~~I~~~L~~kGi~~~~i~~~l~-----~~~~~e~---a~~~~~kk~~~~ 86 (121)
T PF02631_consen 45 PRRIRQKLKQKGIDREIIEEALE-----EYDEEEE---ALELAEKKYRRY 86 (121)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHT-----CS-HHHH---HHHHHHHHHHHT
T ss_pred HHHHHHHHHHHCCChHHHHHHHH-----HhhHHHH---HHHHHHHHHhcc
Confidence 57899999999999999998887 4444444 666677777766
No 145
>PF08708 PriCT_1: Primase C terminal 1 (PriCT-1); InterPro: IPR014820 This alpha helical domain is found at the C-terminal of primases.
Probab=25.95 E-value=1.9e+02 Score=20.77 Aligned_cols=22 Identities=27% Similarity=0.333 Sum_probs=18.4
Q ss_pred hcCCCcHHHHHHHHHHHHhhhh
Q 023901 211 ASMLDDSQVAEILNEISRRFVR 232 (275)
Q Consensus 211 as~L~d~evaeiL~E~s~Ri~~ 232 (275)
.-.|+++||..|.+-++++.++
T Consensus 50 ~~PL~~~Ev~~i~kSi~k~~~r 71 (71)
T PF08708_consen 50 SPPLPESEVKAIAKSIAKWTWR 71 (71)
T ss_pred CCCCCHHHHHHHHHHHHHhccC
Confidence 5679999999999999887653
No 146
>COG3082 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.94 E-value=46 Score=26.55 Aligned_cols=51 Identities=29% Similarity=0.398 Sum_probs=37.5
Q ss_pred hcCCCcHHHHHHHHHHHHhhhhhc----------CCeeeeccccchhhhhhHHHHHHHHHhh
Q 023901 211 ASMLDDSQVAEILNEISRRFVREK----------GPVVMNMSGYSEKGFKRKLAVQALFGKV 262 (275)
Q Consensus 211 as~L~d~evaeiL~E~s~Ri~~~~----------G~vmmn~~G~Te~G~kRK~a~~aLF~K~ 262 (275)
-|..+|++|..||||+..-+=|.+ |+.+.|+---+-.-.+||+-.++ |+..
T Consensus 4 ~SkYsDe~ve~il~e~iaVLeKH~ap~dLsLmvlGNmvtNlintsVa~aQr~alA~~-Fa~a 64 (74)
T COG3082 4 ISKYSDEQVEQILNELIAVLEKHKAPTDLSLMVLGNMVTNLINTSVAPAQRQAIANS-FARA 64 (74)
T ss_pred cccccHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHHhcccHHHHHHHHHH-HHHH
Confidence 467899999999999988666655 55566777777777888876554 4443
No 147
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=25.89 E-value=1.1e+02 Score=21.22 Aligned_cols=28 Identities=29% Similarity=0.418 Sum_probs=23.5
Q ss_pred hHHHHHHHHhCCChHHHHHHHHHHHhcC
Q 023901 167 PALKGLVQKTGFSMEDVLRKYIRYALNE 194 (275)
Q Consensus 167 gvLk~L~~KTGFs~~Ei~RKYirY~LnE 194 (275)
..|+.|..+||-...+++|+=|.-.|.+
T Consensus 15 ~~L~~ls~~t~i~~S~Ll~eAle~~l~k 42 (44)
T PF12651_consen 15 EKLKELSEETGIPKSKLLREALEDYLEK 42 (44)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 4577899999999999999988777654
No 148
>TIGR00017 cmk cytidylate kinase. This family consists of cytidylate kinase, which catalyzes the phosphorylation of cytidine 5-monophosphate (dCMP) to cytidine 5 -diphosphate (dCDP) in the presence of ATP or GTP. UMP and dCMP can also act as acceptors.
Probab=25.81 E-value=3.1e+02 Score=24.03 Aligned_cols=81 Identities=15% Similarity=0.130 Sum_probs=47.7
Q ss_pred CCCchHHHHHHHHhC---CChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCC-------------------------
Q 023901 163 AVNPPALKGLVQKTG---FSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASML------------------------- 214 (275)
Q Consensus 163 a~~~gvLk~L~~KTG---Fs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L------------------------- 214 (275)
+......+.|..+.| ++..+++|..-+++|... ++.+--..++.++...++
T Consensus 13 sGKst~~~~la~~~~~~~~~~g~~~r~~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~v~~~ir~~ 91 (217)
T TIGR00017 13 AGKSTVAKAVAEKLGYAYLDSGAMYRAIALAALQNR-VDLTSEDALAELISHLDIRFIPTNGEVEVFLNGEDVSEAIRTQ 91 (217)
T ss_pred CCHHHHHHHHHHHhCCceeeCchHHHHHHHHHHHcC-CCCCCHHHHHHHHHhCCCEEecCCCceeEEEcCcchHHHhcCH
Confidence 344566777777777 677778777665555443 333322333444444433
Q ss_pred ----------CcHHHHHHHHHHHHhhhhhcCCeeeeccccc
Q 023901 215 ----------DDSQVAEILNEISRRFVREKGPVVMNMSGYS 245 (275)
Q Consensus 215 ----------~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~T 245 (275)
..-.|.+.|.+.-+++.+ .|++||+=..++
T Consensus 92 ~v~~~~s~~a~~p~VR~~l~~~qr~~a~-~~~~Vi~Gr~~~ 131 (217)
T TIGR00017 92 EVANAASKVAVFPKVREALLKRQQALAK-NDGIIADGRDIG 131 (217)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHhh-cCCEEEEEcCcc
Confidence 233456677777788764 477888866533
No 149
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=25.70 E-value=3e+02 Score=22.28 Aligned_cols=49 Identities=10% Similarity=0.132 Sum_probs=31.2
Q ss_pred HHHHHHHhCCChHHHHH------HHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHH
Q 023901 169 LKGLVQKTGFSMEDVLR------KYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQV 219 (275)
Q Consensus 169 Lk~L~~KTGFs~~Ei~R------KYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~ev 219 (275)
++.+..+.|.+.+|+-+ .||.-..|.+. +| -...|..|=.+++++-+++
T Consensus 10 l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~~-~p-s~~~l~kIa~aL~v~~~~L 64 (120)
T PRK13890 10 VLRLLDERHMTKKELSERSGVSISFLSDLTTGKA-NP-SLKVMEAIADALETPLPLL 64 (120)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCC-CC-CHHHHHHHHHHHCCCHHHH
Confidence 34444444555544443 48877788776 66 4477888888999955544
No 150
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=25.63 E-value=3.8e+02 Score=22.01 Aligned_cols=29 Identities=14% Similarity=0.210 Sum_probs=15.4
Q ss_pred CChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 023901 197 FNPDLVVNLIQLRKASMLDDSQVAEILNE 225 (275)
Q Consensus 197 F~~d~VaDLi~Lr~as~L~d~evaeiL~E 225 (275)
++++.+.+.+.-...-|++.+-+...+.-
T Consensus 53 i~~~~i~~~~~~~~~~~~~~~t~~~~~~~ 81 (297)
T PRK00236 53 LDAADLRSFLARRRRQGLSARSLARRLSA 81 (297)
T ss_pred CCHHHHHHHHHHHHhcccChhHHHHHHHH
Confidence 45555655555444445555555555443
No 151
>PF01026 TatD_DNase: TatD related DNase The Pfam entry finds members not in the Prosite definition.; InterPro: IPR001130 This family of proteins are related to a large superfamily of metalloenzymes []. TatD, a member of this family has been shown experimentally to be a DNase enzyme []. Allantoinase 3.5.2.5 from EC, N-isopropylammelide isopropyl amidohydrolase 3.5.1 from EC and the SCN1 protein from fission yeast belong to this family.; GO: 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters; PDB: 3E2V_B 1XWY_A 3GUW_D 3RCM_A 1ZZM_A 2XIO_A 1J6O_A 2GZX_A 3IPW_A 2Y1H_A ....
Probab=25.58 E-value=1.1e+02 Score=26.90 Aligned_cols=35 Identities=20% Similarity=0.336 Sum_probs=28.4
Q ss_pred ChHHHHHHHH-HHhhcCCCcHHHHHHHHHHHHhhhh
Q 023901 198 NPDLVVNLIQ-LRKASMLDDSQVAEILNEISRRFVR 232 (275)
Q Consensus 198 ~~d~VaDLi~-Lr~as~L~d~evaeiL~E~s~Ri~~ 232 (275)
.|..+.+.++ |-+.-+++.+++++++.+-++|+|.
T Consensus 220 ~p~~i~~~~~~la~~~~~~~e~~~~~~~~N~~r~f~ 255 (255)
T PF01026_consen 220 EPSNIPKVAQALAEIKGISLEELAQIIYENAKRLFG 255 (255)
T ss_dssp -GGGHHHHHHHHHHHHTSTHHHHHHHHHHHHHHHHT
T ss_pred ChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhC
Confidence 6777776665 6667789999999999999999983
No 152
>COG0599 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]
Probab=25.33 E-value=56 Score=26.10 Aligned_cols=21 Identities=19% Similarity=0.264 Sum_probs=15.9
Q ss_pred HHHHhhc--CCCcHHHHHHHHHH
Q 023901 206 IQLRKAS--MLDDSQVAEILNEI 226 (275)
Q Consensus 206 i~Lr~as--~L~d~evaeiL~E~ 226 (275)
.|+|.|+ |.|++|+.|+|.-.
T Consensus 75 ~H~~~Al~~GaT~eEI~e~i~~~ 97 (124)
T COG0599 75 VHVRAALENGATKEEIAEAIAVA 97 (124)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHH
Confidence 4666665 99999999988643
No 153
>PRK14038 ADP-dependent glucokinase; Provisional
Probab=25.30 E-value=99 Score=31.26 Aligned_cols=102 Identities=16% Similarity=0.249 Sum_probs=62.6
Q ss_pred hcCChhhhh----hhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhc--CC--------C
Q 023901 131 KFNSPKFKR----KKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALN--EK--------P 196 (275)
Q Consensus 131 K~tSPraKR----kR~VnKNa~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~Ln--Er--------~ 196 (275)
.|++||+-| .+..|-..++.+.+.++|+.-....+--+|-|++.=.+++..+.|++=.+.... ++ +
T Consensus 188 ~~~aPRaNRfI~s~D~~N~~l~~~eef~~~l~ei~~~~Dl~vlSG~q~l~~~~~~~~l~~~~~~l~~l~~~~i~iH~EfA 267 (453)
T PRK14038 188 DFEAPRENRFIGAADDYNPNLYIRPEFRERFEEIAKKAELAIISGLQALTEENYREPFETVREHLKVLNERGIPAHLEFA 267 (453)
T ss_pred eeEcCCCceEEEecCCCCcceeecHHHHHHHHhhccCCCEEEEEchhhhccccHHHHHHHHHHHHHhcCcCCceEEEEee
Confidence 799999988 466777777888888888875555665555555544456666666655444433 22 2
Q ss_pred CC--hHHHHHHHHHHh---hcCCCcHHHHHHHH-----HHHHhhhh
Q 023901 197 FN--PDLVVNLIQLRK---ASMLDDSQVAEILN-----EISRRFVR 232 (275)
Q Consensus 197 F~--~d~VaDLi~Lr~---as~L~d~evaeiL~-----E~s~Ri~~ 232 (275)
|. .+...+++.+=. -.||+..|++-+++ |.|+||.+
T Consensus 268 s~~d~~~r~~i~~ilp~vDSlGmNE~ELa~ll~~lg~~~l~~~i~~ 313 (453)
T PRK14038 268 FTPDETVREEILGLLGKFYSVGLNEVELASIMEVMGEKTLAEKLLA 313 (453)
T ss_pred ccchHHHHHHHHhhCccccccccCHHHHHHHHHHhccchhhhhhhh
Confidence 22 222233332211 27888889999887 44455444
No 154
>COG5590 Uncharacterized conserved protein [Function unknown]
Probab=24.94 E-value=2.9e+02 Score=26.16 Aligned_cols=52 Identities=25% Similarity=0.384 Sum_probs=40.7
Q ss_pred chhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCCh--------------HHHHHHHHH-HHhcC-CCCC
Q 023901 145 KNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSM--------------EDVLRKYIR-YALNE-KPFN 198 (275)
Q Consensus 145 KNa~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~--------------~Ei~RKYir-Y~LnE-r~F~ 198 (275)
|-+-+++++-++.|.++ .|-+.+-+=.+++||+. ...|--|.| |+|.+ ++|+
T Consensus 28 kk~~~l~~llelvP~~g--wnn~li~eal~a~Gys~~~s~ilfP~g~~eLi~f~~~~~d~~aL~~lk~~d 95 (229)
T COG5590 28 KKIVFLQSLLELVPFNG--WNNRLIVEALEALGYSKGYSLILFPEGPMELIKFLEVYLDAYALESLKNID 95 (229)
T ss_pred HHHHHHHHHHHhccccc--cchhHHHHHHHhcCcccchhhhcCCCCHHHHHHHHHHHhHHHHHhcCCccc
Confidence 44568899999999886 57778888889999997 345778889 99977 4555
No 155
>PF03619 Solute_trans_a: Organic solute transporter Ostalpha; InterPro: IPR005178 This is a family of mainly hypothetical proteins of no known function.
Probab=24.89 E-value=87 Score=28.16 Aligned_cols=33 Identities=12% Similarity=0.451 Sum_probs=22.6
Q ss_pred hHHHHHHHhhhhHhhhhh---hhhhhhcCChhhhhh
Q 023901 108 WILAVPLAYVGVSFVIAF---VKTVKKFNSPKFKRK 140 (275)
Q Consensus 108 wiLAlPLAylGiTFviA~---vRTvrK~tSPraKRk 140 (275)
|...+.-.++.+|+.|++ ++-.++|+.|+.||.
T Consensus 3 ~~~~ia~~~~~~~~~is~~~i~~hl~~y~~P~~Qr~ 38 (274)
T PF03619_consen 3 WAWIIAGIFALLTILISLFLIYQHLRNYSKPEEQRY 38 (274)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 344455566666777766 556689999988775
No 156
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=24.81 E-value=1.6e+02 Score=21.69 Aligned_cols=36 Identities=14% Similarity=0.304 Sum_probs=24.4
Q ss_pred HHhcCCCCCCchHHHHHHHHhCCCh-HHHHHHHHHHH
Q 023901 156 LFQKGGDAVNPPALKGLVQKTGFSM-EDVLRKYIRYA 191 (275)
Q Consensus 156 yfp~gRda~~~gvLk~L~~KTGFs~-~Ei~RKYirY~ 191 (275)
++......+....|...-+.+||+. ++-+|.+|++.
T Consensus 6 ~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~m 42 (66)
T PF08461_consen 6 ILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAM 42 (66)
T ss_pred HHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHH
Confidence 4444555667777766666668887 77788888773
No 157
>PRK11172 dkgB 2,5-diketo-D-gluconate reductase B; Provisional
Probab=24.79 E-value=2.4e+02 Score=24.83 Aligned_cols=58 Identities=14% Similarity=0.257 Sum_probs=41.0
Q ss_pred CchHHHHHHHHhCCChHHHHHHHHHHHhcCC------CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 023901 165 NPPALKGLVQKTGFSMEDVLRKYIRYALNEK------PFNPDLVVNLIQLRKASMLDDSQVAEILNEIS 227 (275)
Q Consensus 165 ~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr------~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s 227 (275)
+.+.|+.+.++.|-|..++. |+|.|.-. .-+++-+.+-++.-. .-||++|+++| +++.
T Consensus 188 ~~~~l~~~a~~~~~s~aqva---l~w~l~~~~~~i~g~~~~~~l~~n~~~~~-~~L~~~~~~~i-~~~~ 251 (267)
T PRK11172 188 KDPVIARIAAKHNATPAQVI---LAWAMQLGYSVIPSSTKRENLASNLLAQD-LQLDAEDMAAI-AALD 251 (267)
T ss_pred CCHHHHHHHHHhCCCHHHHH---HHHHHhCCCEeecCCCCHHHHHHHHhhcC-CCcCHHHHHHH-hhhc
Confidence 34789999999999999987 56777642 356777776655432 46999998766 4443
No 158
>TIGR00044 pyridoxal phosphate enzyme, YggS family. Members of this protein family include YggS from Escherichia coli and YBL036C, an uncharacterized pyridoxal protein of Saccharomyces cerevisiae.
Probab=24.71 E-value=1.7e+02 Score=25.58 Aligned_cols=106 Identities=16% Similarity=0.214 Sum_probs=62.0
Q ss_pred HhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHH--HHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 023901 150 CKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKY--IRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEIS 227 (275)
Q Consensus 150 vkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKY--irY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s 227 (275)
.+-+..+...|-+.+--.-++++..|. +.+|+- +.+.+..-.+.+.....+.+..-..-+++.+.++.|++.+
T Consensus 40 ~~~i~~l~~~G~~~fg~~~~~Ea~~k~-----~~lr~~~~~~~~~ig~~q~~~~~~~~~~~~l~~~vds~~~~~~l~~~a 114 (229)
T TIGR00044 40 ASAIQIAYDAGQRAFGENYVQELVEKI-----KLLEDLGKLEWHFIGPLQSNKDRLVVENFDWVHTIDSLKIAKKLNEQR 114 (229)
T ss_pred HHHHHHHHHcCCccccEEcHHHHHHHH-----HHhcccCCceEEEECCCcchHHHHHhhhcCEEEEECCHHHHHHHHHHH
Confidence 334444444555555555566665543 223331 4555666555655543444444456779999999999998
Q ss_pred HhhhhhcC--Ceeeecc-ccchhhhhhHHHHHHHHHhh
Q 023901 228 RRFVREKG--PVVMNMS-GYSEKGFKRKLAVQALFGKV 262 (275)
Q Consensus 228 ~Ri~~~~G--~vmmn~~-G~Te~G~kRK~a~~aLF~K~ 262 (275)
.+- .+.- -|.+|+. ||+..|+.-. .+..++..+
T Consensus 115 ~~~-~~~~~V~l~vdtg~gm~R~G~~~~-e~~~~~~~i 150 (229)
T TIGR00044 115 EKL-QPPLNVLLQINISDEESKSGIQPE-ELLELAIQI 150 (229)
T ss_pred Hhc-CCCceEEEEEECCCCCCCCCCCHH-HHHHHHHHH
Confidence 652 1112 3567877 7999999762 345555554
No 159
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=24.71 E-value=3.4e+02 Score=21.29 Aligned_cols=55 Identities=16% Similarity=0.236 Sum_probs=28.4
Q ss_pred HHHHHHhCCChHHHHHHHHHHHh---------cCCCCChHHHHHHHHHH--hhcCCCcHHHHHHHHH
Q 023901 170 KGLVQKTGFSMEDVLRKYIRYAL---------NEKPFNPDLVVNLIQLR--KASMLDDSQVAEILNE 225 (275)
Q Consensus 170 k~L~~KTGFs~~Ei~RKYirY~L---------nEr~F~~d~VaDLi~Lr--~as~L~d~evaeiL~E 225 (275)
.++.+.+|-|.. -+|.|-+--| +-|-|+++.|+.|..++ +.+|++-++|.++|+.
T Consensus 4 ~eva~~~gvs~~-tlR~ye~~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (108)
T cd04773 4 GELAHLLGVPPS-TLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ 69 (108)
T ss_pred HHHHHHHCcCHH-HHHHHHHCCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 445555555543 3455554433 12346666666554333 2356666666666654
No 160
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=24.64 E-value=2.7e+02 Score=22.06 Aligned_cols=52 Identities=8% Similarity=0.039 Sum_probs=39.5
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHH
Q 023901 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLI 206 (275)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi 206 (275)
.+-..|++||..-.+.-..+.++... .++=|.||+.+|..-..|....|.++
T Consensus 27 ~~~~~l~~~~~~l~~~~~~~~~~~~l-------~~~Er~~i~~aL~~~~gn~s~AAr~L 78 (95)
T PRK00430 27 SVKQALKNYFAQLNGQDVNDLYELVL-------AEVEAPLLDMVMQYTRGNQTRAALML 78 (95)
T ss_pred HHHHHHHHHHHHhcCCCchhHHHHHH-------HHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence 35567899998777766667766653 45678999999999999988887654
No 161
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=24.60 E-value=3.7e+02 Score=21.54 Aligned_cols=12 Identities=17% Similarity=0.166 Sum_probs=5.1
Q ss_pred cCCCcHHHHHHH
Q 023901 212 SMLDDSQVAEIL 223 (275)
Q Consensus 212 s~L~d~evaeiL 223 (275)
+|++=+||+++|
T Consensus 56 ~G~sL~eI~~~l 67 (127)
T TIGR02044 56 VGFSLEECKELL 67 (127)
T ss_pred CCCCHHHHHHHH
Confidence 344444444444
No 162
>smart00229 RasGEFN Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).
Probab=24.49 E-value=3.3e+02 Score=20.96 Aligned_cols=95 Identities=15% Similarity=0.217 Sum_probs=49.2
Q ss_pred hhHhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCC-C--CchHHHHHHHHhCCChHHHHHHHHHHHhcC
Q 023901 118 GVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDA-V--NPPALKGLVQKTGFSMEDVLRKYIRYALNE 194 (275)
Q Consensus 118 GiTFviA~vRTvrK~tSPraKRkR~VnKNa~LvkSLdeyfp~gRda-~--~~gvLk~L~~KTGFs~~Ei~RKYirY~LnE 194 (275)
..+|+-+|.=|+|.|+||.. |++-|-+.|..--.. . .....+.++++ ...|++..+..--.
T Consensus 25 d~~f~~~Flltyr~F~tp~~-----------ll~~L~~rf~~~~~~~~~~~~~~~~~~~~r----v~~~l~~Wv~~~~~- 88 (127)
T smart00229 25 DPFFVETFLLTYRSFITTQE-----------LLQLLLYRYNAIPPESWVERKVNPLRVKNR----VLNILRHWVENYWQ- 88 (127)
T ss_pred CHHHHHHHHHHhhhhCCHHH-----------HHHHHHHHhCCCCcHHHHHHHhhHHHHHHH----HHHHHHHHHHHCCc-
Confidence 45778888889999999983 555555555443222 0 01111122222 35566665554443
Q ss_pred CCCChH--HHHHHHHHHhhcCCC-cHHHHHHHHHHHHh
Q 023901 195 KPFNPD--LVVNLIQLRKASMLD-DSQVAEILNEISRR 229 (275)
Q Consensus 195 r~F~~d--~VaDLi~Lr~as~L~-d~evaeiL~E~s~R 229 (275)
-|+.+ ....|..+-....-+ ..+..+-|.++.++
T Consensus 89 -dF~~~~~l~~~l~~f~~~~~~~~~~~~~~~l~~~~~~ 125 (127)
T smart00229 89 -DFEDDPKLILRLLEFLDLVDQEKGPGLVTSLQELLQR 125 (127)
T ss_pred -ccccCHHHHHHHHHHHHHHhhCcCCCHHHHHHHHHHh
Confidence 46655 555555554433333 33444555555544
No 163
>PRK08123 histidinol-phosphatase; Reviewed
Probab=24.47 E-value=1.2e+02 Score=26.97 Aligned_cols=69 Identities=22% Similarity=0.280 Sum_probs=45.2
Q ss_pred CChHHHHHHHHHHHhc--CC---CCChHHHH--HHHHHH-hhcCC-CcHHHHHHHHHHHHhhhhhcCCeeeeccccch
Q 023901 178 FSMEDVLRKYIRYALN--EK---PFNPDLVV--NLIQLR-KASML-DDSQVAEILNEISRRFVREKGPVVMNMSGYSE 246 (275)
Q Consensus 178 Fs~~Ei~RKYirY~Ln--Er---~F~~d~Va--DLi~Lr-~as~L-~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te 246 (275)
=+.+++++.|....++ +. .|++|.++ |||..- +-... .++...+.+.++.+.+.+.-..|=+|++|+..
T Consensus 145 ~~~~~~~~~Y~~~~~~~~~~~~~~~~~dvlgH~Dli~r~~~~~~~~~~~~~~~~~~~il~~~~~~g~~lEINtsgl~~ 222 (270)
T PRK08123 145 GSIEAVYEAYYETVLQSIEADLGPYKPKRIGHITLVRKFQKLFPPDFDEKNKELIEDILALIKKRGYELDFNTAGLRK 222 (270)
T ss_pred CCHHHHHHHHHHHHHHHHHhcccccCCCEeecchHHHHhCccCCcccCHHHHHHHHHHHHHHHHcCCEEEEEchhhcC
Confidence 3778999999998887 43 25566766 555421 11111 14567777777777776666666699999975
No 164
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=24.36 E-value=91 Score=30.51 Aligned_cols=82 Identities=23% Similarity=0.263 Sum_probs=61.4
Q ss_pred hhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCC--chHHHHHHHHhCCChHHHH----HHHHHHHhcCCCCChHHHH
Q 023901 130 KKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVN--PPALKGLVQKTGFSMEDVL----RKYIRYALNEKPFNPDLVV 203 (275)
Q Consensus 130 rK~tSPraKRkR~VnKNa~LvkSLdeyfp~gRda~~--~gvLk~L~~KTGFs~~Ei~----RKYirY~LnEr~F~~d~Va 203 (275)
++|-+.|.|| |-.+||+. +-|+|||...+.--- ..+=.+|.+|||.+...|- +|-|||.=|=-+|-++ +
T Consensus 183 ~r~ldarRKR-RNFsK~aT--eiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~ee--~ 257 (334)
T KOG0774|consen 183 SRFLDARRKR-RNFSKQAT--EILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQEE--A 257 (334)
T ss_pred HHHHHHHHhh-cccchhHH--HHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhhh--h
Confidence 4566665554 34577764 779999998776433 4466789999999998885 5889999888777554 7
Q ss_pred HHHHHHhhcCCCc
Q 023901 204 NLIQLRKASMLDD 216 (275)
Q Consensus 204 DLi~Lr~as~L~d 216 (275)
||-++|+|-.-+.
T Consensus 258 ~l~~~kk~~~~~~ 270 (334)
T KOG0774|consen 258 NLYAAKKAVDATP 270 (334)
T ss_pred hhHhhcccccCCC
Confidence 9999999876554
No 165
>PRK10026 arsenate reductase; Provisional
Probab=24.28 E-value=1e+02 Score=26.16 Aligned_cols=81 Identities=27% Similarity=0.433 Sum_probs=54.3
Q ss_pred CCCCchHHHHHHHHhCCChHHHHHH----HHHHHhcCCCCChHHHHHHHH--------------HHhhcCCCcHHHHHHH
Q 023901 162 DAVNPPALKGLVQKTGFSMEDVLRK----YIRYALNEKPFNPDLVVNLIQ--------------LRKASMLDDSQVAEIL 223 (275)
Q Consensus 162 da~~~gvLk~L~~KTGFs~~Ei~RK----YirY~LnEr~F~~d~VaDLi~--------------Lr~as~L~d~evaeiL 223 (275)
+..+...|+.+-.++|.+..+++|+ |=.-.+.+...+.+.+-++++ -+...|=..+.|.++|
T Consensus 37 ~ppt~~eL~~~l~~~g~~~~~lint~~~~yr~L~~~~~~ls~~e~l~ll~~~P~LIKRPIi~~~~~a~i~Rp~e~v~~~l 116 (141)
T PRK10026 37 TPPTRDELVKLIADMGISVRALLRKNVEPYEELGLAEDKFTDDQLIDFMLQHPILINRPIVVTPLGTRLCRPSEVVLEIL 116 (141)
T ss_pred CCcCHHHHHHHHHhCCCCHHHHHHcCCchHHHcCCCccCCCHHHHHHHHHhCccceeCcEEEcCCCeEEECCHHHHHHHh
Confidence 5677899999999999999999986 333334444566565555554 2455667778888888
Q ss_pred HHHHHh--hhhhcCCeeeeccc
Q 023901 224 NEISRR--FVREKGPVVMNMSG 243 (275)
Q Consensus 224 ~E~s~R--i~~~~G~vmmn~~G 243 (275)
. .+.+ +|++-|-+++|-.|
T Consensus 117 ~-~~~~~~~~~~~~~~~~~~~~ 137 (141)
T PRK10026 117 P-DAQKGAFTKEDGEKVVDEAG 137 (141)
T ss_pred c-ccccccccccCCeEeecCCC
Confidence 3 2332 56666666666555
No 166
>PRK13848 conjugal transfer protein TraC; Provisional
Probab=24.07 E-value=91 Score=26.09 Aligned_cols=31 Identities=23% Similarity=0.516 Sum_probs=25.4
Q ss_pred HHHHhhcC---CCcHHHHHHHHHHHHhhhhhcCC
Q 023901 206 IQLRKASM---LDDSQVAEILNEISRRFVREKGP 236 (275)
Q Consensus 206 i~Lr~as~---L~d~evaeiL~E~s~Ri~~~~G~ 236 (275)
|+||..++ ++|.|+..++.|++.|+-+-+|.
T Consensus 33 iAlKAGLgeieI~d~eL~~aFeeiAaRFR~g~~~ 66 (98)
T PRK13848 33 IALKAGLGEIEIEEAELQAAFEELAKRFRGGKGA 66 (98)
T ss_pred HHHHcCccccccCHHHHHHHHHHHHHHHhcCCCc
Confidence 56666554 79999999999999999887775
No 167
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=24.04 E-value=3.9e+02 Score=21.58 Aligned_cols=9 Identities=11% Similarity=0.420 Sum_probs=4.2
Q ss_pred HhCCChHHH
Q 023901 175 KTGFSMEDV 183 (275)
Q Consensus 175 KTGFs~~Ei 183 (275)
+.||+..||
T Consensus 55 ~lG~sL~eI 63 (127)
T TIGR02047 55 TLDMSLAEI 63 (127)
T ss_pred HcCCCHHHH
Confidence 444444443
No 168
>PRK13749 transcriptional regulator MerD; Provisional
Probab=23.79 E-value=1.2e+02 Score=25.20 Aligned_cols=56 Identities=18% Similarity=0.229 Sum_probs=41.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHh---------cCCCCChHHHHHHHHHH--hhcCCCcHHHHHHHHH
Q 023901 169 LKGLVQKTGFSMEDVLRKYIRYAL---------NEKPFNPDLVVNLIQLR--KASMLDDSQVAEILNE 225 (275)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~L---------nEr~F~~d~VaDLi~Lr--~as~L~d~evaeiL~E 225 (275)
+.++.++||-|..- +|-|=.=-| +=|-|+++.|..|-.++ +.+|++=+||+++|.-
T Consensus 6 IgelA~~~gvS~~t-iR~YE~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l 72 (121)
T PRK13749 6 VSRLALDAGVSVHI-VRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRA 72 (121)
T ss_pred HHHHHHHHCCCHHH-HHHHHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence 56788888887644 455532222 33679999999998888 5899999999999874
No 169
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=23.72 E-value=2.7e+02 Score=23.78 Aligned_cols=80 Identities=29% Similarity=0.433 Sum_probs=53.0
Q ss_pred hCCChHHHHHHHHHHHhcC--------CCC----ChHHHHHHHHHHhhcC------------CCcHHHHHHHHHHHHhhh
Q 023901 176 TGFSMEDVLRKYIRYALNE--------KPF----NPDLVVNLIQLRKASM------------LDDSQVAEILNEISRRFV 231 (275)
Q Consensus 176 TGFs~~Ei~RKYirY~LnE--------r~F----~~d~VaDLi~Lr~as~------------L~d~evaeiL~E~s~Ri~ 231 (275)
.||+-.=++|--+++-..+ .++ +..+...+-++-+.++ ++| +-+++.++.+-+.
T Consensus 6 lGf~~~~~~r~~~~~~~~~~~~~vilv~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~vd~~d--~~~~~~~v~~~i~ 83 (203)
T TIGR01884 6 VGFDEKFIIRALMEIGIKEEGDLVILVKSPIEDGARRAVESLRAIISDLGGNLVEGTIKEIELKD--VPSILRQMSDIIK 83 (203)
T ss_pred eccchHHHHHHHHhcCCCccCcEEEEEcCCCchHHHHHHHHHHHHHHHhccCCCcceEEEEecCC--HHHHHHHHHHHHH
Confidence 4788888888777776555 222 3445566666655553 444 5699999999999
Q ss_pred hhcCC-eeeeccccchhhhhhHHHHHHHHHhh
Q 023901 232 REKGP-VVMNMSGYSEKGFKRKLAVQALFGKV 262 (275)
Q Consensus 232 ~~~G~-vmmn~~G~Te~G~kRK~a~~aLF~K~ 262 (275)
+.-++ |.+|++| |+ |-+.+..+|.-+
T Consensus 84 ~~~~~~v~vnlsg----G~-R~l~~~~~~a~~ 110 (203)
T TIGR01884 84 EEREPRVIINLSG----GM-RILILILLLLAI 110 (203)
T ss_pred hcccCcEEEEcCC----Cc-hHHHHHHHHHHH
Confidence 99888 9999876 22 444444444433
No 170
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=23.68 E-value=1.3e+02 Score=20.69 Aligned_cols=32 Identities=28% Similarity=0.302 Sum_probs=25.6
Q ss_pred CCChHHHHHHHHHHHhcCCCCChHHHHHHHHH
Q 023901 177 GFSMEDVLRKYIRYALNEKPFNPDLVVNLIQL 208 (275)
Q Consensus 177 GFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~L 208 (275)
-|+..||.+=-.-..|++.-|+++.++.+++|
T Consensus 38 ~y~~~dl~~l~~i~~lr~~g~~~~~i~~~l~l 69 (70)
T smart00422 38 LYSDEDLERLRFIKRLKELGFSLEEIKELLEL 69 (70)
T ss_pred ecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 38888887766666678899999999998876
No 171
>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]
Probab=23.55 E-value=2.2e+02 Score=30.86 Aligned_cols=79 Identities=30% Similarity=0.369 Sum_probs=45.4
Q ss_pred HHhCCChHHHHHHHHHHHhcCCCC-C----hHHHHHHHHHHhhc--CC-------------------------------C
Q 023901 174 QKTGFSMEDVLRKYIRYALNEKPF-N----PDLVVNLIQLRKAS--ML-------------------------------D 215 (275)
Q Consensus 174 ~KTGFs~~Ei~RKYirY~LnEr~F-~----~d~VaDLi~Lr~as--~L-------------------------------~ 215 (275)
..|+|+++ .+||||+||=|=+|= + ...|.--.+||+-. |. +
T Consensus 554 ~~~~~~~e-~vrkYi~yAR~~~P~ls~ea~~~lve~Y~~lR~~~~~~~~~~s~~ITvRqLESlIRLsEA~Ar~~~~devt 632 (764)
T KOG0480|consen 554 RVCVYTLE-QVRKYIRYARNFKPKLSKEASEMLVEKYKGLRQRDAQGNNRSSYRITVRQLESLIRLSEARARVECRDEVT 632 (764)
T ss_pred ccccccHH-HHHHHHHHHHhcCccccHHHHHHHHHHHHHHHHhhccccCcccccccHHHHHHHHHHHHHHHhhhhhhhcc
Confidence 33788875 569999999743321 1 13344445666544 22 2
Q ss_pred cHHHHHHHHHHHHhhhhhcCCeeeecc--------ccchhhhhhHH
Q 023901 216 DSQVAEILNEISRRFVREKGPVVMNMS--------GYSEKGFKRKL 253 (275)
Q Consensus 216 d~evaeiL~E~s~Ri~~~~G~vmmn~~--------G~Te~G~kRK~ 253 (275)
.++|.|+..=.=+-|++.+|+=+=... |++..+-+.|.
T Consensus 633 ~~~v~ea~eLlk~Siv~ve~ddi~~~d~~~~~~~~g~s~~~~~k~~ 678 (764)
T KOG0480|consen 633 KEDVEEAVELLKKSIVRVEGDDIELDDNDGENDSGGESAQKPKKKF 678 (764)
T ss_pred HHHHHHHHHHHHhhheeeccccccccccccccCcccccccchhhHH
Confidence 344445444444568888887655444 67766664333
No 172
>PF01823 MACPF: MAC/Perforin domain; InterPro: IPR020864 The membrane attack complex/perforin (MACPF) domain is conserved in bacteria, fungi, mammals and plants. It was originally identified and named as being common to five complement components (C6, C7, C8-alpha, C8-beta, and C9) and perforin. These molecules perform critical functions in innate and adaptive immunity. The MAC family proteins and perforin are known to participate in lytic pore formation. In response to pathogen infection, a sequential and highly specific interaction between the constituent elements occurs to form transmembrane channels which are known as the membrane-attack complex (MAC).Only a few other MACPF proteins have been characterised and several are thought to form pores for invasion or protection [, , ]. Examples are proteins from malarial parasites [], the cytolytic toxins from sea anemones [], and proteins that provide plant immunity [, ]. Functionally uncharacterised MACPF proteins are also evident in pathogenic bacteria such as Chlamydia spp [] and Photorhabdus luminescens (Xenorhabdus luminescens) []. The MACPF domain is commonly found to be associated with other N- and C-terminal domains, such as TSP1 (see PDOC50092 from PROSITEDOC), LDLRA (see PDOC00929 from PROSITEDOC), EGF-like (see PDOC00021 from PROSITEDOC),Sushi/CCP/SCR (see PDOC50923 from PROSITEDOC), FIMAC or C2 (see PDOC00380 from PROSITEDOC). They probably control or target MACPF function [, ]. The MACPF domain oligomerizes, undergoes conformational change, and is required for lytic activity. The MACPF domain consists of a central kinked four-stranded antiparallel beta sheet surrounded by alpha helices and beta strands, forming two structural segments. Overall, the MACPF domain has a thin L-shaped appearance. MACPF domains exhibit limited sequence similarity but contain a signature [YW]-G-[TS]-H-[FY]-x(6)-G-G motif [, , ]. Some proteins known to contain a MACPF domain are listed below: Vertebrate complement proteins C6 to C9. Complement factors C6 to C9 assemble to form a scaffold, the membrane attack complex (MAC), that permits C9 polymerisation into pores that lyse Gram-negative pathogens [, ]. Vertebrate perforin. It is delivered by natural killer cells and cytotoxic T lymphocytes and forms oligomeric pores (12 to 18 monomers) in the plasma membrane of either virus-infected or transformed cells. Arabidopsis thaliana (Mouse-ear cress) constitutively activated cell death 1 (CAD1) protein. It is likely to act as a mediator that recognises plant signals for pathogen infection []. Arabidopsis thaliana (Mouse-ear cress) necrotic spotted lesions 1 (NSL1) protein []. Venomous sea anemone Phyllodiscus semoni (Night anemone) toxins PsTX-60A and PsTX-60B []. Venomous sea anemone Actineria villosa (Okinawan sea anemone) toxin AvTX-60A []. Plasmodium sporozoite microneme protein essential for cell traversal 2 (SPECT2). It is essential for the membrane-wounding activity of the sporozoite and is involved in its traversal of the sinusoidal cell layer prior to hepatocyte-infection []. P. luminescens Plu-MACPF. Although nonlytic, it was shown to bind to cell membranes []. Chlamydial putative uncharacterised protein CT153 []. ; PDB: 2QP2_A 3OJY_B 3NSJ_A 4E0S_B 3T5O_A 4A5W_B 2QQH_A 2RD7_A.
Probab=23.50 E-value=34 Score=27.93 Aligned_cols=37 Identities=16% Similarity=0.331 Sum_probs=22.9
Q ss_pred CChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCeeee
Q 023901 197 FNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMN 240 (275)
Q Consensus 197 F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn 240 (275)
++++++.||-+|-.-. ++.+ .+.-.+++++|||-++-
T Consensus 45 L~~~F~~~l~~L~~~~--~~~~-----~~~y~~f~~~yGTH~v~ 81 (212)
T PF01823_consen 45 LTPEFLSDLNALPAEY--NSDN-----TDEYYRFFDKYGTHYVT 81 (212)
T ss_dssp BGHHHHHHHHTSHSS----HHH-----HHHHHHHHHHH-SEEEE
T ss_pred cCHHHHHHHHhhCccc--Cccc-----hHHHHHHHHHhCcEEEE
Confidence 7889988887774331 1111 11167899999998763
No 173
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=23.37 E-value=72 Score=25.25 Aligned_cols=45 Identities=7% Similarity=-0.009 Sum_probs=32.0
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 023901 185 RKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRR 229 (275)
Q Consensus 185 RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~R 229 (275)
.|.|+=+-.+..+-..+.+|=-++=++.|||++|.+-+++---+.
T Consensus 7 nrli~~L~~dp~~rerF~~DPea~~~~~gLt~eE~~aL~~~D~~~ 51 (81)
T cd07922 7 NRLIQELFKDPGLIERFQDDPSAVFEEYGLTPAERAALREGTFGA 51 (81)
T ss_pred HHHHHHHhcCHHHHHHHHHCHHHHHHHcCCCHHHHHHHHccCHHH
Confidence 556666555555666777777888889999999998776544333
No 174
>PRK11565 dkgA 2,5-diketo-D-gluconate reductase A; Provisional
Probab=23.26 E-value=2.6e+02 Score=24.90 Aligned_cols=55 Identities=20% Similarity=0.394 Sum_probs=39.3
Q ss_pred CCchHHHHHHHHhCCChHHHHHHHHHHHhcCC------CCChHHHHHHHHHHhhcCCCcHHHHHH
Q 023901 164 VNPPALKGLVQKTGFSMEDVLRKYIRYALNEK------PFNPDLVVNLIQLRKASMLDDSQVAEI 222 (275)
Q Consensus 164 ~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr------~F~~d~VaDLi~Lr~as~L~d~evaei 222 (275)
.....|+.+.++.|-|+.+|. |||.|.-. .-+++-+.|-++.-. ..||++|+++|
T Consensus 197 ~~~~~l~~ia~~~g~s~aq~a---L~w~l~~~~~~I~g~~~~~~i~~n~~a~~-~~Ls~~~~~~i 257 (275)
T PRK11565 197 FDQKVIRDLADKYGKTPAQIV---IRWHLDSGLVVIPKSVTPSRIAENFDVFD-FRLDKDELGEI 257 (275)
T ss_pred ccCHHHHHHHHHhCCCHHHHH---HHHHHcCCCEeeCCCCCHHHHHHHHhccC-CCcCHHHHHHH
Confidence 345789999999999999997 56667542 234566666555433 36999998876
No 175
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=23.26 E-value=4e+02 Score=26.68 Aligned_cols=75 Identities=16% Similarity=0.202 Sum_probs=52.7
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHH
Q 023901 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEI 222 (275)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~R---KYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaei 222 (275)
...+.+.|...+.+.+-.++..+++.|.+.++-|+-+++. +-+-| ....-+.+.|.+++. ..+++.+-++
T Consensus 180 ~~~i~~~l~~il~~egi~~~~~al~~ia~~s~GslR~al~lLdq~ia~--~~~~It~~~V~~~lg-----~~~~~~i~~l 252 (509)
T PRK14958 180 PLQIAAHCQHLLKEENVEFENAALDLLARAANGSVRDALSLLDQSIAY--GNGKVLIADVKTMLG-----TIEPLLLFDI 252 (509)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhc--CCCCcCHHHHHHHHC-----CCCHHHHHHH
Confidence 4567778888898888888999999999999999888755 55556 355677777776642 2344445444
Q ss_pred HHHHH
Q 023901 223 LNEIS 227 (275)
Q Consensus 223 L~E~s 227 (275)
+..++
T Consensus 253 l~al~ 257 (509)
T PRK14958 253 LEALA 257 (509)
T ss_pred HHHHH
Confidence 44443
No 176
>PF14163 SieB: Superinfection exclusion protein B
Probab=23.05 E-value=1.7e+02 Score=24.08 Aligned_cols=12 Identities=42% Similarity=0.717 Sum_probs=6.0
Q ss_pred CCChHHHHHHHH
Q 023901 196 PFNPDLVVNLIQ 207 (275)
Q Consensus 196 ~F~~d~VaDLi~ 207 (275)
+.|...|..|++
T Consensus 101 p~~~~~v~~L~~ 112 (151)
T PF14163_consen 101 PYNNPAVKSLLQ 112 (151)
T ss_pred cCCCHHHHHHHH
Confidence 444555555544
No 177
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=22.84 E-value=2e+02 Score=29.94 Aligned_cols=59 Identities=20% Similarity=0.340 Sum_probs=42.6
Q ss_pred ChHHHHHHHHHHHhc-------CCCCChHHHHHHHHH--Hhh-----cCCCcHHHHHHHHHHHHhhhhhcCCee
Q 023901 179 SMEDVLRKYIRYALN-------EKPFNPDLVVNLIQL--RKA-----SMLDDSQVAEILNEISRRFVREKGPVV 238 (275)
Q Consensus 179 s~~Ei~RKYirY~Ln-------Er~F~~d~VaDLi~L--r~a-----s~L~d~evaeiL~E~s~Ri~~~~G~vm 238 (275)
+..|..++|++|.-. -++|+.++|+-||.- |.| +-|...++++++++ +.-+.++.|.=.
T Consensus 315 d~~e~~~~~~~~iaqe~~~~G~l~~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~-a~~~a~~~~~~~ 387 (637)
T PRK13765 315 DTPENRRKLVRFVAQEVKRDGKIPHFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRV-AGDIARSEGAEL 387 (637)
T ss_pred CCHHHHHHHHHHHHHHhhhccCCCCCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHH-HHHHHHhhccce
Confidence 357889999998653 358999999999963 333 34678899999999 555666655433
No 178
>PRK09459 pspG phage shock protein G; Reviewed
Probab=22.75 E-value=51 Score=26.40 Aligned_cols=17 Identities=18% Similarity=0.579 Sum_probs=8.5
Q ss_pred hhhhhhhhhcCChhhhh
Q 023901 123 IAFVKTVKKFNSPKFKR 139 (275)
Q Consensus 123 iA~vRTvrK~tSPraKR 139 (275)
+=+||.++|-.+||.||
T Consensus 58 vW~~r~~~~~~~~~y~~ 74 (76)
T PRK09459 58 VWVIRAIKAPKVPRYQR 74 (76)
T ss_pred HHHHHHhhccccccccc
Confidence 34556655555555443
No 179
>PLN02196 abscisic acid 8'-hydroxylase
Probab=22.53 E-value=3.5e+02 Score=25.40 Aligned_cols=67 Identities=12% Similarity=0.208 Sum_probs=36.7
Q ss_pred cccccCCCCCCCCCchhHHHHHHHhhhhHhhhhhhhhhhhcCChhhhhhhhhcchhhHH---hhHHHHHhcCCC
Q 023901 92 VTQAIPGPRVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVC---KTIDELFQKGGD 162 (275)
Q Consensus 92 v~qaiPgPrvg~s~lPwiLAlPLAylGiTFviA~vRTvrK~tSPraKRkR~VnKNa~Lv---kSLdeyfp~gRd 162 (275)
..|-||+|- |..++|+++-+...+.+ .....+.+..+||.+. =+-+..+++..++ +-+.+.|.++.+
T Consensus 30 ~~~~~~~Pp-gp~~~P~iG~~~~~~~~-~~~~~~~~~~~~yG~i--~~~~~~~~~~v~v~~p~~~~~vl~~~~~ 99 (463)
T PLN02196 30 SSTKLPLPP-GTMGWPYVGETFQLYSQ-DPNVFFASKQKRYGSV--FKTHVLGCPCVMISSPEAAKFVLVTKSH 99 (463)
T ss_pred CCCCCCCCC-CCCCCCccchHHHHHhc-CHHHHHHHHHHHhhhh--heeeecCCceEEEcCHHHHHHHHhCCCC
Confidence 346678873 55678888754333322 3445567778888642 2444455555444 233444544444
No 180
>PRK14951 DNA polymerase III subunits gamma and tau; Provisional
Probab=22.51 E-value=4.5e+02 Score=27.44 Aligned_cols=59 Identities=19% Similarity=0.283 Sum_probs=44.6
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH---HHHHHHhcCCCCChHHHHHHH
Q 023901 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYALNEKPFNPDLVVNLI 206 (275)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~R---KYirY~LnEr~F~~d~VaDLi 206 (275)
+..+.+.|.+.+.+.+-.++..+|+.|.+.++-|+.+++. +.+.|. .+.-+.+.|.+++
T Consensus 185 ~eei~~~L~~i~~~egi~ie~~AL~~La~~s~GslR~al~lLdq~ia~~--~~~It~~~V~~~L 246 (618)
T PRK14951 185 PETVLEHLTQVLAAENVPAEPQALRLLARAARGSMRDALSLTDQAIAFG--SGQLQEAAVRQML 246 (618)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhc--CCCcCHHHHHHHH
Confidence 4567777777778888888999999999999999988765 456663 5566777766554
No 181
>PF08519 RFC1: Replication factor RFC1 C terminal domain; InterPro: IPR013725 This is the C-terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo [, ]. ; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_A.
Probab=22.48 E-value=39 Score=28.81 Aligned_cols=48 Identities=23% Similarity=0.245 Sum_probs=0.0
Q ss_pred ChHHHHHHHHHHHhc--CCCCCh---HHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 023901 179 SMEDVLRKYIRYALN--EKPFNP---DLVVNLIQLRKASMLDDSQVAEILNEIS 227 (275)
Q Consensus 179 s~~Ei~RKYirY~Ln--Er~F~~---d~VaDLi~Lr~as~L~d~evaeiL~E~s 227 (275)
+..||...|+-++.. -+|.-. |.|.+.|.+-...+|+-+|+ |-|.|++
T Consensus 77 ~~~~v~~~Ylp~L~~~l~~pL~~~~~~~v~~vi~~Md~Y~Ltred~-d~i~el~ 129 (155)
T PF08519_consen 77 SKSEVRLDYLPLLRQKLTQPLIEQGKDGVDEVIDLMDEYGLTREDW-DNIMELS 129 (155)
T ss_dssp ------------------------------------------------------
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCcccHHHHHHHHHHhCCCHHHH-HHHHHhc
Confidence 346666666544332 122222 48999999999999999999 8888887
No 182
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.41 E-value=3.4e+02 Score=21.74 Aligned_cols=12 Identities=17% Similarity=0.216 Sum_probs=5.2
Q ss_pred cCCCcHHHHHHH
Q 023901 212 SMLDDSQVAEIL 223 (275)
Q Consensus 212 s~L~d~evaeiL 223 (275)
+|++=+||.++|
T Consensus 54 ~G~~L~~I~~~l 65 (118)
T cd04776 54 LGFSLEEIRELL 65 (118)
T ss_pred CCCCHHHHHHHH
Confidence 344444444444
No 183
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=22.40 E-value=1e+02 Score=20.50 Aligned_cols=28 Identities=29% Similarity=0.306 Sum_probs=22.6
Q ss_pred ChHHHHHHHHHHHhcCCCCChHHHHHHH
Q 023901 179 SMEDVLRKYIRYALNEKPFNPDLVVNLI 206 (275)
Q Consensus 179 s~~Ei~RKYirY~LnEr~F~~d~VaDLi 206 (275)
|++|+=+.||+.+|..-..|...+|.++
T Consensus 1 sl~~~E~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 1 SLEEFEKQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp -HHHHHHHHHHHHHHHTTT-HHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence 5788899999999999999988887654
No 184
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=22.38 E-value=84 Score=22.23 Aligned_cols=58 Identities=14% Similarity=0.135 Sum_probs=37.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhh-cCCCcHHHHHHHHHH
Q 023901 169 LKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKA-SMLDDSQVAEILNEI 226 (275)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~a-s~L~d~evaeiL~E~ 226 (275)
++-+++..|......-+..|...+++-.|++|.|--+|..=.. -..+-+=+..||+.-
T Consensus 2 ~~~~e~~~~~~~s~~e~~~l~~~~~~~~~~~~~v~~ai~~~~~~~~~~~~Yi~~Il~~W 60 (77)
T PF07261_consen 2 FEFYEKNFGRPPSPSEIEKLEKWIDDYGFSPEVVNEAIEYALENNKRSFNYIEKILNNW 60 (77)
T ss_dssp HHHHHCCCTSS--HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCT--SHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence 4456666788888889999999999889999999776654332 123344455555543
No 185
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=22.35 E-value=4.6e+02 Score=21.84 Aligned_cols=44 Identities=9% Similarity=0.039 Sum_probs=25.6
Q ss_pred HHHHHHHHHhc----CCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023901 183 VLRKYIRYALN----EKPFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (275)
Q Consensus 183 i~RKYirY~Ln----Er~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (275)
.+++|++|.-. =..++++.|.+.+.-...-+++.+.+...+.-+
T Consensus 33 ~~~~~~~~~~~~~~~~~~l~~~~i~~~~~~~~~~~~~~~t~~~~~~~l 80 (299)
T PRK00283 33 DLELFAEWLAARGLSLAEATRDDLQAFLAELAEGGYKATSSARRLSAL 80 (299)
T ss_pred HHHHHHHHHHhcCCChHHCCHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence 34555555431 145677777777766655567776666554433
No 186
>PRK01326 prsA foldase protein PrsA; Reviewed
Probab=22.33 E-value=1.4e+02 Score=27.60 Aligned_cols=61 Identities=8% Similarity=0.221 Sum_probs=36.7
Q ss_pred HHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCeeeeccccchhhhhhHHHHHHHHHhh
Q 023901 201 LVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRKLAVQALFGKV 262 (275)
Q Consensus 201 ~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a~~aLF~K~ 262 (275)
++.+++.-+.+...+|+||.+.++++.++.=..| -=.+.-.|+|+.-+++.+--+-+..++
T Consensus 61 ~i~~~l~~q~~i~Vsd~EVd~~i~~i~~q~g~~f-~~~L~~~G~t~~~~k~~ir~~ll~~~~ 121 (310)
T PRK01326 61 TISRVFEKQYGDKVSDKEVEKAYAKTAKQYGASF-SRALAQAGLTPETYKAQIRTSKLVEYA 121 (310)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhHHH-HHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 4555555455556788888888888877632111 112344688888877766555444443
No 187
>cd03022 DsbA_HCCA_Iso DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1,2-dihydroxynapthalene by a dioxygenase, into cis-o-hydroxybenzylidenepyruvate (cHBPA). This is the fourth reaction in a six-step pathway that converts napthalene into salicylate. HCCA isomerase is unique to bacteria that degrade polycyclic aromatic compounds. It is closely related to the eukaryotic protein, GSH transferase kappa (GSTK).
Probab=22.29 E-value=1.8e+02 Score=23.33 Aligned_cols=37 Identities=19% Similarity=0.434 Sum_probs=27.3
Q ss_pred hhHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHH
Q 023901 147 AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV 183 (275)
Q Consensus 147 a~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei 183 (275)
.++-.-.+.||..+++-.+..+|..+..+.|++.+++
T Consensus 104 ~~~~~lf~a~~~~~~~i~~~~~l~~~a~~~Gld~~~~ 140 (192)
T cd03022 104 AFARAVFRALWGEGLDIADPAVLAAVAAAAGLDADEL 140 (192)
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHHHcCCCHHHH
Confidence 3443444567778887677889999999999987654
No 188
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=22.24 E-value=74 Score=22.05 Aligned_cols=55 Identities=25% Similarity=0.367 Sum_probs=35.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHh--------cCCCCChHHHHHH---HHHHhhcCCCcHHHHHHHHH
Q 023901 169 LKGLVQKTGFSMEDVLRKYIRYAL--------NEKPFNPDLVVNL---IQLRKASMLDDSQVAEILNE 225 (275)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~L--------nEr~F~~d~VaDL---i~Lr~as~L~d~evaeiL~E 225 (275)
++++.+.+|-+. +.+|.|.+=-| +-+-|+++.|.-| ..|++ .|++-+||+++|++
T Consensus 3 i~eva~~~gvs~-~tlr~y~~~gll~~~~~~~g~r~y~~~dv~~l~~i~~l~~-~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 3 IKEVAKLLGVSP-STLRYYEREGLLPPPRDENGYRYYSEEDVERLREIKELRK-QGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHHHTTTTH-HHHHHHHHTTSSTTBESTTSSEEE-HHHHHHHHHHHHHHH-TTTHHHHHHHHH--
T ss_pred HHHHHHHHCcCH-HHHHHHHHhcCcccccccCceeeccHHHHHHHHHHHHHHH-CcCCHHHHHHHHcc
Confidence 457788888764 45677765322 1256777777655 45666 99999999999875
No 189
>PRK08456 flagellar motor protein MotA; Validated
Probab=22.16 E-value=4.8e+02 Score=23.83 Aligned_cols=54 Identities=9% Similarity=0.059 Sum_probs=41.7
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHH
Q 023901 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQ 207 (275)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~ 207 (275)
.+++.+-++..++|... +..|++...=..++++++.+++... ..+++.+.+.+.
T Consensus 76 ~li~~l~~l~~~~r~~g----~laLe~~~~~~~~~fl~~gL~~~~~--g~~~~~i~~~le 129 (257)
T PRK08456 76 ERIKQLVELATLARKDG----VLALEGRVAQIEDEFLKNGLSMLVD--GKDLEEIKESME 129 (257)
T ss_pred HHHHHHHHHHHHhhhhh----HHHHhhcccCcHHHHHHHHHHHhhc--CCCHHHHHHHHH
Confidence 77888999999888743 5567776666678899999998775 338888888876
No 190
>PF01323 DSBA: DSBA-like thioredoxin domain; InterPro: IPR001853 DSBA is a sub-family of the Thioredoxin family []. The efficient and correct folding of bacterial disulphide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyses disulphide-bond formation during the folding of secreted proteins. The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilising active-site interactions in the reduced form. DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulphide at the active site []. In the pathogenic bacterium Vibrio cholerae, the DsbA homologue (TcpG) is responsible for the folding, maturation and secretion of virulence factors. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA [].; GO: 0015035 protein disulfide oxidoreductase activity; PDB: 3GL5_A 3DKS_D 3RPP_C 3RPN_B 1YZX_A 3L9V_C 2IMD_A 2IME_A 2IMF_A 2B3S_B ....
Probab=22.03 E-value=2.2e+02 Score=22.76 Aligned_cols=38 Identities=16% Similarity=0.341 Sum_probs=26.8
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHH
Q 023901 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR 185 (275)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~R 185 (275)
+.-.-.+.||..|++--+..+|..+..+.|++.+++..
T Consensus 105 ~~~al~~a~~~~~~~i~~~~vl~~~~~~~Gld~~~~~~ 142 (193)
T PF01323_consen 105 FADALFRAYFVEGRDISDPDVLAEIAEEAGLDPDEFDA 142 (193)
T ss_dssp HHHHHHHHHHTSST-TSSHHHHHHHHHHTT--HHHHHH
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHHHcCCcHHHHHH
Confidence 33444567788888888899999999999998887543
No 191
>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells. Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....
Probab=21.96 E-value=3.1e+02 Score=21.65 Aligned_cols=82 Identities=22% Similarity=0.308 Sum_probs=47.0
Q ss_pred chHHHHHHHHhCCC---hHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCeeeecc
Q 023901 166 PPALKGLVQKTGFS---MEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMNMS 242 (275)
Q Consensus 166 ~gvLk~L~~KTGFs---~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~ 242 (275)
.-.-+.|.++.||. ..|++|+++.. .--.-..+.+. |..+-.+.|+-+.+++.+.-..-... .
T Consensus 10 ~t~~~~la~~~~~~~is~~~llr~~~~~----~s~~g~~i~~~--l~~g~~vp~~~v~~ll~~~l~~~~~~--------~ 75 (151)
T PF00406_consen 10 GTQAKRLAKRYGLVHISVGDLLREEIKS----DSELGKQIQEY--LDNGELVPDELVIELLKERLEQPPCN--------R 75 (151)
T ss_dssp HHHHHHHHHHHTSEEEEHHHHHHHHHHT----TSHHHHHHHHH--HHTTSS--HHHHHHHHHHHHHSGGTT--------T
T ss_pred HHHHHHHHHhcCcceechHHHHHHHHhh----hhHHHHHHHHH--HHhhccchHHHHHHHHHHHHhhhccc--------c
Confidence 33456788888985 89999999842 11111334444 45777788888888887755544222 3
Q ss_pred ccchhhhhhHHHHHHHHHh
Q 023901 243 GYSEKGFKRKLAVQALFGK 261 (275)
Q Consensus 243 G~Te~G~kRK~a~~aLF~K 261 (275)
|+=..||-|-..=...|.+
T Consensus 76 g~ildGfPrt~~Qa~~l~~ 94 (151)
T PF00406_consen 76 GFILDGFPRTLEQAEALEE 94 (151)
T ss_dssp EEEEESB-SSHHHHHHHHH
T ss_pred eeeeeeccccHHHHHHHHH
Confidence 3334466665553344444
No 192
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=21.92 E-value=33 Score=28.63 Aligned_cols=9 Identities=33% Similarity=0.549 Sum_probs=5.1
Q ss_pred HHHHhcchh
Q 023901 69 VEVEEELPW 77 (275)
Q Consensus 69 ~e~e~e~~w 77 (275)
||+|++|.|
T Consensus 100 ee~ddDmgf 108 (112)
T PTZ00373 100 EEEEDDLGF 108 (112)
T ss_pred ccccccccc
Confidence 444556765
No 193
>PF02459 Adeno_terminal: Adenoviral DNA terminal protein; InterPro: IPR003391 The genome of adenovirus contains a protein covalently bound to the 5' end of each strand of the linear DNA molecule []. Since adenovirus DNA replication is initiated at the termini of the DNA molecule it has been proposed that the terminal protein serves as the primer for initiation of replication. However, the priming function now appears to reside in the precursor form of the terminal protein (pTP) found on the 5' ends of nascent DNA strands replicated in vitro [, ] and as a component of DNA-protein complexes isolated from virions of the protease-deficient adenovirus serotype 2 (Ad2) mutant tsl. The pTP is encoded by the leftward-transcribed strand of the viral genome and comprises part of a transcription unit that also encodes the single-strand DNA binding protein [].; GO: 0003677 DNA binding, 0006260 DNA replication
Probab=21.84 E-value=34 Score=35.49 Aligned_cols=14 Identities=14% Similarity=0.600 Sum_probs=9.3
Q ss_pred HhhhhhhhhhhhcC
Q 023901 120 SFVIAFVKTVKKFN 133 (275)
Q Consensus 120 TFviA~vRTvrK~t 133 (275)
.|..-||.+..+..
T Consensus 360 nFa~~FY~~l~rl~ 373 (548)
T PF02459_consen 360 NFAVDFYELLERLE 373 (548)
T ss_pred HhHHHHHHHHHHHH
Confidence 57777777766543
No 194
>PF11377 DUF3180: Protein of unknown function (DUF3180); InterPro: IPR021517 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.
Probab=21.79 E-value=59 Score=27.28 Aligned_cols=38 Identities=13% Similarity=0.166 Sum_probs=23.0
Q ss_pred CCchhHHHHHHHhhhhHhhhhhhhhhhhcCChhhhhhhhh
Q 023901 104 SKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLV 143 (275)
Q Consensus 104 s~lPwiLAlPLAylGiTFviA~vRTvrK~tSPraKRkR~V 143 (275)
.++||...+.+..+++--+..-+ .+|++. .+..+++++
T Consensus 27 p~~p~~~~~~l~~la~~~~~~a~-~vr~~~-~~~~~~~~~ 64 (138)
T PF11377_consen 27 PPIPWTAGVTLLVLAAVELWLAW-QVRRRI-EIGPGRRQL 64 (138)
T ss_pred CCCchHHHHHHHHHHHHHHHHHH-HHHHHH-hcCCCCCCc
Confidence 35789999999888854444444 445555 333344443
No 195
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=21.55 E-value=33 Score=28.51 Aligned_cols=12 Identities=17% Similarity=0.459 Sum_probs=6.5
Q ss_pred hhHHHHHhcchh
Q 023901 66 EVEVEVEEELPW 77 (275)
Q Consensus 66 ~~e~e~e~e~~w 77 (275)
|+|||+|++|.|
T Consensus 98 e~eeE~ddDmGf 109 (113)
T PLN00138 98 EEKEESDDDMGF 109 (113)
T ss_pred cccccccccccc
Confidence 333455567765
No 196
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=21.45 E-value=2.5e+02 Score=24.28 Aligned_cols=37 Identities=30% Similarity=0.436 Sum_probs=19.1
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHH
Q 023901 169 LKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLI 206 (275)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi 206 (275)
|+.|..+.|++..+|+.+-.+|++. +.|+++...+++
T Consensus 250 l~~ll~~~g~~~~~i~~~l~~~~~~-~~~~~~~l~~~~ 286 (319)
T PRK00440 250 LRDLMIDYGLSGEDIIKQIHREVWS-LDIPEELKVELI 286 (319)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHh-cCCCHHHHHHHH
Confidence 4444444566666666555555442 455555444444
No 197
>PF07308 DUF1456: Protein of unknown function (DUF1456); InterPro: IPR009921 This domain occurs in several hypothetical bacterial proteins of around 150 residues in length. The function of this domain is unknown.
Probab=21.42 E-value=91 Score=23.68 Aligned_cols=39 Identities=28% Similarity=0.572 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 023901 182 DVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNE 225 (275)
Q Consensus 182 Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E 225 (275)
+|+|| |||+|+ ++.+.+.++.+|= ..-+|.+|+...|+.
T Consensus 3 dILrk-LRyal~---l~d~~m~~if~l~-~~~vs~~el~a~lrk 41 (68)
T PF07308_consen 3 DILRK-LRYALD---LKDDDMIEIFALA-GFEVSKAELSAWLRK 41 (68)
T ss_pred HHHHH-HHHHHc---CChHHHHHHHHHc-CCccCHHHHHHHHCC
Confidence 45665 666665 4555555555543 245566666655543
No 198
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=21.34 E-value=26 Score=33.68 Aligned_cols=11 Identities=27% Similarity=0.308 Sum_probs=5.6
Q ss_pred hhHHHHHhcch
Q 023901 66 EVEVEVEEELP 76 (275)
Q Consensus 66 ~~e~e~e~e~~ 76 (275)
|+|||+|++|.
T Consensus 308 ~~~e~~~~d~~ 318 (323)
T PTZ00240 308 EEEESDEDDFG 318 (323)
T ss_pred CCccCcccccC
Confidence 44445555654
No 199
>PRK13477 bifunctional pantoate ligase/cytidylate kinase; Provisional
Probab=21.33 E-value=2.6e+02 Score=28.41 Aligned_cols=82 Identities=17% Similarity=0.196 Sum_probs=52.1
Q ss_pred cCCCCCCchHHHHHHHHhCCC---hHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCC---------------------
Q 023901 159 KGGDAVNPPALKGLVQKTGFS---MEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASML--------------------- 214 (275)
Q Consensus 159 ~gRda~~~gvLk~L~~KTGFs---~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L--------------------- 214 (275)
+.-.+.+....+.|.++.|+. ...++|..=++++.+. +|.+...++..|-.-+.+
T Consensus 291 G~sgsGKst~a~~la~~l~~~~~d~g~~YR~~a~~~l~~~-~~~~~~~~l~~l~~~l~~~~~~~~~~~~~i~~~~~dv~~ 369 (512)
T PRK13477 291 GPAGAGKSTVTRAVAKKLGLLYLDTGAMYRAVTWLVLQEG-IDPQDEEALAELLSDLKIELKPSSGSPQRVWINGEDVTE 369 (512)
T ss_pred CCCCCCHHHHHHHHHHHcCCeEecCCceehHHHHHHHHcC-cCCcCHHHHHHHHhcCCeeeccCCCCCceEEeCCcchHh
Confidence 344455667778888888764 4668888777777654 766554444443322211
Q ss_pred ---------------CcHHHHHHHHHHHHhhhhhcCCeeeecc
Q 023901 215 ---------------DDSQVAEILNEISRRFVREKGPVVMNMS 242 (275)
Q Consensus 215 ---------------~d~evaeiL~E~s~Ri~~~~G~vmmn~~ 242 (275)
...+|-+.|+++=|.+.++ |.+|||-.
T Consensus 370 ~iRs~eV~~~vS~ia~~p~VR~~l~~~qr~~~~~-~~iV~eGR 411 (512)
T PRK13477 370 AIRSPEVTSSVSAIAAQPAVRQALVKQQQRIGEK-GGLVAEGR 411 (512)
T ss_pred hhcchhHHHHHHHHhCCHHHHHHHHHHHHHHhhc-CCEEEEcc
Confidence 3457888899988887654 45777754
No 200
>cd03025 DsbA_FrnE_like DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=21.32 E-value=1.8e+02 Score=23.41 Aligned_cols=36 Identities=25% Similarity=0.470 Sum_probs=26.0
Q ss_pred HHhhH-HHHHhcCCCCCCchHHHHHHHHhCCChHHHH
Q 023901 149 VCKTI-DELFQKGGDAVNPPALKGLVQKTGFSMEDVL 184 (275)
Q Consensus 149 LvkSL-deyfp~gRda~~~gvLk~L~~KTGFs~~Ei~ 184 (275)
+.+.| ..+|..+++-.+..+|+++..+.|++.+++.
T Consensus 107 ~~~~l~~a~~~~~~~i~~~~~l~~ia~~~Gld~~~~~ 143 (193)
T cd03025 107 MLKAIQRAHYVEGRDLADTEVLRELAIELGLDVEEFL 143 (193)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHHHHH
Confidence 34443 4467777776667799999999999887554
No 201
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=21.26 E-value=83 Score=24.91 Aligned_cols=41 Identities=17% Similarity=0.298 Sum_probs=31.5
Q ss_pred hHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 023901 180 MEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNE 225 (275)
Q Consensus 180 ~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E 225 (275)
..|.+|+|+.+...+=+|+ +--.|=+-+|||+++|.+|-.+
T Consensus 2 ~~~~l~~~f~~i~~~V~~~-----~Wk~laR~LGLse~~I~~i~~~ 42 (96)
T cd08315 2 PQETLRRSFDHFIKEVPFD-----SWNRLMRQLGLSENEIDVAKAN 42 (96)
T ss_pred cHhHHHHHHHHHHHHCCHH-----HHHHHHHHcCCCHHHHHHHHHH
Confidence 4688999999988887743 4445556789999999988754
No 202
>PRK01905 DNA-binding protein Fis; Provisional
Probab=21.17 E-value=2.8e+02 Score=20.78 Aligned_cols=53 Identities=9% Similarity=0.159 Sum_probs=39.4
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHH
Q 023901 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQ 207 (275)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~ 207 (275)
.+-+.|.+||-+-.+.-..+.++.. +.++=+.||+.+|.+-..|...+|+++.
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~-------l~~~E~~~i~~aL~~~~gn~s~aAr~LG 61 (77)
T PRK01905 9 CIRDSLDQYFRDLDGSNPHDVYDMV-------LSCVEKPLLEVVMEQAGGNQSLAAEYLG 61 (77)
T ss_pred HHHHHHHHHHHHHcCCCCccHHHHH-------HHHHHHHHHHHHHHHcCCCHHHHHHHHC
Confidence 4557788888887776556666553 4456689999999999999888876543
No 203
>TIGR03290 CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, subunit C. The last step in methanogenesis leaves two coenzymes of methanogenesis, CoM and CoB, linked by a disulfide bond. Members of this protein family are the C subunit of the enzyme that reduces the heterodisulfide to CoB-SH and CoM-SH. Similar enzyme complex subunits are found in various other species, but likely act on a different substrate.
Probab=21.09 E-value=2.1e+02 Score=23.37 Aligned_cols=47 Identities=19% Similarity=0.202 Sum_probs=34.2
Q ss_pred CCCCCCchHHHHHHHHhCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHhhcCCCc
Q 023901 160 GGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDD 216 (275)
Q Consensus 160 gRda~~~gvLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d 216 (275)
|+.-.....+++|.+++|..... -.-++.|+.+.|.+.+=+++|++|
T Consensus 96 g~~~~~~~~~~~lr~~~g~~~~p----------~~~~~~p~~~~~~~~il~~~~~~~ 142 (144)
T TIGR03290 96 GHAVPINDEIKELRKELGLDEIP----------PTTHKYPEALEEVQKLIKALEFDE 142 (144)
T ss_pred CCCCCccHHHHHHHHHcCCCCCC----------CccccCHHHHHHHHHHHHHhChhh
Confidence 33333456778999999973111 233889999999999999999876
No 204
>PRK12657 putative monovalent cation/H+ antiporter subunit F; Reviewed
Probab=21.07 E-value=83 Score=25.64 Aligned_cols=42 Identities=12% Similarity=0.282 Sum_probs=32.1
Q ss_pred chhHHHHHHHhhhhHhhhhhhhhhhhcCChhhhhhhhhcchhhHHh
Q 023901 106 LPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCK 151 (275)
Q Consensus 106 lPwiLAlPLAylGiTFviA~vRTvrK~tSPraKRkR~VnKNa~Lvk 151 (275)
+.|++.+.++.+++++++++||.+|-=|.| -|.|.-|.+-..
T Consensus 6 ~~~~~~~a~~~l~~a~~l~l~Rlv~GPt~~----DRivAlD~l~~~ 47 (100)
T PRK12657 6 THIMIISALIIFGIALIICLFRLIKGPTTA----DRVVTFDTTSAV 47 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCccHH----HHHHHHHHHHHH
Confidence 568888888889999999999998876655 366666665444
No 205
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=21.01 E-value=1.3e+02 Score=22.14 Aligned_cols=33 Identities=24% Similarity=0.424 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHhhhhhcCCeeeeccccchhhhhhHHH
Q 023901 217 SQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRKLA 254 (275)
Q Consensus 217 ~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a 254 (275)
+|+.+|.++ +++.-+|++|++.+...-.+|=++
T Consensus 10 ~D~~~i~~~-----l~~g~~Vivnl~~l~~~~~~Ri~D 42 (73)
T PF04472_consen 10 EDAREIVDA-----LREGKIVIVNLENLDDEEAQRILD 42 (73)
T ss_dssp GGHHHHHHH-----HHTT--EEEE-TTS-HHHHHHHHH
T ss_pred HHHHHHHHH-----HHcCCEEEEECCCCCHHHHHHHHH
Confidence 455554433 355579999999999999888443
No 206
>PF03147 FDX-ACB: Ferredoxin-fold anticodon binding domain; InterPro: IPR005121 Aminoacyl-tRNA synthetases (aaRSs) play a crucial role in the translation of the genetic code by means of covalent attachment of amino acids to their cognate tRNAs. Phenylalanine-tRNA synthetase (PheRS) is known to be among the most complex enzymes of the aaRS family. Bacterial and mitochondrial PheRSs share a ferredoxin-fold anticodon binding (FDX-ACB) domain, which represents a canonical double split alpha+beta motif having no insertions. The FDX-ACB domain displays a typical RNA recognition fold (RRM) (see PDOC00030 from PROSITEDOC) formed by the four-stranded antiparallel beta sheet, with two helices packed against it [, , , , ].; GO: 0000049 tRNA binding, 0000287 magnesium ion binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation, 0008033 tRNA processing; PDB: 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 3PCO_D 2RHS_D 2RHQ_B 2AKW_B 1B70_B ....
Probab=20.99 E-value=93 Score=23.67 Aligned_cols=25 Identities=28% Similarity=0.446 Sum_probs=18.5
Q ss_pred CCCcHHHHHHHHHHHHhhhhhcCCe
Q 023901 213 MLDDSQVAEILNEISRRFVREKGPV 237 (275)
Q Consensus 213 ~L~d~evaeiL~E~s~Ri~~~~G~v 237 (275)
-|+|+||.++.+.+-..+-+++|-.
T Consensus 68 TLt~~ev~~~~~~i~~~l~~~~~~~ 92 (94)
T PF03147_consen 68 TLTDEEVNEIHDKIIKALEKKLGAE 92 (94)
T ss_dssp ---HHHHHHHHHHHHHHHHHTCT-B
T ss_pred CCCHHHHHHHHHHHHHHHHHHhCcE
Confidence 5899999999999999888888743
No 207
>PF00286 Flexi_CP: Viral coat protein; InterPro: IPR000052 Potexviruses and Carlaviruses are plant-infecting viruses whose genome consist of a single-stranded RNA molecule encapsided in a coat protein. The genome of many Potexviruses is known and their coat protein sequence has been shown to be rather well conserved []. The same observation applies to the coat protein of a variety of Carlaviruses whose sequences are related to those of Potexviruses [, ]. The coat proteins of Potexviruses and of Carlaviruses contain from 190 to 300 amino acid residues. The best conserved region of these coat proteins is located in the central part.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 4DOX_B.
Probab=20.98 E-value=2.7e+02 Score=24.09 Aligned_cols=64 Identities=14% Similarity=0.169 Sum_probs=41.2
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCeeeeccccc--hhhhhhHHHHHHHHHh
Q 023901 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMNMSGYS--EKGFKRKLAVQALFGK 261 (275)
Q Consensus 198 ~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~T--e~G~kRK~a~~aLF~K 261 (275)
|++.++-+.++=.++|...+.+++++-++++--++.=----+++.|-+ ..|+-|...+.++-.+
T Consensus 6 t~e~i~~I~~~~~~lgvp~~~~~~~~~~la~~C~d~gSS~~~~~~G~~~~~~g~~~~~la~aiik~ 71 (140)
T PF00286_consen 6 TPEEIAAISAALQGLGVPTESVAKVAWDLARYCADNGSSRYTDPKGTSPFPGGVIRADLAAAIIKE 71 (140)
T ss_dssp -HHHHHHHHHHHHHTT--GGGHHHHHHHHHHHHHHH---TT----SB--SSTT-BHHHHH-HHHHH
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCcccccCCcccCCCCccHHHHHHHHHHc
Confidence 456666777777779999999999999999988887667888999999 4899998888655443
No 208
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=20.88 E-value=66 Score=22.93 Aligned_cols=33 Identities=18% Similarity=0.243 Sum_probs=21.1
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCee
Q 023901 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVV 238 (275)
Q Consensus 198 ~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vm 238 (275)
+.+.|.+.++--...|||++||++-+ ++||+=.
T Consensus 5 ~~~~v~~~l~t~~~~GLs~~ev~~r~--------~~~G~N~ 37 (69)
T PF00690_consen 5 SVEEVLKRLNTSSSQGLSSEEVEERR--------KKYGPNE 37 (69)
T ss_dssp SHHHHHHHHTTBTSSBBTHHHHHHHH--------HHHSSSS
T ss_pred CHHHHHHHHCcCCCCCCCHHHHHHHH--------Hhccccc
Confidence 44555555554457899998887655 5677633
No 209
>PF12385 Peptidase_C70: Papain-like cysteine protease AvrRpt2; InterPro: IPR022118 This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis []. AvrRpt2 from Pseudomonas syringae pv tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2 [].
Probab=20.79 E-value=66 Score=28.93 Aligned_cols=41 Identities=17% Similarity=0.122 Sum_probs=28.1
Q ss_pred HHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhhcCCeeee
Q 023901 200 DLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMN 240 (275)
Q Consensus 200 d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn 240 (275)
..++|+++--...+++...=+-.-.|.-+++.++||||++-
T Consensus 74 ~d~~~~~~~~gl~~v~~P~~~~~t~e~~~~LL~~yGPLwv~ 114 (166)
T PF12385_consen 74 LDPEDFIRNEGLKEVPEPANASYTAEGLANLLREYGPLWVA 114 (166)
T ss_pred ccHHHHHHhcCccccCCCcccccCHHHHHHHHHHcCCeEEE
Confidence 34577777666666665554445556667788999999985
No 210
>PF02410 Oligomerisation: Oligomerisation domain; InterPro: IPR004394 The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. Maize has two RNA polymerases in plastids, but the plastid-encoded one, similar to bacterial RNA polymerases, is missing in iojap mutants. The role of iojap in chloroplast development, and the role of its bacterial orthologs modeled here, is unclear [, ]. This entry contains the bacterial protein YbeB (P0AAT6 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2O5A_A 2ID1_B 3UPS_A.
Probab=20.50 E-value=89 Score=24.40 Aligned_cols=37 Identities=22% Similarity=0.385 Sum_probs=26.1
Q ss_pred hcCCCcHHHHHHHHHHHHhhhhhcCCeeeeccccchh
Q 023901 211 ASMLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEK 247 (275)
Q Consensus 211 as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~ 247 (275)
|+|-|.-++..+-+++.+.+-+++|.....++|....
T Consensus 35 ~T~~S~rh~~aia~~v~~~~~k~~~~~~~~~eG~~~~ 71 (100)
T PF02410_consen 35 ATGRSERHVRAIADEVEKALKKEYGERPLRIEGLDES 71 (100)
T ss_dssp EEESSHHHHHHHHHHHHHHH-HHTT----EEESTTTT
T ss_pred EEcCCHHHHHHHHHHHHHHHHHHcCCcccccCCCCCC
Confidence 5677888999999998888867788888888888554
No 211
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=20.34 E-value=28 Score=32.88 Aligned_cols=10 Identities=40% Similarity=0.564 Sum_probs=4.9
Q ss_pred hhHHHHHhcc
Q 023901 66 EVEVEVEEEL 75 (275)
Q Consensus 66 ~~e~e~e~e~ 75 (275)
|+|||+|++|
T Consensus 295 ~~~ee~~~~~ 304 (310)
T PTZ00135 295 EEEEEEEDDM 304 (310)
T ss_pred ccccCcchhc
Confidence 4444455555
No 212
>PRK14136 recX recombination regulator RecX; Provisional
Probab=20.19 E-value=1.3e+02 Score=29.31 Aligned_cols=72 Identities=24% Similarity=0.267 Sum_probs=50.3
Q ss_pred hCCChHHHHHHHHHHHhcCCCCChHHHHHHHH-HHhhcCCCcHHHHHHHHHHHHhhhhhcCCeeeeccccchhhhhhHHH
Q 023901 176 TGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQ-LRKASMLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRKLA 254 (275)
Q Consensus 176 TGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~-Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a 254 (275)
.-+|..||.+| |.++-|+++.|+.+|. |+.-=-|+|...++.+-.. |+ ++||+..+- .=|-++|+..-+.
T Consensus 175 ReRSe~ELr~K-----L~kkG~~ee~IE~VIerLke~gYLDDeRFAesyVr~--R~-~kkGp~rIr-qELrQKGId~eLI 245 (309)
T PRK14136 175 REYSRAELARK-----LAPYADESDSVEPLLDALEREGWLSDARFAESLVHR--RA-SRVGSARIV-SELKRHAVGDALV 245 (309)
T ss_pred ccccHHHHHHH-----HHHcCCCHHHHHHHHHHHHHcCCcCHHHHHHHHHHH--Hh-hchhHHHHH-HHHHHcCCCHHHH
Confidence 45677776665 5677899999988885 5665668999999988742 43 568997764 4466777765554
Q ss_pred HH
Q 023901 255 VQ 256 (275)
Q Consensus 255 ~~ 256 (275)
-+
T Consensus 246 Eq 247 (309)
T PRK14136 246 ES 247 (309)
T ss_pred HH
Confidence 33
No 213
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.16 E-value=2.9e+02 Score=21.46 Aligned_cols=16 Identities=13% Similarity=0.125 Sum_probs=7.4
Q ss_pred CCCChHHHHHHHHHHh
Q 023901 195 KPFNPDLVVNLIQLRK 210 (275)
Q Consensus 195 r~F~~d~VaDLi~Lr~ 210 (275)
--|+.+.+..++++..
T Consensus 56 ~G~~l~ei~~~l~~~~ 71 (96)
T cd04774 56 LGFSLQEVTHFLERPL 71 (96)
T ss_pred cCCCHHHHHHHHhccc
Confidence 4444444444444433
No 214
>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.
Probab=20.02 E-value=6.9e+02 Score=22.97 Aligned_cols=89 Identities=17% Similarity=0.259 Sum_probs=61.0
Q ss_pred hhhhhhcchhhHHhhHHHHHh--cCCCCCC--chHHHHHHHHhCCChHHHH---------------HHHHHHHhcCCCCC
Q 023901 138 KRKKLVNKNAMVCKTIDELFQ--KGGDAVN--PPALKGLVQKTGFSMEDVL---------------RKYIRYALNEKPFN 198 (275)
Q Consensus 138 KRkR~VnKNa~LvkSLdeyfp--~gRda~~--~gvLk~L~~KTGFs~~Ei~---------------RKYirY~LnEr~F~ 198 (275)
|+++.++....|+.-.-.++- +|++... .-.+++|.+++|=+..=.. .+.|.=+|+..+-|
T Consensus 155 ~~~~~~~eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~~ 234 (290)
T PF04733_consen 155 KNMQQIDEDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDKFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPND 234 (290)
T ss_dssp HHHHCCSCCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCCS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CCH
T ss_pred HHHHhcCCcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccCC
Confidence 455667777776655544433 5667776 7788999988775532111 23455589999999
Q ss_pred hHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 023901 199 PDLVVNLIQLRKASMLDDSQVAEILNEI 226 (275)
Q Consensus 199 ~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (275)
||+.+++|-+-.-.|-+.+.+.+-+++.
T Consensus 235 ~d~LaNliv~~~~~gk~~~~~~~~l~qL 262 (290)
T PF04733_consen 235 PDTLANLIVCSLHLGKPTEAAERYLSQL 262 (290)
T ss_dssp HHHHHHHHHHHHHTT-TCHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHhCCChhHHHHHHHHH
Confidence 9999999999999999988888777763
Done!