Query psy3486
Match_columns 222
No_of_seqs 257 out of 394
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 17:56:34 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3486.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3486hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1464|consensus 100.0 1E-45 2.2E-50 333.1 9.7 133 87-221 46-178 (440)
2 KOG1463|consensus 99.8 1.3E-20 2.8E-25 173.4 7.7 109 20-134 286-408 (411)
3 KOG1463|consensus 99.8 1.9E-19 4.1E-24 165.7 6.1 69 1-69 315-383 (411)
4 COG5159 RPN6 26S proteasome re 99.8 1.8E-18 3.9E-23 157.4 8.3 114 19-138 283-410 (421)
5 COG5159 RPN6 26S proteasome re 99.7 6.6E-18 1.4E-22 153.7 6.3 69 1-69 313-381 (421)
6 KOG1464|consensus 99.6 2E-15 4.4E-20 137.2 8.2 69 1-123 334-402 (440)
7 PF01399 PCI: PCI domain; Int 98.7 4.2E-08 9.1E-13 73.2 5.2 67 2-68 31-97 (105)
8 PF01399 PCI: PCI domain; Int 98.5 3.9E-07 8.4E-12 68.0 7.5 69 52-123 30-98 (105)
9 smart00753 PAM PCI/PINT associ 98.5 1.4E-07 2.9E-12 69.8 4.1 62 8-69 1-62 (88)
10 smart00088 PINT motif in prote 98.5 1.4E-07 2.9E-12 69.8 4.1 62 8-69 1-62 (88)
11 KOG0686|consensus 98.5 1.2E-07 2.5E-12 89.9 4.7 68 3-70 337-404 (466)
12 smart00753 PAM PCI/PINT associ 98.1 4.6E-06 1E-10 61.6 5.5 55 69-123 8-62 (88)
13 smart00088 PINT motif in prote 98.1 4.6E-06 1E-10 61.6 5.5 55 69-123 8-62 (88)
14 KOG0686|consensus 96.9 0.0012 2.5E-08 63.3 4.9 93 51-156 334-426 (466)
15 KOG0687|consensus 95.8 0.0064 1.4E-07 57.0 2.8 66 2-67 288-353 (393)
16 COG5187 RPN7 26S proteasome re 93.9 0.047 1E-06 51.0 3.0 67 2-68 302-368 (412)
17 PF10075 PCI_Csn8: COP9 signal 93.5 0.074 1.6E-06 42.9 3.3 47 4-50 70-116 (143)
18 KOG2581|consensus 93.0 0.21 4.6E-06 48.3 5.9 73 47-123 338-416 (493)
19 KOG1498|consensus 92.4 0.19 4.1E-06 48.3 4.7 61 6-66 328-388 (439)
20 KOG1497|consensus 89.4 0.77 1.7E-05 43.4 5.6 81 69-159 301-388 (399)
21 KOG1498|consensus 89.1 0.72 1.6E-05 44.4 5.2 51 73-123 341-391 (439)
22 PF09743 DUF2042: Uncharacteri 89.0 18 0.00039 32.9 15.0 90 25-122 64-167 (272)
23 cd00189 TPR Tetratricopeptide 86.5 2.7 5.8E-05 27.3 5.5 88 119-218 11-98 (100)
24 COG5071 RPN5 26S proteasome re 86.2 1.1 2.3E-05 42.4 4.4 64 3-66 325-388 (439)
25 PLN03083 E3 UFM1-protein ligas 86.2 19 0.00042 37.6 13.7 145 28-181 71-235 (803)
26 KOG1497|consensus 86.1 0.86 1.9E-05 43.1 3.8 57 12-68 298-354 (399)
27 KOG1840|consensus 85.7 14 0.00031 36.6 12.2 163 38-217 314-479 (508)
28 TIGR03504 FimV_Cterm FimV C-te 81.9 1.2 2.5E-05 29.9 2.1 27 190-216 1-27 (44)
29 KOG0687|consensus 81.0 6.1 0.00013 37.6 7.1 68 53-123 288-355 (393)
30 PF14938 SNAP: Soluble NSF att 80.6 4.8 0.0001 35.7 6.2 98 123-220 89-187 (282)
31 PF13176 TPR_7: Tetratricopept 79.3 0.69 1.5E-05 28.7 0.3 24 115-138 6-29 (36)
32 PF12895 Apc3: Anaphase-promot 77.3 6.3 0.00014 28.1 4.9 82 120-213 1-83 (84)
33 smart00342 HTH_ARAC helix_turn 76.4 17 0.00037 24.8 6.8 68 32-104 2-70 (84)
34 PF09012 FeoC: FeoC like trans 76.0 3.5 7.6E-05 29.3 3.2 45 76-120 5-49 (69)
35 PF09012 FeoC: FeoC like trans 75.4 3 6.5E-05 29.6 2.7 43 21-63 4-46 (69)
36 PF13424 TPR_12: Tetratricopep 74.1 8.4 0.00018 26.7 4.8 33 110-143 7-39 (78)
37 PF08279 HTH_11: HTH domain; 73.9 6.9 0.00015 26.0 4.1 37 18-54 1-38 (55)
38 KOG2582|consensus 73.0 16 0.00034 35.3 7.5 103 19-123 247-355 (422)
39 COG5071 RPN5 26S proteasome re 73.0 6.4 0.00014 37.3 4.9 49 74-122 341-390 (439)
40 TIGR02795 tol_pal_ybgF tol-pal 72.9 32 0.0007 24.7 8.5 93 119-217 13-105 (119)
41 PF14938 SNAP: Soluble NSF att 71.0 19 0.00041 31.9 7.3 99 120-219 47-146 (282)
42 PF08220 HTH_DeoR: DeoR-like h 70.3 5.4 0.00012 27.5 3.0 35 18-52 1-35 (57)
43 smart00345 HTH_GNTR helix_turn 69.9 7.7 0.00017 25.4 3.6 41 13-53 1-42 (60)
44 TIGR02552 LcrH_SycD type III s 69.6 45 0.00098 25.1 9.1 110 91-218 6-115 (135)
45 KOG2235|consensus 69.5 35 0.00076 35.0 9.4 153 26-178 68-251 (776)
46 TIGR02521 type_IV_pilW type IV 69.5 24 0.00053 27.7 7.0 27 191-217 172-198 (234)
47 PF12612 TFCD_C: Tubulin foldi 68.0 28 0.00062 29.4 7.5 74 134-208 89-166 (193)
48 PF12169 DNA_pol3_gamma3: DNA 67.2 11 0.00024 29.7 4.5 105 86-191 1-123 (143)
49 PF08784 RPA_C: Replication pr 66.9 7.4 0.00016 29.4 3.4 36 85-120 65-100 (102)
50 COG2944 Predicted transcriptio 66.3 12 0.00025 29.7 4.4 37 11-47 26-62 (104)
51 KOG1076|consensus 64.8 13 0.00029 38.5 5.5 56 12-67 695-754 (843)
52 PF13404 HTH_AsnC-type: AsnC-t 64.1 11 0.00023 24.7 3.3 35 20-54 6-40 (42)
53 TIGR02997 Sig70-cyanoRpoD RNA 63.2 34 0.00074 30.8 7.5 28 81-112 268-295 (298)
54 PF13429 TPR_15: Tetratricopep 62.0 50 0.0011 28.6 8.1 87 118-216 156-242 (280)
55 PF04760 IF2_N: Translation in 59.2 18 0.0004 24.3 3.9 47 85-131 3-51 (54)
56 PRK11788 tetratricopeptide rep 59.0 26 0.00056 31.3 5.9 94 115-215 148-241 (389)
57 PRK07598 RNA polymerase sigma 58.9 1.1E+02 0.0024 29.6 10.4 77 33-114 280-398 (415)
58 TIGR02521 type_IV_pilW type IV 58.6 77 0.0017 24.8 8.0 23 193-215 208-230 (234)
59 PRK11788 tetratricopeptide rep 58.5 60 0.0013 28.9 8.2 88 117-216 223-310 (389)
60 PF05491 RuvB_C: Holliday junc 57.7 9.5 0.00021 28.6 2.4 30 20-49 12-43 (76)
61 PRK11169 leucine-responsive tr 57.4 34 0.00073 28.1 5.9 49 72-120 15-63 (164)
62 PF13424 TPR_12: Tetratricopep 57.0 37 0.00081 23.4 5.3 58 162-219 19-77 (78)
63 smart00344 HTH_ASNC helix_turn 56.1 20 0.00043 26.8 4.0 45 73-117 5-49 (108)
64 PF10075 PCI_Csn8: COP9 signal 55.9 22 0.00048 28.4 4.5 37 73-109 84-121 (143)
65 PF13374 TPR_10: Tetratricopep 55.9 10 0.00022 22.8 2.0 31 190-220 4-34 (42)
66 PRK12514 RNA polymerase sigma 54.9 24 0.00051 28.6 4.6 45 6-53 123-167 (179)
67 PF09756 DDRGK: DDRGK domain; 54.6 12 0.00026 32.4 2.9 50 18-67 100-149 (188)
68 cd07377 WHTH_GntR Winged helix 54.6 32 0.0007 22.7 4.5 39 11-49 4-43 (66)
69 KOG2908|consensus 54.6 45 0.00097 31.9 6.8 99 12-123 224-332 (380)
70 PRK05949 RNA polymerase sigma 54.4 1.1E+02 0.0024 28.3 9.3 29 81-113 285-313 (327)
71 PF08784 RPA_C: Replication pr 54.3 8.9 0.00019 29.0 1.8 36 31-66 65-100 (102)
72 PF12643 MazG-like: MazG-like 53.9 35 0.00075 26.5 5.1 46 91-140 51-96 (98)
73 PF13404 HTH_AsnC-type: AsnC-t 53.4 21 0.00045 23.4 3.2 35 74-108 6-40 (42)
74 PLN03077 Protein ECB2; Provisi 53.3 27 0.0006 35.6 5.7 90 114-213 360-449 (857)
75 PLN03218 maturation of RBCL 1; 53.1 28 0.00061 37.4 5.9 55 114-173 513-567 (1060)
76 smart00420 HTH_DEOR helix_turn 53.1 18 0.00039 22.9 2.9 25 30-54 13-37 (53)
77 smart00550 Zalpha Z-DNA-bindin 52.9 29 0.00062 24.7 4.2 45 73-117 8-54 (68)
78 PF13412 HTH_24: Winged helix- 51.9 32 0.0007 22.2 4.1 42 75-116 7-48 (48)
79 PF04049 APC8: Anaphase promot 51.6 8.8 0.00019 31.5 1.5 20 194-213 80-99 (142)
80 smart00550 Zalpha Z-DNA-bindin 51.1 23 0.0005 25.1 3.5 35 19-53 8-44 (68)
81 cd02681 MIT_calpain7_1 MIT: do 51.0 40 0.00087 25.0 4.8 38 121-158 19-57 (76)
82 TIGR03001 Sig-70_gmx1 RNA poly 50.9 70 0.0015 28.2 7.2 46 7-55 156-201 (244)
83 PRK05927 hypothetical protein; 50.2 19 0.00042 33.6 3.7 88 8-99 109-201 (350)
84 PF13443 HTH_26: Cro/C1-type H 49.6 24 0.00052 23.8 3.3 47 31-101 10-56 (63)
85 PF04545 Sigma70_r4: Sigma-70, 49.1 36 0.00078 22.2 4.0 26 29-54 18-43 (50)
86 PF09756 DDRGK: DDRGK domain; 48.8 22 0.00048 30.8 3.6 51 74-124 102-153 (188)
87 KOG2300|consensus 48.7 21 0.00046 35.8 3.8 101 111-214 326-430 (629)
88 PLN03081 pentatricopeptide (PP 48.5 39 0.00085 33.7 5.8 55 113-172 295-349 (697)
89 PLN03218 maturation of RBCL 1; 47.2 45 0.00097 35.9 6.2 91 115-215 621-711 (1060)
90 PF13412 HTH_24: Winged helix- 46.6 40 0.00086 21.7 3.8 36 20-55 6-41 (48)
91 PF00392 GntR: Bacterial regul 46.2 50 0.0011 22.7 4.5 44 11-54 3-47 (64)
92 smart00344 HTH_ASNC helix_turn 45.8 29 0.00063 25.9 3.5 40 19-58 5-44 (108)
93 PRK06645 DNA polymerase III su 45.5 2.5E+02 0.0054 27.8 10.7 169 9-190 167-363 (507)
94 PF08220 HTH_DeoR: DeoR-like h 44.5 44 0.00095 22.8 3.9 42 74-115 3-44 (57)
95 PRK10681 DNA-binding transcrip 43.9 29 0.00063 30.6 3.7 38 17-54 7-44 (252)
96 TIGR01610 phage_O_Nterm phage 43.7 81 0.0018 23.7 5.7 39 85-123 47-85 (95)
97 PF08667 BetR: BetR domain; I 43.6 29 0.00064 29.0 3.4 44 34-102 25-68 (147)
98 PF08221 HTH_9: RNA polymerase 43.6 76 0.0017 22.2 5.1 57 52-116 2-58 (62)
99 cd06171 Sigma70_r4 Sigma70, re 43.6 52 0.0011 20.2 4.0 25 30-54 25-49 (55)
100 TIGR02859 spore_sigH RNA polym 43.5 44 0.00095 27.3 4.5 42 9-53 146-187 (198)
101 COG3355 Predicted transcriptio 43.4 1.2E+02 0.0027 24.7 6.9 49 76-124 33-84 (126)
102 PF13181 TPR_8: Tetratricopept 43.4 23 0.0005 20.6 2.1 19 119-137 12-30 (34)
103 PF14769 CLAMP: Flagellar C1a 43.2 47 0.001 25.3 4.3 67 91-161 6-79 (101)
104 PRK10434 srlR DNA-bindng trans 43.2 29 0.00063 30.8 3.6 38 17-54 5-42 (256)
105 PF00515 TPR_1: Tetratricopept 42.8 26 0.00056 20.5 2.3 19 118-136 11-29 (34)
106 PF07719 TPR_2: Tetratricopept 42.5 26 0.00057 20.1 2.3 20 118-137 11-30 (34)
107 PLN03088 SGT1, suppressor of 41.7 1.2E+02 0.0027 28.0 7.6 87 118-216 12-98 (356)
108 PF13174 TPR_6: Tetratricopept 41.4 31 0.00067 19.6 2.4 26 192-217 4-29 (33)
109 PF12844 HTH_19: Helix-turn-he 41.0 51 0.0011 22.2 3.9 47 31-102 12-58 (64)
110 PF12651 RHH_3: Ribbon-helix-h 41.0 34 0.00074 22.6 2.8 28 33-60 16-43 (44)
111 TIGR02844 spore_III_D sporulat 40.8 34 0.00073 25.7 3.1 36 18-54 7-42 (80)
112 PRK13509 transcriptional repre 40.4 35 0.00076 30.1 3.7 48 17-64 5-56 (251)
113 PRK10411 DNA-binding transcrip 40.3 35 0.00076 30.0 3.6 39 17-55 4-42 (240)
114 PF09976 TPR_21: Tetratricopep 40.0 56 0.0012 25.6 4.5 35 180-214 77-111 (145)
115 PRK10219 DNA-binding transcrip 40.0 1.6E+02 0.0034 22.0 7.8 67 29-100 19-85 (107)
116 TIGR03302 OM_YfiO outer membra 39.9 1.1E+02 0.0024 25.4 6.5 20 117-136 79-98 (235)
117 smart00421 HTH_LUXR helix_turn 39.8 58 0.0013 20.5 3.8 27 29-55 16-42 (58)
118 PF14559 TPR_19: Tetratricopep 38.7 20 0.00044 23.9 1.5 36 180-219 21-56 (68)
119 PF13041 PPR_2: PPR repeat fam 38.5 11 0.00024 24.4 0.1 39 113-156 8-46 (50)
120 PRK09234 fbiC FO synthase; Rev 37.7 30 0.00064 36.4 3.1 88 8-99 590-682 (843)
121 PRK14960 DNA polymerase III su 37.6 3.4E+02 0.0074 28.3 10.5 172 11-191 159-351 (702)
122 TIGR03338 phnR_burk phosphonat 37.6 2.4E+02 0.0052 23.4 11.6 39 11-49 14-52 (212)
123 COG5187 RPN7 26S proteasome re 36.7 65 0.0014 30.7 4.9 68 53-123 302-369 (412)
124 PF10602 RPN7: 26S proteasome 36.7 89 0.0019 26.2 5.4 96 108-212 36-137 (177)
125 PF13429 TPR_15: Tetratricopep 36.5 28 0.00061 30.1 2.4 87 116-216 52-138 (280)
126 cd05804 StaR_like StaR_like; a 36.1 1.3E+02 0.0027 26.6 6.6 87 119-214 125-212 (355)
127 KOG3060|consensus 36.1 1.1E+02 0.0023 28.4 6.1 81 122-214 100-180 (289)
128 PRK14961 DNA polymerase III su 35.7 1.4E+02 0.0031 27.5 7.1 171 8-189 157-351 (363)
129 cd02683 MIT_1 MIT: domain cont 35.3 60 0.0013 23.9 3.7 38 121-158 19-56 (77)
130 PF14689 SPOB_a: Sensor_kinase 35.3 13 0.00028 26.2 0.1 28 111-138 26-53 (62)
131 PRK10803 tol-pal system protei 34.8 1.4E+02 0.003 26.7 6.6 91 118-216 153-245 (263)
132 KOG2581|consensus 34.7 37 0.00081 33.3 3.1 64 3-66 345-413 (493)
133 PF13413 HTH_25: Helix-turn-he 34.5 34 0.00073 24.1 2.1 51 31-102 10-62 (62)
134 PRK10370 formate-dependent nit 34.5 29 0.00062 29.4 2.1 27 119-145 155-181 (198)
135 KOG2753|consensus 34.4 1.1E+02 0.0024 29.3 6.0 62 11-72 274-335 (378)
136 PRK07405 RNA polymerase sigma 34.4 1.7E+02 0.0036 26.8 7.2 29 81-113 275-303 (317)
137 PF01022 HTH_5: Bacterial regu 34.3 81 0.0018 20.4 3.8 38 18-66 4-41 (47)
138 PRK11534 DNA-binding transcrip 33.9 76 0.0016 26.8 4.6 41 10-50 9-49 (224)
139 COG2345 Predicted transcriptio 33.5 1.8E+02 0.0039 25.8 7.0 87 73-159 13-113 (218)
140 TIGR02395 rpoN_sigma RNA polym 33.4 1.2E+02 0.0027 29.2 6.4 24 29-52 111-134 (429)
141 cd02656 MIT MIT: domain contai 33.4 1.2E+02 0.0027 21.4 5.0 27 122-148 20-46 (75)
142 TIGR02941 Sigma_B RNA polymera 33.3 1.7E+02 0.0036 25.4 6.8 30 79-112 218-247 (255)
143 PRK00440 rfc replication facto 33.2 3.3E+02 0.0071 23.7 9.5 42 85-136 213-255 (319)
144 PRK11169 leucine-responsive tr 33.1 64 0.0014 26.5 3.9 44 19-62 16-59 (164)
145 cd06170 LuxR_C_like C-terminal 32.7 83 0.0018 19.9 3.7 25 29-53 13-37 (57)
146 KOG2582|consensus 32.2 45 0.00097 32.3 3.1 53 13-66 299-353 (422)
147 PF13428 TPR_14: Tetratricopep 32.1 49 0.0011 20.9 2.4 28 191-218 4-31 (44)
148 PRK12534 RNA polymerase sigma 31.9 77 0.0017 25.7 4.2 26 29-54 151-176 (187)
149 smart00346 HTH_ICLR helix_turn 31.9 78 0.0017 22.6 3.8 35 18-52 6-41 (91)
150 PF08280 HTH_Mga: M protein tr 31.5 87 0.0019 21.5 3.8 34 16-49 4-37 (59)
151 KOG2908|consensus 31.4 94 0.002 29.8 5.1 61 4-66 263-329 (380)
152 PRK13890 conjugal transfer pro 31.3 1.3E+02 0.0029 23.7 5.3 63 14-102 2-64 (120)
153 TIGR00756 PPR pentatricopeptid 31.3 16 0.00034 20.8 -0.0 23 114-136 6-28 (35)
154 PF01535 PPR: PPR repeat; Int 31.0 19 0.00041 20.2 0.3 23 114-136 6-28 (31)
155 KOG3054|consensus 30.8 68 0.0015 29.5 3.9 75 22-96 205-285 (299)
156 KOG1840|consensus 30.6 1.4E+02 0.0031 29.6 6.5 107 108-215 283-394 (508)
157 PRK09047 RNA polymerase factor 30.5 1E+02 0.0022 24.1 4.6 37 15-54 109-145 (161)
158 PRK08691 DNA polymerase III su 30.3 4.3E+02 0.0093 27.6 9.9 168 11-188 160-348 (709)
159 PF04212 MIT: MIT (microtubule 30.2 85 0.0018 21.9 3.6 23 121-143 18-40 (69)
160 PRK12323 DNA polymerase III su 30.2 2.9E+02 0.0062 28.8 8.6 174 8-190 162-355 (700)
161 PRK08444 hypothetical protein; 29.8 52 0.0011 30.8 3.2 88 8-99 113-205 (353)
162 COG1522 Lrp Transcriptional re 29.8 98 0.0021 24.3 4.3 52 74-125 11-62 (154)
163 KOG2376|consensus 29.8 51 0.0011 33.6 3.2 119 87-220 84-207 (652)
164 KOG1076|consensus 29.7 38 0.00083 35.2 2.4 42 82-123 715-756 (843)
165 PRK15359 type III secretion sy 29.4 2.8E+02 0.0062 21.8 7.2 88 119-218 35-122 (144)
166 KOG2672|consensus 29.4 38 0.00083 31.8 2.1 63 153-222 28-94 (360)
167 PLN03081 pentatricopeptide (PP 29.4 1.5E+02 0.0033 29.5 6.5 91 114-213 397-487 (697)
168 PRK06266 transcription initiat 29.1 1.1E+02 0.0025 25.9 4.9 54 1-55 5-60 (178)
169 PF12802 MarR_2: MarR family; 29.0 1.5E+02 0.0033 19.5 4.7 47 76-122 10-58 (62)
170 KOG2002|consensus 28.9 1.6E+02 0.0035 31.8 6.7 34 120-156 624-657 (1018)
171 PRK08215 sporulation sigma fac 28.8 1.7E+02 0.0037 25.5 6.0 19 33-51 141-159 (258)
172 TIGR00990 3a0801s09 mitochondr 28.8 2.5E+02 0.0054 27.5 7.8 30 190-219 544-573 (615)
173 smart00418 HTH_ARSR helix_turn 28.4 83 0.0018 20.0 3.2 25 29-53 8-32 (66)
174 PRK09210 RNA polymerase sigma 28.4 2.4E+02 0.0053 26.3 7.3 29 81-113 324-352 (367)
175 PRK11179 DNA-binding transcrip 28.2 1.1E+02 0.0023 24.8 4.4 36 83-118 21-56 (153)
176 PRK12530 RNA polymerase sigma 28.2 1.1E+02 0.0024 25.2 4.6 45 7-54 129-173 (189)
177 cd00086 homeodomain Homeodomai 28.1 46 0.001 21.7 1.9 24 81-104 22-46 (59)
178 KOG2758|consensus 28.1 1.5E+02 0.0033 28.6 5.8 60 2-61 320-379 (432)
179 TIGR03879 near_KaiC_dom probab 27.9 67 0.0015 23.8 2.8 28 27-54 28-55 (73)
180 PRK14574 hmsH outer membrane p 27.9 1.7E+02 0.0036 30.8 6.7 19 118-136 44-62 (822)
181 PRK04424 fatty acid biosynthes 27.9 75 0.0016 26.9 3.5 40 18-57 8-47 (185)
182 cd02684 MIT_2 MIT: domain cont 27.8 1.1E+02 0.0024 22.3 4.0 36 121-156 19-54 (75)
183 PF08281 Sigma70_r4_2: Sigma-7 27.8 1.3E+02 0.0028 19.6 4.0 45 6-53 4-48 (54)
184 TIGR02917 PEP_TPR_lipo putativ 27.7 2.3E+02 0.0051 27.3 7.3 87 118-217 713-799 (899)
185 PRK14958 DNA polymerase III su 27.3 4.3E+02 0.0093 26.1 9.1 170 11-191 160-349 (509)
186 PRK14964 DNA polymerase III su 27.3 5.1E+02 0.011 25.6 9.6 192 8-215 154-368 (491)
187 PRK03837 transcriptional regul 27.2 1.1E+02 0.0023 26.0 4.5 43 10-52 15-58 (241)
188 PRK08445 hypothetical protein; 26.9 44 0.00095 31.1 2.1 92 8-99 106-198 (348)
189 PF14947 HTH_45: Winged helix- 26.9 2.4E+02 0.0053 20.2 6.0 59 76-137 11-75 (77)
190 PRK09802 DNA-binding transcrip 26.7 77 0.0017 28.3 3.6 40 16-55 16-55 (269)
191 PF00392 GntR: Bacterial regul 26.5 1.9E+02 0.0042 19.7 4.9 44 79-122 17-61 (64)
192 PF09339 HTH_IclR: IclR helix- 26.5 1.2E+02 0.0025 20.0 3.6 31 21-51 7-38 (52)
193 COG1802 GntR Transcriptional r 26.5 99 0.0022 26.3 4.1 40 10-49 18-57 (230)
194 TIGR00990 3a0801s09 mitochondr 26.4 2E+02 0.0043 28.3 6.6 103 94-211 115-217 (615)
195 PRK10906 DNA-binding transcrip 26.3 80 0.0017 28.0 3.6 34 17-50 5-38 (252)
196 COG3860 Uncharacterized protei 26.2 48 0.001 25.5 1.8 18 142-159 43-60 (89)
197 PRK12529 RNA polymerase sigma 26.2 1.3E+02 0.0027 24.6 4.5 43 9-54 124-166 (178)
198 PF13414 TPR_11: TPR repeat; P 26.1 43 0.00092 22.4 1.4 21 118-138 13-33 (69)
199 PRK09642 RNA polymerase sigma 26.1 1.2E+02 0.0025 23.9 4.2 26 29-54 120-145 (160)
200 PF11817 Foie-gras_1: Foie gra 25.9 72 0.0016 27.9 3.2 57 165-221 155-211 (247)
201 COG1349 GlpR Transcriptional r 25.7 80 0.0017 28.0 3.5 37 16-52 4-40 (253)
202 PRK10572 DNA-binding transcrip 25.7 3E+02 0.0065 23.9 7.1 69 27-100 195-263 (290)
203 TIGR02917 PEP_TPR_lipo putativ 25.6 3E+02 0.0065 26.5 7.6 25 192-216 673-697 (899)
204 PRK15186 AraC family transcrip 25.6 1.6E+02 0.0035 26.8 5.5 68 27-100 193-260 (291)
205 PRK09191 two-component respons 25.5 1.2E+02 0.0025 25.5 4.3 46 6-54 82-127 (261)
206 COG4699 Uncharacterized protei 25.4 1.5E+02 0.0032 24.1 4.5 53 122-176 31-89 (120)
207 PRK12520 RNA polymerase sigma 25.3 1.3E+02 0.0029 24.6 4.5 27 29-55 145-171 (191)
208 PF09976 TPR_21: Tetratricopep 25.2 1.7E+02 0.0038 22.8 5.0 87 115-211 55-141 (145)
209 PF02796 HTH_7: Helix-turn-hel 25.2 60 0.0013 21.0 2.0 21 32-52 22-42 (45)
210 PRK09648 RNA polymerase sigma 25.0 1.4E+02 0.0029 24.4 4.5 45 7-54 134-178 (189)
211 PF07638 Sigma70_ECF: ECF sigm 24.9 1.2E+02 0.0026 25.1 4.2 34 18-54 141-174 (185)
212 PF05527 DUF758: Domain of unk 24.8 1.9E+02 0.004 25.2 5.4 113 52-172 26-161 (186)
213 PF13432 TPR_16: Tetratricopep 24.8 59 0.0013 21.5 2.0 23 193-215 2-24 (65)
214 PRK06759 RNA polymerase factor 24.8 1.5E+02 0.0033 22.9 4.6 25 30-54 121-145 (154)
215 TIGR00373 conserved hypothetic 24.7 1.9E+02 0.004 24.0 5.3 54 3-66 1-54 (158)
216 PF12324 HTH_15: Helix-turn-he 24.5 1.2E+02 0.0027 22.8 3.7 36 20-55 27-62 (77)
217 PRK09645 RNA polymerase sigma 24.4 1.5E+02 0.0032 23.7 4.6 45 8-55 114-158 (173)
218 PF13371 TPR_9: Tetratricopept 24.4 1.2E+02 0.0026 20.3 3.5 53 162-220 9-61 (73)
219 PRK05901 RNA polymerase sigma 24.3 2.9E+02 0.0063 27.5 7.3 49 60-113 440-494 (509)
220 PRK09954 putative kinase; Prov 24.2 94 0.002 28.3 3.7 45 73-117 5-49 (362)
221 COG1060 ThiH Thiamine biosynth 24.2 1.2E+02 0.0027 28.7 4.6 89 8-100 123-216 (370)
222 PRK12547 RNA polymerase sigma 24.1 1.6E+02 0.0034 23.5 4.7 44 9-55 109-152 (164)
223 PRK09483 response regulator; P 24.1 85 0.0018 25.1 3.1 39 18-67 152-190 (217)
224 PF13463 HTH_27: Winged helix 24.0 1.8E+02 0.0039 19.4 4.4 37 19-55 5-42 (68)
225 PRK06986 fliA flagellar biosyn 24.0 3.5E+02 0.0076 23.1 7.1 73 33-107 113-222 (236)
226 PLN03077 Protein ECB2; Provisi 23.7 1.3E+02 0.0028 30.8 4.9 93 113-214 559-651 (857)
227 PHA01083 hypothetical protein 23.6 2.5E+02 0.0054 23.7 5.7 60 10-102 3-63 (149)
228 PRK15185 transcriptional regul 23.6 1.8E+02 0.004 27.1 5.5 67 28-100 219-285 (309)
229 PRK07003 DNA polymerase III su 23.5 4.1E+02 0.0089 28.3 8.4 33 156-188 313-348 (830)
230 KOG2758|consensus 23.5 1.2E+02 0.0026 29.2 4.3 86 52-140 319-409 (432)
231 TIGR02885 spore_sigF RNA polym 23.3 3.4E+02 0.0073 23.0 6.8 27 85-112 199-225 (231)
232 PF15469 Sec5: Exocyst complex 23.3 1.9E+02 0.004 23.9 5.1 64 111-182 89-152 (182)
233 KOG2114|consensus 23.3 1.4E+02 0.0031 31.8 5.1 64 91-159 356-421 (933)
234 PF00440 TetR_N: Bacterial reg 23.3 55 0.0012 21.2 1.5 23 27-49 12-34 (47)
235 PRK11414 colanic acid/biofilm 23.2 1.1E+02 0.0023 25.9 3.6 42 11-52 14-55 (221)
236 PF02787 CPSase_L_D3: Carbamoy 23.2 3.9E+02 0.0084 21.3 7.6 18 91-108 78-95 (123)
237 COG3071 HemY Uncharacterized e 23.2 2.7E+02 0.0059 27.0 6.6 79 119-212 274-352 (400)
238 PRK09954 putative kinase; Prov 23.0 1E+02 0.0022 28.1 3.7 43 19-61 5-47 (362)
239 PF12840 HTH_20: Helix-turn-he 22.8 1E+02 0.0023 20.8 2.9 28 22-49 15-42 (61)
240 PRK11447 cellulose synthase su 22.7 2.7E+02 0.0058 29.9 7.2 86 119-216 614-699 (1157)
241 PF13542 HTH_Tnp_ISL3: Helix-t 22.7 2.2E+02 0.0048 18.3 4.5 33 16-51 15-47 (52)
242 PRK09685 DNA-binding transcrip 22.6 1.8E+02 0.004 25.3 5.2 64 32-100 215-279 (302)
243 PRK05685 fliS flagellar protei 22.6 2.2E+02 0.0047 22.8 5.1 48 159-220 20-74 (132)
244 PF01047 MarR: MarR family; I 22.5 2E+02 0.0043 18.9 4.2 46 76-121 8-53 (59)
245 PF01381 HTH_3: Helix-turn-hel 22.3 1.7E+02 0.0038 18.8 3.8 18 32-49 10-27 (55)
246 PHA00428 tail tubular protein 22.1 1.5E+02 0.0032 25.8 4.3 40 149-191 9-57 (193)
247 KOG0164|consensus 22.1 2.2E+02 0.0048 30.1 6.1 102 39-147 254-363 (1001)
248 PF04192 Utp21: Utp21 specific 22.0 4.3E+02 0.0093 23.5 7.3 55 120-177 122-189 (237)
249 PF01402 RHH_1: Ribbon-helix-h 21.8 1.3E+02 0.0027 18.5 2.9 26 33-58 13-38 (39)
250 PRK05657 RNA polymerase sigma 21.8 4.1E+02 0.0088 24.4 7.4 75 33-107 191-304 (325)
251 PF08928 DUF1910: Domain of un 21.4 2.6E+02 0.0056 21.4 5.2 34 148-181 50-83 (117)
252 PRK11179 DNA-binding transcrip 21.3 1.3E+02 0.0027 24.4 3.6 42 21-62 13-54 (153)
253 PRK11511 DNA-binding transcrip 21.3 2.9E+02 0.0064 21.5 5.6 66 30-100 24-89 (127)
254 KOG2004|consensus 21.2 1.6E+02 0.0035 31.1 5.0 48 86-138 320-367 (906)
255 TIGR02983 SigE-fam_strep RNA p 21.1 1.1E+02 0.0024 24.1 3.1 34 19-53 115-148 (162)
256 PRK14959 DNA polymerase III su 21.0 5.1E+02 0.011 26.6 8.4 171 8-189 157-353 (624)
257 smart00346 HTH_ICLR helix_turn 20.9 1.8E+02 0.004 20.6 4.0 34 85-118 20-53 (91)
258 PRK10225 DNA-binding transcrip 20.9 1.8E+02 0.0038 25.2 4.6 42 10-51 11-53 (257)
259 PF04539 Sigma70_r3: Sigma-70 20.8 1.1E+02 0.0025 21.4 2.9 22 87-108 22-43 (78)
260 PRK12539 RNA polymerase sigma 20.8 1.7E+02 0.0036 23.9 4.2 26 29-54 145-170 (184)
261 PRK12540 RNA polymerase sigma 20.8 1.8E+02 0.0039 23.9 4.5 42 10-54 109-150 (182)
262 PF01978 TrmB: Sugar-specific 20.8 2.2E+02 0.0048 19.5 4.3 38 82-119 19-56 (68)
263 PRK14951 DNA polymerase III su 20.7 6E+02 0.013 25.9 8.9 169 11-187 165-353 (618)
264 PRK12512 RNA polymerase sigma 20.6 1.9E+02 0.004 23.4 4.5 26 29-54 145-170 (184)
265 PRK05658 RNA polymerase sigma 20.6 3E+02 0.0064 27.7 6.7 29 81-113 575-603 (619)
266 PF12496 BNIP2: Bcl2-/adenovir 20.6 30 0.00065 28.3 -0.3 10 77-86 108-117 (127)
267 PRK13500 transcriptional activ 20.4 5.4E+02 0.012 23.0 7.8 65 31-100 222-286 (312)
268 cd02678 MIT_VPS4 MIT: domain c 20.3 2.8E+02 0.0061 19.8 4.9 23 121-143 19-41 (75)
269 COG5257 GCD11 Translation init 20.3 91 0.002 30.0 2.8 31 115-145 146-176 (415)
270 PF10304 DUF2411: Domain of un 20.1 1.1E+02 0.0024 19.4 2.4 16 2-17 18-33 (36)
No 1
>KOG1464|consensus
Probab=100.00 E-value=1e-45 Score=333.08 Aligned_cols=133 Identities=67% Similarity=0.972 Sum_probs=129.3
Q ss_pred cHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHH
Q psy3486 87 HIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMEL 166 (222)
Q Consensus 87 ~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~ 166 (222)
-++-+++++.++.+..| |.|++|+|+|++.|++|+|++|+++|+||||||||||||||||||||+|+||+|+|+++++
T Consensus 46 Al~sF~kVlelEgEKge--WGFKALKQmiKI~f~l~~~~eMm~~Y~qlLTYIkSAVTrNySEKsIN~IlDyiStS~~m~L 123 (440)
T KOG1464|consen 46 ALSSFQKVLELEGEKGE--WGFKALKQMIKINFRLGNYKEMMERYKQLLTYIKSAVTRNYSEKSINSILDYISTSKNMDL 123 (440)
T ss_pred HHHHHHHHHhcccccch--hHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHhhhhhhHH
Confidence 35678999999999888 7999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCCceeeecchhhhhhhhchhhHhHHHHHHHHHHHhhhcc
Q psy3486 167 LQDFYETTLEALKDAKNDRLWFKTNTKLGKLYFDREDFNKLSRILKQLHQSCQMK 221 (222)
Q Consensus 167 l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~ld~~ey~~l~~~l~~L~~~c~~~ 221 (222)
+|.||++||+||++++|||||||||+|||+||||++||.++++++++||.|||++
T Consensus 124 LQ~FYeTTL~ALkdAKNeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~e 178 (440)
T KOG1464|consen 124 LQEFYETTLDALKDAKNERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSCQTE 178 (440)
T ss_pred HHHHHHHHHHHHHhhhcceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHhccc
Confidence 9999999999999999999999999999999999999999999999999999986
No 2
>KOG1463|consensus
Probab=99.82 E-value=1.3e-20 Score=173.35 Aligned_cols=109 Identities=19% Similarity=0.386 Sum_probs=92.7
Q ss_pred HHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCCh
Q psy3486 20 QVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIET 99 (222)
Q Consensus 20 q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~ 99 (222)
.++..+-+.|..-.+....++|+-=..+++ .|||++.|++.+|| .|+||||+|||||||+|||+|||+.+|+|+
T Consensus 286 ~AmkavAeA~~nRSLkdF~~AL~~yk~eL~---~D~ivr~Hl~~Lyd---~lLEknl~riIEPyS~Vei~hIA~~IGl~~ 359 (411)
T KOG1463|consen 286 DAMKAVAEAFGNRSLKDFEKALADYKKELA---EDPIVRSHLQSLYD---NLLEKNLCRIIEPYSRVEISHIAEVIGLDV 359 (411)
T ss_pred HHHHHHHHHhcCCcHHHHHHHHHHhHHHHh---cChHHHHHHHHHHH---HHHHHhHHHHcCchhhhhHHHHHHHHCCCc
Confidence 344455566667777777777766555544 79999999999997 689999999999999999999999999999
Q ss_pred HHHHHHHHHHhhccceeeEeeccc--------------hHHHHHHHHHH
Q psy3486 100 SDVESLLVSLILDNTVRGRIDQSN--------------YKEMMSRYKQL 134 (222)
Q Consensus 100 ~~VE~~L~~~iLdq~ik~~idqg~--------------y~~~l~~y~~L 134 (222)
.+||+||++||||+++.|.+|||. |+.+|++.+.|
T Consensus 360 ~~VEkKLsqMILDKkf~G~LDQg~g~Liv~~e~~~d~~y~~aLetI~~m 408 (411)
T KOG1463|consen 360 PQVEKKLSQMILDKKFYGTLDQGEGCLIVFEEPPADNTYDAALETIQNM 408 (411)
T ss_pred HHHHHHHHHHHHHHHhhcccccCCCeEEEeCCCCcchHHHHHHHHHHhc
Confidence 999999999999999999999998 77777776665
No 3
>KOG1463|consensus
Probab=99.78 E-value=1.9e-19 Score=165.70 Aligned_cols=69 Identities=25% Similarity=0.420 Sum_probs=66.8
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhh
Q psy3486 1 MDDPFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLN 69 (222)
Q Consensus 1 ~~D~~I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~ 69 (222)
++||+|+.|++.|||+|++|||+++|+|||||+|+|||+.+|+|.+.||+|||+||||+.+.|.+||-+
T Consensus 315 ~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~hIA~~IGl~~~~VEkKLsqMILDKkf~G~LDQg~ 383 (411)
T KOG1463|consen 315 AEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEISHIAEVIGLDVPQVEKKLSQMILDKKFYGTLDQGE 383 (411)
T ss_pred hcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHHHHHHHHCCCcHHHHHHHHHHHHHHHhhcccccCC
Confidence 479999999999999999999999999999999999999999999999999999999999999999843
No 4
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=99.75 E-value=1.8e-18 Score=157.36 Aligned_cols=114 Identities=20% Similarity=0.425 Sum_probs=101.1
Q ss_pred HHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCC
Q psy3486 19 TQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIE 98 (222)
Q Consensus 19 ~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~ 98 (222)
..++..+-++|..-.+....++|..=.+++. +|+|++.|+.++|| .++++||+|||||||+|+|+|||+.+|++
T Consensus 283 I~am~avaea~~NRsL~df~~aL~qY~~el~---~D~~iRsHl~~LYD---~LLe~Nl~kiiEPfs~VeishIa~viGld 356 (421)
T COG5159 283 IRAMLAVAEAFGNRSLKDFSDALAQYSDELH---QDSFIRSHLQYLYD---VLLEKNLVKIIEPFSVVEISHIADVIGLD 356 (421)
T ss_pred HHHHHHHHHHhCCCcHhhHHHHHHHhhHHhc---cCHHHHHHHHHHHH---HHHHhhhhhhcCcceeeehhHHHHHhccc
Confidence 3466678888888888888888887666654 89999999999997 67999999999999999999999999999
Q ss_pred hHHHHHHHHHHhhccceeeEeeccc--------------hHHHHHHHHHHHhhh
Q psy3486 99 TSDVESLLVSLILDNTVRGRIDQSN--------------YKEMMSRYKQLLLYI 138 (222)
Q Consensus 99 ~~~VE~~L~~~iLdq~ik~~idqg~--------------y~~~l~~y~~LLtyi 138 (222)
+.+||+||++||||+.+.|.+|||+ ||+|++..++|=+-+
T Consensus 357 t~qvEgKLsqMILDKifyG~LDqg~gcLivy~ep~qd~tyd~ale~v~~l~~vV 410 (421)
T COG5159 357 TNQVEGKLSQMILDKIFYGTLDQGDGCLIVYGEPAQDNTYDEALEQVEALDCVV 410 (421)
T ss_pred HHHHHHHHHHHHHHHHHHhhhccCCceEEEeCCccccchHHHHHHHHHHhhhHH
Confidence 9999999999999999999999998 888888877776643
No 5
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=99.72 E-value=6.6e-18 Score=153.70 Aligned_cols=69 Identities=25% Similarity=0.332 Sum_probs=66.9
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhh
Q psy3486 1 MDDPFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLN 69 (222)
Q Consensus 1 ~~D~~I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~ 69 (222)
+.|||||.|++.|||+++++||+++|+||++|+|+|||+.+|++..+||+||||||||+-+.|++||-+
T Consensus 313 ~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGldt~qvEgKLsqMILDKifyG~LDqg~ 381 (421)
T COG5159 313 HQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLDTNQVEGKLSQMILDKIFYGTLDQGD 381 (421)
T ss_pred ccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhcccHHHHHHHHHHHHHHHHHHhhhccCC
Confidence 579999999999999999999999999999999999999999999999999999999999999999853
No 6
>KOG1464|consensus
Probab=99.60 E-value=2e-15 Score=137.20 Aligned_cols=69 Identities=78% Similarity=1.187 Sum_probs=58.8
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhc
Q psy3486 1 MDDPFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLI 80 (222)
Q Consensus 1 ~~D~~I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~ii 80 (222)
|+||||++|+++|++++|+|+|+++|+||++|.|+|
T Consensus 334 M~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipf-------------------------------------------- 369 (440)
T KOG1464|consen 334 MDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPF-------------------------------------------- 369 (440)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHhccccccCchh--------------------------------------------
Confidence 799999999999999999999997666666666655
Q ss_pred cccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccc
Q psy3486 81 KPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSN 123 (222)
Q Consensus 81 epys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~ 123 (222)
||+.+++|..+||+.|+.+|||..|.|+||+.+
T Consensus 370 ----------is~~Lnv~~~dV~~LLV~~ILD~~i~g~Ide~n 402 (440)
T KOG1464|consen 370 ----------ISKELNVPEADVESLLVSCILDDTIDGRIDEVN 402 (440)
T ss_pred ----------hHhhcCCCHHHHHHHHHHHHhccccccchHHhh
Confidence 777777788899999999999999999998753
No 7
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=98.65 E-value=4.2e-08 Score=73.22 Aligned_cols=67 Identities=33% Similarity=0.441 Sum_probs=63.4
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhh
Q psy3486 2 DDPFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQL 68 (222)
Q Consensus 2 ~D~~I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~ 68 (222)
.|+++..|++.+.+.++..++.+++.||++|.++.+|+.+++|.++||.-+.+||.++-+.|-+|+.
T Consensus 31 ~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~ 97 (105)
T PF01399_consen 31 KDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLISNGLIKAKIDQV 97 (105)
T ss_dssp HCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEETT
T ss_pred cCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHHCCCEEEEEECC
Confidence 4788999999999999999999999999999999999999999999999999999999999999864
No 8
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=98.53 E-value=3.9e-07 Score=67.98 Aligned_cols=69 Identities=29% Similarity=0.482 Sum_probs=57.5
Q ss_pred hhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccc
Q psy3486 52 LIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSN 123 (222)
Q Consensus 52 lsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~ 123 (222)
+.++++..|...+.+ .+...++.+++.||++|.++.+|+.++++.++||..+..+|.++.++|+||+.+
T Consensus 30 ~~~~~l~~~~~~l~~---~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~~ 98 (105)
T PF01399_consen 30 FKDPFLAEYVEQLKE---KIRRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLISNGLIKAKIDQVN 98 (105)
T ss_dssp HHCTTHHHHHHHHHH---HHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEETTT
T ss_pred HcCccHHHHHHHHHH---HHHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHHCCCEEEEEECCC
Confidence 344555555555553 567788999999999999999999999999999999999999999999999853
No 9
>smart00753 PAM PCI/PINT associated module.
Probab=98.49 E-value=1.4e-07 Score=69.84 Aligned_cols=62 Identities=26% Similarity=0.359 Sum_probs=58.9
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhh
Q psy3486 8 EHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLN 69 (222)
Q Consensus 8 ~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~ 69 (222)
.|++.+++.+|..++..+.+||++|.++.||+.+++|.++||..+.+||.++.+.|-+||.+
T Consensus 1 ~~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~ 62 (88)
T smart00753 1 QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVN 62 (88)
T ss_pred ChHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcC
Confidence 37899999999999999999999999999999999999999999999999999999998743
No 10
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=98.49 E-value=1.4e-07 Score=69.84 Aligned_cols=62 Identities=26% Similarity=0.359 Sum_probs=58.9
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhh
Q psy3486 8 EHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLN 69 (222)
Q Consensus 8 ~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~ 69 (222)
.|++.+++.+|..++..+.+||++|.++.||+.+++|.++||..+.+||.++.+.|-+||.+
T Consensus 1 ~~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~ 62 (88)
T smart00088 1 QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVN 62 (88)
T ss_pred ChHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcC
Confidence 37899999999999999999999999999999999999999999999999999999998743
No 11
>KOG0686|consensus
Probab=98.49 E-value=1.2e-07 Score=89.93 Aligned_cols=68 Identities=18% Similarity=0.303 Sum_probs=65.9
Q ss_pred chHHHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhh
Q psy3486 3 DPFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNI 70 (222)
Q Consensus 3 D~~I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~ 70 (222)
|++++.|++.||+.||.+.|+++..||+.+.++.||.+||.|+..+|+.|-+.|+++|+.|=+|+.+.
T Consensus 337 D~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~sv~~le~~l~~LI~~~~i~~rIDs~~k 404 (466)
T KOG0686|consen 337 DMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTSVAILESELLELILEGKISGRIDSHNK 404 (466)
T ss_pred chhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhcccHHHHHHHHHHHHHccchheeeccccc
Confidence 89999999999999999999999999999999999999999999999999999999999999998643
No 12
>smart00753 PAM PCI/PINT associated module.
Probab=98.15 E-value=4.6e-06 Score=61.60 Aligned_cols=55 Identities=27% Similarity=0.457 Sum_probs=50.8
Q ss_pred hhhhhhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccc
Q psy3486 69 NIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSN 123 (222)
Q Consensus 69 ~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~ 123 (222)
+.+...++..+.+||++|.++.+|+.+++|.+++|..++.+|.++.+.|++|+.+
T Consensus 8 ~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~ 62 (88)
T smart00753 8 RKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVN 62 (88)
T ss_pred HHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcC
Confidence 3556788999999999999999999999999999999999999999999999854
No 13
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=98.15 E-value=4.6e-06 Score=61.60 Aligned_cols=55 Identities=27% Similarity=0.457 Sum_probs=50.8
Q ss_pred hhhhhhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccc
Q psy3486 69 NIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSN 123 (222)
Q Consensus 69 ~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~ 123 (222)
+.+...++..+.+||++|.++.+|+.+++|.+++|..++.+|.++.+.|++|+.+
T Consensus 8 ~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~ 62 (88)
T smart00088 8 RKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVN 62 (88)
T ss_pred HHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcC
Confidence 3556788999999999999999999999999999999999999999999999854
No 14
>KOG0686|consensus
Probab=96.92 E-value=0.0012 Score=63.26 Aligned_cols=93 Identities=24% Similarity=0.416 Sum_probs=79.6
Q ss_pred hhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccchHHHHHH
Q psy3486 51 KLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSNYKEMMSR 130 (222)
Q Consensus 51 klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~y~~~l~~ 130 (222)
-|-||+|..|...++++. -+.-+++..-|||.+.++.+|.-.|.++...|+.|-..|+++.|+|+||+.+.
T Consensus 334 llLD~yLaphVd~Ly~~I---R~r~llqy~~py~s~~m~~mA~af~~sv~~le~~l~~LI~~~~i~~rIDs~~k------ 404 (466)
T KOG0686|consen 334 LLLDMYLAPHVDNLYSLI---RNRALLQYLSPYSSADMSKMAEAFNTSVAILESELLELILEGKISGRIDSHNK------ 404 (466)
T ss_pred eeechhcchhHHHHHHHH---HHhhHHHhcCccccchHHHHHHHhcccHHHHHHHHHHHHHccchheeeccccc------
Confidence 356999999999999853 45679999999999999999999999999999999999999999999999875
Q ss_pred HHHHHhhhhhccCccccHHHHHHHHH
Q psy3486 131 YKQLLLYIKSAVTRNYSEKSINSILD 156 (222)
Q Consensus 131 y~~LLtyiksaVtrNysEksIn~iLd 156 (222)
.-|++.+=+||..-+-++.|-+
T Consensus 405 ----i~~~~~~~~en~~fe~~~~~~~ 426 (466)
T KOG0686|consen 405 ----ILYARDADSENATFERVLPMGK 426 (466)
T ss_pred ----eeeecccccccchhhhcchhhH
Confidence 6677666677776666665554
No 15
>KOG0687|consensus
Probab=95.81 E-value=0.0064 Score=57.04 Aligned_cols=66 Identities=14% Similarity=0.269 Sum_probs=62.3
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhh
Q psy3486 2 DDPFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQ 67 (222)
Q Consensus 2 ~D~~I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~ 67 (222)
.|-++..|.+---+-||..+=-++.+||..+.++.||+.||+|++=|+.-|+.-|-...|+--+|.
T Consensus 288 ~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDr 353 (393)
T KOG0687|consen 288 DDRYLGPHYRYYVREMRRRVYAQLLESYRSLTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDR 353 (393)
T ss_pred cchhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeec
Confidence 588999999999999999999999999999999999999999999999999999999998888874
No 16
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=93.89 E-value=0.047 Score=51.00 Aligned_cols=67 Identities=16% Similarity=0.332 Sum_probs=63.5
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhh
Q psy3486 2 DDPFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQL 68 (222)
Q Consensus 2 ~D~~I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~ 68 (222)
+|.|+-.|.+-.-+.||-++--++.++|....++.||+.||+|++=|+.-|..-|-++.|.-.+|..
T Consensus 302 ~d~fl~rh~d~fvREMRrrvYaQlLESYr~lsl~sMA~tFgVSV~yvdrDLg~FIp~~~LncvIDRv 368 (412)
T COG5187 302 DDVFLGRHVDLFVREMRRRVYAQLLESYRLLSLESMAQTFGVSVEYVDRDLGEFIPEGRLNCVIDRV 368 (412)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhCccHHHHhhhHHhhCCCCceeeeeecc
Confidence 6899999999999999999999999999999999999999999999999999999999998888843
No 17
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=93.55 E-value=0.074 Score=42.90 Aligned_cols=47 Identities=15% Similarity=0.291 Sum_probs=39.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHH
Q psy3486 4 PFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLI 50 (222)
Q Consensus 4 ~~I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~ 50 (222)
+.+...+..+.+++|...+--+-..|++|.++.+|+.||++.+++++
T Consensus 70 ~~~~~~v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~ 116 (143)
T PF10075_consen 70 PDYKPFVPGFEDTIRERIAHLISKAYSSISLSDLAEMLGLSEEELEK 116 (143)
T ss_dssp -HHHHTSTTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTTS-HHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhCCCHHHHHH
Confidence 57788899999999999999999999999999999999999666553
No 18
>KOG2581|consensus
Probab=93.01 E-value=0.21 Score=48.28 Aligned_cols=73 Identities=18% Similarity=0.354 Sum_probs=58.9
Q ss_pred HHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhh-----hccccccccHhHHHHHhCCChHH-HHHHHHHHhhccceeeEee
Q psy3486 47 DVLIKLIKPYTRIHIPFISRQLNIETSDVLIK-----LIKPYTRIHIPFISRQLNIETSD-VESLLVSLILDNTVRGRID 120 (222)
Q Consensus 47 ~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~-----iiepys~v~i~~ia~~l~l~~~~-VE~~L~~~iLdq~ik~~id 120 (222)
++..+.-|-|...+.+.++ +++.+|.+| |==.||||.+..||+.||++.++ +|-..+.-|-|+.|.+.++
T Consensus 338 ~~leq~k~~f~~D~ty~Li----vRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~EyiVakAIRDGvIea~Id 413 (493)
T KOG2581|consen 338 ETLEQFKDKFQADGTYTLI----VRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDAEYIVAKAIRDGVIEAKID 413 (493)
T ss_pred HHHHHHHHHHhhCCcchHH----HHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhHHHHHHHHHHhccceeeec
Confidence 3444556677777777666 578888765 33489999999999999998876 9999999999999999998
Q ss_pred ccc
Q psy3486 121 QSN 123 (222)
Q Consensus 121 qg~ 123 (222)
.++
T Consensus 414 ~~~ 416 (493)
T KOG2581|consen 414 HED 416 (493)
T ss_pred ccc
Confidence 763
No 19
>KOG1498|consensus
Probab=92.43 E-value=0.19 Score=48.30 Aligned_cols=61 Identities=16% Similarity=0.082 Sum_probs=56.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhh
Q psy3486 6 IREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISR 66 (222)
Q Consensus 6 I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d 66 (222)
-..|.++|...+-+.|+-=+-+=||||.+.++|..+++|+++.|++||+|.-.+++..=+|
T Consensus 328 gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl~~ee~E~~LS~lv~t~ti~aKid 388 (439)
T KOG1498|consen 328 GEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDLPVEEMEKFLSDLVVTGTIYAKID 388 (439)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHHHHHhccceEEEec
Confidence 3579999999999999998899999999999999999999999999999999999985555
No 20
>KOG1497|consensus
Probab=89.39 E-value=0.77 Score=43.39 Aligned_cols=81 Identities=25% Similarity=0.366 Sum_probs=64.2
Q ss_pred hhhhhhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccc----hHH---HHHHHHHHHhhhhhc
Q psy3486 69 NIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSN----YKE---MMSRYKQLLLYIKSA 141 (222)
Q Consensus 69 ~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~----y~~---~l~~y~~LLtyiksa 141 (222)
...+|-||+-+=+=|..+..+-+++.+++|.+++|+.-++||-...++|+|||-+ |+. +-.+-++..+..
T Consensus 301 ra~~EhNlls~Skly~nisf~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~egiihFe~~e~l~~wdkqi~sl~--- 377 (399)
T KOG1497|consen 301 RAVIEHNLLSASKLYNNISFEELGALLKIDAEKAEKIAAQMITQERMNGSIDQIEGIIHFEDREELPQWDKQIQSLC--- 377 (399)
T ss_pred hHHHHHhHHHHHHHHHhccHHHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhhcceEeecchhhhhhhhHHHHHHH---
Confidence 3567899999999999999999999999999999999999999999999999954 333 323344443322
Q ss_pred cCccccHHHHHHHHHHhh
Q psy3486 142 VTRNYSEKSINSILDYIS 159 (222)
Q Consensus 142 VtrNysEksIn~iLd~vs 159 (222)
..+|+|+|-++
T Consensus 378 -------~qvNki~~~i~ 388 (399)
T KOG1497|consen 378 -------NQVNKILDKIS 388 (399)
T ss_pred -------HHHHHHHHHHH
Confidence 34678888665
No 21
>KOG1498|consensus
Probab=89.09 E-value=0.72 Score=44.43 Aligned_cols=51 Identities=22% Similarity=0.447 Sum_probs=44.0
Q ss_pred hhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccc
Q psy3486 73 SDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSN 123 (222)
Q Consensus 73 ~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~ 123 (222)
+-|+-=+=+=||||....+|..+++|+++.|..+++++-.+.+.+.+|++.
T Consensus 341 EHNiRiiA~yYSrIt~~rl~eLLdl~~ee~E~~LS~lv~t~ti~aKidrps 391 (439)
T KOG1498|consen 341 EHNIRIIAKYYSRITLKRLAELLDLPVEEMEKFLSDLVVTGTIYAKIDRPS 391 (439)
T ss_pred HHHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHHHHHhccceEEEecCCC
Confidence 344433345689999999999999999999999999999999999999874
No 22
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=88.96 E-value=18 Score=32.94 Aligned_cols=90 Identities=14% Similarity=0.242 Sum_probs=71.1
Q ss_pred hhcccccccHhHHHHHhccchhHHHHhhhhhhHhh--------------hhhhhhhhhhhhhhhhhhhhccccccccHhH
Q psy3486 25 LIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRI--------------HIPFISRQLNIETSDVLIKLIKPYTRIHIPF 90 (222)
Q Consensus 25 li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~--------------hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ 90 (222)
+..-=-||.+..+|+.||++...||..+.++.=+. ++..+...+|..+ .--..|-|+.
T Consensus 64 l~~~gGRv~~~dL~~~LnVd~~~ie~~~~~i~~~~~~~~l~~gelit~~Yld~l~~Eine~L--------qe~G~vsi~e 135 (272)
T PF09743_consen 64 LYVHGGRVNLVDLAQALNVDLDHIERRAQEIVKSDKSLQLVQGELITDSYLDSLAEEINEKL--------QESGQVSISE 135 (272)
T ss_pred HHHcCCceEHHHHHHhcCcCHHHHHHHHHHHHhCCCcEEEECCEEccHHHHHHHHHHHHHHH--------HHcCeEeHHH
Confidence 33445899999999999999999999998866554 4444444444433 2338899999
Q ss_pred HHHHhCCChHHHHHHHHHHhhccceeeEeecc
Q psy3486 91 ISRQLNIETSDVESLLVSLILDNTVRGRIDQS 122 (222)
Q Consensus 91 ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg 122 (222)
+|+..++|.+=+.+.+..+.+-..|+|+++.+
T Consensus 136 La~~~~Lp~efl~~~li~~~lg~~I~g~~d~~ 167 (272)
T PF09743_consen 136 LAKQYDLPSEFLKEELISKRLGKIIKGRLDGD 167 (272)
T ss_pred HHHhcCCcHHHHHHHHhhhhcCcceeEEEeCC
Confidence 99999999988887788888999999999976
No 23
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=86.53 E-value=2.7 Score=27.33 Aligned_cols=88 Identities=16% Similarity=0.180 Sum_probs=52.1
Q ss_pred eeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhhh
Q psy3486 119 IDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKLY 198 (222)
Q Consensus 119 idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~ 198 (222)
+.+|+++++++.+++.+..- +. . ..+...+-..+....+.+--.+.|+..++.. ..+. .+...+|.++
T Consensus 11 ~~~~~~~~A~~~~~~~~~~~-~~----~-~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~--~~~~----~~~~~~~~~~ 78 (100)
T cd00189 11 YKLGDYDEALEYYEKALELD-PD----N-ADAYYNLAAAYYKLGKYEEALEDYEKALELD--PDNA----KAYYNLGLAY 78 (100)
T ss_pred HHHhcHHHHHHHHHHHHhcC-Cc----c-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC--Ccch----hHHHHHHHHH
Confidence 45799999999999988743 21 1 1333333332222222222233444433321 1122 4556789999
Q ss_pred hchhhHhHHHHHHHHHHHhh
Q psy3486 199 FDREDFNKLSRILKQLHQSC 218 (222)
Q Consensus 199 ld~~ey~~l~~~l~~L~~~c 218 (222)
+..+++.+..+.+....+.|
T Consensus 79 ~~~~~~~~a~~~~~~~~~~~ 98 (100)
T cd00189 79 YKLGKYEEALEAYEKALELD 98 (100)
T ss_pred HHHHhHHHHHHHHHHHHccC
Confidence 99999999998888877655
No 24
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=86.21 E-value=1.1 Score=42.42 Aligned_cols=64 Identities=16% Similarity=0.132 Sum_probs=57.2
Q ss_pred chHHHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhh
Q psy3486 3 DPFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISR 66 (222)
Q Consensus 3 D~~I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d 66 (222)
|..=..|.++|...+-+.|+-=+-+-||||....+...+..|+++.|++.|||.=..|++.=.+
T Consensus 325 ~e~~~~~w~DL~krviEHN~RvI~~yYSrI~~~rl~~lld~~~s~te~~ISdlVN~G~~yaKiN 388 (439)
T COG5071 325 DEKGEKRWSDLRKRVIEHNIRVIANYYSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFYAKIN 388 (439)
T ss_pred cchhhhhHHHHHHHHHHhhHhHHHHHhhhhhHHHHHHHHcCCHHHHHHHHHHHHhcCcEEEEec
Confidence 3444579999999999999988888999999999999999999999999999999888876654
No 25
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=86.16 E-value=19 Score=37.62 Aligned_cols=145 Identities=13% Similarity=0.210 Sum_probs=94.0
Q ss_pred ccccccHhHHHHHhccchhHHHHhhhhhhH--------------hhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHH
Q psy3486 28 PYTRIHIPFISRQLNIETSDVLIKLIKPYT--------------RIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISR 93 (222)
Q Consensus 28 PYsri~i~~ia~~l~l~~~~ve~klsd~il--------------~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~ 93 (222)
-.-||-+-.+|..||++...||..+.++-- +.++..+... +-..+.--+.|-|+.+|+
T Consensus 71 ~gGRvnlvdLa~~LnVD~~hiEr~~~~iv~~d~~~~l~~GeLit~~Yld~iaeE--------Ine~LqE~G~isI~eLa~ 142 (803)
T PLN03083 71 KLGRVSLVDLADTIGVDLYHVERQAQQVVSDDPGLMLVQGEIISQSYWDSIAEE--------INERLQECSQIALAELAR 142 (803)
T ss_pred hCCCeeHHHHhhhcCCCHHHHHHHHHHHhcCCCceEEecCEecchHHHHHHHHH--------HHHHHHHcCcChHHHHHH
Confidence 468999999999999999999999887633 2333333332 334456678999999999
Q ss_pred HhCCChHHHHHHHHHHhhccceeeEeeccch-H-HHHHHHHHHHhhhhhccCccccHHHHHHHHHH-hh---cCCchHHH
Q psy3486 94 QLNIETSDVESLLVSLILDNTVRGRIDQSNY-K-EMMSRYKQLLLYIKSAVTRNYSEKSINSILDY-IS---TSKNMELL 167 (222)
Q Consensus 94 ~l~l~~~~VE~~L~~~iLdq~ik~~idqg~y-~-~~l~~y~~LLtyiksaVtrNysEksIn~iLd~-vs---~s~~~~~l 167 (222)
++++|.+=+.+.++.. +-..|+|+.+-|.. - .-+..-+..+-=+-.|+||.-+=.++.+.+-. +. .+.+..+-
T Consensus 143 ~~~Lpsefl~~~l~~r-lG~iI~g~~~g~~lyT~aYv~r~~a~vRG~l~AiT~Pt~~s~l~~~~q~~l~~~~~~~~v~~~ 221 (803)
T PLN03083 143 QLQVGSELVTSMLEPR-LGTIVKARLEGGQLYTPAYVARVTAMVRGAARGITVPTNLSSLWNSLQQLLREMDGAGGVTVE 221 (803)
T ss_pred hcCChHHHHHHHHHHH-hccceEEEecCCEEecHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhccccccccccch
Confidence 9999999888888776 88899999965542 1 11111111111122577777766666554421 11 11234566
Q ss_pred HHHHHHHHHHHhcC
Q psy3486 168 QDFYETTLEALKDA 181 (222)
Q Consensus 168 ~~fYe~TL~~l~~~ 181 (222)
.++|.-+++-|-..
T Consensus 222 ~~lf~~~l~~Li~~ 235 (803)
T PLN03083 222 GSFFQSIFNGLVKE 235 (803)
T ss_pred HHHHHHHHHHHHhc
Confidence 67776666655533
No 26
>KOG1497|consensus
Probab=86.12 E-value=0.86 Score=43.08 Aligned_cols=57 Identities=18% Similarity=0.103 Sum_probs=53.6
Q ss_pred HHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhh
Q psy3486 12 DLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQL 68 (222)
Q Consensus 12 ~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~ 68 (222)
.+=+.+.+.||+-+-+=|..|+++.+++.|++|.+.+|+--+|||...-+.|-+||.
T Consensus 298 il~ra~~EhNlls~Skly~nisf~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~ 354 (399)
T KOG1497|consen 298 ILDRAVIEHNLLSASKLYNNISFEELGALLKIDAEKAEKIAAQMITQERMNGSIDQI 354 (399)
T ss_pred hhhhHHHHHhHHHHHHHHHhccHHHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhh
Confidence 456778899999999999999999999999999999999999999999999999984
No 27
>KOG1840|consensus
Probab=85.71 E-value=14 Score=36.55 Aligned_cols=163 Identities=13% Similarity=0.144 Sum_probs=113.9
Q ss_pred HHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceee
Q psy3486 38 SRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRG 117 (222)
Q Consensus 38 a~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~ 117 (222)
.+..|.+.++|..-|+....---.-+=+++ +..+-|+.++|++ ......+ ..+..++.-|..+
T Consensus 314 ~~~~~~~~~~v~~~l~~~~~~~~~~~~~Ee-a~~l~q~al~i~~--~~~g~~~------~~~a~~~~nl~~l-------- 376 (508)
T KOG1840|consen 314 EKLLGASHPEVAAQLSELAAILQSMNEYEE-AKKLLQKALKIYL--DAPGEDN------VNLAKIYANLAEL-------- 376 (508)
T ss_pred HHhhccChHHHHHHHHHHHHHHHHhcchhH-HHHHHHHHHHHHH--hhccccc------hHHHHHHHHHHHH--------
Confidence 346778888888888887766555555553 5556677778777 2222222 1234445444443
Q ss_pred EeeccchHHHHHHHHHHHhhhhhccC--ccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCc-eeeecchhh
Q psy3486 118 RIDQSNYKEMMSRYKQLLLYIKSAVT--RNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDR-LWFKTNTKL 194 (222)
Q Consensus 118 ~idqg~y~~~l~~y~~LLtyiksaVt--rNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeR-LWfKtnlKl 194 (222)
...+|+|++|.+.|++-++=.+..-. ..+.-++||.+=.-+..+++.+.-.+.|+.-..-.+..+++- =-.-|..+|
T Consensus 377 ~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL 456 (508)
T KOG1840|consen 377 YLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNL 456 (508)
T ss_pred HHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHH
Confidence 34569999999999999995544444 456689999998877777777777788888777776555544 445678899
Q ss_pred hhhhhchhhHhHHHHHHHHHHHh
Q psy3486 195 GKLYFDREDFNKLSRILKQLHQS 217 (222)
Q Consensus 195 akL~ld~~ey~~l~~~l~~L~~~ 217 (222)
|.+|=.+|.|+...++...+-.+
T Consensus 457 ~~~Y~~~g~~e~a~~~~~~~~~~ 479 (508)
T KOG1840|consen 457 AALYRAQGNYEAAEELEEKVLNA 479 (508)
T ss_pred HHHHHHcccHHHHHHHHHHHHHH
Confidence 99999999999999887766543
No 28
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=81.91 E-value=1.2 Score=29.90 Aligned_cols=27 Identities=19% Similarity=0.421 Sum_probs=24.8
Q ss_pred cchhhhhhhhchhhHhHHHHHHHHHHH
Q psy3486 190 TNTKLGKLYFDREDFNKLSRILKQLHQ 216 (222)
Q Consensus 190 tnlKlakL~ld~~ey~~l~~~l~~L~~ 216 (222)
|++.||+.|+++|+++...++|.++-+
T Consensus 1 ~kLdLA~ayie~Gd~e~Ar~lL~evl~ 27 (44)
T TIGR03504 1 TKLDLARAYIEMGDLEGARELLEEVIE 27 (44)
T ss_pred CchHHHHHHHHcCChHHHHHHHHHHHH
Confidence 578899999999999999999999875
No 29
>KOG0687|consensus
Probab=81.02 E-value=6.1 Score=37.61 Aligned_cols=68 Identities=16% Similarity=0.314 Sum_probs=58.4
Q ss_pred hhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccc
Q psy3486 53 IKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSN 123 (222)
Q Consensus 53 sd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~ 123 (222)
-|-++..|..+..|. |---.--+++|||-.+-++..|+-.|++++=++.-|+.-|-.+.++-.||..+
T Consensus 288 ~D~~l~~h~~yyvRE---MR~rvY~QlLESYrsl~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDrVn 355 (393)
T KOG0687|consen 288 DDRYLGPHYRYYVRE---MRRRVYAQLLESYRSLTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDRVN 355 (393)
T ss_pred cchhcchHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeeccc
Confidence 477899999998873 33344567899999999999999999999999999999999999999998743
No 30
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=80.64 E-value=4.8 Score=35.70 Aligned_cols=98 Identities=12% Similarity=0.205 Sum_probs=68.0
Q ss_pred chHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcC-CchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhhhhch
Q psy3486 123 NYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTS-KNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKLYFDR 201 (222)
Q Consensus 123 ~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s-~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~ld~ 201 (222)
++++|+++|++-+..-...=...-.-+...++=..+... .+.+---+.|+..++.++..+..+.--++..++|.++...
T Consensus 89 ~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l 168 (282)
T PF14938_consen 89 DPDEAIECYEKAIEIYREAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARL 168 (282)
T ss_dssp THHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHh
Confidence 778888888887774422111112233444444444444 5777778899999999988877777788999999999999
Q ss_pred hhHhHHHHHHHHHHHhhhc
Q psy3486 202 EDFNKLSRILKQLHQSCQM 220 (222)
Q Consensus 202 ~ey~~l~~~l~~L~~~c~~ 220 (222)
++|....++..++-..|..
T Consensus 169 ~~y~~A~~~~e~~~~~~l~ 187 (282)
T PF14938_consen 169 GRYEEAIEIYEEVAKKCLE 187 (282)
T ss_dssp T-HHHHHHHHHHHHHTCCC
T ss_pred CCHHHHHHHHHHHHHHhhc
Confidence 9999999999988877743
No 31
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=79.33 E-value=0.69 Score=28.71 Aligned_cols=24 Identities=25% Similarity=0.304 Sum_probs=18.5
Q ss_pred eeeEeeccchHHHHHHHHHHHhhh
Q psy3486 115 VRGRIDQSNYKEMMSRYKQLLLYI 138 (222)
Q Consensus 115 ik~~idqg~y~~~l~~y~~LLtyi 138 (222)
-.+..++|+|++|+++|++.|...
T Consensus 6 g~~~~~~g~~~~Ai~~y~~aL~l~ 29 (36)
T PF13176_consen 6 GRIYRQQGDYEKAIEYYEQALALA 29 (36)
T ss_dssp HHHHHHCT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHcCCHHHHHHHHHHHHHhc
Confidence 345668899999999999988643
No 32
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=77.30 E-value=6.3 Score=28.09 Aligned_cols=82 Identities=21% Similarity=0.288 Sum_probs=44.4
Q ss_pred eccchHHHHHHHHHHHhhhhhccCccccHHH-HHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhhh
Q psy3486 120 DQSNYKEMMSRYKQLLLYIKSAVTRNYSEKS-INSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKLY 198 (222)
Q Consensus 120 dqg~y~~~l~~y~~LLtyiksaVtrNysEks-In~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~ 198 (222)
++|+|++|+..|++++.-. +. |. +.+ .-.+-. .-|...=|+..++.++..+-+.--+.+..-+|+.+
T Consensus 1 ~~~~y~~Ai~~~~k~~~~~-~~---~~-~~~~~~~la~-------~~~~~~~y~~A~~~~~~~~~~~~~~~~~~l~a~~~ 68 (84)
T PF12895_consen 1 DQGNYENAIKYYEKLLELD-PT---NP-NSAYLYNLAQ-------CYFQQGKYEEAIELLQKLKLDPSNPDIHYLLARCL 68 (84)
T ss_dssp HTT-HHHHHHHHHHHHHHH-CG---TH-HHHHHHHHHH-------HHHHTTHHHHHHHHHHCHTHHHCHHHHHHHHHHHH
T ss_pred CCccHHHHHHHHHHHHHHC-CC---Ch-hHHHHHHHHH-------HHHHCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Confidence 5799999999999999955 22 22 222 111111 11222223334444432110000134444569999
Q ss_pred hchhhHhHHHHHHHH
Q psy3486 199 FDREDFNKLSRILKQ 213 (222)
Q Consensus 199 ld~~ey~~l~~~l~~ 213 (222)
++.|+|+..-+.+++
T Consensus 69 ~~l~~y~eAi~~l~~ 83 (84)
T PF12895_consen 69 LKLGKYEEAIKALEK 83 (84)
T ss_dssp HHTT-HHHHHHHHHH
T ss_pred HHhCCHHHHHHHHhc
Confidence 999999999887764
No 33
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=76.43 E-value=17 Score=24.77 Aligned_cols=68 Identities=9% Similarity=0.038 Sum_probs=41.9
Q ss_pred ccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCC-ChHHHHH
Q psy3486 32 IHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNI-ETSDVES 104 (222)
Q Consensus 32 i~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l-~~~~VE~ 104 (222)
+.++.+|+.+|+|...+...+...+-..- ...++ ...+..-+-.+.++ .+.++.+|..+|+ +....-.
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~~~s~-~~~~~--~~r~~~a~~~l~~~--~~~~~~ia~~~g~~s~~~f~r 70 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGTTP-KQYLR--DRRLERARRLLRDT--DLSVTEIALRVGFSSQSYFSR 70 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHhCcCH-HHHHH--HHHHHHHHHHHHcC--CCCHHHHHHHhCCCChHHHHH
Confidence 57889999999999988777665432211 11111 11222222233333 7889999999999 7666554
No 34
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=76.02 E-value=3.5 Score=29.29 Aligned_cols=45 Identities=20% Similarity=0.317 Sum_probs=35.2
Q ss_pred hhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEee
Q psy3486 76 LIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRID 120 (222)
Q Consensus 76 l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~id 120 (222)
|...|+---++.++.||+.+|++.+.||..|.+++-++.|.-.-.
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 445566677889999999999999999999999999998885544
No 35
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=75.40 E-value=3 Score=29.63 Aligned_cols=43 Identities=14% Similarity=0.146 Sum_probs=33.0
Q ss_pred HHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhh
Q psy3486 21 VLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPF 63 (222)
Q Consensus 21 ~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~ 63 (222)
.|.++++--.++.++.||..|++|++.|+.-|..++-+.++..
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~ 46 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRK 46 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEE
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEE
Confidence 4556666778899999999999999999999998887776653
No 36
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=74.07 E-value=8.4 Score=26.74 Aligned_cols=33 Identities=18% Similarity=0.266 Sum_probs=22.3
Q ss_pred hhccceeeEeeccchHHHHHHHHHHHhhhhhccC
Q psy3486 110 ILDNTVRGRIDQSNYKEMMSRYKQLLLYIKSAVT 143 (222)
Q Consensus 110 iLdq~ik~~idqg~y~~~l~~y~~LLtyiksaVt 143 (222)
++...-.....+|+|++|+++|++-++. ...++
T Consensus 7 ~~~~la~~~~~~~~~~~A~~~~~~al~~-~~~~~ 39 (78)
T PF13424_consen 7 AYNNLARVYRELGRYDEALDYYEKALDI-EEQLG 39 (78)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHHHH-HHHTT
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHHHC
Confidence 3344444556789999999999999996 34443
No 37
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=73.88 E-value=6.9 Score=26.00 Aligned_cols=37 Identities=14% Similarity=0.284 Sum_probs=25.0
Q ss_pred HHHHHHHhh-cccccccHhHHHHHhccchhHHHHhhhh
Q psy3486 18 RTQVLIKLI-KPYTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 18 r~q~Ll~li-~PYsri~i~~ia~~l~l~~~~ve~klsd 54 (222)
|.+.+++++ +-=..|..+.||+.||+|...|..-+..
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 455666666 2222299999999999998887754443
No 38
>KOG2582|consensus
Probab=72.99 E-value=16 Score=35.28 Aligned_cols=103 Identities=17% Similarity=0.233 Sum_probs=76.6
Q ss_pred HHHHHHhhcccccccHhHHHHHhccch---hHHHHhhhhhhHhhhhhhhhhhh-hhhhhhhhhhhccccccccHhHHHH-
Q psy3486 19 TQVLIKLIKPYTRIHIPFISRQLNIET---SDVLIKLIKPYTRIHIPFISRQL-NIETSDVLIKLIKPYTRIHIPFISR- 93 (222)
Q Consensus 19 ~q~Ll~li~PYsri~i~~ia~~l~l~~---~~ve~klsd~il~~hl~~l~d~~-~~~~~~~l~~iiepys~v~i~~ia~- 93 (222)
.|+..+.++|++.=-.++.---+.=+. +.|-++=++-|++..=-|+.-|. -.+.-.||.|+=+-|+.+.+++||+
T Consensus 247 s~~~~r~~K~ms~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF~sLsL~dIA~~ 326 (422)
T KOG2582|consen 247 SQNAGRFFKPMSNPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTFLSLSLSDIASR 326 (422)
T ss_pred hhhhHHhcccCCchHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence 488999999998555554433333332 34556667777776655555442 2345589999999999999999999
Q ss_pred -HhCCChHHHHHHHHHHhhccceeeEeeccc
Q psy3486 94 -QLNIETSDVESLLVSLILDNTVRGRIDQSN 123 (222)
Q Consensus 94 -~l~l~~~~VE~~L~~~iLdq~ik~~idqg~ 123 (222)
+|+.+ .+||+...+|+=++.+-+.++ |.
T Consensus 327 vQLa~~-qevek~Ilqmie~~~i~a~iN-G~ 355 (422)
T KOG2582|consen 327 VQLASA-QEVEKYILQMIEDGEIFASIN-GM 355 (422)
T ss_pred HHhcch-HHHHHHHHHHhccCceEEEec-ce
Confidence 66655 689999999999999999998 65
No 39
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=72.97 E-value=6.4 Score=37.33 Aligned_cols=49 Identities=22% Similarity=0.428 Sum_probs=42.5
Q ss_pred hhhhhhcc-ccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeecc
Q psy3486 74 DVLIKLIK-PYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQS 122 (222)
Q Consensus 74 ~~l~~iie-pys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg 122 (222)
.+=+|+|+ -||||.+..++..+++|.++.|.+.+++.=++.+.+.+.+.
T Consensus 341 EHN~RvI~~yYSrI~~~rl~~lld~~~s~te~~ISdlVN~G~~yaKiNrp 390 (439)
T COG5071 341 EHNIRVIANYYSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFYAKINRP 390 (439)
T ss_pred HhhHhHHHHHhhhhhHHHHHHHHcCCHHHHHHHHHHHHhcCcEEEEecCc
Confidence 34455654 58999999999999999999999999999999999988764
No 40
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=72.91 E-value=32 Score=24.73 Aligned_cols=93 Identities=11% Similarity=0.108 Sum_probs=55.0
Q ss_pred eeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhhh
Q psy3486 119 IDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKLY 198 (222)
Q Consensus 119 idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~ 198 (222)
..+|+|++|.+.|++++.-- |. + -+...+-..+-.......+.+--.+.|+..+.. ..+.+.--..-..+|.++
T Consensus 13 ~~~~~~~~A~~~~~~~~~~~-~~-~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~---~p~~~~~~~~~~~~~~~~ 86 (119)
T TIGR02795 13 LKAGDYADAIQAFQAFLKKY-PK-S-TYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKK---YPKSPKAPDALLKLGMSL 86 (119)
T ss_pred HHcCCHHHHHHHHHHHHHHC-CC-c-cccHHHHHHHHHHHHhhccHHHHHHHHHHHHHH---CCCCCcccHHHHHHHHHH
Confidence 45799999999999998732 21 1 122333333333333334444445555554432 122222123356789999
Q ss_pred hchhhHhHHHHHHHHHHHh
Q psy3486 199 FDREDFNKLSRILKQLHQS 217 (222)
Q Consensus 199 ld~~ey~~l~~~l~~L~~~ 217 (222)
.+.++++...+.++++.+.
T Consensus 87 ~~~~~~~~A~~~~~~~~~~ 105 (119)
T TIGR02795 87 QELGDKEKAKATLQQVIKR 105 (119)
T ss_pred HHhCChHHHHHHHHHHHHH
Confidence 9999999999888877553
No 41
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=70.99 E-value=19 Score=31.94 Aligned_cols=99 Identities=11% Similarity=0.154 Sum_probs=64.1
Q ss_pred eccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhhhh
Q psy3486 120 DQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKLYF 199 (222)
Q Consensus 120 dqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~l 199 (222)
..|+|++|.++|.+-...-...=.+...-++....-..+... +.+-.-+.|+...+.+.+.++-+-+-++..++|++|-
T Consensus 47 ~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~-~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye 125 (282)
T PF14938_consen 47 LAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKKG-DPDEAIECYEKAIEIYREAGRFSQAAKCLKELAEIYE 125 (282)
T ss_dssp HTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHC
T ss_pred HHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhh-CHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHH
Confidence 457888888888887774422112222233333333333333 4445557889999988889988999999999999999
Q ss_pred ch-hhHhHHHHHHHHHHHhhh
Q psy3486 200 DR-EDFNKLSRILKQLHQSCQ 219 (222)
Q Consensus 200 d~-~ey~~l~~~l~~L~~~c~ 219 (222)
+. +++++.-+..++-.+..+
T Consensus 126 ~~~~d~e~Ai~~Y~~A~~~y~ 146 (282)
T PF14938_consen 126 EQLGDYEKAIEYYQKAAELYE 146 (282)
T ss_dssp CTT--HHHHHHHHHHHHHHHH
T ss_pred HHcCCHHHHHHHHHHHHHHHH
Confidence 99 999998877766655544
No 42
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=70.32 E-value=5.4 Score=27.46 Aligned_cols=35 Identities=14% Similarity=0.348 Sum_probs=29.4
Q ss_pred HHHHHHHhhcccccccHhHHHHHhccchhHHHHhh
Q psy3486 18 RTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKL 52 (222)
Q Consensus 18 r~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~kl 52 (222)
|.+.++++++--..+.++.+|+.||+|...|-.-|
T Consensus 1 R~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl 35 (57)
T PF08220_consen 1 RQQQILELLKEKGKVSVKELAEEFGVSEMTIRRDL 35 (57)
T ss_pred CHHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHH
Confidence 45778888888999999999999999988866433
No 43
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=69.87 E-value=7.7 Score=25.37 Aligned_cols=41 Identities=15% Similarity=0.254 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHhhcccccc-cHhHHHHHhccchhHHHHhhh
Q psy3486 13 LLRNIRTQVLIKLIKPYTRI-HIPFISRQLNIETSDVLIKLI 53 (222)
Q Consensus 13 L~~~lr~q~Ll~li~PYsri-~i~~ia~~l~l~~~~ve~kls 53 (222)
+++.++.......+.|=.++ ....+|+.+|+|.+.|..-+.
T Consensus 1 i~~~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~ 42 (60)
T smart00345 1 VAERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALS 42 (60)
T ss_pred CHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHH
Confidence 36777888777777887788 899999999999887664443
No 44
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=69.61 E-value=45 Score=25.05 Aligned_cols=110 Identities=13% Similarity=0.147 Sum_probs=64.6
Q ss_pred HHHHhCCChHHHHHHHHHHhhccceeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHH
Q psy3486 91 ISRQLNIETSDVESLLVSLILDNTVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDF 170 (222)
Q Consensus 91 ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~f 170 (222)
+.+.+.++.+..+..+ ......+.+|+|++|++.++++++.- |. .......+-..+....+.+--...
T Consensus 6 ~~~~l~~~p~~~~~~~------~~a~~~~~~~~~~~A~~~~~~~~~~~-p~-----~~~~~~~la~~~~~~~~~~~A~~~ 73 (135)
T TIGR02552 6 LKDLLGLDSEQLEQIY------ALAYNLYQQGRYDEALKLFQLLAAYD-PY-----NSRYWLGLAACCQMLKEYEEAIDA 73 (135)
T ss_pred HHHHHcCChhhHHHHH------HHHHHHHHcccHHHHHHHHHHHHHhC-CC-----cHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455667776665322 12233556799999999999998832 32 223333333322222233333444
Q ss_pred HHHHHHHHhcCCCCceeeecchhhhhhhhchhhHhHHHHHHHHHHHhh
Q psy3486 171 YETTLEALKDAKNDRLWFKTNTKLGKLYFDREDFNKLSRILKQLHQSC 218 (222)
Q Consensus 171 Ye~TL~~l~~~~NeRLWfKtnlKlakL~ld~~ey~~l~~~l~~L~~~c 218 (222)
|+..++. ... .......+|.++...|++++..+.++...+.+
T Consensus 74 ~~~~~~~--~p~----~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~ 115 (135)
T TIGR02552 74 YALAAAL--DPD----DPRPYFHAAECLLALGEPESALKALDLAIEIC 115 (135)
T ss_pred HHHHHhc--CCC----ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhc
Confidence 4443332 122 34445678999999999999988887766654
No 45
>KOG2235|consensus
Probab=69.51 E-value=35 Score=35.04 Aligned_cols=153 Identities=17% Similarity=0.214 Sum_probs=97.7
Q ss_pred hcccccccHhHHHHHhccchhHHHHhhhhhhHh-hh----hhhhhhhh-hhhhhhhhhhhccccccccHhHHHHHhCCCh
Q psy3486 26 IKPYTRIHIPFISRQLNIETSDVLIKLIKPYTR-IH----IPFISRQL-NIETSDVLIKLIKPYTRIHIPFISRQLNIET 99 (222)
Q Consensus 26 i~PYsri~i~~ia~~l~l~~~~ve~klsd~il~-~h----l~~l~d~~-~~~~~~~l~~iiepys~v~i~~ia~~l~l~~ 99 (222)
+..=-|+.+-.+|+.+|++..-||+.-.|.+.. .| ++.++|+= --.+-+.+-.-+.--+.|-|+.+|+++++|.
T Consensus 68 ~v~GgRaslvDla~tlnVDl~hIEk~a~dIv~~d~~v~Lv~geiide~Y~d~iaeEinekLqE~gqvtiaeLakq~dl~s 147 (776)
T KOG2235|consen 68 IVAGGRASLVDLAVTLNVDLDHIEKTARDIVSTDDEVTLVLGEIIDEEYVDRIAEEINEKLQEQGQVTIAELAKQWDLPS 147 (776)
T ss_pred HHhCCcchhHHHHHHhCcCHHHHHHHHHHHhhcCCceEEehhhhhhHHHHHHHHHHHHHHHHHhcchHHHHHHHhcCCcH
Confidence 334458899999999999999999776665542 22 22222210 0000011222233458899999999999999
Q ss_pred HHHHHHHHHHhhccceeeEeeccc-h-HHHHHHHHHHHhhhhhccCcc-----------ccHHHHHHHHHHhhcC-----
Q psy3486 100 SDVESLLVSLILDNTVRGRIDQSN-Y-KEMMSRYKQLLLYIKSAVTRN-----------YSEKSINSILDYISTS----- 161 (222)
Q Consensus 100 ~~VE~~L~~~iLdq~ik~~idqg~-y-~~~l~~y~~LLtyiksaVtrN-----------ysEksIn~iLd~vs~s----- 161 (222)
+-+.+.|..+-|-..|+|++|-|. | ..-++.-+-++.=+-.|+||. .-|+-.++.++.+-+.
T Consensus 148 ellqs~l~ek~lg~iikgr~dggviyT~Ayv~r~ka~iRga~~aItrptnvs~i~~k~gvqek~~~s~feei~n~g~~~g 227 (776)
T KOG2235|consen 148 ELLQSLLIEKLLGSIIKGRVDGGVIYTSAYVNRRKAVIRGALIAITRPTNVSTIQKKVGVQEKRFYSAFEEIQNLGEIPG 227 (776)
T ss_pred HHHHHHHHHHhhccceeeeecCCEEeeHHHHHHHHHHHHHHHHHhhcCCcHHHHHHHhcccHHHHHHHHHHHHhcccCcc
Confidence 999999999999999999999876 2 223344444443333455553 4577777777755421
Q ss_pred -------CchHHHHHHHHHHHHHH
Q psy3486 162 -------KNMELLQDFYETTLEAL 178 (222)
Q Consensus 162 -------~~~~~l~~fYe~TL~~l 178 (222)
....|+.-+|..|....
T Consensus 228 t~igs~qa~~~yvP~iya~tqk~c 251 (776)
T KOG2235|consen 228 TLIGSTQASCSYVPMIYAHTQKSC 251 (776)
T ss_pred cccccCCCCCeechHHHHHHHHHH
Confidence 24456666666665543
No 46
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=69.49 E-value=24 Score=27.70 Aligned_cols=27 Identities=22% Similarity=0.447 Sum_probs=20.1
Q ss_pred chhhhhhhhchhhHhHHHHHHHHHHHh
Q psy3486 191 NTKLGKLYFDREDFNKLSRILKQLHQS 217 (222)
Q Consensus 191 nlKlakL~ld~~ey~~l~~~l~~L~~~ 217 (222)
...+|.++...|+|++....+++..+.
T Consensus 172 ~~~la~~~~~~~~~~~A~~~~~~~~~~ 198 (234)
T TIGR02521 172 LLELAELYYLRGQYKDARAYLERYQQT 198 (234)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 346788888888888888777766554
No 47
>PF12612 TFCD_C: Tubulin folding cofactor D C terminal; InterPro: IPR022577 This region is found in eukaryotes, and is typically between 182 and 199 amino acids in length. There is a single completely conserved residue R that may be functionally important. Tubulin folding cofactor D does not co-polymerise with microtubules either in vivo or in vitro, but instead modulates microtubule dynamics by sequestering beta-tubulin from GTP-bound alphabeta-heterodimers in microtubules [].
Probab=68.01 E-value=28 Score=29.36 Aligned_cols=74 Identities=26% Similarity=0.321 Sum_probs=53.4
Q ss_pred HHhhhhhc--cCccccHHHHHHHHHHhhc-CCchHHHHHHHHHHHHHHhc-CCCCceeeecchhhhhhhhchhhHhHHH
Q psy3486 134 LLLYIKSA--VTRNYSEKSINSILDYIST-SKNMELLQDFYETTLEALKD-AKNDRLWFKTNTKLGKLYFDREDFNKLS 208 (222)
Q Consensus 134 LLtyiksa--VtrNysEksIn~iLd~vs~-s~~~~~l~~fYe~TL~~l~~-~~NeRLWfKtnlKlakL~ld~~ey~~l~ 208 (222)
+.+++-|+ .|..-...|-..+++|+.. +.+.+.+..+....+..+++ .+++|+++.+ ++....+|+.|-++.+.
T Consensus 89 l~Glv~S~G~~tesl~~~s~~AL~~~~~~~~~~~~~~~~v~~~l~~il~~~~~~dRv~vP~-l~tl~~Ll~~~~~~~~~ 166 (193)
T PF12612_consen 89 LSGLVVSAGGLTESLVRASSAALLSYLRELSDSPEELEQVLSDLLSILKENLRNDRVVVPL-LKTLDFLLSSGVFDSLP 166 (193)
T ss_pred HhHHHhcCCCCchhHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHhCCCCCeeecH-HHHHHHHHhCcchhccc
Confidence 45666554 4455556677788888864 45667788888888888884 4799999965 77888888887766644
No 48
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=67.17 E-value=11 Score=29.71 Aligned_cols=105 Identities=19% Similarity=0.256 Sum_probs=58.8
Q ss_pred ccHhHHHHHhCCChHHHHHHHHHHhhccceeeEee-------ccc-----hHHHHHHHHHHHhhhhhc---cCccccHHH
Q psy3486 86 IHIPFISRQLNIETSDVESLLVSLILDNTVRGRID-------QSN-----YKEMMSRYKQLLLYIKSA---VTRNYSEKS 150 (222)
Q Consensus 86 v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~id-------qg~-----y~~~l~~y~~LLtyiksa---VtrNysEks 150 (222)
|..+.+.+.+|+...+.-..+...++++-...-++ +|. .++++++++.++-+-... .....++..
T Consensus 1 It~e~V~~~lG~v~~~~i~~l~~ai~~~d~~~~l~~~~~l~~~G~d~~~~l~~L~~~~R~ll~~k~~~~~~~~~~~~~~~ 80 (143)
T PF12169_consen 1 ITAEDVREILGLVDEEQIFELLDAILEGDAAEALELLNELLEQGKDPKQFLDDLIEYLRDLLLYKITGDKSNLLELSEEE 80 (143)
T ss_dssp B-HHHHHHHHTHTSTHHHHHHHHHHHTT-HHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHHTTSGGGS-SG--CTTT
T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhCCchhhcccCCHHH
Confidence 34566778888665555445666666554443332 222 566777777777643211 111234444
Q ss_pred HHHHHHHhhcCCchHHHHHHHHHHHHHHh---cCCCCceeeecc
Q psy3486 151 INSILDYISTSKNMELLQDFYETTLEALK---DAKNDRLWFKTN 191 (222)
Q Consensus 151 In~iLd~vs~s~~~~~l~~fYe~TL~~l~---~~~NeRLWfKtn 191 (222)
.+.+.+ .+..-+.+.+.++|++..++.. .+.|.|+||-..
T Consensus 81 ~~~~~~-~a~~~~~~~l~~~~~~l~~~~~~lr~s~~pr~~lE~~ 123 (143)
T PF12169_consen 81 EEKLKE-LAKKFSPERLQRILQILLEAENELRYSSNPRILLEMA 123 (143)
T ss_dssp HHHHHH-HHHHS-HHHHHHHHHHHHHHHHHTTTSSSHHHHHHHH
T ss_pred HHHHHH-HHHcCCHHHHHHHHHHHHHHHHHhccCCChHHHHHHH
Confidence 444333 3334468899999999888776 455888887654
No 49
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=66.90 E-value=7.4 Score=29.41 Aligned_cols=36 Identities=25% Similarity=0.369 Sum_probs=31.8
Q ss_pred cccHhHHHHHhCCChHHHHHHHHHHhhccceeeEee
Q psy3486 85 RIHIPFISRQLNIETSDVESLLVSLILDNTVRGRID 120 (222)
Q Consensus 85 ~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~id 120 (222)
-|.++.|++.++++..+|+.-+.+++=++.|.-.+|
T Consensus 65 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD 100 (102)
T PF08784_consen 65 GVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTID 100 (102)
T ss_dssp TEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSS
T ss_pred cccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccC
Confidence 489999999999999999999999999998887766
No 50
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=66.35 E-value=12 Score=29.72 Aligned_cols=37 Identities=14% Similarity=0.160 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhH
Q psy3486 11 EDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSD 47 (222)
Q Consensus 11 ~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ 47 (222)
+...-...++..+.-++|.+..+|..|-+.+|+|++.
T Consensus 26 ~~~~~~~~~~~~l~~~~~ls~~eIk~iRe~~~lSQ~v 62 (104)
T COG2944 26 SQITMRDETKACLLKVKTLSPTEIKAIREKLGLSQPV 62 (104)
T ss_pred cchhhhhHHHHhhccCCCCCHHHHHHHHHHhCCCHHH
Confidence 3444455677888889999999999999999999876
No 51
>KOG1076|consensus
Probab=64.84 E-value=13 Score=38.45 Aligned_cols=56 Identities=13% Similarity=0.135 Sum_probs=46.5
Q ss_pred HHHHHHHHHHH----HHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhh
Q psy3486 12 DLLRNIRTQVL----IKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQ 67 (222)
Q Consensus 12 ~L~~~lr~q~L----l~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~ 67 (222)
-|.+.|++..| +-+-.-|+.|.+..+|+.|.+|.+.|..=+|.||+..-|+.-+||
T Consensus 695 Ml~~rIqEEsLRTYLftYss~Y~SvSl~~LA~mFdLp~~~VhsIiSkmiineEl~AslDq 754 (843)
T KOG1076|consen 695 MLTERIQEESLRTYLFTYSSVYDSVSLAKLADMFDLPEPKVHSIISKMIINEELHASLDQ 754 (843)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHhCCCchhHHHHHHHHHHHHHhhhccCC
Confidence 34455555544 445566788999999999999999999999999999999999996
No 52
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=64.12 E-value=11 Score=24.74 Aligned_cols=35 Identities=14% Similarity=0.286 Sum_probs=25.1
Q ss_pred HHHHHhhcccccccHhHHHHHhccchhHHHHhhhh
Q psy3486 20 QVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 20 q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd 54 (222)
..|++.+.-=.|.....||+.+|+|.+.|-..+..
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 34555555568999999999999999999876654
No 53
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=63.22 E-value=34 Score=30.81 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=21.2
Q ss_pred cccccccHhHHHHHhCCChHHHHHHHHHHhhc
Q psy3486 81 KPYTRIHIPFISRQLNIETSDVESLLVSLILD 112 (222)
Q Consensus 81 epys~v~i~~ia~~l~l~~~~VE~~L~~~iLd 112 (222)
+|+| +..||+.+|++.+.|... -.++++
T Consensus 268 ~~~T---l~EIa~~lgiS~erVrq~-~~rAl~ 295 (298)
T TIGR02997 268 EPLT---LAEIGRRLNLSRERVRQI-EAKALR 295 (298)
T ss_pred CCcC---HHHHHHHHCcCHHHHHHH-HHHHHH
Confidence 6766 788999999999999864 344444
No 54
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=62.03 E-value=50 Score=28.61 Aligned_cols=87 Identities=11% Similarity=0.176 Sum_probs=52.4
Q ss_pred EeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhh
Q psy3486 118 RIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKL 197 (222)
Q Consensus 118 ~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL 197 (222)
..+.|++++|++.|++.+..- | .++...++.+...-...+.+-..+..+...... ..|.++|. .+|..
T Consensus 156 ~~~~G~~~~A~~~~~~al~~~-P-----~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~--~~~~~~~~----~la~~ 223 (280)
T PF13429_consen 156 YEQLGDPDKALRDYRKALELD-P-----DDPDARNALAWLLIDMGDYDEAREALKRLLKAA--PDDPDLWD----ALAAA 223 (280)
T ss_dssp HHHCCHHHHHHHHHHHHHHH--T-----T-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH---HTSCCHCH----HHHHH
T ss_pred HHHcCCHHHHHHHHHHHHHcC-C-----CCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC--cCHHHHHH----HHHHH
Confidence 346788999999999988843 4 345556666654433333333333333333322 34566764 46888
Q ss_pred hhchhhHhHHHHHHHHHHH
Q psy3486 198 YFDREDFNKLSRILKQLHQ 216 (222)
Q Consensus 198 ~ld~~ey~~l~~~l~~L~~ 216 (222)
++..|++.+.-..++...+
T Consensus 224 ~~~lg~~~~Al~~~~~~~~ 242 (280)
T PF13429_consen 224 YLQLGRYEEALEYLEKALK 242 (280)
T ss_dssp HHHHT-HHHHHHHHHHHHH
T ss_pred hcccccccccccccccccc
Confidence 8888888888887777655
No 55
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=59.22 E-value=18 Score=24.31 Aligned_cols=47 Identities=11% Similarity=0.344 Sum_probs=29.9
Q ss_pred cccHhHHHHHhCCChHHHHHHHHH-Hhhc-cceeeEeeccchHHHHHHH
Q psy3486 85 RIHIPFISRQLNIETSDVESLLVS-LILD-NTVRGRIDQSNYKEMMSRY 131 (222)
Q Consensus 85 ~v~i~~ia~~l~l~~~~VE~~L~~-~iLd-q~ik~~idqg~y~~~l~~y 131 (222)
.+.|..+|+.+|++..+|=..|.. +-.. ....-.++...-+...+.|
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e~~~~i~~~~ 51 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEEEAELIAEEF 51 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETTGGGHHHHHH
T ss_pred ceEHHHHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHHHHHHHHHHh
Confidence 467888999999999999887733 5555 5555666655555554444
No 56
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=59.02 E-value=26 Score=31.32 Aligned_cols=94 Identities=10% Similarity=0.112 Sum_probs=43.6
Q ss_pred eeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhh
Q psy3486 115 VRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKL 194 (222)
Q Consensus 115 ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKl 194 (222)
..+...+|++++|++.|++++..- +.............+-..+....+.+--.+.|+..++.- ..+. .+...+
T Consensus 148 a~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~--p~~~----~~~~~l 220 (389)
T PRK11788 148 LEIYQQEKDWQKAIDVAERLEKLG-GDSLRVEIAHFYCELAQQALARGDLDAARALLKKALAAD--PQCV----RASILL 220 (389)
T ss_pred HHHHHHhchHHHHHHHHHHHHHhc-CCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhHC--cCCH----HHHHHH
Confidence 334456778888888888776622 211110000001111111112233333444444444321 1111 234557
Q ss_pred hhhhhchhhHhHHHHHHHHHH
Q psy3486 195 GKLYFDREDFNKLSRILKQLH 215 (222)
Q Consensus 195 akL~ld~~ey~~l~~~l~~L~ 215 (222)
|.++...|++++..+.++++.
T Consensus 221 a~~~~~~g~~~~A~~~~~~~~ 241 (389)
T PRK11788 221 GDLALAQGDYAAAIEALERVE 241 (389)
T ss_pred HHHHHHCCCHHHHHHHHHHHH
Confidence 777777777777766666554
No 57
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=58.87 E-value=1.1e+02 Score=29.61 Aligned_cols=77 Identities=18% Similarity=0.281 Sum_probs=47.8
Q ss_pred cHhHHHHHhccchhHHHHhhh------------------------------------hhhHhhhhhhhhhhhhhhhhhhh
Q psy3486 33 HIPFISRQLNIETSDVLIKLI------------------------------------KPYTRIHIPFISRQLNIETSDVL 76 (222)
Q Consensus 33 ~i~~ia~~l~l~~~~ve~kls------------------------------------d~il~~hl~~l~d~~~~~~~~~l 76 (222)
+.+.||+.+|++.++|..-+. .--+...|...+++|...- +.+
T Consensus 280 t~~EiA~~l~is~~~vr~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~~~pee~~~~~~l~~~L~~~L~~L~~re-R~V 358 (415)
T PRK07598 280 TIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDDISPEEMLMRESLQRDLQHLLADLTSRE-RDV 358 (415)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHccCCcccccccCCCccccHHHhccCCCCCHHHHHHHHHHHHHHHHHHHhCCHHH-HHH
Confidence 367888888888887765321 1122334555665554333 334
Q ss_pred hhh--c----cccccccHhHHHHHhCCChHHHHHHHHHHhhccc
Q psy3486 77 IKL--I----KPYTRIHIPFISRQLNIETSDVESLLVSLILDNT 114 (222)
Q Consensus 77 ~~i--i----epys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ 114 (222)
++. . +|+| +..||+.+|++.+.|... -.+|+++.
T Consensus 359 I~LRygl~d~~~~T---l~EIA~~LGvS~erVRqi-e~rAl~KL 398 (415)
T PRK07598 359 IRMRFGLADGHTYS---LAEIGRALDLSRERVRQI-ESKALQKL 398 (415)
T ss_pred HHHHHhcCCCCCCC---HHHHHHHHCcCHHHHHHH-HHHHHHHH
Confidence 433 2 6776 577999999999999864 44566543
No 58
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=58.61 E-value=77 Score=24.78 Aligned_cols=23 Identities=17% Similarity=-0.055 Sum_probs=14.1
Q ss_pred hhhhhhhchhhHhHHHHHHHHHH
Q psy3486 193 KLGKLYFDREDFNKLSRILKQLH 215 (222)
Q Consensus 193 KlakL~ld~~ey~~l~~~l~~L~ 215 (222)
-++.++...|+++......+.+.
T Consensus 208 ~~~~~~~~~~~~~~a~~~~~~~~ 230 (234)
T TIGR02521 208 LGIRIARALGDVAAAQRYGAQLQ 230 (234)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHH
Confidence 35666666777777666555443
No 59
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=58.50 E-value=60 Score=28.94 Aligned_cols=88 Identities=13% Similarity=0.166 Sum_probs=47.4
Q ss_pred eEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhh
Q psy3486 117 GRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGK 196 (222)
Q Consensus 117 ~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlak 196 (222)
....+|++++|++.|++++..- | ++.....+.+.+.+....+.+-..++++..++. ..+... -..++.
T Consensus 223 ~~~~~g~~~~A~~~~~~~~~~~-p----~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~---~p~~~~----~~~la~ 290 (389)
T PRK11788 223 LALAQGDYAAAIEALERVEEQD-P----EYLSEVLPKLMECYQALGDEAEGLEFLRRALEE---YPGADL----LLALAQ 290 (389)
T ss_pred HHHHCCCHHHHHHHHHHHHHHC-h----hhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCchH----HHHHHH
Confidence 3445667777777777766521 1 223344444444443333333333344443332 222222 266888
Q ss_pred hhhchhhHhHHHHHHHHHHH
Q psy3486 197 LYFDREDFNKLSRILKQLHQ 216 (222)
Q Consensus 197 L~ld~~ey~~l~~~l~~L~~ 216 (222)
++...|+++.....+++..+
T Consensus 291 ~~~~~g~~~~A~~~l~~~l~ 310 (389)
T PRK11788 291 LLEEQEGPEAAQALLREQLR 310 (389)
T ss_pred HHHHhCCHHHHHHHHHHHHH
Confidence 88888888888887776543
No 60
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=57.73 E-value=9.5 Score=28.63 Aligned_cols=30 Identities=13% Similarity=0.276 Sum_probs=20.9
Q ss_pred HHHHHhhcccc--cccHhHHHHHhccchhHHH
Q psy3486 20 QVLIKLIKPYT--RIHIPFISRQLNIETSDVL 49 (222)
Q Consensus 20 q~Ll~li~PYs--ri~i~~ia~~l~l~~~~ve 49 (222)
+.|--+++-|. -|.++-||..+|.+.+.+|
T Consensus 12 ~yL~~l~~~f~ggPvGl~tlA~~l~ed~~Tie 43 (76)
T PF05491_consen 12 RYLKTLIENFKGGPVGLDTLAAALGEDKETIE 43 (76)
T ss_dssp HHHHHHHHCSTTS-B-HHHHHHHTTS-HHHHH
T ss_pred HHHHHHHHHcCCCCeeHHHHHHHHCCCHhHHH
Confidence 34445566666 6999999999999988877
No 61
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=57.41 E-value=34 Score=28.14 Aligned_cols=49 Identities=10% Similarity=0.122 Sum_probs=43.5
Q ss_pred hhhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEee
Q psy3486 72 TSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRID 120 (222)
Q Consensus 72 ~~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~id 120 (222)
++.-|++++.-=+|+..+.||+.+|++...|-.++..+-=.+.|++.--
T Consensus 15 ~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~ 63 (164)
T PRK11169 15 IDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTA 63 (164)
T ss_pred HHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEE
Confidence 4677888999999999999999999999999999999999999986443
No 62
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=57.00 E-value=37 Score=23.37 Aligned_cols=58 Identities=17% Similarity=0.289 Sum_probs=41.1
Q ss_pred CchHHHHHHHHHHHHHHhcCCCCce-eeecchhhhhhhhchhhHhHHHHHHHHHHHhhh
Q psy3486 162 KNMELLQDFYETTLEALKDAKNDRL-WFKTNTKLGKLYFDREDFNKLSRILKQLHQSCQ 219 (222)
Q Consensus 162 ~~~~~l~~fYe~TL~~l~~~~NeRL-WfKtnlKlakL~ld~~ey~~l~~~l~~L~~~c~ 219 (222)
.+.+--...|+-.++..+..+++.. -..+.-++|.+|...|+|++..+..++-.+-|+
T Consensus 19 ~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i~~ 77 (78)
T PF13424_consen 19 GRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALDIFE 77 (78)
T ss_dssp T-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhc
Confidence 4444455566666666555555543 377888999999999999999998888766654
No 63
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=56.11 E-value=20 Score=26.84 Aligned_cols=45 Identities=13% Similarity=0.325 Sum_probs=38.6
Q ss_pred hhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceee
Q psy3486 73 SDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRG 117 (222)
Q Consensus 73 ~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~ 117 (222)
+..+++.+..-.++..+.+|+.+|++...|-..+..+.-++.+.+
T Consensus 5 D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 5 DRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeec
Confidence 455667777778899999999999999999999999888888874
No 64
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=55.92 E-value=22 Score=28.42 Aligned_cols=37 Identities=22% Similarity=0.436 Sum_probs=24.9
Q ss_pred hhhhhhhc-cccccccHhHHHHHhCCChHHHHHHHHHH
Q psy3486 73 SDVLIKLI-KPYTRIHIPFISRQLNIETSDVESLLVSL 109 (222)
Q Consensus 73 ~~~l~~ii-epys~v~i~~ia~~l~l~~~~VE~~L~~~ 109 (222)
-+.++++| ..|+.|.++.+|+.+|++.+++++.....
T Consensus 84 R~~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~~~~~~ 121 (143)
T PF10075_consen 84 RERIAHLISKAYSSISLSDLAEMLGLSEEELEKFIKSR 121 (143)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhHcCHHHHHHHhCCCHHHHHHHHHHc
Confidence 34444544 58999999999999999988777655443
No 65
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=55.86 E-value=10 Score=22.78 Aligned_cols=31 Identities=10% Similarity=0.177 Sum_probs=24.4
Q ss_pred cchhhhhhhhchhhHhHHHHHHHHHHHhhhc
Q psy3486 190 TNTKLGKLYFDREDFNKLSRILKQLHQSCQM 220 (222)
Q Consensus 190 tnlKlakL~ld~~ey~~l~~~l~~L~~~c~~ 220 (222)
+--.||..|..+|+|++.....++..+-|+.
T Consensus 4 ~~~~la~~~~~~g~~~~A~~~~~~al~~~~~ 34 (42)
T PF13374_consen 4 ALNNLANAYRAQGRYEEALELLEEALEIRER 34 (42)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHhhhhcchhhHHHHHHHHHHHH
Confidence 4457999999999999999999998887753
No 66
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=54.91 E-value=24 Score=28.60 Aligned_cols=45 Identities=11% Similarity=0.130 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhh
Q psy3486 6 IREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLI 53 (222)
Q Consensus 6 I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~kls 53 (222)
+...++.|-..-|+-.++.+++.++ .+.||+.+|+|...|.+.+.
T Consensus 123 l~~~l~~L~~~~r~i~~l~~~~g~s---~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 123 IDACLEELEKDRAAAVRRAYLEGLS---YKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred HHHHHHhCCHHHHHHHHHHHHcCCC---HHHHHHHHCCChHHHHHHHH
Confidence 4455666666667777777766554 89999999999999875544
No 67
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=54.61 E-value=12 Score=32.43 Aligned_cols=50 Identities=14% Similarity=0.180 Sum_probs=40.0
Q ss_pred HHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhh
Q psy3486 18 RTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQ 67 (222)
Q Consensus 18 r~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~ 67 (222)
.-+..+++|+-=..|-++.+|..||++.++|-..+.+..-+.-|.|++|.
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~Dd 149 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDD 149 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-T
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcC
Confidence 44667788888899999999999999999999999999999999999983
No 68
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=54.60 E-value=32 Score=22.74 Aligned_cols=39 Identities=21% Similarity=0.342 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHhhccccccc-HhHHHHHhccchhHHH
Q psy3486 11 EDLLRNIRTQVLIKLIKPYTRIH-IPFISRQLNIETSDVL 49 (222)
Q Consensus 11 ~~L~~~lr~q~Ll~li~PYsri~-i~~ia~~l~l~~~~ve 49 (222)
+++++.++...+.....|-..+. ...||+.+|+|.+.|.
T Consensus 4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~ 43 (66)
T cd07377 4 EQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVR 43 (66)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHH
Confidence 45667777766666566666665 8899999999877755
No 69
>KOG2908|consensus
Probab=54.59 E-value=45 Score=31.95 Aligned_cols=99 Identities=18% Similarity=0.303 Sum_probs=67.4
Q ss_pred HHHHHHHH---HHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhcc-cccc--
Q psy3486 12 DLLRNIRT---QVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK-PYTR-- 85 (222)
Q Consensus 12 ~L~~~lr~---q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iie-pys~-- 85 (222)
.++++|+. +.|..++..|..=.+....+.-|. --.+|++-.|=..+..-. +|+-+|| -|+|
T Consensus 224 PilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~-------~~~~p~L~~~e~~L~qKI------~LmaLiEi~F~rpa 290 (380)
T KOG2908|consen 224 PILESLKGTNREWLKDLLIAFNSGDLKRFESLKGV-------WGKQPDLASNEDFLLQKI------RLLALIEITFSRPA 290 (380)
T ss_pred HHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHH-------hccCchHHHHHHHHHHHH------HHHHHHHHHhcCcc
Confidence 34566666 889999999888887776665553 112566666655555432 3344554 2555
Q ss_pred ----ccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccc
Q psy3486 86 ----IHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSN 123 (222)
Q Consensus 86 ----v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~ 123 (222)
|-.+.||+...+|.++||-.+-.-.-.+.|+|.||+..
T Consensus 291 ~~R~lsf~~Ia~~tkip~~eVE~LVMKAlslgLikG~Idqv~ 332 (380)
T KOG2908|consen 291 NERTLSFKEIAEATKIPNKEVELLVMKALSLGLIKGSIDQVE 332 (380)
T ss_pred hhccccHHHHHHHhCCCHHHHHHHHHHHHhccceeeeecccc
Confidence 67888999999999999964443334568999999854
No 70
>PRK05949 RNA polymerase sigma factor; Validated
Probab=54.39 E-value=1.1e+02 Score=28.30 Aligned_cols=29 Identities=21% Similarity=0.327 Sum_probs=21.1
Q ss_pred cccccccHhHHHHHhCCChHHHHHHHHHHhhcc
Q psy3486 81 KPYTRIHIPFISRQLNIETSDVESLLVSLILDN 113 (222)
Q Consensus 81 epys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq 113 (222)
+|+| +..||+.+|++.+.|... -.+++++
T Consensus 285 e~~T---l~EIa~~lgiS~erVrq~-~~rAl~k 313 (327)
T PRK05949 285 KELS---LAKVGERLNLSRERVRQL-EHQALAH 313 (327)
T ss_pred CCCC---HHHHHHHHCcCHHHHHHH-HHHHHHH
Confidence 6655 677899999999999864 3445554
No 71
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=54.30 E-value=8.9 Score=28.99 Aligned_cols=36 Identities=22% Similarity=0.147 Sum_probs=31.7
Q ss_pred cccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhh
Q psy3486 31 RIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISR 66 (222)
Q Consensus 31 ri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d 66 (222)
-|.+++|++.|++|..+|+.-+..+.=..|++..+|
T Consensus 65 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD 100 (102)
T PF08784_consen 65 GVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTID 100 (102)
T ss_dssp TEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSS
T ss_pred cccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccC
Confidence 489999999999999999999999998888887766
No 72
>PF12643 MazG-like: MazG-like family
Probab=53.91 E-value=35 Score=26.55 Aligned_cols=46 Identities=11% Similarity=0.212 Sum_probs=31.0
Q ss_pred HHHHhCCChHHHHHHHHHHhhccceeeEeeccchHHHHHHHHHHHhhhhh
Q psy3486 91 ISRQLNIETSDVESLLVSLILDNTVRGRIDQSNYKEMMSRYKQLLLYIKS 140 (222)
Q Consensus 91 ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~y~~~l~~y~~LLtyiks 140 (222)
+|+.+|+|..+++..+..+.-++..+.... ++.-..++.|..|+++
T Consensus 51 La~rLGid~~~lD~~i~~KL~~~~~k~~~~----Ek~~gdls~l~~~l~~ 96 (98)
T PF12643_consen 51 LADRLGIDFRELDEIIKEKLKKNIEKYPVL----EKWYGDLSKLEQHLKK 96 (98)
T ss_pred HHHHhCCCHHHHHHHHHHHHHhcccccchH----HHHhccHHHHHHHHhc
Confidence 899999998888877777666665555442 4444556666666643
No 73
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=53.44 E-value=21 Score=23.37 Aligned_cols=35 Identities=14% Similarity=0.245 Sum_probs=24.9
Q ss_pred hhhhhhccccccccHhHHHHHhCCChHHHHHHHHH
Q psy3486 74 DVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVS 108 (222)
Q Consensus 74 ~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~ 108 (222)
.-|++++.-=.+.-...||+.+|++...|-.++..
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 34455555558888999999999999999887754
No 74
>PLN03077 Protein ECB2; Provisional
Probab=53.33 E-value=27 Score=35.62 Aligned_cols=90 Identities=12% Similarity=0.142 Sum_probs=49.2
Q ss_pred ceeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchh
Q psy3486 114 TVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTK 193 (222)
Q Consensus 114 ~ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlK 193 (222)
++.+..+.|++++|++.|+++.. ..+..| +-+.+.++...+...+.+...++++...+. .-....-+.-.
T Consensus 360 li~~~~~~g~~~~A~~lf~~M~~---~g~~Pd--~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~-----g~~~~~~~~n~ 429 (857)
T PLN03077 360 MISGYEKNGLPDKALETYALMEQ---DNVSPD--EITIASVLSACACLGDLDVGVKLHELAERK-----GLISYVVVANA 429 (857)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHH---hCCCCC--ceeHHHHHHHHhccchHHHHHHHHHHHHHh-----CCCcchHHHHH
Confidence 46677788888888888888754 233322 345666666665555555555555544331 01111222233
Q ss_pred hhhhhhchhhHhHHHHHHHH
Q psy3486 194 LGKLYFDREDFNKLSRILKQ 213 (222)
Q Consensus 194 lakL~ld~~ey~~l~~~l~~ 213 (222)
|...|...|+++++.++.++
T Consensus 430 Li~~y~k~g~~~~A~~vf~~ 449 (857)
T PLN03077 430 LIEMYSKCKCIDKALEVFHN 449 (857)
T ss_pred HHHHHHHcCCHHHHHHHHHh
Confidence 44555555555555555444
No 75
>PLN03218 maturation of RBCL 1; Provisional
Probab=53.10 E-value=28 Score=37.39 Aligned_cols=55 Identities=11% Similarity=0.151 Sum_probs=33.1
Q ss_pred ceeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHH
Q psy3486 114 TVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYET 173 (222)
Q Consensus 114 ~ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~ 173 (222)
+|.+..+.|++++|++.|++|.. ..+..| .-+.|.+++.+....+.+-..++|+.
T Consensus 513 LI~gy~k~G~~eeAl~lf~~M~~---~Gv~PD--~vTYnsLI~a~~k~G~~deA~~lf~e 567 (1060)
T PLN03218 513 LIDGCARAGQVAKAFGAYGIMRS---KNVKPD--RVVFNALISACGQSGAVDRAFDVLAE 567 (1060)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHH---cCCCCC--HHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence 46677778888888888888754 223332 44566666666655554444444443
No 76
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=53.06 E-value=18 Score=22.91 Aligned_cols=25 Identities=12% Similarity=0.208 Sum_probs=20.0
Q ss_pred ccccHhHHHHHhccchhHHHHhhhh
Q psy3486 30 TRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 30 sri~i~~ia~~l~l~~~~ve~klsd 54 (222)
..+.+..+|+.++++...|..-+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4589999999999999887655544
No 77
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=52.88 E-value=29 Score=24.67 Aligned_cols=45 Identities=13% Similarity=0.225 Sum_probs=34.2
Q ss_pred hhhhhhhcccccc--ccHhHHHHHhCCChHHHHHHHHHHhhccceee
Q psy3486 73 SDVLIKLIKPYTR--IHIPFISRQLNIETSDVESLLVSLILDNTVRG 117 (222)
Q Consensus 73 ~~~l~~iiepys~--v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~ 117 (222)
++.++..+.--.. +....||+.+|++...|..-|..+.-++.|.-
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 3455555555544 78899999999999999998888777776643
No 78
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=51.93 E-value=32 Score=22.15 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=29.8
Q ss_pred hhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhcccee
Q psy3486 75 VLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVR 116 (222)
Q Consensus 75 ~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik 116 (222)
.++..|.-=.++....+|+.+|++...|-+.+..+.=++.|+
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 344444444558889999999999999998888877666553
No 79
>PF04049 APC8: Anaphase promoting complex subunit 8 / Cdc23 ; InterPro: IPR007192 The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8). This entry is for CDC23.; GO: 0030071 regulation of mitotic metaphase/anaphase transition, 0005680 anaphase-promoting complex
Probab=51.62 E-value=8.8 Score=31.45 Aligned_cols=20 Identities=35% Similarity=0.808 Sum_probs=18.6
Q ss_pred hhhhhhchhhHhHHHHHHHH
Q psy3486 194 LGKLYFDREDFNKLSRILKQ 213 (222)
Q Consensus 194 lakL~ld~~ey~~l~~~l~~ 213 (222)
+|+-|||.+||+|+.-.++.
T Consensus 80 lAksyFD~kEy~RaA~~L~~ 99 (142)
T PF04049_consen 80 LAKSYFDCKEYDRAAHVLKD 99 (142)
T ss_pred HHHHHhchhHHHHHHHHHcc
Confidence 89999999999999988875
No 80
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=51.15 E-value=23 Score=25.14 Aligned_cols=35 Identities=9% Similarity=0.166 Sum_probs=24.9
Q ss_pred HHHHHHhhccccc--ccHhHHHHHhccchhHHHHhhh
Q psy3486 19 TQVLIKLIKPYTR--IHIPFISRQLNIETSDVLIKLI 53 (222)
Q Consensus 19 ~q~Ll~li~PYsr--i~i~~ia~~l~l~~~~ve~kls 53 (222)
.+.++.++.--.. +....||+.+|++...|..-|.
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~ 44 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLY 44 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 3455556655545 8999999999999887664433
No 81
>cd02681 MIT_calpain7_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.
Probab=50.99 E-value=40 Score=24.96 Aligned_cols=38 Identities=16% Similarity=0.279 Sum_probs=27.0
Q ss_pred ccchHHHHHHHHHHHhhhhhc-cCccccHHHHHHHHHHh
Q psy3486 121 QSNYKEMMSRYKQLLLYIKSA-VTRNYSEKSINSILDYI 158 (222)
Q Consensus 121 qg~y~~~l~~y~~LLtyiksa-VtrNysEksIn~iLd~v 158 (222)
.|+|++|+.+|++=+.+...+ .-..+.+++-..|..-+
T Consensus 19 ~g~y~eA~~~Y~~aie~l~~~~~~~~~n~~~k~~ir~K~ 57 (76)
T cd02681 19 EGRYSEAVFYYKEAAQLLIYAEMAGTLNDSHLKTIQEKS 57 (76)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHH
Confidence 599999999999999988665 33335556655555433
No 82
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=50.92 E-value=70 Score=28.15 Aligned_cols=46 Identities=15% Similarity=0.210 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhh
Q psy3486 7 REHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP 55 (222)
Q Consensus 7 ~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~ 55 (222)
...++.|=..-|+=.++++++ -.+...||+.+|+|...|...+..-
T Consensus 156 ~~aL~~Lp~~~R~v~~L~~~e---g~S~~EIA~~Lgis~~TVk~rl~RA 201 (244)
T TIGR03001 156 REALAALSERERHLLRLHFVD---GLSMDRIGAMYQVHRSTVSRWVAQA 201 (244)
T ss_pred HHHHHhCCHHHHHHHHHHHHc---CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 344444444455556666554 4458899999999999999877653
No 83
>PRK05927 hypothetical protein; Provisional
Probab=50.24 E-value=19 Score=33.61 Aligned_cols=88 Identities=17% Similarity=0.156 Sum_probs=66.5
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccc---c-
Q psy3486 8 EHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP---Y- 83 (222)
Q Consensus 8 ~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiep---y- 83 (222)
+++.++.+.|++..=---+..||-++|++++..+|++..++-.+|-+-=++...++-.+. ++..+-+++-| +
T Consensus 109 e~~~~~i~~ik~~~p~l~~~~~s~~ei~~~~~~~G~~~~e~l~~Lk~aGl~~l~g~~~Et----~~~~~~~~~~p~k~~~ 184 (350)
T PRK05927 109 DYLEELVRITVKEFPSLHPHFFSAVEIAHAAQVSGISTEQALERLWDAGQRTIPGGGAEI----LSERVRKIISPKKMGP 184 (350)
T ss_pred HHHHHHHHHHHHHCCCCcccCCCHHHHHHHHHhcCCCHHHHHHHHHHcCcccCCCCCchh----CCHHHhhccCCCCCCH
Confidence 466777888887631123568999999999999999999999999888775555545653 45666678878 3
Q ss_pred -ccccHhHHHHHhCCCh
Q psy3486 84 -TRIHIPFISRQLNIET 99 (222)
Q Consensus 84 -s~v~i~~ia~~l~l~~ 99 (222)
-++++=..|+.+|++.
T Consensus 185 ~~rl~~i~~A~~lGi~~ 201 (350)
T PRK05927 185 DGWIQFHKLAHRLGFRS 201 (350)
T ss_pred HHHHHHHHHHHHcCCCc
Confidence 4688888899999987
No 84
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=49.65 E-value=24 Score=23.80 Aligned_cols=47 Identities=17% Similarity=0.080 Sum_probs=25.0
Q ss_pred cccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChHH
Q psy3486 31 RIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSD 101 (222)
Q Consensus 31 ri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~ 101 (222)
.+....+|+..|+|.+.|-..+... ..+.+.-.+.-||+.+|+++++
T Consensus 10 ~it~~~La~~~gis~~tl~~~~~~~------------------------~~~~~~~~l~~ia~~l~~~~~e 56 (63)
T PF13443_consen 10 GITQKDLARKTGISRSTLSRILNGK------------------------PSNPSLDTLEKIAKALNCSPEE 56 (63)
T ss_dssp T--HHHHHHHHT--HHHHHHHHTTT-----------------------------HHHHHHHHHHHT--HHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHhcc------------------------cccccHHHHHHHHHHcCCCHHH
Confidence 4567889999999887755333221 2445556677788889988765
No 85
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=49.07 E-value=36 Score=22.18 Aligned_cols=26 Identities=23% Similarity=0.307 Sum_probs=20.2
Q ss_pred cccccHhHHHHHhccchhHHHHhhhh
Q psy3486 29 YTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 29 Ysri~i~~ia~~l~l~~~~ve~klsd 54 (222)
|...+++.||+.+|+|.+.|-.....
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 66677999999999999988755443
No 86
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=48.76 E-value=22 Score=30.80 Aligned_cols=51 Identities=20% Similarity=0.358 Sum_probs=37.0
Q ss_pred hhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeec-cch
Q psy3486 74 DVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQ-SNY 124 (222)
Q Consensus 74 ~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idq-g~y 124 (222)
+..+.-|+-=-.|.++.+|..+|+..+++-.++..+--++.+.|.+|. |.|
T Consensus 102 ~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkf 153 (188)
T PF09756_consen 102 QEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKF 153 (188)
T ss_dssp HHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--E
T ss_pred HHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCe
Confidence 444556666678999999999999999999999999999999999975 654
No 87
>KOG2300|consensus
Probab=48.75 E-value=21 Score=35.75 Aligned_cols=101 Identities=21% Similarity=0.208 Sum_probs=71.9
Q ss_pred hccceeeEeeccchHHHHHHHHHHHhhhhhc----cCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCce
Q psy3486 111 LDNTVRGRIDQSNYKEMMSRYKQLLLYIKSA----VTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRL 186 (222)
Q Consensus 111 Ldq~ik~~idqg~y~~~l~~y~~LLtyiksa----VtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRL 186 (222)
|..++--+.-.|+|.+|++....++.+.... .+| |.+--|--++.-+|-| +.+.+..=.-...+.+.+..+.+
T Consensus 326 LE~iv~c~lv~~~~~~al~~i~dm~~w~~r~p~~~Llr-~~~~~ih~LlGlys~s--v~~~enAe~hf~~a~k~t~~~dl 402 (629)
T KOG2300|consen 326 LEHIVMCRLVRGDYVEALEEIVDMKNWCTRFPTPLLLR-AHEAQIHMLLGLYSHS--VNCYENAEFHFIEATKLTESIDL 402 (629)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHhCCchHHHH-HhHHHHHHHHhhHhhh--cchHHHHHHHHHHHHHhhhHHHH
Confidence 5556666667789999999999999887522 444 4555666677766654 33444444455667777888899
Q ss_pred eeecchhhhhhhhchhhHhHHHHHHHHH
Q psy3486 187 WFKTNTKLGKLYFDREDFNKLSRILKQL 214 (222)
Q Consensus 187 WfKtnlKlakL~ld~~ey~~l~~~l~~L 214 (222)
|.-+|+++|-.|+..++-+.+.+++.-+
T Consensus 403 ~a~~nlnlAi~YL~~~~~ed~y~~ld~i 430 (629)
T KOG2300|consen 403 QAFCNLNLAISYLRIGDAEDLYKALDLI 430 (629)
T ss_pred HHHHHHhHHHHHHHhccHHHHHHHHHhc
Confidence 9999999999999877777666665543
No 88
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=48.55 E-value=39 Score=33.67 Aligned_cols=55 Identities=13% Similarity=0.107 Sum_probs=30.6
Q ss_pred cceeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHH
Q psy3486 113 NTVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYE 172 (222)
Q Consensus 113 q~ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe 172 (222)
-++.+..+.|++++|++.|++|.. ..+.. ..-+.+.++..++.....+.-.++++
T Consensus 295 ~li~~y~~~g~~~eA~~lf~~M~~---~g~~p--d~~t~~~ll~a~~~~g~~~~a~~i~~ 349 (697)
T PLN03081 295 SMLAGYALHGYSEEALCLYYEMRD---SGVSI--DQFTFSIMIRIFSRLALLEHAKQAHA 349 (697)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHH---cCCCC--CHHHHHHHHHHHHhccchHHHHHHHH
Confidence 456677777888888888888754 22221 12355555555544434333333333
No 89
>PLN03218 maturation of RBCL 1; Provisional
Probab=47.20 E-value=45 Score=35.94 Aligned_cols=91 Identities=10% Similarity=0.175 Sum_probs=42.1
Q ss_pred eeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhh
Q psy3486 115 VRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKL 194 (222)
Q Consensus 115 ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKl 194 (222)
|.+..+.|++++|++.|.+|.. ..+..+ +-+.|.+++.+....+.+-..++|+...+. +-..-..|.--+
T Consensus 621 I~ay~k~G~~deAl~lf~eM~~---~Gv~PD--~~TynsLI~a~~k~G~~eeA~~l~~eM~k~-----G~~pd~~tynsL 690 (1060)
T PLN03218 621 VNSCSQKGDWDFALSIYDDMKK---KGVKPD--EVFFSALVDVAGHAGDLDKAFEILQDARKQ-----GIKLGTVSYSSL 690 (1060)
T ss_pred HHHHHhcCCHHHHHHHHHHHHH---cCCCCC--HHHHHHHHHHHHhCCCHHHHHHHHHHHHHc-----CCCCCHHHHHHH
Confidence 3444556666666666666654 222222 445566666555544444444444333321 001111233334
Q ss_pred hhhhhchhhHhHHHHHHHHHH
Q psy3486 195 GKLYFDREDFNKLSRILKQLH 215 (222)
Q Consensus 195 akL~ld~~ey~~l~~~l~~L~ 215 (222)
...|...|+++.+.++.+++.
T Consensus 691 I~ay~k~G~~eeA~~lf~eM~ 711 (1060)
T PLN03218 691 MGACSNAKNWKKALELYEDIK 711 (1060)
T ss_pred HHHHHhCCCHHHHHHHHHHHH
Confidence 445555555555555555443
No 90
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=46.57 E-value=40 Score=21.72 Aligned_cols=36 Identities=22% Similarity=0.252 Sum_probs=24.1
Q ss_pred HHHHHhhcccccccHhHHHHHhccchhHHHHhhhhh
Q psy3486 20 QVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP 55 (222)
Q Consensus 20 q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~ 55 (222)
..++.++.-=.++....+|+.+|+|.+.|-.-+.++
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 344555555566999999999999988876554443
No 91
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=46.20 E-value=50 Score=22.67 Aligned_cols=44 Identities=16% Similarity=0.273 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHhhcccccc-cHhHHHHHhccchhHHHHhhhh
Q psy3486 11 EDLLRNIRTQVLIKLIKPYTRI-HIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 11 ~~L~~~lr~q~Ll~li~PYsri-~i~~ia~~l~l~~~~ve~klsd 54 (222)
+.+++.|+....-.-+.|=+++ ....+|+.+|+|...|..-+..
T Consensus 3 ~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~ 47 (64)
T PF00392_consen 3 EQIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRR 47 (64)
T ss_dssp HHHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHH
Confidence 4678889999999999999999 9999999999998887754443
No 92
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=45.75 E-value=29 Score=25.93 Aligned_cols=40 Identities=10% Similarity=0.233 Sum_probs=30.5
Q ss_pred HHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHh
Q psy3486 19 TQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTR 58 (222)
Q Consensus 19 ~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~ 58 (222)
...++..+..-.++..+.||+.+|+|.+.|-..+..+.=+
T Consensus 5 D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 5 DRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4566777777789999999999999999877555544433
No 93
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=45.54 E-value=2.5e+02 Score=27.83 Aligned_cols=169 Identities=15% Similarity=0.108 Sum_probs=82.1
Q ss_pred HHHHHHHHHHHHHHHHhhcccccccHh-HH---HHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccc
Q psy3486 9 HIEDLLRNIRTQVLIKLIKPYTRIHIP-FI---SRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYT 84 (222)
Q Consensus 9 hi~~L~~~lr~q~Ll~li~PYsri~i~-~i---a~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys 84 (222)
..+.+..+|+..+..--+.|++.-++. ++ ++.-|+.. +..--+.|. ..-.|-.+..-.++++-+.=-=..-.
T Consensus 167 e~~kI~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~egi~i---e~eAL~~Ia-~~s~GslR~al~~Ldkai~~~~~~~~ 242 (507)
T PRK06645 167 EVQKIPATIISRCQRYDLRRLSFEEIFKLLEYITKQENLKT---DIEALRIIA-YKSEGSARDAVSILDQAASMSAKSDN 242 (507)
T ss_pred ChHHhhHHHHhcceEEEccCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHH-HHcCCCHHHHHHHHHHHHHhhccCCC
Confidence 345667777776654345566554432 22 22223321 111112222 23445554433333332110000112
Q ss_pred cccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccchHHHHHHHHHHH-----------------hhhh-hccCccc
Q psy3486 85 RIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSNYKEMMSRYKQLL-----------------LYIK-SAVTRNY 146 (222)
Q Consensus 85 ~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~y~~~l~~y~~LL-----------------tyik-saVtrNy 146 (222)
.|..+.+.+.+|...++.=-.+...++++ +.++|+..|.+++ .++. -.+..+|
T Consensus 243 ~It~~~V~~llg~~~~~~if~L~~ai~~~---------d~~~Al~~l~~L~~~g~~~~~~l~~l~~~~~~l~~~k~~~~~ 313 (507)
T PRK06645 243 IISPQVINQMLGLVDSSVIIEFVEYIIHR---------ETEKAINLINKLYGSSVNLEIFIESVSDFIAYLNKVKMLPNY 313 (507)
T ss_pred CcCHHHHHHHHCCCCHHHHHHHHHHHHcC---------CHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhcccc
Confidence 58889999999977665433344444443 3333333333321 1110 1122245
Q ss_pred cHH---HHHHHHHHhhcCCchHHHHHHHHHHHHHHh---cCCCCceeeec
Q psy3486 147 SEK---SINSILDYISTSKNMELLQDFYETTLEALK---DAKNDRLWFKT 190 (222)
Q Consensus 147 sEk---sIn~iLd~vs~s~~~~~l~~fYe~TL~~l~---~~~NeRLWfKt 190 (222)
++. +-..-+...+..-+++.+.++|++.++..+ .+.|.|+|+-.
T Consensus 314 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~e~ 363 (507)
T PRK06645 314 SLPIYESFNDRTKSILDKISLPHLSILWQIYNKGVGEIKISYNQLTETEM 363 (507)
T ss_pred ccccchhHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhccCCCchHHHHH
Confidence 443 112223333344568899999999999866 55688888644
No 94
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=44.54 E-value=44 Score=22.85 Aligned_cols=42 Identities=10% Similarity=0.243 Sum_probs=33.8
Q ss_pred hhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccce
Q psy3486 74 DVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTV 115 (222)
Q Consensus 74 ~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~i 115 (222)
+.|+..++--..+.+..+|+.+|++...+-.-|..+.-.+.+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 345677777889999999999999999999877776665553
No 95
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=43.92 E-value=29 Score=30.62 Aligned_cols=38 Identities=16% Similarity=0.199 Sum_probs=33.8
Q ss_pred HHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhh
Q psy3486 17 IRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 17 lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd 54 (222)
=|.+.+++++....+|+++.+|+.||+|...|-.-|..
T Consensus 7 eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~ 44 (252)
T PRK10681 7 ERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNA 44 (252)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence 48899999999999999999999999999888766553
No 96
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=43.74 E-value=81 Score=23.72 Aligned_cols=39 Identities=13% Similarity=0.094 Sum_probs=30.6
Q ss_pred cccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccc
Q psy3486 85 RIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSN 123 (222)
Q Consensus 85 ~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~ 123 (222)
.+.-..||+.+|++.+.|-+.+..+.-++.|...-..|.
T Consensus 47 ~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~~~~~ 85 (95)
T TIGR01610 47 RVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQGMMGI 85 (95)
T ss_pred ccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeecCCce
Confidence 344567999999999999999999999999875433344
No 97
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=43.64 E-value=29 Score=29.04 Aligned_cols=44 Identities=20% Similarity=0.246 Sum_probs=35.0
Q ss_pred HhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChHHH
Q psy3486 34 IPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDV 102 (222)
Q Consensus 34 i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~V 102 (222)
.+.||+.||++.+.+-.||. |- -||+.-||..||+.+|++.+..
T Consensus 25 ~s~LA~iL~Is~ssa~RKL~---------G~----------------~~ftl~EI~~Ia~~fgvS~d~l 68 (147)
T PF08667_consen 25 ASELADILGISYSSAYRKLN---------GK----------------SPFTLEEIKKIAKHFGVSPDEL 68 (147)
T ss_pred HHHHHHHHCCCHHHHHHHhc---------CC----------------CCCCHHHHHHHHHHhCcCHHHH
Confidence 57899999999888765543 22 3899999999999999997653
No 98
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=43.61 E-value=76 Score=22.24 Aligned_cols=57 Identities=23% Similarity=0.233 Sum_probs=41.7
Q ss_pred hhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhcccee
Q psy3486 52 LIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVR 116 (222)
Q Consensus 52 lsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik 116 (222)
|--.++..|++.+.. .+...+--+.+.-++.|++..++|..+|.+-|.-+|--+.+.
T Consensus 2 L~~~ii~~~fG~~~~--------~V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 2 LCTLIIEEHFGEIVA--------KVGEVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp HHHHHHHHHHHHHHH--------HHHHHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcChHHH--------HHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCee
Confidence 344677788888774 455666678889999999999999999998888887666553
No 99
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=43.57 E-value=52 Score=20.16 Aligned_cols=25 Identities=24% Similarity=0.230 Sum_probs=20.6
Q ss_pred ccccHhHHHHHhccchhHHHHhhhh
Q psy3486 30 TRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 30 sri~i~~ia~~l~l~~~~ve~klsd 54 (222)
.......||+.+|+|.+.|...+..
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 7889999999999999887655543
No 100
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=43.52 E-value=44 Score=27.29 Aligned_cols=42 Identities=19% Similarity=0.189 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhh
Q psy3486 9 HIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLI 53 (222)
Q Consensus 9 hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~kls 53 (222)
.++.|....+...++.+ |...+++.||+.+|+|...|...+.
T Consensus 146 ~l~~Ll~~~~~~i~~~~---~~~~s~~eIA~~l~~s~~tV~~~l~ 187 (198)
T TIGR02859 146 KMNELLSDLEWKVLQSY---LDGKSYQEIACDLNRHVKSIDNALQ 187 (198)
T ss_pred HHHHhcCHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34444434444444433 5788899999999999999876543
No 101
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=43.43 E-value=1.2e+02 Score=24.74 Aligned_cols=49 Identities=18% Similarity=0.214 Sum_probs=34.4
Q ss_pred hhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccce---eeEeeccch
Q psy3486 76 LIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTV---RGRIDQSNY 124 (222)
Q Consensus 76 l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~i---k~~idqg~y 124 (222)
+..++++=.-..++.||+.+|.+...|.+-|...+-.+.| +...+.|.|
T Consensus 33 ~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy 84 (126)
T COG3355 33 YKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGY 84 (126)
T ss_pred HHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCce
Confidence 3455556666778999999999999999655555555544 455677774
No 102
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=43.41 E-value=23 Score=20.57 Aligned_cols=19 Identities=16% Similarity=0.354 Sum_probs=16.6
Q ss_pred eeccchHHHHHHHHHHHhh
Q psy3486 119 IDQSNYKEMMSRYKQLLLY 137 (222)
Q Consensus 119 idqg~y~~~l~~y~~LLty 137 (222)
.+.|++++|+++|++.+.+
T Consensus 12 ~~~~~~~~A~~~~~~a~~~ 30 (34)
T PF13181_consen 12 EQLGDYEEALEYFEKALEL 30 (34)
T ss_dssp HHTTSHHHHHHHHHHHHHH
T ss_pred HHcCCHHHHHHHHHHHHhh
Confidence 4579999999999999884
No 103
>PF14769 CLAMP: Flagellar C1a complex subunit C1a-32
Probab=43.22 E-value=47 Score=25.34 Aligned_cols=67 Identities=21% Similarity=0.455 Sum_probs=48.7
Q ss_pred HHHHhCCChHHHHHHHHHHhhccceeeEe-eccchHHHHHHHHHHHhhhhhccCcc------ccHHHHHHHHHHhhcC
Q psy3486 91 ISRQLNIETSDVESLLVSLILDNTVRGRI-DQSNYKEMMSRYKQLLLYIKSAVTRN------YSEKSINSILDYISTS 161 (222)
Q Consensus 91 ia~~l~l~~~~VE~~L~~~iLdq~ik~~i-dqg~y~~~l~~y~~LLtyiksaVtrN------ysEksIn~iLd~vs~s 161 (222)
.|+.-|.+.+++=.-++ +++......+ ...+.++..+.+++++- .-.|.|. ++.+-+..|+||+.++
T Consensus 6 Fa~~~~fs~~q~s~~~~--i~~~ll~~~i~~~~~~~~~~~~fk~~l~--~~sv~rpp~~~~iFs~~~~~~i~~y~~~t 79 (101)
T PF14769_consen 6 FAKEQGFSWEQTSAFLS--ILKELLEKNIEKGMSLEDSFKYFKELLL--RHSVQRPPFSIGIFSVDQVKAIIDYFHNT 79 (101)
T ss_pred hHhhCCCCHHHHHHHHH--HHHHHHHHHHHccCCHHHHHHHHHHHHH--HhccCCCCcccCcCCHHHHHHHHHHHHHH
Confidence 57788888887774333 4566655333 56789999999999984 2345554 9999999999998643
No 104
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=43.16 E-value=29 Score=30.75 Aligned_cols=38 Identities=5% Similarity=0.203 Sum_probs=33.0
Q ss_pred HHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhh
Q psy3486 17 IRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 17 lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd 54 (222)
=|.+.|+.+++...+|.++.+|+.||+|...|-.-|..
T Consensus 5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~ 42 (256)
T PRK10434 5 QRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVI 42 (256)
T ss_pred HHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHH
Confidence 38889999999999999999999999998887655543
No 105
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=42.79 E-value=26 Score=20.48 Aligned_cols=19 Identities=21% Similarity=0.440 Sum_probs=15.8
Q ss_pred EeeccchHHHHHHHHHHHh
Q psy3486 118 RIDQSNYKEMMSRYKQLLL 136 (222)
Q Consensus 118 ~idqg~y~~~l~~y~~LLt 136 (222)
...+|+|++|+++|++-++
T Consensus 11 ~~~~~~~~~A~~~~~~al~ 29 (34)
T PF00515_consen 11 YFQLGDYEEALEYYQRALE 29 (34)
T ss_dssp HHHTT-HHHHHHHHHHHHH
T ss_pred HHHhCCchHHHHHHHHHHH
Confidence 4567999999999999988
No 106
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=42.54 E-value=26 Score=20.11 Aligned_cols=20 Identities=20% Similarity=0.361 Sum_probs=16.0
Q ss_pred EeeccchHHHHHHHHHHHhh
Q psy3486 118 RIDQSNYKEMMSRYKQLLLY 137 (222)
Q Consensus 118 ~idqg~y~~~l~~y~~LLty 137 (222)
...+|+|++|+++|++.+..
T Consensus 11 ~~~~~~~~~A~~~~~~al~l 30 (34)
T PF07719_consen 11 YYQLGNYEEAIEYFEKALEL 30 (34)
T ss_dssp HHHTT-HHHHHHHHHHHHHH
T ss_pred HHHhCCHHHHHHHHHHHHHH
Confidence 35679999999999999873
No 107
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=41.66 E-value=1.2e+02 Score=27.99 Aligned_cols=87 Identities=10% Similarity=0.049 Sum_probs=50.3
Q ss_pred EeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhh
Q psy3486 118 RIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKL 197 (222)
Q Consensus 118 ~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL 197 (222)
-+..|+|++|++.|++.+..- |. .. ....+.-..+....+.+--...++..++. ... +......+|.+
T Consensus 12 a~~~~~~~~Ai~~~~~Al~~~-P~----~~-~a~~~~a~~~~~~g~~~eAl~~~~~Al~l--~P~----~~~a~~~lg~~ 79 (356)
T PLN03088 12 AFVDDDFALAVDLYTQAIDLD-PN----NA-ELYADRAQANIKLGNFTEAVADANKAIEL--DPS----LAKAYLRKGTA 79 (356)
T ss_pred HHHcCCHHHHHHHHHHHHHhC-CC----CH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcC----CHHHHHHHHHH
Confidence 456799999999999999833 32 11 12222211111222322223334444332 122 23455678999
Q ss_pred hhchhhHhHHHHHHHHHHH
Q psy3486 198 YFDREDFNKLSRILKQLHQ 216 (222)
Q Consensus 198 ~ld~~ey~~l~~~l~~L~~ 216 (222)
++..|+|+.+...++...+
T Consensus 80 ~~~lg~~~eA~~~~~~al~ 98 (356)
T PLN03088 80 CMKLEEYQTAKAALEKGAS 98 (356)
T ss_pred HHHhCCHHHHHHHHHHHHH
Confidence 9999999998887766543
No 108
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=41.38 E-value=31 Score=19.59 Aligned_cols=26 Identities=15% Similarity=0.448 Sum_probs=22.8
Q ss_pred hhhhhhhhchhhHhHHHHHHHHHHHh
Q psy3486 192 TKLGKLYFDREDFNKLSRILKQLHQS 217 (222)
Q Consensus 192 lKlakL~ld~~ey~~l~~~l~~L~~~ 217 (222)
.++|.++...|++++..+.++++.+.
T Consensus 4 ~~~a~~~~~~g~~~~A~~~~~~~~~~ 29 (33)
T PF13174_consen 4 YRLARCYYKLGDYDEAIEYFQRLIKR 29 (33)
T ss_dssp HHHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHH
Confidence 56899999999999999999988764
No 109
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=41.03 E-value=51 Score=22.20 Aligned_cols=47 Identities=11% Similarity=0.090 Sum_probs=25.9
Q ss_pred cccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChHHH
Q psy3486 31 RIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDV 102 (222)
Q Consensus 31 ri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~V 102 (222)
.++...+|+.+|++...+-.-.+.- .+.+.-.+..||+.+|++.+..
T Consensus 12 ~lt~~~~a~~~~i~~~~i~~~e~g~-------------------------~~~~~~~l~~i~~~~~v~~~~l 58 (64)
T PF12844_consen 12 GLTQKDLAEKLGISRSTISKIENGK-------------------------RKPSVSTLKKIAEALGVSLDEL 58 (64)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHTTS-------------------------S--BHHHHHHHHHHHTS-HHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHCCC-------------------------cCCCHHHHHHHHHHhCCCHHHH
Confidence 5678888999998866544222221 1233444566889999987653
No 110
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=40.99 E-value=34 Score=22.59 Aligned_cols=28 Identities=18% Similarity=0.248 Sum_probs=23.0
Q ss_pred cHhHHHHHhccchhHHHHhhhhhhHhhh
Q psy3486 33 HIPFISRQLNIETSDVLIKLIKPYTRIH 60 (222)
Q Consensus 33 ~i~~ia~~l~l~~~~ve~klsd~il~~h 60 (222)
+++.+|+..|+|.+.+-.+--+.+|.+|
T Consensus 16 ~L~~ls~~t~i~~S~Ll~eAle~~l~ky 43 (44)
T PF12651_consen 16 KLKELSEETGIPKSKLLREALEDYLEKY 43 (44)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHhc
Confidence 5788999999999988777777777665
No 111
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=40.84 E-value=34 Score=25.70 Aligned_cols=36 Identities=17% Similarity=0.177 Sum_probs=30.7
Q ss_pred HHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhh
Q psy3486 18 RTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 18 r~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd 54 (222)
|-..++.++.- .++.+..+|+.+|+|.+.|-.-|.+
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 77778888888 9999999999999999998865543
No 112
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=40.36 E-value=35 Score=30.11 Aligned_cols=48 Identities=15% Similarity=0.114 Sum_probs=38.4
Q ss_pred HHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhh----hHhhhhhhh
Q psy3486 17 IRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP----YTRIHIPFI 64 (222)
Q Consensus 17 lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~----il~~hl~~l 64 (222)
=|.+.+++++.....+.++.+|+.||+|...|..-|.++ .+.++-+|.
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~~gga 56 (251)
T PRK13509 5 QRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLKKVRNGA 56 (251)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCc
Confidence 377889999999999999999999999999988766665 444444443
No 113
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=40.27 E-value=35 Score=30.01 Aligned_cols=39 Identities=21% Similarity=0.289 Sum_probs=33.8
Q ss_pred HHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhh
Q psy3486 17 IRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP 55 (222)
Q Consensus 17 lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~ 55 (222)
=|.+.++.+++-...++.+.+|+.||+|...|..=|..+
T Consensus 4 ~R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L 42 (240)
T PRK10411 4 ARQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNEL 42 (240)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 377889999999999999999999999999887666654
No 114
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=40.01 E-value=56 Score=25.63 Aligned_cols=35 Identities=14% Similarity=0.309 Sum_probs=27.2
Q ss_pred cCCCCceeeecchhhhhhhhchhhHhHHHHHHHHH
Q psy3486 180 DAKNDRLWFKTNTKLGKLYFDREDFNKLSRILKQL 214 (222)
Q Consensus 180 ~~~NeRLWfKtnlKlakL~ld~~ey~~l~~~l~~L 214 (222)
.++++.+---..+.||.++++.|+|+.....|..+
T Consensus 77 ~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~ 111 (145)
T PF09976_consen 77 NAPDPELKPLARLRLARILLQQGQYDEALATLQQI 111 (145)
T ss_pred hCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhc
Confidence 33445555567888999999999999999888664
No 115
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=39.99 E-value=1.6e+02 Score=21.96 Aligned_cols=67 Identities=15% Similarity=0.040 Sum_probs=38.3
Q ss_pred cccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChH
Q psy3486 29 YTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETS 100 (222)
Q Consensus 29 Ysri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~ 100 (222)
-..+.++.+|+.+|+|...+....... ....+...++.+....-.. .+.. +...|..||..+|.+..
T Consensus 19 ~~~~~~~~lA~~~~~S~~~l~r~f~~~-~g~s~~~~i~~~Rl~~a~~--~L~~--~~~~i~~iA~~~Gf~~~ 85 (107)
T PRK10219 19 DQPLNIDVVAKKSGYSKWYLQRMFRTV-THQTLGDYIRQRRLLLAAV--ELRT--TERPIFDIAMDLGYVSQ 85 (107)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH-HCcCHHHHHHHHHHHHHHH--HHHc--cCCCHHHHHHHHCCCCH
Confidence 344899999999999988877555443 2333333443221111111 1222 23457777777777643
No 116
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=39.90 E-value=1.1e+02 Score=25.36 Aligned_cols=20 Identities=10% Similarity=0.285 Sum_probs=15.2
Q ss_pred eEeeccchHHHHHHHHHHHh
Q psy3486 117 GRIDQSNYKEMMSRYKQLLL 136 (222)
Q Consensus 117 ~~idqg~y~~~l~~y~~LLt 136 (222)
..+.+|++++|++.|++++.
T Consensus 79 ~~~~~~~~~~A~~~~~~~l~ 98 (235)
T TIGR03302 79 AYYKSGDYAEAIAAADRFIR 98 (235)
T ss_pred HHHhcCCHHHHHHHHHHHHH
Confidence 44456888888888888876
No 117
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=39.78 E-value=58 Score=20.49 Aligned_cols=27 Identities=19% Similarity=0.116 Sum_probs=21.6
Q ss_pred cccccHhHHHHHhccchhHHHHhhhhh
Q psy3486 29 YTRIHIPFISRQLNIETSDVLIKLIKP 55 (222)
Q Consensus 29 Ysri~i~~ia~~l~l~~~~ve~klsd~ 55 (222)
+.......||+.+|+|.+.|...+...
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 456788999999999999987665543
No 118
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=38.73 E-value=20 Score=23.91 Aligned_cols=36 Identities=14% Similarity=0.351 Sum_probs=27.3
Q ss_pred cCCCCceeeecchhhhhhhhchhhHhHHHHHHHHHHHhhh
Q psy3486 180 DAKNDRLWFKTNTKLGKLYFDREDFNKLSRILKQLHQSCQ 219 (222)
Q Consensus 180 ~~~NeRLWfKtnlKlakL~ld~~ey~~l~~~l~~L~~~c~ 219 (222)
..+|...|+ .+|.+|+..|+|++....++.+.....
T Consensus 21 ~p~~~~~~~----~la~~~~~~g~~~~A~~~l~~~~~~~~ 56 (68)
T PF14559_consen 21 NPDNPEARL----LLAQCYLKQGQYDEAEELLERLLKQDP 56 (68)
T ss_dssp TTTSHHHHH----HHHHHHHHTT-HHHHHHHHHCCHGGGT
T ss_pred CCCCHHHHH----HHHHHHHHcCCHHHHHHHHHHHHHHCc
Confidence 344555555 599999999999999999988776554
No 119
>PF13041 PPR_2: PPR repeat family
Probab=38.47 E-value=11 Score=24.40 Aligned_cols=39 Identities=10% Similarity=0.323 Sum_probs=27.3
Q ss_pred cceeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHH
Q psy3486 113 NTVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILD 156 (222)
Q Consensus 113 q~ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd 156 (222)
-.+.+.++.|++++|.+.|+++.. ..+.. ...+-|.+++
T Consensus 8 ~li~~~~~~~~~~~a~~l~~~M~~---~g~~P--~~~Ty~~li~ 46 (50)
T PF13041_consen 8 TLISGYCKAGKFEEALKLFKEMKK---RGIKP--DSYTYNILIN 46 (50)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHH---cCCCC--CHHHHHHHHH
Confidence 357788899999999999999987 33332 2344455554
No 120
>PRK09234 fbiC FO synthase; Reviewed
Probab=37.71 E-value=30 Score=36.39 Aligned_cols=88 Identities=11% Similarity=0.117 Sum_probs=64.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccc----c
Q psy3486 8 EHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP----Y 83 (222)
Q Consensus 8 ~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiep----y 83 (222)
.++.++++.|++..----+..||.+++.|+|..+|++..++-.+|.+-=++..-++-= ..++..+-++|-| +
T Consensus 590 ~~y~~lir~IK~~~p~i~i~afsp~Ei~~~a~~~Gl~~~e~l~~LkeAGLds~pgt~a----eil~d~vr~~i~p~k~~~ 665 (843)
T PRK09234 590 TGYADLVRAVKARVPSMHVHAFSPMEIVNGAARLGLSIREWLTALREAGLDTIPGTAA----EILDDEVRWVLTKGKLPT 665 (843)
T ss_pred HHHHHHHHHHHHhCCCeeEEecChHHHHHHHHHcCCCHHHHHHHHHHhCcCccCCCch----hhCCHHHHhhcCCCCCCH
Confidence 4666888888887654456889999999999999999999999999987776543222 1233344455554 3
Q ss_pred -ccccHhHHHHHhCCCh
Q psy3486 84 -TRIHIPFISRQLNIET 99 (222)
Q Consensus 84 -s~v~i~~ia~~l~l~~ 99 (222)
.++++=..|+.+|+++
T Consensus 666 ~~wle~i~~Ah~lGi~~ 682 (843)
T PRK09234 666 AEWIEVVTTAHEVGLRS 682 (843)
T ss_pred HHHHHHHHHHHHcCCCc
Confidence 3477777888888886
No 121
>PRK14960 DNA polymerase III subunits gamma and tau; Provisional
Probab=37.64 E-value=3.4e+02 Score=28.30 Aligned_cols=172 Identities=16% Similarity=0.102 Sum_probs=87.9
Q ss_pred HHHHHHHHHHHHHHhhcccccccHh----HHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccc
Q psy3486 11 EDLLRNIRTQVLIKLIKPYTRIHIP----FISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRI 86 (222)
Q Consensus 11 ~~L~~~lr~q~Ll~li~PYsri~i~----~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v 86 (222)
..+..+++..+..=-++|.+.-++. ++++.-|++.+ ..--.. |-+.-.|-+|....+++|-+.- --..|
T Consensus 159 ~kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~kEgI~id---~eAL~~-IA~~S~GdLRdALnLLDQaIay---g~g~I 231 (702)
T PRK14960 159 QKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQIAAD---QDAIWQ-IAESAQGSLRDALSLTDQAIAY---GQGAV 231 (702)
T ss_pred HhhhHHHHHhhheeeccCCCHHHHHHHHHHHHHHcCCCCC---HHHHHH-HHHHcCCCHHHHHHHHHHHHHh---cCCCc
Confidence 3455667777665555666555432 22222232211 111112 2233445555444445443321 13468
Q ss_pred cHhHHHHHhCCChHH-HHHHHHHHhhcccee-------eEeeccc-----hHHHHHHHHHHHhhhh-hccCccccHHHHH
Q psy3486 87 HIPFISRQLNIETSD-VESLLVSLILDNTVR-------GRIDQSN-----YKEMMSRYKQLLLYIK-SAVTRNYSEKSIN 152 (222)
Q Consensus 87 ~i~~ia~~l~l~~~~-VE~~L~~~iLdq~ik-------~~idqg~-----y~~~l~~y~~LLtyik-saVtrNysEksIn 152 (222)
..+.|.+.+|....+ +.. +...+.++... .-..+|. +++++.+++.++-+-. +...-.++ +.+.
T Consensus 232 T~edV~~lLG~~d~e~Ifd-LldAI~k~d~~~al~~L~el~~~g~d~~~~l~~Ll~~lrdlll~~~~~~~~~~~~-~~~~ 309 (702)
T PRK14960 232 HHQDVKEMLGLIDRTIIYD-LILAVHQNQREKVSQLLLQFRYQALDVSLVLDQLISTLHELALLQYLPELGLKYS-EEIN 309 (702)
T ss_pred CHHHHHHHhccCCHHHHHH-HHHHHHhcCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhccccccccc-HHHH
Confidence 899999999965543 322 22222322221 1111121 5567777777665331 11111223 2344
Q ss_pred HHHHHhhcCCchHHHHHHHHHHHHHHh---cCCCCceeeecc
Q psy3486 153 SILDYISTSKNMELLQDFYETTLEALK---DAKNDRLWFKTN 191 (222)
Q Consensus 153 ~iLd~vs~s~~~~~l~~fYe~TL~~l~---~~~NeRLWfKtn 191 (222)
..+...+..-+.+.++.+|+..++..+ -+.+.|++|-.-
T Consensus 310 ~~~~~la~~~s~~~l~~~~qi~l~~~~~l~~s~~~r~~lEm~ 351 (702)
T PRK14960 310 AKILQLSKLISAQDLQLYYQIACKGRSDLQLAVTQEQGFEMC 351 (702)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHhccCCChhHHHHHH
Confidence 445555555568899999999988866 556888887654
No 122
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=37.59 E-value=2.4e+02 Score=23.42 Aligned_cols=39 Identities=15% Similarity=0.197 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHH
Q psy3486 11 EDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVL 49 (222)
Q Consensus 11 ~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve 49 (222)
+.+|+.|++..+-.-+.|=+++.-..+|+.||+|..-|-
T Consensus 14 ~~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVR 52 (212)
T TIGR03338 14 TLVQDEIERAILSGELPPGAKLNESDIAARLGVSRGPVR 52 (212)
T ss_pred HHHHHHHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHH
Confidence 457777887777777788888777777777777766554
No 123
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=36.74 E-value=65 Score=30.65 Aligned_cols=68 Identities=16% Similarity=0.265 Sum_probs=57.9
Q ss_pred hhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccc
Q psy3486 53 IKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSN 123 (222)
Q Consensus 53 sd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~ 123 (222)
.|-|+-.|....++ .|--..-.+++|+|--.-++-.|+..|++++=|+.-|..-|-++.+.-.||..+
T Consensus 302 ~d~fl~rh~d~fvR---EMRrrvYaQlLESYr~lsl~sMA~tFgVSV~yvdrDLg~FIp~~~LncvIDRvn 369 (412)
T COG5187 302 DDVFLGRHVDLFVR---EMRRRVYAQLLESYRLLSLESMAQTFGVSVEYVDRDLGEFIPEGRLNCVIDRVN 369 (412)
T ss_pred chHHHHHHHHHHHH---HHHHHHHHHHHHHHHHhhHHHHHHHhCccHHHHhhhHHhhCCCCceeeeeeccc
Confidence 46788888888886 455566678899999999999999999999999999999999998888887643
No 124
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=36.66 E-value=89 Score=26.19 Aligned_cols=96 Identities=15% Similarity=0.305 Sum_probs=59.3
Q ss_pred HHhhccceeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhc---CCchHHHHHHHHHHHHHHhcCCCC
Q psy3486 108 SLILDNTVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYIST---SKNMELLQDFYETTLEALKDAKND 184 (222)
Q Consensus 108 ~~iLdq~ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~---s~~~~~l~~fYe~TL~~l~~~~Ne 184 (222)
.+++.....-..+.|++++|+++|.+...|..+ ...-|+-.+.-+.. -.|...+++..+..-..++....
T Consensus 36 r~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~------~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d- 108 (177)
T PF10602_consen 36 RMALEDLADHYCKIGDLEEALKAYSRARDYCTS------PGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGD- 108 (177)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCC------HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccch-
Confidence 366777777788889999999999999998722 12233333332222 24777788887777777766443
Q ss_pred cee-eecchhh--hhhhhchhhHhHHHHHHH
Q psy3486 185 RLW-FKTNTKL--GKLYFDREDFNKLSRILK 212 (222)
Q Consensus 185 RLW-fKtnlKl--akL~ld~~ey~~l~~~l~ 212 (222)
| .+..+|- |=..+-.++|....+.+=
T Consensus 109 --~~~~nrlk~~~gL~~l~~r~f~~AA~~fl 137 (177)
T PF10602_consen 109 --WERRNRLKVYEGLANLAQRDFKEAAELFL 137 (177)
T ss_pred --HHHHHHHHHHHHHHHHHhchHHHHHHHHH
Confidence 4 1222222 223345778877776543
No 125
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=36.51 E-value=28 Score=30.14 Aligned_cols=87 Identities=15% Similarity=0.315 Sum_probs=11.8
Q ss_pred eeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhh
Q psy3486 116 RGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLG 195 (222)
Q Consensus 116 k~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKla 195 (222)
...-..|++++|.+.|++++..- ++ +......+..++..+.. .+-.++....++..++.+.|.. .+
T Consensus 52 ~La~~~~~~~~A~~ay~~l~~~~-~~-----~~~~~~~l~~l~~~~~~----~~A~~~~~~~~~~~~~~~~l~~----~l 117 (280)
T PF13429_consen 52 DLAWSLGDYDEAIEAYEKLLASD-KA-----NPQDYERLIQLLQDGDP----EEALKLAEKAYERDGDPRYLLS----AL 117 (280)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccccccccccccccccccccccc-cc-----ccccccccccccccccc----cccccccccccccccccchhhH----HH
Confidence 34456677888888888887621 11 22233333333221111 1112222222232333444422 44
Q ss_pred hhhhchhhHhHHHHHHHHHHH
Q psy3486 196 KLYFDREDFNKLSRILKQLHQ 216 (222)
Q Consensus 196 kL~ld~~ey~~l~~~l~~L~~ 216 (222)
.++...++|+++...++.+..
T Consensus 118 ~~~~~~~~~~~~~~~l~~~~~ 138 (280)
T PF13429_consen 118 QLYYRLGDYDEAEELLEKLEE 138 (280)
T ss_dssp H-HHHTT-HHHHHHHHHHHHH
T ss_pred HHHHHHhHHHHHHHHHHHHHh
Confidence 555666666666666666553
No 126
>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
Probab=36.14 E-value=1.3e+02 Score=26.55 Aligned_cols=87 Identities=11% Similarity=0.071 Sum_probs=53.7
Q ss_pred eeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHh-hcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhh
Q psy3486 119 IDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYI-STSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKL 197 (222)
Q Consensus 119 idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~v-s~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL 197 (222)
..+|++++|.+.+++.+... |.- . .....+-.+ ....+.+--..+|+..++.... +..+.......+|.+
T Consensus 125 ~~~G~~~~A~~~~~~al~~~-p~~-----~-~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~--~~~~~~~~~~~la~~ 195 (355)
T cd05804 125 EEAGQYDRAEEAARRALELN-PDD-----A-WAVHAVAHVLEMQGRFKEGIAFMESWRDTWDC--SSMLRGHNWWHLALF 195 (355)
T ss_pred HHcCCHHHHHHHHHHHHhhC-CCC-----c-HHHHHHHHHHHHcCCHHHHHHHHHhhhhccCC--CcchhHHHHHHHHHH
Confidence 46799999999999999843 332 1 111222211 1223444445555555553222 234444455678999
Q ss_pred hhchhhHhHHHHHHHHH
Q psy3486 198 YFDREDFNKLSRILKQL 214 (222)
Q Consensus 198 ~ld~~ey~~l~~~l~~L 214 (222)
++..|++++....+++.
T Consensus 196 ~~~~G~~~~A~~~~~~~ 212 (355)
T cd05804 196 YLERGDYEAALAIYDTH 212 (355)
T ss_pred HHHCCCHHHHHHHHHHH
Confidence 99999999999888876
No 127
>KOG3060|consensus
Probab=36.09 E-value=1.1e+02 Score=28.43 Aligned_cols=81 Identities=26% Similarity=0.453 Sum_probs=45.6
Q ss_pred cchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhhhhch
Q psy3486 122 SNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKLYFDR 201 (222)
Q Consensus 122 g~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~ld~ 201 (222)
|+|++|+++|..+|. ..=|-+..-| -++.-.-+.|++.+.++.+=+-+-.... .--.|- -||.+|+..
T Consensus 100 ~~~~~A~e~y~~lL~---ddpt~~v~~K--RKlAilka~GK~l~aIk~ln~YL~~F~~---D~EAW~----eLaeiY~~~ 167 (289)
T KOG3060|consen 100 GNYKEAIEYYESLLE---DDPTDTVIRK--RKLAILKAQGKNLEAIKELNEYLDKFMN---DQEAWH----ELAEIYLSE 167 (289)
T ss_pred hchhhHHHHHHHHhc---cCcchhHHHH--HHHHHHHHcCCcHHHHHHHHHHHHHhcC---cHHHHH----HHHHHHHhH
Confidence 789999999999986 2222111112 2222222344555444443332222111 124553 389999999
Q ss_pred hhHhHHHHHHHHH
Q psy3486 202 EDFNKLSRILKQL 214 (222)
Q Consensus 202 ~ey~~l~~~l~~L 214 (222)
++|++..=.+.|+
T Consensus 168 ~~f~kA~fClEE~ 180 (289)
T KOG3060|consen 168 GDFEKAAFCLEEL 180 (289)
T ss_pred hHHHHHHHHHHHH
Confidence 9999988766665
No 128
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=35.70 E-value=1.4e+02 Score=27.53 Aligned_cols=171 Identities=16% Similarity=0.129 Sum_probs=83.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccHh-H---HHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhcccc
Q psy3486 8 EHIEDLLRNIRTQVLIKLIKPYTRIHIP-F---ISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPY 83 (222)
Q Consensus 8 ~hi~~L~~~lr~q~Ll~li~PYsri~i~-~---ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepy 83 (222)
.+.+.+..+|+.....=-+.|++.=++. + +++.-|.+.+. .--+.| -.+-.|-.+....++++-... .-
T Consensus 157 ~~~~~l~~tI~SRc~~~~~~~l~~~el~~~L~~~~~~~g~~i~~---~al~~i-a~~s~G~~R~al~~l~~~~~~---~~ 229 (363)
T PRK14961 157 TDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKESIDTDE---YALKLI-AYHAHGSMRDALNLLEHAINL---GK 229 (363)
T ss_pred CChHhhhHHHHhhceEEeCCCCCHHHHHHHHHHHHHHcCCCCCH---HHHHHH-HHHcCCCHHHHHHHHHHHHHh---cC
Confidence 3456678888888766666777655543 2 33333432211 111222 224455555444445443321 23
Q ss_pred ccccHhHHHHHhCCChHHHHHHHHHHhhcccee-------eEeeccc-----hHHHHHHHHHHHhhhhhccCcc-----c
Q psy3486 84 TRIHIPFISRQLNIETSDVESLLVSLILDNTVR-------GRIDQSN-----YKEMMSRYKQLLLYIKSAVTRN-----Y 146 (222)
Q Consensus 84 s~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik-------~~idqg~-----y~~~l~~y~~LLtyiksaVtrN-----y 146 (222)
..|..+.+.+.++.+.+..=..+...+.++-.. -.+..|. .+.++.+++.++-+- ++.+ +
T Consensus 230 ~~It~~~v~~~l~~~~~~~i~~l~~ai~~~~~~~~~~~~~~l~~~g~~~~~il~~l~~~~~d~l~~~---~~~~~~~~~~ 306 (363)
T PRK14961 230 GNINIKNVTDMLGLLNEKQSFLLTDALLKKDSKKTMLLLNKISSIGIEWENILIEMLRFLHHISMSQ---SFPKIWNTIF 306 (363)
T ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH---hcCchhhccc
Confidence 568888888888866433222222222221111 0012222 445566666666642 2222 2
Q ss_pred cHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHh---cCCCCceeee
Q psy3486 147 SEKSINSILDYISTSKNMELLQDFYETTLEALK---DAKNDRLWFK 189 (222)
Q Consensus 147 sEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~---~~~NeRLWfK 189 (222)
.+...+.+- ..+..-+.+.+.++++..+++.. .+.|-|+|+-
T Consensus 307 ~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~e 351 (363)
T PRK14961 307 IKNYKNQIQ-KIAQNNKKTNIQLCYQILLNGRKELKFAPDQKIGVE 351 (363)
T ss_pred chHHHHHHH-HHHHcCCHHHHHHHHHHHHHHHHHHccCCCchHHHH
Confidence 222222222 22233457788888888887765 4445666553
No 129
>cd02683 MIT_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with unknown function, co-occuring with an as yet undescribed domain. The molecular function of the MIT domain is unclear.
Probab=35.29 E-value=60 Score=23.86 Aligned_cols=38 Identities=11% Similarity=0.218 Sum_probs=26.5
Q ss_pred ccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHh
Q psy3486 121 QSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYI 158 (222)
Q Consensus 121 qg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~v 158 (222)
.|+|++|+.+|.+=+.+...++..--.++.-+.+-..+
T Consensus 19 ~g~y~eAl~~Y~~aie~l~~~lk~e~d~~~k~~~r~ki 56 (77)
T cd02683 19 EGRFQEALVCYQEGIDLLMQVLKGTKDEAKKKNLRQKI 56 (77)
T ss_pred hccHHHHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence 49999999999998888877665444444444444444
No 130
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=35.28 E-value=13 Score=26.16 Aligned_cols=28 Identities=18% Similarity=0.201 Sum_probs=23.0
Q ss_pred hccceeeEeeccchHHHHHHHHHHHhhh
Q psy3486 111 LDNTVRGRIDQSNYKEMMSRYKQLLLYI 138 (222)
Q Consensus 111 Ldq~ik~~idqg~y~~~l~~y~~LLtyi 138 (222)
-=|+|.|.+..|++|+|.++.+++..-+
T Consensus 26 hLqvI~gllqlg~~~~a~eYi~~~~~~~ 53 (62)
T PF14689_consen 26 HLQVIYGLLQLGKYEEAKEYIKELSKDL 53 (62)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3467889999999999999999988766
No 131
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=34.81 E-value=1.4e+02 Score=26.74 Aligned_cols=91 Identities=12% Similarity=0.161 Sum_probs=54.0
Q ss_pred EeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhh-cCCchHHHHHHHHHHHHHHh-cCCCCceeeecchhhh
Q psy3486 118 RIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYIS-TSKNMELLQDFYETTLEALK-DAKNDRLWFKTNTKLG 195 (222)
Q Consensus 118 ~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs-~s~~~~~l~~fYe~TL~~l~-~~~NeRLWfKtnlKla 195 (222)
.++.|+|++|+..|+.+++-- |. -.|...+--.+=+.+- .+...+-+.. |+..++..- +.+... .-.|+|
T Consensus 153 ~~~~~~y~~Ai~af~~fl~~y-P~--s~~a~~A~y~LG~~y~~~g~~~~A~~~-f~~vv~~yP~s~~~~d----Al~klg 224 (263)
T PRK10803 153 VQDKSRQDDAIVAFQNFVKKY-PD--STYQPNANYWLGQLNYNKGKKDDAAYY-FASVVKNYPKSPKAAD----AMFKVG 224 (263)
T ss_pred HHhcCCHHHHHHHHHHHHHHC-cC--CcchHHHHHHHHHHHHHcCCHHHHHHH-HHHHHHHCCCCcchhH----HHHHHH
Confidence 344599999999999999833 32 2355555444434222 2322233333 333333222 223333 344589
Q ss_pred hhhhchhhHhHHHHHHHHHHH
Q psy3486 196 KLYFDREDFNKLSRILKQLHQ 216 (222)
Q Consensus 196 kL~ld~~ey~~l~~~l~~L~~ 216 (222)
.++.+.|++++..+.++++-+
T Consensus 225 ~~~~~~g~~~~A~~~~~~vi~ 245 (263)
T PRK10803 225 VIMQDKGDTAKAKAVYQQVIK 245 (263)
T ss_pred HHHHHcCCHHHHHHHHHHHHH
Confidence 999999999999998887754
No 132
>KOG2581|consensus
Probab=34.70 E-value=37 Score=33.31 Aligned_cols=64 Identities=20% Similarity=0.272 Sum_probs=47.6
Q ss_pred chHHHHHHHHHHHHHHHHHH----HHhhcccccccHhHHHHHhccchhH-HHHhhhhhhHhhhhhhhhh
Q psy3486 3 DPFIREHIEDLLRNIRTQVL----IKLIKPYTRIHIPFISRQLNIETSD-VLIKLIKPYTRIHIPFISR 66 (222)
Q Consensus 3 D~~I~~hi~~L~~~lr~q~L----l~li~PYsri~i~~ia~~l~l~~~~-ve~klsd~il~~hl~~l~d 66 (222)
|.|.+.+.-.|.-.||..++ -+|=-.||||.+.-||+.|+++-++ +|--++..|=|..|.+-+|
T Consensus 345 ~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~EyiVakAIRDGvIea~Id 413 (493)
T KOG2581|consen 345 DKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDAEYIVAKAIRDGVIEAKID 413 (493)
T ss_pred HHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhHHHHHHHHHHhccceeeec
Confidence 34455555555555665544 3444589999999999999998877 9988888888888877775
No 133
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=34.54 E-value=34 Score=24.12 Aligned_cols=51 Identities=16% Similarity=0.233 Sum_probs=27.7
Q ss_pred cccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhh-hhhhccc-cccccHhHHHHHhCCChHHH
Q psy3486 31 RIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDV-LIKLIKP-YTRIHIPFISRQLNIETSDV 102 (222)
Q Consensus 31 ri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~-l~~iiep-ys~v~i~~ia~~l~l~~~~V 102 (222)
.++++.+|..+++|.+.++. +|++ .-.+=.| |.+=-+.-.|+.+|++.++|
T Consensus 10 glsl~~va~~t~I~~~~l~a---------------------iE~~~~~~lp~~~y~rg~lr~Ya~~Lgld~~~l 62 (62)
T PF13413_consen 10 GLSLEDVAEETKISVSYLEA---------------------IENGDFDSLPSPVYARGYLRKYARFLGLDPDEL 62 (62)
T ss_dssp T--HHHHHHHCS--HHHHHH---------------------HHCT-GCCSSSHHHHHHHHHHHHHHTT--HHHH
T ss_pred CCCHHHHHHHhCCCHHHHHH---------------------HHCcChhhCCcHHHHHHHHHHHHHHhCcCcccC
Confidence 45788889999998777652 2222 2222222 55556666888899988764
No 134
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=34.50 E-value=29 Score=29.41 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=23.5
Q ss_pred eeccchHHHHHHHHHHHhhhhhccCcc
Q psy3486 119 IDQSNYKEMMSRYKQLLLYIKSAVTRN 145 (222)
Q Consensus 119 idqg~y~~~l~~y~~LLtyiksaVtrN 145 (222)
+.+|+|++|+.+|++++...-+.++|-
T Consensus 155 ~~~g~~~~Ai~~~~~aL~l~~~~~~r~ 181 (198)
T PRK10370 155 FMQADYAQAIELWQKVLDLNSPRVNRT 181 (198)
T ss_pred HHcCCHHHHHHHHHHHHhhCCCCccHH
Confidence 467999999999999999887778774
No 135
>KOG2753|consensus
Probab=34.38 E-value=1.1e+02 Score=29.29 Aligned_cols=62 Identities=18% Similarity=0.221 Sum_probs=55.5
Q ss_pred HHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhh
Q psy3486 11 EDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIET 72 (222)
Q Consensus 11 ~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~ 72 (222)
+.....||-=-++.+-+|=-.|..+.+|+.|.++.++||-...|-|--+-+.|=+||.|...
T Consensus 274 E~~~~KMRLLTlm~LA~es~eisy~~l~k~LqI~edeVE~fVIdaI~aklV~~kidq~~~~v 335 (378)
T KOG2753|consen 274 EQNMAKMRLLTLMSLAEESNEISYDTLAKELQINEDEVELFVIDAIRAKLVEGKIDQMNRTV 335 (378)
T ss_pred HHHHHHHHHHHHHHHhccCCCCCHHHHHHHhccCHHHHHHHHHHHHHHHHHHhhHHhhcceE
Confidence 36778888888999999999999999999999999999999999999999999999875433
No 136
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=34.35 E-value=1.7e+02 Score=26.83 Aligned_cols=29 Identities=28% Similarity=0.413 Sum_probs=21.0
Q ss_pred cccccccHhHHHHHhCCChHHHHHHHHHHhhcc
Q psy3486 81 KPYTRIHIPFISRQLNIETSDVESLLVSLILDN 113 (222)
Q Consensus 81 epys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq 113 (222)
+|.| +..||+.+|++.+.|... -..|+++
T Consensus 275 ~~~T---l~EIa~~lgiS~erVRqi-~~rAl~k 303 (317)
T PRK07405 275 QPLT---LAKIGERLNISRERVRQI-EREALSK 303 (317)
T ss_pred CCcC---HHHHHHHHCcCHHHHHHH-HHHHHHH
Confidence 5554 788999999999998863 3444443
No 137
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=34.31 E-value=81 Score=20.42 Aligned_cols=38 Identities=16% Similarity=0.286 Sum_probs=24.3
Q ss_pred HHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhh
Q psy3486 18 RTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISR 66 (222)
Q Consensus 18 r~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d 66 (222)
|-+.|..+.+ ....+..||+.+|+|++. +.+||.-+.+
T Consensus 4 R~~Il~~L~~--~~~~~~el~~~l~~s~~~---------vs~hL~~L~~ 41 (47)
T PF01022_consen 4 RLRILKLLSE--GPLTVSELAEELGLSQST---------VSHHLKKLRE 41 (47)
T ss_dssp HHHHHHHHTT--SSEEHHHHHHHHTS-HHH---------HHHHHHHHHH
T ss_pred HHHHHHHHHh--CCCchhhHHHhccccchH---------HHHHHHHHHH
Confidence 4444444444 667788999999997665 4466655554
No 138
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=33.89 E-value=76 Score=26.83 Aligned_cols=41 Identities=7% Similarity=0.215 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHH
Q psy3486 10 IEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLI 50 (222)
Q Consensus 10 i~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~ 50 (222)
.+.+|+.|+++.+-.-+.|=+++.-..+|+.||+|..-|-.
T Consensus 9 ~~~vy~~i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVRE 49 (224)
T PRK11534 9 ALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLRE 49 (224)
T ss_pred hHHHHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHH
Confidence 46799999999999999999999999999999999776553
No 139
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=33.55 E-value=1.8e+02 Score=25.82 Aligned_cols=87 Identities=20% Similarity=0.264 Sum_probs=61.3
Q ss_pred hhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeecc---ch-----------HHHHHHHHHHHhhh
Q psy3486 73 SDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQS---NY-----------KEMMSRYKQLLLYI 138 (222)
Q Consensus 73 ~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg---~y-----------~~~l~~y~~LLtyi 138 (222)
.+-|+.++.-=.-+....+|+.||++...|-.-|..+.-++.+.....++ +. ...=..|-.++.-.
T Consensus 13 r~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~~f~~~y~~l~~~~ 92 (218)
T COG2345 13 RERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGREQFPKRYGELALAL 92 (218)
T ss_pred HHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchhhcchhhHHHHHHH
Confidence 34555666656677788899999999999999999999999888887654 31 22224454544444
Q ss_pred hhccCccccHHHHHHHHHHhh
Q psy3486 139 KSAVTRNYSEKSINSILDYIS 159 (222)
Q Consensus 139 ksaVtrNysEksIn~iLd~vs 159 (222)
-..+....-++.+|.|++...
T Consensus 93 l~~l~~~~G~~~l~~~l~~r~ 113 (218)
T COG2345 93 LDALEETGGEEALNAFLEKRA 113 (218)
T ss_pred HHHHHHhccHHHHHHHHHHHH
Confidence 455667777888888887444
No 140
>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=33.42 E-value=1.2e+02 Score=29.21 Aligned_cols=24 Identities=25% Similarity=0.390 Sum_probs=20.8
Q ss_pred cccccHhHHHHHhccchhHHHHhh
Q psy3486 29 YTRIHIPFISRQLNIETSDVLIKL 52 (222)
Q Consensus 29 Ysri~i~~ia~~l~l~~~~ve~kl 52 (222)
|=+..++.||+.+|++.++|+.-+
T Consensus 111 yL~~~~~eia~~l~~~~~~ve~~l 134 (429)
T TIGR02395 111 YLEIDLEEIADELEVSEEEVEKVL 134 (429)
T ss_pred CCCCCHHHHHHHcCCCHHHHHHHH
Confidence 667889999999999999998744
No 141
>cd02656 MIT MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear.
Probab=33.38 E-value=1.2e+02 Score=21.40 Aligned_cols=27 Identities=30% Similarity=0.486 Sum_probs=21.2
Q ss_pred cchHHHHHHHHHHHhhhhhccCccccH
Q psy3486 122 SNYKEMMSRYKQLLLYIKSAVTRNYSE 148 (222)
Q Consensus 122 g~y~~~l~~y~~LLtyiksaVtrNysE 148 (222)
|+|++|+.+|.+=+.+...++...-.+
T Consensus 20 g~~~~Al~~Y~~a~e~l~~~~~~~~~~ 46 (75)
T cd02656 20 GNYEEALELYKEALDYLLQALKAEKEP 46 (75)
T ss_pred CCHHHHHHHHHHHHHHHHHHhccCCCH
Confidence 999999999999998887766443333
No 142
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=33.34 E-value=1.7e+02 Score=25.40 Aligned_cols=30 Identities=13% Similarity=0.120 Sum_probs=21.1
Q ss_pred hccccccccHhHHHHHhCCChHHHHHHHHHHhhc
Q psy3486 79 LIKPYTRIHIPFISRQLNIETSDVESLLVSLILD 112 (222)
Q Consensus 79 iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLd 112 (222)
.++.+| ...||+.+|++...|... ...+++
T Consensus 218 ~~~g~s---~~eIA~~lgis~~~V~~~-~~ra~~ 247 (255)
T TIGR02941 218 FEENLS---QKETGERLGISQMHVSRL-QRQAIS 247 (255)
T ss_pred HcCCCC---HHHHHHHHCcCHHHHHHH-HHHHHH
Confidence 356554 588999999999999754 344444
No 143
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=33.18 E-value=3.3e+02 Score=23.71 Aligned_cols=42 Identities=10% Similarity=0.348 Sum_probs=28.2
Q ss_pred cccHhHHHHHhCCCh-HHHHHHHHHHhhccceeeEeeccchHHHHHHHHHHHh
Q psy3486 85 RIHIPFISRQLNIET-SDVESLLVSLILDNTVRGRIDQSNYKEMMSRYKQLLL 136 (222)
Q Consensus 85 ~v~i~~ia~~l~l~~-~~VE~~L~~~iLdq~ik~~idqg~y~~~l~~y~~LLt 136 (222)
.|..++|.+.++.+. +.|.. +...++ .+++++|++.|..|+.
T Consensus 213 ~it~~~v~~~~~~~~~~~i~~-l~~~~~---------~~~~~~a~~~l~~ll~ 255 (319)
T PRK00440 213 EVTEEAVYKITGTARPEEIRE-MIELAL---------NGDFTEAREKLRDLMI 255 (319)
T ss_pred CCCHHHHHHHhCCCCHHHHHH-HHHHHH---------cCCHHHHHHHHHHHHH
Confidence 588888888887554 34433 333333 3678889988888874
No 144
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=33.08 E-value=64 Score=26.49 Aligned_cols=44 Identities=11% Similarity=0.150 Sum_probs=36.7
Q ss_pred HHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhh
Q psy3486 19 TQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIP 62 (222)
Q Consensus 19 ~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~ 62 (222)
...|+++++-=.|+....||+.+|+|.+.|-..+..+-=...+.
T Consensus 16 D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 16 DRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 67788899999999999999999999999987776666555544
No 145
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=32.66 E-value=83 Score=19.93 Aligned_cols=25 Identities=20% Similarity=0.021 Sum_probs=20.6
Q ss_pred cccccHhHHHHHhccchhHHHHhhh
Q psy3486 29 YTRIHIPFISRQLNIETSDVLIKLI 53 (222)
Q Consensus 29 Ysri~i~~ia~~l~l~~~~ve~kls 53 (222)
+.......||+.+|+|...|...+.
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4567899999999999999886554
No 146
>KOG2582|consensus
Probab=32.19 E-value=45 Score=32.30 Aligned_cols=53 Identities=13% Similarity=0.130 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHhhcccccccHhHHHH--HhccchhHHHHhhhhhhHhhhhhhhhh
Q psy3486 13 LLRNIRTQVLIKLIKPYTRIHIPFISR--QLNIETSDVLIKLIKPYTRIHIPFISR 66 (222)
Q Consensus 13 L~~~lr~q~Ll~li~PYsri~i~~ia~--~l~l~~~~ve~klsd~il~~hl~~l~d 66 (222)
....+--++|.++-+-|+.++++.||+ +|+. .++||+-.-|||=++-++...+
T Consensus 299 av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~-~qevek~Ilqmie~~~i~a~iN 353 (422)
T KOG2582|consen 299 AVSSLYKKNIQRLTKTFLSLSLSDIASRVQLAS-AQEVEKYILQMIEDGEIFASIN 353 (422)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcc-hHHHHHHHHHHhccCceEEEec
Confidence 345566789999999999999999999 7775 4679999999999998888775
No 147
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=32.08 E-value=49 Score=20.86 Aligned_cols=28 Identities=14% Similarity=0.105 Sum_probs=24.3
Q ss_pred chhhhhhhhchhhHhHHHHHHHHHHHhh
Q psy3486 191 NTKLGKLYFDREDFNKLSRILKQLHQSC 218 (222)
Q Consensus 191 nlKlakL~ld~~ey~~l~~~l~~L~~~c 218 (222)
-+.+|..|.+.|++++..+.++.+.+.+
T Consensus 4 ~~~la~~~~~~G~~~~A~~~~~~~l~~~ 31 (44)
T PF13428_consen 4 WLALARAYRRLGQPDEAERLLRRALALD 31 (44)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence 3568999999999999999999887765
No 148
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=31.94 E-value=77 Score=25.74 Aligned_cols=26 Identities=8% Similarity=0.081 Sum_probs=21.6
Q ss_pred cccccHhHHHHHhccchhHHHHhhhh
Q psy3486 29 YTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 29 Ysri~i~~ia~~l~l~~~~ve~klsd 54 (222)
|.......||+.+|+|...|...++-
T Consensus 151 ~~g~s~~eIA~~lgis~~~v~~~l~R 176 (187)
T PRK12534 151 FEGITYEELAARTDTPIGTVKSWIRR 176 (187)
T ss_pred HcCCCHHHHHHHhCCChhHHHHHHHH
Confidence 46778899999999999998876653
No 149
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=31.85 E-value=78 Score=22.59 Aligned_cols=35 Identities=11% Similarity=0.194 Sum_probs=26.2
Q ss_pred HHHHHHHhhccc-ccccHhHHHHHhccchhHHHHhh
Q psy3486 18 RTQVLIKLIKPY-TRIHIPFISRQLNIETSDVLIKL 52 (222)
Q Consensus 18 r~q~Ll~li~PY-sri~i~~ia~~l~l~~~~ve~kl 52 (222)
|...++.++.-. ..+.++.||+.+|+|.+.|..-|
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l 41 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLL 41 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHH
Confidence 445567777655 47999999999999988766433
No 150
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=31.47 E-value=87 Score=21.45 Aligned_cols=34 Identities=21% Similarity=0.281 Sum_probs=24.6
Q ss_pred HHHHHHHHHhhcccccccHhHHHHHhccchhHHH
Q psy3486 16 NIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVL 49 (222)
Q Consensus 16 ~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve 49 (222)
..|.-.|+.++---..+.++.+|+.+|+|...|.
T Consensus 4 i~rq~~Ll~~L~~~~~~~~~ela~~l~~S~rti~ 37 (59)
T PF08280_consen 4 IKRQLKLLELLLKNKWITLKELAKKLNISERTIK 37 (59)
T ss_dssp HHHHHHHHHHHHHHTSBBHHHHHHHCTS-HHHHH
T ss_pred HHHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHH
Confidence 3455566666644778899999999999977655
No 151
>KOG2908|consensus
Probab=31.36 E-value=94 Score=29.83 Aligned_cols=61 Identities=21% Similarity=0.264 Sum_probs=45.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhccccc------ccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhh
Q psy3486 4 PFIREHIEDLLRNIRTQVLIKLIKPYTR------IHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISR 66 (222)
Q Consensus 4 ~~I~~hi~~L~~~lr~q~Ll~li~PYsr------i~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d 66 (222)
|.+.+|-+.|.+.|+-=+|+.++ |+| |.++.||+..++|..+||--+=..+=-.-+.|-+|
T Consensus 263 p~L~~~e~~L~qKI~LmaLiEi~--F~rpa~~R~lsf~~Ia~~tkip~~eVE~LVMKAlslgLikG~Id 329 (380)
T KOG2908|consen 263 PDLASNEDFLLQKIRLLALIEIT--FSRPANERTLSFKEIAEATKIPNKEVELLVMKALSLGLIKGSID 329 (380)
T ss_pred chHHHHHHHHHHHHHHHHHHHHH--hcCcchhccccHHHHHHHhCCCHHHHHHHHHHHHhccceeeeec
Confidence 77889999999999999998875 555 88999999999999999943333333333344444
No 152
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=31.35 E-value=1.3e+02 Score=23.69 Aligned_cols=63 Identities=11% Similarity=0.059 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHH
Q psy3486 14 LRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISR 93 (222)
Q Consensus 14 ~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~ 93 (222)
|+.+.-.++.++++ -..++.+.+|+..|+|.+.+- .+. ++= ..| |.=-+..||+
T Consensus 2 ~~~i~~~~l~~ll~-~~Glsq~eLA~~~Gis~~~is-------------~iE--------~g~---~~p-s~~~l~kIa~ 55 (120)
T PRK13890 2 YNYIFFTNVLRLLD-ERHMTKKELSERSGVSISFLS-------------DLT--------TGK---ANP-SLKVMEAIAD 55 (120)
T ss_pred HHHHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHH-------------HHH--------cCC---CCC-CHHHHHHHHH
Confidence 66777788888877 557888999999999866532 111 110 123 3344677899
Q ss_pred HhCCChHHH
Q psy3486 94 QLNIETSDV 102 (222)
Q Consensus 94 ~l~l~~~~V 102 (222)
.+|++++.+
T Consensus 56 aL~v~~~~L 64 (120)
T PRK13890 56 ALETPLPLL 64 (120)
T ss_pred HHCCCHHHH
Confidence 999987653
No 153
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=31.29 E-value=16 Score=20.76 Aligned_cols=23 Identities=17% Similarity=0.343 Sum_probs=19.3
Q ss_pred ceeeEeeccchHHHHHHHHHHHh
Q psy3486 114 TVRGRIDQSNYKEMMSRYKQLLL 136 (222)
Q Consensus 114 ~ik~~idqg~y~~~l~~y~~LLt 136 (222)
.+.+..+.|++++|.+.|.++..
T Consensus 6 li~~~~~~~~~~~a~~~~~~M~~ 28 (35)
T TIGR00756 6 LIDGLCKAGRVEEALELFKEMLE 28 (35)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 46677888999999999999865
No 154
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=31.02 E-value=19 Score=20.22 Aligned_cols=23 Identities=9% Similarity=0.309 Sum_probs=19.1
Q ss_pred ceeeEeeccchHHHHHHHHHHHh
Q psy3486 114 TVRGRIDQSNYKEMMSRYKQLLL 136 (222)
Q Consensus 114 ~ik~~idqg~y~~~l~~y~~LLt 136 (222)
.+.+..+.|++++|.+.|+++..
T Consensus 6 li~~~~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 6 LISGYCKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HHHHHHccchHHHHHHHHHHHhH
Confidence 46677788999999999998864
No 155
>KOG3054|consensus
Probab=30.85 E-value=68 Score=29.51 Aligned_cols=75 Identities=13% Similarity=0.175 Sum_probs=58.1
Q ss_pred HHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhh------hhhhhhhccccccccHhHHHHHh
Q psy3486 22 LIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIET------SDVLIKLIKPYTRIHIPFISRQL 95 (222)
Q Consensus 22 Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~------~~~l~~iiepys~v~i~~ia~~l 95 (222)
.+.+|+--.+|-|+.+|..||+-.+++-.++.+.+.+..+.|+.|-=-..+ -.-..+.|+-=-||.|.++|..-
T Consensus 205 Fv~YIk~nKvV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS~eEl~AVAkfIkqrGRVSIaelAe~S 284 (299)
T KOG3054|consen 205 FVEYIKKNKVVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYISMEELAAVAKFIKQRGRVSIAELAEKS 284 (299)
T ss_pred HHHHHHhcCeeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEecHHHHHHHHHHHHHcCceeHHHHHHhh
Confidence 456777778999999999999999999999999999999999887311100 03445777888888888888754
Q ss_pred C
Q psy3486 96 N 96 (222)
Q Consensus 96 ~ 96 (222)
|
T Consensus 285 N 285 (299)
T KOG3054|consen 285 N 285 (299)
T ss_pred c
Confidence 4
No 156
>KOG1840|consensus
Probab=30.64 E-value=1.4e+02 Score=29.63 Aligned_cols=107 Identities=13% Similarity=0.182 Sum_probs=62.8
Q ss_pred HHhhccceeeEeeccchHHHHHHHHHHHhhhhhccC---ccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcC--C
Q psy3486 108 SLILDNTVRGRIDQSNYKEMMSRYKQLLLYIKSAVT---RNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDA--K 182 (222)
Q Consensus 108 ~~iLdq~ik~~idqg~y~~~l~~y~~LLtyiksaVt---rNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~--~ 182 (222)
...|.+.-.+...+|.|++|-.++++-+.-. ..+. ..-....++++..-...-...+-....|.-.++-...+ .
T Consensus 283 a~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~-~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~ 361 (508)
T KOG1840|consen 283 AATLNNLAVLYYKQGKFAEAEEYCERALEIY-EKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGE 361 (508)
T ss_pred HHHHHHHHHHHhccCChHHHHHHHHHHHHHH-HHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccc
Confidence 3445555566688999999999999988844 3332 22223344444443332233444444444444433311 1
Q ss_pred CCceeeecchhhhhhhhchhhHhHHHHHHHHHH
Q psy3486 183 NDRLWFKTNTKLGKLYFDREDFNKLSRILKQLH 215 (222)
Q Consensus 183 NeRLWfKtnlKlakL~ld~~ey~~l~~~l~~L~ 215 (222)
.+---=|+.-.||.+|+-+|.|....++.++.-
T Consensus 362 ~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai 394 (508)
T KOG1840|consen 362 DNVNLAKIYANLAELYLKMGKYKEAEELYKKAI 394 (508)
T ss_pred cchHHHHHHHHHHHHHHHhcchhHHHHHHHHHH
Confidence 111234677889999999999999887666543
No 157
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=30.47 E-value=1e+02 Score=24.10 Aligned_cols=37 Identities=8% Similarity=0.142 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhh
Q psy3486 15 RNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 15 ~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd 54 (222)
..-|+=.++.++ .......||+.+|+|...|...+..
T Consensus 109 ~~~r~v~~l~~~---~g~s~~EIA~~lgis~~tV~~~l~r 145 (161)
T PRK09047 109 ARQREAFLLRYW---EDMDVAETAAAMGCSEGSVKTHCSR 145 (161)
T ss_pred HHHHHHHHHHHH---hcCCHHHHHHHHCCCHHHHHHHHHH
Confidence 333444444454 4556899999999999998866554
No 158
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=30.30 E-value=4.3e+02 Score=27.59 Aligned_cols=168 Identities=13% Similarity=0.107 Sum_probs=79.1
Q ss_pred HHHHHHHHHHHHHHhhcccccccH----hHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccc
Q psy3486 11 EDLLRNIRTQVLIKLIKPYTRIHI----PFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRI 86 (222)
Q Consensus 11 ~~L~~~lr~q~Ll~li~PYsri~i----~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v 86 (222)
..+..+||..++.=-|.|++.-++ .++++.-|++ ++..--+.|.+. -.|-++....+++|-+.- -..+|
T Consensus 160 ~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi~---id~eAL~~Ia~~-A~GslRdAlnLLDqaia~---g~g~I 232 (709)
T PRK08691 160 HKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIA---YEPPALQLLGRA-AAGSMRDALSLLDQAIAL---GSGKV 232 (709)
T ss_pred cccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHcCCC---cCHHHHHHHHHH-hCCCHHHHHHHHHHHHHh---cCCCc
Confidence 355667777765544556655542 2333333332 122222333332 245555454555553331 24578
Q ss_pred cHhHHHHHhCCChHHHHHHHHHHhhcccee-----------eEeeccc-hHHHHHHHHHHHhhhh--hccCccccHHHHH
Q psy3486 87 HIPFISRQLNIETSDVESLLVSLILDNTVR-----------GRIDQSN-YKEMMSRYKQLLLYIK--SAVTRNYSEKSIN 152 (222)
Q Consensus 87 ~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik-----------~~idqg~-y~~~l~~y~~LLtyik--saVtrNysEksIn 152 (222)
..+.|...+|...+..=-.+...++++-.. .-++-.+ ..+.+.++++++-+-. +.++... .-.
T Consensus 233 t~e~V~~lLG~~d~~~If~LldAL~~~d~~~al~~l~~L~~~G~d~~~~l~~L~~~l~~l~~~~~~~~~~~~~~---~~~ 309 (709)
T PRK08691 233 AENDVRQMIGAVDKQYLYELLTGIINQDGAALLAKAQEMAACAVGFDNALGELAILLQQLALIQAVPSALAHDD---PDS 309 (709)
T ss_pred CHHHHHHHHcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhcCchhccccc---hHH
Confidence 888899999966543222222222222111 1111100 2233334444333210 0111111 113
Q ss_pred HHHHHhhcCCchHHHHHHHHHHHHHHhc---CCCCceee
Q psy3486 153 SILDYISTSKNMELLQDFYETTLEALKD---AKNDRLWF 188 (222)
Q Consensus 153 ~iLd~vs~s~~~~~l~~fYe~TL~~l~~---~~NeRLWf 188 (222)
..+...+..-..+.++.+|+++++..++ +.+.|+-|
T Consensus 310 ~~~~~~a~~~~~~~l~~~~q~~l~~~~~l~~a~~~~~~~ 348 (709)
T PRK08691 310 DILHRLAQTISGEQIQLYYQIAVHGKRDLSLAPDEYAGF 348 (709)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHhccCCCHHHHH
Confidence 4455555556789999999999998763 33455444
No 159
>PF04212 MIT: MIT (microtubule interacting and transport) domain; InterPro: IPR007330 The MIT domain is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking.; PDB: 2DL1_A 2JQK_A 1WR0_A 2CPT_A 2JQH_A 2V6Y_A 2JQ9_A 2K3W_A 1YXR_A 3EAB_E ....
Probab=30.18 E-value=85 Score=21.88 Aligned_cols=23 Identities=30% Similarity=0.608 Sum_probs=19.7
Q ss_pred ccchHHHHHHHHHHHhhhhhccC
Q psy3486 121 QSNYKEMMSRYKQLLLYIKSAVT 143 (222)
Q Consensus 121 qg~y~~~l~~y~~LLtyiksaVt 143 (222)
.|+|++|+++|++=+.+...++.
T Consensus 18 ~g~~~~A~~~Y~~ai~~l~~~~~ 40 (69)
T PF04212_consen 18 AGNYEEALELYKEAIEYLMQALK 40 (69)
T ss_dssp TTSHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHhc
Confidence 59999999999999998866654
No 160
>PRK12323 DNA polymerase III subunits gamma and tau; Provisional
Probab=30.16 E-value=2.9e+02 Score=28.82 Aligned_cols=174 Identities=10% Similarity=0.026 Sum_probs=82.7
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccHhH----HHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhcccc
Q psy3486 8 EHIEDLLRNIRTQVLIKLIKPYTRIHIPF----ISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPY 83 (222)
Q Consensus 8 ~hi~~L~~~lr~q~Ll~li~PYsri~i~~----ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepy 83 (222)
+..+.|..+||+.+..--|.|.+.-++.. +++.-|++.+. .--+. |-++-.|-.+....+++|-+. .-+
T Consensus 162 tep~kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~Egi~~d~---eAL~~-IA~~A~Gs~RdALsLLdQaia---~~~ 234 (700)
T PRK12323 162 TDPQKIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEGIAHEV---NALRL-LAQAAQGSMRDALSLTDQAIA---YSA 234 (700)
T ss_pred CChHhhhhHHHHHHHhcccCCCChHHHHHHHHHHHHHcCCCCCH---HHHHH-HHHHcCCCHHHHHHHHHHHHH---hcc
Confidence 45678889999999876666666544332 22222332211 11112 223344444433344444332 223
Q ss_pred ccccHhHHHHHhCCChH-HHHHHHHHHhhccceeeEee------ccchHHHHHHHHHHHhhhhhc-cCcccc-----HHH
Q psy3486 84 TRIHIPFISRQLNIETS-DVESLLVSLILDNTVRGRID------QSNYKEMMSRYKQLLLYIKSA-VTRNYS-----EKS 150 (222)
Q Consensus 84 s~v~i~~ia~~l~l~~~-~VE~~L~~~iLdq~ik~~id------qg~y~~~l~~y~~LLtyiksa-VtrNys-----Eks 150 (222)
..|..+.+.+.+|+... .+...+. .+.++-...-+. ...++ .....+.++.+++.. +.+... +..
T Consensus 235 ~~It~~~V~~~LG~~d~~~i~~Ll~-aL~~~d~~~~l~l~~~l~~~G~d-~~~~L~dLl~~l~~l~l~q~~~~~~~~~~~ 312 (700)
T PRK12323 235 GNVSEEAVRGMLGAIDQSYLVRLLD-ALAAEDGAALLAIADEMAGRSLS-FAGALQDLASLLQKIALAQVVPAAVQDDWP 312 (700)
T ss_pred CCcCHHHHHHHhCCCCHHHHHHHHH-HHHcCCHHHHHHHHHHHHHcCCC-HHHHHHHHHHHHHHHHHHhhCchhcccccc
Confidence 56777888888886653 3333322 222221111110 01111 233344444443221 111110 000
Q ss_pred HHHHHHHhhcCCchHHHHHHHHHHHHHHhc---CCCCceeeec
Q psy3486 151 INSILDYISTSKNMELLQDFYETTLEALKD---AKNDRLWFKT 190 (222)
Q Consensus 151 In~iLd~vs~s~~~~~l~~fYe~TL~~l~~---~~NeRLWfKt 190 (222)
-..-+...+..-+.+.++.+|+++++..++ +.+.|+.|-.
T Consensus 313 ~~~~~~~~a~~~s~~~l~~~~q~~~~~~~el~~a~~~~~~~Em 355 (700)
T PRK12323 313 EADDIRRLAGRFDAQEVQLFYQIANLGRSELALAPDEYAGFTM 355 (700)
T ss_pred hHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhccCCCHHHHHHH
Confidence 112222333344688999999999998874 4577776643
No 161
>PRK08444 hypothetical protein; Provisional
Probab=29.84 E-value=52 Score=30.84 Aligned_cols=88 Identities=14% Similarity=0.063 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccc---c-
Q psy3486 8 EHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP---Y- 83 (222)
Q Consensus 8 ~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiep---y- 83 (222)
+++.++.+.|+..-----+..||..||.|+|+.+|+|.+++-.+|-+-=++..-++=-+ .++..+-+.|-| |
T Consensus 113 e~y~e~ir~Ik~~~p~i~i~a~s~~Ei~~~a~~~g~~~~e~l~~LkeAGl~~~~g~~aE----i~~~~vr~~I~p~k~~~ 188 (353)
T PRK08444 113 EWYLEIFKKIKEAYPNLHVKAMTAAEVDFLSRKFGKSYEEVLEDMLEYGVDSMPGGGAE----IFDEEVRKKICKGKVSS 188 (353)
T ss_pred HHHHHHHHHHHHHCCCceEeeCCHHHHHHHHHHcCCCHHHHHHHHHHhCcccCCCCCch----hcCHHHHhhhCCCCCCH
Confidence 45677888888632111255699999999999999999999999988877764442222 234455566666 2
Q ss_pred -ccccHhHHHHHhCCCh
Q psy3486 84 -TRIHIPFISRQLNIET 99 (222)
Q Consensus 84 -s~v~i~~ia~~l~l~~ 99 (222)
-.++|-..|+.+|++.
T Consensus 189 ~~~~~i~~~a~~~Gi~~ 205 (353)
T PRK08444 189 ERWLEIHKYWHKKGKMS 205 (353)
T ss_pred HHHHHHHHHHHHcCCCc
Confidence 2356666788888886
No 162
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=29.81 E-value=98 Score=24.34 Aligned_cols=52 Identities=13% Similarity=0.220 Sum_probs=41.0
Q ss_pred hhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccchH
Q psy3486 74 DVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSNYK 125 (222)
Q Consensus 74 ~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~y~ 125 (222)
--|+++++==+++...-||+.+|++...|-.++..+-=++.|++.--.-++.
T Consensus 11 ~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~~ 62 (154)
T COG1522 11 RRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDPE 62 (154)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECHH
Confidence 3445555555678889999999999999999998888888888876655554
No 163
>KOG2376|consensus
Probab=29.80 E-value=51 Score=33.64 Aligned_cols=119 Identities=15% Similarity=0.229 Sum_probs=73.9
Q ss_pred cHhHHHHHhCCChHHHHH-----HHHHHhhccceeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcC
Q psy3486 87 HIPFISRQLNIETSDVES-----LLVSLILDNTVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTS 161 (222)
Q Consensus 87 ~i~~ia~~l~l~~~~VE~-----~L~~~iLdq~ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s 161 (222)
|=.|+.=++|-+.+-.+- ++...++.=.-+...++|+||++++.|+.|...- ..-|.|.=-.+++..++.+
T Consensus 84 EKAYc~Yrlnk~Dealk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~----~dd~d~~~r~nl~a~~a~l 159 (652)
T KOG2376|consen 84 EKAYCEYRLNKLDEALKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNN----SDDQDEERRANLLAVAAAL 159 (652)
T ss_pred HHHHHHHHcccHHHHHHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC----CchHHHHHHHHHHHHHHhh
Confidence 455666777766654442 1112233333345678999999999999998744 2246666667777766544
Q ss_pred CchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhhhhchhhHhHHHHHHHHHHHhhhc
Q psy3486 162 KNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKLYFDREDFNKLSRILKQLHQSCQM 220 (222)
Q Consensus 162 ~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~ld~~ey~~l~~~l~~L~~~c~~ 220 (222)
... +++..=+++.. .-.+.| +.|-.+++.|.|+.+.++|..-.+-|++
T Consensus 160 ~~~-~~q~v~~v~e~------syel~y----N~Ac~~i~~gky~qA~elL~kA~~~~~e 207 (652)
T KOG2376|consen 160 QVQ-LLQSVPEVPED------SYELLY----NTACILIENGKYNQAIELLEKALRICRE 207 (652)
T ss_pred hHH-HHHhccCCCcc------hHHHHH----HHHHHHHhcccHHHHHHHHHHHHHHHHH
Confidence 321 33333332211 112333 3588899999999999999988777764
No 164
>KOG1076|consensus
Probab=29.74 E-value=38 Score=35.23 Aligned_cols=42 Identities=14% Similarity=0.441 Sum_probs=39.2
Q ss_pred ccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccc
Q psy3486 82 PYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSN 123 (222)
Q Consensus 82 pys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~ 123 (222)
-|+.|-++.+|+...+|+..|-+.++.||.+.-+.+..||-.
T Consensus 715 ~Y~SvSl~~LA~mFdLp~~~VhsIiSkmiineEl~AslDqpt 756 (843)
T KOG1076|consen 715 VYDSVSLAKLADMFDLPEPKVHSIISKMIINEELHASLDQPT 756 (843)
T ss_pred hhhhccHHHHHHHhCCCchhHHHHHHHHHHHHHhhhccCCCc
Confidence 499999999999999999999999999999999999998853
No 165
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=29.43 E-value=2.8e+02 Score=21.84 Aligned_cols=88 Identities=11% Similarity=0.051 Sum_probs=53.8
Q ss_pred eeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhhh
Q psy3486 119 IDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKLY 198 (222)
Q Consensus 119 idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~ 198 (222)
..+|+|++|+++|++++..- |.-..-+...+ .-.....+.+--..+|+..+.. ..++-. +-..+|..+
T Consensus 35 ~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg-----~~~~~~g~~~~A~~~y~~Al~l--~p~~~~----a~~~lg~~l 102 (144)
T PRK15359 35 WQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALA-----GTWMMLKEYTTAINFYGHALML--DASHPE----PVYQTGVCL 102 (144)
T ss_pred HHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHH-----HHHHHHhhHHHHHHHHHHHHhc--CCCCcH----HHHHHHHHH
Confidence 56899999999999998843 43222221111 1111122344455666666652 233334 445689999
Q ss_pred hchhhHhHHHHHHHHHHHhh
Q psy3486 199 FDREDFNKLSRILKQLHQSC 218 (222)
Q Consensus 199 ld~~ey~~l~~~l~~L~~~c 218 (222)
...|+++......+..-+.|
T Consensus 103 ~~~g~~~eAi~~~~~Al~~~ 122 (144)
T PRK15359 103 KMMGEPGLAREAFQTAIKMS 122 (144)
T ss_pred HHcCCHHHHHHHHHHHHHhC
Confidence 99999999887777765544
No 166
>KOG2672|consensus
Probab=29.41 E-value=38 Score=31.78 Aligned_cols=63 Identities=30% Similarity=0.529 Sum_probs=42.2
Q ss_pred HHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCc--eeeecchhhhhhhhchhhHhHHHHHHHHH--HHhhhccC
Q psy3486 153 SILDYISTSKNMELLQDFYETTLEALKDAKNDR--LWFKTNTKLGKLYFDREDFNKLSRILKQL--HQSCQMKR 222 (222)
Q Consensus 153 ~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeR--LWfKtnlKlakL~ld~~ey~~l~~~l~~L--~~~c~~~~ 222 (222)
++-|+++...+..-...||.-.+..+. ..--| =|+||.+-+++ .|.++..-+++| |.-|++.|
T Consensus 28 s~~DFv~~d~~~~~~~~~e~~~~~~~~-~~~~rlP~WLK~~iP~G~------n~~~iK~~lr~l~L~TVCEEAr 94 (360)
T KOG2672|consen 28 SFADFVSGDKPLRADWDFEKGRKKREG-EERLRLPPWLKTKIPLGE------NYNKIKKDLRELKLHTVCEEAR 94 (360)
T ss_pred chhhhhcCCcccccccchhhchhhhhc-cccccCChhhcccCCCCc------cHHHHHHHHhhCchhhhhhhcc
Confidence 466788766555555677877776542 11123 39999988764 688899888874 56777654
No 167
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=29.36 E-value=1.5e+02 Score=29.50 Aligned_cols=91 Identities=8% Similarity=0.068 Sum_probs=49.8
Q ss_pred ceeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchh
Q psy3486 114 TVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTK 193 (222)
Q Consensus 114 ~ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlK 193 (222)
+|.|..+.|++++|++.+++|.. ..+.. ..-+.+.++...+.+...+--.++|+...+. .+-.-...+.--
T Consensus 397 lI~~y~~~G~~~~A~~lf~~M~~---~g~~P--d~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~----~g~~p~~~~y~~ 467 (697)
T PLN03081 397 LIAGYGNHGRGTKAVEMFERMIA---EGVAP--NHVTFLAVLSACRYSGLSEQGWEIFQSMSEN----HRIKPRAMHYAC 467 (697)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHH---hCCCC--CHHHHHHHHHHHhcCCcHHHHHHHHHHHHHh----cCCCCCccchHh
Confidence 45566667777777777777764 22322 2444666666666555554444555444331 111122234444
Q ss_pred hhhhhhchhhHhHHHHHHHH
Q psy3486 194 LGKLYFDREDFNKLSRILKQ 213 (222)
Q Consensus 194 lakL~ld~~ey~~l~~~l~~ 213 (222)
+..+|...|.++.+.+++++
T Consensus 468 li~~l~r~G~~~eA~~~~~~ 487 (697)
T PLN03081 468 MIELLGREGLLDEAYAMIRR 487 (697)
T ss_pred HHHHHHhcCCHHHHHHHHHH
Confidence 66667777777776666554
No 168
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=29.13 E-value=1.1e+02 Score=25.91 Aligned_cols=54 Identities=20% Similarity=0.258 Sum_probs=0.0
Q ss_pred CCchHHHHHHHHHH--HHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhh
Q psy3486 1 MDDPFIREHIEDLL--RNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP 55 (222)
Q Consensus 1 ~~D~~I~~hi~~L~--~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~ 55 (222)
++||.|+..+..+. ..-.-.+|-.+. .=..++-+.+|+.+|++...|-+-|..+
T Consensus 5 ~~~~~v~~~l~~~~~~~~~~~~Vl~~L~-~~g~~tdeeLA~~Lgi~~~~VRk~L~~L 60 (178)
T PRK06266 5 LNNPLVQKVLFEIMEGDEEGFEVLKALI-KKGEVTDEEIAEQTGIKLNTVRKILYKL 60 (178)
T ss_pred hcCHHHHHHHHHHhcCCccHhHHHHHHH-HcCCcCHHHHHHHHCCCHHHHHHHHHHH
No 169
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=29.00 E-value=1.5e+02 Score=19.46 Aligned_cols=47 Identities=15% Similarity=0.178 Sum_probs=35.3
Q ss_pred hhhhcccccc--ccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeecc
Q psy3486 76 LIKLIKPYTR--IHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQS 122 (222)
Q Consensus 76 l~~iiepys~--v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg 122 (222)
++..|.-+.. +.+..||+.++++...|-..+..+.-++.|.-.-+.+
T Consensus 10 vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~ 58 (62)
T PF12802_consen 10 VLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPG 58 (62)
T ss_dssp HHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SS
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCC
Confidence 3445555555 8999999999999999999888888888887665543
No 170
>KOG2002|consensus
Probab=28.92 E-value=1.6e+02 Score=31.76 Aligned_cols=34 Identities=15% Similarity=0.301 Sum_probs=21.6
Q ss_pred eccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHH
Q psy3486 120 DQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILD 156 (222)
Q Consensus 120 dqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd 156 (222)
.++.+++|++.|+++|+.= |. --|.--+|--+|.
T Consensus 624 ~kk~~~KAlq~y~kvL~~d-pk--N~yAANGIgiVLA 657 (1018)
T KOG2002|consen 624 EKKHQEKALQLYGKVLRND-PK--NMYAANGIGIVLA 657 (1018)
T ss_pred HHHHHHHHHHHHHHHHhcC-cc--hhhhccchhhhhh
Confidence 3467899999999999843 21 1255555555554
No 171
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=28.80 E-value=1.7e+02 Score=25.53 Aligned_cols=19 Identities=16% Similarity=0.420 Sum_probs=15.5
Q ss_pred cHhHHHHHhccchhHHHHh
Q psy3486 33 HIPFISRQLNIETSDVLIK 51 (222)
Q Consensus 33 ~i~~ia~~l~l~~~~ve~k 51 (222)
....+|+.+|++.++|..-
T Consensus 141 ~~~eia~~l~v~~~~v~~~ 159 (258)
T PRK08215 141 TVEEIAKELEVPREEVVFA 159 (258)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 5788999999998887763
No 172
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=28.79 E-value=2.5e+02 Score=27.52 Aligned_cols=30 Identities=7% Similarity=0.293 Sum_probs=23.6
Q ss_pred cchhhhhhhhchhhHhHHHHHHHHHHHhhh
Q psy3486 190 TNTKLGKLYFDREDFNKLSRILKQLHQSCQ 219 (222)
Q Consensus 190 tnlKlakL~ld~~ey~~l~~~l~~L~~~c~ 219 (222)
+...+|.++++.|+|+..-+.+++..+.+.
T Consensus 544 a~~~la~~~~~~g~~~eAi~~~e~A~~l~~ 573 (615)
T TIGR00990 544 AVATMAQLLLQQGDVDEALKLFERAAELAR 573 (615)
T ss_pred HHHHHHHHHHHccCHHHHHHHHHHHHHHhc
Confidence 456789999999999998887777655443
No 173
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=28.44 E-value=83 Score=20.04 Aligned_cols=25 Identities=16% Similarity=0.106 Sum_probs=18.3
Q ss_pred cccccHhHHHHHhccchhHHHHhhh
Q psy3486 29 YTRIHIPFISRQLNIETSDVLIKLI 53 (222)
Q Consensus 29 Ysri~i~~ia~~l~l~~~~ve~kls 53 (222)
-..+.+..|++.+|++...|-.-+.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~ 32 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLK 32 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHH
Confidence 3557888999999998776554443
No 174
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=28.38 E-value=2.4e+02 Score=26.35 Aligned_cols=29 Identities=7% Similarity=0.220 Sum_probs=20.9
Q ss_pred cccccccHhHHHHHhCCChHHHHHHHHHHhhcc
Q psy3486 81 KPYTRIHIPFISRQLNIETSDVESLLVSLILDN 113 (222)
Q Consensus 81 epys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq 113 (222)
+|+| +..||+.+|++.+.|-. +-.++|.+
T Consensus 324 ~~~t---l~EIa~~lgvs~erVrQ-i~~~Al~k 352 (367)
T PRK09210 324 RTRT---LEEVGKVFGVTRERIRQ-IEAKALRK 352 (367)
T ss_pred CCcc---HHHHHHHHCCCHHHHHH-HHHHHHHH
Confidence 5555 68899999999988875 34555554
No 175
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=28.22 E-value=1.1e+02 Score=24.76 Aligned_cols=36 Identities=8% Similarity=0.202 Sum_probs=32.6
Q ss_pred cccccHhHHHHHhCCChHHHHHHHHHHhhccceeeE
Q psy3486 83 YTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGR 118 (222)
Q Consensus 83 ys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~ 118 (222)
=.|.-.+.||+.+|++...|-.++..+.=.+.|.+.
T Consensus 21 d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 21 NARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence 378888999999999999999999999999999854
No 176
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=28.22 E-value=1.1e+02 Score=25.22 Aligned_cols=45 Identities=13% Similarity=0.205 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhh
Q psy3486 7 REHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 7 ~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd 54 (222)
...++.|=..-|+=.++++++ -.+...||+.+|+|...|...+..
T Consensus 129 ~~~l~~Lp~~~R~v~~L~~~~---g~s~~EIA~~lgis~~tVk~~l~R 173 (189)
T PRK12530 129 EACLNHLPAQQARVFMMREYL---ELSSEQICQECDISTSNLHVLLYR 173 (189)
T ss_pred HHHHHhCCHHHHHHHhHHHHc---CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 445555555555555665544 566889999999999999877654
No 177
>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=28.11 E-value=46 Score=21.73 Aligned_cols=24 Identities=21% Similarity=0.447 Sum_probs=21.2
Q ss_pred ccc-ccccHhHHHHHhCCChHHHHH
Q psy3486 81 KPY-TRIHIPFISRQLNIETSDVES 104 (222)
Q Consensus 81 epy-s~v~i~~ia~~l~l~~~~VE~ 104 (222)
-|| +.-++..+|..+|++..+|..
T Consensus 22 ~~~P~~~~~~~la~~~~l~~~qV~~ 46 (59)
T cd00086 22 NPYPSREEREELAKELGLTERQVKI 46 (59)
T ss_pred CCCCCHHHHHHHHHHHCcCHHHHHH
Confidence 677 778899999999999999984
No 178
>KOG2758|consensus
Probab=28.06 E-value=1.5e+02 Score=28.57 Aligned_cols=60 Identities=15% Similarity=0.304 Sum_probs=41.2
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhh
Q psy3486 2 DDPFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHI 61 (222)
Q Consensus 2 ~D~~I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl 61 (222)
+|+|+-...++..++-|-=.---+.+--+||+|+-+|+.|+++.++.|.-..+.|=...|
T Consensus 320 nDfFLva~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~~eeaErwivnlIr~~rl 379 (432)
T KOG2758|consen 320 NDFFLVALLDEFLENARLLIFETFCRIHQCITIDMLADKLNMDPEEAERWIVNLIRTARL 379 (432)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCCHHHHHHHHHHHHHHhhh
Confidence 688887777776666554333333333477899999999999999999665555544333
No 179
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=27.95 E-value=67 Score=23.80 Aligned_cols=28 Identities=14% Similarity=0.019 Sum_probs=22.5
Q ss_pred cccccccHhHHHHHhccchhHHHHhhhh
Q psy3486 27 KPYTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 27 ~PYsri~i~~ia~~l~l~~~~ve~klsd 54 (222)
.=+...+...||+.+|+|...|...+..
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 3347788999999999999998866553
No 180
>PRK14574 hmsH outer membrane protein; Provisional
Probab=27.94 E-value=1.7e+02 Score=30.78 Aligned_cols=19 Identities=5% Similarity=0.046 Sum_probs=16.9
Q ss_pred EeeccchHHHHHHHHHHHh
Q psy3486 118 RIDQSNYKEMMSRYKQLLL 136 (222)
Q Consensus 118 ~idqg~y~~~l~~y~~LLt 136 (222)
.+++|+|+.|++.+++.+.
T Consensus 44 ~~r~Gd~~~Al~~L~qaL~ 62 (822)
T PRK14574 44 RARAGDTAPVLDYLQEESK 62 (822)
T ss_pred HHhCCCHHHHHHHHHHHHh
Confidence 4678999999999999997
No 181
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=27.92 E-value=75 Score=26.87 Aligned_cols=40 Identities=13% Similarity=0.162 Sum_probs=33.6
Q ss_pred HHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhH
Q psy3486 18 RTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYT 57 (222)
Q Consensus 18 r~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il 57 (222)
|.+.++.++.-...+.+..+|+.||+|.+.|-.=|.++=-
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~ 47 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGI 47 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhc
Confidence 8889999999999999999999999998887755544433
No 182
>cd02684 MIT_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with an n-terminal serine/threonine kinase domain. The molecular function of the MIT domain is unclear.
Probab=27.79 E-value=1.1e+02 Score=22.27 Aligned_cols=36 Identities=14% Similarity=0.204 Sum_probs=27.1
Q ss_pred ccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHH
Q psy3486 121 QSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILD 156 (222)
Q Consensus 121 qg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd 156 (222)
.|+|++|+..|.+=+.+...++...-.++.-+.+-.
T Consensus 19 ~g~y~eA~~lY~~ale~~~~~~k~e~~~~~k~~lr~ 54 (75)
T cd02684 19 RGDAAAALSLYCSALQYFVPALHYETDAQRKEALRQ 54 (75)
T ss_pred hccHHHHHHHHHHHHHHHHHHHhhCCCHHHHHHHHH
Confidence 499999999999999998877755555555554444
No 183
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=27.79 E-value=1.3e+02 Score=19.57 Aligned_cols=45 Identities=20% Similarity=0.288 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhh
Q psy3486 6 IREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLI 53 (222)
Q Consensus 6 I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~kls 53 (222)
|..++..|-..-|.-..+.++. ..+...||+.+|+|.+.|...+.
T Consensus 4 l~~~l~~L~~~~r~i~~l~~~~---g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 4 LQQALAQLPERQREIFLLRYFQ---GMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp HHHHHHCS-HHHHHHHHHHHTS------HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHCCCHHHHHHHHHHHHH---CcCHHHHHHHHCcCHHHHHHHHH
Confidence 4556666666666666666654 44567889999999999986654
No 184
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=27.66 E-value=2.3e+02 Score=27.29 Aligned_cols=87 Identities=20% Similarity=0.282 Sum_probs=45.8
Q ss_pred EeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhh
Q psy3486 118 RIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKL 197 (222)
Q Consensus 118 ~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL 197 (222)
.+.+|+|++|++.|++.+..- +. + .+..++...+....+.+--.+.|+..+ +...++ ......+|.+
T Consensus 713 ~~~~g~~~~A~~~~~~~~~~~-~~---~---~~~~~l~~~~~~~g~~~~A~~~~~~~l---~~~~~~---~~~~~~la~~ 779 (899)
T TIGR02917 713 YLRQKDYPAAIQAYRKALKRA-PS---S---QNAIKLHRALLASGNTAEAVKTLEAWL---KTHPND---AVLRTALAEL 779 (899)
T ss_pred HHHCCCHHHHHHHHHHHHhhC-CC---c---hHHHHHHHHHHHCCCHHHHHHHHHHHH---HhCCCC---HHHHHHHHHH
Confidence 345677777777777766632 11 1 233333333322223222223333332 222222 2344567888
Q ss_pred hhchhhHhHHHHHHHHHHHh
Q psy3486 198 YFDREDFNKLSRILKQLHQS 217 (222)
Q Consensus 198 ~ld~~ey~~l~~~l~~L~~~ 217 (222)
+...|++++....++++.+.
T Consensus 780 ~~~~g~~~~A~~~~~~~~~~ 799 (899)
T TIGR02917 780 YLAQKDYDKAIKHYRTVVKK 799 (899)
T ss_pred HHHCcCHHHHHHHHHHHHHh
Confidence 88888888888888777654
No 185
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=27.31 E-value=4.3e+02 Score=26.06 Aligned_cols=170 Identities=12% Similarity=0.108 Sum_probs=84.5
Q ss_pred HHHHHHHHHHHHHHhhcccccccHh----HHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccc
Q psy3486 11 EDLLRNIRTQVLIKLIKPYTRIHIP----FISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRI 86 (222)
Q Consensus 11 ~~L~~~lr~q~Ll~li~PYsri~i~----~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v 86 (222)
..+..+|+..+..=-++|.+.-++. ++++.-|++.+. .--+.|. +.-.|-.+....+++|-+.- ...+|
T Consensus 160 ~kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi~~~~---~al~~ia-~~s~GslR~al~lLdq~ia~---~~~~I 232 (509)
T PRK14958 160 HKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEENVEFEN---AALDLLA-RAANGSVRDALSLLDQSIAY---GNGKV 232 (509)
T ss_pred HhchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCCCCCH---HHHHHHH-HHcCCcHHHHHHHHHHHHhc---CCCCc
Confidence 4566678888877777777776554 344444553221 1122232 33455555554555554321 24579
Q ss_pred cHhHHHHHhCCChH-HHHHHHHHHhhccce-------eeEeeccc-----hHHHHHHHHHHHhhhhhccCccccHHHHHH
Q psy3486 87 HIPFISRQLNIETS-DVESLLVSLILDNTV-------RGRIDQSN-----YKEMMSRYKQLLLYIKSAVTRNYSEKSINS 153 (222)
Q Consensus 87 ~i~~ia~~l~l~~~-~VE~~L~~~iLdq~i-------k~~idqg~-----y~~~l~~y~~LLtyiksaVtrNysEksIn~ 153 (222)
..+.|.+.+|...+ .+-..+. .+..+-. ..-+..|. ..+.+..+.+++-+ +. +.-...+..- .
T Consensus 233 t~~~V~~~lg~~~~~~i~~ll~-al~~~d~~~~l~~~~~l~~~g~~~~~il~~l~~~~~~~~~~-~~-~~~~~~~~~~-~ 308 (509)
T PRK14958 233 LIADVKTMLGTIEPLLLFDILE-ALAAKAGDRLLGCVTRLVEQGVDFSNALADLLSLLHQIAII-QT-VPEALIENDS-E 308 (509)
T ss_pred CHHHHHHHHCCCCHHHHHHHHH-HHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH-hh-CccccccchH-H
Confidence 99999999996654 3333322 2222111 11112221 12333333333221 10 1000011111 1
Q ss_pred HHHHhhcCCchHHHHHHHHHHHHHHh---cCCCCceeeecc
Q psy3486 154 ILDYISTSKNMELLQDFYETTLEALK---DAKNDRLWFKTN 191 (222)
Q Consensus 154 iLd~vs~s~~~~~l~~fYe~TL~~l~---~~~NeRLWfKtn 191 (222)
-+...+..-+.+.++.||++.+...+ -+.+.|+||-.-
T Consensus 309 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 349 (509)
T PRK14958 309 QLRQLAKLLDREDVQLFYQIGLIGQRDLAYSPTPQTGFEMT 349 (509)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHHHHhccCCChhHHHHHH
Confidence 23333333457788999999887655 556889887643
No 186
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=27.27 E-value=5.1e+02 Score=25.61 Aligned_cols=192 Identities=14% Similarity=0.123 Sum_probs=89.7
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccH----hHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhcccc
Q psy3486 8 EHIEDLLRNIRTQVLIKLIKPYTRIHI----PFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPY 83 (222)
Q Consensus 8 ~hi~~L~~~lr~q~Ll~li~PYsri~i----~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepy 83 (222)
...+.+..+|+..+..--++|.+.-++ ..+++.-|+..+ ..--+.| -+.-.|-++....+++|-+.-. .
T Consensus 154 te~~Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~Egi~i~---~eAL~lI-a~~s~GslR~alslLdqli~y~---~ 226 (491)
T PRK14964 154 TEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENIEHD---EESLKLI-AENSSGSMRNALFLLEQAAIYS---N 226 (491)
T ss_pred CChHHHHHHHHHhheeeecccccHHHHHHHHHHHHHHcCCCCC---HHHHHHH-HHHcCCCHHHHHHHHHHHHHhc---C
Confidence 345667788888886655555554332 223333333211 1111222 2233454444444444433211 1
Q ss_pred ccccHhHHHHHhCCChHHHHHHHHHHhhccceeeE-------eeccc----hHHHHHHHHHHHhhhhhccCc----cccH
Q psy3486 84 TRIHIPFISRQLNIETSDVESLLVSLILDNTVRGR-------IDQSN----YKEMMSRYKQLLLYIKSAVTR----NYSE 148 (222)
Q Consensus 84 s~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~-------idqg~----y~~~l~~y~~LLtyiksaVtr----NysE 148 (222)
..|..+.+.+.+|......=-.+...++++-...- +++|+ +.+++.++..++.+ .++. ..++
T Consensus 227 ~~It~e~V~~llg~~~~~~If~L~~aI~~~d~~~Al~~l~~Ll~~g~~~~i~~~l~~~~~~~~~~---~~~~~~~~~~~~ 303 (491)
T PRK14964 227 NKISEKSVRDLLGCVDKHILEDLVEAILLGDAQSALNVFRELCNTSNPVIILEGMLQIIYEICYF---SITKEIDFLLGE 303 (491)
T ss_pred CCCCHHHHHHHHccCCHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH---hcCccccccCCH
Confidence 36888889888886655432223333332221110 11122 12223333332221 1222 1223
Q ss_pred HHHHHHHHHhhcCCchHHHHHHHHHHHHHHh---cCCCCceeeecch-hhhhhhhchhhHhHHHHHHHHHH
Q psy3486 149 KSINSILDYISTSKNMELLQDFYETTLEALK---DAKNDRLWFKTNT-KLGKLYFDREDFNKLSRILKQLH 215 (222)
Q Consensus 149 ksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~---~~~NeRLWfKtnl-KlakL~ld~~ey~~l~~~l~~L~ 215 (222)
+-.+.+-+ .+. -.+.++.++|++.++.++ .+.|.|+.+-.-+ ++| ...+......+++.|.
T Consensus 304 ~~~~~~~~-~~~-~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~e~~~~rl~----~~~~~~~~~~~~~~~~ 368 (491)
T PRK14964 304 DLITRIKS-LKI-GSTIFLSRLWQMLLKGIQEVKSSTCVKQAAEMMIIRLC----YLSDLPSPQQIIKKIL 368 (491)
T ss_pred HHHHHHHH-HhC-CCHHHHHHHHHHHHHHHHHhccCCCchHHHHHHHHHHH----hcCCCCCHHHHHHHHH
Confidence 22233332 223 568899999999999988 4457777765432 222 2234445555556554
No 187
>PRK03837 transcriptional regulator NanR; Provisional
Probab=27.22 E-value=1.1e+02 Score=26.02 Aligned_cols=43 Identities=9% Similarity=0.054 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHhhcccccc-cHhHHHHHhccchhHHHHhh
Q psy3486 10 IEDLLRNIRTQVLIKLIKPYTRI-HIPFISRQLNIETSDVLIKL 52 (222)
Q Consensus 10 i~~L~~~lr~q~Ll~li~PYsri-~i~~ia~~l~l~~~~ve~kl 52 (222)
-+.+++.|+++.+-.-+.|=+++ ....+|+.+|+|..-|-.-|
T Consensus 15 ~~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL 58 (241)
T PRK03837 15 SEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREAL 58 (241)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 35799999999999999999999 89999999999988876444
No 188
>PRK08445 hypothetical protein; Provisional
Probab=26.90 E-value=44 Score=31.15 Aligned_cols=92 Identities=14% Similarity=0.175 Sum_probs=58.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhh-hccccccc
Q psy3486 8 EHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIK-LIKPYTRI 86 (222)
Q Consensus 8 ~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~-iiepys~v 86 (222)
+++.++++.|++..--.-+..|+.++++++|+..+++.+++-++|-+-=++...+.=+++++..+.+.+.. ..-+=..+
T Consensus 106 e~~~~l~~~Ik~~~p~i~~~a~s~~ei~~~a~~~~~~~~e~L~~LkeAGl~~~~g~glE~~~d~v~~~~~pk~~t~~~~i 185 (348)
T PRK08445 106 EWYENLVSHIAQKYPTITIHGFSAVEIDYIAKISKISIKEVLERLQAKGLSSIPGAGAEILSDRVRDIIAPKKLDSDRWL 185 (348)
T ss_pred HHHHHHHHHHHHHCCCcEEEEccHHHHHHHHHHhCCCHHHHHHHHHHcCCCCCCCCceeeCCHHHHHhhCCCCCCHHHHH
Confidence 56778888888876422246699999999999999998888888888777754443344333223222211 22222335
Q ss_pred cHhHHHHHhCCCh
Q psy3486 87 HIPFISRQLNIET 99 (222)
Q Consensus 87 ~i~~ia~~l~l~~ 99 (222)
+.=..|+.+|++.
T Consensus 186 ~~i~~a~~~Gi~~ 198 (348)
T PRK08445 186 EVHRQAHLIGMKS 198 (348)
T ss_pred HHHHHHHHcCCee
Confidence 5556666666654
No 189
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=26.90 E-value=2.4e+02 Score=20.22 Aligned_cols=59 Identities=17% Similarity=0.287 Sum_probs=39.1
Q ss_pred hhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccch------HHHHHHHHHHHhh
Q psy3486 76 LIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSNY------KEMMSRYKQLLLY 137 (222)
Q Consensus 76 l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~y------~~~l~~y~~LLty 137 (222)
+++.+. ......+.|+...|++...+.+-+..+.-++.|.. +.+.| .++++.|+++...
T Consensus 11 IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~--~~~~Y~lTekG~~~l~~l~~~~~~ 75 (77)
T PF14947_consen 11 ILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK--KDGKYRLTEKGKEFLEELEELIEL 75 (77)
T ss_dssp HHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE--ETTEEEE-HHHHHHHHHHHHHHHH
T ss_pred HHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC--CCCEEEECccHHHHHHHHHHHHHH
Confidence 445565 56777899999999999999999999999999854 33443 3455555555543
No 190
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=26.73 E-value=77 Score=28.33 Aligned_cols=40 Identities=13% Similarity=0.148 Sum_probs=33.6
Q ss_pred HHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhh
Q psy3486 16 NIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP 55 (222)
Q Consensus 16 ~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~ 55 (222)
.-|-+.++++++...+|+++.+|+.||+|...|..-|..+
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~L 55 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFL 55 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHH
Confidence 4578889999999989999999999999998877655443
No 191
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=26.52 E-value=1.9e+02 Score=19.65 Aligned_cols=44 Identities=14% Similarity=0.209 Sum_probs=32.7
Q ss_pred hccccccc-cHhHHHHHhCCChHHHHHHHHHHhhccceeeEeecc
Q psy3486 79 LIKPYTRI-HIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQS 122 (222)
Q Consensus 79 iiepys~v-~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg 122 (222)
-++|=+++ -...+|+.+|++...|..-+..+.-.+.+...-..|
T Consensus 17 ~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~~G 61 (64)
T PF00392_consen 17 RLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPGRG 61 (64)
T ss_dssp SS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE
T ss_pred CCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECCce
Confidence 45666777 788899999999999999888888888877654443
No 192
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=26.51 E-value=1.2e+02 Score=20.01 Aligned_cols=31 Identities=16% Similarity=0.205 Sum_probs=22.2
Q ss_pred HHHHhhccccc-ccHhHHHHHhccchhHHHHh
Q psy3486 21 VLIKLIKPYTR-IHIPFISRQLNIETSDVLIK 51 (222)
Q Consensus 21 ~Ll~li~PYsr-i~i~~ia~~l~l~~~~ve~k 51 (222)
.+++.+..-.. +.+..||+.+|+|.+.|..-
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~ 38 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRL 38 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHH
Confidence 45555555555 79999999999998886643
No 193
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=26.48 E-value=99 Score=26.33 Aligned_cols=40 Identities=15% Similarity=0.302 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHH
Q psy3486 10 IEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVL 49 (222)
Q Consensus 10 i~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve 49 (222)
-+.+|+.||+..+-.-+.|=+++.-..||+.+|+|..-|-
T Consensus 18 ~~~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVR 57 (230)
T COG1802 18 ADQVYEELREAILSGELAPGERLSEEELAEELGVSRTPVR 57 (230)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHH
Confidence 4678999999999999999999999999999999877655
No 194
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=26.38 E-value=2e+02 Score=28.25 Aligned_cols=103 Identities=13% Similarity=0.102 Sum_probs=57.9
Q ss_pred HhCCChHHHHHHHHHHhhccceeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHH
Q psy3486 94 QLNIETSDVESLLVSLILDNTVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYET 173 (222)
Q Consensus 94 ~l~l~~~~VE~~L~~~iLdq~ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~ 173 (222)
...++.++-+. -...++..=...+.+|+|++|+++|++.+... |.. -.|+ |.-.-|.. -.+.+---+.|+.
T Consensus 115 ~~~~~~~~~~~--~a~~~k~~G~~~~~~~~~~~Ai~~y~~al~~~-p~~-~~~~----n~a~~~~~-l~~~~~Ai~~~~~ 185 (615)
T TIGR00990 115 VANLSEEERKK--YAAKLKEKGNKAYRNKDFNKAIKLYSKAIECK-PDP-VYYS----NRAACHNA-LGDWEKVVEDTTA 185 (615)
T ss_pred cccCCHHHHHH--HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-Cch-HHHH----HHHHHHHH-hCCHHHHHHHHHH
Confidence 34555544332 23456666666789999999999999999854 420 0111 11111221 1233222333333
Q ss_pred HHHHHhcCCCCceeeecchhhhhhhhchhhHhHHHHHH
Q psy3486 174 TLEALKDAKNDRLWFKTNTKLGKLYFDREDFNKLSRIL 211 (222)
Q Consensus 174 TL~~l~~~~NeRLWfKtnlKlakL~ld~~ey~~l~~~l 211 (222)
.++. +.. +.++...+|..|...|+|+....-+
T Consensus 186 al~l--~p~----~~~a~~~~a~a~~~lg~~~eA~~~~ 217 (615)
T TIGR00990 186 ALEL--DPD----YSKALNRRANAYDGLGKYADALLDL 217 (615)
T ss_pred HHHc--CCC----CHHHHHHHHHHHHHcCCHHHHHHHH
Confidence 3331 222 3566677999999999998775433
No 195
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=26.28 E-value=80 Score=27.96 Aligned_cols=34 Identities=12% Similarity=0.230 Sum_probs=30.9
Q ss_pred HHHHHHHHhhcccccccHhHHHHHhccchhHHHH
Q psy3486 17 IRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLI 50 (222)
Q Consensus 17 lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~ 50 (222)
=|.+.|+.+++-...+++..+|+.|++|...|-.
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRR 38 (252)
T PRK10906 5 QRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRR 38 (252)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHH
Confidence 4888999999999999999999999999988765
No 196
>COG3860 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.20 E-value=48 Score=25.54 Aligned_cols=18 Identities=39% Similarity=0.547 Sum_probs=16.1
Q ss_pred cCccccHHHHHHHHHHhh
Q psy3486 142 VTRNYSEKSINSILDYIS 159 (222)
Q Consensus 142 VtrNysEksIn~iLd~vs 159 (222)
-.|+|||+-+|.+|..+.
T Consensus 43 ~~r~YsEkeVN~ii~ryh 60 (89)
T COG3860 43 NERQYSEKEVNLIIKRYH 60 (89)
T ss_pred cccccCHHHHHHHHHHhC
Confidence 478999999999999876
No 197
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=26.18 E-value=1.3e+02 Score=24.56 Aligned_cols=43 Identities=14% Similarity=0.220 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhh
Q psy3486 9 HIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 9 hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd 54 (222)
.++.|=..-|+=.+++.+ .....+.||+.+|+|+..|.+.+..
T Consensus 124 ~l~~Lp~~~R~v~~L~~~---~g~s~~EIA~~lgis~~tVk~~l~r 166 (178)
T PRK12529 124 LLDTLRPRVKQAFLMATL---DGMKQKDIAQALDIALPTVKKYIHQ 166 (178)
T ss_pred HHHhCCHHHHHHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 333333333444444443 5667889999999999999977763
No 198
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=26.12 E-value=43 Score=22.41 Aligned_cols=21 Identities=14% Similarity=0.335 Sum_probs=18.1
Q ss_pred EeeccchHHHHHHHHHHHhhh
Q psy3486 118 RIDQSNYKEMMSRYKQLLLYI 138 (222)
Q Consensus 118 ~idqg~y~~~l~~y~~LLtyi 138 (222)
.+.+|+|++|+++|++.+.+-
T Consensus 13 ~~~~~~~~~A~~~~~~ai~~~ 33 (69)
T PF13414_consen 13 YFQQGDYEEAIEYFEKAIELD 33 (69)
T ss_dssp HHHTTHHHHHHHHHHHHHHHS
T ss_pred HHHcCCHHHHHHHHHHHHHcC
Confidence 456899999999999999964
No 199
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=26.12 E-value=1.2e+02 Score=23.93 Aligned_cols=26 Identities=27% Similarity=0.217 Sum_probs=21.5
Q ss_pred cccccHhHHHHHhccchhHHHHhhhh
Q psy3486 29 YTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 29 Ysri~i~~ia~~l~l~~~~ve~klsd 54 (222)
|.......||+.+|+|...|.+.+.-
T Consensus 120 ~~g~s~~EIA~~lgis~~tV~~~l~R 145 (160)
T PRK09642 120 LEEKSYQEIALQEKIEVKTVEMKLYR 145 (160)
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 46677889999999999999876653
No 200
>PF11817 Foie-gras_1: Foie gras liver health family 1; InterPro: IPR021773 Mutating the gene foie gras in zebrafish has been shown to affect development; the mutants develop large, lipid-filled hepatocytes in the liver, resembling those in individuals with fatty liver disease []. Foie-gras protein is long and has several well-defined domains though none of them has a known function. We have annotated this one as the first []. THe C terminus of this region contains TPR repeats.
Probab=25.86 E-value=72 Score=27.93 Aligned_cols=57 Identities=19% Similarity=0.345 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHhcCCCCceeeecchhhhhhhhchhhHhHHHHHHHHHHHhhhcc
Q psy3486 165 ELLQDFYETTLEALKDAKNDRLWFKTNTKLGKLYFDREDFNKLSRILKQLHQSCQMK 221 (222)
Q Consensus 165 ~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~ld~~ey~~l~~~l~~L~~~c~~~ 221 (222)
...-..++...+.++..+..|+--.....+|.-|+..|+|++..+.++.+..+...|
T Consensus 155 ~~iI~lL~~A~~~f~~~~~~R~~~~l~~~~A~ey~~~g~~~~A~~~l~~~~~~yr~e 211 (247)
T PF11817_consen 155 KLIIELLEKAYEQFKKYGQNRMASYLSLEMAEEYFRLGDYDKALKLLEPAASSYRRE 211 (247)
T ss_pred HHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhC
Confidence 344455556666666677789999999999999999999999999999987766654
No 201
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=25.68 E-value=80 Score=27.97 Aligned_cols=37 Identities=14% Similarity=0.280 Sum_probs=32.5
Q ss_pred HHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhh
Q psy3486 16 NIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKL 52 (222)
Q Consensus 16 ~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~kl 52 (222)
.-|.+.|+++++.-..|+++.+|+.||+|...|-.=|
T Consensus 4 ~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL 40 (253)
T COG1349 4 EERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDL 40 (253)
T ss_pred HHHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhH
Confidence 3488999999999999999999999999998877533
No 202
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=25.68 E-value=3e+02 Score=23.91 Aligned_cols=69 Identities=14% Similarity=0.219 Sum_probs=38.9
Q ss_pred cccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChH
Q psy3486 27 KPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETS 100 (222)
Q Consensus 27 ~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~ 100 (222)
.+...++++.+|+.+|+|.+.+-....+- +..-....+++.-...-..++. .+...|+.||..+|.+..
T Consensus 195 ~~~~~isl~~lA~~~~lS~~~l~r~Fk~~-~G~tp~~~l~~~Rl~~A~~lL~----~t~~sI~eIA~~~GF~d~ 263 (290)
T PRK10572 195 HLASEFDIESVAQHVCLSPSRLAHLFRQQ-LGISVLRWREDQRISRAKLLLQ----TTRMPIATIGRNVGYDDQ 263 (290)
T ss_pred cccCCCCHHHHHHHHCCCHHHHHHHHHHH-HCcCHHHHHHHHHHHHHHHHHH----cCCCCHHHHHHHhCCCCH
Confidence 45578999999999999987644332222 1111222222111111122222 367888888888888743
No 203
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=25.63 E-value=3e+02 Score=26.54 Aligned_cols=25 Identities=20% Similarity=0.316 Sum_probs=13.7
Q ss_pred hhhhhhhhchhhHhHHHHHHHHHHH
Q psy3486 192 TKLGKLYFDREDFNKLSRILKQLHQ 216 (222)
Q Consensus 192 lKlakL~ld~~ey~~l~~~l~~L~~ 216 (222)
..++.++.+.|+++....+++.+.+
T Consensus 673 ~~l~~~~~~~~~~~~A~~~~~~~~~ 697 (899)
T TIGR02917 673 IGLAQLLLAAKRTESAKKIAKSLQK 697 (899)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 4455555566666555555555443
No 204
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=25.63 E-value=1.6e+02 Score=26.79 Aligned_cols=68 Identities=13% Similarity=0.122 Sum_probs=44.4
Q ss_pred cccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChH
Q psy3486 27 KPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETS 100 (222)
Q Consensus 27 ~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~ 100 (222)
.|-..+.++.+|+.+|+|...+..++.+. ..-+...+.++ ++.. -.+.+. .+...|..||..+|.+..
T Consensus 193 ~~~~~~sl~~lA~~~gmS~stl~R~Fk~~--g~s~~~~~~~~--Rl~~-A~~lL~-~~~~sI~~IA~~~GY~s~ 260 (291)
T PRK15186 193 DISRKWALKDISDSLYMSCSTLKRKLKQE--NTSFSEVYLNA--RMNK-ATKLLR-NSEYNITRVAYMCGYDSA 260 (291)
T ss_pred CccCCCCHHHHHHHHCcCHHHHHHHHHHc--CCCHHHHHHHH--HHHH-HHHHHH-cCCCCHHHHHHHhCCCCH
Confidence 35567899999999999999988888774 34455555432 3322 112222 345678888888887653
No 205
>PRK09191 two-component response regulator; Provisional
Probab=25.47 E-value=1.2e+02 Score=25.52 Aligned_cols=46 Identities=11% Similarity=0.188 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhh
Q psy3486 6 IREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 6 I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd 54 (222)
+...++.|-..-|+-.+++.++.+| ...||+.+|+|...|.+.+..
T Consensus 82 l~~~l~~L~~~~r~v~~l~~~~~~s---~~eIA~~l~~s~~tV~~~l~r 127 (261)
T PRK09191 82 AERRLAGLTPLPRQAFLLTALEGFS---VEEAAEILGVDPAEAEALLDD 127 (261)
T ss_pred HHHHHHhCCHHHhHHHHHHHHhcCC---HHHHHHHHCCCHHHHHHHHHH
Confidence 4445555555556666676666665 889999999999999988764
No 206
>COG4699 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.38 E-value=1.5e+02 Score=24.08 Aligned_cols=53 Identities=25% Similarity=0.349 Sum_probs=35.9
Q ss_pred cchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCC------chHHHHHHHHHHHH
Q psy3486 122 SNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSK------NMELLQDFYETTLE 176 (222)
Q Consensus 122 g~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~------~~~~l~~fYe~TL~ 176 (222)
.++++|+++|+++-.=++ +--.||..++ +.+..+.-+.. =-+.+|+|+..+|=
T Consensus 31 ~d~~~alkyYqq~w~~l~-~~~p~y~skk-~ll~afwn~eD~~wCEDCeedLQ~fhsliLl 89 (120)
T COG4699 31 SDFYDALKYYQQLWFRLK-VNFPNYVSKK-DLLTAFWNNEDMEWCEDCEEDLQQFHSLILL 89 (120)
T ss_pred hHHHHHHHHHHHHHHHHH-HhCcccccch-hHHHHHhcchhhhHHHHHHHHHHHHHHHhhh
Confidence 578999999999988663 3455676665 33444443321 15679999998875
No 207
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=25.30 E-value=1.3e+02 Score=24.56 Aligned_cols=27 Identities=15% Similarity=0.351 Sum_probs=22.0
Q ss_pred cccccHhHHHHHhccchhHHHHhhhhh
Q psy3486 29 YTRIHIPFISRQLNIETSDVLIKLIKP 55 (222)
Q Consensus 29 Ysri~i~~ia~~l~l~~~~ve~klsd~ 55 (222)
|.....+.||+.+|+|...|.+.|...
T Consensus 145 ~~g~s~~EIA~~lgis~~tV~~~l~Ra 171 (191)
T PRK12520 145 WLELETEEICQELQITATNAWVLLYRA 171 (191)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 456778999999999999999776543
No 208
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=25.20 E-value=1.7e+02 Score=22.78 Aligned_cols=87 Identities=17% Similarity=0.276 Sum_probs=47.0
Q ss_pred eeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhh
Q psy3486 115 VRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKL 194 (222)
Q Consensus 115 ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKl 194 (222)
-+..+++|+|++|.+.|++++... ...+...-+--+ |-.+- +-+.=|+..+..|+...+...---...-+
T Consensus 55 A~~~~~~g~~~~A~~~l~~~~~~~---~d~~l~~~a~l~-LA~~~------~~~~~~d~Al~~L~~~~~~~~~~~~~~~~ 124 (145)
T PF09976_consen 55 AKAAYEQGDYDEAKAALEKALANA---PDPELKPLARLR-LARIL------LQQGQYDEALATLQQIPDEAFKALAAELL 124 (145)
T ss_pred HHHHHHCCCHHHHHHHHHHHHhhC---CCHHHHHHHHHH-HHHHH------HHcCCHHHHHHHHHhccCcchHHHHHHHH
Confidence 344578899999999999998833 111121111111 11111 11222444444444332222222244568
Q ss_pred hhhhhchhhHhHHHHHH
Q psy3486 195 GKLYFDREDFNKLSRIL 211 (222)
Q Consensus 195 akL~ld~~ey~~l~~~l 211 (222)
|.+|+..|++++....-
T Consensus 125 Gdi~~~~g~~~~A~~~y 141 (145)
T PF09976_consen 125 GDIYLAQGDYDEARAAY 141 (145)
T ss_pred HHHHHHCCCHHHHHHHH
Confidence 99999999998876543
No 209
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=25.15 E-value=60 Score=21.04 Aligned_cols=21 Identities=29% Similarity=0.379 Sum_probs=15.2
Q ss_pred ccHhHHHHHhccchhHHHHhh
Q psy3486 32 IHIPFISRQLNIETSDVLIKL 52 (222)
Q Consensus 32 i~i~~ia~~l~l~~~~ve~kl 52 (222)
..+..||+.+|+|...|-.-|
T Consensus 22 ~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 22 MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp --HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 678999999999999876544
No 210
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=25.04 E-value=1.4e+02 Score=24.37 Aligned_cols=45 Identities=11% Similarity=0.214 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhh
Q psy3486 7 REHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 7 ~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd 54 (222)
...++.|-..-|+=..+.+++- .++..||+.+|+|...|...+..
T Consensus 134 ~~~l~~L~~~~r~i~~l~~~~g---~s~~EIA~~lgis~~tV~~~l~R 178 (189)
T PRK09648 134 RELLDTLPEKQREILILRVVVG---LSAEETAEAVGSTPGAVRVAQHR 178 (189)
T ss_pred HHHHHhCCHHHHHHHHHHHHcC---CCHHHHHHHHCCCHHHHHHHHHH
Confidence 3444444444455555556664 45889999999999998876643
No 211
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=24.95 E-value=1.2e+02 Score=25.15 Aligned_cols=34 Identities=21% Similarity=0.308 Sum_probs=25.0
Q ss_pred HHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhh
Q psy3486 18 RTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 18 r~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd 54 (222)
+....+..+.=| +.+.||+.+|+|+..|+..|.-
T Consensus 141 ~~~v~l~~~~Gl---s~~EIA~~lgiS~~tV~r~l~~ 174 (185)
T PF07638_consen 141 RRVVELRFFEGL---SVEEIAERLGISERTVRRRLRR 174 (185)
T ss_pred HHHHHHHHHCCC---CHHHHHHHHCcCHHHHHHHHHH
Confidence 444445555544 7888999999999999987753
No 212
>PF05527 DUF758: Domain of unknown function (DUF758) ; InterPro: IPR008477 This is a family of eukaryotic proteins with unknown function, which are induced by tumour necrosis factor.; PDB: 3F4M_A.
Probab=24.83 E-value=1.9e+02 Score=25.21 Aligned_cols=113 Identities=14% Similarity=0.176 Sum_probs=47.8
Q ss_pred hhhhhHhhhhhhhhhhhhhhhh-------------hhhhhhccccccccHhHHHHHhCCChHHHHH--HHHHHhhc----
Q psy3486 52 LIKPYTRIHIPFISRQLNIETS-------------DVLIKLIKPYTRIHIPFISRQLNIETSDVES--LLVSLILD---- 112 (222)
Q Consensus 52 lsd~il~~hl~~l~d~~~~~~~-------------~~l~~iiepys~v~i~~ia~~l~l~~~~VE~--~L~~~iLd---- 112 (222)
...+|+|..-..++|.+..++. .||+|++ |.|.-+.+.=.++.++... ++..+.-.
T Consensus 26 ~ak~fIddtsselLD~ly~l~K~~t~~kkeA~ki~KniIKi~-----vKigvl~rn~qf~~eEl~~~~~fr~k~~~~amt 100 (186)
T PF05527_consen 26 VAKMFIDDTSSELLDELYRLLKEYTGNKKEAEKIIKNIIKIV-----VKIGVLYRNNQFSDEELALAEKFRKKFHQLAMT 100 (186)
T ss_dssp -------HHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHH-----HHHHHHHHTT---HHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHhcCchHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH-----HHhheeeecCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4567888888888874422221 3333332 5555565555566655541 12111111
Q ss_pred ----cceeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHH
Q psy3486 113 ----NTVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYE 172 (222)
Q Consensus 113 ----q~ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe 172 (222)
..+.=.+|..-..+++.--+++|. +.|+|--++||+..|=.-.+-=.+.+|+..+|.
T Consensus 101 ~iSF~eV~fTfD~~~L~~~L~ec~~~L~---~lv~~HLT~KS~~Ri~~vF~~f~~~efL~~lf~ 161 (186)
T PF05527_consen 101 AISFYEVDFTFDRNYLSKLLKECRDLLH---QLVEPHLTPKSHGRIDHVFNFFSDPEFLDALFS 161 (186)
T ss_dssp HHHHTSTTS---HHHHHHHHHHHHHHHH---HHHTTTS-HHHHHHHHHHHHHHT-HHHHHHHTS
T ss_pred HhhhcccchhhhHHHHHHHHHHHHHHHH---HHHHHhCChhhHHHHHHHHHhhCChHHHHHHhC
Confidence 112223343334444443444433 567777888887655432222236777777776
No 213
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=24.81 E-value=59 Score=21.52 Aligned_cols=23 Identities=13% Similarity=0.348 Sum_probs=15.9
Q ss_pred hhhhhhhchhhHhHHHHHHHHHH
Q psy3486 193 KLGKLYFDREDFNKLSRILKQLH 215 (222)
Q Consensus 193 KlakL~ld~~ey~~l~~~l~~L~ 215 (222)
.+|..+++.|+|++..+.++++.
T Consensus 2 ~~a~~~~~~g~~~~A~~~~~~~l 24 (65)
T PF13432_consen 2 ALARALYQQGDYDEAIAAFEQAL 24 (65)
T ss_dssp HHHHHHHHCTHHHHHHHHHHHHH
T ss_pred hHHHHHHHcCCHHHHHHHHHHHH
Confidence 46677777777777777766654
No 214
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=24.76 E-value=1.5e+02 Score=22.95 Aligned_cols=25 Identities=8% Similarity=-0.081 Sum_probs=20.6
Q ss_pred ccccHhHHHHHhccchhHHHHhhhh
Q psy3486 30 TRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 30 sri~i~~ia~~l~l~~~~ve~klsd 54 (222)
.-.+...||+.+|+|...|.+.+..
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4566899999999999999876654
No 215
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=24.68 E-value=1.9e+02 Score=24.02 Aligned_cols=54 Identities=17% Similarity=0.094 Sum_probs=38.8
Q ss_pred chHHHHHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhh
Q psy3486 3 DPFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISR 66 (222)
Q Consensus 3 D~~I~~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d 66 (222)
||.|+..+..++..-=-+++-.++ +=+-++-+.||+.+|++... +++++..+++
T Consensus 1 ~~~~~~~~~~~~g~~~v~Vl~aL~-~~~~~tdEeLa~~Lgi~~~~---------VRk~L~~L~e 54 (158)
T TIGR00373 1 EELLNEVVGRAAEEEVGLVLFSLG-IKGEFTDEEISLELGIKLNE---------VRKALYALYD 54 (158)
T ss_pred ChHHHHHHHHHcChhHHHHHHHHh-ccCCCCHHHHHHHHCCCHHH---------HHHHHHHHHH
Confidence 688888888888754444444333 45569999999999997665 5566666666
No 216
>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=24.49 E-value=1.2e+02 Score=22.79 Aligned_cols=36 Identities=14% Similarity=0.200 Sum_probs=26.3
Q ss_pred HHHHHhhcccccccHhHHHHHhccchhHHHHhhhhh
Q psy3486 20 QVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP 55 (222)
Q Consensus 20 q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~ 55 (222)
..|++++.-=.-|..+.+|.++|+|.++|..-|.++
T Consensus 27 r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~ 62 (77)
T PF12324_consen 27 RPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAM 62 (77)
T ss_dssp HHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-
T ss_pred HHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhC
Confidence 347788887888999999999999999999877654
No 217
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=24.43 E-value=1.5e+02 Score=23.66 Aligned_cols=45 Identities=16% Similarity=0.146 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhh
Q psy3486 8 EHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP 55 (222)
Q Consensus 8 ~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~ 55 (222)
..++.|-..-|+=.+++++ .......||+.+|+|...|.+.+..-
T Consensus 114 ~~l~~L~~~~r~vl~L~~~---~g~s~~EIA~~lgis~~tV~~~l~ra 158 (173)
T PRK09645 114 DALAQLSPEHRAVLVRSYY---RGWSTAQIAADLGIPEGTVKSRLHYA 158 (173)
T ss_pred HHHHhCCHHHHHHHHHHHH---cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3444444444554455554 46668999999999999998766543
No 218
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=24.43 E-value=1.2e+02 Score=20.31 Aligned_cols=53 Identities=17% Similarity=0.305 Sum_probs=36.9
Q ss_pred CchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhhhhchhhHhHHHHHHHHHHHhhhc
Q psy3486 162 KNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKLYFDREDFNKLSRILKQLHQSCQM 220 (222)
Q Consensus 162 ~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~ld~~ey~~l~~~l~~L~~~c~~ 220 (222)
++.+-..+.++..+.. ...+-.+|+. +|.+++..|+|+.....+....+.|.+
T Consensus 9 ~~~~~A~~~~~~~l~~--~p~~~~~~~~----~a~~~~~~g~~~~A~~~l~~~l~~~p~ 61 (73)
T PF13371_consen 9 EDYEEALEVLERALEL--DPDDPELWLQ----RARCLFQLGRYEEALEDLERALELSPD 61 (73)
T ss_pred CCHHHHHHHHHHHHHh--CcccchhhHH----HHHHHHHhccHHHHHHHHHHHHHHCCC
Confidence 3444445555555553 2334455554 899999999999999999988887754
No 219
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=24.27 E-value=2.9e+02 Score=27.54 Aligned_cols=49 Identities=14% Similarity=0.213 Sum_probs=28.4
Q ss_pred hhhhhhhhhhhhhhhhhhhh------ccccccccHhHHHHHhCCChHHHHHHHHHHhhcc
Q psy3486 60 HIPFISRQLNIETSDVLIKL------IKPYTRIHIPFISRQLNIETSDVESLLVSLILDN 113 (222)
Q Consensus 60 hl~~l~d~~~~~~~~~l~~i------iepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq 113 (222)
.|...+++|+.. ++.+++. -+|+| +..||+.+|++.+.|-. +-.++|++
T Consensus 440 ~L~~aL~~L~eR-Er~VI~lRyGL~~~e~~T---L~EIa~~lGVSrERVRQ-Ie~kAL~K 494 (509)
T PRK05901 440 QLQEVLETLSER-EAGVIRMRFGLTDGQPKT---LDEIGQVYGVTRERIRQ-IESKTLRK 494 (509)
T ss_pred HHHHHHhhCCHH-HHHHHHHHhhccCCCCCC---HHHHHHHHCCCHHHHHH-HHHHHHHH
Confidence 344444444333 2444443 14554 77889999999987764 44445543
No 220
>PRK09954 putative kinase; Provisional
Probab=24.20 E-value=94 Score=28.30 Aligned_cols=45 Identities=18% Similarity=0.333 Sum_probs=35.9
Q ss_pred hhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceee
Q psy3486 73 SDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRG 117 (222)
Q Consensus 73 ~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~ 117 (222)
++.|+++++=-.++....||+.+|++...|...+..+--++.+++
T Consensus 5 ~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~ 49 (362)
T PRK09954 5 EKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKG 49 (362)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCC
Confidence 345666666667899999999999999999988888776666653
No 221
>COG1060 ThiH Thiamine biosynthesis enzyme ThiH and related uncharacterized enzymes [Coenzyme metabolism / General function prediction only]
Probab=24.17 E-value=1.2e+02 Score=28.73 Aligned_cols=89 Identities=21% Similarity=0.170 Sum_probs=68.2
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccc-----
Q psy3486 8 EHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP----- 82 (222)
Q Consensus 8 ~hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiep----- 82 (222)
.+..+++++|++...---+..||-.++.++|...++|.++|-++|-+.=++....+--+ .++.-.-+++-|
T Consensus 123 ~y~~~~~~~ik~~~p~~~i~a~s~~ei~~~~~~~~~s~~E~l~~Lk~aGldsmpg~~ae----il~e~vr~~~~p~K~~~ 198 (370)
T COG1060 123 EYYEELFRTIKEEFPDLHIHALSAGEILFLAREGGLSYEEVLKRLKEAGLDSMPGGGAE----ILSEEVRKIHCPPKKSP 198 (370)
T ss_pred HHHHHHHHHHHHhCcchhhcccCHHHhHHHHhccCCCHHHHHHHHHHcCCCcCcCccee----echHHHHHhhCCCCCCH
Confidence 48889999999876666688999999999999999999999999987766666655443 333333344444
Q ss_pred cccccHhHHHHHhCCChH
Q psy3486 83 YTRIHIPFISRQLNIETS 100 (222)
Q Consensus 83 ys~v~i~~ia~~l~l~~~ 100 (222)
--++++-..|..+|+|..
T Consensus 199 ~~wle~~~~Ah~lGI~~t 216 (370)
T COG1060 199 EEWLEIHERAHRLGIPTT 216 (370)
T ss_pred HHHHHHHHHHHHcCCCcc
Confidence 457888899999999863
No 222
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=24.14 E-value=1.6e+02 Score=23.51 Aligned_cols=44 Identities=5% Similarity=0.024 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhh
Q psy3486 9 HIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP 55 (222)
Q Consensus 9 hi~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~ 55 (222)
.++.|-..=|+=.++.++ ...+.+.||+.+|+|...|.+.|...
T Consensus 109 ~l~~L~~~~r~v~~l~~~---~g~s~~eIA~~lgis~~tV~~~l~Ra 152 (164)
T PRK12547 109 ALNLLSADQREAIILIGA---SGFSYEDAAAICGCAVGTIKSRVSRA 152 (164)
T ss_pred HHHhCCHHHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 333333333443444444 55668999999999999999777654
No 223
>PRK09483 response regulator; Provisional
Probab=24.10 E-value=85 Score=25.13 Aligned_cols=39 Identities=21% Similarity=0.145 Sum_probs=24.5
Q ss_pred HHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhh
Q psy3486 18 RTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQ 67 (222)
Q Consensus 18 r~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~ 67 (222)
|+..+++++. .-.....||+.+++|...|+ .|+..+++-
T Consensus 152 rE~~vl~~~~--~G~~~~~Ia~~l~is~~TV~---------~~~~~i~~K 190 (217)
T PRK09483 152 RELQIMLMIT--KGQKVNEISEQLNLSPKTVN---------SYRYRMFSK 190 (217)
T ss_pred HHHHHHHHHH--CCCCHHHHHHHhCCCHHHHH---------HHHHHHHHH
Confidence 4445555553 23455689999999888866 455555543
No 224
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=23.99 E-value=1.8e+02 Score=19.43 Aligned_cols=37 Identities=14% Similarity=0.103 Sum_probs=24.4
Q ss_pred HHHHHHhhc-ccccccHhHHHHHhccchhHHHHhhhhh
Q psy3486 19 TQVLIKLIK-PYTRIHIPFISRQLNIETSDVLIKLIKP 55 (222)
Q Consensus 19 ~q~Ll~li~-PYsri~i~~ia~~l~l~~~~ve~klsd~ 55 (222)
+..++..+. +...+++..||+.++++.+.|-.-+..+
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L 42 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKL 42 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 445666666 8999999999999999988766444443
No 225
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=23.97 E-value=3.5e+02 Score=23.06 Aligned_cols=73 Identities=15% Similarity=0.091 Sum_probs=0.0
Q ss_pred cHhHHHHHhccchhHH-------------------------------------HHhhhhhhHhhhhhhhhhhhhhhhhhh
Q psy3486 33 HIPFISRQLNIETSDV-------------------------------------LIKLIKPYTRIHIPFISRQLNIETSDV 75 (222)
Q Consensus 33 ~i~~ia~~l~l~~~~v-------------------------------------e~klsd~il~~hl~~l~d~~~~~~~~~ 75 (222)
....||+.+|++.++| +..+.+--....+...+++|...--+-
T Consensus 113 ~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v 192 (236)
T PRK06986 113 TDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDHQDEDPLQQLEDEELREALVEAIESLPEREQLV 192 (236)
T ss_pred CHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHH
Q ss_pred hhhhccccccccHhHHHHHhCCChHHHHHHHH
Q psy3486 76 LIKLIKPYTRIHIPFISRQLNIETSDVESLLV 107 (222)
Q Consensus 76 l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~ 107 (222)
+.... +.......||+.+|++...|...+.
T Consensus 193 l~l~~--~~g~s~~EIA~~lgis~~tV~~~~~ 222 (236)
T PRK06986 193 LSLYY--QEELNLKEIGAVLGVSESRVSQIHS 222 (236)
T ss_pred HHhHh--ccCCCHHHHHHHHCCCHHHHHHHHH
No 226
>PLN03077 Protein ECB2; Provisional
Probab=23.72 E-value=1.3e+02 Score=30.81 Aligned_cols=93 Identities=12% Similarity=0.109 Sum_probs=61.5
Q ss_pred cceeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecch
Q psy3486 113 NTVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNT 192 (222)
Q Consensus 113 q~ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnl 192 (222)
-+|.+....|+.++|++.+++|.. ..+..| +-+.+.+|...+.+...+--.++|+...+.. +-.-...+.-
T Consensus 559 ~lI~~~~~~G~~~~A~~lf~~M~~---~g~~Pd--~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~----gi~P~~~~y~ 629 (857)
T PLN03077 559 ILLTGYVAHGKGSMAVELFNRMVE---SGVNPD--EVTFISLLCACSRSGMVTQGLEYFHSMEEKY----SITPNLKHYA 629 (857)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHH---cCCCCC--cccHHHHHHHHhhcChHHHHHHHHHHHHHHh----CCCCchHHHH
Confidence 356677788889999999998875 233322 3457788887776655555555555444221 1222345666
Q ss_pred hhhhhhhchhhHhHHHHHHHHH
Q psy3486 193 KLGKLYFDREDFNKLSRILKQL 214 (222)
Q Consensus 193 KlakL~ld~~ey~~l~~~l~~L 214 (222)
-+..+|...|.++++.++++++
T Consensus 630 ~lv~~l~r~G~~~eA~~~~~~m 651 (857)
T PLN03077 630 CVVDLLGRAGKLTEAYNFINKM 651 (857)
T ss_pred HHHHHHHhCCCHHHHHHHHHHC
Confidence 7888888889998888888764
No 227
>PHA01083 hypothetical protein
Probab=23.64 E-value=2.5e+02 Score=23.72 Aligned_cols=60 Identities=10% Similarity=0.117 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhh-ccccccccH
Q psy3486 10 IEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKL-IKPYTRIHI 88 (222)
Q Consensus 10 i~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~i-iepys~v~i 88 (222)
.++|+|...++ ++++.-..+|+.||++.+.|-+ .-+= -.|.+.-++
T Consensus 3 tnkLLda~K~a--------~~~~sdkqLA~~LGVs~q~IS~-------------------------~R~G~r~~i~de~A 49 (149)
T PHA01083 3 TNKLLDAYKKA--------KNYVQYKQIAHDLGVSPQKISK-------------------------MRTGVRTYISDEEA 49 (149)
T ss_pred HHHHHHHHHHH--------HhhccHHHHHHHhCCCHHHHHH-------------------------HHcCCCCCCCHHHH
Confidence 45555555544 5678889999999999776431 1111 346777888
Q ss_pred hHHHHHhCCChHHH
Q psy3486 89 PFISRQLNIETSDV 102 (222)
Q Consensus 89 ~~ia~~l~l~~~~V 102 (222)
-++|+.+|++++++
T Consensus 50 ~~LAe~aGiDp~ea 63 (149)
T PHA01083 50 IFLAESAGIDPEIA 63 (149)
T ss_pred HHHHHHhCCCHHHH
Confidence 89999999998653
No 228
>PRK15185 transcriptional regulator HilD; Provisional
Probab=23.58 E-value=1.8e+02 Score=27.09 Aligned_cols=67 Identities=12% Similarity=0.154 Sum_probs=43.4
Q ss_pred ccccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChH
Q psy3486 28 PYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETS 100 (222)
Q Consensus 28 PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~ 100 (222)
|-..+.++.+|+.+|+|+..+..++.. . ..-+...+... +++.-. +.+. .+...|..||..+|.+..
T Consensus 219 ~~~~~SledLA~~lgmS~~tL~R~FK~-~-G~S~~~yl~~~--Ri~~A~-~LL~-~t~~sIseIA~~~GFss~ 285 (309)
T PRK15185 219 PSRQWKLTDVADHIFMSTSTLKRKLAE-E-GTSFSDIYLSA--RMNQAA-KLLR-IGNHNVNAVALKCGYDST 285 (309)
T ss_pred ccCCCCHHHHHHHHCcCHHHHHHHHHH-c-CCCHHHHHHHH--HHHHHH-HHHH-cCCCCHHHHHHHhCCCCH
Confidence 457789999999999999998877654 2 44444444432 332222 2222 355678888888888653
No 229
>PRK07003 DNA polymerase III subunits gamma and tau; Validated
Probab=23.53 E-value=4.1e+02 Score=28.28 Aligned_cols=33 Identities=15% Similarity=0.133 Sum_probs=22.8
Q ss_pred HHhhcCCchHHHHHHHHHHHHHHhcC---CCCceee
Q psy3486 156 DYISTSKNMELLQDFYETTLEALKDA---KNDRLWF 188 (222)
Q Consensus 156 d~vs~s~~~~~l~~fYe~TL~~l~~~---~NeRLWf 188 (222)
...+..-..+.++.||++.++..++- .+.|+-|
T Consensus 313 ~~~a~~~s~~~l~~~~qi~l~g~~el~~ap~~~~~~ 348 (830)
T PRK07003 313 RRFAELLSPEQVQLFYQIATVGRGELGLAPDEYAGF 348 (830)
T ss_pred HHHHHhCCHHHHHHHHHHHHhHHHHhhcCCCHHHHH
Confidence 33444456889999999999987743 3555544
No 230
>KOG2758|consensus
Probab=23.46 E-value=1.2e+02 Score=29.17 Aligned_cols=86 Identities=17% Similarity=0.219 Sum_probs=58.9
Q ss_pred hhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccch-----HH
Q psy3486 52 LIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSNY-----KE 126 (222)
Q Consensus 52 lsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~y-----~~ 126 (222)
+.|.||-.-+...++.-..++..--+|| -++|.|+-+|..+|++.++.|.-.+..|-+..+.+.+|..-= ..
T Consensus 319 ~nDfFLva~l~~F~E~ARl~ifEtfCRI---HqcIti~mLA~kLnm~~eeaErwivnlIr~~rl~AkidSklg~Vvmg~~ 395 (432)
T KOG2758|consen 319 VNDFFLVALLDEFLENARLLIFETFCRI---HQCITIDMLADKLNMDPEEAERWIVNLIRTARLDAKIDSKLGHVVMGHP 395 (432)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHHHHH---HHheeHHHHHHHhcCCHHHHHHHHHHHHHHhhhhhhhccccCceeecCC
Confidence 4678876666666553333333333443 256789999999999999999888999999888888875321 12
Q ss_pred HHHHHHHHHhhhhh
Q psy3486 127 MMSRYKQLLLYIKS 140 (222)
Q Consensus 127 ~l~~y~~LLtyiks 140 (222)
...-|+|+..-+||
T Consensus 396 ~~s~~qQ~ie~tks 409 (432)
T KOG2758|consen 396 TVSPHQQLIEKTKS 409 (432)
T ss_pred CCCHHHHHHHhccc
Confidence 34567777776654
No 231
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=23.35 E-value=3.4e+02 Score=22.98 Aligned_cols=27 Identities=19% Similarity=0.183 Sum_probs=18.8
Q ss_pred cccHhHHHHHhCCChHHHHHHHHHHhhc
Q psy3486 85 RIHIPFISRQLNIETSDVESLLVSLILD 112 (222)
Q Consensus 85 ~v~i~~ia~~l~l~~~~VE~~L~~~iLd 112 (222)
...+..||+.+|++...|-. +...+++
T Consensus 199 ~~t~~eIA~~lgis~~~V~~-~~~~al~ 225 (231)
T TIGR02885 199 DKTQTEVANMLGISQVQVSR-LEKKVLK 225 (231)
T ss_pred CCCHHHHHHHHCcCHHHHHH-HHHHHHH
Confidence 34578899999999888763 4444444
No 232
>PF15469 Sec5: Exocyst complex component Sec5
Probab=23.28 E-value=1.9e+02 Score=23.93 Aligned_cols=64 Identities=16% Similarity=0.314 Sum_probs=39.0
Q ss_pred hccceeeEeeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCC
Q psy3486 111 LDNTVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAK 182 (222)
Q Consensus 111 Ldq~ik~~idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~ 182 (222)
|-..+.-++.+|+|+.++..|++.-....+... .-..+.+|.+-|. ..+++|-+.+.+.|.+..
T Consensus 89 LP~~L~~~i~~~dy~~~i~dY~kak~l~~~~~~---~~~vf~~v~~eve-----~ii~~~r~~l~~~L~~~~ 152 (182)
T PF15469_consen 89 LPSNLRECIKKGDYDQAINDYKKAKSLFEKYKQ---QVPVFQKVWSEVE-----KIIEEFREKLWEKLLSPP 152 (182)
T ss_pred hHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhhh---hHHHHHHHHHHHH-----HHHHHHHHHHHHHHhCCC
Confidence 334555667889999999999988886643211 3344555555442 234566666666555443
No 233
>KOG2114|consensus
Probab=23.27 E-value=1.4e+02 Score=31.78 Aligned_cols=64 Identities=8% Similarity=0.277 Sum_probs=45.7
Q ss_pred HHHHhCCChHHHHHHHHHHhhccceeeEeeccchHHHHHHHHHHHhhhhhc-cC-ccccHHHHHHHHHHhh
Q psy3486 91 ISRQLNIETSDVESLLVSLILDNTVRGRIDQSNYKEMMSRYKQLLLYIKSA-VT-RNYSEKSINSILDYIS 159 (222)
Q Consensus 91 ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~y~~~l~~y~~LLtyiksa-Vt-rNysEksIn~iLd~vs 159 (222)
+|+..+++.+.++..... --.-.+..|+|++|+++|-+-++++-|+ |- |--..+.|-+..+|..
T Consensus 356 LAk~~~~d~d~~~~i~~k-----Ygd~Ly~Kgdf~~A~~qYI~tI~~le~s~Vi~kfLdaq~IknLt~YLe 421 (933)
T KOG2114|consen 356 LAKSQHLDEDTLAEIHRK-----YGDYLYGKGDFDEATDQYIETIGFLEPSEVIKKFLDAQRIKNLTSYLE 421 (933)
T ss_pred HHHhcCCCHHHHHHHHHH-----HHHHHHhcCCHHHHHHHHHHHcccCChHHHHHHhcCHHHHHHHHHHHH
Confidence 899999999988863222 1122356799999999999999998654 54 4444566777777665
No 234
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=23.26 E-value=55 Score=21.16 Aligned_cols=23 Identities=22% Similarity=0.365 Sum_probs=19.9
Q ss_pred cccccccHhHHHHHhccchhHHH
Q psy3486 27 KPYTRIHIPFISRQLNIETSDVL 49 (222)
Q Consensus 27 ~PYsri~i~~ia~~l~l~~~~ve 49 (222)
++|..+.+..||+..|+|...+-
T Consensus 12 ~G~~~~s~~~Ia~~~gvs~~~~y 34 (47)
T PF00440_consen 12 KGYEAVSIRDIARRAGVSKGSFY 34 (47)
T ss_dssp HHTTTSSHHHHHHHHTSCHHHHH
T ss_pred hCHHhCCHHHHHHHHccchhhHH
Confidence 68999999999999999876543
No 235
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=23.18 E-value=1.1e+02 Score=25.90 Aligned_cols=42 Identities=21% Similarity=0.291 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhh
Q psy3486 11 EDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKL 52 (222)
Q Consensus 11 ~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~kl 52 (222)
+.+++.|+++.+-.-++|=+++.-..+|+.||+|..-|-.-|
T Consensus 14 e~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL 55 (221)
T PRK11414 14 LQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREAL 55 (221)
T ss_pred HHHHHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHH
Confidence 679999999999999999999999999999999988766433
No 236
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=23.16 E-value=3.9e+02 Score=21.29 Aligned_cols=18 Identities=22% Similarity=0.340 Sum_probs=11.5
Q ss_pred HHHHhCCChHHHHHHHHH
Q psy3486 91 ISRQLNIETSDVESLLVS 108 (222)
Q Consensus 91 ia~~l~l~~~~VE~~L~~ 108 (222)
||+..|.+.++|...-..
T Consensus 78 IA~l~~~~e~~vr~~R~~ 95 (123)
T PF02787_consen 78 IARLWGVSEEEVRELRKE 95 (123)
T ss_dssp HHHHHTS-HHHHHHHHHH
T ss_pred HHhccCCCHHHHHHHHHH
Confidence 777778888777754333
No 237
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=23.15 E-value=2.7e+02 Score=27.03 Aligned_cols=79 Identities=19% Similarity=0.227 Sum_probs=46.1
Q ss_pred eeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhhh
Q psy3486 119 IDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKLY 198 (222)
Q Consensus 119 idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~ 198 (222)
++.|.+++|.+..++-|+ +++.+. +-..++.+-.+++. -+++.-+ +.++..+++- ..+.-||.|+
T Consensus 274 i~l~~~~~A~~~i~~~Lk-------~~~D~~-L~~~~~~l~~~d~~-~l~k~~e---~~l~~h~~~p---~L~~tLG~L~ 338 (400)
T COG3071 274 IRLGDHDEAQEIIEDALK-------RQWDPR-LCRLIPRLRPGDPE-PLIKAAE---KWLKQHPEDP---LLLSTLGRLA 338 (400)
T ss_pred HHcCChHHHHHHHHHHHH-------hccChh-HHHHHhhcCCCCch-HHHHHHH---HHHHhCCCCh---hHHHHHHHHH
Confidence 345666666665554443 455555 55555555433332 2333333 2334445555 3445599999
Q ss_pred hchhhHhHHHHHHH
Q psy3486 199 FDREDFNKLSRILK 212 (222)
Q Consensus 199 ld~~ey~~l~~~l~ 212 (222)
+.+++|++.+.-++
T Consensus 339 ~k~~~w~kA~~~le 352 (400)
T COG3071 339 LKNKLWGKASEALE 352 (400)
T ss_pred HHhhHHHHHHHHHH
Confidence 99999999997776
No 238
>PRK09954 putative kinase; Provisional
Probab=23.03 E-value=1e+02 Score=28.13 Aligned_cols=43 Identities=16% Similarity=0.223 Sum_probs=33.7
Q ss_pred HHHHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhh
Q psy3486 19 TQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHI 61 (222)
Q Consensus 19 ~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl 61 (222)
.+.++++++=-.++..+.||+.||+|...|...+..+-=+..+
T Consensus 5 ~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i 47 (362)
T PRK09954 5 EKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRI 47 (362)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 3456677776679999999999999999999888866544443
No 239
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=22.83 E-value=1e+02 Score=20.84 Aligned_cols=28 Identities=18% Similarity=0.377 Sum_probs=19.8
Q ss_pred HHHhhcccccccHhHHHHHhccchhHHH
Q psy3486 22 LIKLIKPYTRIHIPFISRQLNIETSDVL 49 (222)
Q Consensus 22 Ll~li~PYsri~i~~ia~~l~l~~~~ve 49 (222)
+++.+..-....+..||+.+|+|.+.+-
T Consensus 15 Il~~L~~~~~~t~~ela~~l~~~~~t~s 42 (61)
T PF12840_consen 15 ILRLLASNGPMTVSELAEELGISQSTVS 42 (61)
T ss_dssp HHHHHHHCSTBEHHHHHHHHTS-HHHHH
T ss_pred HHHHHhcCCCCCHHHHHHHHCCCHHHHH
Confidence 3444456677888999999999877644
No 240
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=22.65 E-value=2.7e+02 Score=29.91 Aligned_cols=86 Identities=10% Similarity=0.165 Sum_probs=55.1
Q ss_pred eeccchHHHHHHHHHHHhhhhhccCccccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhhh
Q psy3486 119 IDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKLY 198 (222)
Q Consensus 119 idqg~y~~~l~~y~~LLtyiksaVtrNysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~ 198 (222)
..+|++++|++.|++.+..- |. ...+..++...+....+.+--.+.|+..++. ..+. ..+...+|.+|
T Consensus 614 ~~~g~~~~A~~~y~~al~~~-P~-----~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~----~p~~--~~~~~~la~~~ 681 (1157)
T PRK11447 614 QQRGDYAAARAAYQRVLTRE-PG-----NADARLGLIEVDIAQGDLAAARAQLAKLPAT----ANDS--LNTQRRVALAW 681 (1157)
T ss_pred HHcCCHHHHHHHHHHHHHhC-CC-----CHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc----CCCC--hHHHHHHHHHH
Confidence 45688999999999988832 32 3456666666555555555455555543331 1111 12345678888
Q ss_pred hchhhHhHHHHHHHHHHH
Q psy3486 199 FDREDFNKLSRILKQLHQ 216 (222)
Q Consensus 199 ld~~ey~~l~~~l~~L~~ 216 (222)
...|++++....++.+.+
T Consensus 682 ~~~g~~~eA~~~~~~al~ 699 (1157)
T PRK11447 682 AALGDTAAAQRTFNRLIP 699 (1157)
T ss_pred HhCCCHHHHHHHHHHHhh
Confidence 899999988888887765
No 241
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=22.65 E-value=2.2e+02 Score=18.26 Aligned_cols=33 Identities=18% Similarity=0.152 Sum_probs=22.2
Q ss_pred HHHHHHHHHhhcccccccHhHHHHHhccchhHHHHh
Q psy3486 16 NIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIK 51 (222)
Q Consensus 16 ~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~k 51 (222)
.+...++-.+.+. ..+..+|+.+|+|.+.|..-
T Consensus 15 ~~~~~i~~~~~~~---~s~~~vA~~~~vs~~TV~ri 47 (52)
T PF13542_consen 15 RLEQYILKLLRES---RSFKDVARELGVSWSTVRRI 47 (52)
T ss_pred HHHHHHHHHHhhc---CCHHHHHHHHCCCHHHHHHH
Confidence 3344444444333 67889999999999988743
No 242
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=22.57 E-value=1.8e+02 Score=25.32 Aligned_cols=64 Identities=14% Similarity=0.184 Sum_probs=42.3
Q ss_pred ccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccc-cccccHhHHHHHhCCChH
Q psy3486 32 IHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKP-YTRIHIPFISRQLNIETS 100 (222)
Q Consensus 32 i~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiep-ys~v~i~~ia~~l~l~~~ 100 (222)
+.++.||+.+|+|...+.....+. ..-....+. +.+++.- .+.+.| .+...|..||...|.+..
T Consensus 215 ls~~~lA~~~giS~r~L~r~Fk~~--G~T~~~yi~--~~RL~~A-~~lL~~~~~~~sI~eIA~~~GF~d~ 279 (302)
T PRK09685 215 LRPEWIAGELGISVRSLYRLFAEQ--GLVVAQYIR--NRRLDRC-ADDLRPAADDEKITSIAYKWGFSDS 279 (302)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHc--CCCHHHHHH--HHHHHHH-HHHhhhhccCCCHHHHHHHhCCCCH
Confidence 789999999999988776665542 333444443 2334322 233366 577889999999998753
No 243
>PRK05685 fliS flagellar protein FliS; Validated
Probab=22.56 E-value=2.2e+02 Score=22.83 Aligned_cols=48 Identities=31% Similarity=0.432 Sum_probs=37.1
Q ss_pred hcCCchHHHHHHHHHHHHHHhcCCCCceeeecchhhhhhhhchhhHh-------HHHHHHHHHHHhhhc
Q psy3486 159 STSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKLGKLYFDREDFN-------KLSRILKQLHQSCQM 220 (222)
Q Consensus 159 s~s~~~~~l~~fYe~TL~~l~~~~NeRLWfKtnlKlakL~ld~~ey~-------~l~~~l~~L~~~c~~ 220 (222)
.++.+.+++--+|+-.+..+ +.|+..++.+++. |+..+|.+|..+...
T Consensus 20 ~tasp~~Li~mLydgai~~l--------------~~A~~ai~~~~~~~~~~~l~ka~~Ii~eL~~sLd~ 74 (132)
T PRK05685 20 SSASPHKLIQMLYEGALSFL--------------AQAKLAIEQGDIEAKGEYLSKAINIINGLRNSLDM 74 (132)
T ss_pred hcCCHHHHHHHHHHHHHHHH--------------HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 35678889999999998854 4677778878877 777888888877653
No 244
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=22.50 E-value=2e+02 Score=18.86 Aligned_cols=46 Identities=15% Similarity=0.242 Sum_probs=35.4
Q ss_pred hhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeec
Q psy3486 76 LIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQ 121 (222)
Q Consensus 76 l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idq 121 (222)
++..|.-+-.+....||+.++++...+-..+..+.-++.|.-.-+.
T Consensus 8 iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~ 53 (59)
T PF01047_consen 8 ILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDP 53 (59)
T ss_dssp HHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCC
Confidence 3445555666889999999999999999888888888887766554
No 245
>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=22.32 E-value=1.7e+02 Score=18.80 Aligned_cols=18 Identities=17% Similarity=0.253 Sum_probs=11.2
Q ss_pred ccHhHHHHHhccchhHHH
Q psy3486 32 IHIPFISRQLNIETSDVL 49 (222)
Q Consensus 32 i~i~~ia~~l~l~~~~ve 49 (222)
+....+|+.+|+|.+.|-
T Consensus 10 ls~~~la~~~gis~~~i~ 27 (55)
T PF01381_consen 10 LSQKELAEKLGISRSTIS 27 (55)
T ss_dssp S-HHHHHHHHTS-HHHHH
T ss_pred CCHHHHHHHhCCCcchhH
Confidence 345678888888776654
No 246
>PHA00428 tail tubular protein A
Probab=22.13 E-value=1.5e+02 Score=25.78 Aligned_cols=40 Identities=25% Similarity=0.436 Sum_probs=32.7
Q ss_pred HHHHHHHHHhhcC---------CchHHHHHHHHHHHHHHhcCCCCceeeecc
Q psy3486 149 KSINSILDYISTS---------KNMELLQDFYETTLEALKDAKNDRLWFKTN 191 (222)
Q Consensus 149 ksIn~iLd~vs~s---------~~~~~l~~fYe~TL~~l~~~~NeRLWfKtn 191 (222)
+++|.+|..++.+ +++.....+|+.+...+++.. =||.|.
T Consensus 9 davN~~L~~IGe~pV~SLd~~~~~aa~a~~il~~~~~~vl~~g---W~Fnt~ 57 (193)
T PHA00428 9 DAVNDILASIGESPVTSLDETNPDVANARRILEEINRQLQSEG---WWFNTE 57 (193)
T ss_pred HHHHHHHHHhccCccCccccCCHHHHHHHHHHHHHHHHHHHcC---ceeccc
Confidence 5788999988854 368899999999999999664 788875
No 247
>KOG0164|consensus
Probab=22.09 E-value=2.2e+02 Score=30.15 Aligned_cols=102 Identities=16% Similarity=0.155 Sum_probs=57.9
Q ss_pred HHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeE
Q psy3486 39 RQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGR 118 (222)
Q Consensus 39 ~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~ 118 (222)
..+|.++++||+-++=.=---||+-+-=. .--+.+.+.-. -++.++|+.++++.+++|.-|...-.--.=...
T Consensus 254 ~vIgFs~eEVe~v~~iiAavLhLGNv~f~--~~ed~~~~~~~-----~~l~~~aell~v~~del~~aL~~Rtvaa~~e~v 326 (1001)
T KOG0164|consen 254 RVIGFSEEEVESVLSIIAAVLHLGNVEFA--DNEDSSGIVNG-----AQLKYIAELLSVTGDELERALTSRTVAAGGEIV 326 (1001)
T ss_pred HHcCCCHHHHHHHHHHHHHHHhccceEEe--ecCcccccchh-----HHHHHHHHHHcCCHHHHHHHHHHHHHHhccchh
Confidence 45788999999877654444455433210 00011111111 578899999999999999766554332211111
Q ss_pred eeccch--------HHHHHHHHHHHhhhhhccCcccc
Q psy3486 119 IDQSNY--------KEMMSRYKQLLLYIKSAVTRNYS 147 (222)
Q Consensus 119 idqg~y--------~~~l~~y~~LLtyiksaVtrNys 147 (222)
.++.+- .-|-.-|.+|.+||.+.+++.-.
T Consensus 327 ~k~hn~~qA~YaRDAlAKaiY~RlF~Wiv~rIn~~i~ 363 (1001)
T KOG0164|consen 327 LKQHNVEQASYARDALAKAIYSRLFTWIVNRINRSIE 363 (1001)
T ss_pred hccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhee
Confidence 122221 12336799999999776664433
No 248
>PF04192 Utp21: Utp21 specific WD40 associated putative domain ; InterPro: IPR007319 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp21 is a component of the SSU processome, which is required for pre-18S rRNA processing. It interacts with Utp18 [].; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=22.02 E-value=4.3e+02 Score=23.46 Aligned_cols=55 Identities=25% Similarity=0.496 Sum_probs=34.3
Q ss_pred eccchHHHHHHHHHHHhhhhhccC---cccc------HHHHHHHHHHhh----cCCchHHHHHHHHHHHHH
Q psy3486 120 DQSNYKEMMSRYKQLLLYIKSAVT---RNYS------EKSINSILDYIS----TSKNMELLQDFYETTLEA 177 (222)
Q Consensus 120 dqg~y~~~l~~y~~LLtyiksaVt---rNys------EksIn~iLd~vs----~s~~~~~l~~fYe~TL~~ 177 (222)
..++|+++++|.+.|-. |+|. |+-+ ..-+..+++++. +..|.+++|.+..+.|+.
T Consensus 122 ~~~dy~~~~~~LkslsP---S~iDlEIRsL~~~~~~~~~~l~~Fl~~l~~~L~~~~dfElvQa~l~vFLk~ 189 (237)
T PF04192_consen 122 ESEDYSEFLEYLKSLSP---SAIDLEIRSLSPESGGSYEELVSFLRFLTYRLKSRRDFELVQAYLSVFLKV 189 (237)
T ss_pred ccccHHHHHHHHHhCCh---hHHHHHHHhccCccCCcHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 33666666666665533 3332 3333 555666666544 457999999999888875
No 249
>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=21.77 E-value=1.3e+02 Score=18.47 Aligned_cols=26 Identities=15% Similarity=0.377 Sum_probs=19.1
Q ss_pred cHhHHHHHhccchhHHHHhhhhhhHh
Q psy3486 33 HIPFISRQLNIETSDVLIKLIKPYTR 58 (222)
Q Consensus 33 ~i~~ia~~l~l~~~~ve~klsd~il~ 58 (222)
.++.+|+..|.|.+++-..+.+.+++
T Consensus 13 ~l~~~a~~~g~s~s~~ir~ai~~~l~ 38 (39)
T PF01402_consen 13 RLDELAKELGRSRSELIREAIREYLE 38 (39)
T ss_dssp HHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCcCHHHHHHHHHHHHHh
Confidence 46789999999998876665555443
No 250
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=21.77 E-value=4.1e+02 Score=24.44 Aligned_cols=75 Identities=17% Similarity=0.153 Sum_probs=0.0
Q ss_pred cHhHHHHHhccchhHH-------------------------------------HHhhhhhhHhhhhhhhhhhhhhhhhhh
Q psy3486 33 HIPFISRQLNIETSDV-------------------------------------LIKLIKPYTRIHIPFISRQLNIETSDV 75 (222)
Q Consensus 33 ~i~~ia~~l~l~~~~v-------------------------------------e~klsd~il~~hl~~l~d~~~~~~~~~ 75 (222)
+...+|+.+|++.++| +..+...-+...+...+++|+...-+.
T Consensus 191 t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~e~~~~L~~aL~~L~~~~R~v 270 (325)
T PRK05657 191 SAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREV 270 (325)
T ss_pred CHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHH
Q ss_pred hhhh--ccccccccHhHHHHHhCCChHHHHHHHH
Q psy3486 76 LIKL--IKPYTRIHIPFISRQLNIETSDVESLLV 107 (222)
Q Consensus 76 l~~i--iepys~v~i~~ia~~l~l~~~~VE~~L~ 107 (222)
|... +.=|-......||+.+|++...|.+.+.
T Consensus 271 l~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~ 304 (325)
T PRK05657 271 LARRFGLLGYEAATLEDVAREIGLTRERVRQIQV 304 (325)
T ss_pred HHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHH
No 251
>PF08928 DUF1910: Domain of unknown function (DUF1910); InterPro: IPR015024 This domain is found in hypothetical bacterial proteins.
Probab=21.42 E-value=2.6e+02 Score=21.40 Aligned_cols=34 Identities=15% Similarity=0.368 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhhcCCchHHHHHHHHHHHHHHhcC
Q psy3486 148 EKSINSILDYISTSKNMELLQDFYETTLEALKDA 181 (222)
Q Consensus 148 EksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~~~ 181 (222)
...+..++-.+|.|.+.+-+...|...+++++..
T Consensus 50 ~~~~~~l~~~YS~G~~i~~l~~~~~~~l~~~e~~ 83 (117)
T PF08928_consen 50 DYYLELLIAKYSAGDSIEELKPYYPNILDYFEEI 83 (117)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHh
Confidence 4567788889999999999999999999999863
No 252
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=21.33 E-value=1.3e+02 Score=24.35 Aligned_cols=42 Identities=10% Similarity=0.146 Sum_probs=31.1
Q ss_pred HHHHhhcccccccHhHHHHHhccchhHHHHhhhhhhHhhhhh
Q psy3486 21 VLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIP 62 (222)
Q Consensus 21 ~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd~il~~hl~ 62 (222)
.|++.++==.|...+.||+.+|+|++.|...+..+.=..-+.
T Consensus 13 ~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 13 GILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 344444444899999999999999999988777666555554
No 253
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=21.33 E-value=2.9e+02 Score=21.50 Aligned_cols=66 Identities=11% Similarity=0.134 Sum_probs=35.5
Q ss_pred ccccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChH
Q psy3486 30 TRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETS 100 (222)
Q Consensus 30 sri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~ 100 (222)
..+.++.+|+.+|+|+..+...+...+=.. +...+.. ..++.-...+.. +...|..||...|.+..
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s-~~~~l~~--~Rl~~A~~~L~~--t~~~i~eIA~~~Gf~s~ 89 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKKETGHS-LGQYIRS--RKMTEIAQKLKE--SNEPILYLAERYGFESQ 89 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHCcC-HHHHHHH--HHHHHHHHHHHc--CCCCHHHHHHHhCCCCH
Confidence 458999999999999888775544332111 1111111 112111111222 35567777777776643
No 254
>KOG2004|consensus
Probab=21.19 E-value=1.6e+02 Score=31.14 Aligned_cols=48 Identities=17% Similarity=0.174 Sum_probs=29.0
Q ss_pred ccHhHHHHHhCCChHHHHHHHHHHhhccceeeEeeccchHHHHHHHHHHHhhh
Q psy3486 86 IHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSNYKEMMSRYKQLLLYI 138 (222)
Q Consensus 86 v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~idqg~y~~~l~~y~~LLtyi 138 (222)
=|+..|.++||++. +.++.++.++...+.. .+-.+.+++...+=|+=.
T Consensus 320 eQlk~IKkeLg~e~-Ddkd~~~~~~~er~~~----~~~P~~v~kv~~eEl~kL 367 (906)
T KOG2004|consen 320 EQLKAIKKELGIEK-DDKDALVEKFRERIKS----LKMPDHVLKVIDEELTKL 367 (906)
T ss_pred HHHHHHHHhhCCCc-cchhhHHHHHHHHhhh----ccCcHHHHHHHHHHHHHH
Confidence 35888999999875 3344455555554443 355666666555544434
No 255
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=21.12 E-value=1.1e+02 Score=24.07 Aligned_cols=34 Identities=18% Similarity=0.267 Sum_probs=24.4
Q ss_pred HHHHHHhhcccccccHhHHHHHhccchhHHHHhhh
Q psy3486 19 TQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLI 53 (222)
Q Consensus 19 ~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~kls 53 (222)
.+.++.+.- +.....+.||+.+|+|.+.|.+.+.
T Consensus 115 ~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ 148 (162)
T TIGR02983 115 QRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLS 148 (162)
T ss_pred HHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHH
Confidence 344443332 6678899999999999999886544
No 256
>PRK14959 DNA polymerase III subunits gamma and tau; Provisional
Probab=21.04 E-value=5.1e+02 Score=26.55 Aligned_cols=171 Identities=12% Similarity=0.148 Sum_probs=82.4
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccHh-HHHH---Hhc--cchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhcc
Q psy3486 8 EHIEDLLRNIRTQVLIKLIKPYTRIHIP-FISR---QLN--IETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK 81 (222)
Q Consensus 8 ~hi~~L~~~lr~q~Ll~li~PYsri~i~-~ia~---~l~--l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iie 81 (222)
.+...+..+|+..+..--|.|++.-++. ++.+ .-| ++.+.++ .+. ..-.|-.+..-.++++.+ ..
T Consensus 157 t~~~kll~TI~SRcq~i~F~pLs~~eL~~~L~~il~~egi~id~eal~-----lIA-~~s~GdlR~Al~lLeqll-~~-- 227 (624)
T PRK14959 157 TEPHKFPVTIVSRCQHFTFTRLSEAGLEAHLTKVLGREGVDYDPAAVR-----LIA-RRAAGSVRDSMSLLGQVL-AL-- 227 (624)
T ss_pred CChhhhhHHHHhhhhccccCCCCHHHHHHHHHHHHHHcCCCCCHHHHH-----HHH-HHcCCCHHHHHHHHHHHH-Hh--
Confidence 3445677788877765556666655544 2222 223 3333222 222 233344443333444432 11
Q ss_pred ccccccHhHHHHHhCCChHH-HHHHHHHHh----------hccceeeEeeccc-hHHHHHHHHHHHhhhhhccCc-----
Q psy3486 82 PYTRIHIPFISRQLNIETSD-VESLLVSLI----------LDNTVRGRIDQSN-YKEMMSRYKQLLLYIKSAVTR----- 144 (222)
Q Consensus 82 pys~v~i~~ia~~l~l~~~~-VE~~L~~~i----------Ldq~ik~~idqg~-y~~~l~~y~~LLtyiksaVtr----- 144 (222)
.=..|.+++|.+.++....+ +.+.+..+. +...++...+-.. .+.++.+|+.|+-+ +.+..+
T Consensus 228 g~~~It~d~V~~~lg~~~~e~vfeLl~AL~~~D~~aal~~l~~Ll~~g~d~~~iL~~Ll~~~RdLLl~-k~~~~~~~~~l 306 (624)
T PRK14959 228 GESRLTIDGARGVLGLAGQELFLRLMEALAAQDCLGVANVVRELLDRGVDMGFFLRELVATWRNLFML-RQAGEAALASL 306 (624)
T ss_pred cCCCcCHHHHHHHhCCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHh-hhccccchhhc
Confidence 22368889999999876554 433322211 1111111111111 56677888888864 222211
Q ss_pred cccHHHHHHHHHHhhcCCchHHHHHHHHHHHHHHh---cCCCCceeee
Q psy3486 145 NYSEKSINSILDYISTSKNMELLQDFYETTLEALK---DAKNDRLWFK 189 (222)
Q Consensus 145 NysEksIn~iLd~vs~s~~~~~l~~fYe~TL~~l~---~~~NeRLWfK 189 (222)
-..+.-+..+.... ..-....+..+++.++++-. .+.|-||.+-
T Consensus 307 ~i~~~~~~~~~~~A-~~~s~~~L~~~l~~il~~~~~l~~n~n~rl~lE 353 (624)
T PRK14959 307 DLPEDEARQWLGWA-KRFEPAHIHACWQMTLEGQRRVLTSLEPAMALE 353 (624)
T ss_pred ccCHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHHhCCCHHHHHH
Confidence 12333333333322 22346677888888887754 4445555543
No 257
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=20.92 E-value=1.8e+02 Score=20.60 Aligned_cols=34 Identities=18% Similarity=0.199 Sum_probs=28.6
Q ss_pred cccHhHHHHHhCCChHHHHHHHHHHhhccceeeE
Q psy3486 85 RIHIPFISRQLNIETSDVESLLVSLILDNTVRGR 118 (222)
Q Consensus 85 ~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~ 118 (222)
.+.++.||+.+|+|...|-..+..+.-.+.+...
T Consensus 20 ~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 20 GLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence 5889999999999999999988887767777543
No 258
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=20.90 E-value=1.8e+02 Score=25.16 Aligned_cols=42 Identities=17% Similarity=0.158 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHHhhcccccc-cHhHHHHHhccchhHHHHh
Q psy3486 10 IEDLLRNIRTQVLIKLIKPYTRI-HIPFISRQLNIETSDVLIK 51 (222)
Q Consensus 10 i~~L~~~lr~q~Ll~li~PYsri-~i~~ia~~l~l~~~~ve~k 51 (222)
.+.+|+.|++..+-.-++|=+++ .-..+|+.||+|..-|-.-
T Consensus 11 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREA 53 (257)
T PRK10225 11 YQEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREA 53 (257)
T ss_pred HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHH
Confidence 46899999999999999999999 6999999999998876533
No 259
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=20.79 E-value=1.1e+02 Score=21.38 Aligned_cols=22 Identities=27% Similarity=0.332 Sum_probs=17.4
Q ss_pred cHhHHHHHhCCChHHHHHHHHH
Q psy3486 87 HIPFISRQLNIETSDVESLLVS 108 (222)
Q Consensus 87 ~i~~ia~~l~l~~~~VE~~L~~ 108 (222)
....||+.+|++.++|...+..
T Consensus 22 t~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHHHHh
Confidence 4567999999999999986664
No 260
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.78 E-value=1.7e+02 Score=23.85 Aligned_cols=26 Identities=8% Similarity=0.158 Sum_probs=22.1
Q ss_pred cccccHhHHHHHhccchhHHHHhhhh
Q psy3486 29 YTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 29 Ysri~i~~ia~~l~l~~~~ve~klsd 54 (222)
|...+.+.||+.+|+|...|.+.+..
T Consensus 145 ~~g~s~~eIA~~lgis~~tV~~~l~r 170 (184)
T PRK12539 145 LEGLSVAEAATRSGMSESAVKVSVHR 170 (184)
T ss_pred HcCCcHHHHHHHHCcCHHHHHHHHHH
Confidence 35788999999999999999977654
No 261
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=20.78 E-value=1.8e+02 Score=23.92 Aligned_cols=42 Identities=5% Similarity=0.078 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHHhhcccccccHhHHHHHhccchhHHHHhhhh
Q psy3486 10 IEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 10 i~~L~~~lr~q~Ll~li~PYsri~i~~ia~~l~l~~~~ve~klsd 54 (222)
++.|=..-|+=.+++.+ .-.+...||+.+|+|...|...++.
T Consensus 109 l~~Lp~~~R~v~~L~~~---~g~s~~EIA~~Lgis~~tV~~~l~R 150 (182)
T PRK12540 109 LDKLPQDQREALILVGA---SGFSYEDAAAICGCAVGTIKSRVNR 150 (182)
T ss_pred HHhCCHHHHHHhhHHHH---cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33333333444444444 5556888999999999999876653
No 262
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=20.75 E-value=2.2e+02 Score=19.50 Aligned_cols=38 Identities=24% Similarity=0.089 Sum_probs=31.4
Q ss_pred ccccccHhHHHHHhCCChHHHHHHHHHHhhccceeeEe
Q psy3486 82 PYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRI 119 (222)
Q Consensus 82 pys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~i 119 (222)
-......+.||+.+|+|...|-.-+..+.-++.|...-
T Consensus 19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 19 KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 34566788899999999999999999988888876554
No 263
>PRK14951 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.73 E-value=6e+02 Score=25.92 Aligned_cols=169 Identities=8% Similarity=0.040 Sum_probs=77.8
Q ss_pred HHHHHHHHHHHHHHhhcccccccH----hHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccc
Q psy3486 11 EDLLRNIRTQVLIKLIKPYTRIHI----PFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRI 86 (222)
Q Consensus 11 ~~L~~~lr~q~Ll~li~PYsri~i----~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v 86 (222)
..+..++++.+..=-++|.+.-++ .++++.-|++.+. .--+.|. ++-.|-++....+++|-+.- -..+|
T Consensus 165 ~kil~TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi~ie~---~AL~~La-~~s~GslR~al~lLdq~ia~---~~~~I 237 (618)
T PRK14951 165 QKVPVTVLSRCLQFNLRPMAPETVLEHLTQVLAAENVPAEP---QALRLLA-RAARGSMRDALSLTDQAIAF---GSGQL 237 (618)
T ss_pred hhhhHHHHHhceeeecCCCCHHHHHHHHHHHHHHcCCCCCH---HHHHHHH-HHcCCCHHHHHHHHHHHHHh---cCCCc
Confidence 345666777766655556555443 2222333443221 1112222 34455555444455554432 24678
Q ss_pred cHhHHHHHhCCChHHHHHHHHHHhhccceeeEe-------eccc-----hHHHHHHHHHHHhhhh-hccCccccHHHHHH
Q psy3486 87 HIPFISRQLNIETSDVESLLVSLILDNTVRGRI-------DQSN-----YKEMMSRYKQLLLYIK-SAVTRNYSEKSINS 153 (222)
Q Consensus 87 ~i~~ia~~l~l~~~~VE~~L~~~iLdq~ik~~i-------dqg~-----y~~~l~~y~~LLtyik-saVtrNysEksIn~ 153 (222)
..+.+.+.+|...++.=..+...+..+-...-+ ..|. .++++.+++.++-+-- +......++.- -.
T Consensus 238 t~~~V~~~Lg~~~~~~i~~LldaL~~~d~~~al~~l~~l~~~G~~~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~ 316 (618)
T PRK14951 238 QEAAVRQMLGSVDRSHVFRLIDALAQGDGRTVVETADELRLNGLSAASTLEEMAAVLQRMAVLQAVPQAAAAATDPE-AA 316 (618)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhCcccccccChHH-HH
Confidence 999999999965433222233333322221111 1111 2344444444443210 00001111111 11
Q ss_pred HHHHhhcCCchHHHHHHHHHHHHHHhcC---CCCcee
Q psy3486 154 ILDYISTSKNMELLQDFYETTLEALKDA---KNDRLW 187 (222)
Q Consensus 154 iLd~vs~s~~~~~l~~fYe~TL~~l~~~---~NeRLW 187 (222)
-+...+..-+.+.++.+|+++++...+- .+.|+=
T Consensus 317 ~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 353 (618)
T PRK14951 317 EVARLAALMPADETQLLYSICLHGRAELGLAPDEYAA 353 (618)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHHHHhccCCCHHHH
Confidence 2223333346889999999999987743 355543
No 264
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=20.60 E-value=1.9e+02 Score=23.37 Aligned_cols=26 Identities=15% Similarity=0.178 Sum_probs=21.4
Q ss_pred cccccHhHHHHHhccchhHHHHhhhh
Q psy3486 29 YTRIHIPFISRQLNIETSDVLIKLIK 54 (222)
Q Consensus 29 Ysri~i~~ia~~l~l~~~~ve~klsd 54 (222)
+...+...||+.+|+|...|...++.
T Consensus 145 ~~g~s~~eIA~~l~is~~tV~~~l~r 170 (184)
T PRK12512 145 VEGASIKETAAKLSMSEGAVRVALHR 170 (184)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 35788899999999999998866553
No 265
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=20.56 E-value=3e+02 Score=27.68 Aligned_cols=29 Identities=10% Similarity=0.245 Sum_probs=20.3
Q ss_pred cccccccHhHHHHHhCCChHHHHHHHHHHhhcc
Q psy3486 81 KPYTRIHIPFISRQLNIETSDVESLLVSLILDN 113 (222)
Q Consensus 81 epys~v~i~~ia~~l~l~~~~VE~~L~~~iLdq 113 (222)
+|+| +..||+.+|++.+.|-. +-.++|++
T Consensus 575 ~~~t---l~ei~~~lgvs~eRVrQ-ie~~al~k 603 (619)
T PRK05658 575 TDHT---LEEVGKQFDVTRERIRQ-IEAKALRK 603 (619)
T ss_pred CCcc---HHHHHHHhCCCHHHHHH-HHHHHHHH
Confidence 4554 78899999999987764 44455543
No 266
>PF12496 BNIP2: Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2; InterPro: IPR022181 This domain family is found in eukaryotes, and is typically between 119 and 133 amino acids in length. There is a conserved HGGY sequence motif. This family is Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2. It interacts with pro- and anti- apoptotic molecules in the cell.
Probab=20.55 E-value=30 Score=28.31 Aligned_cols=10 Identities=50% Similarity=1.198 Sum_probs=8.3
Q ss_pred hhhccccccc
Q psy3486 77 IKLIKPYTRI 86 (222)
Q Consensus 77 ~~iiepys~v 86 (222)
.++||||-||
T Consensus 108 MkvIEPYkrV 117 (127)
T PF12496_consen 108 MKVIEPYKRV 117 (127)
T ss_pred eEecccceee
Confidence 4789999887
No 267
>PRK13500 transcriptional activator RhaR; Provisional
Probab=20.40 E-value=5.4e+02 Score=22.98 Aligned_cols=65 Identities=15% Similarity=0.156 Sum_probs=38.4
Q ss_pred cccHhHHHHHhccchhHHHHhhhhhhHhhhhhhhhhhhhhhhhhhhhhhccccccccHhHHHHHhCCChH
Q psy3486 31 RIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETS 100 (222)
Q Consensus 31 ri~i~~ia~~l~l~~~~ve~klsd~il~~hl~~l~d~~~~~~~~~l~~iiepys~v~i~~ia~~l~l~~~ 100 (222)
.+.++.+|+.+|+|+..+-....+-. ..-....+.++....-..+++ .|...|..||..+|.+..
T Consensus 222 ~isl~~lA~~~~iS~~~L~r~FK~~t-G~T~~~yi~~~RL~~A~~LL~----~t~~sI~eIA~~~GF~d~ 286 (312)
T PRK13500 222 PFALDKFCDEASCSERVLRQQFRQQT-GMTINQYLRQVRVCHAQYLLQ----HSRLLISDISTECGFEDS 286 (312)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH-CcCHHHHHHHHHHHHHHHHHH----cCCCCHHHHHHHhCCCCH
Confidence 58999999999999776543332221 111222222222222233333 577889999999988754
No 268
>cd02678 MIT_VPS4 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.
Probab=20.28 E-value=2.8e+02 Score=19.76 Aligned_cols=23 Identities=30% Similarity=0.556 Sum_probs=18.8
Q ss_pred ccchHHHHHHHHHHHhhhhhccC
Q psy3486 121 QSNYKEMMSRYKQLLLYIKSAVT 143 (222)
Q Consensus 121 qg~y~~~l~~y~~LLtyiksaVt 143 (222)
.|+|++|+.+|.+=+.+...++.
T Consensus 19 ~g~y~eA~~~Y~~aie~l~~~~k 41 (75)
T cd02678 19 AGNYEEALRLYQHALEYFMHALK 41 (75)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHh
Confidence 49999999999998888765553
No 269
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=20.27 E-value=91 Score=30.04 Aligned_cols=31 Identities=26% Similarity=0.513 Sum_probs=25.9
Q ss_pred eeeEeeccchHHHHHHHHHHHhhhhhccCcc
Q psy3486 115 VRGRIDQSNYKEMMSRYKQLLLYIKSAVTRN 145 (222)
Q Consensus 115 ik~~idqg~y~~~l~~y~~LLtyiksaVtrN 145 (222)
++-.+|.-+-++|++.|+|...|+|..+.-|
T Consensus 146 vQNKIDlV~~E~AlE~y~qIk~FvkGt~Ae~ 176 (415)
T COG5257 146 VQNKIDLVSRERALENYEQIKEFVKGTVAEN 176 (415)
T ss_pred EecccceecHHHHHHHHHHHHHHhcccccCC
Confidence 3457888899999999999999999776544
No 270
>PF10304 DUF2411: Domain of unknown function (DUF2411); InterPro: IPR019414 This entry represents a 38 residue domain of unknown function that is found at the extreme C-terminal end of some HEAT repeats.
Probab=20.13 E-value=1.1e+02 Score=19.45 Aligned_cols=16 Identities=38% Similarity=0.794 Sum_probs=14.1
Q ss_pred CchHHHHHHHHHHHHH
Q psy3486 2 DDPFIREHIEDLLRNI 17 (222)
Q Consensus 2 ~D~~I~~hi~~L~~~l 17 (222)
.|+.++.|...+++.|
T Consensus 18 ~D~lvr~hA~~~Le~L 33 (36)
T PF10304_consen 18 NDDLVREHAQDALEEL 33 (36)
T ss_pred CcHHHHHHHHHHHHHH
Confidence 5999999999998876
Done!