Query psy1861
Match_columns 661
No_of_seqs 425 out of 1363
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 18:11:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1861.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1861hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1598|consensus 100.0 2.3E-57 5.1E-62 493.4 19.6 367 173-564 18-493 (521)
2 PRK00423 tfb transcription ini 100.0 1.4E-41 3E-46 360.0 21.2 236 174-417 30-306 (310)
3 COG1405 SUA7 Transcription ini 100.0 1E-40 2.3E-45 347.6 19.8 232 174-416 20-280 (285)
4 COG5030 APS2 Clathrin adaptor 100.0 9.5E-41 2.1E-45 306.5 13.4 119 2-178 22-140 (152)
5 KOG0934|consensus 100.0 3.4E-41 7.3E-46 309.1 9.6 117 2-176 22-138 (145)
6 KOG1597|consensus 100.0 2.9E-39 6.2E-44 330.0 19.4 237 176-417 20-290 (308)
7 KOG0936|consensus 100.0 1.3E-39 2.9E-44 302.4 11.5 127 2-180 22-148 (182)
8 KOG0935|consensus 100.0 2E-36 4.4E-41 271.3 10.3 120 1-178 21-141 (143)
9 PF07741 BRF1: Brf1-like TBP-b 99.9 4.8E-26 1E-30 202.9 3.7 90 469-558 1-97 (97)
10 KOG0936|consensus 99.9 3E-24 6.5E-29 200.3 2.3 60 32-91 58-117 (182)
11 PF01217 Clat_adaptor_s: Clath 99.9 2.5E-22 5.5E-27 189.7 10.6 119 2-178 22-140 (141)
12 PF00382 TFIIB: Transcription 99.7 2.9E-17 6.3E-22 137.9 9.9 71 250-320 1-71 (71)
13 PRK00423 tfb transcription ini 99.6 5.3E-15 1.2E-19 157.4 9.2 187 114-335 121-308 (310)
14 COG1405 SUA7 Transcription ini 99.4 3.7E-13 7.9E-18 141.4 8.1 165 145-335 118-283 (285)
15 KOG0934|consensus 99.0 3.3E-11 7.1E-16 112.0 -0.8 36 56-91 76-111 (145)
16 KOG1597|consensus 99.0 2.1E-09 4.4E-14 111.6 10.5 184 116-332 105-289 (308)
17 cd00043 CYCLIN Cyclin box fold 98.9 8.2E-09 1.8E-13 86.7 11.1 83 245-327 4-87 (88)
18 COG5030 APS2 Clathrin adaptor 98.9 9.6E-11 2.1E-15 109.1 -1.0 35 57-91 77-111 (152)
19 KOG0835|consensus 98.9 3.9E-08 8.4E-13 103.4 14.7 154 235-389 15-189 (367)
20 smart00385 CYCLIN domain prese 98.9 1.4E-08 3E-13 84.6 9.2 79 249-328 2-82 (83)
21 TIGR00569 ccl1 cyclin ccl1. Un 98.8 2.6E-08 5.6E-13 106.1 12.9 149 240-389 52-212 (305)
22 KOG0834|consensus 98.8 3.6E-08 7.9E-13 105.3 12.5 153 237-389 32-201 (323)
23 KOG0935|consensus 98.7 2.1E-09 4.5E-14 97.9 -0.3 51 38-91 62-112 (143)
24 PF00382 TFIIB: Transcription 98.6 2.6E-08 5.7E-13 83.6 3.4 56 344-402 1-65 (71)
25 COG5333 CCL1 Cdk activating ki 98.5 4.5E-07 9.8E-12 95.2 9.6 145 244-389 46-198 (297)
26 KOG1598|consensus 98.5 5.2E-08 1.1E-12 108.3 2.1 239 114-389 63-323 (521)
27 KOG0656|consensus 98.1 2.7E-05 5.8E-10 83.7 13.3 146 244-389 79-232 (335)
28 PF00134 Cyclin_N: Cyclin, N-t 97.7 0.00056 1.2E-08 62.5 11.5 94 241-334 29-125 (127)
29 KOG0794|consensus 97.6 8E-05 1.7E-09 75.6 5.7 142 246-389 44-200 (264)
30 PF01857 RB_B: Retinoblastoma- 97.4 0.00079 1.7E-08 64.0 8.6 85 242-326 10-96 (135)
31 KOG3343|consensus 96.8 0.0015 3.3E-08 62.9 4.7 85 90-174 59-144 (175)
32 KOG0937|consensus 96.4 0.013 2.7E-07 64.9 9.2 134 25-176 2-135 (424)
33 cd00043 CYCLIN Cyclin box fold 96.3 0.0063 1.4E-07 50.7 5.1 63 338-403 3-74 (88)
34 KOG0653|consensus 96.0 0.044 9.5E-07 60.9 10.8 144 243-389 158-305 (391)
35 KOG2496|consensus 95.8 0.04 8.7E-07 58.5 8.9 83 258-340 73-159 (325)
36 COG5024 Cyclin [Cell division 95.2 0.074 1.6E-06 59.7 9.1 139 247-389 217-359 (440)
37 KOG2740|consensus 95.1 0.023 5.1E-07 61.4 4.6 70 102-172 64-133 (418)
38 smart00385 CYCLIN domain prese 95.0 0.028 6E-07 46.3 3.9 59 342-403 1-68 (83)
39 KOG0938|consensus 95.0 0.044 9.5E-07 58.8 6.2 88 87-174 46-133 (446)
40 PF02984 Cyclin_C: Cyclin, C-t 94.6 0.15 3.3E-06 45.5 8.0 87 246-332 3-90 (118)
41 PF01217 Clat_adaptor_s: Clath 94.4 0.0069 1.5E-07 57.4 -1.5 34 56-89 76-109 (141)
42 KOG0835|consensus 91.9 0.53 1.2E-05 50.7 7.8 105 246-353 141-248 (367)
43 PF08271 TF_Zn_Ribbon: TFIIB z 91.1 0.083 1.8E-06 40.3 0.6 24 174-202 19-42 (43)
44 KOG0655|consensus 89.4 1.8 3.9E-05 46.9 9.0 111 246-356 148-262 (408)
45 PF08613 Cyclin: Cyclin; Inte 88.7 6.5 0.00014 37.7 11.7 89 246-334 54-148 (149)
46 KOG3343|consensus 87.0 0.85 1.8E-05 44.5 4.3 71 5-78 35-105 (175)
47 KOG4557|consensus 86.3 8.4 0.00018 39.6 11.1 157 249-415 2-177 (262)
48 KOG4164|consensus 82.2 4.1 8.8E-05 45.1 7.4 88 246-333 385-477 (497)
49 smart00342 HTH_ARAC helix_turn 79.6 6.3 0.00014 32.3 6.3 72 250-328 4-76 (84)
50 PF05460 ORC6: Origin recognit 79.5 0.59 1.3E-05 51.4 0.0 78 258-335 11-89 (353)
51 KOG1010|consensus 75.6 6 0.00013 47.7 6.6 83 245-327 679-763 (920)
52 KOG4557|consensus 74.9 9.4 0.0002 39.3 6.9 85 246-331 92-181 (262)
53 cd06571 Bac_DnaA_C C-terminal 72.1 10 0.00023 33.2 5.9 47 285-333 28-75 (90)
54 COG5541 RET3 Vesicle coat comp 71.2 4.1 9E-05 39.7 3.3 85 90-174 66-151 (187)
55 TIGR00569 ccl1 cyclin ccl1. Un 71.1 44 0.00095 36.2 11.5 71 260-331 180-252 (305)
56 KOG2635|consensus 71.0 4.2 9.2E-05 45.6 3.8 66 24-89 43-115 (512)
57 PF15001 AP-5_subunit_s1: AP-5 67.0 19 0.00041 36.5 7.1 75 93-167 104-179 (189)
58 TIGR02010 IscR iron-sulfur clu 66.5 12 0.00025 35.3 5.4 47 284-330 6-52 (135)
59 PF00325 Crp: Bacterial regula 66.0 9.8 0.00021 27.6 3.6 27 303-329 2-28 (32)
60 PF02082 Rrf2: Transcriptional 65.3 9.9 0.00021 32.7 4.2 46 285-330 7-52 (83)
61 PF13545 HTH_Crp_2: Crp-like h 63.4 18 0.00039 29.9 5.4 29 302-330 27-55 (76)
62 TIGR03697 NtcA_cyano global ni 63.0 26 0.00057 33.8 7.3 46 285-330 115-170 (193)
63 KOG2635|consensus 61.5 13 0.00029 41.8 5.3 73 87-159 48-120 (512)
64 PF08279 HTH_11: HTH domain; 58.0 25 0.00054 27.4 5.0 34 298-331 10-43 (55)
65 PF02984 Cyclin_C: Cyclin, C-t 57.9 4.3 9.4E-05 36.0 0.7 48 339-389 2-49 (118)
66 PF13613 HTH_Tnp_4: Helix-turn 57.6 19 0.00041 28.5 4.3 37 300-336 16-52 (53)
67 PRK10857 DNA-binding transcrip 56.9 21 0.00046 35.1 5.4 47 284-330 6-52 (164)
68 PRK11920 rirA iron-responsive 55.8 24 0.00053 34.1 5.6 46 284-330 6-51 (153)
69 PF01325 Fe_dep_repress: Iron 54.6 34 0.00073 28.0 5.4 37 292-329 12-48 (60)
70 KOG0937|consensus 52.4 14 0.0003 41.6 3.6 58 23-80 41-98 (424)
71 cd00092 HTH_CRP helix_turn_hel 51.8 50 0.0011 26.3 6.0 30 301-330 23-52 (67)
72 KOG1010|consensus 50.9 57 0.0012 39.8 8.4 78 247-325 35-113 (920)
73 PF13542 HTH_Tnp_ISL3: Helix-t 50.8 48 0.001 25.5 5.5 43 282-327 9-51 (52)
74 PF07022 Phage_CI_repr: Bacter 49.5 12 0.00025 31.0 2.0 51 305-382 14-64 (66)
75 PF12802 MarR_2: MarR family; 49.4 42 0.00092 26.5 5.2 40 290-329 8-47 (62)
76 TIGR00738 rrf2_super rrf2 fami 48.4 36 0.00078 31.4 5.3 45 285-329 7-51 (132)
77 TIGR02944 suf_reg_Xantho FeS a 47.1 43 0.00093 31.0 5.6 46 284-330 7-52 (130)
78 PF00356 LacI: Bacterial regul 46.6 23 0.00049 27.7 3.0 41 305-353 1-43 (46)
79 COG3877 Uncharacterized protei 46.0 87 0.0019 29.0 7.0 71 291-369 50-121 (122)
80 PF00165 HTH_AraC: Bacterial r 45.5 29 0.00062 25.8 3.4 27 301-327 6-32 (42)
81 KOG2740|consensus 45.4 20 0.00043 39.6 3.4 82 33-157 53-136 (418)
82 PRK11161 fumarate/nitrate redu 45.1 73 0.0016 32.0 7.4 30 302-331 183-212 (235)
83 PRK11753 DNA-binding transcrip 42.3 94 0.002 30.5 7.5 29 302-330 167-195 (211)
84 smart00419 HTH_CRP helix_turn_ 41.6 40 0.00087 25.0 3.7 29 302-330 7-35 (48)
85 PRK10219 DNA-binding transcrip 41.4 1.2E+02 0.0026 26.9 7.4 39 288-327 7-45 (107)
86 PF04545 Sigma70_r4: Sigma-70, 40.4 52 0.0011 25.3 4.2 31 301-331 18-48 (50)
87 KOG0834|consensus 40.0 19 0.0004 39.4 2.2 88 245-332 150-246 (323)
88 PRK11511 DNA-binding transcrip 39.9 1.1E+02 0.0023 28.5 7.0 43 284-327 7-49 (127)
89 PF00196 GerE: Bacterial regul 38.7 48 0.001 26.3 3.9 32 302-333 17-48 (58)
90 KOG0794|consensus 38.7 93 0.002 32.7 6.8 82 248-330 155-237 (264)
91 smart00478 ENDO3c endonuclease 38.6 3.2E+02 0.0069 25.6 10.2 105 244-354 8-114 (149)
92 PF13412 HTH_24: Winged helix- 37.5 92 0.002 23.6 5.2 28 302-329 16-43 (48)
93 PF09862 DUF2089: Protein of u 37.1 95 0.0021 29.0 6.0 61 305-368 51-112 (113)
94 PRK05901 RNA polymerase sigma 36.8 4.7E+02 0.01 30.6 12.9 89 237-325 271-396 (509)
95 COG1959 Predicted transcriptio 36.4 67 0.0014 31.1 5.2 46 285-330 7-52 (150)
96 TIGR02297 HpaA 4-hydroxyphenyl 36.2 1.7E+02 0.0037 30.3 8.6 49 289-346 189-237 (287)
97 PRK10402 DNA-binding transcrip 35.3 91 0.002 31.4 6.3 46 285-330 151-196 (226)
98 PF13463 HTH_27: Winged helix 35.1 77 0.0017 25.4 4.7 32 299-330 14-45 (68)
99 PF13404 HTH_AsnC-type: AsnC-t 34.9 85 0.0019 23.9 4.5 30 298-327 12-41 (42)
100 PRK10572 DNA-binding transcrip 33.7 1.6E+02 0.0036 30.6 8.1 84 249-348 201-286 (290)
101 PRK06030 hypothetical protein; 33.2 94 0.002 29.4 5.5 39 291-331 59-97 (124)
102 smart00550 Zalpha Z-DNA-bindin 33.2 1E+02 0.0022 25.6 5.2 39 293-331 11-50 (68)
103 smart00421 HTH_LUXR helix_turn 33.1 79 0.0017 23.7 4.3 30 304-333 19-48 (58)
104 PF04967 HTH_10: HTH DNA bindi 31.9 2.3E+02 0.005 22.9 6.7 44 268-329 6-49 (53)
105 PF01047 MarR: MarR family; I 31.7 1.3E+02 0.0028 23.6 5.3 37 292-330 8-44 (59)
106 TIGR01610 phage_O_Nterm phage 31.5 1.3E+02 0.0028 26.7 5.8 30 300-329 44-73 (95)
107 cd06170 LuxR_C_like C-terminal 31.4 91 0.002 23.6 4.4 31 303-333 15-45 (57)
108 PRK09391 fixK transcriptional 30.8 1.8E+02 0.004 29.4 7.7 29 302-330 178-206 (230)
109 PF10668 Phage_terminase: Phag 29.9 1.2E+02 0.0026 25.3 4.8 21 303-323 22-42 (60)
110 PRK14088 dnaA chromosomal repl 29.7 75 0.0016 36.0 5.0 68 261-331 345-415 (440)
111 PF09339 HTH_IclR: IclR helix- 29.6 97 0.0021 24.1 4.2 34 296-329 11-44 (52)
112 PRK13918 CRP/FNR family transc 29.4 1.7E+02 0.0037 28.4 7.0 29 302-330 148-176 (202)
113 smart00345 HTH_GNTR helix_turn 29.4 92 0.002 23.9 4.1 26 305-330 22-47 (60)
114 COG0177 Nth Predicted EndoIII- 29.2 3.5E+02 0.0075 28.0 9.2 113 246-371 54-167 (211)
115 smart00351 PAX Paired Box doma 28.9 4E+02 0.0086 24.8 8.9 85 237-324 21-124 (125)
116 PF08281 Sigma70_r4_2: Sigma-7 28.2 87 0.0019 24.2 3.7 28 304-331 27-54 (54)
117 PRK11014 transcriptional repre 28.2 1E+02 0.0022 29.1 5.0 46 285-330 7-52 (141)
118 PRK15121 right oriC-binding tr 27.3 1.5E+02 0.0033 31.2 6.5 41 286-327 5-45 (289)
119 PRK10130 transcriptional regul 27.2 5.2E+02 0.011 28.5 10.8 52 285-345 239-290 (350)
120 PF05344 DUF746: Domain of Unk 27.2 1.2E+02 0.0026 25.7 4.4 47 298-348 8-54 (65)
121 PF04703 FaeA: FaeA-like prote 27.0 1.5E+02 0.0032 24.8 5.0 34 300-333 12-45 (62)
122 PF01978 TrmB: Sugar-specific 26.5 1.1E+02 0.0025 24.9 4.3 36 293-329 13-48 (68)
123 COG1725 Predicted transcriptio 26.5 77 0.0017 30.1 3.6 26 305-330 37-62 (125)
124 COG5333 CCL1 Cdk activating ki 26.3 1.1E+02 0.0025 33.1 5.3 45 262-306 168-212 (297)
125 PF12833 HTH_18: Helix-turn-he 26.1 3.8E+02 0.0082 22.2 8.8 78 253-346 1-81 (81)
126 PF08299 Bac_DnaA_C: Bacterial 26.0 1.3E+02 0.0028 25.3 4.6 35 291-327 35-70 (70)
127 PF13936 HTH_38: Helix-turn-he 25.3 1.3E+02 0.0028 22.9 4.1 26 300-325 17-42 (44)
128 PF13730 HTH_36: Helix-turn-he 25.3 1.4E+02 0.003 23.1 4.4 25 305-329 27-51 (55)
129 PF08220 HTH_DeoR: DeoR-like h 24.9 1.2E+02 0.0025 24.4 4.0 31 301-331 12-42 (57)
130 TIGR01889 Staph_reg_Sar staphy 24.6 1.9E+02 0.0042 26.0 5.8 41 289-330 30-70 (109)
131 PRK09685 DNA-binding transcrip 24.4 3.8E+02 0.0083 27.9 8.9 53 284-345 195-247 (302)
132 PRK09392 ftrB transcriptional 23.9 1.9E+02 0.0042 29.0 6.3 28 302-329 172-199 (236)
133 PRK07921 RNA polymerase sigma 23.2 3.1E+02 0.0067 29.9 8.1 145 244-419 149-310 (324)
134 COG4565 CitB Response regulato 23.0 5.4E+02 0.012 26.9 9.2 91 239-331 110-201 (224)
135 PRK09210 RNA polymerase sigma 23.0 1E+03 0.023 26.2 14.7 88 240-327 132-256 (367)
136 PF01710 HTH_Tnp_IS630: Transp 22.9 3.3E+02 0.0071 25.1 7.1 88 237-332 6-100 (119)
137 PF13384 HTH_23: Homeodomain-l 22.7 1.3E+02 0.0028 22.8 3.8 27 303-329 17-43 (50)
138 PF04855 SNF5: SNF5 / SMARCB1 22.7 1.2E+02 0.0026 31.9 4.6 50 335-384 139-189 (244)
139 PRK07406 RNA polymerase sigma 22.6 3.1E+02 0.0066 30.7 8.0 23 302-325 239-261 (373)
140 TIGR02297 HpaA 4-hydroxyphenyl 22.4 4.8E+02 0.01 26.9 9.1 72 249-328 204-277 (287)
141 PF05066 HARE-HTH: HB1, ASXL, 21.7 81 0.0018 26.3 2.6 32 267-298 20-53 (72)
142 PF08006 DUF1700: Protein of u 21.1 2.5E+02 0.0055 27.5 6.4 51 248-306 5-56 (181)
143 smart00418 HTH_ARSR helix_turn 21.0 2.2E+02 0.0048 21.5 4.9 30 301-330 8-37 (66)
144 PRK15435 bifunctional DNA-bind 20.8 2.5E+02 0.0055 31.0 6.9 50 286-346 85-134 (353)
145 PRK13501 transcriptional activ 20.7 2.8E+02 0.0061 28.9 7.0 72 250-328 195-267 (290)
146 PF04552 Sigma54_DBD: Sigma-54 20.2 34 0.00074 33.7 0.0 24 302-325 48-71 (160)
147 PRK09978 DNA-binding transcrip 20.1 7.7E+02 0.017 26.4 10.1 87 250-353 161-249 (274)
148 KOG1921|consensus 20.1 2.6E+02 0.0056 29.8 6.3 111 237-354 90-202 (286)
149 cd07377 WHTH_GntR Winged helix 20.0 1.5E+02 0.0032 23.2 3.7 25 305-329 27-51 (66)
No 1
>KOG1598|consensus
Probab=100.00 E-value=2.3e-57 Score=493.45 Aligned_cols=367 Identities=35% Similarity=0.502 Sum_probs=303.5
Q ss_pred HhhhhhccCCCCcceeeeccccccccceeecCCCCccccccccccCCCCCCcCCCCccCCCCCCCchhHHHHHHHHHHHH
Q psy1861 173 LRVLRSRCGPSPWRHILEDSVIVSEMQFEENAHGGTSALGHFVSSDSKGGCQGFGGALRGGLNRESREITLDNCKRNISS 252 (661)
Q Consensus 173 L~~lcs~CG~~~~g~VLeE~~Ivse~tF~e~~~G~~~~~G~fv~~~~~~~~~~~g~~~~~~~~~~srEr~L~~a~~~I~~ 252 (661)
-...|+.|| +|+|+++|++++||.++ ++|+||+.++.|.+ .+.+++++++++|++.|..
T Consensus 18 g~~~C~~CG-----~v~E~~~ivsev~F~e~------~~G~~v~~~~~g~~----------~s~e~r~~t~~n~r~~i~~ 76 (521)
T KOG1598|consen 18 GNLYCTACG-----TVLEYNNIVAEVTFVEG------AQGQFVRVGQSGAG----------SSLESREKTIYNARRLIEE 76 (521)
T ss_pred CCceecccc-----ceeeccceeEEeeeecc------cceeEEeccccCCc----------cchHHHHHHHHHHHhHHHH
Confidence 346788888 99999999999999986 89999999877642 1579999999999999999
Q ss_pred HHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHhc
Q psy1861 253 LCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQALC 332 (661)
Q Consensus 253 i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~ 332 (661)
++.+|+|++ +++.|.+||++|.++||++||+...|+|||+|++||+++++|+|+||+++++|+++.||++|++|++.|.
T Consensus 77 ~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~Lqv~Vy~LG~~~l~l~~~L~ 155 (521)
T KOG1598|consen 77 LTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQVSVYDLGSNFLEVTDSLS 155 (521)
T ss_pred HHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccceEEehhhhhHHHHHHHHHhc
Confidence 999999999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cc---CCCCChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCccceeecc---------cccCHHHHHHH
Q psy1861 333 IS---IPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLIGKY---------SCDSHVDISRV 400 (661)
Q Consensus 333 i~---~p~~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIAaAA---------~~rT~~eIa~~ 400 (661)
+. .|.+||+.||+||+++|.+++++++|+.+|.+|+++|++|||++||||+|||||| +++|+.||+++
T Consensus 156 i~en~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~v 235 (521)
T KOG1598|consen 156 IGENVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKV 235 (521)
T ss_pred cccccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHH
Confidence 98 8999999999999999999999999999999999999999999999999999999 89999999998
Q ss_pred Hh----hhhhhhhcchHHHHHhhhhccc-------cc----------------------------ccc------------
Q psy1861 401 AG----DDYIKSNELPRVIKECLEDADL-------EE----------------------------ETE------------ 429 (661)
Q Consensus 401 ag----tiR~~ykeL~~~~~~~l~~~~~-------e~----------------------------~~e------------ 429 (661)
+. |++.||+|+.+.+...|+..+- ++ +.+
T Consensus 236 vhV~e~Tl~kRl~Ef~~T~s~~Lti~ef~~~d~e~~~~ppsft~~~~~~~k~~~~~k~~l~~~~~~~e~~~~~~~~~~~~ 315 (521)
T KOG1598|consen 236 VHVCESTLSKRLKEFSDTLSGDLTIDELAEIDLEYESDPPSFTASPSKEAKYVEDKKKMLSRTMQLVELANETWLVTLRH 315 (521)
T ss_pred HHHhHHHHHHHHHHHhccccccccHHHHHhhhhhhccCcchhhcccchhhhhhhhhhhhhhhhhhhhhcccchhhhcccc
Confidence 76 8999998888876655542110 00 000
Q ss_pred ------ccccCCCCCcccc-cccc------------cccc-------------------c-----cccccCCCCCCcCCC
Q psy1861 430 ------GEIRGIGPTPAML-GMAT------------NQDA-------------------E-----RNDQIVDDAEDDLGD 466 (661)
Q Consensus 430 ------~~~~g~~p~~~~~-~~~~------------~~~~-------------------~-----~~~~~~~~~~~~lsd 466 (661)
+.+.++..++... ...+ ++.. + .......+....+++
T Consensus 316 ~~~~~~~~l~~~~q~~~~~~~~~e~~~~~~~e~~~ssE~~dk~~~g~~~~~~~~~sd~~~~~~~~~~~~~~~d~~~~~~~ 395 (521)
T KOG1598|consen 316 SLPVITGGLFLAWQDLQPRDRLVESYDDLASECPLSSEDEDKPASGRLAELLAVLSDMAEQLASVWLRVLTLDKRSGVKH 395 (521)
T ss_pred CCcccchhhhcccccchhhhhhhhhhhhhhhcCcccccccCCcCccccchhhhcccccchhhhhcchhhhhccccccccc
Confidence 0011110000000 0000 0000 0 001223456678999
Q ss_pred CChHHHHhhcCCHHHHHHHHHHHHHhcHHHHHHHHH---HHHhHHhhCCcccccCCccccCCCCCCCCHHHHHHHHHHhc
Q psy1861 467 IDDEEINSYILTEGEATNKAKLWEVLNREYLTLQAE---RKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEK 543 (661)
Q Consensus 467 iDD~Eid~yil~eeE~~~K~~lW~~~N~eyl~eq~~---r~~~e~~~~~~~kkk~k~~~~k~~~~~~Ta~EA~~~ml~~K 543 (661)
+||.+++.++|++++...++.+ | .|++|+.|+.. +.+++.++|+... ++|..++++.+++.||.||+++|++.|
T Consensus 396 ~~~~~l~r~~l~~~a~~~a~~~-~-~n~e~l~E~~~~~~~~ak~~~~g~~~~-~~k~~~r~~s~~~~t~~eavk~~~~i~ 472 (521)
T KOG1598|consen 396 IDDLLLERQLLEESAGRDATEP-M-ENAETLVEERPGKAKAAKEREEGINSL-SKKVGERRNSPELLTAPEAVKSMKEIK 472 (521)
T ss_pred cCHHHHHHHHhhhHHhhhcchh-h-hhHHHHHhhchhhhhhhHhhhhccccc-ccccccccCCCcccccHHHHHHHHhcc
Confidence 9999999999999999999999 7 99999999986 4555556665222 223345678899999999999999999
Q ss_pred CCCCCCCHHHHhcccCCCCCC
Q psy1861 544 KISTKINYDVLKSLDFTVDVN 564 (661)
Q Consensus 544 k~S~KINYd~L~~L~~~~~~~ 564 (661)
++|++|||++|.+||+...+.
T Consensus 473 ~~s~~in~~~L~~i~d~~~e~ 493 (521)
T KOG1598|consen 473 PVSSVINYSVLENISDAEIEQ 493 (521)
T ss_pred ccccchHHHHHHHHhhhhccc
Confidence 999999999999999988765
No 2
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=1.4e-41 Score=360.04 Aligned_cols=236 Identities=25% Similarity=0.394 Sum_probs=204.7
Q ss_pred hhhhhccCCCCcceeeecccccccccee---ecCCCCcccccccccc---C-CCCCCcC------CCCc-----------
Q psy1861 174 RVLRSRCGPSPWRHILEDSVIVSEMQFE---ENAHGGTSALGHFVSS---D-SKGGCQG------FGGA----------- 229 (661)
Q Consensus 174 ~~lcs~CG~~~~g~VLeE~~Ivse~tF~---e~~~G~~~~~G~fv~~---~-~~~~~~~------~g~~----------- 229 (661)
..+|.+|| +||+|++||.+++|. +++.++++++|..++. + +.+.... .|..
T Consensus 30 e~vC~~CG-----~Vl~e~~iD~g~EWR~f~~~~~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~~~g~~l~~~~~~~~~r 104 (310)
T PRK00423 30 EIVCADCG-----LVIEENIIDQGPEWRAFDPEQREKRSRVGAPMTYTIHDKGLSTDIDWRNKDSYGKSISGKNRAQLYR 104 (310)
T ss_pred eEeecccC-----CcccccccccCCCccCCCccccCCccccCCCCCccccCCCCceEeecCCcccccccccHHHHHHHHH
Confidence 46788888 899999999999664 5555567777765542 1 1111011 1111
Q ss_pred ---cCCC-CCCCchhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCccc
Q psy1861 230 ---LRGG-LNRESREITLDNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHL 305 (661)
Q Consensus 230 ---~~~~-~~~~srEr~L~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~Prt 305 (661)
||.. ...++.|++|..|++.|+++|+.|+||+.++++|+.+|++++++++++||+.++++|||||+|||++++|||
T Consensus 105 l~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prt 184 (310)
T PRK00423 105 LRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRT 184 (310)
T ss_pred HHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcC
Confidence 1111 124788999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCccce
Q psy1861 306 LIDFSELLQICIFELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGL 385 (661)
Q Consensus 306 LkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gI 385 (661)
|+||++++++++++|+++|+.|.+.|++++|+++|++||+|||+.|+|+. .|.+.|.+|++.+.+.|++.||+|.+|
T Consensus 185 l~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~---~v~~~A~~i~~~a~~~~l~~Gr~P~sI 261 (310)
T PRK00423 185 LDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSG---EVQKKAIEILQKAKEKGLTSGKGPTGL 261 (310)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCH---HHHHHHHHHHHHHHhcCcccCCCHHHH
Confidence 99999999999999999999999999999999999999999999999987 589999999999999999999999999
Q ss_pred eecc---------cccCHHHHHHHHh----hhhhhhhcchHHHHH
Q psy1861 386 IGKY---------SCDSHVDISRVAG----DDYIKSNELPRVIKE 417 (661)
Q Consensus 386 AaAA---------~~rT~~eIa~~ag----tiR~~ykeL~~~~~~ 417 (661)
|||| .++|++||+.++| |||++|++|.+.++.
T Consensus 262 AAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~~ 306 (310)
T PRK00423 262 AAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKLDI 306 (310)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCc
Confidence 9999 6799999999999 799999999987753
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=1e-40 Score=347.61 Aligned_cols=232 Identities=27% Similarity=0.472 Sum_probs=202.0
Q ss_pred hhhhhccCCCCcceeeecccccccccee---ecCCCCcccccccccc---CCCCC-CcCCC--------CccCC-CCCCC
Q psy1861 174 RVLRSRCGPSPWRHILEDSVIVSEMQFE---ENAHGGTSALGHFVSS---DSKGG-CQGFG--------GALRG-GLNRE 237 (661)
Q Consensus 174 ~~lcs~CG~~~~g~VLeE~~Ivse~tF~---e~~~G~~~~~G~fv~~---~~~~~-~~~~g--------~~~~~-~~~~~ 237 (661)
..+|.+|| +|++|+.||.+++|. +++.. ++|..++. +.+.. ...++ .+||. ....+
T Consensus 20 e~VC~~CG-----~Vi~~~~id~gpewr~f~e~~~~---r~g~P~t~~~~d~~l~t~i~~~~~~~~~rlr~~~~~~~v~~ 91 (285)
T COG1405 20 EIVCADCG-----LVLEDSLIDPGPEWRAFDERHER---RVGAPLTPSIHDKGLSTIIGWGDKDKMYRLRKWQIRIRVSS 91 (285)
T ss_pred eEEeccCC-----EEeccccccCCCCcccccccccc---cccCCCccccCccchhhhcccchhHHHHHHHHHHhcccccc
Confidence 46788888 999999999999887 44332 55544332 22111 11111 12332 23456
Q ss_pred chhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCH
Q psy1861 238 SREITLDNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICI 317 (661)
Q Consensus 238 srEr~L~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv 317 (661)
++|+++..++..|.++|++|+||.++.++|..||++++++++++||+.+.++|||+|+|||++++||||.||+++++|++
T Consensus 92 ~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V~~ 171 (285)
T COG1405 92 AKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVSK 171 (285)
T ss_pred chhhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCCH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcccCCCCChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCccceeecc--------
Q psy1861 318 FELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLIGKY-------- 389 (661)
Q Consensus 318 ~~Lgrtyk~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIAaAA-------- 389 (661)
++||++|+.+.+.|++.+|+.+|.+||+|||+.|+|++ +|.+.|.+|++.+.+.|++.||+|+|+||||
T Consensus 172 kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~---~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~ 248 (285)
T COG1405 172 KEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSD---EVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLL 248 (285)
T ss_pred HHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCH---HHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999997 6999999999999999999999999999999
Q ss_pred -cccCHHHHHHHHh----hhhhhhhcchHHHH
Q psy1861 390 -SCDSHVDISRVAG----DDYIKSNELPRVIK 416 (661)
Q Consensus 390 -~~rT~~eIa~~ag----tiR~~ykeL~~~~~ 416 (661)
+++||++||+++| |||++|++|.+.++
T Consensus 249 ~~~~tq~eva~v~~vtevTIrnrykel~~~~~ 280 (285)
T COG1405 249 GERRTQKEVAKVAGVTEVTIRNRYKELADALD 280 (285)
T ss_pred CCchHHHHHHHHhCCeeeHHHHHHHHHHHhhc
Confidence 7999999999999 89999999887754
No 4
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=100.00 E-value=9.5e-41 Score=306.49 Aligned_cols=119 Identities=52% Similarity=0.876 Sum_probs=110.2
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCcccceecCeEEEeeecceEEEEEEEcCCCchhhHHhhhhhheeeccccccccccc
Q psy1861 2 NFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCEL 81 (661)
Q Consensus 2 ~~~~~~~~~l~~ei~~~~~~R~~~~cnf~e~~~~kivyrryAsL~f~~~vd~~enel~~l~~i~~~ve~ld~~f~~vcel 81 (661)
+++..+|++|+++|++++++|++++|||+|+++.||||||||+|||+||||.+|
T Consensus 22 ~~~~~e~~kli~~i~~lIs~R~~ke~N~~e~k~~kiVYrrYA~LyF~f~Vd~~d-------------------------- 75 (152)
T COG5030 22 PVSDPEQAKLIADIYELISARKPKESNFIEGKNEKIVYRRYATLYFVFGVDNDD-------------------------- 75 (152)
T ss_pred cCCcHHHHHHHHHHHHHHHcCCchhcccccccCcEEEeeecCcEEEEEEEcCCC--------------------------
Confidence 678999999999999999999999999999999999999999999888888754
Q ss_pred ccccccccccceeeeeeccccEEEEEeeeCCCchhHHHHHHHHHHHhhhhhhcccceeeeeechHHHHHHhhHHhhcceE
Q psy1861 82 DLVFNFYKFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEI 161 (661)
Q Consensus 82 d~~~nf~k~~~~k~vyr~ya~l~f~~~~d~~enel~~l~~i~~~ve~ld~~f~~vcEld~~f~~~k~~~ildE~i~~G~v 161 (661)
|||+|||+||+|||+||+|||||||||+||||.|+|.|||||++||++
T Consensus 76 --------------------------------nEl~iL~lIh~FVE~lDr~FgnVCELdlIFNF~kv~~ILdE~i~gG~i 123 (152)
T COG5030 76 --------------------------------NELIILELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILGGEI 123 (152)
T ss_pred --------------------------------CcchHHHHHHHHHHHHHHHhccceeeEeEeeHHHHHHHHHHHHhCCee
Confidence 555888888889999999999999999999999999999999999999
Q ss_pred eecchHHHHHHHhhhhh
Q psy1861 162 RETSQTKVLKELRVLRS 178 (661)
Q Consensus 162 ~Ets~~~Il~~L~~lcs 178 (661)
+|+|+.+|++++..+++
T Consensus 124 ~Es~~~~vl~~v~~lda 140 (152)
T COG5030 124 IESSKNEVLEHVYALDA 140 (152)
T ss_pred eecCHHHHHHHHHHHHh
Confidence 99999999999887743
No 5
>KOG0934|consensus
Probab=100.00 E-value=3.4e-41 Score=309.13 Aligned_cols=117 Identities=47% Similarity=0.849 Sum_probs=108.7
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCcccceecCeEEEeeecceEEEEEEEcCCCchhhHHhhhhhheeeccccccccccc
Q psy1861 2 NFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCEL 81 (661)
Q Consensus 2 ~~~~~~~~~l~~ei~~~~~~R~~~~cnf~e~~~~kivyrryAsL~f~~~vd~~enel~~l~~i~~~ve~ld~~f~~vcel 81 (661)
.++.++|.+|+||+++.||+|++++|||+||+++|+||||||||||++||+.+
T Consensus 22 ~~~~~er~~i~re~i~~~Lar~pk~csfie~kd~kvVyrryasl~f~~~v~~~--------------------------- 74 (145)
T KOG0934|consen 22 ALSIKERKKIERELIKSVLARKPKMCSFIEYKDEKVVYRRYASLFFCVGVEDN--------------------------- 74 (145)
T ss_pred hhcHHHHHHHHHHHHHHHHhCCcccccchhccCceehhhhhhhEEEEEEEecC---------------------------
Confidence 57899999999999999999999999999999999999999999999998865
Q ss_pred ccccccccccceeeeeeccccEEEEEeeeCCCchhHHHHHHHHHHHhhhhhhcccceeeeeechHHHHHHhhHHhhcceE
Q psy1861 82 DLVFNFYKFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEI 161 (661)
Q Consensus 82 d~~~nf~k~~~~k~vyr~ya~l~f~~~~d~~enel~~l~~i~~~ve~ld~~f~~vcEld~~f~~~k~~~ildE~i~~G~v 161 (661)
||||++||+||+|||+||+|||||||||+||||+|+|+||||++++|++
T Consensus 75 -------------------------------dNEL~~LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~ 123 (145)
T KOG0934|consen 75 -------------------------------DNELAILEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEI 123 (145)
T ss_pred -------------------------------CchhhHHHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcch
Confidence 4555888888889999999999999999999999999999999999999
Q ss_pred eecchHHHHHHHhhh
Q psy1861 162 RETSQTKVLKELRVL 176 (661)
Q Consensus 162 ~Ets~~~Il~~L~~l 176 (661)
+|+++..++.++...
T Consensus 124 ~e~~k~~~~~~i~~a 138 (145)
T KOG0934|consen 124 QETSKNDVLKAIAQA 138 (145)
T ss_pred HhhhcccHHHHHHHh
Confidence 999999999887654
No 6
>KOG1597|consensus
Probab=100.00 E-value=2.9e-39 Score=329.98 Aligned_cols=237 Identities=18% Similarity=0.320 Sum_probs=202.8
Q ss_pred hhhccCCCCcceeeeccccccccce---eecC-CCCcccccc----ccccCCCCCCcCCC-----------CccCCCCCC
Q psy1861 176 LRSRCGPSPWRHILEDSVIVSEMQF---EENA-HGGTSALGH----FVSSDSKGGCQGFG-----------GALRGGLNR 236 (661)
Q Consensus 176 lcs~CG~~~~g~VLeE~~Ivse~tF---~e~~-~G~~~~~G~----fv~~~~~~~~~~~g-----------~~~~~~~~~ 236 (661)
-++.|+ +||.|+++++|+...+| .++. +.+++++|. |+.........+.| +++|+..++
T Consensus 20 gdtvC~--~CGlVl~~r~Id~~sEwrtfsnd~~~~DPsrvG~~sNPlL~~g~L~T~I~~g~g~~s~~~s~l~~~Q~~~sm 97 (308)
T KOG1597|consen 20 GDTVCS--ECGLVLEDRIIDEGSEWRTFSNDDSDADPSRVGASSNPLLDGGDLSTFISKGTGTSSSFASSLGKAQNRNSM 97 (308)
T ss_pred Cceecc--cCCeeeccccccccccccccccCCCCCCccccCCCCCCCCCCCCcceeeecCCCCCHHHHHHHHHHhccccc
Confidence 344444 44499999999988754 4444 447777773 44433322111111 124666688
Q ss_pred CchhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCC
Q psy1861 237 ESREITLDNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQIC 316 (661)
Q Consensus 237 ~srEr~L~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vs 316 (661)
.+.|+.+..|++.|..||+.|+||..+.++|.++||++.+.+.+|||+.++++|||||+|||+++.||||+||+.+++|+
T Consensus 98 ~~~d~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~anv~ 177 (308)
T KOG1597|consen 98 SNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVANVS 177 (308)
T ss_pred CCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcccCCC--CChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCccceeecc-----
Q psy1861 317 IFELGRTYLRLSQALCISIPS--MDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLIGKY----- 389 (661)
Q Consensus 317 v~~Lgrtyk~L~k~L~i~~p~--~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIAaAA----- 389 (661)
.++|||+++.|.+.|++..+. +...+||+|||+.|+|+. .+++.|.++++++..-.+..||+|.+||||+
T Consensus 178 kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~---~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmis 254 (308)
T KOG1597|consen 178 KKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPK---SAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMIS 254 (308)
T ss_pred HHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCH---HHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHH
Confidence 999999999999999986654 447899999999999987 5899999999999999999999999999999
Q ss_pred ----cccCHHHHHHHHh----hhhhhhhcchHHHHH
Q psy1861 390 ----SCDSHVDISRVAG----DDYIKSNELPRVIKE 417 (661)
Q Consensus 390 ----~~rT~~eIa~~ag----tiR~~ykeL~~~~~~ 417 (661)
.++||+||..++| |||+.||+|....++
T Consensus 255 qls~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~~~ 290 (308)
T KOG1597|consen 255 QLSDEKKTQKEIGEVTGVAEVTIRNSYKDLYPHADK 290 (308)
T ss_pred HhccCcccHHHHHHHhhhhHHHHHHHHHHHhhchhh
Confidence 7899999999998 899999999988764
No 7
>KOG0936|consensus
Probab=100.00 E-value=1.3e-39 Score=302.42 Aligned_cols=127 Identities=34% Similarity=0.593 Sum_probs=114.6
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCcccceecCeEEEeeecceEEEEEEEcCCCchhhHHhhhhhheeeccccccccccc
Q psy1861 2 NFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCEL 81 (661)
Q Consensus 2 ~~~~~~~~~l~~ei~~~~~~R~~~~cnf~e~~~~kivyrryAsL~f~~~vd~~enel~~l~~i~~~ve~ld~~f~~vcel 81 (661)
+++.+.||+|++++|+++++|++++|||+|....
T Consensus 22 p~~~~~Qq~lir~vf~lvs~R~~n~~nFLe~~~l---------------------------------------------- 55 (182)
T KOG0936|consen 22 PVDEEKQQQLIREVFHLVSKRPDNVCNFLEGNSL---------------------------------------------- 55 (182)
T ss_pred cCChHHHHHHHHHHHHHHHcCCchHhhhhccccc----------------------------------------------
Confidence 6889999999999999999999999999975432
Q ss_pred ccccccccccceeeeeeccccEEEEEeeeCCCchhHHHHHHHHHHHhhhhhhcccceeeeeechHHHHHHhhHHhhcceE
Q psy1861 82 DLVFNFYKFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEI 161 (661)
Q Consensus 82 d~~~nf~k~~~~k~vyr~ya~l~f~~~~d~~enel~~l~~i~~~ve~ld~~f~~vcEld~~f~~~k~~~ildE~i~~G~v 161 (661)
.-..|.||||||||||||+||||++||||+|||+||.|||+||+||+||||||||||++|+|+||+|+++||+|
T Consensus 56 ------~g~~d~rlIYrhYATLYFvfvvD~sEsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h~iL~EiV~GGmV 129 (182)
T KOG0936|consen 56 ------IGGSDNRLIYRHYATLYFVFVVDSSESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVHAILAEIVMGGMV 129 (182)
T ss_pred ------cCCccceeehheeeeEEEEEEEcCCcchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHHHHHHHHHhCCeE
Confidence 12357888999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecchHHHHHHHhhhhhcc
Q psy1861 162 RETSQTKVLKELRVLRSRC 180 (661)
Q Consensus 162 ~Ets~~~Il~~L~~lcs~C 180 (661)
.|||..+|+.++..+-+--
T Consensus 130 lETn~neIv~av~~~nkle 148 (182)
T KOG0936|consen 130 LETNMNEIVAAVDEQNKLE 148 (182)
T ss_pred EeccHHHHHHHHHHhchhh
Confidence 9999999999987665433
No 8
>KOG0935|consensus
Probab=100.00 E-value=2e-36 Score=271.32 Aligned_cols=120 Identities=85% Similarity=1.356 Sum_probs=105.8
Q ss_pred CCCCHHHHHHHHHHHHHHHhcCCCCCcccceecCeEEEee-ecceEEEEEEEcCCCchhhHHhhhhhheeeccccccccc
Q psy1861 1 MNFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYR-RYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVC 79 (661)
Q Consensus 1 ~~~~~~~~~~l~~ei~~~~~~R~~~~cnf~e~~~~kivyr-ryAsL~f~~~vd~~enel~~l~~i~~~ve~ld~~f~~vc 79 (661)
+++++.|||+++.||++++++|+.+.-||++.++.+++|| |||+|||++|||.
T Consensus 21 v~~dd~ek~~~~~~vh~lvs~Rd~K~~~~~~~~~~~~~~~rryagLyf~~~vd~-------------------------- 74 (143)
T KOG0935|consen 21 VQFDDDEKQKLIEEVHALVTVRDAKHTNFVEFRNFKIIYRRRYAGLYFCICVDV-------------------------- 74 (143)
T ss_pred eccCchHHHHHHHHHHHHHhhccchhhhheeeeeceEEEEEeeCCEEEEEEEec--------------------------
Confidence 4678899999999999999999999888888777666544 7777777666665
Q ss_pred ccccccccccccceeeeeeccccEEEEEeeeCCCchhHHHHHHHHHHHhhhhhhcccceeeeeechHHHHHHhhHHhhcc
Q psy1861 80 ELDLVFNFYKFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAG 159 (661)
Q Consensus 80 eld~~~nf~k~~~~k~vyr~ya~l~f~~~~d~~enel~~l~~i~~~ve~ld~~f~~vcEld~~f~~~k~~~ildE~i~~G 159 (661)
.+|||++|+.||+|||+||.||+|||||||+|||+|+|.|+|||++||
T Consensus 75 --------------------------------tDnelayLe~IHlFVEvLd~fF~NVCELDlvFNFyKVy~i~DEm~l~G 122 (143)
T KOG0935|consen 75 --------------------------------TDNELAYLEHIHLFVEVLDEFFHNVCELDLVFNFYKVYTIVDEMFLAG 122 (143)
T ss_pred --------------------------------CCchHHHHHHHHHHHHHHHHHhccccceeeeeeeeeHHHHHHHHHHhh
Confidence 566779999999999999999999999999999999999999999999
Q ss_pred eEeecchHHHHHHHhhhhh
Q psy1861 160 EIRETSQTKVLKELRVLRS 178 (661)
Q Consensus 160 ~v~Ets~~~Il~~L~~lcs 178 (661)
+++|||+..|++++..+.+
T Consensus 123 Ei~Etsk~~vlerl~~L~~ 141 (143)
T KOG0935|consen 123 EIRETSKTKVLERLLMLQS 141 (143)
T ss_pred hhhhhhHHHHHHHHHHHhc
Confidence 9999999999999887653
No 9
>PF07741 BRF1: Brf1-like TBP-binding domain; InterPro: IPR011665 The Vaccinia virus has an infection-induced host cell cycle control mechanism. p53 and Rb, which are associated with the is inactivated Rb, which are associated with the RNA polymerase III transcription factor B (TFIIIB) subunits, TBP and Brf1, are inactivated [, ]. TFIIB, Brf1, and Brf2 share related N-terminal zinc ribbon and core domains. TFIIB bridges RNA polymerase II (Pol II) with the promoter-bound pre-initiation complex, whereas Brf1 and Brf2 are involved in the recruitment of Pol III. Brf1 and Brf2 both have a C-terminal extension absent in TFIIB, but their C-terminal extensions are unrelated. In yeast Brf1, the C-terminal extension interacts with the TBP/TATA box complex and contributes to the recruitment of Bdp1 []. It is suggested that the structure of the TBP-DNA complex may be altered upon entry of Brf1 and Bdp1 into the complex. Entry of Brf1 and Bdp1 into the complex imposes a strict sequence preference for the downstream half of the TATA box []. This region covers both the Brf homology II and III regions []. ; GO: 0008270 zinc ion binding, 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1NGM_J.
Probab=99.92 E-value=4.8e-26 Score=202.89 Aligned_cols=90 Identities=47% Similarity=0.714 Sum_probs=32.2
Q ss_pred hHHHHhhcCCHHHHHHHHHHHHHhcHHHHHHHHHHHHhHH---hhCC--ccccc-CCccccCC-CCCCCCHHHHHHHHHH
Q psy1861 469 DEEINSYILTEGEATNKAKLWEVLNREYLTLQAERKAREE---VEGK--KEKKK-RKPKANKA-TSVAKTAGEAIEKMLK 541 (661)
Q Consensus 469 D~Eid~yil~eeE~~~K~~lW~~~N~eyl~eq~~r~~~e~---~~~~--~~kkk-~k~~~~k~-~~~~~Ta~EA~~~ml~ 541 (661)
|+|||.|||||+|+++|++||+++|+|||++|++|+.+.+ +.+. +++++ +|++..+. .+|+.||+||+++||+
T Consensus 1 DdEid~~il~eeE~~~K~~iW~~~NkdyL~~~~~K~~~~~~~~~~~~~~~k~k~~rk~~~~~~~~~~a~ta~EA~~~ml~ 80 (97)
T PF07741_consen 1 DDEIDNYILSEEEVKIKERIWMEMNKDYLEEQEEKELKAKAEEEAGAKSRKKKKKRKRRKKKNQAPPAETAAEAARKMLK 80 (97)
T ss_dssp -HHHHTTC--HHHHHHHHHHHHHHTHHHHHHHHHCCCCT-----------------------------------------
T ss_pred ChHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCccccccccccccCCCCCCCCHHHHHHHHHH
Confidence 5699999999999999999999999999999999443221 1222 22222 22223344 6899999999999999
Q ss_pred hcCCCCCCCHHHHhccc
Q psy1861 542 EKKISTKINYDVLKSLD 558 (661)
Q Consensus 542 ~Kk~S~KINYd~L~~L~ 558 (661)
+|+||+|||||+|++||
T Consensus 81 ~k~~S~KINYd~L~~LF 97 (97)
T PF07741_consen 81 KKKFSKKINYDALESLF 97 (97)
T ss_dssp -----------------
T ss_pred hcCcccccCHHHHHhhC
Confidence 99999999999999998
No 10
>KOG0936|consensus
Probab=99.89 E-value=3e-24 Score=200.25 Aligned_cols=60 Identities=45% Similarity=0.831 Sum_probs=58.1
Q ss_pred ecCeEEEeeecceEEEEEEEcCCCchhhHHhhhhhheeeccccccccccccccccccccc
Q psy1861 32 FRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKFR 91 (661)
Q Consensus 32 ~~~~kivyrryAsL~f~~~vd~~enel~~l~~i~~~ve~ld~~f~~vceld~~~nf~k~~ 91 (661)
..|++||||+||+|||++|||.+||||+|||+||+|||+||+||+||||||+||||.|.|
T Consensus 58 ~~d~rlIYrhYATLYFvfvvD~sEsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h 117 (182)
T KOG0936|consen 58 GSDNRLIYRHYATLYFVFVVDSSESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVH 117 (182)
T ss_pred CccceeehheeeeEEEEEEEcCCcchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHH
Confidence 358999999999999999999999999999999999999999999999999999999977
No 11
>PF01217 Clat_adaptor_s: Clathrin adaptor complex small chain; InterPro: IPR022775 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the small sigma and mu subunits of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and the zeta and delta subunits of various coatomer (COP) adaptors. The small sigma subunit of AP proteins have been characterised in several species [, , , ]. The sigma subunit plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The zeta subunit of coatomers (zeta-COP) is required for coatomer binding to Golgi membranes and for coat-vesicle assembly [, ]. More information about these proteins can be found at Protein of the Month: Clathrin [].; PDB: 1W63_W 2JKR_I 2VGL_S 2JKT_I 2XA7_S 2HF6_A 3TJZ_C.
Probab=99.87 E-value=2.5e-22 Score=189.69 Aligned_cols=119 Identities=39% Similarity=0.666 Sum_probs=104.4
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCcccceecCeEEEeeecceEEEEEEEcCCCchhhHHhhhhhheeeccccccccccc
Q psy1861 2 NFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCEL 81 (661)
Q Consensus 2 ~~~~~~~~~l~~ei~~~~~~R~~~~cnf~e~~~~kivyrryAsL~f~~~vd~~enel~~l~~i~~~ve~ld~~f~~vcel 81 (661)
+.+.++++++.+++++.+..|+++.|+++.++++++||++|+.|||++++|.+
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~--------------------------- 74 (141)
T PF01217_consen 22 DVSEEERQKLFEKFIKKKSSRNSKQSPIFEHDNYRIVYKRYSDLYFVVVGDEN--------------------------- 74 (141)
T ss_dssp TSTSHHHHHHHHHHHHHHHTSSSSSTSEEEETTEEEEEEEETTEEEEEEESST---------------------------
T ss_pred CccHHHHHHHHHHHHHHHHhcccccceeeecccceeeeEeeccEEEEEEeecc---------------------------
Confidence 46778999999999999999999999999999999888888888888877765
Q ss_pred ccccccccccceeeeeeccccEEEEEeeeCCCchhHHHHHHHHHHHhhhhhhcccceeeeeechHHHHHHhhHHhhcceE
Q psy1861 82 DLVFNFYKFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEI 161 (661)
Q Consensus 82 d~~~nf~k~~~~k~vyr~ya~l~f~~~~d~~enel~~l~~i~~~ve~ld~~f~~vcEld~~f~~~k~~~ildE~i~~G~v 161 (661)
+|||.++++||.||++|+.||++|||+|+++||+++|.+||||+.+|.+
T Consensus 75 -------------------------------eNel~~~e~l~~~v~~l~~~~~~v~e~~i~~N~~~v~~~LDEiid~G~i 123 (141)
T PF01217_consen 75 -------------------------------ENELLLLEFLHRLVEVLDDYFGNVSEKDILENFDLVYLILDEIIDGGII 123 (141)
T ss_dssp -------------------------------SBHHHHHHHHHHHHHHHHHHHSS-SHHHHHHTHHHHHHHHHHHEETTEE
T ss_pred -------------------------------cchHHHHHHHHHhhhhhhhhhccccHHHHHHCHHHHHHHHHHHHhCCEE
Confidence 5555788888889999999999999999999999999999999999999
Q ss_pred eecchHHHHHHHhhhhh
Q psy1861 162 RETSQTKVLKELRVLRS 178 (661)
Q Consensus 162 ~Ets~~~Il~~L~~lcs 178 (661)
+||+++.|++++...++
T Consensus 124 ~etd~~~I~~~v~~~~~ 140 (141)
T PF01217_consen 124 LETDPNVILKRVTMQDS 140 (141)
T ss_dssp S--THHHHHHHHHHCCC
T ss_pred EECCHHHHHHHHHHhhc
Confidence 99999999999887643
No 12
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=99.72 E-value=2.9e-17 Score=137.90 Aligned_cols=71 Identities=32% Similarity=0.601 Sum_probs=66.6
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHH
Q psy1861 250 ISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFEL 320 (661)
Q Consensus 250 I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~L 320 (661)
|+++|+.|+||+++.++|.++|+++.+.++++||++..++|||||+|||+++.|+|++||+++++|++++|
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999886
No 13
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.57 E-value=5.3e-15 Score=157.41 Aligned_cols=187 Identities=18% Similarity=0.216 Sum_probs=142.7
Q ss_pred chhHHHHHHHHHHHhhhhhhcccceeeeeechHHHHHHhhHHhhcceEeecchHHHHHH-HhhhhhccCCCCcceeeecc
Q psy1861 114 NNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKE-LRVLRSRCGPSPWRHILEDS 192 (661)
Q Consensus 114 nel~~l~~i~~~ve~ld~~f~~vcEld~~f~~~k~~~ildE~i~~G~v~Ets~~~Il~~-L~~lcs~CG~~~~g~VLeE~ 192 (661)
|-...+..|+.+.+.|.-- .+| .++|..|+..+...|.+.+.+.+.|+.+ +...|+..| +|+.+.|-
T Consensus 121 ~l~~a~~~I~~~~~~L~Lp-~~v--------~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~---~prtl~eI 188 (310)
T PRK00423 121 NLAFALSELDRIASQLGLP-RSV--------REEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCK---VPRTLDEI 188 (310)
T ss_pred HHHHHHHHHHHHHHHcCCC-HHH--------HHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcC---CCcCHHHH
Confidence 4455666677776666333 344 5689999999999999999999999877 789999999 57777765
Q ss_pred ccccccceeecCCCCccccccccccCCCCCCcCCCCccCCCCCCCchhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Q psy1861 193 VIVSEMQFEENAHGGTSALGHFVSSDSKGGCQGFGGALRGGLNRESREITLDNCKRNISSLCNQLRLNQHCLETSFNLYK 272 (661)
Q Consensus 193 ~Ivse~tF~e~~~G~~~~~G~fv~~~~~~~~~~~g~~~~~~~~~~srEr~L~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk 272 (661)
.-...+.-. ..|.....- ...++ +.. . ......+|.++|+.|+||..+.++|..+++
T Consensus 189 ~~~~~v~~k--------~i~~~~~~l----~k~L~--~~~----~-----~~~p~~~i~r~~~~L~L~~~v~~~A~~i~~ 245 (310)
T PRK00423 189 AEVSRVSRK--------EIGRCYRFL----LRELN--LKL----P-----PTDPIDYVPRFASELGLSGEVQKKAIEILQ 245 (310)
T ss_pred HHHhCCCHH--------HHHHHHHHH----HHHhC--CCC----C-----CCCHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 433322111 011000000 00000 000 0 112569999999999999999999999999
Q ss_pred HHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHhcccC
Q psy1861 273 MALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQALCISI 335 (661)
Q Consensus 273 ~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~ 335 (661)
++.+.+++.||++..++|||||+|||.+|.|+|++|||++++|+..+|++.|+.|.+.|++.+
T Consensus 246 ~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~~~~ 308 (310)
T PRK00423 246 KAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKLDIKI 308 (310)
T ss_pred HHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCccc
Confidence 999999999999999999999999999999999999999999999999999999999998754
No 14
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.41 E-value=3.7e-13 Score=141.37 Aligned_cols=165 Identities=15% Similarity=0.153 Sum_probs=132.3
Q ss_pred hHHHHHHhhHHhhcceEeecchHHHHHH-HhhhhhccCCCCcceeeeccccccccceeecCCCCccccccccccCCCCCC
Q psy1861 145 FYKVYTVVDEMFLAGEIRETSQTKVLKE-LRVLRSRCGPSPWRHILEDSVIVSEMQFEENAHGGTSALGHFVSSDSKGGC 223 (661)
Q Consensus 145 ~~k~~~ildE~i~~G~v~Ets~~~Il~~-L~~lcs~CG~~~~g~VLeE~~Ivse~tF~e~~~G~~~~~G~fv~~~~~~~~ 223 (661)
-+.+..|+-..+-.|.+...|.+.++.+ +...|..+| .++.++|-.-..++.-. ..|....- ..
T Consensus 118 ~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~---~prtl~eIa~a~~V~~k--------ei~rtyr~----~~ 182 (285)
T COG1405 118 RETAARIYRKAVDKGLLRGRSIESVAAACIYAACRING---VPRTLDEIAKALGVSKK--------EIGRTYRL----LV 182 (285)
T ss_pred HHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcC---CCccHHHHHHHHCCCHH--------HHHHHHHH----HH
Confidence 5678899999999999999999999998 779999999 47778775444432111 11111000 00
Q ss_pred cCCCCccCCCCCCCchhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCc
Q psy1861 224 QGFGGALRGGLNRESREITLDNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTS 303 (661)
Q Consensus 224 ~~~g~~~~~~~~~~srEr~L~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~P 303 (661)
+.++.. ..+ .+...+|.++|+.||||+.+...|.++.+++...|++.||++..++|||||+||+.++.+
T Consensus 183 ~~L~l~------~~~-----~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~ 251 (285)
T COG1405 183 RELKLK------IPP-----VDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGER 251 (285)
T ss_pred HhcCCC------CCC-----CCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCc
Confidence 000000 011 346789999999999999999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHHHhcccC
Q psy1861 304 HLLIDFSELLQICIFELGRTYLRLSQALCISI 335 (661)
Q Consensus 304 rtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~ 335 (661)
+|.+||+.+++|++.+|.+.|+.|...+++..
T Consensus 252 ~tq~eva~v~~vtevTIrnrykel~~~~~i~~ 283 (285)
T COG1405 252 RTQKEVAKVAGVTEVTIRNRYKELADALDIEV 283 (285)
T ss_pred hHHHHHHHHhCCeeeHHHHHHHHHHHhhcccc
Confidence 99999999999999999999999999998754
No 15
>KOG0934|consensus
Probab=99.02 E-value=3.3e-11 Score=111.96 Aligned_cols=36 Identities=58% Similarity=1.022 Sum_probs=33.4
Q ss_pred chhhHHhhhhhheeeccccccccccccccccccccc
Q psy1861 56 NNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKFR 91 (661)
Q Consensus 56 nel~~l~~i~~~ve~ld~~f~~vceld~~~nf~k~~ 91 (661)
|||++||+||+|||+||+|||+|||||+||||.|.+
T Consensus 76 NEL~~LE~IH~~vE~lDkYFg~VCELDiiFNfekay 111 (145)
T KOG0934|consen 76 NELAILEFIHNYVELLDKYFGSVCELDIIFNFEKAY 111 (145)
T ss_pred chhhHHHHHHHHHHHHHHHhccceeeEEEEehHhHH
Confidence 048999999999999999999999999999999966
No 16
>KOG1597|consensus
Probab=98.98 E-value=2.1e-09 Score=111.61 Aligned_cols=184 Identities=16% Similarity=0.195 Sum_probs=132.4
Q ss_pred hHHHHHHHHHHHhhhhhhcccceeeeeechHHHHHHhhHHhhcceEeecchHHHHHH-HhhhhhccCCCCcceeeecccc
Q psy1861 116 LCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKE-LRVLRSRCGPSPWRHILEDSVI 194 (661)
Q Consensus 116 l~~l~~i~~~ve~ld~~f~~vcEld~~f~~~k~~~ildE~i~~G~v~Ets~~~Il~~-L~~lcs~CG~~~~g~VLeE~~I 194 (661)
...+..|..+-+.++--. +. -+++..|+--+--.-...+.|.+.|..+ |.-.|+.=+ .|+.+-|-..
T Consensus 105 ~~a~~~I~~m~d~~~Lp~--------~I-~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~---~pRT~kEI~~ 172 (308)
T KOG1597|consen 105 KAAFKEITAMCDRLSLPA--------TI-KDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQED---VPRTFKEISA 172 (308)
T ss_pred HHHHHHHHHHHHHhCCch--------HH-HHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcC---CCchHHHHHH
Confidence 344555555555544322 21 2566666644444456677888888888 667788887 4666666554
Q ss_pred ccccceeecCCCCccccccccccCCCCCCcCCCCccCCCCCCCchhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Q psy1861 195 VSEMQFEENAHGGTSALGHFVSSDSKGGCQGFGGALRGGLNRESREITLDNCKRNISSLCNQLRLNQHCLETSFNLYKMA 274 (661)
Q Consensus 195 vse~tF~e~~~G~~~~~G~fv~~~~~~~~~~~g~~~~~~~~~~srEr~L~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a 274 (661)
++.++=.| .|-.+.- .+..+ ..+.+..-...-.+|.++|+.|+||..+++.|.++.+++
T Consensus 173 ~anv~kKE--------Igr~~K~--------i~~~l-----~~s~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka 231 (308)
T KOG1597|consen 173 VANVSKKE--------IGRCVKL--------IGEAL-----ETSVDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKA 231 (308)
T ss_pred HHcCCHHH--------HHHHHHH--------HHHHH-----hccchhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 44432222 1111110 00001 122233334467999999999999999999999999999
Q ss_pred HhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHhc
Q psy1861 275 LSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQALC 332 (661)
Q Consensus 275 ~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~ 332 (661)
.+.++..||+|-.|+||.+|++|+....++|++||.+++||...+|..+|+.|..++.
T Consensus 232 ~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~~ 289 (308)
T KOG1597|consen 232 EEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLYPHAD 289 (308)
T ss_pred HHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHHHHHHhhchh
Confidence 9999999999999999999999999999999999999999999999999999988775
No 17
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.95 E-value=8.2e-09 Score=86.69 Aligned_cols=83 Identities=23% Similarity=0.214 Sum_probs=79.1
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCC-CHHHHHHH
Q psy1861 245 NCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQI-CIFELGRT 323 (661)
Q Consensus 245 ~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~V-sv~~Lgrt 323 (661)
.+...|.+++..+++++.+...|..+++++...+...++++..+++||||+||+.++.|.++.++...++. +..+|.+.
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~ 83 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEILRM 83 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999 99999999
Q ss_pred HHHH
Q psy1861 324 YLRL 327 (661)
Q Consensus 324 yk~L 327 (661)
++.|
T Consensus 84 e~~i 87 (88)
T cd00043 84 EKLL 87 (88)
T ss_pred HHHh
Confidence 8876
No 18
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=98.94 E-value=9.6e-11 Score=109.06 Aligned_cols=35 Identities=63% Similarity=1.079 Sum_probs=32.1
Q ss_pred hhhHHhhhhhheeeccccccccccccccccccccc
Q psy1861 57 NLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKFR 91 (661)
Q Consensus 57 el~~l~~i~~~ve~ld~~f~~vceld~~~nf~k~~ 91 (661)
||++||+||+|||+||+||+||||||+||||.|.+
T Consensus 77 El~iL~lIh~FVE~lDr~FgnVCELdlIFNF~kv~ 111 (152)
T COG5030 77 ELIILELIHNFVEILDRFFGNVCELDLIFNFQKVY 111 (152)
T ss_pred cchHHHHHHHHHHHHHHHhccceeeEeEeeHHHHH
Confidence 03799999999999999999999999999999966
No 19
>KOG0835|consensus
Probab=98.86 E-value=3.9e-08 Score=103.37 Aligned_cols=154 Identities=14% Similarity=0.139 Sum_probs=136.6
Q ss_pred CCCchhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhC
Q psy1861 235 NRESREITLDNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQ 314 (661)
Q Consensus 235 ~~~srEr~L~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~ 314 (661)
..+..+-...-|...|++-|-.|+||+...-+++.+|.+.....-..+-..+++++|||.+|.+.+..|++++||..|++
T Consensus 15 ~~e~e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh 94 (367)
T KOG0835|consen 15 SLETEEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFH 94 (367)
T ss_pred ccchHHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHH
Confidence 34566666677999999999999999999999999999999988888899999999999999999999999999988863
Q ss_pred C---------------------CHHHHHHHHHHHHHHhcccCCCCChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhc
Q psy1861 315 I---------------------CIFELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKK 373 (661)
Q Consensus 315 V---------------------sv~~Lgrtyk~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~ 373 (661)
- -+-.+-++...|.+.||......+|..+|-.|..-|++.+. .++...++...+...+
T Consensus 95 ~L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~-~~l~Q~~wNfmNDslR 173 (367)
T KOG0835|consen 95 YLEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPN-LKLLQAAWNFMNDSLR 173 (367)
T ss_pred HHHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCc-hhHHHHHHHhhhhccc
Confidence 2 12245677778999999999999999999999999999875 3689999999999999
Q ss_pred ccccCCCCccceeecc
Q psy1861 374 DMLHSGRRPNGLIGKY 389 (661)
Q Consensus 374 d~i~tGRrP~gIAaAA 389 (661)
..+..--+|.+||+||
T Consensus 174 T~v~vry~pe~iACac 189 (367)
T KOG0835|consen 174 TDVFVRYSPESIACAC 189 (367)
T ss_pred cceeeecCHHHHHHHH
Confidence 9999999999999999
No 20
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.86 E-value=1.4e-08 Score=84.58 Aligned_cols=79 Identities=22% Similarity=0.246 Sum_probs=73.3
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHh-CCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCC-CHHHHHHHHHH
Q psy1861 249 NISSLCNQLRLNQHCLETSFNLYKMALS-RNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQI-CIFELGRTYLR 326 (661)
Q Consensus 249 ~I~~i~~~L~Lp~~V~e~A~~iyk~a~e-~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~V-sv~~Lgrtyk~ 326 (661)
.|.+++..+++|+.+...|..+++++.. .++.+ +++..++|||+|+||+.++.+.+..++...+++ +..+|.+.++.
T Consensus 2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~-~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~~~ 80 (83)
T smart00385 2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLK-YSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRMEKL 80 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhccc-CCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHHHH
Confidence 5889999999999999999999999998 55555 999999999999999999999999999999999 99999999988
Q ss_pred HH
Q psy1861 327 LS 328 (661)
Q Consensus 327 L~ 328 (661)
|.
T Consensus 81 il 82 (83)
T smart00385 81 LL 82 (83)
T ss_pred Hh
Confidence 75
No 21
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=98.84 E-value=2.6e-08 Score=106.12 Aligned_cols=149 Identities=14% Similarity=0.180 Sum_probs=123.4
Q ss_pred hHHHH-HHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCC
Q psy1861 240 EITLD-NCKRNISSLCNQLR--LNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQIC 316 (661)
Q Consensus 240 Er~L~-~a~~~I~~i~~~L~--Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vs 316 (661)
|+.|. .....|.++|..|+ ||+.++-+|..+|++.+-.+.+.--.+..+++||||+||+.+..|+++.+|...+.-+
T Consensus 52 E~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~ 131 (305)
T TIGR00569 52 ELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKET 131 (305)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCC
Confidence 45554 46699999999999 9999999999999999998888878999999999999999999999999999876544
Q ss_pred ----HHHHHHHHHHHHHHhcccCCCCChhhHHHHHHhhcC-----CCcccHHHHHHHHHHHHHhhcccccCCCCccceee
Q psy1861 317 ----IFELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLD-----FGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLIG 387 (661)
Q Consensus 317 ----v~~Lgrtyk~L~k~L~i~~p~~dP~~yI~Rf~~~L~-----L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIAa 387 (661)
...|...-..|.+.|+.++-...|..++..|...|+ +. ....+...|+.+++.+...-+.-=-.|.-||.
T Consensus 132 ~~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~-~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAl 210 (305)
T TIGR00569 132 PLKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLE-NPEYLRKHADKFLNRTLLTDAYLLYTPSQIAL 210 (305)
T ss_pred chhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhcccc-chHHHHHHHHHHHHHHHcCCceecCCHHHHHH
Confidence 378999999999999998887889888888875442 22 22357888999988766654444478998888
Q ss_pred cc
Q psy1861 388 KY 389 (661)
Q Consensus 388 AA 389 (661)
||
T Consensus 211 AA 212 (305)
T TIGR00569 211 AA 212 (305)
T ss_pred HH
Confidence 88
No 22
>KOG0834|consensus
Probab=98.80 E-value=3.6e-08 Score=105.28 Aligned_cols=153 Identities=18% Similarity=0.273 Sum_probs=123.8
Q ss_pred CchhH-HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhC-
Q psy1861 237 ESREI-TLDNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQ- 314 (661)
Q Consensus 237 ~srEr-~L~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~- 314 (661)
...|. .-..+.+.|.++|.+|++|+..+.+|..+|.+.+-....+.-....+|+||||+||+.+++|+.++||..+..
T Consensus 32 ~~~E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~ 111 (323)
T KOG0834|consen 32 LKKELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYR 111 (323)
T ss_pred hhHHHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHH
Confidence 33443 3367899999999999999999999999999999988888888889999999999999999999999988752
Q ss_pred -CCH--HHHHHHH-----------HHHHHHhcccCCCCChhhHHHHHHhhcCCCcccH-HHHHHHHHHHHHhhcccccCC
Q psy1861 315 -ICI--FELGRTY-----------LRLSQALCISIPSMDPCLYVLRYSNRLDFGAKTH-EVTMTALRILQRMKKDMLHSG 379 (661)
Q Consensus 315 -Vsv--~~Lgrty-----------k~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~~~~~-~V~~~A~~Iv~~m~~d~i~tG 379 (661)
.++ .++...| +.|.+.|+.++..-.|..|+-+|+.+|+.....+ .++..|+.+++...+..+.--
T Consensus 112 ~~~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~ 191 (323)
T KOG0834|consen 112 YLNPKDLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQ 191 (323)
T ss_pred HcCcccccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEe
Confidence 333 2333333 4456677777778889999999999998766422 588999999998777555555
Q ss_pred CCccceeecc
Q psy1861 380 RRPNGLIGKY 389 (661)
Q Consensus 380 RrP~gIAaAA 389 (661)
-.|..||.||
T Consensus 192 y~p~~IAva~ 201 (323)
T KOG0834|consen 192 YSPHSIAVAC 201 (323)
T ss_pred ecCcEEEeeh
Confidence 6899999998
No 23
>KOG0935|consensus
Probab=98.71 E-value=2.1e-09 Score=97.89 Aligned_cols=51 Identities=57% Similarity=0.851 Sum_probs=43.2
Q ss_pred EeeecceEEEEEEEcCCCchhhHHhhhhhheeeccccccccccccccccccccc
Q psy1861 38 VYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKFR 91 (661)
Q Consensus 38 vyrryAsL~f~~~vd~~enel~~l~~i~~~ve~ld~~f~~vceld~~~nf~k~~ 91 (661)
=|-..+-++.+=..|. ||+.|+-||.|||+||.+|+||||||++|||+|..
T Consensus 62 ryagLyf~~~vd~tDn---elayLe~IHlFVEvLd~fF~NVCELDlvFNFyKVy 112 (143)
T KOG0935|consen 62 RYAGLYFCICVDVTDN---ELAYLEHIHLFVEVLDEFFHNVCELDLVFNFYKVY 112 (143)
T ss_pred eeCCEEEEEEEecCCc---hHHHHHHHHHHHHHHHHHhccccceeeeeeeeeHH
Confidence 3444455666777777 79999999999999999999999999999999843
No 24
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=98.61 E-value=2.6e-08 Score=83.62 Aligned_cols=56 Identities=21% Similarity=0.349 Sum_probs=50.6
Q ss_pred HHHHHhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCccceeecc---------cccCHHHHHHHHh
Q psy1861 344 VLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLIGKY---------SCDSHVDISRVAG 402 (661)
Q Consensus 344 I~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIAaAA---------~~rT~~eIa~~ag 402 (661)
|+|||+.|+|++ .|.+.|.+|++.+.+.|+..||+|.++|||| .++|++||+++++
T Consensus 1 I~r~~~~L~L~~---~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~ 65 (71)
T PF00382_consen 1 IPRICSKLGLPE---DVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAG 65 (71)
T ss_dssp HHHHHHHTT--H---HHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCT
T ss_pred ChHHHhHcCCCH---HHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhC
Confidence 689999999998 5999999999999999999999999999999 7899999999988
No 25
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=98.49 E-value=4.5e-07 Score=95.22 Aligned_cols=145 Identities=19% Similarity=0.184 Sum_probs=123.5
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHh--------CC
Q psy1861 244 DNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELL--------QI 315 (661)
Q Consensus 244 ~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~--------~V 315 (661)
..++..|..+|.+|+||..+..+|..+|++..-++..++-....++++|||+||+-+.+|+-+.-.+-.. --
T Consensus 46 i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~ 125 (297)
T COG5333 46 IYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKS 125 (297)
T ss_pred HHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccc
Confidence 4578999999999999999999999999999999999999999999999999999999865544333333 23
Q ss_pred CHHHHHHHHHHHHHHhcccCCCCChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCccceeecc
Q psy1861 316 CIFELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLIGKY 389 (661)
Q Consensus 316 sv~~Lgrtyk~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIAaAA 389 (661)
+...|-..-..+.+.|+...-...|..++..|...+.+... .++...|+.++..+.+..++-=-.|..||.||
T Consensus 126 sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~-~~~~~~aw~~inDa~~t~~~llypphiIA~a~ 198 (297)
T COG5333 126 SRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDK-YKLLQIAWKIINDALRTDLCLLYPPHIIALAA 198 (297)
T ss_pred cHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccH-HHHHHHHHHHHHhhhhceeeeecChHHHHHHH
Confidence 57888888899999999988888899999999988876553 35889999999998877666666799999998
No 26
>KOG1598|consensus
Probab=98.47 E-value=5.2e-08 Score=108.32 Aligned_cols=239 Identities=18% Similarity=0.209 Sum_probs=144.6
Q ss_pred chhHHHH---HHHHHHHhhhhhhcccceeeeeechHHHHHHhhHHhhcceEeecchHHHHHH-HhhhhhccCCCCcceee
Q psy1861 114 NNLCYLE---AIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKE-LRVLRSRCGPSPWRHIL 189 (661)
Q Consensus 114 nel~~l~---~i~~~ve~ld~~f~~vcEld~~f~~~k~~~ildE~i~~G~v~Ets~~~Il~~-L~~lcs~CG~~~~g~VL 189 (661)
.+.-+.+ .|+..-+.|+- ++ =.|+.|||.| -++-++...+.+.+.++.. ++.+|..=| .+++.+-
T Consensus 63 r~~t~~n~r~~i~~~~~~l~l--~~--~~~~a~~~~k------~a~~~nftkGr~~~~vvasClY~vcR~e~-t~hlliD 131 (521)
T KOG1598|consen 63 REKTIYNARRLIEELTERLNL--GN--KTEVAFNFFK------LAPDRNFTKGRRSTEVVAACLYLVCRLEK-TDHLLID 131 (521)
T ss_pred HHHHHHHHHhHHHHHHHhcCc--ch--HHHHHHHHHH------HHhhCCCCCCcchHHHHHHHHHHHHHhhC-CceEEEE
Confidence 3556666 67766666653 34 3788888877 3567788888999999988 445555444 1222333
Q ss_pred eccccccccceeecCCCCccccc-ccccc-CCCCCCcCCCCccCCCCCCCchhHHHHHHHHHHHHHHHhcCCC-HH--HH
Q psy1861 190 EDSVIVSEMQFEENAHGGTSALG-HFVSS-DSKGGCQGFGGALRGGLNRESREITLDNCKRNISSLCNQLRLN-QH--CL 264 (661)
Q Consensus 190 eE~~Ivse~tF~e~~~G~~~~~G-~fv~~-~~~~~~~~~g~~~~~~~~~~srEr~L~~a~~~I~~i~~~L~Lp-~~--V~ 264 (661)
..+++. +++.+ .| .|+-- +.... +.+ .-.|....-+|.+++..|-.. .+ |+
T Consensus 132 fS~~Lq--v~Vy~--------LG~~~l~l~~~L~i----~en----------~~plvDpsL~i~Rfa~~L~~g~~~~~Vv 187 (521)
T KOG1598|consen 132 FSSYLQ--VSVYD--------LGSNFLEVTDSLSI----GEN----------VSPLVDPSLYIVRFSCRLLFGDKTEDVA 187 (521)
T ss_pred eccceE--Eehhh--------hhHHHHHHHHHhcc----ccc----------cccccCcceeeechhHhhhcCCchHHHH
Confidence 333322 33322 12 12110 00000 000 112223345677777776443 33 55
Q ss_pred HHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCC-------
Q psy1861 265 ETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQALCISIPS------- 337 (661)
Q Consensus 265 e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~p~------- 337 (661)
.+|.++..++..-=...||++..+++||||+|||+||+++|..||+.+.+|+..+|.+.|++|...+...++.
T Consensus 188 ~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl~Ef~~T~s~~Lti~ef~~~d 267 (521)
T KOG1598|consen 188 KTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRLKEFSDTLSGDLTIDELAEID 267 (521)
T ss_pred HHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHHHHHhccccccccHHHHHhhh
Confidence 5555555444433345799999999999999999999999999999999999999999999999887654432
Q ss_pred ----CChhhHHHHH--HhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCccceeecc
Q psy1861 338 ----MDPCLYVLRY--SNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLIGKY 389 (661)
Q Consensus 338 ----~dP~~yI~Rf--~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIAaAA 389 (661)
.||-.|-..= ..+--. ..++....-...+.-+...|..+++.|...+-++
T Consensus 268 ~e~~~~ppsft~~~~~~~k~~~--~~k~~l~~~~~~~e~~~~~~~~~~~~~~~~~~~~ 323 (521)
T KOG1598|consen 268 LEYESDPPSFTASPSKEAKYVE--DKKKMLSRTMQLVELANETWLVTLRHSLPVITGG 323 (521)
T ss_pred hhhccCcchhhcccchhhhhhh--hhhhhhhhhhhhhhcccchhhhccccCCcccchh
Confidence 2331111100 000000 1112344445566677788999999999888877
No 27
>KOG0656|consensus
Probab=98.14 E-value=2.7e-05 Score=83.75 Aligned_cols=146 Identities=15% Similarity=0.161 Sum_probs=121.4
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCC-CCC--chHHHHHHHHHHHHHHhCC--cccHHHHHHHh--CCC
Q psy1861 244 DNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLT-KGR--RQILVCAACVYMTCRLEGT--SHLLIDFSELL--QIC 316 (661)
Q Consensus 244 ~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~-rGR--~~~~VaAACLYiACR~~~~--PrtLkDIsdv~--~Vs 316 (661)
..|...|-+.|...+..+.+.--|.+++.+.+...-+ +++ -.+.+++|||.+|.+.+.+ |.++-=..+.+ -+.
T Consensus 79 ~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~fe 158 (335)
T KOG0656|consen 79 KQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFE 158 (335)
T ss_pred HHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcccccccc
Confidence 3589999999999999999999999999999975443 333 3789999999999999886 65555444442 367
Q ss_pred HHHHHHHHHHHHHHhcccCCCCChhhHHHHHHhhcCCCcc-cHHHHHHHHHHHHHhhcccccCCCCccceeecc
Q psy1861 317 IFELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLDFGAK-THEVTMTALRILQRMKKDMLHSGRRPNGLIGKY 389 (661)
Q Consensus 317 v~~Lgrtyk~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~~~-~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIAaAA 389 (661)
.++|.|.-+.|+..|+..+..+.|..|+..|+++++.... .+.+...|..++-....+.-..+-.|+.||||+
T Consensus 159 aktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~ 232 (335)
T KOG0656|consen 159 AKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAA 232 (335)
T ss_pred HHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHH
Confidence 8999999999999999999999999999999999998643 456778887777766667667788999999997
No 28
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=97.66 E-value=0.00056 Score=62.49 Aligned_cols=94 Identities=17% Similarity=0.266 Sum_probs=79.6
Q ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCC-cccHHHHHHHhC--CCH
Q psy1861 241 ITLDNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGT-SHLLIDFSELLQ--ICI 317 (661)
Q Consensus 241 r~L~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~-PrtLkDIsdv~~--Vsv 317 (661)
..-....+.|..++..++++..+.-.|..++.+..............+++||+|+||+.+.. +.++.++....+ .++
T Consensus 29 ~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~ 108 (127)
T PF00134_consen 29 EMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTK 108 (127)
T ss_dssp HHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHH
T ss_pred HHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCH
Confidence 44456789999999999999999999999999999988888889999999999999999887 788899988873 678
Q ss_pred HHHHHHHHHHHHHhccc
Q psy1861 318 FELGRTYLRLSQALCIS 334 (661)
Q Consensus 318 ~~Lgrtyk~L~k~L~i~ 334 (661)
.+|-..-..|.+.|+.+
T Consensus 109 ~~i~~~E~~iL~~L~f~ 125 (127)
T PF00134_consen 109 KDILEMEREILSALNFD 125 (127)
T ss_dssp HHHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHHCCCC
Confidence 99999999999988754
No 29
>KOG0794|consensus
Probab=97.62 E-value=8e-05 Score=75.64 Aligned_cols=142 Identities=18% Similarity=0.246 Sum_probs=109.5
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCc----ccHHHHHHHh--------
Q psy1861 246 CKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTS----HLLIDFSELL-------- 313 (661)
Q Consensus 246 a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~P----rtLkDIsdv~-------- 313 (661)
..+.|+.++..|+|.+.|+-+|..+|++.+-++..++-.+..+|+.|||+||+-+..| |+|.-=+.++
T Consensus 44 ~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~~ 123 (264)
T KOG0794|consen 44 MANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYWP 123 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccch
Confidence 4589999999999999999999999999999999999999999999999999999988 2332222222
Q ss_pred ---CCCHHHHHHHHHHHHHHhcccCCCCChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCccceeecc
Q psy1861 314 ---QICIFELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLIGKY 389 (661)
Q Consensus 314 ---~Vsv~~Lgrtyk~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIAaAA 389 (661)
......|-..--.|.+.|+--+-.-.|..-+..|....|+.+. +....|+.|++..-+..++-=-.|.-||-||
T Consensus 124 e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d~--~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAc 200 (264)
T KOG0794|consen 124 EKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGINDQ--KLLQLAWSIVNDSYRMDLCLLYPPHQIALAC 200 (264)
T ss_pred hhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccch--hhhhhhHhhhcchhhcceeeecCHHHHHHHH
Confidence 1223344444555666666433345566668899999988442 4788999999988777776677899999999
No 30
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=97.36 E-value=0.00079 Score=64.02 Aligned_cols=85 Identities=15% Similarity=0.254 Sum_probs=65.9
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHh--CCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHH
Q psy1861 242 TLDNCKRNISSLCNQLRLNQHCLETSFNLYKMALS--RNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFE 319 (661)
Q Consensus 242 ~L~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e--~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~ 319 (661)
.+.-|..+|+.+|..|+|++.+.+....+|..+.. ..++++|..+.++.+|+|+.||.++.+.|++||-..-.--+..
T Consensus 10 vy~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~qpq~ 89 (135)
T PF01857_consen 10 VYKLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRKQPQA 89 (135)
T ss_dssp HHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTTSTT-
T ss_pred HHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHhcccc
Confidence 44558899999999999999999999999999885 4578999999999999999999999999999988766544444
Q ss_pred HHHHHHH
Q psy1861 320 LGRTYLR 326 (661)
Q Consensus 320 Lgrtyk~ 326 (661)
-..+|+.
T Consensus 90 ~~~Vyr~ 96 (135)
T PF01857_consen 90 SSHVYRS 96 (135)
T ss_dssp -THHHHS
T ss_pred cccceEE
Confidence 4444443
No 31
>KOG3343|consensus
Probab=96.81 E-value=0.0015 Score=62.93 Aligned_cols=85 Identities=19% Similarity=0.347 Sum_probs=72.7
Q ss_pred ccceeeeeeccccEEEEEeeeCCCchhHHHHHHHHHHHhhhhhhcccce-eeeeechHHHHHHhhHHhhcceEeecchHH
Q psy1861 90 FRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCE-LDLVFNFYKVYTVVDEMFLAGEIRETSQTK 168 (661)
Q Consensus 90 ~~~~k~vyr~ya~l~f~~~~d~~enel~~l~~i~~~ve~ld~~f~~vcE-ld~~f~~~k~~~ildE~i~~G~v~Ets~~~ 168 (661)
..+..+||+.+.-|||-++--..||||......+.+...++..+.+.-| --++=|+|-+..++|||+-+|-|+||..+.
T Consensus 59 ldg~~vvYk~~~Dl~fyv~G~~~ENEl~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ 138 (175)
T KOG3343|consen 59 LDGNTVVYKSVIDLHFYVVGSEEENELMLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQ 138 (175)
T ss_pred ecCcEEEEEecccEEEEEecCcchhHHHHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHH
Confidence 3567899999999999999999999999999999999999999966433 234556777778999999999999999999
Q ss_pred HHHHHh
Q psy1861 169 VLKELR 174 (661)
Q Consensus 169 Il~~L~ 174 (661)
|..++.
T Consensus 139 ia~rv~ 144 (175)
T KOG3343|consen 139 IAQRVA 144 (175)
T ss_pred HHHHhc
Confidence 887743
No 32
>KOG0937|consensus
Probab=96.41 E-value=0.013 Score=64.90 Aligned_cols=134 Identities=19% Similarity=0.258 Sum_probs=107.1
Q ss_pred CCcccceecCeEEEeeecceEEEEEEEcCCCchhhHHhhhhhheeecccccccccccccccccccccceeeeeeccccEE
Q psy1861 25 KHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKFRNFKIVYRRYAGLY 104 (661)
Q Consensus 25 ~~cnf~e~~~~kivyrryAsL~f~~~vd~~enel~~l~~i~~~ve~ld~~f~~vceld~~~nf~k~~~~k~vyr~ya~l~ 104 (661)
.+|-++++++--+|+|+|-+. |+.+.-|. |+.. .|+.- +.|..=-|..+++...+|=++-.||
T Consensus 2 sa~fild~~G~~lisr~yr~d-----v~~s~~~~----F~~~-------l~~~e-~~~~~~p~l~~~g~~~~~ik~s~ly 64 (424)
T KOG0937|consen 2 SAVFILDHKGEVLISRDYRGD-----VPMSSTEK----FFRK-------LFEKE-EGDESPPFLVHDGSRFIHIKHSNLY 64 (424)
T ss_pred ceEEEEcCCCcEeEeeccccc-----CChhhhhh----HHHH-------Hhhhc-ccCCCCCeEEeCCceEEEEeecceE
Confidence 357788889999999999877 33222111 2211 12222 4666777788999999999999999
Q ss_pred EEEeeeCCCchhHHHHHHHHHHHhhhhhhcccceeeeeechHHHHHHhhHHhhcceEeecchHHHHHHHhhh
Q psy1861 105 FCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKELRVL 176 (661)
Q Consensus 105 f~~~~d~~enel~~l~~i~~~ve~ld~~f~~vcEld~~f~~~k~~~ildE~i~~G~v~Ets~~~Il~~L~~l 176 (661)
++.++-.+-|-..+|+|+|.+|+++-.||+..-|+=+.=||.-+|-+|||++-=|..+ |+...|++..-.+
T Consensus 65 lv~~~~~n~~a~~v~~~l~~~~~v~~~y~~~l~e~si~~n~vlvyElLde~mDFGypQ-~t~s~iL~~yi~~ 135 (424)
T KOG0937|consen 65 LVAGTRPNVSAALVLSFLYAVADVFGDYLSELEEESIRDNFVLVYELLDEVMDFGYPQ-TTDSEILKNYITQ 135 (424)
T ss_pred EEEEeccCCCHHHHHHHHHHHHHHHHHHhccCCccceecchHHHHHHHHHHhccCCcc-cchHHHHHHHhcc
Confidence 9999988899999999999999999999999999999999999999999999999995 4555588775443
No 33
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=96.34 E-value=0.0063 Score=50.68 Aligned_cols=63 Identities=22% Similarity=0.243 Sum_probs=55.7
Q ss_pred CChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCccceeecc---------cccCHHHHHHHHhh
Q psy1861 338 MDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLIGKY---------SCDSHVDISRVAGD 403 (661)
Q Consensus 338 ~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIAaAA---------~~rT~~eIa~~agt 403 (661)
..|..||.++++.++++. .+...|..+++++...+...|++|..||+|| ...+.++++..++.
T Consensus 3 ~~~~~~l~~~~~~~~~~~---~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~ 74 (88)
T cd00043 3 PTPLDFLRRVAKALGLSP---ETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGY 74 (88)
T ss_pred chHHHHHHHHHHHcCCCH---HHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCC
Confidence 457899999999999987 5899999999999888888899999999999 45788899888774
No 34
>KOG0653|consensus
Probab=95.97 E-value=0.044 Score=60.86 Aligned_cols=144 Identities=14% Similarity=0.119 Sum_probs=114.1
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHH-HHHHHhC-CcccHHHHHHHhC--CCHH
Q psy1861 243 LDNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVY-MTCRLEG-TSHLLIDFSELLQ--ICIF 318 (661)
Q Consensus 243 L~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLY-iACR~~~-~PrtLkDIsdv~~--Vsv~ 318 (661)
...-.+.+-++-..++|.....-.|..++.+......+..++...|..+|++ |||+.+. .+-++.|+.-+++ .+..
T Consensus 158 R~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~ 237 (391)
T KOG0653|consen 158 RAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSRE 237 (391)
T ss_pred HHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchH
Confidence 3344688889999999999999999999999999877888888888888856 9999644 3344677766654 7899
Q ss_pred HHHHHHHHHHHHhcccCCCCChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCccceeecc
Q psy1861 319 ELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLIGKY 389 (661)
Q Consensus 319 ~Lgrtyk~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIAaAA 389 (661)
+|-+.-+.+...|+..+....|-.|+.||........ .....+..+++...-+.-+....|..+|||+
T Consensus 238 ~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d~---~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~ 305 (391)
T KOG0653|consen 238 EILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADYDI---KTRTLVKYLLELSLCDYSMLSIPPSSSAAAS 305 (391)
T ss_pred HHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhcch---hHHHHHHHHHHHHHhhhHHhccCcHHHHHHH
Confidence 9999999999999988888899999999998887433 3455666666666556555667778888877
No 35
>KOG2496|consensus
Probab=95.78 E-value=0.04 Score=58.48 Aligned_cols=83 Identities=17% Similarity=0.263 Sum_probs=68.2
Q ss_pred CCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhC----CCHHHHHHHHHHHHHHhcc
Q psy1861 258 RLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQ----ICIFELGRTYLRLSQALCI 333 (661)
Q Consensus 258 ~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~----Vsv~~Lgrtyk~L~k~L~i 333 (661)
+||.+|+-+|..+|++++=.+...--.+..|.++|+|+||+.+..-+|.-+|+.-.. -+...+-+--..+.+.|+.
T Consensus 73 ~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~~k~~e~vLk~E~~llqsL~f 152 (325)
T KOG2496|consen 73 NLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRKWKTHEIVLKYEFLLLQSLKF 152 (325)
T ss_pred CCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhccCcccccHHHHHhchHHHHHhhhh
Confidence 899999999999999999888888888999999999999999999999999998776 4445555555667777776
Q ss_pred cCCCCCh
Q psy1861 334 SIPSMDP 340 (661)
Q Consensus 334 ~~p~~dP 340 (661)
.+-.-.|
T Consensus 153 ~L~vh~P 159 (325)
T KOG2496|consen 153 SLTVHNP 159 (325)
T ss_pred hheecCC
Confidence 5433333
No 36
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=95.24 E-value=0.074 Score=59.69 Aligned_cols=139 Identities=14% Similarity=0.082 Sum_probs=105.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCC-cccHHHHHHHhC--CCHHHHHHH
Q psy1861 247 KRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGT-SHLLIDFSELLQ--ICIFELGRT 323 (661)
Q Consensus 247 ~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~-PrtLkDIsdv~~--Vsv~~Lgrt 323 (661)
-+.|.++=..++|-+.....|..|..+.+..+.+.=.+...|.++|+||||+-+.+ +.+++++.-++. .+.++|.++
T Consensus 217 v~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~a 296 (440)
T COG5024 217 VDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRA 296 (440)
T ss_pred HHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHH
Confidence 46677777888998999999999999999999888888999999999999998774 567889988874 789999999
Q ss_pred HHHHHHHhcccCCCCChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcc-cccCCCCccceeecc
Q psy1861 324 YLRLSQALCISIPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKD-MLHSGRRPNGLIGKY 389 (661)
Q Consensus 324 yk~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d-~i~tGRrP~gIAaAA 389 (661)
++.+...|+.++....|.-|+.|+.....-...+ ...|..+..-..-+ -+...+ |+-+||||
T Consensus 297 E~~ml~~l~f~is~P~P~sFLRriSka~dyd~~s---rt~~k~~~e~s~~~~~f~~~~-~S~~~aaa 359 (440)
T COG5024 297 ERYMLEVLDFNISWPSPMSFLRRISKASDYDIFS---RTPAKFSSEISPVDYKFIQIS-PSWCAAAA 359 (440)
T ss_pred HHHHhhhcccccCCCChHHHHHHHHhhcccchhh---hhhHhhhCCchHhhhhhccCC-chHHHHHH
Confidence 9999999999888888999977777655544321 22333333322211 133344 77777776
No 37
>KOG2740|consensus
Probab=95.13 E-value=0.023 Score=61.36 Aligned_cols=70 Identities=34% Similarity=0.499 Sum_probs=60.3
Q ss_pred cEEEEEeeeCCCchhHHHHHHHHHHHhhhhhhcccceeeeeechHHHHHHhhHHhhcceEeecchHHHHHH
Q psy1861 102 GLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKE 172 (661)
Q Consensus 102 ~l~f~~~~d~~enel~~l~~i~~~ve~ld~~f~~vcEld~~f~~~k~~~ildE~i~~G~v~Ets~~~Il~~ 172 (661)
.+|||.+....---|.+.||.|..|.+|-.|||...|=-|.=|+..+|.+||||+-+|.=.-|-. +|++.
T Consensus 64 ~i~~~~~st~e~pPL~~iefL~rv~dv~~eyFg~~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~-NiLke 133 (418)
T KOG2740|consen 64 LIFFCAVSTVETPPLMVIEFLHRVVDVLLEYFGGLSESKIKDNVVVVYELLDEMIDNGFPLVTEP-NILKE 133 (418)
T ss_pred CcEEEEEEeccCCChhHHHHHHHHHHHHHHHhcccCHhHhhcceeeHHHHHHHHHHcCCCcccCh-hHHHh
Confidence 46888888766669999999999999999999988887788899999999999999998776666 45655
No 38
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=95.03 E-value=0.028 Score=46.32 Aligned_cols=59 Identities=15% Similarity=0.155 Sum_probs=48.8
Q ss_pred hHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCccceeecc---------cccCHHHHHHHHhh
Q psy1861 342 LYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLIGKY---------SCDSHVDISRVAGD 403 (661)
Q Consensus 342 ~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIAaAA---------~~rT~~eIa~~agt 403 (661)
+||.|+++.++++. ++...|..+++++..+.-..+++|..||+|| ...+..+++..++-
T Consensus 1 ~~l~~~~~~~~~~~---~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~ 68 (83)
T smart00385 1 DFLRRVCKALNLDP---ETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGY 68 (83)
T ss_pred CHHHHHHHHcCCCH---HHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC
Confidence 48999999999976 5899999999998875444569999999999 44678888887763
No 39
>KOG0938|consensus
Probab=95.02 E-value=0.044 Score=58.84 Aligned_cols=88 Identities=20% Similarity=0.268 Sum_probs=79.7
Q ss_pred cccccceeeeeeccccEEEEEeeeCCCchhHHHHHHHHHHHhhhhhhcccceeeeeechHHHHHHhhHHhhcceEeecch
Q psy1861 87 FYKFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQ 166 (661)
Q Consensus 87 f~k~~~~k~vyr~ya~l~f~~~~d~~enel~~l~~i~~~ve~ld~~f~~vcEld~~f~~~k~~~ildE~i~~G~v~Ets~ 166 (661)
.......+.+|=|--.||.+.++-++-|-.+++||..-.+..+..|||...|=-|-=||-=.|-+||||+-.|..+.|..
T Consensus 46 V~~igsttf~~~r~~nl~lvaitksN~Nva~v~eFl~kl~avm~aYfgk~~Eeaiknnf~lI~ElLDemld~G~pqnte~ 125 (446)
T KOG0938|consen 46 VLTIGSTTFHHIRSSNLWLVAITKSNANVAAVFEFLYKLDAVMNAYFGKDREEAIKNNFVLIYELLDEMLDFGIPQNTEP 125 (446)
T ss_pred eeEecceeEEEEeeccEEEEEEecCCCchhhHHHHHHHHHHHHHHHhcccchhhhhhceEeHHHHHHHHHhcCCCccCCh
Confidence 34566788899999999999999999999999999999999999999999998888999999999999999999999999
Q ss_pred HHHHHHHh
Q psy1861 167 TKVLKELR 174 (661)
Q Consensus 167 ~~Il~~L~ 174 (661)
..+...+.
T Consensus 126 ~al~~~is 133 (446)
T KOG0938|consen 126 NALKAQIS 133 (446)
T ss_pred hHHHhhhh
Confidence 87665554
No 40
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=94.63 E-value=0.15 Score=45.46 Aligned_cols=87 Identities=10% Similarity=0.029 Sum_probs=66.0
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCC-cccHHHHHHHhCCCHHHHHHHH
Q psy1861 246 CKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGT-SHLLIDFSELLQICIFELGRTY 324 (661)
Q Consensus 246 a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~-PrtLkDIsdv~~Vsv~~Lgrty 324 (661)
.+..|+.+....+....+...|..+...+.-..-.-+-++..+||||+|+|.+..+. +.--..+...++++..+|..++
T Consensus 3 p~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c~ 82 (118)
T PF02984_consen 3 PYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKECI 82 (118)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHHH
Confidence 456777775555556678888888888876554455678899999999999999765 4445567777899999999999
Q ss_pred HHHHHHhc
Q psy1861 325 LRLSQALC 332 (661)
Q Consensus 325 k~L~k~L~ 332 (661)
+.|.+.+.
T Consensus 83 ~~i~~~~~ 90 (118)
T PF02984_consen 83 ELIQELLS 90 (118)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 99988775
No 41
>PF01217 Clat_adaptor_s: Clathrin adaptor complex small chain; InterPro: IPR022775 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the small sigma and mu subunits of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and the zeta and delta subunits of various coatomer (COP) adaptors. The small sigma subunit of AP proteins have been characterised in several species [, , , ]. The sigma subunit plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The zeta subunit of coatomers (zeta-COP) is required for coatomer binding to Golgi membranes and for coat-vesicle assembly [, ]. More information about these proteins can be found at Protein of the Month: Clathrin [].; PDB: 1W63_W 2JKR_I 2VGL_S 2JKT_I 2XA7_S 2HF6_A 3TJZ_C.
Probab=94.37 E-value=0.0069 Score=57.36 Aligned_cols=34 Identities=50% Similarity=0.749 Sum_probs=30.4
Q ss_pred chhhHHhhhhhheeeccccccccccccccccccc
Q psy1861 56 NNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYK 89 (661)
Q Consensus 56 nel~~l~~i~~~ve~ld~~f~~vceld~~~nf~k 89 (661)
|||.++++||.+|++|+.||++|||.++++||+.
T Consensus 76 Nel~~~e~l~~~v~~l~~~~~~v~e~~i~~N~~~ 109 (141)
T PF01217_consen 76 NELLLLEFLHRLVEVLDDYFGNVSEKDILENFDL 109 (141)
T ss_dssp BHHHHHHHHHHHHHHHHHHHSS-SHHHHHHTHHH
T ss_pred chHHHHHHHHHhhhhhhhhhccccHHHHHHCHHH
Confidence 0478999999999999999999999999999986
No 42
>KOG0835|consensus
Probab=91.92 E-value=0.53 Score=50.74 Aligned_cols=105 Identities=16% Similarity=0.211 Sum_probs=76.1
Q ss_pred HHHHHHHHHHhcCCCHHH--HHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHH-HHHHHhCCCHHHHHH
Q psy1861 246 CKRNISSLCNQLRLNQHC--LETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLI-DFSELLQICIFELGR 322 (661)
Q Consensus 246 a~~~I~~i~~~L~Lp~~V--~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLk-DIsdv~~Vsv~~Lgr 322 (661)
..+.|-.+...|++|++. ...|.+|.....--.+..--+++.||+||+|+|.|..++|.+.. .--.+++.++.+|-.
T Consensus 141 Phklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ 220 (367)
T KOG0835|consen 141 PHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDE 220 (367)
T ss_pred cHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHH
Confidence 457788888999999765 67777777666665555556899999999999999999886554 455678888888887
Q ss_pred HHHHHHHHhcccCCCCChhhHHHHHHhhcCC
Q psy1861 323 TYLRLSQALCISIPSMDPCLYVLRYSNRLDF 353 (661)
Q Consensus 323 tyk~L~k~L~i~~p~~dP~~yI~Rf~~~L~L 353 (661)
....+........| + ..+|.-|+..+..
T Consensus 221 ic~~l~~lY~~~~p--~-~~li~~~vd~~k~ 248 (367)
T KOG0835|consen 221 ICYRLIPLYKRAKP--D-ETLIEAFVDRLKR 248 (367)
T ss_pred HHHHHHHHHHhccc--C-HHHHHHHHHHhhH
Confidence 77777665543222 1 3467777766643
No 43
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=91.06 E-value=0.083 Score=40.33 Aligned_cols=24 Identities=25% Similarity=0.605 Sum_probs=19.0
Q ss_pred hhhhhccCCCCcceeeeccccccccceee
Q psy1861 174 RVLRSRCGPSPWRHILEDSVIVSEMQFEE 202 (661)
Q Consensus 174 ~~lcs~CG~~~~g~VLeE~~Ivse~tF~e 202 (661)
..+|+.|| .||+|+.|+++++|.+
T Consensus 19 ~~vC~~CG-----~Vl~e~~i~~~~e~r~ 42 (43)
T PF08271_consen 19 ELVCPNCG-----LVLEENIIDEGPEWRE 42 (43)
T ss_dssp EEEETTT------BBEE-TTBSCCCSCCH
T ss_pred eEECCCCC-----CEeecccccCCccccc
Confidence 35789999 8999999999999863
No 44
>KOG0655|consensus
Probab=89.43 E-value=1.8 Score=46.92 Aligned_cols=111 Identities=12% Similarity=0.178 Sum_probs=90.8
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCC-CCCCchHHHHHHHHHHHHHHhCC-cccHHHHHHHhC--CCHHHHH
Q psy1861 246 CKRNISSLCNQLRLNQHCLETSFNLYKMALSRNL-TKGRRQILVCAACVYMTCRLEGT-SHLLIDFSELLQ--ICIFELG 321 (661)
Q Consensus 246 a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l-~rGR~~~~VaAACLYiACR~~~~-PrtLkDIsdv~~--Vsv~~Lg 321 (661)
-.+.+-++|..-.|....---|..+|.+...-.. ..--....+--+|||||.+.+.+ |--+.|||-++. ++..+|.
T Consensus 148 LlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIl 227 (408)
T KOG0655|consen 148 LLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDIL 227 (408)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHHHH
Confidence 4688889999999998888889999988775321 11224466778999999999884 788999999974 7899999
Q ss_pred HHHHHHHHHhcccCCCCChhhHHHHHHhhcCCCcc
Q psy1861 322 RTYLRLSQALCISIPSMDPCLYVLRYSNRLDFGAK 356 (661)
Q Consensus 322 rtyk~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~~~ 356 (661)
+.-+.|.+.|+..+.++....++.-|..-+.+++.
T Consensus 228 tmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~ 262 (408)
T KOG0655|consen 228 TMELIILKALKWELSPITIISWLNVYLQVDALNDA 262 (408)
T ss_pred HHHHHHHHHhcccccceehHHHHHHHHHHHhcCCC
Confidence 99999999999998888888888888887776653
No 45
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=88.72 E-value=6.5 Score=37.75 Aligned_cols=89 Identities=8% Similarity=0.073 Sum_probs=68.4
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHh---CCC--CCCCchHHHHHHHHHHHHHH-hCCcccHHHHHHHhCCCHHH
Q psy1861 246 CKRNISSLCNQLRLNQHCLETSFNLYKMALS---RNL--TKGRRQILVCAACVYMTCRL-EGTSHLLIDFSELLQICIFE 319 (661)
Q Consensus 246 a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e---~~l--~rGR~~~~VaAACLYiACR~-~~~PrtLkDIsdv~~Vsv~~ 319 (661)
..++|.++....+++..+.-.|..+..+... ... +.......+..+|+-+|.+. .....+.+.+|.+.|++.++
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~e 133 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKE 133 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHH
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHH
Confidence 4578888999999999999999999999888 222 34456777899999999996 55889999999999999999
Q ss_pred HHHHHHHHHHHhccc
Q psy1861 320 LGRTYLRLSQALCIS 334 (661)
Q Consensus 320 Lgrtyk~L~k~L~i~ 334 (661)
|.+.-..+...|+.+
T Consensus 134 ln~lE~~fL~~l~~~ 148 (149)
T PF08613_consen 134 LNELEREFLKLLDYN 148 (149)
T ss_dssp HHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHCCCc
Confidence 999999999988754
No 46
>KOG3343|consensus
Probab=86.98 E-value=0.85 Score=44.51 Aligned_cols=71 Identities=11% Similarity=0.251 Sum_probs=58.9
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCcccceecCeEEEeeecceEEEEEEEcCCCchhhHHhhhhhheeecccccccc
Q psy1861 5 DDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNV 78 (661)
Q Consensus 5 ~~~~~~l~~ei~~~~~~R~~~~cnf~e~~~~kivyrryAsL~f~~~vd~~enel~~l~~i~~~ve~ld~~f~~v 78 (661)
-++|...++-+|++-.+ ...-.+-+.+..+|||-+--|||-+.=...||||......+.+.+.++..+.+.
T Consensus 35 vkeqkaFEK~lF~KT~k---t~~eI~~ldg~~vvYk~~~Dl~fyv~G~~~ENEl~L~svL~~l~dal~llLr~n 105 (175)
T KOG3343|consen 35 VKEQKAFEKNLFSKTSK---TESEILLLDGNTVVYKSVIDLHFYVVGSEEENELMLMSVLTCLFDALSLLLRKN 105 (175)
T ss_pred HHHHHHHHHHHhccccc---ccceeEEecCcEEEEEecccEEEEEecCcchhHHHHHHHHHHHHHHHHHHHHhC
Confidence 67899999999998644 445566678999999999999999998999999998888888887777766543
No 47
>KOG4557|consensus
Probab=86.33 E-value=8.4 Score=39.59 Aligned_cols=157 Identities=16% Similarity=0.149 Sum_probs=109.1
Q ss_pred HHHHHHHhcCCC--HHHHHHHHHHHHHHHhC--CCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHH
Q psy1861 249 NISSLCNQLRLN--QHCLETSFNLYKMALSR--NLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTY 324 (661)
Q Consensus 249 ~I~~i~~~L~Lp--~~V~e~A~~iyk~a~e~--~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrty 324 (661)
.|.+++.+|||. +.+.+.|.+|.+...-+ +..-|-.-..-+.-|+=+|.-.-++|.-=.-.-...|.+++.-.+.+
T Consensus 2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKLSGl~k~~Y~~~~ 81 (262)
T KOG4557|consen 2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKLSGLSKKAYSRSF 81 (262)
T ss_pred cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHhccccHHHHHHHH
Confidence 478999999994 68999999998887643 44445444555777888888888888766666677899999999999
Q ss_pred HHHHHHhcccCCCCChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcc-------cccCCCCccceeecc--------
Q psy1861 325 LRLSQALCISIPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKD-------MLHSGRRPNGLIGKY-------- 389 (661)
Q Consensus 325 k~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d-------~i~tGRrP~gIAaAA-------- 389 (661)
+.+...||++.. .-|..+|-.||.- +|++.|..++...+.. .... -+|.=.+||.
T Consensus 82 ~sfe~llgln~~-----~~VrdlaVQfgc~----evi~~a~~vl~syk~~lpaT~~~~~D~-SrP~ft~aA~~~ack~lK 151 (262)
T KOG4557|consen 82 NSFENLLGLNIK-----LNVRDLAVQFGCV----EVIKSAQNVLSSYKERLPATRRANADF-SRPVFTAAAFYLACKKLK 151 (262)
T ss_pred HHHHHHhcchhh-----cCHHHHHHHHhHH----HHHHHHHHHHHHHHhcCchhhhcCCcc-cchHHHHHHHHHHHHHHH
Confidence 999999998533 2456677777764 4888898888876641 1111 2355444444
Q ss_pred cccCHHHHHHHHhhhhhhhhcchHHH
Q psy1861 390 SCDSHVDISRVAGDDYIKSNELPRVI 415 (661)
Q Consensus 390 ~~rT~~eIa~~agtiR~~ykeL~~~~ 415 (661)
.+++......++|+..-.+.-|.+.+
T Consensus 152 lKVdK~kli~~sg~~~s~F~~l~kql 177 (262)
T KOG4557|consen 152 LKVDKLKLIEVSGTSESEFSCLSKQL 177 (262)
T ss_pred HhhhHhhcccccCCCHHHHHHHHHHH
Confidence 45555666667776655444444333
No 48
>KOG4164|consensus
Probab=82.25 E-value=4.1 Score=45.13 Aligned_cols=88 Identities=15% Similarity=0.247 Sum_probs=65.5
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCc-c---cHHHH-HHHhCCCHHHH
Q psy1861 246 CKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTS-H---LLIDF-SELLQICIFEL 320 (661)
Q Consensus 246 a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~P-r---tLkDI-sdv~~Vsv~~L 320 (661)
..+++++++..-+|....+.+|..+|.+..=+|++.-.+...+|+|||.+|.+.+..- . +|+|= -+.+..+..+|
T Consensus 385 lKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrrdL 464 (497)
T KOG4164|consen 385 LKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRRDL 464 (497)
T ss_pred HHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHHhh
Confidence 4467777777778888899999999999999999887788899999999999988653 2 33332 23467777776
Q ss_pred HHHHHHHHHHhcc
Q psy1861 321 GRTYLRLSQALCI 333 (661)
Q Consensus 321 grtyk~L~k~L~i 333 (661)
-..-.-++-.|.+
T Consensus 465 ia~Ef~VlvaLef 477 (497)
T KOG4164|consen 465 IAFEFPVLVALEF 477 (497)
T ss_pred hhhhhhHHHhhhh
Confidence 6655555555544
No 49
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=79.60 E-value=6.3 Score=32.28 Aligned_cols=72 Identities=13% Similarity=0.110 Sum_probs=45.5
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCC-CHHHHHHHHHHHH
Q psy1861 250 ISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQI-CIFELGRTYLRLS 328 (661)
Q Consensus 250 I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~V-sv~~Lgrtyk~L~ 328 (661)
|..+|..+|++....... |+.........-.....+..|+-|+.. .+.++.|+|..+|. +...+.+.|++..
T Consensus 4 ~~~la~~~~~s~~~l~~~---f~~~~~~s~~~~~~~~r~~~a~~~l~~----~~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 4 LEDLAEALGMSPRHLQRL---FKKETGTTPKQYLRDRRLERARRLLRD----TDLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred HHHHHHHhCCCHHHHHHH---HHHHhCcCHHHHHHHHHHHHHHHHHHc----CCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 678899999987554333 333332222111112233445555532 28999999999999 9999999997653
No 50
>PF05460 ORC6: Origin recognition complex subunit 6 (ORC6); InterPro: IPR008721 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 6, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; interacts with Spp1 and with trimethylated histone H3; phosphorylated by Cdc28 [, ]. In Saccharomyces cerevisiae (Baker's yeast), both ends of the Orc6 interact with Cdt1 [] and the N terminus mediates an interaction with the S-phase cyclin Clb5 []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex; PDB: 3M03_B.
Probab=79.49 E-value=0.59 Score=51.39 Aligned_cols=78 Identities=14% Similarity=0.081 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHHHHH-hCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHhcccC
Q psy1861 258 RLNQHCLETSFNLYKMAL-SRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQALCISI 335 (661)
Q Consensus 258 ~Lp~~V~e~A~~iyk~a~-e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~ 335 (661)
++|+.++..|..||++.. ....+++..-.+-+.+|+||||...+.+.-+.......+++++...+.|..|.+.|+...
T Consensus 11 ~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~pl~pk~y~~l~~~~~~~L~~~s 89 (353)
T PF05460_consen 11 GLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRSPLPPKVYKKLLNTFENLLGNSS 89 (353)
T ss_dssp -------------------------------------------------------------------------------
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCCCCCHHHHHHHHHHHHHHHhCCC
Confidence 456899999999999998 455667666666789999999999999998888888889999999999999999888754
No 51
>KOG1010|consensus
Probab=75.57 E-value=6 Score=47.68 Aligned_cols=83 Identities=13% Similarity=0.250 Sum_probs=71.1
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhC--CCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHH
Q psy1861 245 NCKRNISSLCNQLRLNQHCLETSFNLYKMALSR--NLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGR 322 (661)
Q Consensus 245 ~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~--~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgr 322 (661)
-|..+|+.+|.+|.|.+...+.-..+|.-...+ .+++-|..+.+.-+|+|+.||..+...|+.+|-....--+.....
T Consensus 679 LAavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~QPqa~~~ 758 (920)
T KOG1010|consen 679 LAAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRRQPQAVSL 758 (920)
T ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhcCchhhhh
Confidence 478899999999999999999988888877654 578899999999999999999999999999998877666666666
Q ss_pred HHHHH
Q psy1861 323 TYLRL 327 (661)
Q Consensus 323 tyk~L 327 (661)
+|+.+
T Consensus 759 vyRsV 763 (920)
T KOG1010|consen 759 VYRSV 763 (920)
T ss_pred hhhhe
Confidence 66654
No 52
>KOG4557|consensus
Probab=74.87 E-value=9.4 Score=39.27 Aligned_cols=85 Identities=15% Similarity=0.147 Sum_probs=57.8
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhC-----CCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHH
Q psy1861 246 CKRNISSLCNQLRLNQHCLETSFNLYKMALSR-----NLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFEL 320 (661)
Q Consensus 246 a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~-----~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~L 320 (661)
..-.|+.+|-++|+.+ ++..|.++.+...++ ..-.--+.....+|++|.|||..+....=.-+-.+.|+++..+
T Consensus 92 ~~~~VrdlaVQfgc~e-vi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~~sg~~~s~F 170 (262)
T KOG4557|consen 92 IKLNVRDLAVQFGCVE-VIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIEVSGTSESEF 170 (262)
T ss_pred hhcCHHHHHHHHhHHH-HHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhcccccCCCHHHH
Confidence 3455778888888866 677788887766552 1111234457899999999999887655555556678888777
Q ss_pred HHHHHHHHHHh
Q psy1861 321 GRTYLRLSQAL 331 (661)
Q Consensus 321 grtyk~L~k~L 331 (661)
....+++.+..
T Consensus 171 ~~l~kqler~~ 181 (262)
T KOG4557|consen 171 SCLSKQLERNY 181 (262)
T ss_pred HHHHHHHHHHH
Confidence 66666665544
No 53
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=72.06 E-value=10 Score=33.24 Aligned_cols=47 Identities=13% Similarity=0.080 Sum_probs=38.1
Q ss_pred hHHHHHHHHHHHHHHhCCcccHHHHHHHhC-CCHHHHHHHHHHHHHHhcc
Q psy1861 285 QILVCAACVYMTCRLEGTSHLLIDFSELLQ-ICIFELGRTYLRLSQALCI 333 (661)
Q Consensus 285 ~~~VaAACLYiACR~~~~PrtLkDIsdv~~-Vsv~~Lgrtyk~L~k~L~i 333 (661)
....=..|+|++-+..| .|+.+|+..+| .+-.++..+++++.+.+..
T Consensus 28 ~~~aR~ia~yl~~~~~~--~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 28 IALARQIAMYLARELTG--LSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred cchHHHHHHHHHHHHhC--CCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 33334467887777665 78999999999 9999999999999998864
No 54
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=71.17 E-value=4.1 Score=39.73 Aligned_cols=85 Identities=15% Similarity=0.219 Sum_probs=69.9
Q ss_pred ccceeeeeeccccEEEEEeeeCCCchhHHHHHHHHHHHhhhhhhcccce-eeeeechHHHHHHhhHHhhcceEeecchHH
Q psy1861 90 FRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCE-LDLVFNFYKVYTVVDEMFLAGEIRETSQTK 168 (661)
Q Consensus 90 ~~~~k~vyr~ya~l~f~~~~d~~enel~~l~~i~~~ve~ld~~f~~vcE-ld~~f~~~k~~~ildE~i~~G~v~Ets~~~ 168 (661)
+.|--++|++|--.-|.++.--.|||.-+.....-|--.|+-.|..+-. =.+.=|+|..-.+.||.|-+|-|+||....
T Consensus 66 f~d~lV~~k~~~dv~~yiv~~meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet~s~~ 145 (187)
T COG5541 66 FYDRLVMCKRLDDVLLYIVSPMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDE 145 (187)
T ss_pred EcceeeeeeeehhEEEEEecccccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeecChHH
Confidence 3455678999988888888888899999998888888888888876632 336668888888889999999999999999
Q ss_pred HHHHHh
Q psy1861 169 VLKELR 174 (661)
Q Consensus 169 Il~~L~ 174 (661)
|.+++.
T Consensus 146 ia~rv~ 151 (187)
T COG5541 146 IADRVP 151 (187)
T ss_pred HHHhCC
Confidence 987743
No 55
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=71.09 E-value=44 Score=36.25 Aligned_cols=71 Identities=11% Similarity=-0.048 Sum_probs=48.1
Q ss_pred CHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCC--CHHHHHHHHHHHHHHh
Q psy1861 260 NQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQI--CIFELGRTYLRLSQAL 331 (661)
Q Consensus 260 p~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~V--sv~~Lgrtyk~L~k~L 331 (661)
++.+...|..+...+.---+.=--.+..+|+||||+|+|..++...-.+ .+++.+ +...++.....+.+..
T Consensus 180 ~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA~~~~~~~l~~~~-~e~~~~~~~~~~~~~l~~~~~~~~ 252 (305)
T TIGR00569 180 PEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNMESYL-TEQLSVPGNREELPQLIDIMRELR 252 (305)
T ss_pred hHHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHHHHHHhCCCCcccc-hhhhcccccHHHHHHHHHHHHHHH
Confidence 4567788888877766544322367899999999999999997433322 256666 5677776666665543
No 56
>KOG2635|consensus
Probab=71.03 E-value=4.2 Score=45.56 Aligned_cols=66 Identities=30% Similarity=0.522 Sum_probs=54.5
Q ss_pred CCCcccceecCeEEEeeecceEEEEEEEcCCCchhhHHhhhhhheeecccccccccc-------ccccccccc
Q psy1861 24 AKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCE-------LDLVFNFYK 89 (661)
Q Consensus 24 ~~~cnf~e~~~~kivyrryAsL~f~~~vd~~enel~~l~~i~~~ve~ld~~f~~vce-------ld~~~nf~k 89 (661)
..+--|+|-+.++.||+-.-.||.+++...+-|-|--|+.++.|..+...|-.++=| +++||-|++
T Consensus 43 ~~qhT~vEt~~VRYVYqP~d~lY~vLITtk~SNIleDl~TL~Lfskvipey~~slde~eI~~~~FelifAFDE 115 (512)
T KOG2635|consen 43 GKQHTFVETDSVRYVYQPLDNLYIVLITTKQSNILEDLETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDE 115 (512)
T ss_pred CCCccEEecccEEEEEEecccEEEEEEeccccchhhHHHHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccch
Confidence 457789999999999999999999999999999998888888888888887654433 456666665
No 57
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=67.01 E-value=19 Score=36.48 Aligned_cols=75 Identities=12% Similarity=0.254 Sum_probs=65.6
Q ss_pred eeeeeeccccEEEEEeeeCCCchhHHHHHHHHHHHhhhhhhcccce-eeeeechHHHHHHhhHHhhcceEeecchH
Q psy1861 93 FKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCE-LDLVFNFYKVYTVVDEMFLAGEIRETSQT 167 (661)
Q Consensus 93 ~k~vyr~ya~l~f~~~~d~~enel~~l~~i~~~ve~ld~~f~~vcE-ld~~f~~~k~~~ildE~i~~G~v~Ets~~ 167 (661)
-.+|+....++.|..+.|..||-+..--+...|+-.|=.+|...-- -++....|++..||+.++=.|.+.=.|..
T Consensus 104 k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~ 179 (189)
T PF15001_consen 104 KIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQLLFLNHR 179 (189)
T ss_pred cEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHH
Confidence 3688999999999999999999999999999999998877744432 55677999999999999999999988877
No 58
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=66.54 E-value=12 Score=35.30 Aligned_cols=47 Identities=21% Similarity=0.207 Sum_probs=40.4
Q ss_pred chHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 284 RQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 284 ~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
+.+.-+.|++|+|-+..+.|.+..+||+.++++...+.+....|.+.
T Consensus 6 ~~~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 6 KGRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45566788999997766678999999999999999999999998873
No 59
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=65.98 E-value=9.8 Score=27.64 Aligned_cols=27 Identities=15% Similarity=0.183 Sum_probs=22.4
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy1861 303 SHLLIDFSELLQICIFELGRTYLRLSQ 329 (661)
Q Consensus 303 PrtLkDIsdv~~Vsv~~Lgrtyk~L~k 329 (661)
|.|-.|||+.+|++..++.|++++|.+
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLER 28 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 678899999999999999999999876
No 60
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=65.30 E-value=9.9 Score=32.70 Aligned_cols=46 Identities=17% Similarity=0.161 Sum_probs=37.4
Q ss_pred hHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 285 QILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 285 ~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
.+.-+-+.+|+|-...+.|.+..+||+.++++...+.+....|.+.
T Consensus 7 ~~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 7 TDYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA 52 (83)
T ss_dssp HHHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC
Confidence 3445667788888777788999999999999999999999999883
No 61
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=63.36 E-value=18 Score=29.91 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=26.7
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 302 TSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 302 ~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
.|.|..+||+.+|++..++.++.+.|.+.
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~ 55 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDE 55 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 47899999999999999999999999874
No 62
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=63.02 E-value=26 Score=33.84 Aligned_cols=46 Identities=13% Similarity=0.035 Sum_probs=35.5
Q ss_pred hHHHHHHHHHHHHHHhC----------CcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 285 QILVCAACVYMTCRLEG----------TSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 285 ~~~VaAACLYiACR~~~----------~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
...=+|..|+.-|+..+ .|.|..|||+.+|++..++.|+.++|.+.
T Consensus 115 ~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 115 MGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred HHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 33345556555455543 67899999999999999999999999884
No 63
>KOG2635|consensus
Probab=61.55 E-value=13 Score=41.80 Aligned_cols=73 Identities=25% Similarity=0.411 Sum_probs=62.1
Q ss_pred cccccceeeeeeccccEEEEEeeeCCCchhHHHHHHHHHHHhhhhhhcccceeeeeechHHHHHHhhHHhhcc
Q psy1861 87 FYKFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAG 159 (661)
Q Consensus 87 f~k~~~~k~vyr~ya~l~f~~~~d~~enel~~l~~i~~~ve~ld~~f~~vcEld~~f~~~k~~~ildE~i~~G 159 (661)
|.+...+|-||+=.-.||++++...+-|.|.-|+..++|..+...|-..+=|.-|+=|---..+-.||++.=|
T Consensus 48 ~vEt~~VRYVYqP~d~lY~vLITtk~SNIleDl~TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLG 120 (512)
T KOG2635|consen 48 FVETDSVRYVYQPLDNLYIVLITTKQSNILEDLETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLG 120 (512)
T ss_pred EEecccEEEEEEecccEEEEEEeccccchhhHHHHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhc
Confidence 5567789999999999999999999999999999999999999999988877776655444445558888888
No 64
>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=57.96 E-value=25 Score=27.44 Aligned_cols=34 Identities=12% Similarity=-0.034 Sum_probs=28.8
Q ss_pred HHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy1861 298 RLEGTSHLLIDFSELLQICIFELGRTYLRLSQAL 331 (661)
Q Consensus 298 R~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L 331 (661)
..++-|.|..++|+.++|+..+|.+..+.|...+
T Consensus 10 ~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 10 LESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 3556679999999999999999999999997766
No 65
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=57.93 E-value=4.3 Score=36.00 Aligned_cols=48 Identities=17% Similarity=0.115 Sum_probs=37.5
Q ss_pred ChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCccceeecc
Q psy1861 339 DPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLIGKY 389 (661)
Q Consensus 339 dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIAaAA 389 (661)
.|..|+.+|....+. ..++...|..+++.+..+.-..+-+|+-|||||
T Consensus 2 Tp~~Fl~~~~~~~~~---~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAa 49 (118)
T PF02984_consen 2 TPYDFLRRFLKISNA---DQEVRNLARYLLELSLLDYEFLQYPPSVIAAAA 49 (118)
T ss_dssp -HHHHHHHHHTSSSH---HHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHH
T ss_pred cHHHHHHHHHHHcCC---cHHHHHHHHHHHHHHHhhccccCCCHHHHHHHH
Confidence 578999999554333 346889999999988877778889999999999
No 66
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=57.61 E-value=19 Score=28.51 Aligned_cols=37 Identities=11% Similarity=0.045 Sum_probs=31.2
Q ss_pred hCCcccHHHHHHHhCCCHHHHHHHHHHHHHHhcccCC
Q psy1861 300 EGTSHLLIDFSELLQICIFELGRTYLRLSQALCISIP 336 (661)
Q Consensus 300 ~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~p 336 (661)
-+.-.+..++|..+||+..++.+.+..+...|....|
T Consensus 16 LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l~ 52 (53)
T PF13613_consen 16 LRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVLK 52 (53)
T ss_pred HHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhcC
Confidence 3445899999999999999999999999998865443
No 67
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=56.94 E-value=21 Score=35.08 Aligned_cols=47 Identities=21% Similarity=0.186 Sum_probs=39.6
Q ss_pred chHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 284 RQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 284 ~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
+.+.-+.+++|+|-...+-|.+..+||+.++++..-+.+....|.+.
T Consensus 6 ~~~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~a 52 (164)
T PRK10857 6 KGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKN 52 (164)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45666788899995555678999999999999999999999998873
No 68
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=55.84 E-value=24 Score=34.14 Aligned_cols=46 Identities=11% Similarity=0.093 Sum_probs=38.6
Q ss_pred chHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 284 RQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 284 ~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
+.+.-+-|++|+| ...+.+.+..+||+..+++..-|.+....|.+.
T Consensus 6 ~~~YAlr~L~~LA-~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 6 QTNYAIRMLMYCA-ANDGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HHhHHHHHHHHHH-hCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4456677899999 445668899999999999999999999999884
No 69
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=54.65 E-value=34 Score=28.00 Aligned_cols=37 Identities=22% Similarity=0.257 Sum_probs=31.0
Q ss_pred HHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy1861 292 CVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQ 329 (661)
Q Consensus 292 CLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k 329 (661)
+||.... .+.+.+..|||..++|++.++....++|.+
T Consensus 12 ~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 12 AIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 4566555 778899999999999999999999999876
No 70
>KOG0937|consensus
Probab=52.43 E-value=14 Score=41.59 Aligned_cols=58 Identities=14% Similarity=0.240 Sum_probs=52.0
Q ss_pred CCCCcccceecCeEEEeeecceEEEEEEEcCCCchhhHHhhhhhheeecccccccccc
Q psy1861 23 DAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCE 80 (661)
Q Consensus 23 ~~~~cnf~e~~~~kivyrryAsL~f~~~vd~~enel~~l~~i~~~ve~ld~~f~~vce 80 (661)
.+..--|+.+++...+|-++-.||++.+.-.+-|-..+|+|++.+++++-.||+..-|
T Consensus 41 ~~~~~p~l~~~g~~~~~ik~s~lylv~~~~~n~~a~~v~~~l~~~~~v~~~y~~~l~e 98 (424)
T KOG0937|consen 41 GDESPPFLVHDGSRFIHIKHSNLYLVAGTRPNVSAALVLSFLYAVADVFGDYLSELEE 98 (424)
T ss_pred cCCCCCeEEeCCceEEEEeecceEEEEEeccCCCHHHHHHHHHHHHHHHHHHhccCCc
Confidence 3456788999999999999999999999988899999999999999999999985544
No 71
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=51.80 E-value=50 Score=26.30 Aligned_cols=30 Identities=13% Similarity=0.122 Sum_probs=26.9
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 301 GTSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 301 ~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
..+.+..|||+.++++..++.+.+..|.+.
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 357899999999999999999999999874
No 72
>KOG1010|consensus
Probab=50.86 E-value=57 Score=39.78 Aligned_cols=78 Identities=17% Similarity=0.303 Sum_probs=57.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHH-hCCCHHHHHHHHH
Q psy1861 247 KRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSEL-LQICIFELGRTYL 325 (661)
Q Consensus 247 ~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv-~~Vsv~~Lgrtyk 325 (661)
.......|..|+|++.....|..-|..+...--+-| +-.++.|.++|.+||..++|.-.+-+... ..|+--.|-++++
T Consensus 35 ~q~~~~~c~~lnld~~~~~ea~d~yta~~q~~sleg-s~~hW~~cAlY~~~r~S~~~~v~~~~~~~~n~vsL~~Ilrs~k 113 (920)
T KOG1010|consen 35 EQDSDELCRPLNLDEQTETEAWDTYTAVSQRLSLEG-SESHWLACALYTACRRSSVPTVGGGIVEGKNEVSLTRILRSFK 113 (920)
T ss_pred hhhhhhhhhhhcccchhhhhhHHHHHHHHhHhCCCc-cHHHHHHHHHHHHHHhccCCccCcceeeecceehHHHHHHHHH
Confidence 456778899999999999999999998887555555 46799999999999999776544444333 3344444444443
No 73
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=50.81 E-value=48 Score=25.51 Aligned_cols=43 Identities=14% Similarity=0.040 Sum_probs=30.3
Q ss_pred CCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHH
Q psy1861 282 GRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRL 327 (661)
Q Consensus 282 GR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L 327 (661)
+.+...-..+-++-.|+.. .|+++||..++++..++++.+...
T Consensus 9 ~~r~T~~~~~~i~~~~~~~---~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 9 YCRITKRLEQYILKLLRES---RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCcHHHHHHHHHHHHHhhc---CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3344444444444444433 799999999999999999998753
No 74
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=49.50 E-value=12 Score=31.04 Aligned_cols=51 Identities=16% Similarity=0.209 Sum_probs=31.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCc
Q psy1861 305 LLIDFSELLQICIFELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRP 382 (661)
Q Consensus 305 tLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP 382 (661)
+..|+|+.++|+..+|.+.+++ - ..-|.+++.+++..++++- +|+.+|..|
T Consensus 14 ~~~~lA~~lgis~st~s~~~~~----r-----~~~P~~~l~~ia~~~gvsl------------------~WLltG~g~ 64 (66)
T PF07022_consen 14 SDKELAERLGISKSTLSNNWKK----R-----GSIPAEWLIKIALETGVSL------------------DWLLTGKGE 64 (66)
T ss_dssp SCHHHHCCTT--HHHHH-HHHH----S-----SS--HHHHHHHHHHH---H------------------HHHHC-SS-
T ss_pred CHHHHHHHhCcCHHHhhHHHHh----C-----CCCCHHHHHHHHHHHCcCH------------------HHHHhCCCC
Confidence 6679999999999999843322 1 1236889999999888754 788888765
No 75
>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=49.40 E-value=42 Score=26.48 Aligned_cols=40 Identities=20% Similarity=0.189 Sum_probs=31.6
Q ss_pred HHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy1861 290 AACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQ 329 (661)
Q Consensus 290 AACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k 329 (661)
..+|++.....+.+.|+.||++.+++++..+.+..+.|.+
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4455555555555689999999999999999999999876
No 76
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=48.41 E-value=36 Score=31.37 Aligned_cols=45 Identities=11% Similarity=0.002 Sum_probs=35.7
Q ss_pred hHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy1861 285 QILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQ 329 (661)
Q Consensus 285 ~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k 329 (661)
.+.-+.+.+|++-...+.|.+..+||+.++++...+.+....|.+
T Consensus 7 ~~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 7 TEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRR 51 (132)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344566677777332345999999999999999999999999987
No 77
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=47.12 E-value=43 Score=31.02 Aligned_cols=46 Identities=9% Similarity=-0.028 Sum_probs=37.9
Q ss_pred chHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 284 RQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 284 ~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
..+..+.+.+|++- ..+.|.+..|||+.++++...+.+....|.+.
T Consensus 7 ~~~yal~~l~~la~-~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~ 52 (130)
T TIGR02944 7 LTDYATLVLTTLAQ-NDSQPYSAAEIAEQTGLNAPTVSKILKQLSLA 52 (130)
T ss_pred HHhHHHHHHHHHHh-CCCCCccHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45566777888874 34568999999999999999999999999873
No 78
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=46.63 E-value=23 Score=27.67 Aligned_cols=41 Identities=12% Similarity=0.139 Sum_probs=28.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCCh--hhHHHHHHhhcCC
Q psy1861 305 LLIDFSELLQICIFELGRTYLRLSQALCISIPSMDP--CLYVLRYSNRLDF 353 (661)
Q Consensus 305 tLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~p~~dP--~~yI~Rf~~~L~L 353 (661)
||+|||..+||+..++.+++ +- .+.+.| ..-|...+.+||.
T Consensus 1 Ti~dIA~~agvS~~TVSr~l-------n~-~~~vs~~tr~rI~~~a~~lgY 43 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVL-------NG-PPRVSEETRERILEAAEELGY 43 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHH-------TT-CSSSTHHHHHHHHHHHHHHTB
T ss_pred CHHHHHHHHCcCHHHHHHHH-------hC-CCCCCHHHHHHHHHHHHHHCC
Confidence 78999999999999998774 22 244554 3456666666654
No 79
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.01 E-value=87 Score=29.02 Aligned_cols=71 Identities=15% Similarity=0.206 Sum_probs=50.1
Q ss_pred HHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCChhhH-HHHHHhhcCCCcccHHHHHHHHHHHH
Q psy1861 291 ACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQALCISIPSMDPCLY-VLRYSNRLDFGAKTHEVTMTALRILQ 369 (661)
Q Consensus 291 ACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~p~~dP~~y-I~Rf~~~L~L~~~~~~V~~~A~~Iv~ 369 (661)
.-||+-|| =.|+||-..+|++-.+++.-+-++.+.+|.++...+|.+. =..+.+.|+-|+-+ ...|.++++
T Consensus 50 v~lf~r~R-----GnlKEvEr~lg~sYptvR~kld~vlramgy~p~~e~~~~i~~~~i~~qle~Gei~---peeA~~~L~ 121 (122)
T COG3877 50 VELFLRCR-----GNLKEVERELGISYPTVRTKLDEVLRAMGYNPDSENSVNIGKKKIIDQLEKGEIS---PEEAIKMLN 121 (122)
T ss_pred HHHHHHHc-----cCHHHHHHHHCCccHHHHHHHHHHHHHcCCCCCCCChhhhhHHHHHHHHHcCCCC---HHHHHHHhc
Confidence 34677777 3689999999999999999999999999998777777544 12344555444321 245555543
No 80
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=45.54 E-value=29 Score=25.80 Aligned_cols=27 Identities=15% Similarity=0.070 Sum_probs=20.1
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHH
Q psy1861 301 GTSHLLIDFSELLQICIFELGRTYLRL 327 (661)
Q Consensus 301 ~~PrtLkDIsdv~~Vsv~~Lgrtyk~L 327 (661)
..+.++.|||+.++++...+.+.|++.
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 457899999999999999999888654
No 81
>KOG2740|consensus
Probab=45.42 E-value=20 Score=39.57 Aligned_cols=82 Identities=27% Similarity=0.435 Sum_probs=57.0
Q ss_pred cCeEE--EeeecceEEEEEEEcCCCchhhHHhhhhhheeecccccccccccccccccccccceeeeeeccccEEEEEeee
Q psy1861 33 RNFKI--VYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKFRNFKIVYRRYAGLYFCICVD 110 (661)
Q Consensus 33 ~~~ki--vyrryAsL~f~~~vd~~enel~~l~~i~~~ve~ld~~f~~vceld~~~nf~k~~~~k~vyr~ya~l~f~~~~d 110 (661)
..+.+ |||. .+|||.+...+--.|-+.||+|..+.++-.||+...|--|-=|
T Consensus 53 p~hylfsv~~~--~i~~~~~st~e~pPL~~iefL~rv~dv~~eyFg~~s~~~Ik~N------------------------ 106 (418)
T KOG2740|consen 53 PHHYLFSVYRD--LIFFCAVSTVETPPLMVIEFLHRVVDVLLEYFGGLSESKIKDN------------------------ 106 (418)
T ss_pred Cceeeeeeecc--CcEEEEEEeccCCChhHHHHHHHHHHHHHHHhcccCHhHhhcc------------------------
Confidence 34444 4554 5788888876666999999999999999999994333211111
Q ss_pred CCCchhHHHHHHHHHHHhhhhhhcccceeeeeechHHHHHHhhHHhh
Q psy1861 111 VNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFL 157 (661)
Q Consensus 111 ~~enel~~l~~i~~~ve~ld~~f~~vcEld~~f~~~k~~~ildE~i~ 157 (661)
-.-|. +++-|.+|.=|-++.|- .||-|+|-
T Consensus 107 ----~~vv~---ell~emiDnGfpl~tE~----------NiLke~i~ 136 (418)
T KOG2740|consen 107 ----VVVVY---ELLDEMIDNGFPLVTEP----------NILKELIP 136 (418)
T ss_pred ----eeeHH---HHHHHHHHcCCCcccCh----------hHHHhhcC
Confidence 11222 45778889999999984 67777764
No 82
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=45.10 E-value=73 Score=32.00 Aligned_cols=30 Identities=13% Similarity=0.109 Sum_probs=26.9
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy1861 302 TSHLLIDFSELLQICIFELGRTYLRLSQAL 331 (661)
Q Consensus 302 ~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L 331 (661)
.|.|..+||+.+|++..++.|..++|.+.=
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g 212 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKSG 212 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHCC
Confidence 578999999999999999999999887743
No 83
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=42.27 E-value=94 Score=30.48 Aligned_cols=29 Identities=10% Similarity=0.059 Sum_probs=26.5
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 302 TSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 302 ~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
.|.|.++||+.+|++..++.|..++|.+.
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 48899999999999999999999999774
No 84
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=41.63 E-value=40 Score=24.99 Aligned_cols=29 Identities=24% Similarity=0.241 Sum_probs=26.2
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 302 TSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 302 ~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
.|.+..|+|+.++++..++.+..+.|.+.
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 57899999999999999999999998773
No 85
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=41.41 E-value=1.2e+02 Score=26.87 Aligned_cols=39 Identities=5% Similarity=0.043 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHH
Q psy1861 288 VCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRL 327 (661)
Q Consensus 288 VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L 327 (661)
+..++-|+.... ..|.++.++|+.++++...|.+.|++.
T Consensus 7 ~~~~~~~i~~~~-~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEHI-DQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHhc-CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 444555655553 457999999999999999999988775
No 86
>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=40.41 E-value=52 Score=25.29 Aligned_cols=31 Identities=23% Similarity=0.115 Sum_probs=25.9
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy1861 301 GTSHLLIDFSELLQICIFELGRTYLRLSQAL 331 (661)
Q Consensus 301 ~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L 331 (661)
..+.|+.|||+.+|++..++.+......+.|
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 5578999999999999999999888776655
No 87
>KOG0834|consensus
Probab=39.96 E-value=19 Score=39.41 Aligned_cols=88 Identities=10% Similarity=0.116 Sum_probs=58.9
Q ss_pred HHHHHHHHHHHhcCCCHH----HHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHH---HHHHhC--C
Q psy1861 245 NCKRNISSLCNQLRLNQH----CLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLID---FSELLQ--I 315 (661)
Q Consensus 245 ~a~~~I~~i~~~L~Lp~~----V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkD---Isdv~~--V 315 (661)
.....+-.++..|+-..+ +.-.|..+...+.--.+.=--.+.+||+||||+||...+++..... -...++ +
T Consensus 150 hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~v 229 (323)
T KOG0834|consen 150 HPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETV 229 (323)
T ss_pred CchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccC
Confidence 355666666666655543 6777777777666544322346789999999999999997644432 244556 7
Q ss_pred CHHHHHHHHHHHHHHhc
Q psy1861 316 CIFELGRTYLRLSQALC 332 (661)
Q Consensus 316 sv~~Lgrtyk~L~k~L~ 332 (661)
+...|......+...+.
T Consensus 230 t~e~l~~i~~~~l~~y~ 246 (323)
T KOG0834|consen 230 TNELLDDICHEFLDLYE 246 (323)
T ss_pred CHHHHHHHHHHHHHHHh
Confidence 77777777777666654
No 88
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=39.92 E-value=1.1e+02 Score=28.46 Aligned_cols=43 Identities=19% Similarity=0.178 Sum_probs=32.4
Q ss_pred chHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHH
Q psy1861 284 RQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRL 327 (661)
Q Consensus 284 ~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L 327 (661)
....+..+.-||.-... .|.++.++|+.+++++..|.+.|++.
T Consensus 7 ~~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 7 DAITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred cHHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34455556666665544 47999999999999999999888764
No 89
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=38.74 E-value=48 Score=26.34 Aligned_cols=32 Identities=16% Similarity=0.075 Sum_probs=27.2
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHHHhcc
Q psy1861 302 TSHLLIDFSELLQICIFELGRTYLRLSQALCI 333 (661)
Q Consensus 302 ~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i 333 (661)
...+.++||+.++++..++......+.+.|++
T Consensus 17 ~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 17 QGMSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred hcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 34788999999999999999999999998886
No 90
>KOG0794|consensus
Probab=38.70 E-value=93 Score=32.68 Aligned_cols=82 Identities=11% Similarity=0.234 Sum_probs=50.4
Q ss_pred HHHHHHHHhcCC-CHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHH
Q psy1861 248 RNISSLCNQLRL-NQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLR 326 (661)
Q Consensus 248 ~~I~~i~~~L~L-p~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~ 326 (661)
+-+.++-.-+|+ .+....-|..+....+...+.---.+..++-|||||||-..+.+.+ +-.-..+.++-..+..+.+.
T Consensus 155 rsL~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~~-~~w~~el~vD~ekV~~~v~~ 233 (264)
T KOG0794|consen 155 RSLLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDIP-KAWFAELSVDMEKVKDIVQE 233 (264)
T ss_pred ccHHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCChH-HHHHHHHhccHHHHHHHHHH
Confidence 335555556666 3446666777666666555544456888999999999999887653 22222245555555555555
Q ss_pred HHHH
Q psy1861 327 LSQA 330 (661)
Q Consensus 327 L~k~ 330 (661)
|.+.
T Consensus 234 I~~l 237 (264)
T KOG0794|consen 234 ILKL 237 (264)
T ss_pred HHHH
Confidence 5443
No 91
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=38.60 E-value=3.2e+02 Score=25.61 Aligned_cols=105 Identities=12% Similarity=0.085 Sum_probs=60.7
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHh-CCCCCCCchHHHHHHHHHHHHHHh-CCcccHHHHHHHhCCCHHHHH
Q psy1861 244 DNCKRNISSLCNQLRLNQHCLETSFNLYKMALS-RNLTKGRRQILVCAACVYMTCRLE-GTSHLLIDFSELLQICIFELG 321 (661)
Q Consensus 244 ~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e-~~l~rGR~~~~VaAACLYiACR~~-~~PrtLkDIsdv~~Vsv~~Lg 321 (661)
..+...+.+++..++=|+.+......-...+.. .|+.+ ++...+...|-++.-... ..|-...++...-||-.++..
T Consensus 8 ~~a~~~~~~l~~~~~~~~~l~~~~~~eL~~~l~~~g~~~-~ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~ 86 (149)
T smart00478 8 EAVNKATERLFEKFPTPEDLAAADEEELEELIRPLGFYR-RKAKYLIELARILVEEYGGEVPDDREELLKLPGVGRKTAN 86 (149)
T ss_pred HHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHHcCChH-HHHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCCcHHHHH
Confidence 345566666666666555555544433333332 35433 455566666655544433 355555666666788888643
Q ss_pred HHHHHHHHHhcccCCCCChhhHHHHHHhhcCCC
Q psy1861 322 RTYLRLSQALCISIPSMDPCLYVLRYSNRLDFG 354 (661)
Q Consensus 322 rtyk~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~ 354 (661)
- + +...++...|++|. ++.|++.+|++-
T Consensus 87 ~-~--l~~~~~~~~~~~D~--~v~r~~~rl~~~ 114 (149)
T smart00478 87 A-V--LSFALGKPFIPVDT--HVLRIAKRLGLV 114 (149)
T ss_pred H-H--HHHHCCCCCCccch--HHHHHHHHhCCC
Confidence 3 2 23345555677776 899999999864
No 92
>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=37.53 E-value=92 Score=23.61 Aligned_cols=28 Identities=18% Similarity=0.160 Sum_probs=23.3
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy1861 302 TSHLLIDFSELLQICIFELGRTYLRLSQ 329 (661)
Q Consensus 302 ~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k 329 (661)
-+.|..|+|+.++++..++.+..++|.+
T Consensus 16 ~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 16 PRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3489999999999999999999998876
No 93
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=37.11 E-value=95 Score=29.01 Aligned_cols=61 Identities=16% Similarity=0.082 Sum_probs=45.9
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHHhccc-CCCCChhhHHHHHHhhcCCCcccHHHHHHHHHHH
Q psy1861 305 LLIDFSELLQICIFELGRTYLRLSQALCIS-IPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRIL 368 (661)
Q Consensus 305 tLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~-~p~~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv 368 (661)
+|+|++..+||+=-+++.....|.+.|+.. .+..........+.++|.-|+=+ ...|.+++
T Consensus 51 nlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~GeIs---~eeA~~~L 112 (113)
T PF09862_consen 51 NLKEMEKELGISYPTVRNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEKGEIS---VEEALEIL 112 (113)
T ss_pred CHHHHHHHHCCCcHHHHHHHHHHHHHhCCCCCcccccchhHHHHHHHHHcCCCC---HHHHHHHh
Confidence 789999999999999999999999999983 33344456777777877755532 34555554
No 94
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=36.79 E-value=4.7e+02 Score=30.59 Aligned_cols=89 Identities=13% Similarity=0.081 Sum_probs=49.3
Q ss_pred CchhHHHHHHHHHHHHHHHhc---CCC--HHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHH--------------
Q psy1861 237 ESREITLDNCKRNISSLCNQL---RLN--QHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTC-------------- 297 (661)
Q Consensus 237 ~srEr~L~~a~~~I~~i~~~L---~Lp--~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiAC-------------- 297 (661)
..+++.+..-++.+..+|.++ |++ +=|.+--.-|.+-+..-...+|-+....|.=+|--+.
T Consensus 271 ~Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP 350 (509)
T PRK05901 271 RAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIP 350 (509)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecC
Confidence 445555555566666666664 333 3344444445555555555566544444433332221
Q ss_pred ------------------HHhCCcccHHHHHHHhCCCHHHHHHHHH
Q psy1861 298 ------------------RLEGTSHLLIDFSELLQICIFELGRTYL 325 (661)
Q Consensus 298 ------------------R~~~~PrtLkDIsdv~~Vsv~~Lgrtyk 325 (661)
...|.+-|..+||..+++++..+.....
T Consensus 351 ~~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~ 396 (509)
T PRK05901 351 VHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK 396 (509)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 1123344678899999999988887744
No 95
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=36.38 E-value=67 Score=31.07 Aligned_cols=46 Identities=17% Similarity=0.100 Sum_probs=40.1
Q ss_pred hHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 285 QILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 285 ~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
.+..+-|-+|+|....+-|.+..+||+..++++.-|.+.+..|.+.
T Consensus 7 ~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~ka 52 (150)
T COG1959 7 GEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKA 52 (150)
T ss_pred HhHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHc
Confidence 3455778899998887779999999999999999999999999884
No 96
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=36.16 E-value=1.7e+02 Score=30.26 Aligned_cols=49 Identities=14% Similarity=0.159 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCChhhHHHH
Q psy1861 289 CAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQALCISIPSMDPCLYVLR 346 (661)
Q Consensus 289 aAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~p~~dP~~yI~R 346 (661)
..++-||...- ..++|+.++|+.+++++..|.+.|++.. | ..|..||.+
T Consensus 189 ~~~~~~I~~~~-~~~~sl~~lA~~~~~S~~~l~r~Fk~~~---G-----~t~~~yi~~ 237 (287)
T TIGR02297 189 NRFNFLIEENY-KQHLRLPEYADRLGISESRLNDICRRFS---A-----LSPKRLIIE 237 (287)
T ss_pred HHHHHHHHHhh-ccCCCHHHHHHHHCCCHHHHHHHHHHHh---C-----CCHHHHHHH
Confidence 34555666443 3489999999999999999999988754 3 346677543
No 97
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=35.30 E-value=91 Score=31.43 Aligned_cols=46 Identities=15% Similarity=-0.042 Sum_probs=33.5
Q ss_pred hHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 285 QILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 285 ~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
...=+|.-|+..+.....|.+..|||+.+|++..++.|+.++|.+.
T Consensus 151 ~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~ 196 (226)
T PRK10402 151 LENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQD 196 (226)
T ss_pred HHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHC
Confidence 3333444444333333456789999999999999999999999884
No 98
>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=35.05 E-value=77 Score=25.42 Aligned_cols=32 Identities=19% Similarity=0.155 Sum_probs=24.7
Q ss_pred HhCCcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 299 LEGTSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 299 ~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
..+-|.++.+|++.++++...+.+..+.|.+.
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 56778999999999999999999999998774
No 99
>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=34.88 E-value=85 Score=23.87 Aligned_cols=30 Identities=20% Similarity=0.161 Sum_probs=23.5
Q ss_pred HHhCCcccHHHHHHHhCCCHHHHHHHHHHH
Q psy1861 298 RLEGTSHLLIDFSELLQICIFELGRTYLRL 327 (661)
Q Consensus 298 R~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L 327 (661)
-+.+..+++.+||..+|++..++.+.+++|
T Consensus 12 Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 12 LQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 355677899999999999999999998876
No 100
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=33.72 E-value=1.6e+02 Score=30.59 Aligned_cols=84 Identities=12% Similarity=0.131 Sum_probs=54.1
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHh-CCcccHHHHHHHhCCC-HHHHHHHHHH
Q psy1861 249 NISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLE-GTSHLLIDFSELLQIC-IFELGRTYLR 326 (661)
Q Consensus 249 ~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~-~~PrtLkDIsdv~~Vs-v~~Lgrtyk~ 326 (661)
.|..+|..++++.. +=.++||+........ .+--.-|--|++.- ....++.+||..+|-+ ...+.|.|++
T Consensus 201 sl~~lA~~~~lS~~---~l~r~Fk~~~G~tp~~-----~l~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~Fsr~FKk 272 (290)
T PRK10572 201 DIESVAQHVCLSPS---RLAHLFRQQLGISVLR-----WREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKK 272 (290)
T ss_pred CHHHHHHHHCCCHH---HHHHHHHHHHCcCHHH-----HHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHH
Confidence 36778888888874 4456777776554433 22222333344432 3569999999999975 7888888776
Q ss_pred HHHHhcccCCCCChhhHHHHHH
Q psy1861 327 LSQALCISIPSMDPCLYVLRYS 348 (661)
Q Consensus 327 L~k~L~i~~p~~dP~~yI~Rf~ 348 (661)
.. | ..|..|-.+..
T Consensus 273 ~~---G-----~SP~~yR~~~~ 286 (290)
T PRK10572 273 CT---G-----ASPSEFRARCE 286 (290)
T ss_pred HH---C-----cCHHHHHHHhh
Confidence 53 3 46877765543
No 101
>PRK06030 hypothetical protein; Provisional
Probab=33.24 E-value=94 Score=29.42 Aligned_cols=39 Identities=8% Similarity=0.034 Sum_probs=33.0
Q ss_pred HHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy1861 291 ACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQAL 331 (661)
Q Consensus 291 ACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L 331 (661)
.|+|++-...+ .+|.+|+..+|-+=.++..+++++.+.+
T Consensus 59 IAMYL~r~~~~--~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 59 IAMYVAHVSLG--WPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred HHHHHHHHHcC--CCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 57888777655 5899999999999999999999888754
No 102
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=33.16 E-value=1e+02 Score=25.62 Aligned_cols=39 Identities=13% Similarity=0.121 Sum_probs=30.4
Q ss_pred HHHHHHHhCC-cccHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy1861 293 VYMTCRLEGT-SHLLIDFSELLQICIFELGRTYLRLSQAL 331 (661)
Q Consensus 293 LYiACR~~~~-PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L 331 (661)
|+-.-+..+- +.++.|||..+|++..++.+....|.+.=
T Consensus 11 IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G 50 (68)
T smart00550 11 ILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKG 50 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 3444455555 49999999999999999999988887643
No 103
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=33.10 E-value=79 Score=23.72 Aligned_cols=30 Identities=13% Similarity=0.057 Sum_probs=27.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHHHhcc
Q psy1861 304 HLLIDFSELLQICIFELGRTYLRLSQALCI 333 (661)
Q Consensus 304 rtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i 333 (661)
.+..+||+.++++..++.+....+.+.|+.
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~~kl~~ 48 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIMRKLGV 48 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 588999999999999999999988888875
No 104
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=31.93 E-value=2.3e+02 Score=22.87 Aligned_cols=44 Identities=18% Similarity=0.110 Sum_probs=30.8
Q ss_pred HHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy1861 268 FNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQ 329 (661)
Q Consensus 268 ~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k 329 (661)
.++.+.|++.|+..--+ -.++.|+|+.+||+..++....+.-.+
T Consensus 6 ~e~L~~A~~~GYfd~PR------------------~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 6 REILKAAYELGYFDVPR------------------RITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred HHHHHHHHHcCCCCCCC------------------cCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45677777777754211 158999999999999877766655443
No 105
>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=31.69 E-value=1.3e+02 Score=23.57 Aligned_cols=37 Identities=16% Similarity=0.099 Sum_probs=28.0
Q ss_pred HHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 292 CVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 292 CLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
+|.+..... |.++.+||+.++++...+.+..+.|.+.
T Consensus 8 iL~~l~~~~--~~~~~~la~~~~~~~~~~t~~i~~L~~~ 44 (59)
T PF01047_consen 8 ILRILYENG--GITQSELAEKLGISRSTVTRIIKRLEKK 44 (59)
T ss_dssp HHHHHHHHS--SEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHcC--CCCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence 344443333 3899999999999999999999998773
No 106
>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=31.48 E-value=1.3e+02 Score=26.69 Aligned_cols=30 Identities=10% Similarity=0.049 Sum_probs=27.1
Q ss_pred hCCcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy1861 300 EGTSHLLIDFSELLQICIFELGRTYLRLSQ 329 (661)
Q Consensus 300 ~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k 329 (661)
...+.|..|||+.++++..++.++...|.+
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 456899999999999999999999999876
No 107
>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=31.37 E-value=91 Score=23.56 Aligned_cols=31 Identities=10% Similarity=0.129 Sum_probs=28.1
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHHHhcc
Q psy1861 303 SHLLIDFSELLQICIFELGRTYLRLSQALCI 333 (661)
Q Consensus 303 PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i 333 (661)
..+..+||..+++++.++.+....+.+.++.
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 3699999999999999999999999888876
No 108
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=30.80 E-value=1.8e+02 Score=29.39 Aligned_cols=29 Identities=17% Similarity=0.201 Sum_probs=26.6
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 302 TSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 302 ~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
.|.|..+||+.+|++..++.|+.++|.+.
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 57889999999999999999999999874
No 109
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=29.91 E-value=1.2e+02 Score=25.28 Aligned_cols=21 Identities=19% Similarity=0.123 Sum_probs=18.7
Q ss_pred cccHHHHHHHhCCCHHHHHHH
Q psy1861 303 SHLLIDFSELLQICIFELGRT 323 (661)
Q Consensus 303 PrtLkDIsdv~~Vsv~~Lgrt 323 (661)
-.+++|||+.++|+..+|++.
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHH
Confidence 478999999999999999865
No 110
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=29.66 E-value=75 Score=36.04 Aligned_cols=68 Identities=12% Similarity=0.088 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCCchHHHHHH---HHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy1861 261 QHCLETSFNLYKMALSRNLTKGRRQILVCAA---CVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQAL 331 (661)
Q Consensus 261 ~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAA---CLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L 331 (661)
+.+++..+.+|..-.+.=..++|. ..++-| |+|++-+ -+..++.+|+..+|.+-.++.+++++|.+.+
T Consensus 345 ~~I~~~V~~~~~i~~~~l~s~~R~-~~i~~aR~iamyl~r~--~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 345 DELIEIVAKVTGVSREEILSNSRN-VKALLARRIGMYVAKN--YLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred HHHHHHHHHHcCCcHHHHhCCCCC-ccccHHHHHHHHHHHH--HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 567777777775544322233333 344555 8888844 5567999999999999999999999999976
No 111
>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=29.64 E-value=97 Score=24.10 Aligned_cols=34 Identities=15% Similarity=0.092 Sum_probs=26.9
Q ss_pred HHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy1861 296 TCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQ 329 (661)
Q Consensus 296 ACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k 329 (661)
+-..++.|.++.|||+.++++..++.|....|.+
T Consensus 11 ~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 11 ALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp CHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3445566789999999999999999888877765
No 112
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=29.41 E-value=1.7e+02 Score=28.42 Aligned_cols=29 Identities=7% Similarity=-0.074 Sum_probs=26.9
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 302 TSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 302 ~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
.|.|..+||+.+|++..++.|..++|.+.
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 176 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSRE 176 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHC
Confidence 57899999999999999999999999874
No 113
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=29.38 E-value=92 Score=23.88 Aligned_cols=26 Identities=12% Similarity=0.089 Sum_probs=24.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 305 LLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 305 tLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
|..++|+.++++..++.+.++.|.+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 89999999999999999999999873
No 114
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=29.21 E-value=3.5e+02 Score=28.02 Aligned_cols=113 Identities=15% Similarity=0.074 Sum_probs=65.2
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHh-CCcccHHHHHHHhCCCHHHHHHHH
Q psy1861 246 CKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLE-GTSHLLIDFSELLQICIFELGRTY 324 (661)
Q Consensus 246 a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~-~~PrtLkDIsdv~~Vsv~~Lgrty 324 (661)
-|+.....-+.+.++..-++.. ...-||.+.| ...+.+.|=-+.=+-. .+|.++.++-+.-||-.|+- .
T Consensus 54 Lf~~~~t~e~l~~a~~~~l~~~------I~~iGlyr~K-Ak~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVGrKTA---n 123 (211)
T COG0177 54 LFKRYPTPEDLLNADEEELEEL------IKSIGLYRNK-AKNIKELARILLEKFGGEVPDTREELLSLPGVGRKTA---N 123 (211)
T ss_pred HHHHcCCHHHHHcCCHHHHHHH------HHhcCCcHHH-HHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcchHHH---H
Confidence 3444444445556665333322 2245666543 3344444444443333 47999999999999998874 3
Q ss_pred HHHHHHhcccCCCCChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHh
Q psy1861 325 LRLSQALCISIPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRM 371 (661)
Q Consensus 325 k~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m 371 (661)
..|...++...-.+|. .|.|.++++|+.+. +.....-..+.+.+
T Consensus 124 vVL~~a~g~p~i~VDT--HV~Rvs~R~gl~~~-~~p~~ve~~L~~~i 167 (211)
T COG0177 124 VVLSFAFGIPAIAVDT--HVHRVSNRLGLVPG-KTPEEVEEALMKLI 167 (211)
T ss_pred HHHHhhcCCCcccccc--hHHHHHHHhCCCCC-CCHHHHHHHHHHHC
Confidence 3445556654334454 89999999999862 22333444444444
No 115
>smart00351 PAX Paired Box domain.
Probab=28.87 E-value=4e+02 Score=24.79 Aligned_cols=85 Identities=11% Similarity=0.217 Sum_probs=46.7
Q ss_pred CchhHHHHHHH--HHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCC-----CCchHHHH-HHHHHH-HHHHhCCcccHH
Q psy1861 237 ESREITLDNCK--RNISSLCNQLRLNQHCLETSFNLYKMALSRNLTK-----GRRQILVC-AACVYM-TCRLEGTSHLLI 307 (661)
Q Consensus 237 ~srEr~L~~a~--~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~r-----GR~~~~Va-AACLYi-ACR~~~~PrtLk 307 (661)
+-|.+.+.-.. .....+|..|+++..++.. +.+++.+.|.++ |+++..+. ....+| ..+.+.-..|+.
T Consensus 21 ~~R~riv~~~~~G~s~~~iA~~~gvs~~tV~k---wi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~ 97 (125)
T smart00351 21 EERQRIVELAQNGVRPCDISRQLCVSHGCVSK---ILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAW 97 (125)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHH---HHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHH
Confidence 44454443222 2478999999999866554 445545444432 32332221 222233 345566667899
Q ss_pred HHHHHhC---C-------CHHHHHHHH
Q psy1861 308 DFSELLQ---I-------CIFELGRTY 324 (661)
Q Consensus 308 DIsdv~~---V-------sv~~Lgrty 324 (661)
++++.+. | ++.+|++.+
T Consensus 98 el~~~L~~~gv~~~~~~Ps~sti~~~l 124 (125)
T smart00351 98 EIRDRLLSEGVCDKDNVPSVSSINRIL 124 (125)
T ss_pred HHHHHHHHcCCCcCCCCCChhhHHHhh
Confidence 9987652 2 456666654
No 116
>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=28.23 E-value=87 Score=24.22 Aligned_cols=28 Identities=21% Similarity=0.239 Sum_probs=21.1
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy1861 304 HLLIDFSELLQICIFELGRTYLRLSQAL 331 (661)
Q Consensus 304 rtLkDIsdv~~Vsv~~Lgrtyk~L~k~L 331 (661)
.+..|||+.+|+++.++...+..-.+.|
T Consensus 27 ~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 27 MSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp --HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 5789999999999999998887766543
No 117
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=28.21 E-value=1e+02 Score=29.07 Aligned_cols=46 Identities=20% Similarity=0.195 Sum_probs=37.7
Q ss_pred hHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 285 QILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 285 ~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
.+.-+-+.+|++-...|.+.+..+||+.++|+..-|.+++..|.+.
T Consensus 7 ~~YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 7 TDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HhHHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 3445666777776566678899999999999999999999999874
No 118
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=27.31 E-value=1.5e+02 Score=31.20 Aligned_cols=41 Identities=10% Similarity=0.165 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHH
Q psy1861 286 ILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRL 327 (661)
Q Consensus 286 ~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L 327 (661)
..+..++-||-.... .|.++.++|+.++++...+.|.|+..
T Consensus 5 ~~i~~~~~~i~~~~~-~~~~l~~lA~~~~~S~~~l~r~F~~~ 45 (289)
T PRK15121 5 GIIRDLLIWLEGHLD-QPLSLDNVAAKAGYSKWHLQRMFKDV 45 (289)
T ss_pred HHHHHHHHHHHhccc-CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 345667777776544 57999999999999999999998775
No 119
>PRK10130 transcriptional regulator EutR; Provisional
Probab=27.23 E-value=5.2e+02 Score=28.48 Aligned_cols=52 Identities=15% Similarity=0.284 Sum_probs=39.0
Q ss_pred hHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCChhhHHH
Q psy1861 285 QILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQALCISIPSMDPCLYVL 345 (661)
Q Consensus 285 ~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~p~~dP~~yI~ 345 (661)
...+..++=||.-.. ..|.++.|||..++|+...|.+.|++. +| ..|..||.
T Consensus 239 ~~~v~~~~~~i~~~~-~~~ltv~~lA~~~gvS~r~L~r~Fk~~---~G-----~sp~~ylr 290 (350)
T PRK10130 239 RRLLSRAREYVLENM-SEPVTVLDLCNQLHVSRRTLQNAFHAI---LG-----IGPNAWLK 290 (350)
T ss_pred HHHHHHHHHHHHhhh-cCCCCHHHHHHHHCCCHHHHHHHHHHH---HC-----cCHHHHHH
Confidence 445666777776544 458999999999999999999998765 33 35666665
No 120
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=27.16 E-value=1.2e+02 Score=25.75 Aligned_cols=47 Identities=17% Similarity=-0.047 Sum_probs=38.5
Q ss_pred HHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCChhhHHHHHH
Q psy1861 298 RLEGTSHLLIDFSELLQICIFELGRTYLRLSQALCISIPSMDPCLYVLRYS 348 (661)
Q Consensus 298 R~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~p~~dP~~yI~Rf~ 348 (661)
|.-+.|+++.+.|+.+|+++..+.+....+.+.|-. .||+-...+-+
T Consensus 8 rlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~----LDPSG~~E~RV 54 (65)
T PF05344_consen 8 RLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQ----LDPSGHWEARV 54 (65)
T ss_pred HHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHH----cCCCCChHHHh
Confidence 667889999999999999999999999999887753 57766555433
No 121
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=27.01 E-value=1.5e+02 Score=24.76 Aligned_cols=34 Identities=9% Similarity=0.123 Sum_probs=27.3
Q ss_pred hCCcccHHHHHHHhCCCHHHHHHHHHHHHHHhcc
Q psy1861 300 EGTSHLLIDFSELLQICIFELGRTYLRLSQALCI 333 (661)
Q Consensus 300 ~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i 333 (661)
.+.|.+-.|||+.++++.+...+....|.+.=.+
T Consensus 12 ~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V 45 (62)
T PF04703_consen 12 QNGPLKTREIADALGLSIYQARYYLEKLEKEGKV 45 (62)
T ss_dssp HTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSE
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence 3789999999999999999999988888775444
No 122
>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=26.48 E-value=1.1e+02 Score=24.86 Aligned_cols=36 Identities=19% Similarity=0.186 Sum_probs=29.0
Q ss_pred HHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy1861 293 VYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQ 329 (661)
Q Consensus 293 LYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k 329 (661)
+|.+-- ..-|.|..|||+.++++..++.++.+.|.+
T Consensus 13 vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 13 VYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344333 445789999999999999999999998876
No 123
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=26.46 E-value=77 Score=30.09 Aligned_cols=26 Identities=15% Similarity=0.222 Sum_probs=24.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 305 LLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 305 tLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
|.+++|..++|++.++.|+|..|.+.
T Consensus 37 SvRelA~~~~VNpnTv~raY~eLE~e 62 (125)
T COG1725 37 SVRELAKDLGVNPNTVQRAYQELERE 62 (125)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 88999999999999999999999873
No 124
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=26.34 E-value=1.1e+02 Score=33.06 Aligned_cols=45 Identities=16% Similarity=0.287 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccH
Q psy1861 262 HCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLL 306 (661)
Q Consensus 262 ~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtL 306 (661)
.+.+.|..+...+...-+.---.+-.+|.||++|||+..|.|.-.
T Consensus 168 ~~~~~aw~~inDa~~t~~~llypphiIA~a~l~ia~~~~~~~~~~ 212 (297)
T COG5333 168 KLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPIIK 212 (297)
T ss_pred HHHHHHHHHHHhhhhceeeeecChHHHHHHHHHHHHHhcCCccch
Confidence 366677777777766554444467889999999999999987443
No 125
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=26.10 E-value=3.8e+02 Score=22.15 Aligned_cols=78 Identities=15% Similarity=0.210 Sum_probs=41.9
Q ss_pred HHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHh--CCcccHHHHHHHhCCC-HHHHHHHHHHHHH
Q psy1861 253 LCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLE--GTSHLLIDFSELLQIC-IFELGRTYLRLSQ 329 (661)
Q Consensus 253 i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~--~~PrtLkDIsdv~~Vs-v~~Lgrtyk~L~k 329 (661)
+|+.++++..- -..+|+......+. +.+...-+-.|++.- +...++.|||..+|.+ ...+.+.|++.
T Consensus 1 lA~~~~~s~~~---l~~~f~~~~g~s~~-----~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~fk~~-- 70 (81)
T PF12833_consen 1 LADELGMSERY---LSRIFKKETGMSFK-----QYLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSRAFKRY-- 70 (81)
T ss_dssp HHHHCTS-HHH---HHHHHHHHHSS-HH-----HHHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHHHHHHH--
T ss_pred ChHHhCcCHHH---HHHHHHHHHCcCHH-----HHHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHHHHHHH--
Confidence 46777777643 33455555443331 233333444455532 3678999999999965 77777777665
Q ss_pred HhcccCCCCChhhHHHH
Q psy1861 330 ALCISIPSMDPCLYVLR 346 (661)
Q Consensus 330 ~L~i~~p~~dP~~yI~R 346 (661)
+| ..|..|..|
T Consensus 71 -~g-----~tP~~~r~r 81 (81)
T PF12833_consen 71 -FG-----MTPSEYRKR 81 (81)
T ss_dssp -HS-----S-HHHHHHH
T ss_pred -HC-----cCHHHHHcc
Confidence 44 346666543
No 126
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=26.02 E-value=1.3e+02 Score=25.25 Aligned_cols=35 Identities=9% Similarity=0.097 Sum_probs=24.7
Q ss_pred HHHHHHHHHhCCcccHHHHHHHhC-CCHHHHHHHHHHH
Q psy1861 291 ACVYMTCRLEGTSHLLIDFSELLQ-ICIFELGRTYLRL 327 (661)
Q Consensus 291 ACLYiACR~~~~PrtLkDIsdv~~-Vsv~~Lgrtyk~L 327 (661)
.|+|++-... ..++.+|+..+| -+-.++..+++++
T Consensus 35 va~yL~r~~~--~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 35 VAMYLARELT--GLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHS-----HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred HHHHHHHHHh--CCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 3456655544 488999999999 8999998888764
No 127
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=25.33 E-value=1.3e+02 Score=22.90 Aligned_cols=26 Identities=8% Similarity=-0.027 Sum_probs=17.6
Q ss_pred hCCcccHHHHHHHhCCCHHHHHHHHH
Q psy1861 300 EGTSHLLIDFSELLQICIFELGRTYL 325 (661)
Q Consensus 300 ~~~PrtLkDIsdv~~Vsv~~Lgrtyk 325 (661)
.....++.+||..+|++..+|.+..+
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 34458999999999999999988765
No 128
>PF13730 HTH_36: Helix-turn-helix domain
Probab=25.33 E-value=1.4e+02 Score=23.15 Aligned_cols=25 Identities=12% Similarity=0.056 Sum_probs=23.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHH
Q psy1861 305 LLIDFSELLQICIFELGRTYLRLSQ 329 (661)
Q Consensus 305 tLkDIsdv~~Vsv~~Lgrtyk~L~k 329 (661)
+...||+.++++..++.++.+.|.+
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999999998876
No 129
>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=24.94 E-value=1.2e+02 Score=24.41 Aligned_cols=31 Identities=10% Similarity=0.114 Sum_probs=27.1
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy1861 301 GTSHLLIDFSELLQICIFELGRTYLRLSQAL 331 (661)
Q Consensus 301 ~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L 331 (661)
+-..+..|+|+.++|+..++.+-+..|.+.-
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g 42 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKLEKQG 42 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 4468999999999999999999999987643
No 130
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=24.59 E-value=1.9e+02 Score=25.97 Aligned_cols=41 Identities=12% Similarity=-0.053 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 289 CAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 289 aAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
+-.+|+. |...+-+.++.++++.++++...+.+....|.+.
T Consensus 30 vL~~l~~-~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~k 70 (109)
T TIGR01889 30 ILYYLGK-LENNEGKLTLKEIIKEILIKQSALVKIIKKLSKK 70 (109)
T ss_pred HHHHHHh-hhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3334443 5666778999999999999999999999999874
No 131
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=24.43 E-value=3.8e+02 Score=27.91 Aligned_cols=53 Identities=11% Similarity=0.029 Sum_probs=39.0
Q ss_pred chHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCChhhHHH
Q psy1861 284 RQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQALCISIPSMDPCLYVL 345 (661)
Q Consensus 284 ~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~p~~dP~~yI~ 345 (661)
....+..++-||.-....-..++.+||..+++++..|.+.|++ . | ..|..||.
T Consensus 195 ~~~~l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~---~-G-----~T~~~yi~ 247 (302)
T PRK09685 195 RERQFQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAE---Q-G-----LVVAQYIR 247 (302)
T ss_pred cHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHH---c-C-----CCHHHHHH
Confidence 3445566777777666555589999999999999999999864 2 4 34666665
No 132
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=23.90 E-value=1.9e+02 Score=29.02 Aligned_cols=28 Identities=14% Similarity=0.094 Sum_probs=25.3
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy1861 302 TSHLLIDFSELLQICIFELGRTYLRLSQ 329 (661)
Q Consensus 302 ~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k 329 (661)
.|.+..|||+.+|++..++.|+.++|.+
T Consensus 172 i~~t~~~iA~~lG~tretvsR~l~~L~~ 199 (236)
T PRK09392 172 LPYEKRVLASYLGMTPENLSRAFAALAS 199 (236)
T ss_pred eeCCHHHHHHHhCCChhHHHHHHHHHHh
Confidence 4777899999999999999999999866
No 133
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=23.23 E-value=3.1e+02 Score=29.93 Aligned_cols=145 Identities=13% Similarity=0.126 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHH
Q psy1861 244 DNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRT 323 (661)
Q Consensus 244 ~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrt 323 (661)
+...+.|.+-.....+|.++.+....+.+...+..-.-||.+ |..|||..+++++.++...
T Consensus 149 ~aI~~~i~~~~r~vrlP~~~~~~~~~l~~~~~~l~~~lgr~p-------------------t~~EiA~~lgi~~~~v~~~ 209 (324)
T PRK07921 149 QAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREA-------------------TDEELAEESGIPEEKIADL 209 (324)
T ss_pred HHHHHHHHHcCCCccCCHHHHHHHHHHHHHHHHHHHHhCCCC-------------------CHHHHHHHhCcCHHHHHHH
Q ss_pred HHHHHHHhcccCC-----------------CCChhhHHHHHHhhcCCCcccHHHHHHHHHHHHHhhcccccCCCCcccee
Q psy1861 324 YLRLSQALCISIP-----------------SMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGLI 386 (661)
Q Consensus 324 yk~L~k~L~i~~p-----------------~~dP~~yI~Rf~~~L~L~~~~~~V~~~A~~Iv~~m~~d~i~tGRrP~gIA 386 (661)
.......+-++.| ..+|...+.+-...-.|..--..+-..=..|+.. +-++..|.
T Consensus 210 ~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~~~~~l~~~L~~L~eREr~Vl~~--rygl~~~~------ 281 (324)
T PRK07921 210 LEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDEREQQVIRL--RFGLDDGQ------ 281 (324)
T ss_pred HHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH--HHhcCCCC------
Q ss_pred ecccccCHHHHHHHHhhhhhhhhcchHHHHHhh
Q psy1861 387 GKYSCDSHVDISRVAGDDYIKSNELPRVIKECL 419 (661)
Q Consensus 387 aAA~~rT~~eIa~~agtiR~~ykeL~~~~~~~l 419 (661)
..|++||++.-|..|.+-+++++.-.++|
T Consensus 282 ----~~Tl~eIa~~lgvS~eRVrQIe~~Al~KL 310 (324)
T PRK07921 282 ----PRTLDQIGKLFGLSRERVRQIEREVMSKL 310 (324)
T ss_pred ----CcCHHHHHHHHCCCHHHHHHHHHHHHHHH
No 134
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=23.03 E-value=5.4e+02 Score=26.87 Aligned_cols=91 Identities=15% Similarity=0.131 Sum_probs=71.5
Q ss_pred hhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHH-hCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCCCH
Q psy1861 239 REITLDNCKRNISSLCNQLRLNQHCLETSFNLYKMAL-SRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICI 317 (661)
Q Consensus 239 rEr~L~~a~~~I~~i~~~L~Lp~~V~e~A~~iyk~a~-e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv 317 (661)
-+.+|..-.++-..+...=.+++.-+|.......+.. ...+.+|-+...+-.-|-.+. ..+.|+|.-|+|..+++|.
T Consensus 110 l~~aL~~y~~~r~~l~~~~~~sQ~~lD~l~~~~~k~~~~~~LPkGi~~~Tl~~i~~~~~--~~~~~~Taeela~~~giSR 187 (224)
T COG4565 110 LQQALTRYRQKRHALESHQQLSQKELDQLFNIQSKEQPPDDLPKGLDELTLQKVREALK--EPDQELTAEELAQALGISR 187 (224)
T ss_pred HHHHHHHHHHHHHHHhhhcccCHHHHHHHHhccccccCcccCCCCcCHHHHHHHHHHHh--CcCCccCHHHHHHHhCccH
Confidence 3566777777788888888999999999998885533 345778877777666666666 6679999999999999999
Q ss_pred HHHHHHHHHHHHHh
Q psy1861 318 FELGRTYLRLSQAL 331 (661)
Q Consensus 318 ~~Lgrtyk~L~k~L 331 (661)
.+.+|-...+...-
T Consensus 188 vTaRRYLeyl~~~~ 201 (224)
T COG4565 188 VTARRYLEYLVSNG 201 (224)
T ss_pred HHHHHHHHHHHhcC
Confidence 99998887776643
No 135
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=22.99 E-value=1e+03 Score=26.20 Aligned_cols=88 Identities=10% Similarity=0.003 Sum_probs=52.8
Q ss_pred hHHHHHHHHHHHHHHHhcC---CC--HHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHH---------------
Q psy1861 240 EITLDNCKRNISSLCNQLR---LN--QHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRL--------------- 299 (661)
Q Consensus 240 Er~L~~a~~~I~~i~~~L~---Lp--~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~--------------- 299 (661)
++-+..-...+..+|.++. ++ +-+.+.-..+++-+..-.-.+|-+....|.-+|+-+-+.
T Consensus 132 ~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~ 211 (367)
T PRK09210 132 QRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 211 (367)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHH
Confidence 3333444556666666652 22 345555566666666655566766666666566544311
Q ss_pred -----------------hCCcccHHHHHHHhCCCHHHHHHHHHHH
Q psy1861 300 -----------------EGTSHLLIDFSELLQICIFELGRTYLRL 327 (661)
Q Consensus 300 -----------------~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L 327 (661)
.|.+-|..|||..+++++..+......-
T Consensus 212 ~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~ 256 (367)
T PRK09210 212 VETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA 256 (367)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh
Confidence 1233367789999999999998876543
No 136
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=22.92 E-value=3.3e+02 Score=25.06 Aligned_cols=88 Identities=16% Similarity=0.147 Sum_probs=52.1
Q ss_pred CchhHHHHHHH--HHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCC----CCC-chHHHHHHHHHHHHHHhCCcccHHHH
Q psy1861 237 ESREITLDNCK--RNISSLCNQLRLNQHCLETSFNLYKMALSRNLT----KGR-RQILVCAACVYMTCRLEGTSHLLIDF 309 (661)
Q Consensus 237 ~srEr~L~~a~--~~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~----rGR-~~~~VaAACLYiACR~~~~PrtLkDI 309 (661)
+-|++.+.... ..+..+|..++++.. +..+|+++- +.|-+ +|+ +.+. =-..+.-.+.--.|+.|+
T Consensus 6 DlR~rVl~~~~~g~s~~eaa~~F~VS~~---Tv~~W~k~~-~~G~~~~k~r~~~Kid~----~~L~~~v~~~pd~tl~El 77 (119)
T PF01710_consen 6 DLRQRVLAYIEKGKSIREAAKRFGVSRN---TVYRWLKRK-ETGDLEPKPRGRKKIDR----DELKALVEENPDATLREL 77 (119)
T ss_pred HHHHHHHHHHHccchHHHHHHHhCcHHH---HHHHHHHhc-ccccccccccccccccH----HHHHHHHHHCCCcCHHHH
Confidence 34555554222 368888999998764 444666632 23322 233 2211 112233333444899999
Q ss_pred HHHhCCCHHHHHHHHHHHHHHhc
Q psy1861 310 SELLQICIFELGRTYLRLSQALC 332 (661)
Q Consensus 310 sdv~~Vsv~~Lgrtyk~L~k~L~ 332 (661)
|..++|+..+|++..+++--...
T Consensus 78 a~~l~Vs~~ti~~~Lkrlg~t~K 100 (119)
T PF01710_consen 78 AERLGVSPSTIWRALKRLGITRK 100 (119)
T ss_pred HHHcCCCHHHHHHHHHHcCchhc
Confidence 99999999999988777644443
No 137
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=22.75 E-value=1.3e+02 Score=22.79 Aligned_cols=27 Identities=11% Similarity=0.064 Sum_probs=18.4
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHHHH
Q psy1861 303 SHLLIDFSELLQICIFELGRTYLRLSQ 329 (661)
Q Consensus 303 PrtLkDIsdv~~Vsv~~Lgrtyk~L~k 329 (661)
..|..+||..+||+..++.+..+...+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYRE 43 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT----
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccc
Confidence 578999999999999999998777643
No 138
>PF04855 SNF5: SNF5 / SMARCB1 / INI1; InterPro: IPR006939 SNF5 is a component of the yeast SWI/SNF complex, which is an ATP-dependent nucleosome-remodelling complex that regulates the transcription of a subset of yeast genes. SNF5 is a key component of all SWI/SNF-class complexes characterised so far []. This family consists of the conserved region of SNF5, including a direct repeat motif. SNF5 is essential for the assembly promoter targeting and chromatin remodelling activity of the SWI-SNF complex []. SNF5 is also known as SMARCB1, for SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, and also INI1 for integrase interactor 1. Loss-of function mutations in SNF5 are thought to contribute to oncogenesis in malignant rhabdoid tumours (MRTs) [].; GO: 0006338 chromatin remodeling, 0000228 nuclear chromosome
Probab=22.66 E-value=1.2e+02 Score=31.88 Aligned_cols=50 Identities=18% Similarity=0.226 Sum_probs=35.5
Q ss_pred CCCCChhhHHHHHHhhcCCCccc-HHHHHHHHHHHHHhhcccccCCCCccc
Q psy1861 335 IPSMDPCLYVLRYSNRLDFGAKT-HEVTMTALRILQRMKKDMLHSGRRPNG 384 (661)
Q Consensus 335 ~p~~dP~~yI~Rf~~~L~L~~~~-~~V~~~A~~Iv~~m~~d~i~tGRrP~g 384 (661)
-|..+|+.|-..+|..|||+..- ..|+..-.+-+.+.++.++..|.-..+
T Consensus 139 ~~~~~PE~FA~~~c~dLgL~~Ef~~aIahsIrEq~~~~kK~~~~~g~~~~~ 189 (244)
T PF04855_consen 139 NPPNSPEEFARVLCADLGLPGEFVPAIAHSIREQLLKYKKELCESGYLFDG 189 (244)
T ss_pred CCCCCHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHhcccccCC
Confidence 46789999999999999998752 234444455666677777776655444
No 139
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=22.64 E-value=3.1e+02 Score=30.69 Aligned_cols=23 Identities=13% Similarity=0.042 Sum_probs=18.9
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHH
Q psy1861 302 TSHLLIDFSELLQICIFELGRTYL 325 (661)
Q Consensus 302 ~PrtLkDIsdv~~Vsv~~Lgrtyk 325 (661)
.| |..+||..+++++.++.....
T Consensus 239 ~P-t~~EIA~~lg~~~e~v~~~~~ 261 (373)
T PRK07406 239 KP-TEEEIAESMEMTIEKLRFIAK 261 (373)
T ss_pred CC-CHHHHHHHhCCCHHHHHHHHH
Confidence 44 789999999999999976644
No 140
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=22.38 E-value=4.8e+02 Score=26.86 Aligned_cols=72 Identities=11% Similarity=0.074 Sum_probs=48.6
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHH-hCCcccHHHHHHHhCCC-HHHHHHHHHH
Q psy1861 249 NISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRL-EGTSHLLIDFSELLQIC-IFELGRTYLR 326 (661)
Q Consensus 249 ~I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~-~~~PrtLkDIsdv~~Vs-v~~Lgrtyk~ 326 (661)
.+..+|..++++.. +-.++||+.....+ .+.+..--|--||++ ..+..++.|||..+|-+ ...+.+.|++
T Consensus 204 sl~~lA~~~~~S~~---~l~r~Fk~~~G~t~-----~~yi~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~s~s~Fsr~FKk 275 (287)
T TIGR02297 204 RLPEYADRLGISES---RLNDICRRFSALSP-----KRLIIERVMQEARRLLLFTQHSINQIAYDLGYKDPAYFARFFQK 275 (287)
T ss_pred CHHHHHHHHCCCHH---HHHHHHHHHhCCCH-----HHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHH
Confidence 46778888888863 33556666653322 234444456667774 45779999999999975 7888888876
Q ss_pred HH
Q psy1861 327 LS 328 (661)
Q Consensus 327 L~ 328 (661)
..
T Consensus 276 ~~ 277 (287)
T TIGR02297 276 ET 277 (287)
T ss_pred HH
Confidence 54
No 141
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 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. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=21.65 E-value=81 Score=26.26 Aligned_cols=32 Identities=22% Similarity=0.273 Sum_probs=25.4
Q ss_pred HHHHHHHHHhCCCCC--CCchHHHHHHHHHHHHH
Q psy1861 267 SFNLYKMALSRNLTK--GRRQILVCAACVYMTCR 298 (661)
Q Consensus 267 A~~iyk~a~e~~l~r--GR~~~~VaAACLYiACR 298 (661)
..+|++.+.+.++.. |+.+...++|.||--++
T Consensus 20 ~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~ 53 (72)
T PF05066_consen 20 FKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIK 53 (72)
T ss_dssp HHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH
T ss_pred HHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcc
Confidence 456777888878777 89999999999999888
No 142
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=21.09 E-value=2.5e+02 Score=27.54 Aligned_cols=51 Identities=14% Similarity=0.173 Sum_probs=39.0
Q ss_pred HHHHHHHHhc-CCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccH
Q psy1861 248 RNISSLCNQL-RLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLL 306 (661)
Q Consensus 248 ~~I~~i~~~L-~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtL 306 (661)
++++++-..| +||++-++.+.++|+...+.+.-.|++-+.+ |..-|.|+.+
T Consensus 5 efL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeei--------i~~LG~P~~i 56 (181)
T PF08006_consen 5 EFLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEI--------IAELGSPKEI 56 (181)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHH--------HHHcCCHHHH
Confidence 3455555555 4999999999999999999988899988774 4567777443
No 143
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=20.96 E-value=2.2e+02 Score=21.54 Aligned_cols=30 Identities=13% Similarity=0.223 Sum_probs=26.5
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy1861 301 GTSHLLIDFSELLQICIFELGRTYLRLSQA 330 (661)
Q Consensus 301 ~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~ 330 (661)
+-|.++.+|+..++++..++.+....|.+.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~ 37 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREA 37 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 557899999999999999999999888763
No 144
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=20.81 E-value=2.5e+02 Score=30.99 Aligned_cols=50 Identities=18% Similarity=0.242 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHhCCcccHHHHHHHhCCCHHHHHHHHHHHHHHhcccCCCCChhhHHHH
Q psy1861 286 ILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQALCISIPSMDPCLYVLR 346 (661)
Q Consensus 286 ~~VaAACLYiACR~~~~PrtLkDIsdv~~Vsv~~Lgrtyk~L~k~L~i~~p~~dP~~yI~R 346 (661)
..+..|+-||-- +.+.++.++|..++++...|.|.|++.. + ..|..|+.+
T Consensus 85 ~~i~~a~~~I~~---~~~lsl~eLA~~lG~S~~~L~R~Fkk~~---G-----~TP~~yl~~ 134 (353)
T PRK15435 85 DKITHACRLLEQ---ETPVTLEALADQVAMSPFHLHRLFKATT---G-----MTPKAWQQA 134 (353)
T ss_pred HHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHHH---C-----cCHHHHHHH
Confidence 345666666633 4678999999999999999999887653 3 458778765
No 145
>PRK13501 transcriptional activator RhaR; Provisional
Probab=20.70 E-value=2.8e+02 Score=28.94 Aligned_cols=72 Identities=18% Similarity=0.328 Sum_probs=0.0
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhCC-CHHHHHHHHHHHH
Q psy1861 250 ISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQI-CIFELGRTYLRLS 328 (661)
Q Consensus 250 I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~V-sv~~Lgrtyk~L~ 328 (661)
|.++|+.+++++.-. .++||+.....+.+=.....+.-||-.+ ..+..++.|||..+|- +...+.|.|++..
T Consensus 195 l~~lA~~~~lS~~~l---~r~Fk~~~G~T~~qyi~~~Ri~~A~~LL----~~t~~sI~eIA~~~GF~~~s~F~r~FKk~~ 267 (290)
T PRK13501 195 MADFCHKNQLVERSL---KQLFRQQTGMSISHYLRQIRLCHAKCLL----RGSEHRISDIAARCGFEDSNYFSAVFTREA 267 (290)
T ss_pred HHHHHHHHCcCHHHH---HHHHHHHHCcCHHHHHHHHHHHHHHHHH----HcCCCCHHHHHHHhCCCCHHHHHHHHHHHH
No 146
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=20.23 E-value=34 Score=33.66 Aligned_cols=24 Identities=13% Similarity=0.112 Sum_probs=0.0
Q ss_pred CcccHHHHHHHhCCCHHHHHHHHH
Q psy1861 302 TSHLLIDFSELLQICIFELGRTYL 325 (661)
Q Consensus 302 ~PrtLkDIsdv~~Vsv~~Lgrtyk 325 (661)
.|.|++|||+.+|+++.+|.|+.+
T Consensus 48 ~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 48 KPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp ------------------------
T ss_pred cCCCHHHHHHHhCCCHhHHHHHHc
Confidence 589999999999999999999865
No 147
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=20.12 E-value=7.7e+02 Score=26.42 Aligned_cols=87 Identities=11% Similarity=0.049 Sum_probs=0.0
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhC-CcccHHHHHHHhCCC-HHHHHHHHHHH
Q psy1861 250 ISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEG-TSHLLIDFSELLQIC-IFELGRTYLRL 327 (661)
Q Consensus 250 I~~i~~~L~Lp~~V~e~A~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~-~PrtLkDIsdv~~Vs-v~~Lgrtyk~L 327 (661)
|..+|..++++... +.+...+.|.+- .+.+--.-+=.||++-. ...++.+||..+|.+ ...+.++|++.
T Consensus 161 l~~lA~~~g~S~~~------L~R~Fk~~G~S~---~~yl~~~Rl~~A~~LL~~t~~sI~eIA~~~GF~s~S~Fsr~FKk~ 231 (274)
T PRK09978 161 LARIASELLMSPSL------LKKKLREEETSY---SQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNY 231 (274)
T ss_pred HHHHHHHHCcCHHH------HHHHHHhcCCCH---HHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHH
Q ss_pred HHHhcccCCCCChhhHHHHHHhhcCC
Q psy1861 328 SQALCISIPSMDPCLYVLRYSNRLDF 353 (661)
Q Consensus 328 ~k~L~i~~p~~dP~~yI~Rf~~~L~L 353 (661)
.- ..|..|-.++...+.+
T Consensus 232 ~G--------~TPs~yRk~~~~~~~~ 249 (274)
T PRK09978 232 YG--------MTPTEYQERSAQGLPN 249 (274)
T ss_pred HC--------cCHHHHHHHhhccCCc
No 148
>KOG1921|consensus
Probab=20.12 E-value=2.6e+02 Score=29.76 Aligned_cols=111 Identities=13% Similarity=0.023 Sum_probs=62.4
Q ss_pred CchhHHHHHHHHHHHHHHHhcCCCHHHHHHH--HHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHhCCcccHHHHHHHhC
Q psy1861 237 ESREITLDNCKRNISSLCNQLRLNQHCLETS--FNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQ 314 (661)
Q Consensus 237 ~srEr~L~~a~~~I~~i~~~L~Lp~~V~e~A--~~iyk~a~e~~l~rGR~~~~VaAACLYiACR~~~~PrtLkDIsdv~~ 314 (661)
..+|.....|...|.+.| ||...-+..+ ..+-+....-||...+-...--.|-|..-=-..++|.++.|+-..-|
T Consensus 90 QTKDevt~~Am~rL~~~~---gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~gDIP~~v~dLlsLPG 166 (286)
T KOG1921|consen 90 QTKDEVTAAAMLRLKEYG---GLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDGDIPDTVEDLLSLPG 166 (286)
T ss_pred chHHHHHHHHHHHHHHhc---CCCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCCCCchhHHHHhcCCC
Confidence 445666677888888777 5553222211 22333344446654332222222222222222389999999999999
Q ss_pred CCHHHHHHHHHHHHHHhcccCCCCChhhHHHHHHhhcCCC
Q psy1861 315 ICIFELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLDFG 354 (661)
Q Consensus 315 Vsv~~Lgrtyk~L~k~L~i~~p~~dP~~yI~Rf~~~L~L~ 354 (661)
|-++- +|+-|...-|. +-.+.-...++|+|++|+.-
T Consensus 167 VGPKM---a~L~m~~AWn~-i~GI~VDtHVHRi~nrlgWv 202 (286)
T KOG1921|consen 167 VGPKM---AHLTMQVAWNK-IVGICVDTHVHRICNRLGWV 202 (286)
T ss_pred CchHH---HHHHHHHHhcc-ceeEEeehHHHHHHHHhccc
Confidence 98863 34455554442 22233345899999999973
No 149
>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=20.04 E-value=1.5e+02 Score=23.16 Aligned_cols=25 Identities=12% Similarity=0.066 Sum_probs=23.4
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHHHH
Q psy1861 305 LLIDFSELLQICIFELGRTYLRLSQ 329 (661)
Q Consensus 305 tLkDIsdv~~Vsv~~Lgrtyk~L~k 329 (661)
+..++|+.++++...+.+.+..|.+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6899999999999999999999977
Done!