Query 029202
Match_columns 197
No_of_seqs 117 out of 230
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 09:08:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029202.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029202hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4414 COP9 signalosome, subu 100.0 3.2E-52 6.9E-57 319.6 12.6 196 1-197 1-197 (197)
2 PF10075 PCI_Csn8: COP9 signal 100.0 4.9E-38 1.1E-42 244.1 9.6 131 41-171 6-136 (143)
3 KOG3151 26S proteasome regulat 99.9 3.8E-27 8.3E-32 193.2 15.1 122 42-164 103-225 (260)
4 PF03399 SAC3_GANP: SAC3/GANP/ 99.3 3E-11 6.4E-16 98.1 10.0 102 42-144 102-204 (204)
5 KOG3252 Uncharacterized conser 99.0 8.5E-09 1.8E-13 82.6 10.6 135 53-195 79-216 (217)
6 KOG1861 Leucine permease trans 98.7 7.6E-07 1.7E-11 80.3 15.5 162 7-174 356-521 (540)
7 PF01399 PCI: PCI domain; Int 97.8 0.00015 3.2E-09 52.0 8.0 91 79-169 3-103 (105)
8 smart00088 PINT motif in prote 97.3 0.0023 4.9E-08 44.9 8.2 65 110-174 2-72 (88)
9 smart00753 PAM PCI/PINT associ 97.3 0.0023 4.9E-08 44.9 8.2 65 110-174 2-72 (88)
10 COG5187 RPN7 26S proteasome re 96.2 0.044 9.6E-07 47.7 9.6 122 72-193 266-403 (412)
11 KOG0687 26S proteasome regulat 95.9 0.069 1.5E-06 47.0 9.5 156 37-192 214-388 (393)
12 KOG2581 26S proteasome regulat 94.9 0.05 1.1E-06 49.1 5.4 108 42-155 290-400 (493)
13 KOG1076 Translation initiation 92.5 0.66 1.4E-05 44.6 8.3 94 78-171 656-763 (843)
14 KOG1498 26S proteasome regulat 91.6 1.7 3.7E-05 39.3 9.4 93 103-195 324-426 (439)
15 KOG1860 Nuclear protein export 91.4 4.3 9.3E-05 40.3 12.6 147 15-171 254-426 (927)
16 KOG1464 COP9 signalosome, subu 90.1 3.2 6.9E-05 36.3 9.4 107 46-156 278-388 (440)
17 PF03374 ANT: Phage antirepres 90.0 0.77 1.7E-05 33.5 5.0 42 121-162 13-54 (111)
18 PF14559 TPR_19: Tetratricopep 89.3 1.7 3.7E-05 28.0 5.9 65 9-80 1-65 (68)
19 COG5071 RPN5 26S proteasome re 87.5 2.8 6E-05 37.0 7.4 52 109-160 330-384 (439)
20 PF09976 TPR_21: Tetratricopep 85.5 11 0.00024 28.4 9.2 104 3-117 15-126 (145)
21 smart00071 Galanin Galanin. Ga 84.2 1.6 3.5E-05 31.3 3.6 42 154-195 10-77 (103)
22 KOG2908 26S proteasome regulat 82.6 36 0.00077 30.5 13.2 106 77-190 235-355 (380)
23 PF14938 SNAP: Soluble NSF att 82.1 6.8 0.00015 33.2 7.4 111 9-122 165-281 (282)
24 COG3071 HemY Uncharacterized e 80.0 21 0.00046 32.3 9.9 100 6-114 194-305 (400)
25 PF07037 DUF1323: Putative tra 79.2 3.4 7.3E-05 31.2 4.0 30 134-163 2-31 (122)
26 PF02042 RWP-RK: RWP-RK domain 77.8 4.5 9.8E-05 26.0 3.7 30 128-157 11-40 (52)
27 PF03683 UPF0175: Uncharacteri 74.7 4.6 0.0001 27.7 3.4 30 131-160 33-62 (76)
28 PF10255 Paf67: RNA polymerase 74.6 11 0.00023 34.4 6.6 47 106-152 291-341 (404)
29 KOG2758 Translation initiation 74.5 32 0.00069 30.8 9.2 110 43-155 255-372 (432)
30 PF12840 HTH_20: Helix-turn-he 74.0 12 0.00026 24.1 5.2 49 109-158 2-53 (61)
31 PF10668 Phage_terminase: Phag 73.3 9.2 0.0002 25.3 4.4 46 119-164 9-54 (60)
32 PF04760 IF2_N: Translation in 72.7 3.1 6.7E-05 26.4 2.0 28 132-159 3-31 (54)
33 PF08727 P3A: Poliovirus 3A pr 72.3 2.3 5.1E-05 27.8 1.3 18 145-162 28-45 (57)
34 PF12728 HTH_17: Helix-turn-he 71.5 6.1 0.00013 24.4 3.2 24 133-156 2-25 (51)
35 PF04800 ETC_C1_NDUFA4: ETC co 71.4 4.6 9.9E-05 29.6 2.9 25 145-173 57-81 (101)
36 PF05687 DUF822: Plant protein 71.0 4.4 9.6E-05 31.6 2.8 23 146-168 47-70 (150)
37 PLN03238 probable histone acet 70.4 12 0.00025 32.5 5.6 58 114-171 205-262 (290)
38 PF14555 UBA_4: UBA-like domai 68.6 6.1 0.00013 23.9 2.6 28 135-162 4-31 (43)
39 KOG3389 NADH:ubiquinone oxidor 67.8 3.3 7.3E-05 32.3 1.6 30 133-162 120-150 (178)
40 COG2522 Predicted transcriptio 66.9 21 0.00046 26.9 5.7 44 111-156 3-46 (119)
41 KOG0686 COP9 signalosome, subu 66.1 1.1E+02 0.0024 28.2 11.8 90 79-168 308-407 (466)
42 TIGR02795 tol_pal_ybgF tol-pal 66.1 41 0.00089 23.2 7.3 61 4-67 7-67 (119)
43 cd01104 HTH_MlrA-CarA Helix-Tu 66.0 28 0.0006 22.5 5.7 52 134-195 2-54 (68)
44 PF13412 HTH_24: Winged helix- 61.4 32 0.00069 20.8 5.0 42 116-158 2-46 (48)
45 PF12218 End_N_terminal: N ter 60.7 0.61 1.3E-05 31.2 -3.1 16 53-68 42-57 (67)
46 cd07377 WHTH_GntR Winged helix 60.7 33 0.00072 21.5 5.2 49 112-160 4-56 (66)
47 PF12854 PPR_1: PPR repeat 60.6 19 0.00041 20.4 3.6 30 37-66 5-34 (34)
48 PF04801 Sin_N: Sin-like prote 60.0 8.1 0.00018 35.0 2.8 106 41-160 270-387 (421)
49 PF03484 B5: tRNA synthetase B 59.6 15 0.00033 24.5 3.5 37 132-168 5-44 (70)
50 TIGR01764 excise DNA binding d 59.2 14 0.0003 21.9 3.0 23 133-155 2-24 (49)
51 PF14056 DUF4250: Domain of un 58.8 19 0.00042 23.4 3.7 31 134-164 22-52 (55)
52 smart00550 Zalpha Z-DNA-bindin 58.5 34 0.00074 22.7 5.1 46 116-161 5-54 (68)
53 COG3415 Transposase and inacti 58.3 84 0.0018 24.2 7.8 67 121-192 10-76 (138)
54 COG3357 Predicted transcriptio 58.0 25 0.00053 25.4 4.4 30 116-145 2-31 (97)
55 KOG2066 Vacuolar assembly/sort 57.3 2.1E+02 0.0045 28.5 12.5 121 6-131 399-562 (846)
56 smart00874 B5 tRNA synthetase 56.2 55 0.0012 21.4 6.7 32 132-163 5-38 (71)
57 PRK12686 carbamate kinase; Rev 55.3 27 0.00058 30.7 5.2 21 143-163 133-153 (312)
58 KOG2582 COP9 signalosome, subu 54.5 84 0.0018 28.5 8.1 166 7-178 148-368 (422)
59 KOG3250 COP9 signalosome, subu 54.5 34 0.00073 28.8 5.3 43 15-66 42-85 (258)
60 PF13463 HTH_27: Winged helix 54.2 26 0.00057 22.4 3.9 40 121-160 7-49 (68)
61 PF01418 HTH_6: Helix-turn-hel 53.9 35 0.00077 23.1 4.7 29 131-159 33-61 (77)
62 PF08280 HTH_Mga: M protein tr 53.4 58 0.0013 20.9 5.7 34 121-155 9-42 (59)
63 PRK13503 transcriptional activ 52.6 29 0.00062 28.8 4.8 35 121-155 175-210 (278)
64 PF12324 HTH_15: Helix-turn-he 51.6 34 0.00074 23.8 4.2 45 122-167 29-74 (77)
65 COG2956 Predicted N-acetylgluc 50.6 72 0.0016 28.6 7.0 84 11-100 153-239 (389)
66 cd04762 HTH_MerR-trunc Helix-T 50.2 24 0.00051 20.6 3.0 23 133-155 1-23 (49)
67 cd04235 AAK_CK AAK_CK: Carbama 50.1 21 0.00045 31.3 3.6 32 143-174 131-166 (308)
68 PF05584 Sulfolobus_pRN: Sulfo 48.7 67 0.0015 22.1 5.2 43 117-161 5-55 (72)
69 PF05344 DUF746: Domain of Unk 48.6 14 0.0003 24.9 1.8 40 127-166 8-50 (65)
70 COG0549 ArcC Carbamate kinase 48.2 40 0.00087 29.4 5.0 41 145-188 136-180 (312)
71 PF13411 MerR_1: MerR HTH fami 46.9 39 0.00084 21.8 3.9 50 134-194 2-52 (69)
72 PF01853 MOZ_SAS: MOZ/SAS fami 46.5 80 0.0017 25.7 6.3 55 114-168 130-186 (188)
73 COG5079 SAC3 Nuclear protein e 46.4 65 0.0014 30.5 6.3 136 15-161 218-377 (646)
74 PF00165 HTH_AraC: Bacterial r 46.2 31 0.00066 20.3 3.0 30 130-159 6-36 (42)
75 PLN03239 histone acetyltransfe 46.2 64 0.0014 28.8 6.1 55 114-168 263-320 (351)
76 PF09339 HTH_IclR: IclR helix- 45.6 32 0.00069 21.3 3.1 40 121-160 7-49 (52)
77 COG5484 Uncharacterized conser 45.1 23 0.0005 30.3 3.0 29 132-160 19-47 (279)
78 smart00345 HTH_GNTR helix_turn 45.0 30 0.00064 21.2 3.0 44 117-160 4-51 (60)
79 PF00627 UBA: UBA/TS-N domain; 44.9 28 0.00061 20.1 2.6 26 135-161 6-31 (37)
80 TIGR01128 holA DNA polymerase 44.8 1.8E+02 0.004 24.2 9.8 117 42-161 134-266 (302)
81 PRK12354 carbamate kinase; Rev 44.6 49 0.0011 29.0 5.1 30 144-173 127-159 (307)
82 COG3645 Uncharacterized phage- 44.2 41 0.00089 25.9 4.0 50 121-170 36-85 (135)
83 TIGR00122 birA_repr_reg BirA b 44.2 88 0.0019 20.3 5.9 40 121-162 4-46 (69)
84 smart00420 HTH_DEOR helix_turn 43.6 69 0.0015 18.9 5.4 39 122-161 5-46 (53)
85 PF06250 DUF1016: Protein of u 43.3 1.2E+02 0.0025 26.8 7.3 85 75-161 24-127 (320)
86 PF08279 HTH_11: HTH domain; 42.5 80 0.0017 19.4 4.8 41 120-160 3-46 (55)
87 KOG1497 COP9 signalosome, subu 42.3 59 0.0013 29.1 5.2 55 117-171 302-362 (399)
88 COG2886 Uncharacterized small 41.8 83 0.0018 22.4 5.0 39 121-161 32-70 (88)
89 PF01296 Galanin: Galanin; In 41.4 17 0.00036 20.3 1.1 19 157-175 1-19 (29)
90 PF08784 RPA_C: Replication pr 41.0 55 0.0012 23.2 4.2 46 116-161 46-97 (102)
91 PF01022 HTH_5: Bacterial regu 40.7 50 0.0011 20.0 3.4 35 117-153 2-36 (47)
92 COG5159 RPN6 26S proteasome re 40.3 2.7E+02 0.0058 24.8 11.8 148 46-194 253-412 (421)
93 PF08220 HTH_DeoR: DeoR-like h 40.0 79 0.0017 20.1 4.4 48 119-167 2-52 (57)
94 smart00419 HTH_CRP helix_turn_ 39.9 77 0.0017 18.5 4.5 30 132-161 8-40 (48)
95 PRK11161 fumarate/nitrate redu 39.8 1.7E+02 0.0037 23.4 7.5 36 133-168 185-223 (235)
96 smart00418 HTH_ARSR helix_turn 39.7 63 0.0014 19.6 3.9 37 122-160 2-41 (66)
97 PF13404 HTH_AsnC-type: AsnC-t 39.5 85 0.0019 18.8 5.1 34 120-154 6-39 (42)
98 TIGR02844 spore_III_D sporulat 39.5 52 0.0011 22.9 3.7 33 119-153 8-40 (80)
99 PF09035 Tn916-Xis: Excisionas 39.1 47 0.001 22.4 3.3 30 132-161 13-45 (67)
100 cd04761 HTH_MerR-SF Helix-Turn 39.0 43 0.00093 19.9 2.9 24 134-158 2-25 (49)
101 PF13545 HTH_Crp_2: Crp-like h 38.6 80 0.0017 20.6 4.5 38 132-169 28-68 (76)
102 PF13730 HTH_36: Helix-turn-he 38.5 51 0.0011 20.3 3.3 25 134-158 27-54 (55)
103 cd05513 Bromo_brd7_like Bromod 38.5 18 0.00038 26.1 1.2 29 1-29 42-70 (98)
104 PF06056 Terminase_5: Putative 38.4 46 0.001 21.6 3.1 30 131-160 12-41 (58)
105 COG4004 Uncharacterized protei 38.2 1.1E+02 0.0024 22.1 5.2 54 143-196 9-79 (96)
106 smart00342 HTH_ARAC helix_turn 38.2 1.1E+02 0.0023 19.6 6.0 38 121-160 41-80 (84)
107 PF12802 MarR_2: MarR family; 38.2 84 0.0018 19.6 4.4 40 121-160 9-52 (62)
108 PF04433 SWIRM: SWIRM domain; 37.8 1.3E+02 0.0028 20.6 5.6 42 117-158 37-83 (86)
109 PRK12454 carbamate kinase-like 37.2 69 0.0015 28.1 4.9 30 144-173 136-169 (313)
110 TIGR03573 WbuX N-acetyl sugar 36.9 51 0.0011 29.0 4.1 37 116-153 302-342 (343)
111 PF00392 GntR: Bacterial regul 36.9 64 0.0014 20.7 3.7 48 114-161 5-56 (64)
112 PRK10906 DNA-binding transcrip 36.4 2.3E+02 0.0049 23.7 7.8 54 117-171 5-61 (252)
113 PRK10747 putative protoheme IX 36.0 2.6E+02 0.0057 24.7 8.6 98 7-110 195-301 (398)
114 smart00422 HTH_MERR helix_turn 35.7 56 0.0012 21.0 3.3 21 134-154 2-22 (70)
115 PF13542 HTH_Tnp_ISL3: Helix-t 35.5 1E+02 0.0022 18.6 5.3 35 117-154 15-49 (52)
116 cd05503 Bromo_BAZ2A_B_like Bro 34.7 22 0.00048 25.3 1.2 29 1-29 41-69 (97)
117 PF03793 PASTA: PASTA domain; 34.5 39 0.00084 21.5 2.3 21 140-160 5-25 (63)
118 KOG3614 Ca2+/Mg2+-permeable ca 34.2 2.9E+02 0.0063 29.2 9.2 85 40-142 561-647 (1381)
119 COG1349 GlpR Transcriptional r 34.1 1.8E+02 0.0039 24.4 6.9 56 119-175 7-65 (253)
120 cd05505 Bromo_WSTF_like Bromod 33.7 24 0.00051 25.3 1.2 29 1-29 41-69 (97)
121 cd03568 VHS_STAM VHS domain fa 33.6 1.2E+02 0.0026 23.3 5.3 96 58-161 39-136 (144)
122 TIGR01610 phage_O_Nterm phage 33.5 1.1E+02 0.0024 21.5 4.8 33 129-161 44-79 (95)
123 KOG1463 26S proteasome regulat 33.4 3.7E+02 0.008 24.4 9.7 98 71-168 280-387 (411)
124 cd05498 Bromo_Brdt_II_like Bro 33.3 25 0.00053 25.1 1.3 29 1-29 46-74 (102)
125 COG1777 Predicted transcriptio 33.2 79 0.0017 26.3 4.3 44 107-152 5-48 (217)
126 TIGR03338 phnR_burk phosphonat 33.1 2.5E+02 0.0053 22.2 7.6 49 112-160 14-65 (212)
127 PF10108 DNA_pol_B_exo2: Predi 32.8 89 0.0019 25.8 4.6 48 1-60 134-181 (209)
128 PF06971 Put_DNA-bind_N: Putat 32.7 1E+02 0.0022 19.4 3.9 27 125-151 21-47 (50)
129 PF13384 HTH_23: Homeodomain-l 32.3 94 0.002 18.6 3.7 35 117-154 5-39 (50)
130 PF01535 PPR: PPR repeat; Int 32.1 52 0.0011 17.0 2.3 26 42-67 3-28 (31)
131 PLN00104 MYST -like histone ac 32.0 1.8E+02 0.004 26.9 6.9 55 114-168 356-410 (450)
132 TIGR02702 SufR_cyano iron-sulf 32.0 1.1E+02 0.0025 24.5 5.2 43 118-161 2-47 (203)
133 COG2909 MalT ATP-dependent tra 32.0 5.1E+02 0.011 26.2 10.2 88 9-97 468-568 (894)
134 PF06627 DUF1153: Protein of u 31.9 1.4E+02 0.003 21.4 4.8 37 119-155 36-72 (90)
135 PF04769 MAT_Alpha1: Mating-ty 31.6 2.3E+02 0.005 23.2 6.8 29 139-169 116-146 (201)
136 PF04539 Sigma70_r3: Sigma-70 31.5 1.6E+02 0.0034 19.4 5.7 25 130-154 18-42 (78)
137 smart00497 IENR1 Intron encode 31.5 1E+02 0.0023 18.6 3.9 27 133-160 18-44 (53)
138 TIGR02479 FliA_WhiG RNA polyme 31.4 2.8E+02 0.006 22.3 7.6 23 131-153 98-120 (224)
139 cd05501 Bromo_SP100C_like Brom 31.4 28 0.0006 25.4 1.3 30 1-30 41-70 (102)
140 cd04764 HTH_MlrA-like_sg1 Heli 30.8 75 0.0016 20.5 3.3 22 134-155 2-23 (67)
141 PRK11511 DNA-binding transcrip 30.7 1.5E+02 0.0033 21.8 5.3 36 120-155 12-48 (127)
142 PRK13239 alkylmercury lyase; P 30.6 2.1E+02 0.0045 23.6 6.4 51 117-168 22-73 (206)
143 smart00165 UBA Ubiquitin assoc 30.6 40 0.00086 19.2 1.7 21 142-162 11-31 (37)
144 cd05520 Bromo_polybromo_III Br 30.5 28 0.00061 25.2 1.2 29 1-29 47-75 (103)
145 cd05492 Bromo_ZMYND11 Bromodom 30.4 36 0.00077 25.1 1.7 30 1-30 47-76 (109)
146 cd05507 Bromo_brd8_like Bromod 30.1 29 0.00062 25.1 1.2 30 1-30 44-73 (104)
147 cd05506 Bromo_plant1 Bromodoma 30.0 29 0.00064 24.5 1.2 29 1-29 43-71 (99)
148 PRK09411 carbamate kinase; Rev 29.9 1.1E+02 0.0024 26.7 4.9 41 145-188 129-172 (297)
149 PF07721 TPR_4: Tetratricopept 29.8 54 0.0012 17.2 2.0 19 46-64 8-26 (26)
150 cd05516 Bromo_SNF2L2 Bromodoma 29.7 30 0.00065 25.2 1.2 29 1-29 48-76 (107)
151 PF13986 DUF4224: Domain of un 29.3 1.4E+02 0.0031 18.4 4.8 34 133-166 3-39 (47)
152 cd04763 HTH_MlrA-like Helix-Tu 29.2 81 0.0018 20.4 3.2 52 134-195 2-54 (68)
153 PF13518 HTH_28: Helix-turn-he 29.2 1.3E+02 0.0028 17.9 4.3 34 119-155 2-35 (52)
154 PF00325 Crp: Bacterial regula 29.1 88 0.0019 17.9 2.9 17 133-149 3-19 (32)
155 cd05518 Bromo_polybromo_IV Bro 29.1 32 0.00069 24.9 1.3 29 1-29 47-75 (103)
156 PRK06288 RNA polymerase sigma 29.1 2.3E+02 0.005 23.7 6.7 24 130-153 132-155 (268)
157 cd05495 Bromo_cbp_like Bromodo 29.0 31 0.00067 25.2 1.2 29 1-29 47-75 (108)
158 cd00197 VHS_ENTH_ANTH VHS, ENT 29.0 2.2E+02 0.0047 20.4 7.8 49 40-90 18-69 (115)
159 TIGR02302 aProt_lowcomp conser 28.8 6.2E+02 0.013 25.5 12.6 119 11-143 432-575 (851)
160 PRK10803 tol-pal system protei 28.6 2.9E+02 0.0064 23.3 7.3 80 10-98 154-240 (263)
161 PF12244 DUF3606: Protein of u 28.5 74 0.0016 20.5 2.8 24 135-158 23-46 (57)
162 KOG2264 Exostosin EXT1L [Signa 28.1 1.4E+02 0.0031 28.7 5.5 72 20-98 438-515 (907)
163 KOG2747 Histone acetyltransfer 27.8 1.2E+02 0.0025 27.7 4.8 50 115-164 311-361 (396)
164 PHA02591 hypothetical protein; 27.8 83 0.0018 22.1 3.1 37 116-155 46-82 (83)
165 PF06262 DUF1025: Possibl zinc 27.8 42 0.00092 24.3 1.7 17 135-151 78-94 (97)
166 cd05512 Bromo_brd1_like Bromod 27.5 36 0.00078 24.4 1.3 29 1-29 42-70 (98)
167 cd05509 Bromo_gcn5_like Bromod 27.5 34 0.00074 24.3 1.2 29 1-29 42-70 (101)
168 PF13512 TPR_18: Tetratricopep 27.4 1.7E+02 0.0037 22.6 5.1 56 5-65 16-73 (142)
169 PF12046 DUF3529: Protein of u 27.3 90 0.002 25.1 3.6 26 147-172 47-75 (173)
170 PRK10434 srlR DNA-bindng trans 27.2 2.7E+02 0.0058 23.3 6.8 50 119-169 7-59 (256)
171 cd05508 Bromo_RACK7 Bromodomai 27.1 36 0.00079 24.5 1.3 30 1-30 43-72 (99)
172 cd05504 Bromo_Acf1_like Bromod 27.1 35 0.00076 25.2 1.2 29 1-29 53-81 (115)
173 PF04703 FaeA: FaeA-like prote 26.9 1.2E+02 0.0027 19.9 3.7 42 119-160 2-46 (62)
174 PRK14584 hmsS hemin storage sy 26.8 1.9E+02 0.0041 22.8 5.3 44 128-171 94-139 (153)
175 cd05519 Bromo_SNF2 Bromodomain 26.8 36 0.00079 24.4 1.2 29 1-29 47-75 (103)
176 smart00513 SAP Putative DNA-bi 26.7 68 0.0015 18.3 2.2 19 143-161 3-21 (35)
177 PF11193 DUF2812: Protein of u 26.6 2.1E+02 0.0045 20.5 5.3 44 147-190 54-102 (115)
178 PRK13500 transcriptional activ 26.6 1.6E+02 0.0034 25.2 5.4 41 120-160 209-251 (312)
179 PF09494 Slx4: Slx4 endonuclea 26.6 74 0.0016 20.9 2.6 32 129-160 21-61 (64)
180 PF13551 HTH_29: Winged helix- 26.5 1.5E+02 0.0033 20.5 4.6 33 121-155 3-35 (112)
181 cd05497 Bromo_Brdt_I_like Brom 26.5 37 0.0008 24.8 1.2 29 1-29 48-76 (107)
182 COG2207 AraC AraC-type DNA-bin 26.2 2.2E+02 0.0047 19.8 5.4 37 117-154 21-58 (127)
183 cd05510 Bromo_SPT7_like Bromod 25.7 38 0.00083 25.0 1.2 30 1-30 49-78 (112)
184 PF14791 DNA_pol_B_thumb: DNA 25.2 48 0.001 22.0 1.5 18 147-164 13-30 (64)
185 PRK11534 DNA-binding transcrip 24.8 3.6E+02 0.0079 21.5 7.7 53 108-160 6-61 (224)
186 PRK13501 transcriptional activ 24.7 1.8E+02 0.0038 24.4 5.3 40 121-160 180-221 (290)
187 cd05517 Bromo_polybromo_II Bro 24.7 41 0.0009 24.3 1.2 29 1-29 47-75 (103)
188 PF10116 Host_attach: Protein 24.5 74 0.0016 23.9 2.6 58 81-142 81-138 (138)
189 PF01047 MarR: MarR family; I 24.5 1.2E+02 0.0027 18.7 3.4 38 122-160 8-48 (59)
190 cd05525 Bromo_ASH1 Bromodomain 24.5 42 0.00091 24.5 1.2 29 1-29 49-77 (106)
191 PF13167 GTP-bdg_N: GTP-bindin 24.4 2.3E+02 0.005 20.3 5.0 44 147-193 11-54 (95)
192 PRK10141 DNA-binding transcrip 24.3 2.5E+02 0.0055 20.8 5.4 53 107-160 6-61 (117)
193 PF00531 Death: Death domain; 24.1 2.2E+02 0.0047 18.7 4.7 26 130-155 10-35 (83)
194 PF10607 CLTH: CTLH/CRA C-term 24.1 3E+02 0.0065 20.3 8.7 58 4-63 6-64 (145)
195 COG1466 HolA DNA polymerase II 24.0 4.8E+02 0.01 22.6 9.9 53 13-66 174-235 (334)
196 PF13601 HTH_34: Winged helix 23.9 2.4E+02 0.0053 19.2 5.4 71 118-196 1-77 (80)
197 PRK07408 RNA polymerase sigma 23.8 1.9E+02 0.0041 24.1 5.3 20 133-152 130-149 (256)
198 TIGR00400 mgtE Mg2+ transporte 23.7 2.4E+02 0.0051 25.8 6.2 100 5-126 10-114 (449)
199 PF13591 MerR_2: MerR HTH fami 23.5 1.2E+02 0.0025 21.0 3.3 27 133-160 1-27 (84)
200 TIGR02297 HpaA 4-hydroxyphenyl 23.4 2E+02 0.0043 23.8 5.4 40 120-159 189-230 (287)
201 PRK09464 pdhR transcriptional 23.2 2.9E+02 0.0063 22.6 6.2 59 110-168 11-74 (254)
202 PRK10681 DNA-binding transcrip 23.1 79 0.0017 26.4 2.8 42 117-160 7-52 (252)
203 PF02002 TFIIE_alpha: TFIIE al 23.1 77 0.0017 22.6 2.4 34 121-155 17-50 (105)
204 cd08311 Death_p75NR Death doma 22.9 1.7E+02 0.0037 20.0 4.0 36 119-154 2-37 (77)
205 cd05524 Bromo_polybromo_I Brom 22.9 86 0.0019 23.0 2.6 30 1-30 49-78 (113)
206 cd01107 HTH_BmrR Helix-Turn-He 22.9 2.9E+02 0.0063 19.7 5.7 48 134-190 2-50 (108)
207 PF01709 Transcrip_reg: Transc 22.8 93 0.002 26.0 3.1 44 149-197 179-222 (234)
208 PF12536 DUF3734: Patatin phos 22.8 80 0.0017 23.1 2.4 34 58-95 24-57 (108)
209 PF11360 DUF3110: Protein of u 22.7 95 0.0021 21.9 2.7 27 144-170 55-84 (86)
210 PRK06266 transcription initiat 22.6 2.9E+02 0.0063 22.0 5.8 37 118-155 23-59 (178)
211 PF12169 DNA_pol3_gamma3: DNA 22.5 1.5E+02 0.0033 21.9 4.1 50 79-128 18-68 (143)
212 PRK00430 fis global DNA-bindin 22.5 2.9E+02 0.0063 19.6 8.1 61 92-157 33-93 (95)
213 TIGR01033 DNA-binding regulato 22.4 1.6E+02 0.0035 24.7 4.5 42 150-196 184-225 (238)
214 cd05515 Bromo_polybromo_V Brom 22.4 74 0.0016 22.9 2.2 29 1-29 47-75 (105)
215 TIGR02795 tol_pal_ybgF tol-pal 22.4 2.6E+02 0.0056 18.9 5.2 57 6-65 46-102 (119)
216 smart00346 HTH_ICLR helix_turn 22.3 2.4E+02 0.0052 18.9 4.8 41 121-161 9-52 (91)
217 PF11112 PyocinActivator: Pyoc 22.3 2E+02 0.0043 19.8 4.2 54 131-192 13-68 (76)
218 PF07146 DUF1389: Protein of u 22.3 1.6E+02 0.0036 25.8 4.6 66 76-146 171-236 (314)
219 smart00668 CTLH C-terminal to 22.2 1.5E+02 0.0032 18.1 3.4 27 3-29 5-31 (58)
220 cd05511 Bromo_TFIID Bromodomai 22.2 50 0.0011 24.2 1.2 29 1-29 41-69 (112)
221 PRK09940 transcriptional regul 21.9 3.6E+02 0.0078 22.8 6.6 36 122-157 139-175 (253)
222 KOG2072 Translation initiation 21.9 1E+02 0.0023 30.8 3.6 63 108-170 423-492 (988)
223 TIGR00746 arcC carbamate kinas 21.9 1.6E+02 0.0035 25.8 4.5 20 144-163 133-152 (310)
224 PF08898 DUF1843: Domain of un 21.8 1.1E+02 0.0024 19.7 2.6 25 5-29 6-30 (53)
225 PF07304 SRA1: Steroid recepto 21.8 3.9E+02 0.0085 20.8 6.3 43 73-115 88-139 (157)
226 PF04967 HTH_10: HTH DNA bindi 21.7 1.5E+02 0.0033 18.9 3.3 22 131-152 22-43 (53)
227 PF13443 HTH_26: Cro/C1-type H 21.7 79 0.0017 19.9 2.0 24 132-155 10-33 (63)
228 TIGR02394 rpoS_proteo RNA poly 21.7 1.6E+02 0.0034 25.0 4.4 33 129-161 239-282 (285)
229 TIGR03697 NtcA_cyano global ni 21.6 3.7E+02 0.008 20.5 7.8 38 132-169 143-183 (193)
230 cd05500 Bromo_BDF1_2_I Bromodo 21.5 52 0.0011 23.6 1.2 29 1-29 47-75 (103)
231 PF04545 Sigma70_r4: Sigma-70, 21.5 2E+02 0.0043 17.3 3.9 23 130-152 18-40 (50)
232 cd00256 VATPase_H VATPase_H, r 21.3 3.4E+02 0.0073 25.0 6.6 83 75-159 200-291 (429)
233 PF11084 DUF2621: Protein of u 21.3 3.9E+02 0.0084 20.6 7.5 78 42-127 13-91 (141)
234 cd04369 Bromodomain Bromodomai 21.2 54 0.0012 22.1 1.2 29 1-29 43-71 (99)
235 PF00376 MerR: MerR family reg 21.2 1.2E+02 0.0027 17.7 2.6 21 134-154 1-21 (38)
236 PF01710 HTH_Tnp_IS630: Transp 21.1 2.4E+02 0.0053 20.6 4.8 36 127-162 66-101 (119)
237 PRK07670 RNA polymerase sigma 21.1 3.2E+02 0.007 22.5 6.1 23 132-154 125-147 (251)
238 smart00344 HTH_ASNC helix_turn 21.0 3E+02 0.0065 19.2 5.2 40 120-160 6-48 (108)
239 PF11428 DUF3196: Protein of u 20.9 2.5E+02 0.0055 24.4 5.4 58 79-137 47-109 (286)
240 cd05528 Bromo_AAA Bromodomain; 20.8 62 0.0013 23.8 1.5 29 1-29 44-72 (112)
241 PF03704 BTAD: Bacterial trans 20.6 3.5E+02 0.0075 19.8 5.8 58 7-70 70-127 (146)
242 TIGR03879 near_KaiC_dom probab 20.6 2.9E+02 0.0063 18.9 4.8 27 128-154 28-54 (73)
243 COG1724 Predicted RNA binding 20.5 81 0.0018 21.3 1.8 21 140-160 3-23 (66)
244 PRK13918 CRP/FNR family transc 20.5 4.1E+02 0.0088 20.5 7.6 38 132-169 149-189 (202)
245 cd00092 HTH_CRP helix_turn_hel 20.4 2.3E+02 0.005 17.6 5.1 32 131-162 24-58 (67)
246 COG1522 Lrp Transcriptional re 20.3 2.6E+02 0.0056 20.8 5.0 38 116-154 7-44 (154)
247 cd04766 HTH_HspR Helix-Turn-He 20.2 1.4E+02 0.0031 20.6 3.2 26 133-159 2-27 (91)
248 PF01329 Pterin_4a: Pterin 4 a 20.1 1.5E+02 0.0033 20.9 3.4 19 144-162 5-24 (95)
249 PF07453 NUMOD1: NUMOD1 domain 20.0 1E+02 0.0023 17.5 2.1 17 134-150 18-34 (37)
No 1
>KOG4414 consensus COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=3.2e-52 Score=319.64 Aligned_cols=196 Identities=50% Similarity=0.895 Sum_probs=185.1
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHH
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAW 80 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~ 80 (197)
||...+.+.+++.+|++++++||++||+.+..|+.++++|||+++|+.|++.||..||||||||||..+|+.+|++..+|
T Consensus 1 M~la~m~EalaA~SFdKi~D~Cdn~~Lea~~eGIa~~~dw~Ya~~L~~Yf~~dD~dnARfLWKRIP~AIKe~k~El~aaW 80 (197)
T KOG4414|consen 1 MDLAPMAEALAAFSFDKIADICDNLELEAAGEGIATHDDWPYAIHLAGYFLHDDCDNARFLWKRIPPAIKEAKPELGAAW 80 (197)
T ss_pred CCchHHHHHHHhhhHHHHHHHhhhhhhcccCCCccCCCcchHHHHHHHHHHhccchhHHHHHHhCCHHHhhcCchhhhhh
Confidence 89999999999999999999999999997667999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHhcCCee
Q 029202 81 KIGQHLWTRDYAGVYDAIRGFDWSQEAQALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTL 160 (197)
Q Consensus 81 ~l~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~ 160 (197)
.+||.+|++||+++|.+++.+.||+..+++|+.|.+..|.|.|.++.+||+||..+++|.+|||+++|+.+.+.+.||+.
T Consensus 81 giGQkiWq~Df~GiYeaI~~~dWSeeak~imaAf~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~~ddAtk~ilEnGWqa 160 (197)
T KOG4414|consen 81 GIGQKIWQHDFAGIYEAINAHDWSEEAKDIMAAFRDATRKRAFALLLQAYSSIIADDFAAFLGLPEDDATKGILENGWQA 160 (197)
T ss_pred hhhHHHHhcccchHHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcccch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCceE-eecCCCCCCCCCCChHHHHHHHHHHHhhcC
Q 029202 161 DPASRML-TVKKQPLVTEQKLDPSKLQRLTEYVFHLEH 197 (197)
Q Consensus 161 d~~~~~~-~P~~~~~~~~~~~~~~qL~~LT~~v~fLE~ 197 (197)
|+.++|. .|+++..- ...++-.++..||+++.|||+
T Consensus 161 DaasqMasl~kk~V~~-a~~Vd~nK~~~LsE~a~~~~~ 197 (197)
T KOG4414|consen 161 DAASQMASLKKKAVAG-ALDVDFNKFIPLSEPAFHLEH 197 (197)
T ss_pred hhHHHHhhccchhccc-ccccchhhceecCCccCCCCC
Confidence 9999998 45544332 234588899999999999996
No 2
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=100.00 E-value=4.9e-38 Score=244.13 Aligned_cols=131 Identities=34% Similarity=0.714 Sum_probs=108.0
Q ss_pred hHHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHHHHH
Q 029202 41 PYVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRDYAGVYDAIRGFDWSQEAQALVAAFSELYTK 120 (197)
Q Consensus 41 py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~iR~ 120 (197)
+|+++|+.||++||+++||++|+|||.++++.||+|+++|.|+++||+|+|++||..+++.+|++.+.++|..|++++|+
T Consensus 6 ~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~iR~ 85 (143)
T PF10075_consen 6 IYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDTIRE 85 (143)
T ss_dssp HHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHHHHH
T ss_pred HHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHHHHH
Confidence 39999999999999999999999999999998899999999999999999999999999989999999999999999999
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHhcCCeecCCCceEeecC
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKK 171 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~P~~ 171 (197)
+|+.||++||++|+++++++|||++++|+.++++++||++|+++.++.|.+
T Consensus 86 ~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~~~~~~gW~~d~~~~~~~~~~ 136 (143)
T PF10075_consen 86 RIAHLISKAYSSISLSDLAEMLGLSEEELEKFIKSRGWTVDGDGVLFPPNP 136 (143)
T ss_dssp HHHHHHHHH-SEE-HHHHHHHTTS-HHHHHHHHHHHT-EE-----EE---H
T ss_pred HHHHHHHHHHhHcCHHHHHHHhCCCHHHHHHHHHHcCCEECCCccEEecCC
Confidence 999999999999999999999999999999999999999997775555443
No 3
>KOG3151 consensus 26S proteasome regulatory complex, subunit RPN12/PSMD8 [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=3.8e-27 Score=193.22 Aligned_cols=122 Identities=17% Similarity=0.230 Sum_probs=118.0
Q ss_pred HHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHHHHHH
Q 029202 42 YVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRDYAGVYDAIRGFDWSQEAQALVAAFSELYTKR 121 (197)
Q Consensus 42 y~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~iR~~ 121 (197)
.|++|+.+|.+|++++||++++++|...++.+|.|+++++|+|++|+|.|++||.++++ .+++.|..||+.+.++||++
T Consensus 103 ~GLnLL~LLsqNRiaeFHteLe~lp~~~l~~~~~I~~~v~LEq~~MEGaYnKv~~a~~s-~p~~~y~~FmdIl~~tiRdE 181 (260)
T KOG3151|consen 103 LGLNLLYLLSQNRIAEFHTELELLPKKILQHNPYISHPVSLEQSLMEGAYNKVLSAKQS-IPSEEYTYFMDILLDTIRDE 181 (260)
T ss_pred HHHHHHHHHHhccHHHHHHHHHhccHHHhhccchhhhHHHHHHHHHhhHHHHHHHHHhc-CCcHHHHHHHHHHHHHHHHH
Confidence 79999999999999999999999999999999999999999999999999999999999 88999999999999999999
Q ss_pred HHHHHHHhhcccCHHHHHHHcCCC-HHHHHHHHHhcCCeecCCC
Q 029202 122 MFQLLLSAYSTISTQDTALFLGMN-EDDAAYYVQQQGWTLDPAS 164 (197)
Q Consensus 122 i~~lis~AY~sIs~~~~a~~Lgls-~~e~~~~~~~~GW~~d~~~ 164 (197)
|+.|++++|..|++++++++|+|+ ++++.+|+++|+|.+++.+
T Consensus 182 IA~c~EKsYd~l~~s~a~~~L~f~~~~e~~~~~~~r~W~l~~~~ 225 (260)
T KOG3151|consen 182 IAGCIEKSYDKLSASDATQMLLFNNDKELKKFATERQWPLDEKG 225 (260)
T ss_pred HHHHHHHHHhhcCHHHHHHHHhcCChHHHHHHHHhcCCcccccc
Confidence 999999999999999999999997 8999999999999998433
No 4
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=99.27 E-value=3e-11 Score=98.07 Aligned_cols=102 Identities=22% Similarity=0.208 Sum_probs=85.2
Q ss_pred HHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHHHHHH
Q 029202 42 YVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRDYAGVYDAIRGFDWSQEAQALVAAFSELYTKR 121 (197)
Q Consensus 42 y~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~iR~~ 121 (197)
.+.+|+.+|.+|+..+++..+.++|.++. .+|.++.+..|.+++++|+|.+||..+++...+...+.++..+.+.+|.+
T Consensus 102 ~~y~lL~~l~~~~~~~~~~~l~~l~~~~~-~~~~i~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~l~~~~~~~iR~~ 180 (204)
T PF03399_consen 102 IAYYLLYLLCQNNIPDFHMELELLPSEIL-SSPYIQFALELCRALMEGNYVRFFRLYRSKSAPYLFACLMERFFNRIRLR 180 (204)
T ss_dssp HHHHHHHTT-T---THHHHHHTTS-HHHH-TSHHHHHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHHHHGGGHHHHHHH
T ss_pred HHHHHHHHHHcccchHHHHHHHHCchhhh-cCHHHHHHHHHHHHHHcCCHHHHHHHHhccCCChHHHHHHHHHHHHHHHH
Confidence 78888888889999999999999999877 56999999999999999999999999955577788999999999999999
Q ss_pred HHHHHHHhhcc-cCHHHHHHHcCC
Q 029202 122 MFQLLLSAYST-ISTQDTALFLGM 144 (197)
Q Consensus 122 i~~lis~AY~s-Is~~~~a~~Lgl 144 (197)
+++++++||.+ |+++.++++|||
T Consensus 181 al~~i~~ay~~~i~l~~l~~~L~F 204 (204)
T PF03399_consen 181 ALQSISKAYRSSIPLSFLAELLGF 204 (204)
T ss_dssp HHHHHHHHS-T-EEHHHHHHHTT-
T ss_pred HHHHHHHHcCCCCCHHHHHHHcCC
Confidence 99999999999 999999999996
No 5
>KOG3252 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.95 E-value=8.5e-09 Score=82.59 Aligned_cols=135 Identities=14% Similarity=0.256 Sum_probs=107.8
Q ss_pred cCHHHHHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 029202 53 NDINSARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRDYAGVYDAIRGFDWSQEAQALVAAFSELYTKRMFQLLLSAYST 132 (197)
Q Consensus 53 ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~iR~~i~~lis~AY~s 132 (197)
.|..-|++| ||..... +..++.+.-|+..|..|+|..||...+. ...+-.=|.+|++.||.-+-..++-.|..
T Consensus 79 tDF~l~kcl---i~~~~~~-ee~~r~ii~L~~~LEt~~Fq~FW~~~~~---N~~mle~itGFedsvr~yachvv~iTyQk 151 (217)
T KOG3252|consen 79 TDFTLAKCL---IDERVQM-EEPFRSIIDLGDYLETCRFQQFWQEADE---NRDMLEGITGFEDSVRKYACHVVGITYQK 151 (217)
T ss_pred cchhHHHHh---cCHHHhc-ccchhHHHhHHHHHhhchHHHHhhhhcc---chHHhcCCCcHHHHHHHHHHHheechHhh
Confidence 455555554 5666554 4789999999999999999999987744 46677778899999999999999999999
Q ss_pred cCHHHHHHHcCCC-HHHHHHHHHhcCCeecCCCceEeecCCCCCCCCC-C-ChHHHHHHHHHHHhh
Q 029202 133 ISTQDTALFLGMN-EDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQK-L-DPSKLQRLTEYVFHL 195 (197)
Q Consensus 133 Is~~~~a~~Lgls-~~e~~~~~~~~GW~~d~~~~~~~P~~~~~~~~~~-~-~~~qL~~LT~~v~fL 195 (197)
|.-.-+|.+||-. +.++..++++-||..+.+|.+++|.... ..+++ + +..++...++++.++
T Consensus 152 I~k~lLaellG~~sDs~le~~~~~~GW~a~e~G~ifv~~qE~-~iKtkNi~EkI~fd~Va~ima~~ 216 (217)
T KOG3252|consen 152 IDKWLLAELLGGLSDSQLEVWMTKYGWIADESGQIFVASQEE-EIKTKNIVEKIDFDHVASIMASL 216 (217)
T ss_pred chHHHHHHhhCcccHHHHHHHHHHccceecCCceEEEecccc-ccccCCccccCCcchHHHHHHhc
Confidence 9999999999975 7899999999999999999666666544 33332 2 667777777766543
No 6
>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]
Probab=98.70 E-value=7.6e-07 Score=80.25 Aligned_cols=162 Identities=17% Similarity=0.213 Sum_probs=129.3
Q ss_pred HHHHccccHHHHHHHHhHHhhhhhhCCCc--CCCcchHHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHHHHHH
Q 029202 7 TDALASKSYEKIADICDDLMLKVAAEGIV--FQDEWPYVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAWKIGQ 84 (197)
Q Consensus 7 ~~~~~~~~~~~l~~~~e~~El~~~~~g~~--~~~~~py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~~ 84 (197)
+=++..||.++.-+=--.+-.-. +.|+. ..++ -+--+|.|+...+-.+=-.++.++..++|+ |+.+.++.+|-.
T Consensus 356 RIALEkGD~~EfNQCQtQLk~LY-~egipg~~~EF--~AYriLY~i~tkN~~di~sll~~lt~E~ke-d~~V~hAL~vR~ 431 (540)
T KOG1861|consen 356 RIALEKGDLEEFNQCQTQLKALY-SEGIPGAYLEF--TAYRILYYIFTKNYPDILSLLRDLTEEDKE-DEAVAHALEVRS 431 (540)
T ss_pred HHHHhcCCHHHHHHHHHHHHHHH-ccCCCCchhhH--HHHHHHHHHHhcCchHHHHHHHhccHhhcc-CHHHHHHHHHHH
Confidence 34667787666533222222221 22332 2444 444488888888888888999999999995 699999999999
Q ss_pred HHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhc-ccCHHHHHHHcCCC-HHHHHHHHHhcCCeecC
Q 029202 85 HLWTRDYAGVYDAIRGFDWSQEAQALVAAFSELYTKRMFQLLLSAYS-TISTQDTALFLGMN-EDDAAYYVQQQGWTLDP 162 (197)
Q Consensus 85 ~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~iR~~i~~lis~AY~-sIs~~~~a~~Lgls-~~e~~~~~~~~GW~~d~ 162 (197)
+.--|+|-+||......+ -.-..+|+.|.++-|...+..|.|+|. +|+++-+++.|.|+ .+++..|..+++|+.+.
T Consensus 432 A~~~GNY~kFFrLY~~AP--~M~~yLmdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~e~c~~~l~~~~~~~~~ 509 (540)
T KOG1861|consen 432 AVTLGNYHKFFRLYLTAP--NMSGYLMDLFLERERKKALTIICKSYRPTITVDFIASELAFDSMEDCVNFLNEQNLTYDS 509 (540)
T ss_pred HHHhccHHHHHHHHhhcc--cchhHHHHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchHHHHHHHHhccCccccc
Confidence 999999999999987722 334679999999999999999999999 99999999999997 58899999999999999
Q ss_pred CCceEeecCCCC
Q 029202 163 ASRMLTVKKQPL 174 (197)
Q Consensus 163 ~~~~~~P~~~~~ 174 (197)
.|..+.+++..+
T Consensus 510 ~g~~~~~~~~~s 521 (540)
T KOG1861|consen 510 LGPQILDKNASS 521 (540)
T ss_pred cCCccccccccc
Confidence 998988887654
No 7
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=97.79 E-value=0.00015 Score=51.97 Aligned_cols=91 Identities=14% Similarity=0.166 Sum_probs=69.4
Q ss_pred HHHHHHHHHcCChHHHHHHhhCCC----CcHHHHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHH
Q 029202 79 AWKIGQHLWTRDYAGVYDAIRGFD----WSQEAQALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQ 154 (197)
Q Consensus 79 ~~~l~~~L~~~~y~~v~~~l~~~~----ws~~~~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~ 154 (197)
...+.+++..|+|..+...++... -.+.+...++.+...+|.+.+.-+.+.|++|+++++|+.++++.+++..++.
T Consensus 3 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~ 82 (105)
T PF01399_consen 3 YSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLSEEEVESILI 82 (105)
T ss_dssp HHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHH
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHH
Confidence 346778999999999988887641 1245667899999999999999999999999999999999999988887755
Q ss_pred h---c---CCeecCCCceEee
Q 029202 155 Q---Q---GWTLDPASRMLTV 169 (197)
Q Consensus 155 ~---~---GW~~d~~~~~~~P 169 (197)
+ . .=++|...+++..
T Consensus 83 ~~I~~~~i~~~ID~~~~~v~~ 103 (105)
T PF01399_consen 83 DLISNGLIKAKIDQVNGVVVF 103 (105)
T ss_dssp HHHHTTSSEEEEETTTTEEEE
T ss_pred HHHHCCCEEEEEECCCCEEEe
Confidence 3 1 3355555555543
No 8
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=97.28 E-value=0.0023 Score=44.93 Aligned_cols=65 Identities=20% Similarity=0.245 Sum_probs=53.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh------cCCeecCCCceEeecCCCC
Q 029202 110 LVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ------QGWTLDPASRMLTVKKQPL 174 (197)
Q Consensus 110 ~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~------~GW~~d~~~~~~~P~~~~~ 174 (197)
.+..+...+|.+.+..+.+.|++|+++++++.++++.+++..++.+ ...++|..++++......+
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~ 72 (88)
T smart00088 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDP 72 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCch
Confidence 4577899999999999999999999999999999998887777553 2578888777877765433
No 9
>smart00753 PAM PCI/PINT associated module.
Probab=97.28 E-value=0.0023 Score=44.93 Aligned_cols=65 Identities=20% Similarity=0.245 Sum_probs=53.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh------cCCeecCCCceEeecCCCC
Q 029202 110 LVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ------QGWTLDPASRMLTVKKQPL 174 (197)
Q Consensus 110 ~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~------~GW~~d~~~~~~~P~~~~~ 174 (197)
.+..+...+|.+.+..+.+.|++|+++++++.++++.+++..++.+ ...++|..++++......+
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~ 72 (88)
T smart00753 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDP 72 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCch
Confidence 4577899999999999999999999999999999998887777553 2578888777877765433
No 10
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=96.23 E-value=0.044 Score=47.72 Aligned_cols=122 Identities=17% Similarity=0.263 Sum_probs=91.6
Q ss_pred hcHHHHHHHHHHHHHHcCChHHHHHHhhC-----CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCH
Q 029202 72 SRAEVVAAWKIGQHLWTRDYAGVYDAIRG-----FDWSQEAQALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNE 146 (197)
Q Consensus 72 ~~~~l~~~~~l~~~L~~~~y~~v~~~l~~-----~~ws~~~~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~ 146 (197)
++..+.++..+..+|..+||.+.|..+-. -..-.-+...++-|..-.|.|+-.-+--+|..++++..|+-+|+|.
T Consensus 266 ~~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYaQlLESYr~lsl~sMA~tFgVSV 345 (412)
T COG5187 266 SSEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYAQLLESYRLLSLESMAQTFGVSV 345 (412)
T ss_pred chhhhhhHHHHHHHHHHhccchhhHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhCccH
Confidence 45668899999999999999987765533 1222344566777888889999888888999999999999999995
Q ss_pred ----HHHHHHHHh-cCCe-ecCCCceEeecCCCCCCCC---CC--ChHHHHHHHHHHH
Q 029202 147 ----DDAAYYVQQ-QGWT-LDPASRMLTVKKQPLVTEQ---KL--DPSKLQRLTEYVF 193 (197)
Q Consensus 147 ----~e~~~~~~~-~GW~-~d~~~~~~~P~~~~~~~~~---~~--~~~qL~~LT~~v~ 193 (197)
.++.+|+-. +=|. +|--.+++....|++...+ ++ +++-|.||-+|++
T Consensus 346 ~yvdrDLg~FIp~~~LncvIDRvnGvVetnrpdekn~qy~~vVkqGd~ll~klqKy~a 403 (412)
T COG5187 346 EYVDRDLGEFIPEGRLNCVIDRVNGVVETNRPDEKNQQYSSVVKQGDDLLRKLQKYVA 403 (412)
T ss_pred HHHhhhHHhhCCCCceeeeeecccceEeccCcchhhhhHHHHHhcchHHHHHHHHHHH
Confidence 578888764 4454 4655567776666653333 22 8899999999885
No 11
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=95.94 E-value=0.069 Score=47.01 Aligned_cols=156 Identities=12% Similarity=0.183 Sum_probs=100.8
Q ss_pred CCcchHHHHHHHHHhhcCHHHHHHHHh--cCC-hhhhhhcHHHHHHHHHHHHHHcCChHHHHHHhhCC-----CCcHHHH
Q 029202 37 QDEWPYVIHLLGYYYVNDINSARFLWK--SIP-STIKDSRAEVVAAWKIGQHLWTRDYAGVYDAIRGF-----DWSQEAQ 108 (197)
Q Consensus 37 ~~~~py~~~Ll~~L~~ndl~~ar~l~k--RiP-~~~~~~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~-----~ws~~~~ 108 (197)
-+..||..+...-.+.+=++-=|--+| -|. +++.+.-+.|..+..+..+|.+|+|..||..+-.. ..---+.
T Consensus 214 ~El~~Y~~~v~Ytv~~g~i~leR~dlktKVi~~~Evl~vl~~l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~ 293 (393)
T KOG0687|consen 214 YELMSYETFVRYTVITGLIALERVDLKTKVIKCPEVLEVLHKLPSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLG 293 (393)
T ss_pred eecccHHHHHHHHHHHhhheeccchHHhhhcCcHHHHHHhhcCchHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcc
Confidence 455778877665555544433222111 111 23333333456677888899999999999988431 1112334
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCH----HHHHHHHHh-c-CCeecCCCceEeecCCCCCCCC---C
Q 029202 109 ALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNE----DDAAYYVQQ-Q-GWTLDPASRMLTVKKQPLVTEQ---K 179 (197)
Q Consensus 109 ~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~----~e~~~~~~~-~-GW~~d~~~~~~~P~~~~~~~~~---~ 179 (197)
|..+-+..-+|.++-.-+--+|.+++++..|+-+|+|. .|+-.|+.. + .=++|.-++++-...|++...+ +
T Consensus 294 ~h~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDrVnGVVEtNrpD~KN~qyq~v 373 (393)
T KOG0687|consen 294 PHYRYYVREMRRRVYAQLLESYRSLTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDRVNGVVETNRPDEKNAQYQAV 373 (393)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeecccceeecCCccccchHHHHH
Confidence 55566666788888888889999999999999999995 688888765 4 4456766778877777655422 2
Q ss_pred C--ChHHHHHHHHHH
Q 029202 180 L--DPSKLQRLTEYV 192 (197)
Q Consensus 180 ~--~~~qL~~LT~~v 192 (197)
+ ++.-|.++-++.
T Consensus 374 ikqGd~LLnriQK~~ 388 (393)
T KOG0687|consen 374 IKQGDLLLNRIQKLS 388 (393)
T ss_pred HhhhHHHHHHHHHHH
Confidence 2 665555554443
No 12
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=94.93 E-value=0.05 Score=49.11 Aligned_cols=108 Identities=19% Similarity=0.302 Sum_probs=73.7
Q ss_pred HHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCChHHHHHHhhCCC---CcHHHHHHHHHHHHHH
Q 029202 42 YVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRDYAGVYDAIRGFD---WSQEAQALVAAFSELY 118 (197)
Q Consensus 42 y~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~~---ws~~~~~~i~~l~~~i 118 (197)
..+.+++-|+.++|.+=-+ ... | .+ ..-|+.-..|.+++--||-.+|=..+.++- -.+..-.++-.|.-.|
T Consensus 290 ~k~~ivv~ll~geiPers~-F~Q-p-~~---~ksL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NV 363 (493)
T KOG2581|consen 290 NKLMIVVELLLGEIPERSV-FRQ-P-GM---RKSLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNV 363 (493)
T ss_pred HHHHHHHHHHcCCCcchhh-hcC-c-cH---HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHH
Confidence 4445666666666654111 110 1 11 124677778899999999988877776521 1234455677788888
Q ss_pred HHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh
Q 029202 119 TKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 119 R~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 155 (197)
-..-.+.||-+|+.||+.|+|.-||++.++-.+|+.+
T Consensus 364 IkTgIR~ISlsYSRISl~DIA~kL~l~Seed~EyiVa 400 (493)
T KOG2581|consen 364 IKTGIRKISLSYSRISLQDIAKKLGLNSEEDAEYIVA 400 (493)
T ss_pred HHHhhhheeeeeeeccHHHHHHHhcCCCchhHHHHHH
Confidence 8888899999999999999999999987665555443
No 13
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=92.53 E-value=0.66 Score=44.62 Aligned_cols=94 Identities=12% Similarity=0.237 Sum_probs=68.7
Q ss_pred HHHHHHHHHHcCChHHHHHHhhC--CCCc--HHHHHHHHHHHHHHHHHHHH----HHHHhhcccCHHHHHHHcCCCHHHH
Q 029202 78 AAWKIGQHLWTRDYAGVYDAIRG--FDWS--QEAQALVAAFSELYTKRMFQ----LLLSAYSTISTQDTALFLGMNEDDA 149 (197)
Q Consensus 78 ~~~~l~~~L~~~~y~~v~~~l~~--~~ws--~~~~~~i~~l~~~iR~~i~~----lis~AY~sIs~~~~a~~Lgls~~e~ 149 (197)
+++.-.++|..|++.+-+.-+.+ -.|. +....+.+++.+.|+++.++ .-++.|.|+|+..+|.|+.+++..+
T Consensus 656 hVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftYss~Y~SvSl~~LA~mFdLp~~~V 735 (843)
T KOG1076|consen 656 HVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTYSSVYDSVSLAKLADMFDLPEPKV 735 (843)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHhCCCchhH
Confidence 56677889999999998774433 2454 56677888999999998887 4678899999999999999998887
Q ss_pred HHHHHh------cCCeecCCCceEeecC
Q 029202 150 AYYVQQ------QGWTLDPASRMLTVKK 171 (197)
Q Consensus 150 ~~~~~~------~GW~~d~~~~~~~P~~ 171 (197)
-..+.+ .-=++|..++.++..+
T Consensus 736 hsIiSkmiineEl~AslDqpt~~iv~hr 763 (843)
T KOG1076|consen 736 HSIISKMIINEELHASLDQPTQCIVMHR 763 (843)
T ss_pred HHHHHHHHHHHHhhhccCCCcceEEEee
Confidence 666443 2334454444544433
No 14
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=91.59 E-value=1.7 Score=39.27 Aligned_cols=93 Identities=19% Similarity=0.214 Sum_probs=64.4
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh---cCCee---cCCCceEeecCCCCCC
Q 029202 103 WSQEAQALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ---QGWTL---DPASRMLTVKKQPLVT 176 (197)
Q Consensus 103 ws~~~~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~---~GW~~---d~~~~~~~P~~~~~~~ 176 (197)
-++.-..-...+..+|-+.=++-+++=|++|+...++.+||++.+++.+|... .|=-. |-.++.+....+.+..
T Consensus 324 ~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl~~ee~E~~LS~lv~t~ti~aKidrpsgII~F~k~K~~~ 403 (439)
T KOG1498|consen 324 GGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDLPVEEMEKFLSDLVVTGTIYAKIDRPSGIINFQKVKDSN 403 (439)
T ss_pred ccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHHHHHhccceEEEecCCCceEEEEecccHH
Confidence 34555666778889999999999999999999999999999999999888553 24333 5555566555544332
Q ss_pred CCC----CChHHHHHHHHHHHhh
Q 029202 177 EQK----LDPSKLQRLTEYVFHL 195 (197)
Q Consensus 177 ~~~----~~~~qL~~LT~~v~fL 195 (197)
... .+.++|-.+.+-++||
T Consensus 404 ~~LneW~~nve~L~~ll~K~~HL 426 (439)
T KOG1498|consen 404 EILNEWASNVEKLLGLLEKVSHL 426 (439)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHH
Confidence 221 1455555555555665
No 15
>KOG1860 consensus Nuclear protein export factor [Intracellular trafficking, secretion, and vesicular transport; Cell cycle control, cell division, chromosome partitioning]
Probab=91.35 E-value=4.3 Score=40.26 Aligned_cols=147 Identities=11% Similarity=0.116 Sum_probs=104.4
Q ss_pred HHHHHHHHhHHhhhhhhCCCcC---CCcchHHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCCh
Q 029202 15 YEKIADICDDLMLKVAAEGIVF---QDEWPYVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRDY 91 (197)
Q Consensus 15 ~~~l~~~~e~~El~~~~~g~~~---~~~~py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~y 91 (197)
...|.+..++++-- |+.- +++ +|-++++.|=..++.. .....|.++.+ +++.+-...+.++...|+|
T Consensus 254 l~sL~elYdD~r~~----g~~cpnE~EF--R~Y~vLl~Lgd~~~~~---~iq~~~~evr~-~~~Vk~al~~~~a~~~nn~ 323 (927)
T KOG1860|consen 254 LQSLGELYDDLRKG----GIPCPNEPEF--RGYYVLLSLGDPQVVR---DIQAWPDEVRQ-DSEVKLALCLRRAFQSNNF 323 (927)
T ss_pred HHHHHHHHHHHHhc----CCCCCChHHH--HHHHHHHhcCCchHHH---HHHhcCccccc-chhHHHHHHHHHHhccCCe
Confidence 34455555555544 3322 456 8999998887665543 34567888875 5999999999999999999
Q ss_pred HHHHH-----------------HhhCCCCcHH-HHHHHHHHHHHHHHHHHHHHHHhhcc----cCHHHHHHHcCCC-HHH
Q 029202 92 AGVYD-----------------AIRGFDWSQE-AQALVAAFSELYTKRMFQLLLSAYST----ISTQDTALFLGMN-EDD 148 (197)
Q Consensus 92 ~~v~~-----------------~l~~~~ws~~-~~~~i~~l~~~iR~~i~~lis~AY~s----Is~~~~a~~Lgls-~~e 148 (197)
..++. .+.+..-++. .-.++..|...+|.-..+.++++|.+ |+...+..+|+++ .++
T Consensus 324 ~~~~r~~~~~t~a~~~l~~~~~~l~q~p~~~~L~~~v~~~~f~~ir~~al~~~~~~~~~~~~~vp~~~l~~~l~f~~~e~ 403 (927)
T KOG1860|consen 324 RRFFRLSSLRTEALQNLYTRFFKLMQSPALPYLMGCVLELFFPDIRWAALRAMSHAYNSKHVPVPLGKLDRILLFDGEEE 403 (927)
T ss_pred eeeeeccchhHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcchhHHHHHHhcCChhh
Confidence 88852 1222133332 33455567888999999999999975 7889999999997 789
Q ss_pred HHHHHHhcCCeecCCCceEeecC
Q 029202 149 AAYYVQQQGWTLDPASRMLTVKK 171 (197)
Q Consensus 149 ~~~~~~~~GW~~d~~~~~~~P~~ 171 (197)
+..+|..+|=+++.+...+.+.+
T Consensus 404 ~~~~~~~y~Leis~~~~~~~~~~ 426 (927)
T KOG1860|consen 404 LKVVCNYYGLEISVDDKIVLSIG 426 (927)
T ss_pred hHhhhhheeeEeecccccccccc
Confidence 99999999999976554444443
No 16
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=90.07 E-value=3.2 Score=36.25 Aligned_cols=107 Identities=12% Similarity=0.072 Sum_probs=80.8
Q ss_pred HHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCChHHHHHHhhCCCC----cHHHHHHHHHHHHHHHHH
Q 029202 46 LLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRDYAGVYDAIRGFDW----SQEAQALVAAFSELYTKR 121 (197)
Q Consensus 46 Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~~w----s~~~~~~i~~l~~~iR~~ 121 (197)
|+-.|+..+++.|--- --.+.| +||+|-+.-.+-++...++-..|=..+++..- -+-+..-+..|...||..
T Consensus 278 LANMLmkS~iNPFDsQ---EAKPyK-NdPEIlAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQ 353 (440)
T KOG1464|consen 278 LANMLMKSGINPFDSQ---EAKPYK-NDPEILAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQ 353 (440)
T ss_pred HHHHHHHcCCCCCccc---ccCCCC-CCHHHHHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHH
Confidence 5556666666654320 012234 58999999999999999998888777765221 134566677889999999
Q ss_pred HHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHhc
Q 029202 122 MFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQQ 156 (197)
Q Consensus 122 i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~~ 156 (197)
++--+-+-|+.|.+.-+++-|++++.|+.....++
T Consensus 354 VLlkLIkPYt~i~Ipfis~~Lnv~~~dV~~LLV~~ 388 (440)
T KOG1464|consen 354 VLLKLIKPYTNIGIPFISKELNVPEADVESLLVSC 388 (440)
T ss_pred HHHHHhccccccCchhhHhhcCCCHHHHHHHHHHH
Confidence 99999999999999999999999999988886653
No 17
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=90.05 E-value=0.77 Score=33.49 Aligned_cols=42 Identities=12% Similarity=0.446 Sum_probs=35.7
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHhcCCeecC
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDP 162 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~ 162 (197)
+.++.+..+=.++++.++|+.||+++.++.++..+.||-+..
T Consensus 13 ~~~d~~~~~~~~~ti~~~AK~L~i~~~~l~~~Lr~~g~l~~~ 54 (111)
T PF03374_consen 13 EFYDAFVDSDGLYTIREAAKLLGIGRNKLFQWLREKGWLYRR 54 (111)
T ss_pred HHHHHHHcCCCCccHHHHHHHhCCCHHHHHHHHHhCCceEEC
Confidence 344455555689999999999999999999999999999983
No 18
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=89.30 E-value=1.7 Score=27.96 Aligned_cols=65 Identities=11% Similarity=0.161 Sum_probs=46.5
Q ss_pred HHccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHH
Q 029202 9 ALASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAW 80 (197)
Q Consensus 9 ~~~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~ 80 (197)
++..|+|++-+..++..--. .|+ .++. +-.+--+|+-+++...|+..+++++..-.. ++.+..++
T Consensus 1 ll~~~~~~~A~~~~~~~l~~-~p~---~~~~--~~~la~~~~~~g~~~~A~~~l~~~~~~~~~-~~~~~~l~ 65 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKALQR-NPD---NPEA--RLLLAQCYLKQGQYDEAEELLERLLKQDPD-NPEYQQLL 65 (68)
T ss_dssp HHHTTHHHHHHHHHHHHHHH-TTT---SHHH--HHHHHHHHHHTT-HHHHHHHHHCCHGGGTT-HHHHHHHH
T ss_pred ChhccCHHHHHHHHHHHHHH-CCC---CHHH--HHHHHHHHHHcCCHHHHHHHHHHHHHHCcC-HHHHHHHH
Confidence 57889999999999987433 222 1334 445566788889999999999999877764 37666544
No 19
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=87.52 E-value=2.8 Score=37.01 Aligned_cols=52 Identities=12% Similarity=0.259 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh---cCCee
Q 029202 109 ALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ---QGWTL 160 (197)
Q Consensus 109 ~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~---~GW~~ 160 (197)
.-.+.|..++-+.-++.|++-|++|++..+...|.+++++..+++.. +|--+
T Consensus 330 ~~w~DL~krviEHN~RvI~~yYSrI~~~rl~~lld~~~s~te~~ISdlVN~G~~y 384 (439)
T COG5071 330 KRWSDLRKRVIEHNIRVIANYYSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFY 384 (439)
T ss_pred hhHHHHHHHHHHhhHhHHHHHhhhhhHHHHHHHHcCCHHHHHHHHHHHHhcCcEE
Confidence 45567777888888999999999999999999999999998888653 56654
No 20
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=85.46 E-value=11 Score=28.40 Aligned_cols=104 Identities=15% Similarity=0.152 Sum_probs=67.5
Q ss_pred cchHHHHHccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHH----HH-HHHhhcCHHHHHHHHhcCChhhhhhcHHHH
Q 029202 3 FSPLTDALASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIH----LL-GYYYVNDINSARFLWKSIPSTIKDSRAEVV 77 (197)
Q Consensus 3 ~~~i~~~~~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~----Ll-~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~ 77 (197)
|..+...+..++..++...++.+--.. +++ ||+.+ ++ .+.-++|+.+|...++.+-... .++.++
T Consensus 15 y~~~~~~~~~~~~~~~~~~~~~l~~~~-~~s-------~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~--~d~~l~ 84 (145)
T PF09976_consen 15 YEQALQALQAGDPAKAEAAAEQLAKDY-PSS-------PYAALAALQLAKAAYEQGDYDEAKAALEKALANA--PDPELK 84 (145)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHC-CCC-------hHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCHHHH
Confidence 445666777889999877777776552 211 24433 22 3444799999999999987655 356655
Q ss_pred HHHH--H-HHHHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHH
Q 029202 78 AAWK--I-GQHLWTRDYAGVYDAIRGFDWSQEAQALVAAFSEL 117 (197)
Q Consensus 78 ~~~~--l-~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~ 117 (197)
.+.. | .-.+-+|+|......++. ...+.+.+.+..+...
T Consensus 85 ~~a~l~LA~~~~~~~~~d~Al~~L~~-~~~~~~~~~~~~~~Gd 126 (145)
T PF09976_consen 85 PLARLRLARILLQQGQYDEALATLQQ-IPDEAFKALAAELLGD 126 (145)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHh-ccCcchHHHHHHHHHH
Confidence 4443 2 344668899999999977 4455566665554443
No 21
>smart00071 Galanin Galanin. Galanin [1,2,3] is a neuropeptide that controls various biological activities: it regulates the release growth hormone, inhibits the release of insulin and somatostatin, contracts smooth muscle of the gastrointestinal and genitourinary tract and may be involved in the control of adrenal secretion
Probab=84.19 E-value=1.6 Score=31.30 Aligned_cols=42 Identities=21% Similarity=0.437 Sum_probs=28.7
Q ss_pred HhcCCeecCCCceEeecCCCCCC--------------------CC-----CC-ChHHHHHHHHHHHhh
Q 029202 154 QQQGWTLDPASRMLTVKKQPLVT--------------------EQ-----KL-DPSKLQRLTEYVFHL 195 (197)
Q Consensus 154 ~~~GW~~d~~~~~~~P~~~~~~~--------------------~~-----~~-~~~qL~~LT~~v~fL 195 (197)
.+|||+++..|..+-|...++.. ++ .. ++.-+..+-+|.+||
T Consensus 10 eKRgwtlnsagyllgp~aid~hrs~~dk~g~~gKREl~pEde~r~g~~~r~l~e~~~vrTiiEFLsfL 77 (103)
T smart00071 10 EKRGWTLNSAGYLLGPHAIDNHRSFHDKHGLTGKRELEPEDEARPGSFDRPLSESNIVRTIIEFLTFL 77 (103)
T ss_pred cccCceeccCceeeCccccccccccccCCCccccccCChhhhcccCccCCcCchhhHHHHHHHHHHHH
Confidence 56999999988887787654311 11 11 566677788888887
No 22
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=82.61 E-value=36 Score=30.48 Aligned_cols=106 Identities=12% Similarity=0.176 Sum_probs=71.0
Q ss_pred HHHHHHHHHHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHHHHH--HHHHHHHHhhcc------cCHHHHHHHcCCCHHH
Q 029202 77 VAAWKIGQHLWTRDYAGVYDAIRGFDWSQEAQALVAAFSELYTK--RMFQLLLSAYST------ISTQDTALFLGMNEDD 148 (197)
Q Consensus 77 ~~~~~l~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~iR~--~i~~lis~AY~s------Is~~~~a~~Lgls~~e 148 (197)
+-+..+..++-.||.++|.+..+ .|+. .|+.+.-++.+|+ +...+|+.+|+. ||.++.|+.+-++.++
T Consensus 235 eWL~dll~Afn~Gdl~~f~~l~~--~~~~--~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~e 310 (380)
T KOG2908|consen 235 EWLKDLLIAFNSGDLKRFESLKG--VWGK--QPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIPNKE 310 (380)
T ss_pred HHHHHHHHHhccCCHHHHHHHHH--Hhcc--CchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCCHHH
Confidence 44567888999999999877664 4655 4444444444444 567889999987 9999999999999888
Q ss_pred HHHHHHh------cCCeecCCCceEeecCCCCCCCCCC-ChHHHHHHHH
Q 029202 149 AAYYVQQ------QGWTLDPASRMLTVKKQPLVTEQKL-DPSKLQRLTE 190 (197)
Q Consensus 149 ~~~~~~~------~GW~~d~~~~~~~P~~~~~~~~~~~-~~~qL~~LT~ 190 (197)
+.-.+.+ ..|.+|.-++++...- ..+.+ +.+||-++.+
T Consensus 311 VE~LVMKAlslgLikG~Idqv~~~v~~sw----vqPRvl~~~qI~~Mk~ 355 (380)
T KOG2908|consen 311 VELLVMKALSLGLIKGSIDQVEGVVYMSW----VQPRVLDRSQIVKMKD 355 (380)
T ss_pred HHHHHHHHHhccceeeeecccccEEEEec----ccccccCHHHHHhHHH
Confidence 7655443 2566776666655321 11222 6666665543
No 23
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=82.12 E-value=6.8 Score=33.22 Aligned_cols=111 Identities=12% Similarity=0.106 Sum_probs=70.5
Q ss_pred HHccccHHHHHHHHhHHhhhhhhCCCcC---CCcchHHHHHHHHHhhcCHHHHHHHHhcC---ChhhhhhcHHHHHHHHH
Q 029202 9 ALASKSYEKIADICDDLMLKVAAEGIVF---QDEWPYVIHLLGYYYVNDINSARFLWKSI---PSTIKDSRAEVVAAWKI 82 (197)
Q Consensus 9 ~~~~~~~~~l~~~~e~~El~~~~~g~~~---~~~~py~~~Ll~~L~~ndl~~ar~l~kRi---P~~~~~~~~~l~~~~~l 82 (197)
.+..|+|++-+..+|+.--....+.... .+. |-.-+++||..+|...|+-.+++. .+.... ..+-+.+-.|
T Consensus 165 ~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~--~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~-s~E~~~~~~l 241 (282)
T PF14938_consen 165 YARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEY--FLKAILCHLAMGDYVAARKALERYCSQDPSFAS-SREYKFLEDL 241 (282)
T ss_dssp HHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHH--HHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTT-SHHHHHHHHH
T ss_pred HHHhCCHHHHHHHHHHHHHHhhcccccchhHHHH--HHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCC-cHHHHHHHHH
Confidence 4567789998888887643311111110 122 333478999999999999999984 334443 4777888899
Q ss_pred HHHHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHHHHHHH
Q 029202 83 GQHLWTRDYAGVYDAIRGFDWSQEAQALVAAFSELYTKRM 122 (197)
Q Consensus 83 ~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~iR~~i 122 (197)
..+.-++|-..|=.++..++=...+.+....+.-.|++.|
T Consensus 242 ~~A~~~~D~e~f~~av~~~d~~~~ld~w~~~~l~~~k~~~ 281 (282)
T PF14938_consen 242 LEAYEEGDVEAFTEAVAEYDSISRLDNWKTKMLLKIKKKI 281 (282)
T ss_dssp HHHHHTT-CCCHHHHCHHHTTSS---HHHHHHHHHHHHHH
T ss_pred HHHHHhCCHHHHHHHHHHHcccCccHHHHHHHHHHHHhhc
Confidence 9999999988887777765555566666666666666554
No 24
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=79.96 E-value=21 Score=32.29 Aligned_cols=100 Identities=18% Similarity=0.305 Sum_probs=68.0
Q ss_pred HHHHHccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHH-------HHHHH-hhcCHHHHHHHHhcCChhhhhhcHHHH
Q 029202 6 LTDALASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIH-------LLGYY-YVNDINSARFLWKSIPSTIKDSRAEVV 77 (197)
Q Consensus 6 i~~~~~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~-------Ll~~L-~~ndl~~ar~l~kRiP~~~~~~~~~l~ 77 (197)
.+.++.+|++.++....++++=. |..+.+. +..+ ++--. -.++...=+.-|+++|..++. +|+|.
T Consensus 194 ~r~y~~~g~~~~ll~~l~~L~ka----~~l~~~e--~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~lr~-~p~l~ 266 (400)
T COG3071 194 LRAYIRLGAWQALLAILPKLRKA----GLLSDEE--AARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRKLRN-DPELV 266 (400)
T ss_pred HHHHHHhccHHHHHHHHHHHHHc----cCCChHH--HHHHHHHHHHHHHHHHhccccchHHHHHHHhccHHhhc-ChhHH
Confidence 57889999999999999998744 5555555 4444 22211 236666678999999999995 59988
Q ss_pred HHHHHHHHHHcCChHHHHHHh----hCCCCcHHHHHHHHHH
Q 029202 78 AAWKIGQHLWTRDYAGVYDAI----RGFDWSQEAQALVAAF 114 (197)
Q Consensus 78 ~~~~l~~~L~~~~y~~v~~~l----~~~~ws~~~~~~i~~l 114 (197)
.... .+.+.-|++...+..+ +. .|-+.+-.++..+
T Consensus 267 ~~~a-~~li~l~~~~~A~~~i~~~Lk~-~~D~~L~~~~~~l 305 (400)
T COG3071 267 VAYA-ERLIRLGDHDEAQEIIEDALKR-QWDPRLCRLIPRL 305 (400)
T ss_pred HHHH-HHHHHcCChHHHHHHHHHHHHh-ccChhHHHHHhhc
Confidence 6554 5667777887765544 44 5666655555544
No 25
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=79.24 E-value=3.4 Score=31.20 Aligned_cols=30 Identities=20% Similarity=0.583 Sum_probs=26.9
Q ss_pred CHHHHHHHcCCCHHHHHHHHHhcCCeecCC
Q 029202 134 STQDTALFLGMNEDDAAYYVQQQGWTLDPA 163 (197)
Q Consensus 134 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~ 163 (197)
..+.+|.++|++.+=+-+++.+.||+-.+-
T Consensus 2 T~eELA~~tG~srQTINrWvRkegW~T~p~ 31 (122)
T PF07037_consen 2 TPEELAELTGYSRQTINRWVRKEGWKTEPK 31 (122)
T ss_pred CHHHHHHHhCccHHHHHHHHHhcCceeccC
Confidence 467899999999999999999999998654
No 26
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=77.81 E-value=4.5 Score=26.02 Aligned_cols=30 Identities=20% Similarity=0.274 Sum_probs=26.4
Q ss_pred HhhcccCHHHHHHHcCCCHHHHHHHHHhcC
Q 029202 128 SAYSTISTQDTALFLGMNEDDAAYYVQQQG 157 (197)
Q Consensus 128 ~AY~sIs~~~~a~~Lgls~~e~~~~~~~~G 157 (197)
+.|=.+++.++|+-||++...+...|.+.|
T Consensus 11 ~~~fhlp~~eAA~~Lgv~~T~LKr~CR~~G 40 (52)
T PF02042_consen 11 SQYFHLPIKEAAKELGVSVTTLKRRCRRLG 40 (52)
T ss_pred HHHhCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 357779999999999999999999999876
No 27
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=74.75 E-value=4.6 Score=27.71 Aligned_cols=30 Identities=20% Similarity=0.264 Sum_probs=27.0
Q ss_pred cccCHHHHHHHcCCCHHHHHHHHHhcCCee
Q 029202 131 STISTQDTALFLGMNEDDAAYYVQQQGWTL 160 (197)
Q Consensus 131 ~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~ 160 (197)
..||+..+|.++|+|.-++.+++.++|=.+
T Consensus 33 g~iS~gkAAelag~s~~eF~~~L~~~gI~~ 62 (76)
T PF03683_consen 33 GKISLGKAAELAGMSRWEFLELLKERGIPI 62 (76)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHCCCCC
Confidence 579999999999999999999999988554
No 28
>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 [].
Probab=74.60 E-value=11 Score=34.36 Aligned_cols=47 Identities=19% Similarity=0.282 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHH----HHHHHHHHhhcccCHHHHHHHcCCCHHHHHHH
Q 029202 106 EAQALVAAFSELYTK----RMFQLLLSAYSTISTQDTALFLGMNEDDAAYY 152 (197)
Q Consensus 106 ~~~~~i~~l~~~iR~----~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~ 152 (197)
++..-+..|.+.|+. ..++..-|-|++|+++.+|++|+++++++...
T Consensus 291 ~~~~Ql~~Fl~eV~~q~~l~~lRSyLKLYtti~l~KLA~fl~vd~~~lr~~ 341 (404)
T PF10255_consen 291 PYRRQLKLFLDEVKQQQKLPTLRSYLKLYTTIPLEKLASFLDVDEEELRSQ 341 (404)
T ss_pred HHHHHHHHHHHHHHHhhhhhHHHHHHHhhcCCCHHHHHHHcCCCHHHHHHH
Confidence 444444445555544 56788889999999999999999999876554
No 29
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=74.52 E-value=32 Score=30.78 Aligned_cols=110 Identities=17% Similarity=0.074 Sum_probs=67.6
Q ss_pred HHHHHHHHhhcC---HHHHHHHHhcCChhhhh-hcHHHHHHHHHHHHHHcCChHHHHHHhhCC--CCc--HHHHHHHHHH
Q 029202 43 VIHLLGYYYVND---INSARFLWKSIPSTIKD-SRAEVVAAWKIGQHLWTRDYAGVYDAIRGF--DWS--QEAQALVAAF 114 (197)
Q Consensus 43 ~~~Ll~~L~~nd---l~~ar~l~kRiP~~~~~-~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~--~ws--~~~~~~i~~l 114 (197)
--||+.-.+.|. =..-|-|-|-|.++--. .||-...+ .-...+=||.+.-.-++.- +.. --+.+..+.|
T Consensus 255 lRYLatAvvtnk~~rr~~lkdlvkVIqqE~ysYkDPiteFl---~clyvn~DFdgAq~kl~eCeeVl~nDfFLva~l~~F 331 (432)
T KOG2758|consen 255 LRYLATAVVTNKRRRRNRLKDLVKVIQQESYSYKDPITEFL---ECLYVNYDFDGAQKKLRECEEVLVNDFFLVALLDEF 331 (432)
T ss_pred HHHHHHHhhcchHhhHHHHHHHHHHHHHhccccCCcHHHHH---HHHhhccchHHHHHHHHHHHHHHhcchhHHHHHHHH
Confidence 446777777773 23334455555433222 24544322 2223344666655444320 011 1235566778
Q ss_pred HHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh
Q 029202 115 SELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 115 ~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 155 (197)
.+.-|--||...-+--+.|+++-+|.-|+|+++|+..++..
T Consensus 332 ~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~~eeaErwivn 372 (432)
T KOG2758|consen 332 LENARLLIFETFCRIHQCITIDMLADKLNMDPEEAERWIVN 372 (432)
T ss_pred HHHHHHHHHHHHHHHHHheeHHHHHHHhcCCHHHHHHHHHH
Confidence 88888888888888889999999999999999998887553
No 30
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=74.05 E-value=12 Score=24.10 Aligned_cols=49 Identities=20% Similarity=0.411 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHH---hcCC
Q 029202 109 ALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGW 158 (197)
Q Consensus 109 ~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW 158 (197)
.+...|.+..|.+|++.+ ......++.+++..+|++..-+-.... +.|+
T Consensus 2 ~i~~aL~~p~R~~Il~~L-~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGl 53 (61)
T PF12840_consen 2 EIFKALSDPTRLRILRLL-ASNGPMTVSELAEELGISQSTVSYHLKKLEEAGL 53 (61)
T ss_dssp HHHHHHTSHHHHHHHHHH-HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHHhCCHHHHHHHHHH-hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 356677888999999999 888999999999999999876644433 3455
No 31
>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=73.35 E-value=9.2 Score=25.32 Aligned_cols=46 Identities=17% Similarity=0.320 Sum_probs=37.7
Q ss_pred HHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHhcCCeecCCC
Q 029202 119 TKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPAS 164 (197)
Q Consensus 119 R~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~ 164 (197)
|++++.+--..=..|.+.++|..||+++..+..+=..-.|.-.-.|
T Consensus 9 rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~dkW~~~~~~ 54 (60)
T PF10668_consen 9 RDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSRDKWDEKLKG 54 (60)
T ss_pred HHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhhcchhhHhcc
Confidence 6677777766667899999999999999999998887788765444
No 32
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=72.74 E-value=3.1 Score=26.38 Aligned_cols=28 Identities=18% Similarity=0.221 Sum_probs=23.3
Q ss_pred ccCHHHHHHHcCCCHHHHHHHH-HhcCCe
Q 029202 132 TISTQDTALFLGMNEDDAAYYV-QQQGWT 159 (197)
Q Consensus 132 sIs~~~~a~~Lgls~~e~~~~~-~~~GW~ 159 (197)
.+++.++|+-||++..++++.+ .+.|=.
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKLFKELGIM 31 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH-HHHTS-
T ss_pred ceEHHHHHHHHCcCHHHHHHHHHHhCCcC
Confidence 5789999999999999999999 548876
No 33
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=72.28 E-value=2.3 Score=27.82 Aligned_cols=18 Identities=22% Similarity=0.698 Sum_probs=12.1
Q ss_pred CHHHHHHHHHhcCCeecC
Q 029202 145 NEDDAAYYVQQQGWTLDP 162 (197)
Q Consensus 145 s~~e~~~~~~~~GW~~d~ 162 (197)
+.+|+++||+++||-+-.
T Consensus 28 ~~~eV~~YC~~~GWIip~ 45 (57)
T PF08727_consen 28 DSPEVREYCEEQGWIIPA 45 (57)
T ss_dssp --HHHHHHHHHHT--TT-
T ss_pred CCHHHHHHHHHCCccccC
Confidence 468999999999999853
No 34
>PF12728 HTH_17: Helix-turn-helix domain
Probab=71.50 E-value=6.1 Score=24.40 Aligned_cols=24 Identities=17% Similarity=0.447 Sum_probs=20.8
Q ss_pred cCHHHHHHHcCCCHHHHHHHHHhc
Q 029202 133 ISTQDTALFLGMNEDDAAYYVQQQ 156 (197)
Q Consensus 133 Is~~~~a~~Lgls~~e~~~~~~~~ 156 (197)
++++++|.+||++..-+..++.+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 578999999999999999988643
No 35
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=71.44 E-value=4.6 Score=29.61 Aligned_cols=25 Identities=28% Similarity=0.646 Sum_probs=17.4
Q ss_pred CHHHHHHHHHhcCCeecCCCceEeecCCC
Q 029202 145 NEDDAAYYVQQQGWTLDPASRMLTVKKQP 173 (197)
Q Consensus 145 s~~e~~~~~~~~GW~~d~~~~~~~P~~~~ 173 (197)
+.++++.||+++||.+. +..|+...
T Consensus 57 skE~Ai~yaer~G~~Y~----V~~p~~r~ 81 (101)
T PF04800_consen 57 SKEDAIAYAERNGWDYE----VEEPKKRK 81 (101)
T ss_dssp SHHHHHHHHHHCT-EEE----EE-STT--
T ss_pred CHHHHHHHHHHcCCeEE----EeCCCCCc
Confidence 57999999999999994 55566543
No 36
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=71.00 E-value=4.4 Score=31.59 Aligned_cols=23 Identities=17% Similarity=0.592 Sum_probs=17.7
Q ss_pred HHHH-HHHHHhcCCeecCCCceEe
Q 029202 146 EDDA-AYYVQQQGWTLDPASRMLT 168 (197)
Q Consensus 146 ~~e~-~~~~~~~GW~~d~~~~~~~ 168 (197)
.+|+ ...|.+-||++++||..+-
T Consensus 47 ~NeVLkALc~eAGw~Ve~DGTtyr 70 (150)
T PF05687_consen 47 NNEVLKALCREAGWTVEPDGTTYR 70 (150)
T ss_pred HHHHHHHHHHhCCEEEccCCCeec
Confidence 3565 4779999999999986654
No 37
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=70.42 E-value=12 Score=32.53 Aligned_cols=58 Identities=16% Similarity=0.192 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHhcCCeecCCCceEeecC
Q 029202 114 FSELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKK 171 (197)
Q Consensus 114 l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~P~~ 171 (197)
+..-=|+.+++.+.+...+|++++++...|+..+|++...+..|.-.--.|+.++-.+
T Consensus 205 Y~~YW~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l~~l~~~~g~~~i~~~ 262 (290)
T PLN03238 205 FRSYWTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSLNLIKYWKGQHVIHVD 262 (290)
T ss_pred HHHHHHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCCcEEEECCcEEEEeC
Confidence 4444556666666666789999999999999999999999999976544566555433
No 38
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=68.64 E-value=6.1 Score=23.93 Aligned_cols=28 Identities=25% Similarity=0.496 Sum_probs=22.4
Q ss_pred HHHHHHHcCCCHHHHHHHHHhcCCeecC
Q 029202 135 TQDTALFLGMNEDDAAYYVQQQGWTLDP 162 (197)
Q Consensus 135 ~~~~a~~Lgls~~e~~~~~~~~GW~~d~ 162 (197)
+..+.+..|.+++.+..+.+..+|.++.
T Consensus 4 i~~F~~iTg~~~~~A~~~L~~~~wdle~ 31 (43)
T PF14555_consen 4 IAQFMSITGADEDVAIQYLEANNWDLEA 31 (43)
T ss_dssp HHHHHHHH-SSHHHHHHHHHHTTT-HHH
T ss_pred HHHHHHHHCcCHHHHHHHHHHcCCCHHH
Confidence 4677888899999999999999999864
No 39
>KOG3389 consensus NADH:ubiquinone oxidoreductase, NDUFS4/18 kDa subunit [Energy production and conversion]
Probab=67.83 E-value=3.3 Score=32.33 Aligned_cols=30 Identities=20% Similarity=0.540 Sum_probs=22.6
Q ss_pred cCHHHHHHHcCCC-HHHHHHHHHhcCCeecC
Q 029202 133 ISTQDTALFLGMN-EDDAAYYVQQQGWTLDP 162 (197)
Q Consensus 133 Is~~~~a~~Lgls-~~e~~~~~~~~GW~~d~ 162 (197)
=+++.+..-|-|+ .++++.||++.||.+|-
T Consensus 120 DPlsNvgm~L~F~tkEdA~sFaEkngW~ydv 150 (178)
T KOG3389|consen 120 DPLSNVGMALAFDTKEDAKSFAEKNGWDYDV 150 (178)
T ss_pred CcccccceeeeeccHHHHHHHHHHcCCcccc
Confidence 3445555556665 78999999999999984
No 40
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=66.94 E-value=21 Score=26.92 Aligned_cols=44 Identities=16% Similarity=0.235 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHhc
Q 029202 111 VAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQQ 156 (197)
Q Consensus 111 i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~~ 156 (197)
+..+.-+||..++.-+..- -.|..+.|.+||++..-+-+|+.+.
T Consensus 3 ~~~vlPaiRa~lA~~L~ee--G~Sq~~iA~LLGltqaAVS~Yls~k 46 (119)
T COG2522 3 VEEVLPAIRALLAKELIEE--GLSQYRIAKLLGLTQAAVSQYLSGK 46 (119)
T ss_pred hHHHHHHHHHHHHHHHHHc--CCcHHHHHHHhCCCHHHHHHHHccC
Confidence 3445667777777644433 7889999999999999999999864
No 41
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=66.11 E-value=1.1e+02 Score=28.18 Aligned_cols=90 Identities=16% Similarity=0.187 Sum_probs=70.1
Q ss_pred HHHHHHHHHcCChHHHHHHhhCCCC----cHHHHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCH----HHHH
Q 029202 79 AWKIGQHLWTRDYAGVYDAIRGFDW----SQEAQALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNE----DDAA 150 (197)
Q Consensus 79 ~~~l~~~L~~~~y~~v~~~l~~~~w----s~~~~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~----~e~~ 150 (197)
++.+......+.|..-+..++.-.+ -..+.+=|+.|-+.||+|.+--.-+-|+++..+..|.-+|.+. .++.
T Consensus 308 lr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~sv~~le~~l~ 387 (466)
T KOG0686|consen 308 LREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTSVAILESELL 387 (466)
T ss_pred HHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhcccHHHHHHHHH
Confidence 4477778889999999888876322 2456888899999999999999999999999999999999986 4566
Q ss_pred HHHHhc--CCeecCCCceEe
Q 029202 151 YYVQQQ--GWTLDPASRMLT 168 (197)
Q Consensus 151 ~~~~~~--GW~~d~~~~~~~ 168 (197)
+.+.+. .=++|...+.++
T Consensus 388 ~LI~~~~i~~rIDs~~ki~~ 407 (466)
T KOG0686|consen 388 ELILEGKISGRIDSHNKILY 407 (466)
T ss_pred HHHHccchheeeccccceee
Confidence 666543 556775554444
No 42
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=66.07 E-value=41 Score=23.22 Aligned_cols=61 Identities=10% Similarity=0.049 Sum_probs=42.0
Q ss_pred chHHHHHccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHHHHHHHhhcCHHHHHHHHhcCCh
Q 029202 4 SPLTDALASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIHLLGYYYVNDINSARFLWKSIPS 67 (197)
Q Consensus 4 ~~i~~~~~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~Ll~~L~~ndl~~ar~l~kRiP~ 67 (197)
.....+...|+|++-...++...-. .++....+.. +-.+-.+|+-.++...|...++++-.
T Consensus 7 ~~~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~--~~~l~~~~~~~~~~~~A~~~~~~~~~ 67 (119)
T TIGR02795 7 DAALLVLKAGDYADAIQAFQAFLKK-YPKSTYAPNA--HYWLGEAYYAQGKYADAAKAFLAVVK 67 (119)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHH-CCCccccHHH--HHHHHHHHHhhccHHHHHHHHHHHHH
Confidence 4566788999999999999888644 3332222222 33345566677999999999998753
No 43
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=66.05 E-value=28 Score=22.46 Aligned_cols=52 Identities=13% Similarity=0.171 Sum_probs=33.0
Q ss_pred CHHHHHHHcCCCHHHHHHHHHhcCCeecCCCceEeecCCCCCCCCCC-ChHHHHHHHHHHHhh
Q 029202 134 STQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKLQRLTEYVFHL 195 (197)
Q Consensus 134 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~P~~~~~~~~~~~-~~~qL~~LT~~v~fL 195 (197)
++.++|+.+|++..-+..+.++.| ...|.+. ...... +++++.+|-.+....
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~g--------~~~~~r~--~~~~r~yt~~~v~~l~~i~~l~ 54 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRYG--------LPAPQRT--DGGHRLYSEADVARLRLIRRLT 54 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhCC--------CCCCCcC--CCCCeecCHHHHHHHHHHHHHH
Confidence 678999999999999998876433 2222221 112222 777887776665443
No 44
>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=61.39 E-value=32 Score=20.76 Aligned_cols=42 Identities=17% Similarity=0.358 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHH---HhcCC
Q 029202 116 ELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYV---QQQGW 158 (197)
Q Consensus 116 ~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW 158 (197)
+..+.+|+..+...-. ++..++|..+|+|..-+...+ .+.|+
T Consensus 2 ~~~~~~Il~~l~~~~~-~t~~ela~~~~is~~tv~~~l~~L~~~g~ 46 (48)
T PF13412_consen 2 DETQRKILNYLRENPR-ITQKELAEKLGISRSTVNRYLKKLEEKGL 46 (48)
T ss_dssp -HHHHHHHHHHHHCTT-S-HHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred CHHHHHHHHHHHHcCC-CCHHHHHHHhCCCHHHHHHHHHHHHHCcC
Confidence 4567788888888544 999999999999976555544 34565
No 45
>PF12218 End_N_terminal: N terminal extension of bacteriophage endosialidase; InterPro: IPR024429 This entry represents the N-terminal extension domain of endosialidases which is approximately 70 amino acids in length. The two N-terminal domains (this domain and the beta propeller) assemble in the compact 'cap' whereas the C-terminal domain forms an extended tail-like structure. The very N-terminal part of the 'cap' region (residues 246 to 312) holds the only alpha-helix of the protein and is presumably the residual part of the deleted N-terminal head-binding domain [].; PDB: 3JU4_A 3GVL_A 3GVK_B 3GVJ_A 1V0E_B 1V0F_E.
Probab=60.70 E-value=0.61 Score=31.15 Aligned_cols=16 Identities=31% Similarity=0.756 Sum_probs=11.0
Q ss_pred cCHHHHHHHHhcCChh
Q 029202 53 NDINSARFLWKSIPST 68 (197)
Q Consensus 53 ndl~~ar~l~kRiP~~ 68 (197)
+..-|+||+|+|||-.
T Consensus 42 srf~N~rF~~eri~gq 57 (67)
T PF12218_consen 42 SRFKNARFVYERIPGQ 57 (67)
T ss_dssp GGEES-EEEE-SSTT-
T ss_pred HhhccceEEEeecCCC
Confidence 5677999999999943
No 46
>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=60.70 E-value=33 Score=21.49 Aligned_cols=49 Identities=10% Similarity=0.131 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHhhcccC-HHHHHHHcCCCHHHHHH---HHHhcCCee
Q 029202 112 AAFSELYTKRMFQLLLSAYSTIS-TQDTALFLGMNEDDAAY---YVQQQGWTL 160 (197)
Q Consensus 112 ~~l~~~iR~~i~~lis~AY~sIs-~~~~a~~Lgls~~e~~~---~~~~~GW~~ 160 (197)
..+.+.+++.+....-..-..++ ..++|..+|+|..-+.+ -..+.||-.
T Consensus 4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 4 EQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 34455555555554333444555 99999999999755444 455679953
No 47
>PF12854 PPR_1: PPR repeat
Probab=60.64 E-value=19 Score=20.43 Aligned_cols=30 Identities=20% Similarity=0.279 Sum_probs=25.6
Q ss_pred CCcchHHHHHHHHHhhcCHHHHHHHHhcCC
Q 029202 37 QDEWPYVIHLLGYYYVNDINSARFLWKSIP 66 (197)
Q Consensus 37 ~~~~py~~~Ll~~L~~ndl~~ar~l~kRiP 66 (197)
|+..-|..++-.|--.+++.+|.-++++++
T Consensus 5 Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~ 34 (34)
T PF12854_consen 5 PDVVTYNTLIDGYCKAGRVDEAFELFDEMK 34 (34)
T ss_pred CcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence 555459999999999999999999998764
No 48
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=59.95 E-value=8.1 Score=34.96 Aligned_cols=106 Identities=14% Similarity=0.172 Sum_probs=71.2
Q ss_pred hHHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCChHHHHHHhhCCCCcHHHHH----HHHHHHH
Q 029202 41 PYVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRDYAGVYDAIRGFDWSQEAQA----LVAAFSE 116 (197)
Q Consensus 41 py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~~ws~~~~~----~i~~l~~ 116 (197)
|....+-.+|....+..|-.|-+-+|......+..|+.+-.++. |.+| .|-..-.. .-.....
T Consensus 270 pl~eqi~~ll~~~~v~~Fs~L~~ll~~~~~~~~~lL~~L~~~Av-LV~G------------~WV~kS~ll~~~~~~e~~~ 336 (421)
T PF04801_consen 270 PLEEQIKALLKKARVISFSELRKLLPSNSDTDEELLRALQQVAV-LVQG------------NWVVKSELLYPDVPAEQLC 336 (421)
T ss_pred CHHHHHHHHHHhCCcccHHHHHHHhccccchHHHHHHHHHhheE-EEee------------eEEEehhhccCCCcchhhh
Confidence 45556778888888888888888888666422344554444332 2222 34221111 1234788
Q ss_pred HHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHH----HH----hcCCee
Q 029202 117 LYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYY----VQ----QQGWTL 160 (197)
Q Consensus 117 ~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~----~~----~~GW~~ 160 (197)
..|+-|+-++.+. ..|+.+++....+++.+++.++ |. .+||++
T Consensus 337 ~aRD~iL~~F~~~-~~v~r~~l~~~~~l~~~~~~eiL~~~a~~~~~~~~W~l 387 (421)
T PF04801_consen 337 RARDYILLLFTKS-RYVKRKELMSATKLPPEDVKEILKEIAVLRPSNRGWKL 387 (421)
T ss_pred hhHHHHHHHhcCC-CceeHHHhhhhcCCCHHHHHHHHHHHhhccCCCCceEE
Confidence 8999999999998 7799999999999998776555 32 458887
No 49
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=59.61 E-value=15 Score=24.54 Aligned_cols=37 Identities=16% Similarity=0.388 Sum_probs=28.4
Q ss_pred ccCHHHHHHHcCCC--HHHHHHHHHhcCCeecC-CCceEe
Q 029202 132 TISTQDTALFLGMN--EDDAAYYVQQQGWTLDP-ASRMLT 168 (197)
Q Consensus 132 sIs~~~~a~~Lgls--~~e~~~~~~~~GW~~d~-~~~~~~ 168 (197)
.++.+.+.++||++ .+++.+..+..|-+++. ++..+.
T Consensus 5 ~~~~~~i~~~lG~~i~~~~i~~~L~~lg~~~~~~~~~~~~ 44 (70)
T PF03484_consen 5 TLSLDKINKLLGIDISPEEIIKILKRLGFKVEKIDGDTLE 44 (70)
T ss_dssp EEEHHHHHHHHTS---HHHHHHHHHHTT-EEEE-CTTEEE
T ss_pred EecHHHHHHHhCCCCCHHHHHHHHHHCCCEEEECCCCEEE
Confidence 46788999999985 78999999999999987 454443
No 50
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=59.21 E-value=14 Score=21.88 Aligned_cols=23 Identities=17% Similarity=0.509 Sum_probs=20.2
Q ss_pred cCHHHHHHHcCCCHHHHHHHHHh
Q 029202 133 ISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 133 Is~~~~a~~Lgls~~e~~~~~~~ 155 (197)
+++.++|.+||++..-+..++.+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 57899999999999999888864
No 51
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=58.85 E-value=19 Score=23.38 Aligned_cols=31 Identities=10% Similarity=0.212 Sum_probs=28.5
Q ss_pred CHHHHHHHcCCCHHHHHHHHHhcCCeecCCC
Q 029202 134 STQDTALFLGMNEDDAAYYVQQQGWTLDPAS 164 (197)
Q Consensus 134 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~ 164 (197)
|++.++..++++.+++.+-..+.|..+|+..
T Consensus 22 sLd~Lc~~~~id~~~l~~kL~~~Gy~Y~~~~ 52 (55)
T PF14056_consen 22 SLDELCYDYDIDKEELEEKLASIGYEYDEEQ 52 (55)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHcCCeEchhh
Confidence 8899999999999999999999999998754
No 52
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=58.50 E-value=34 Score=22.71 Aligned_cols=46 Identities=13% Similarity=0.239 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHhhc-ccCHHHHHHHcCCCHHHHHHHH---HhcCCeec
Q 029202 116 ELYTKRMFQLLLSAYS-TISTQDTALFLGMNEDDAAYYV---QQQGWTLD 161 (197)
Q Consensus 116 ~~iR~~i~~lis~AY~-sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~d 161 (197)
+..+++|+.++...=. .++..++|..||++...+.... .+.|+-..
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 4578899999998844 4999999999999987776664 45688764
No 53
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=58.32 E-value=84 Score=24.25 Aligned_cols=67 Identities=16% Similarity=0.089 Sum_probs=43.4
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHhcCCeecCCCceEeecCCCCCCCCCCChHHHHHHHHHH
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKLQRLTEYV 192 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~P~~~~~~~~~~~~~~qL~~LT~~v 192 (197)
|....+.--|.-+|...+|+++|++..=+..++. .|.- .|.. .|.++..-.+..+++.|++.|-+.+
T Consensus 10 R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~--r~~e--~G~~-l~~~~~~GrP~kl~~~q~~~l~e~~ 76 (138)
T COG3415 10 RERVVDAVVGEGLSCREAAKRFGVSISTVYRWVR--RYRE--TGLD-LPPKPRKGRPRKLSEEQLEILLERL 76 (138)
T ss_pred HHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHH--Hhcc--cccc-ccCccCCCCCcccCHHHHHHHHHHH
Confidence 4444555668999999999999999888777776 2332 2322 3444444444555777777665543
No 54
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=57.96 E-value=25 Score=25.37 Aligned_cols=30 Identities=17% Similarity=0.263 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHhhcccCHHHHHHHcCCC
Q 029202 116 ELYTKRMFQLLLSAYSTISTQDTALFLGMN 145 (197)
Q Consensus 116 ~~iR~~i~~lis~AY~sIs~~~~a~~Lgls 145 (197)
.+.|++|+.++.-+-+-+++..+..++|..
T Consensus 2 ~t~rEkii~lL~e~~eplt~~ei~~~~~~~ 31 (97)
T COG3357 2 ETTREKIISLLLESDEPLTVAEIFELLNGE 31 (97)
T ss_pred chHHHHHHHHHHcCCCcchHHHHHHHHcCC
Confidence 468999999999888999999999999997
No 55
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=57.31 E-value=2.1e+02 Score=28.50 Aligned_cols=121 Identities=16% Similarity=0.204 Sum_probs=77.0
Q ss_pred HHHHHccccHHHHHHHHhHH--------hhhh---------------hhCCCc--CCCcchHHHHHHHHHhhcCHHHHHH
Q 029202 6 LTDALASKSYEKIADICDDL--------MLKV---------------AAEGIV--FQDEWPYVIHLLGYYYVNDINSARF 60 (197)
Q Consensus 6 i~~~~~~~~~~~l~~~~e~~--------El~~---------------~~~g~~--~~~~~py~~~Ll~~L~~ndl~~ar~ 60 (197)
|..++..|+|++.+..|-.+ |... -|.|.+ .|.+ |-..|..+|. +|...|+.
T Consensus 399 I~HLl~~~~y~~Aas~~p~m~gn~~~eWe~~V~~f~e~~~l~~Ia~~lPt~~~rL~p~v--YemvLve~L~-~~~~~F~e 475 (846)
T KOG2066|consen 399 IDHLLFEGKYDEAASLCPKMLGNNAAEWELWVFKFAELDQLTDIAPYLPTGPPRLKPLV--YEMVLVEFLA-SDVKGFLE 475 (846)
T ss_pred HHHHHhcchHHHHHhhhHHHhcchHHHHHHHHHHhccccccchhhccCCCCCcccCchH--HHHHHHHHHH-HHHHHHHH
Confidence 67889999999988777432 2221 134554 2455 7776776666 88888887
Q ss_pred HHhc--------------CChhhhhhcH--HHHHHHHHHHHHHcCChHHHHHHhhCCCCcHHHHHHHH--HHHHHHHHHH
Q 029202 61 LWKS--------------IPSTIKDSRA--EVVAAWKIGQHLWTRDYAGVYDAIRGFDWSQEAQALVA--AFSELYTKRM 122 (197)
Q Consensus 61 l~kR--------------iP~~~~~~~~--~l~~~~~l~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~--~l~~~iR~~i 122 (197)
+.+- +|..++++.. .+... -++-++.+|+|++++...-. --..++..+|. .|.+.+|..|
T Consensus 476 ~i~~Wp~~Lys~l~iisa~~~q~~q~Se~~~L~e~-La~LYl~d~~Y~~Al~~ylk-lk~~~vf~lI~k~nL~d~i~~~I 553 (846)
T KOG2066|consen 476 LIKEWPGHLYSVLTIISATEPQIKQNSESTALLEV-LAHLYLYDNKYEKALPIYLK-LQDKDVFDLIKKHNLFDQIKDQI 553 (846)
T ss_pred HHHhCChhhhhhhHHHhhcchHHHhhccchhHHHH-HHHHHHHccChHHHHHHHHh-ccChHHHHHHHHHhhHHHHHHHH
Confidence 7764 4455554311 12222 34567889999998765543 23356666655 4888888888
Q ss_pred HHHHHHhhc
Q 029202 123 FQLLLSAYS 131 (197)
Q Consensus 123 ~~lis~AY~ 131 (197)
..++--.+.
T Consensus 554 v~Lmll~sk 562 (846)
T KOG2066|consen 554 VLLMLLDSK 562 (846)
T ss_pred HHHHccchh
Confidence 888755444
No 56
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=56.24 E-value=55 Score=21.44 Aligned_cols=32 Identities=13% Similarity=0.408 Sum_probs=27.5
Q ss_pred ccCHHHHHHHcCCC--HHHHHHHHHhcCCeecCC
Q 029202 132 TISTQDTALFLGMN--EDDAAYYVQQQGWTLDPA 163 (197)
Q Consensus 132 sIs~~~~a~~Lgls--~~e~~~~~~~~GW~~d~~ 163 (197)
+++.+.+.+++|++ .+++.+...+.|.+++.+
T Consensus 5 ~~~~~~i~~llG~~i~~~ei~~~L~~lg~~~~~~ 38 (71)
T smart00874 5 TLRRERINRLLGLDLSAEEIEEILKRLGFEVEVS 38 (71)
T ss_pred EecHHHHHHHHCCCCCHHHHHHHHHHCCCeEEec
Confidence 56788999999986 789999999999999643
No 57
>PRK12686 carbamate kinase; Reviewed
Probab=55.25 E-value=27 Score=30.69 Aligned_cols=21 Identities=24% Similarity=0.232 Sum_probs=17.5
Q ss_pred CCCHHHHHHHHHhcCCeecCC
Q 029202 143 GMNEDDAAYYVQQQGWTLDPA 163 (197)
Q Consensus 143 gls~~e~~~~~~~~GW~~d~~ 163 (197)
+++++|+...++++||++.+|
T Consensus 133 ~~~~~~a~~~~~~~g~~~~~d 153 (312)
T PRK12686 133 FYTEEEAKQQAEQPGSTFKED 153 (312)
T ss_pred ccCHHHHHHHHHHcCCccccc
Confidence 457899999999999988766
No 58
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=54.52 E-value=84 Score=28.51 Aligned_cols=166 Identities=16% Similarity=0.152 Sum_probs=87.3
Q ss_pred HHHHccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHHHHHHHhh--------cCHHHHHHHHhc---CChhhhhh---
Q 029202 7 TDALASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIHLLGYYYV--------NDINSARFLWKS---IPSTIKDS--- 72 (197)
Q Consensus 7 ~~~~~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~Ll~~L~~--------ndl~~ar~l~kR---iP~~~~~~--- 72 (197)
+-.+.+++|.......+....+- .|. .+-. -+.+++.|++- +|+..|.++++- +|.-..++
T Consensus 148 ~~~L~ak~y~~~~p~ld~divei--~~~-n~h~--~~k~fL~Y~yYgg~iciglk~fe~Al~~~e~~v~~Pa~~vs~~hl 222 (422)
T KOG2582|consen 148 QLCLEAKDYASVLPYLDDDIVEI--CKA-NPHL--DPKYFLLYLYYGGMICIGLKRFERALYLLEICVTTPAMAVSHIHL 222 (422)
T ss_pred HHHHHhhcccccCCccchhHHHH--hcc-CCCC--CHHHHHHHHHhcceeeeccccHHHHHHHHHHHHhcchhHHHHHHH
Confidence 44566777777666666555542 111 2222 24555555553 788888888873 45333222
Q ss_pred cHH----HHHHHHHHHH--------------H--HcCChHHHHHHhhCCCCcHHHH----------------HHHHHHHH
Q 029202 73 RAE----VVAAWKIGQH--------------L--WTRDYAGVYDAIRGFDWSQEAQ----------------ALVAAFSE 116 (197)
Q Consensus 73 ~~~----l~~~~~l~~~--------------L--~~~~y~~v~~~l~~~~ws~~~~----------------~~i~~l~~ 116 (197)
+.+ |-.++.-|+- . |.+-|..+-....... +..+. .++.....
T Consensus 223 EaYkkylLvsLI~~GK~~ql~k~ts~~~~r~~K~ms~pY~ef~~~Y~~~~-~~eLr~lVk~~~~rF~kDnnt~l~k~av~ 301 (422)
T KOG2582|consen 223 EAYKKYLLVSLILTGKVFQLPKNTSQNAGRFFKPMSNPYHEFLNVYLKDS-STELRTLVKKHSERFTKDNNTGLAKQAVS 301 (422)
T ss_pred HHHHHHHHHHhhhcCceeeccccchhhhHHhcccCCchHHHHHHHHhcCC-cHHHHHHHHHHHHHHhhcCcHHHHHHHHH
Confidence 111 2222222211 1 2233444444443322 22232 23444444
Q ss_pred HHHHHHHHHHHHhhcccCHHHHHHHcCCC-HHHHHHHHHh----cCCeecCCCceEeecCCCCCCCC
Q 029202 117 LYTKRMFQLLLSAYSTISTQDTALFLGMN-EDDAAYYVQQ----QGWTLDPASRMLTVKKQPLVTEQ 178 (197)
Q Consensus 117 ~iR~~i~~lis~AY~sIs~~~~a~~Lgls-~~e~~~~~~~----~GW~~d~~~~~~~P~~~~~~~~~ 178 (197)
.+-.+.+.-..+.|+||++++.|++..+. .+|+.+++-+ ..=....+|.+++-.++.....+
T Consensus 302 sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~Ilqmie~~~i~a~iNG~v~f~~n~e~~~Sp 368 (422)
T KOG2582|consen 302 SLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKYILQMIEDGEIFASINGMVFFTDNPEKYNSP 368 (422)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHHHHHHhccCceEEEecceEEEecCcccCCCH
Confidence 55556667788999999999999987775 5666665443 22222235666666665544433
No 59
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=54.46 E-value=34 Score=28.76 Aligned_cols=43 Identities=9% Similarity=0.092 Sum_probs=34.6
Q ss_pred HHHHHHHHhHHhhhhhhCCCcCCCcchHH-HHHHHHHhhcCHHHHHHHHhcCC
Q 029202 15 YEKIADICDDLMLKVAAEGIVFQDEWPYV-IHLLGYYYVNDINSARFLWKSIP 66 (197)
Q Consensus 15 ~~~l~~~~e~~El~~~~~g~~~~~~~py~-~~Ll~~L~~ndl~~ar~l~kRiP 66 (197)
|.+|...|...++.. +.+ .+ +-|+-....+++.++...|.|+|
T Consensus 42 F~ELl~l~nv~qlae-------~~d--sa~lrlL~lFa~Gt~~Dy~aea~rlp 85 (258)
T KOG3250|consen 42 FGELLILPNVVQLAE-------PID--SAYLRLLELFAYGTYRDYSAEALRLP 85 (258)
T ss_pred HHHHHhhhhHHHHcc-------ccc--HHHHHHHHHHhcCchhhhhhhhhcCC
Confidence 899999999999883 222 22 33777888899999999999999
No 60
>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=54.17 E-value=26 Score=22.44 Aligned_cols=40 Identities=15% Similarity=0.256 Sum_probs=26.8
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCCCHHH---HHHHHHhcCCee
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGMNEDD---AAYYVQQQGWTL 160 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgls~~e---~~~~~~~~GW~~ 160 (197)
.++.+|......++..+++..+|++... .++-..++||-.
T Consensus 7 ~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~ 49 (68)
T PF13463_consen 7 QVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVE 49 (68)
T ss_dssp HHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 5666777788999999999999999654 444455689983
No 61
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=53.94 E-value=35 Score=23.08 Aligned_cols=29 Identities=14% Similarity=0.283 Sum_probs=22.7
Q ss_pred cccCHHHHHHHcCCCHHHHHHHHHhcCCe
Q 029202 131 STISTQDTALFLGMNEDDAAYYVQQQGWT 159 (197)
Q Consensus 131 ~sIs~~~~a~~Lgls~~e~~~~~~~~GW~ 159 (197)
...++.++|.-.|.|+.=+..||++.|-+
T Consensus 33 ~~~si~elA~~~~vS~sti~Rf~kkLG~~ 61 (77)
T PF01418_consen 33 AFMSISELAEKAGVSPSTIVRFCKKLGFS 61 (77)
T ss_dssp CT--HHHHHHHCTS-HHHHHHHHHHCTTT
T ss_pred HHccHHHHHHHcCCCHHHHHHHHHHhCCC
Confidence 47889999999999999999999998753
No 62
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=53.39 E-value=58 Score=20.86 Aligned_cols=34 Identities=21% Similarity=0.313 Sum_probs=27.5
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 155 (197)
+++.++.. -..++++++|..||+|.--+...+.+
T Consensus 9 ~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~ 42 (59)
T PF08280_consen 9 KLLELLLK-NKWITLKELAKKLNISERTIKNDINE 42 (59)
T ss_dssp HHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence 67777777 88999999999999998777766654
No 63
>PRK13503 transcriptional activator RhaS; Provisional
Probab=52.63 E-value=29 Score=28.77 Aligned_cols=35 Identities=9% Similarity=0.119 Sum_probs=29.4
Q ss_pred HHHHHHHHhhc-ccCHHHHHHHcCCCHHHHHHHHHh
Q 029202 121 RMFQLLLSAYS-TISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 121 ~i~~lis~AY~-sIs~~~~a~~Lgls~~e~~~~~~~ 155 (197)
++.+.|...|. .++++++|+.+|+|+.-+....++
T Consensus 175 ~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~ 210 (278)
T PRK13503 175 QLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQ 210 (278)
T ss_pred HHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 56678888888 999999999999999877666654
No 64
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=51.62 E-value=34 Score=23.82 Aligned_cols=45 Identities=16% Similarity=0.243 Sum_probs=33.5
Q ss_pred HHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh-cCCeecCCCceE
Q 029202 122 MFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ-QGWTLDPASRML 167 (197)
Q Consensus 122 i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~-~GW~~d~~~~~~ 167 (197)
+++++.+ =.-+++.++|.-+|.+.+++.+.... .+=++|.+|+++
T Consensus 29 LLr~LA~-G~PVt~~~LA~a~g~~~e~v~~~L~~~p~tEyD~~GrIV 74 (77)
T PF12324_consen 29 LLRLLAK-GQPVTVEQLAAALGWPVEEVRAALAAMPDTEYDDQGRIV 74 (77)
T ss_dssp HHHHHTT-TS-B-HHHHHHHHT--HHHHHHHHHH-TTSEEETTSEEE
T ss_pred HHHHHHc-CCCcCHHHHHHHHCCCHHHHHHHHHhCCCceEcCCCCee
Confidence 5555655 57799999999999999999998766 699999888765
No 65
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=50.63 E-value=72 Score=28.59 Aligned_cols=84 Identities=21% Similarity=0.258 Sum_probs=58.1
Q ss_pred ccccHHHHHHHHhHHhhhhh-hCCCcCCCcchHHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHH-HHHHHHHHH-HHH
Q 029202 11 ASKSYEKIADICDDLMLKVA-AEGIVFQDEWPYVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAE-VVAAWKIGQ-HLW 87 (197)
Q Consensus 11 ~~~~~~~l~~~~e~~El~~~-~~g~~~~~~~py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~-l~~~~~l~~-~L~ 87 (197)
+.+++++-++.++++.--.. ..+.--..+ |+-+=..++..+|...|+.+++|- .+.||. .+.-+.+|+ .+-
T Consensus 153 ~treW~KAId~A~~L~k~~~q~~~~eIAqf--yCELAq~~~~~~~~d~A~~~l~kA----lqa~~~cvRAsi~lG~v~~~ 226 (389)
T COG2956 153 ATREWEKAIDVAERLVKLGGQTYRVEIAQF--YCELAQQALASSDVDRARELLKKA----LQADKKCVRASIILGRVELA 226 (389)
T ss_pred HhhHHHHHHHHHHHHHHcCCccchhHHHHH--HHHHHHHHhhhhhHHHHHHHHHHH----HhhCccceehhhhhhHHHHh
Confidence 46788999999988775521 111111334 888888999999999999999983 233444 666666666 466
Q ss_pred cCChHHHHHHhhC
Q 029202 88 TRDYAGVYDAIRG 100 (197)
Q Consensus 88 ~~~y~~v~~~l~~ 100 (197)
+|+|++.-.++..
T Consensus 227 ~g~y~~AV~~~e~ 239 (389)
T COG2956 227 KGDYQKAVEALER 239 (389)
T ss_pred ccchHHHHHHHHH
Confidence 7899997665544
No 66
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=50.16 E-value=24 Score=20.62 Aligned_cols=23 Identities=22% Similarity=0.485 Sum_probs=19.7
Q ss_pred cCHHHHHHHcCCCHHHHHHHHHh
Q 029202 133 ISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 133 Is~~~~a~~Lgls~~e~~~~~~~ 155 (197)
+++.++|.+||++..-+..++.+
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 36789999999999999988773
No 67
>cd04235 AAK_CK AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an essential precursor of arginine and pyrimidine bases, in the presence of ATP, bicarbonate, and ammonia. CK is a homodimer of 33 kDa subunits and is a member of the Amino Acid Kinase Superfamily (AAK).
Probab=50.08 E-value=21 Score=31.32 Aligned_cols=32 Identities=22% Similarity=0.448 Sum_probs=24.9
Q ss_pred CCCHHHHHHHHHhcCCeecCCC----ceEeecCCCC
Q 029202 143 GMNEDDAAYYVQQQGWTLDPAS----RMLTVKKQPL 174 (197)
Q Consensus 143 gls~~e~~~~~~~~GW~~d~~~----~~~~P~~~~~ 174 (197)
.++++|+.+..+++||++-+|+ +.++|.|.+.
T Consensus 131 ~y~~~~a~~~~~~~g~~~~~d~~~g~rrvV~SP~P~ 166 (308)
T cd04235 131 FYSEEEAEELAAEKGWTFKEDAGRGYRRVVPSPKPK 166 (308)
T ss_pred CcCHHHHHHHHHHcCCEEEEeCCCCceeeeCCCCCc
Confidence 3478999999999999998887 5667766543
No 68
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=48.74 E-value=67 Score=22.06 Aligned_cols=43 Identities=12% Similarity=0.270 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHH--------hcCCeec
Q 029202 117 LYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQ--------QQGWTLD 161 (197)
Q Consensus 117 ~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~--------~~GW~~d 161 (197)
++.+.|+..+++. +++++.+.+..|++.+++.-+.. .|+|..-
T Consensus 5 t~~~~IL~~ls~~--c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rkw~~~ 55 (72)
T PF05584_consen 5 TVTQKILIILSKR--CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERKWRKF 55 (72)
T ss_pred hHHHHHHHHHHhc--cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeeEEe
Confidence 5678888888888 99999999999999888765533 3567664
No 69
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=48.57 E-value=14 Score=24.92 Aligned_cols=40 Identities=25% Similarity=0.366 Sum_probs=30.5
Q ss_pred HHhhcccCHHHHHHHcCCCHHHHHHHHHh-cCCe--ecCCCce
Q 029202 127 LSAYSTISTQDTALFLGMNEDDAAYYVQQ-QGWT--LDPASRM 166 (197)
Q Consensus 127 s~AY~sIs~~~~a~~Lgls~~e~~~~~~~-~GW~--~d~~~~~ 166 (197)
..--.-+++.++|..||.++.-+.+++.. +-|- +||+|.+
T Consensus 8 rlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~LDPSG~~ 50 (65)
T PF05344_consen 8 RLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQLDPSGHW 50 (65)
T ss_pred HHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCCCh
Confidence 33345689999999999999988888776 5664 5777753
No 70
>COG0549 ArcC Carbamate kinase [Amino acid transport and metabolism]
Probab=48.16 E-value=40 Score=29.43 Aligned_cols=41 Identities=15% Similarity=0.412 Sum_probs=27.0
Q ss_pred CHHHHHHHHHhcCCeecCCCce----EeecCCCCCCCCCCChHHHHHH
Q 029202 145 NEDDAAYYVQQQGWTLDPASRM----LTVKKQPLVTEQKLDPSKLQRL 188 (197)
Q Consensus 145 s~~e~~~~~~~~GW~~d~~~~~----~~P~~~~~~~~~~~~~~qL~~L 188 (197)
+++|+.+..++.||.+..|++. ++|.|.+ ...++.+-+..|
T Consensus 136 ~~eea~~l~~~~gw~~keD~~rG~RRVVpSP~P---~~IvE~~~Ik~L 180 (312)
T COG0549 136 SEEEAEELAKEYGWVFKEDAGRGYRRVVPSPKP---VRIVEAEAIKAL 180 (312)
T ss_pred CHHHHHHHHhhcCcEEEecCCCCeeEecCCCCC---ccchhHHHHHHH
Confidence 6799999999999999777644 4454433 222355555544
No 71
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=46.88 E-value=39 Score=21.83 Aligned_cols=50 Identities=20% Similarity=0.327 Sum_probs=32.0
Q ss_pred CHHHHHHHcCCCHHHHHHHHHhcCCeecCCCceEeecCCCCCCCCCC-ChHHHHHHHHHHHh
Q 029202 134 STQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKLQRLTEYVFH 194 (197)
Q Consensus 134 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~P~~~~~~~~~~~-~~~qL~~LT~~v~f 194 (197)
+++++|+++|++..-+..+.. +|- +.|.. ....... +++++..|..+...
T Consensus 2 ti~eva~~~gvs~~tlr~y~~-~gl--------l~~~~--~~~g~r~y~~~dv~~l~~i~~l 52 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYER-EGL--------LPPPR--DENGYRYYSEEDVERLREIKEL 52 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHH-TTS--------STTBE--STTSSEEE-HHHHHHHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHHH-hcC--------ccccc--ccCceeeccHHHHHHHHHHHHH
Confidence 578999999999999998865 222 23333 1222223 88888888766543
No 72
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=46.53 E-value=80 Score=25.74 Aligned_cols=55 Identities=18% Similarity=0.258 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHHhhc--ccCHHHHHHHcCCCHHHHHHHHHhcCCeecCCCceEe
Q 029202 114 FSELYTKRMFQLLLSAYS--TISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLT 168 (197)
Q Consensus 114 l~~~iR~~i~~lis~AY~--sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~ 168 (197)
+..--|..+++.+...-. +|++++++...|+..+|++...+..|+-.--.++.++
T Consensus 130 Y~sYW~~~i~~~L~~~~~~~~isi~~is~~Tgi~~~DIi~tL~~l~~l~~~~~~~~i 186 (188)
T PF01853_consen 130 YRSYWRRVILEYLLEFKGKKSISIKDISQETGIRPEDIISTLQQLGMLKYYKGQHII 186 (188)
T ss_dssp HHHHHHHHHHHHHHHTSSE--EEHHHHHHHH-BTHHHHHHHHHHTT-EEEETTEEEE
T ss_pred HHHHHHHHHHHHHHhcCCCCeEEHHHHHHHHCCCHHHHHHHHHHCCCEEEECCcEEE
Confidence 344445566666665555 5999999999999999999999999998765555443
No 73
>COG5079 SAC3 Nuclear protein export factor [Intracellular trafficking and secretion / Cell division and chromosome partitioning]
Probab=46.39 E-value=65 Score=30.49 Aligned_cols=136 Identities=14% Similarity=0.110 Sum_probs=81.6
Q ss_pred HHHHHHHHhHHhhhhhhCCCcCCCcchHHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCC----
Q 029202 15 YEKIADICDDLMLKVAAEGIVFQDEWPYVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRD---- 90 (197)
Q Consensus 15 ~~~l~~~~e~~El~~~~~g~~~~~~~py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~---- 90 (197)
...|....+..+.-. ....--+++ |+-.++..|=..+...- ..+.|..+-. ++-.+-...+-+....++
T Consensus 218 L~sL~elYdd~r~~~-~~cpneaEF--raYaiL~slgDp~yv~~---iq~wp~~if~-d~~vq~alkl~~laq~nn~r~~ 290 (646)
T COG5079 218 LASLIELYDDGRAGK-KECPNEAEF--RAYAILASLGDPRYVAG---IQGWPGGIFC-DLPVQIALKLMQLAQSNNFRLL 290 (646)
T ss_pred HHHHHHHHHHHHhhc-CCCCCHHHH--HHHHHHHHhCCchhhhc---cccCCccccc-cchHHHHHHHHHHhhccCeeec
Confidence 444555555555431 111111345 66667776654444331 2345555543 344444444444433333
Q ss_pred -----------hHHHHHHhhCCCCcHHHHHHHHHHHH----HHHHHHHHHHHHhh----cccCHHHHHHHcCCC-HHHHH
Q 029202 91 -----------YAGVYDAIRGFDWSQEAQALVAAFSE----LYTKRMFQLLLSAY----STISTQDTALFLGMN-EDDAA 150 (197)
Q Consensus 91 -----------y~~v~~~l~~~~ws~~~~~~i~~l~~----~iR~~i~~lis~AY----~sIs~~~~a~~Lgls-~~e~~ 150 (197)
|..||..+++ +.+..+|..|.+ .||.-++..++++| ..|+.-++..+|.++ .+|.+
T Consensus 291 ~~rnteac~nlytrFfkl~qS----psv~~lmg~lle~h~~sir~~aLkAm~k~~~sahk~ipf~~l~~il~f~~~~e~~ 366 (646)
T COG5079 291 GRRNTEACFNLYTRFFKLIQS----PSVQYLMGCLLEKHNISIRGGALKAMEKEIESAHKNIPFVDLSGILDFEEKGEGE 366 (646)
T ss_pred cccchhhhhHHHHHHHHHHhC----ccHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhhcCCCeehhhhhccccccchhH
Confidence 4567777766 667777776655 46766666555554 679999999999997 68999
Q ss_pred HHHHhcCCeec
Q 029202 151 YYVQQQGWTLD 161 (197)
Q Consensus 151 ~~~~~~GW~~d 161 (197)
+||+=.|=++.
T Consensus 367 efckyy~lei~ 377 (646)
T COG5079 367 EFCKYYGLEIR 377 (646)
T ss_pred HHhhhcceeee
Confidence 99998888883
No 74
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=46.21 E-value=31 Score=20.29 Aligned_cols=30 Identities=17% Similarity=0.217 Sum_probs=19.4
Q ss_pred hcccCHHHHHHHcCCCHHHHHHHHHhc-CCe
Q 029202 130 YSTISTQDTALFLGMNEDDAAYYVQQQ-GWT 159 (197)
Q Consensus 130 Y~sIs~~~~a~~Lgls~~e~~~~~~~~-GW~ 159 (197)
-++++++++|..+|+|..-+....++. |.+
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~g~t 36 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKETGMT 36 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHTSS-
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 357899999999999887776665553 655
No 75
>PLN03239 histone acetyltransferase; Provisional
Probab=46.16 E-value=64 Score=28.83 Aligned_cols=55 Identities=16% Similarity=0.192 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHhh---cccCHHHHHHHcCCCHHHHHHHHHhcCCeecCCCceEe
Q 029202 114 FSELYTKRMFQLLLSAY---STISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLT 168 (197)
Q Consensus 114 l~~~iR~~i~~lis~AY---~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~ 168 (197)
+..-=+++++..+...- .++++++++...|+..+|++...+..|.-..-.|+.++
T Consensus 263 Y~~YW~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l~~l~~~~g~~~i 320 (351)
T PLN03239 263 YIPYWGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQLGILKFINGIYFI 320 (351)
T ss_pred HHHHHHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHCCcEEEECCeEEE
Confidence 44445556666655442 46999999999999999999999999977655565544
No 76
>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=45.60 E-value=32 Score=21.30 Aligned_cols=40 Identities=15% Similarity=0.292 Sum_probs=31.3
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCCCHHHHHH---HHHhcCCee
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGMNEDDAAY---YVQQQGWTL 160 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~ 160 (197)
+|++++...=..+++.+++.-+|++..-+-. -..+.||-.
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 6788899998999999999999999755444 455678865
No 77
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=45.07 E-value=23 Score=30.28 Aligned_cols=29 Identities=21% Similarity=0.475 Sum_probs=26.4
Q ss_pred ccCHHHHHHHcCCCHHHHHHHHHhcCCee
Q 029202 132 TISTQDTALFLGMNEDDAAYYVQQQGWTL 160 (197)
Q Consensus 132 sIs~~~~a~~Lgls~~e~~~~~~~~GW~~ 160 (197)
+..+.++|..||+++..+.++-..-||+.
T Consensus 19 gmk~~dIAeklGvspntiksWKrr~gWs~ 47 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKRRDGWSA 47 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHHhcCCCc
Confidence 37889999999999999999999999963
No 78
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=44.96 E-value=30 Score=21.25 Aligned_cols=44 Identities=16% Similarity=0.165 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHhhccc-CHHHHHHHcCCCHHH---HHHHHHhcCCee
Q 029202 117 LYTKRMFQLLLSAYSTI-STQDTALFLGMNEDD---AAYYVQQQGWTL 160 (197)
Q Consensus 117 ~iR~~i~~lis~AY~sI-s~~~~a~~Lgls~~e---~~~~~~~~GW~~ 160 (197)
.++..+....-..=..+ +..++|..+|+|..- +.+...+.||-.
T Consensus 4 ~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 4 RLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred HHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 34444444321122346 899999999999644 444555679853
No 79
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=44.95 E-value=28 Score=20.08 Aligned_cols=26 Identities=12% Similarity=0.162 Sum_probs=19.4
Q ss_pred HHHHHHHcCCCHHHHHHHHHhcCCeec
Q 029202 135 TQDTALFLGMNEDDAAYYVQQQGWTLD 161 (197)
Q Consensus 135 ~~~~a~~Lgls~~e~~~~~~~~GW~~d 161 (197)
+..+..| ||+.+++.+.....||.++
T Consensus 6 v~~L~~m-Gf~~~~~~~AL~~~~~nve 31 (37)
T PF00627_consen 6 VQQLMEM-GFSREQAREALRACNGNVE 31 (37)
T ss_dssp HHHHHHH-TS-HHHHHHHHHHTTTSHH
T ss_pred HHHHHHc-CCCHHHHHHHHHHcCCCHH
Confidence 3456667 9999999999888888664
No 80
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=44.81 E-value=1.8e+02 Score=24.17 Aligned_cols=117 Identities=12% Similarity=0.079 Sum_probs=72.4
Q ss_pred HHHHHHHHHhhcCHHHHHHHHhcCChh---------hhh---hcHHHHHHHHHHHHHHcCChHHHHHHhhCCC-CcHHHH
Q 029202 42 YVIHLLGYYYVNDINSARFLWKSIPST---------IKD---SRAEVVAAWKIGQHLWTRDYAGVYDAIRGFD-WSQEAQ 108 (197)
Q Consensus 42 y~~~Ll~~L~~ndl~~ar~l~kRiP~~---------~~~---~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~~-ws~~~~ 108 (197)
-+...++..+.+|+..++.+.+++-.- ... ....-..++.+..++.+|+..+++..++... -..+.-
T Consensus 134 ~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~~~~~~if~l~dal~~~~~~~a~~~l~~l~~~~~~~~ 213 (302)
T TIGR01128 134 DAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSDSARFNVFDLTDALLEGKAARALRILKGLLGEGEEPL 213 (302)
T ss_pred HHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhhhhcCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCcHH
Confidence 456667777888999998888875211 110 0111224789999999999998877776511 123335
Q ss_pred HHHHHHHHHHHH--HHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh-cCCeec
Q 029202 109 ALVAAFSELYTK--RMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ-QGWTLD 161 (197)
Q Consensus 109 ~~i~~l~~~iR~--~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~-~GW~~d 161 (197)
.++..+...+|. .+-.+..+. .+.+.+++.+|+.+.....+... +.|+.+
T Consensus 214 ~il~~l~~~~~~L~~~k~~~~~~---~~~~~i~~~~~~~~~~~~~~~~~~~~~s~~ 266 (302)
T TIGR01128 214 ILLALLQRQLRLLLQLKRLAQQG---GPLAQLASKLGIWPYRRKLALKALRRLSLA 266 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcC---CCHHHHHHHcCCCHHHHHHHHHHHhcCCHH
Confidence 556666666655 222233333 37888999999887665554443 577764
No 81
>PRK12354 carbamate kinase; Reviewed
Probab=44.61 E-value=49 Score=29.02 Aligned_cols=30 Identities=27% Similarity=0.640 Sum_probs=22.6
Q ss_pred CCHHHHHHHHHhcCCeecCCC---ceEeecCCC
Q 029202 144 MNEDDAAYYVQQQGWTLDPAS---RMLTVKKQP 173 (197)
Q Consensus 144 ls~~e~~~~~~~~GW~~d~~~---~~~~P~~~~ 173 (197)
++++|+.+..+++||++-.+| +.++|.|.+
T Consensus 127 y~~~~a~~~~~e~g~~~~~dg~g~rrVv~SP~P 159 (307)
T PRK12354 127 YDEAEAERLAAEKGWTIKPDGDYFRRVVPSPRP 159 (307)
T ss_pred cCHHHHHHHHHhcCCEEeecCCceEEEecCCCC
Confidence 478999999999999997776 345555543
No 82
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=44.21 E-value=41 Score=25.92 Aligned_cols=50 Identities=10% Similarity=0.138 Sum_probs=39.9
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHhcCCeecCCCceEeec
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVK 170 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~P~ 170 (197)
.-++-+..+-.+|.+.++|+++++.+..+.+|..+.|--+...++...|.
T Consensus 36 ~f~D~v~~~~gli~~re~AK~lkige~~l~~~L~e~~~l~~~~~~~n~p~ 85 (135)
T COG3645 36 EFADAVVEASGLILFRELAKLLKIGENRLFAWLRENKYLIKRGGDKNLPT 85 (135)
T ss_pred HHHHHHhcCccceeHHHHHHHHccCHHHHHHHHHHCCEEEEccCCCCCCc
Confidence 34556778889999999999999999999999999988887523343443
No 83
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=44.18 E-value=88 Score=20.34 Aligned_cols=40 Identities=20% Similarity=0.199 Sum_probs=29.2
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCCCHHHH---HHHHHhcCCeecC
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGMNEDDA---AYYVQQQGWTLDP 162 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgls~~e~---~~~~~~~GW~~d~ 162 (197)
+++..+...+. +.+++|..+|+|..-+ .+...+.|+.+..
T Consensus 4 ~il~~L~~~~~--~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~ 46 (69)
T TIGR00122 4 RLLALLADNPF--SGEKLGEALGMSRTAVNKHIQTLREWGVDVLT 46 (69)
T ss_pred HHHHHHHcCCc--CHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 56777888874 4999999999997544 4445567997643
No 84
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=43.60 E-value=69 Score=18.91 Aligned_cols=39 Identities=23% Similarity=0.357 Sum_probs=26.3
Q ss_pred HHHHHHHhhcccCHHHHHHHcCCCHHH---HHHHHHhcCCeec
Q 029202 122 MFQLLLSAYSTISTQDTALFLGMNEDD---AAYYVQQQGWTLD 161 (197)
Q Consensus 122 i~~lis~AY~sIs~~~~a~~Lgls~~e---~~~~~~~~GW~~d 161 (197)
++..+.+ -..+++.+++..+|++..- ..+...+.||-..
T Consensus 5 il~~l~~-~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 5 ILELLAQ-QGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred HHHHHHH-cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 4444433 3568999999999998644 4444556798654
No 85
>PF06250 DUF1016: Protein of unknown function (DUF1016); InterPro: IPR009362 This is a family of proteins which is found in viruses, archaea and bacteria. The function of these proteins has not been experimetnally determined, but computational analysis suggests that they may function as nucleases which enhance the activity of nearby restriction endonucleases []. Cooperation of this kind between a restriction endonuclease and exonucleases has been shown to be essential in allowing some restriction enzymes to perform multiple rounds of DNA cleavage [].
Probab=43.32 E-value=1.2e+02 Score=26.82 Aligned_cols=85 Identities=14% Similarity=0.371 Sum_probs=53.8
Q ss_pred HHHHHHHHHHHHHcCCh--------HHHHHHhhC-------CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHH
Q 029202 75 EVVAAWKIGQHLWTRDY--------AGVYDAIRG-------FDWSQEAQALVAAFSELYTKRMFQLLLSAYSTISTQDTA 139 (197)
Q Consensus 75 ~l~~~~~l~~~L~~~~y--------~~v~~~l~~-------~~ws~~~~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a 139 (197)
.+..=|.+|+.+-+..- .++...+.. ..+|..--.-|..|-..+-+. ..+...-..||-.+..
T Consensus 24 l~~lYW~IG~~I~e~~~~g~ra~yG~~vi~~LS~dL~~~fpkGFS~rNL~~MrqFy~~y~~~--~i~~~l~~qLsW~H~~ 101 (320)
T PF06250_consen 24 LVLLYWEIGKRIVEKEQQGERAGYGKKVIKRLSKDLTEEFPKGFSRRNLKYMRQFYEAYPDE--EIVQTLVAQLSWHHIR 101 (320)
T ss_pred HHHHHHHHHHHHHHHHhcCcccccchhHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhh--hhccchhcccchhhHh
Confidence 36667888888877543 233333332 135554455555666655532 3455666688888899
Q ss_pred HHcCCCHHHHHHH----HHhcCCeec
Q 029202 140 LFLGMNEDDAAYY----VQQQGWTLD 161 (197)
Q Consensus 140 ~~Lgls~~e~~~~----~~~~GW~~d 161 (197)
-+.-+...+...| |.+.||+.+
T Consensus 102 iL~kikd~~eR~fY~~~ai~~gWS~r 127 (320)
T PF06250_consen 102 ILSKIKDPEERLFYIQEAIENGWSRR 127 (320)
T ss_pred hhccCCCHHHHHHHHHHHHHhCCCHH
Confidence 8888886666555 667899983
No 86
>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=42.51 E-value=80 Score=19.38 Aligned_cols=41 Identities=22% Similarity=0.360 Sum_probs=26.3
Q ss_pred HHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHH---HHhcCCee
Q 029202 120 KRMFQLLLSAYSTISTQDTALFLGMNEDDAAYY---VQQQGWTL 160 (197)
Q Consensus 120 ~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~ 160 (197)
.+++.++..+=..++.+++|..||+|..-+... .++.|..+
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~~~I 46 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWGIPI 46 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeE
Confidence 366777744444599999999999997554444 34456443
No 87
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=42.31 E-value=59 Score=29.06 Aligned_cols=55 Identities=13% Similarity=0.202 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh-----c-CCeecCCCceEeecC
Q 029202 117 LYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ-----Q-GWTLDPASRMLTVKK 171 (197)
Q Consensus 117 ~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~-----~-GW~~d~~~~~~~P~~ 171 (197)
.+-+.=+-.+|+-|..|+.+.++++|+++.+.+.+.+.+ | .=.+|.-.+++.+-+
T Consensus 302 a~~EhNlls~Skly~nisf~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~egiihFe~ 362 (399)
T KOG1497|consen 302 AVIEHNLLSASKLYNNISFEELGALLKIDAEKAEKIAAQMITQERMNGSIDQIEGIIHFED 362 (399)
T ss_pred HHHHHhHHHHHHHHHhccHHHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhhcceEeecc
Confidence 344444557899999999999999999998887776543 2 445666566776654
No 88
>COG2886 Uncharacterized small protein [Function unknown]
Probab=41.83 E-value=83 Score=22.44 Aligned_cols=39 Identities=18% Similarity=0.237 Sum_probs=31.3
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHhcCCeec
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLD 161 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d 161 (197)
-...++.+ ..+|+..++.+.|++..++..-..+||=...
T Consensus 32 iaI~L~qe--g~vSlg~Aaela~~sl~ef~~eL~~R~i~l~ 70 (88)
T COG2886 32 IAIELFQE--GAVSLGRAAELAGMSLNEFEEELRKRGIPLY 70 (88)
T ss_pred HHHHHHHH--hhhHHHHHHHHhcCCHHHHHHHHHHhCCCcc
Confidence 33445555 7899999999999999999999998886554
No 89
>PF01296 Galanin: Galanin; InterPro: IPR008174 Galanin is a peptide hormone that controls various biological activities []. Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons []. Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence []; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function []. Galanin is a 29 amino acid peptide processed from a larger precursor protein. Except in human, galanin is C-terminally amidated. Its sequence is highly conserved and the first 14 residues are identical in all currently known sequences.; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=41.38 E-value=17 Score=20.30 Aligned_cols=19 Identities=32% Similarity=0.482 Sum_probs=15.3
Q ss_pred CCeecCCCceEeecCCCCC
Q 029202 157 GWTLDPASRMLTVKKQPLV 175 (197)
Q Consensus 157 GW~~d~~~~~~~P~~~~~~ 175 (197)
||+++..|-.+-|...++.
T Consensus 1 gwtlnsagyLlGPhaiD~H 19 (29)
T PF01296_consen 1 GWTLNSAGYLLGPHAIDNH 19 (29)
T ss_pred CccccccceEeccccccCc
Confidence 8999988888888876653
No 90
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=41.02 E-value=55 Score=23.18 Aligned_cols=46 Identities=13% Similarity=0.293 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHH---hhcccCHHHHHHHcCCCHHHHHHHHH---hcCCeec
Q 029202 116 ELYTKRMFQLLLS---AYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTLD 161 (197)
Q Consensus 116 ~~iR~~i~~lis~---AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~d 161 (197)
..++++|+..|.. .=.-++++.+++-||++.+++.+.+. ..|.-+.
T Consensus 46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 97 (102)
T PF08784_consen 46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYS 97 (102)
T ss_dssp -HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEec
Confidence 3455666666666 22349999999999999877666554 4577664
No 91
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=40.72 E-value=50 Score=19.98 Aligned_cols=35 Identities=17% Similarity=0.263 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHH
Q 029202 117 LYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYV 153 (197)
Q Consensus 117 ~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~ 153 (197)
-.|-+|+.++.. ...++.+++.-+|++..-+-...
T Consensus 2 ~~R~~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL 36 (47)
T PF01022_consen 2 PTRLRILKLLSE--GPLTVSELAEELGLSQSTVSHHL 36 (47)
T ss_dssp HHHHHHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHh--CCCchhhHHHhccccchHHHHHH
Confidence 468899999988 88999999999999987665543
No 92
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=40.26 E-value=2.7e+02 Score=24.79 Aligned_cols=148 Identities=14% Similarity=0.193 Sum_probs=85.8
Q ss_pred HHHHHhhcCHHHHHHHHhcCChhhhh-hcHHHHHHHHHHHHHHcCChHHHHHHhhCCCCc---HH-HHHHHHHHHHHHHH
Q 029202 46 LLGYYYVNDINSARFLWKSIPSTIKD-SRAEVVAAWKIGQHLWTRDYAGVYDAIRGFDWS---QE-AQALVAAFSELYTK 120 (197)
Q Consensus 46 Ll~~L~~ndl~~ar~l~kRiP~~~~~-~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~~ws---~~-~~~~i~~l~~~iR~ 120 (197)
|+.-+.-|...+-+.++.- -..++. .+.-|+...++.++.-+|+...|=.++.++..- ++ +..=...|-|..-+
T Consensus 253 lLSkIMlN~~~evk~vl~~-K~t~~~y~~r~I~am~avaea~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe 331 (421)
T COG5159 253 LLSKIMLNRREEVKAVLRN-KNTLKHYDDRMIRAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLE 331 (421)
T ss_pred HHHHHHHhhHHHHHHHHcc-chhHhhhhhhhHHHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHH
Confidence 4445555776666666543 223332 345588999999999999888877777764321 11 11222233344444
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCCCHHHH----HHHHHhc--CCeecCCCceEeecCCCCCCCCCC-ChHHHHHHHHHHH
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGMNEDDA----AYYVQQQ--GWTLDPASRMLTVKKQPLVTEQKL-DPSKLQRLTEYVF 193 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgls~~e~----~~~~~~~--GW~~d~~~~~~~P~~~~~~~~~~~-~~~qL~~LT~~v~ 193 (197)
.-+--|---|+.+.+++.|..+|++..++ .+.+..+ -=++|..++.++.-..+++...-- ..++++.|..+|.
T Consensus 332 ~Nl~kiiEPfs~VeishIa~viGldt~qvEgKLsqMILDKifyG~LDqg~gcLivy~ep~qd~tyd~ale~v~~l~~vVd 411 (421)
T COG5159 332 KNLVKIIEPFSVVEISHIADVIGLDTNQVEGKLSQMILDKIFYGTLDQGDGCLIVYGEPAQDNTYDEALEQVEALDCVVD 411 (421)
T ss_pred hhhhhhcCcceeeehhHHHHHhcccHHHHHHHHHHHHHHHHHHhhhccCCceEEEeCCccccchHHHHHHHHHHhhhHHH
Confidence 44444455799999999999999996553 4444332 114444344555444433333211 5667777777764
Q ss_pred h
Q 029202 194 H 194 (197)
Q Consensus 194 f 194 (197)
.
T Consensus 412 ~ 412 (421)
T COG5159 412 S 412 (421)
T ss_pred H
Confidence 3
No 93
>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=40.05 E-value=79 Score=20.09 Aligned_cols=48 Identities=17% Similarity=0.236 Sum_probs=30.9
Q ss_pred HHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHH---HHhcCCeecCCCceE
Q 029202 119 TKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYY---VQQQGWTLDPASRML 167 (197)
Q Consensus 119 R~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~d~~~~~~ 167 (197)
++.|+..+.. -..++++++|..||+|..=+..- ..+.|--.-.-|+..
T Consensus 2 ~~~Il~~l~~-~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~GG~~ 52 (57)
T PF08220_consen 2 QQQILELLKE-KGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRTHGGAV 52 (57)
T ss_pred HHHHHHHHHH-cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCEEE
Confidence 3566777655 58999999999999997544333 334565433334443
No 94
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=39.91 E-value=77 Score=18.45 Aligned_cols=30 Identities=17% Similarity=0.388 Sum_probs=22.3
Q ss_pred ccCHHHHHHHcCCCHHHHHH---HHHhcCCeec
Q 029202 132 TISTQDTALFLGMNEDDAAY---YVQQQGWTLD 161 (197)
Q Consensus 132 sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~d 161 (197)
.++..++|.++|++..-+.. -..+.||-..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 47889999999999755544 4556799764
No 95
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=39.79 E-value=1.7e+02 Score=23.45 Aligned_cols=36 Identities=14% Similarity=0.228 Sum_probs=23.9
Q ss_pred cCHHHHHHHcCCCHHHHHH---HHHhcCCeecCCCceEe
Q 029202 133 ISTQDTALFLGMNEDDAAY---YVQQQGWTLDPASRMLT 168 (197)
Q Consensus 133 Is~~~~a~~Lgls~~e~~~---~~~~~GW~~d~~~~~~~ 168 (197)
++..++|+|||++.+-+-. -.++.|+---..+.+.+
T Consensus 185 lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~~~~i~i 223 (235)
T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKGKYITI 223 (235)
T ss_pred ccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEE
Confidence 6778999999999765544 45567885543344433
No 96
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=39.71 E-value=63 Score=19.63 Aligned_cols=37 Identities=16% Similarity=0.290 Sum_probs=26.5
Q ss_pred HHHHHHHhhcccCHHHHHHHcCCCHHHH---HHHHHhcCCee
Q 029202 122 MFQLLLSAYSTISTQDTALFLGMNEDDA---AYYVQQQGWTL 160 (197)
Q Consensus 122 i~~lis~AY~sIs~~~~a~~Lgls~~e~---~~~~~~~GW~~ 160 (197)
++.++. -..++..+++..+|++...+ .+-..+.||-.
T Consensus 2 il~~l~--~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 2 ILKLLA--EGELCVCELAEILGLSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred HHHHhh--cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 344554 56789999999999986554 44455678886
No 97
>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=39.50 E-value=85 Score=18.83 Aligned_cols=34 Identities=21% Similarity=0.311 Sum_probs=23.4
Q ss_pred HHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHH
Q 029202 120 KRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQ 154 (197)
Q Consensus 120 ~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~ 154 (197)
.+|+..+..- ..+|...+|..+|+|+..+..=+.
T Consensus 6 ~~Il~~Lq~d-~r~s~~~la~~lglS~~~v~~Ri~ 39 (42)
T PF13404_consen 6 RKILRLLQED-GRRSYAELAEELGLSESTVRRRIR 39 (42)
T ss_dssp HHHHHHHHH--TTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHc-CCccHHHHHHHHCcCHHHHHHHHH
Confidence 4555555555 889999999999999988765443
No 98
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=39.49 E-value=52 Score=22.92 Aligned_cols=33 Identities=12% Similarity=0.223 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHH
Q 029202 119 TKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYV 153 (197)
Q Consensus 119 R~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~ 153 (197)
+.+|+..+.. .++++.++|..+|+|..-+-...
T Consensus 8 ~~~I~e~l~~--~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 8 VLEIGKYIVE--TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHH--CCCCHHHHHHHhCCCHHHHHHHh
Confidence 5678888888 99999999999999987666544
No 99
>PF09035 Tn916-Xis: Excisionase from transposon Tn916; InterPro: IPR015122 The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures []. ; PDB: 1Y6U_A.
Probab=39.13 E-value=47 Score=22.41 Aligned_cols=30 Identities=17% Similarity=0.319 Sum_probs=22.2
Q ss_pred ccCHHHHHHHcCCCHHHHHHHH-H--hcCCeec
Q 029202 132 TISTQDTALFLGMNEDDAAYYV-Q--QQGWTLD 161 (197)
Q Consensus 132 sIs~~~~a~~Lgls~~e~~~~~-~--~~GW~~d 161 (197)
.++++.||.|.|+...-+.+.+ . ..+|.+-
T Consensus 13 ~LTi~EAa~Y~gIG~~klr~l~~~~~~~~f~~~ 45 (67)
T PF09035_consen 13 TLTIEEAAEYFGIGEKKLRELAEENPDCPFVLW 45 (67)
T ss_dssp EEEHHHHHHHT-S-HHHHHHHHHH-TT-SSEEE
T ss_pred ccCHHHHHHHhCccHHHHHHHHHhCCCCCEEEE
Confidence 5789999999999999999999 3 3477654
No 100
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=38.99 E-value=43 Score=19.89 Aligned_cols=24 Identities=21% Similarity=0.401 Sum_probs=19.1
Q ss_pred CHHHHHHHcCCCHHHHHHHHHhcCC
Q 029202 134 STQDTALFLGMNEDDAAYYVQQQGW 158 (197)
Q Consensus 134 s~~~~a~~Lgls~~e~~~~~~~~GW 158 (197)
++.++|.++|++..-+..+.. +|+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~-~g~ 25 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYER-IGL 25 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHH-CCC
Confidence 678999999999998887754 443
No 101
>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=38.56 E-value=80 Score=20.62 Aligned_cols=38 Identities=11% Similarity=0.276 Sum_probs=26.2
Q ss_pred ccCHHHHHHHcCCCHHH---HHHHHHhcCCeecCCCceEee
Q 029202 132 TISTQDTALFLGMNEDD---AAYYVQQQGWTLDPASRMLTV 169 (197)
Q Consensus 132 sIs~~~~a~~Lgls~~e---~~~~~~~~GW~~d~~~~~~~P 169 (197)
.++..++|.++|++.+- +.+..++.||---..+.+.++
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~~i~I~ 68 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRGKIIIL 68 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETTEEEES
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCCEEEEC
Confidence 46789999999999654 455566689976444444443
No 102
>PF13730 HTH_36: Helix-turn-helix domain
Probab=38.51 E-value=51 Score=20.33 Aligned_cols=25 Identities=20% Similarity=0.270 Sum_probs=18.4
Q ss_pred CHHHHHHHcCCCHHHHHHH---HHhcCC
Q 029202 134 STQDTALFLGMNEDDAAYY---VQQQGW 158 (197)
Q Consensus 134 s~~~~a~~Lgls~~e~~~~---~~~~GW 158 (197)
|.+.+|..+|++..-+.+. ..++||
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~ 54 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGL 54 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcC
Confidence 6889999999986554444 555787
No 103
>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=38.45 E-value=18 Score=26.11 Aligned_cols=29 Identities=31% Similarity=0.635 Sum_probs=27.7
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
|||+.|+.=+.++.|..+.+++.+..|-.
T Consensus 42 mDL~tI~~kl~~~~Y~s~~~f~~D~~li~ 70 (98)
T cd05513 42 MDFSTMKEKIKNNDYQSIEEFKDDFKLMC 70 (98)
T ss_pred cCHHHHHHHHhCCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999886
No 104
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=38.42 E-value=46 Score=21.60 Aligned_cols=30 Identities=17% Similarity=0.222 Sum_probs=26.2
Q ss_pred cccCHHHHHHHcCCCHHHHHHHHHhcCCee
Q 029202 131 STISTQDTALFLGMNEDDAAYYVQQQGWTL 160 (197)
Q Consensus 131 ~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~ 160 (197)
.-.++.++|..||++..-+-.+...-||.-
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~~W~~ 41 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRYKWDE 41 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhhCccc
Confidence 356789999999999888999999889975
No 105
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=38.24 E-value=1.1e+02 Score=22.07 Aligned_cols=54 Identities=22% Similarity=0.338 Sum_probs=34.2
Q ss_pred CCC--HHHHHHHHHhcCCeecCCCceEeecCCCC-------CCC-----C--CC-ChHHHHHHHHHHHhhc
Q 029202 143 GMN--EDDAAYYVQQQGWTLDPASRMLTVKKQPL-------VTE-----Q--KL-DPSKLQRLTEYVFHLE 196 (197)
Q Consensus 143 gls--~~e~~~~~~~~GW~~d~~~~~~~P~~~~~-------~~~-----~--~~-~~~qL~~LT~~v~fLE 196 (197)
|+. ++-+....++.||++...|..++-.-|.- +.. . .. ++..|+-+-.|+-|||
T Consensus 9 Gf~~~~dri~~~l~e~g~~v~~eGD~ivas~pgis~ieik~E~kkL~v~t~~~~~d~~~l~~~ktyndfle 79 (96)
T COG4004 9 GFKPDPDRIMRGLSELGWTVSEEGDRIVASSPGISRIEIKPENKKLLVNTTDYTDDETKLQTAKTYNDFLE 79 (96)
T ss_pred CCCCCHHHHHHHHHHhCeeEeecccEEEEecCCceEEEEecccceEEEecccccCchhHHHHHHHHHHHHH
Confidence 563 57788889999999988887654332220 111 0 11 4677777777777776
No 106
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=38.24 E-value=1.1e+02 Score=19.63 Aligned_cols=38 Identities=24% Similarity=0.267 Sum_probs=27.3
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCC-CHHHHHHHHHhc-CCee
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGM-NEDDAAYYVQQQ-GWTL 160 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgl-s~~e~~~~~~~~-GW~~ 160 (197)
++...+... .++++++|..+|+ +...+....++. |.+.
T Consensus 41 ~a~~~l~~~--~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~sp 80 (84)
T smart00342 41 RARRLLRDT--DLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80 (84)
T ss_pred HHHHHHHcC--CCCHHHHHHHhCCCChHHHHHHHHHHHCcCh
Confidence 344455443 7999999999999 788887776553 6553
No 107
>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=38.20 E-value=84 Score=19.56 Aligned_cols=40 Identities=15% Similarity=0.233 Sum_probs=27.6
Q ss_pred HHHHHHHHhhcc-cCHHHHHHHcCCCHH---HHHHHHHhcCCee
Q 029202 121 RMFQLLLSAYST-ISTQDTALFLGMNED---DAAYYVQQQGWTL 160 (197)
Q Consensus 121 ~i~~lis~AY~s-Is~~~~a~~Lgls~~---e~~~~~~~~GW~~ 160 (197)
+++..|...=.. ++..+++..+|++.. .+++-..++||-.
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 444455554443 899999999999864 4555566789976
No 108
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=37.76 E-value=1.3e+02 Score=20.61 Aligned_cols=42 Identities=5% Similarity=0.107 Sum_probs=30.6
Q ss_pred HHHHHHHHH-HHHhhcccCHHHHHHHcC-CCH---HHHHHHHHhcCC
Q 029202 117 LYTKRMFQL-LLSAYSTISTQDTALFLG-MNE---DDAAYYVQQQGW 158 (197)
Q Consensus 117 ~iR~~i~~l-is~AY~sIs~~~~a~~Lg-ls~---~e~~~~~~~~GW 158 (197)
.+|+.|+.. ..+.-..++.+++.+.+. .+. .-+-+|....||
T Consensus 37 ~iRn~il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~FL~~~G~ 83 (86)
T PF04433_consen 37 KIRNTILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYDFLERWGL 83 (86)
T ss_dssp HHHHHHHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHHHHHHcCc
Confidence 467788877 677888899999999998 665 446778888898
No 109
>PRK12454 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed
Probab=37.20 E-value=69 Score=28.15 Aligned_cols=30 Identities=20% Similarity=0.543 Sum_probs=21.9
Q ss_pred CCHHHHHHHHHhcCCeecCC-C---ceEeecCCC
Q 029202 144 MNEDDAAYYVQQQGWTLDPA-S---RMLTVKKQP 173 (197)
Q Consensus 144 ls~~e~~~~~~~~GW~~d~~-~---~~~~P~~~~ 173 (197)
++++|+.+..+++||++-+| | +.++|.|.+
T Consensus 136 y~~~~a~~~~~~~g~~~~~d~g~g~RrvV~SP~P 169 (313)
T PRK12454 136 YDEEEAKKLAKEKGWIVKEDAGRGWRRVVPSPDP 169 (313)
T ss_pred cCHHHHHHHHHHcCCEEEEcCCCceEEEeCCCCC
Confidence 46899999999999999766 3 245555543
No 110
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=36.93 E-value=51 Score=29.00 Aligned_cols=37 Identities=16% Similarity=0.248 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHhhcc----cCHHHHHHHcCCCHHHHHHHH
Q 029202 116 ELYTKRMFQLLLSAYST----ISTQDTALFLGMNEDDAAYYV 153 (197)
Q Consensus 116 ~~iR~~i~~lis~AY~s----Is~~~~a~~Lgls~~e~~~~~ 153 (197)
..-|++.+.+|.+ |.. -.++.+.++||++++|..+.+
T Consensus 302 ~itReeal~~v~~-~d~~~~~~~~~~~~~~lg~t~~ef~~~~ 342 (343)
T TIGR03573 302 RITREEAIELVKE-YDGEFPKEDLEYFLKYLGISEEEFWKTV 342 (343)
T ss_pred CCCHHHHHHHHHH-hcccccHHHHHHHHHHhCCCHHHHHHHh
Confidence 3458999999999 765 457889999999999987654
No 111
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=36.91 E-value=64 Score=20.74 Aligned_cols=48 Identities=13% Similarity=0.147 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHhhccc-CHHHHHHHcCCCH---HHHHHHHHhcCCeec
Q 029202 114 FSELYTKRMFQLLLSAYSTI-STQDTALFLGMNE---DDAAYYVQQQGWTLD 161 (197)
Q Consensus 114 l~~~iR~~i~~lis~AY~sI-s~~~~a~~Lgls~---~e~~~~~~~~GW~~d 161 (197)
+.+.+++.|...--+.=+.+ +..++++.+|+|. -++.....+.||-.-
T Consensus 5 i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 5 IYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIER 56 (64)
T ss_dssp HHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEE
Confidence 34445555554444444688 9999999999985 556666777898753
No 112
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=36.37 E-value=2.3e+02 Score=23.73 Aligned_cols=54 Identities=9% Similarity=0.064 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHH---HHHhcCCeecCCCceEeecC
Q 029202 117 LYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAY---YVQQQGWTLDPASRMLTVKK 171 (197)
Q Consensus 117 ~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~d~~~~~~~P~~ 171 (197)
.-|++|..++ +....+++.++++.||+|..-+.. ...++|--.-.-|+.+.|..
T Consensus 5 ~R~~~Il~~l-~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~~GGa~~~~~ 61 (252)
T PRK10906 5 QRHDAIIELV-KQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRHHGGAALPSS 61 (252)
T ss_pred HHHHHHHHHH-HHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCEEecCC
Confidence 3466777777 678999999999999999876544 34557876554566665543
No 113
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=35.98 E-value=2.6e+02 Score=24.73 Aligned_cols=98 Identities=8% Similarity=0.080 Sum_probs=61.0
Q ss_pred HHHHccccHHHHHHHHhHHhhhhhhCCCcCCCc------chHHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHH
Q 029202 7 TDALASKSYEKIADICDDLMLKVAAEGIVFQDE------WPYVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAW 80 (197)
Q Consensus 7 ~~~~~~~~~~~l~~~~e~~El~~~~~g~~~~~~------~py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~ 80 (197)
+.++..|++++....++.++=.. ..+++. ..|..++....-+.|.....-.|+.+|...+. +|.+....
T Consensus 195 ~~~~~~gdw~~a~~~l~~l~k~~----~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~-~~~~~~~~ 269 (398)
T PRK10747 195 QAYIRTGAWSSLLDILPSMAKAH----VGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRH-QVALQVAM 269 (398)
T ss_pred HHHHHHHhHHHHHHHHHHHHHcC----CCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhC-CHHHHHHH
Confidence 45677788888887777777441 111222 11333455555567888999999999998874 57766443
Q ss_pred HHHHHHHcCChHHHHHHhhC---CCCcHHHHHH
Q 029202 81 KIGQHLWTRDYAGVYDAIRG---FDWSQEAQAL 110 (197)
Q Consensus 81 ~l~~~L~~~~y~~v~~~l~~---~~ws~~~~~~ 110 (197)
. ...+..|++.+....+.. ..|.+.+..+
T Consensus 270 A-~~l~~~g~~~~A~~~L~~~l~~~~~~~l~~l 301 (398)
T PRK10747 270 A-EHLIECDDHDTAQQIILDGLKRQYDERLVLL 301 (398)
T ss_pred H-HHHHHCCCHHHHHHHHHHHHhcCCCHHHHHH
Confidence 3 345667788886665543 2555544433
No 114
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=35.72 E-value=56 Score=20.98 Aligned_cols=21 Identities=19% Similarity=0.382 Sum_probs=18.7
Q ss_pred CHHHHHHHcCCCHHHHHHHHH
Q 029202 134 STQDTALFLGMNEDDAAYYVQ 154 (197)
Q Consensus 134 s~~~~a~~Lgls~~e~~~~~~ 154 (197)
++.++|+++|++...+..+..
T Consensus 2 s~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999998865
No 115
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=35.47 E-value=1e+02 Score=18.61 Aligned_cols=35 Identities=20% Similarity=0.172 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHH
Q 029202 117 LYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQ 154 (197)
Q Consensus 117 ~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~ 154 (197)
.++..|+.++... .+..++|..+|+|..-+.....
T Consensus 15 ~~~~~i~~~~~~~---~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 15 RLEQYILKLLRES---RSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHHHhhc---CCHHHHHHHHCCCHHHHHHHHH
Confidence 3344444444433 7999999999999877766543
No 116
>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=34.67 E-value=22 Score=25.31 Aligned_cols=29 Identities=31% Similarity=0.627 Sum_probs=27.6
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||++.|++=+..|.|..+.+.+.+..+-.
T Consensus 41 mdL~tI~~kl~~~~Y~s~~ef~~D~~li~ 69 (97)
T cd05503 41 MDFSTIREKLESGQYKTLEEFAEDVRLVF 69 (97)
T ss_pred CCHHHHHHHHccCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999986
No 117
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=34.46 E-value=39 Score=21.52 Aligned_cols=21 Identities=29% Similarity=0.455 Sum_probs=17.5
Q ss_pred HHcCCCHHHHHHHHHhcCCee
Q 029202 140 LFLGMNEDDAAYYVQQQGWTL 160 (197)
Q Consensus 140 ~~Lgls~~e~~~~~~~~GW~~ 160 (197)
.+.|++.+++.+.+++.||++
T Consensus 5 d~~g~~~~~a~~~l~~~g~~~ 25 (63)
T PF03793_consen 5 DLVGMTYDEAKSILEAAGLTV 25 (63)
T ss_dssp TTTTSBHHHHHHHHHHTT-EE
T ss_pred CcCCCcHHHHHHHHHHCCCEE
Confidence 467999999999999999965
No 118
>KOG3614 consensus Ca2+/Mg2+-permeable cation channels (LTRPC family) [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=34.20 E-value=2.9e+02 Score=29.20 Aligned_cols=85 Identities=20% Similarity=0.298 Sum_probs=59.6
Q ss_pred chHHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCChHHHHHHhhCC--CCcHHHHHHHHHHHHH
Q 029202 40 WPYVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRDYAGVYDAIRGF--DWSQEAQALVAAFSEL 117 (197)
Q Consensus 40 ~py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~--~ws~~~~~~i~~l~~~ 117 (197)
-||..+|+=-+++|+-.=|+++|..=.+.+. +++.. .++|+++... +| ..+..-...+.+.
T Consensus 561 yP~~dLlIWAvL~~R~~MA~~~W~~gee~~A------kALvA----------~rLykslA~ea~d~-~~~s~el~~~s~~ 623 (1381)
T KOG3614|consen 561 YPIRDLLIWAVLLNRQGMAKCLWAHGEEAVA------KALVA----------SRLYKSLAHEAHDW-HEAAKELKTLSDE 623 (1381)
T ss_pred ccHHHHHHHHHHhccHHHHHHHHHhchhHHH------HHHHH----------HHHHHHHhhhcchh-hHHHHHHHHHHHH
Confidence 5899999999999999999999998543332 22222 2444444431 22 3456666788999
Q ss_pred HHHHHHHHHHHhhcccCHHHHHHHc
Q 029202 118 YTKRMFQLLLSAYSTISTQDTALFL 142 (197)
Q Consensus 118 iR~~i~~lis~AY~sIs~~~~a~~L 142 (197)
+++....+...+|++= -+.+.++|
T Consensus 624 f~~lAveLfd~cy~~d-e~~A~~LL 647 (1381)
T KOG3614|consen 624 FEGLAVELFDECYSSD-EARALQLL 647 (1381)
T ss_pred HHHHHHHHHHHHhcCC-HHHHHHHH
Confidence 9999999999999874 34444444
No 119
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=34.09 E-value=1.8e+02 Score=24.36 Aligned_cols=56 Identities=16% Similarity=0.241 Sum_probs=40.5
Q ss_pred HHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHH---HHHhcCCeecCCCceEeecCCCCC
Q 029202 119 TKRMFQLLLSAYSTISTQDTALFLGMNEDDAAY---YVQQQGWTLDPASRMLTVKKQPLV 175 (197)
Q Consensus 119 R~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~d~~~~~~~P~~~~~~ 175 (197)
|++|++++.+ -.++++++++..||.|+.=+.. ...++|=-.---|+...|......
T Consensus 7 ~~~Il~~l~~-~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~hGGa~~~~~~~~~ 65 (253)
T COG1349 7 HQKILELLKE-KGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVHGGAVLPDSESEY 65 (253)
T ss_pred HHHHHHHHHH-cCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEeCCEecCCCcccc
Confidence 5677777776 7899999999999999865433 334466665555778777766543
No 120
>cd05505 Bromo_WSTF_like Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=33.67 E-value=24 Score=25.33 Aligned_cols=29 Identities=24% Similarity=0.471 Sum_probs=27.6
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||++-|+.-+..|.|..+-+.+.+..|-.
T Consensus 41 mDL~tI~~kl~~~~Y~s~~ef~~D~~li~ 69 (97)
T cd05505 41 MDLQTMQTKCSCGSYSSVQEFLDDMKLVF 69 (97)
T ss_pred CCHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999986
No 121
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=33.56 E-value=1.2e+02 Score=23.31 Aligned_cols=96 Identities=11% Similarity=0.063 Sum_probs=57.2
Q ss_pred HHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCChHHHHHHhhCCCCcHHHHHHHHH-HHHHHHHHHHHHHHHhhcccCHH
Q 029202 58 ARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRDYAGVYDAIRGFDWSQEAQALVAA-FSELYTKRMFQLLLSAYSTISTQ 136 (197)
Q Consensus 58 ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~-l~~~iR~~i~~lis~AY~sIs~~ 136 (197)
.|.+-|||-. +..+..+.++- |...++++==..|+..+.+..+-+.+..++.. ....||++++.+|..=+.+..
T Consensus 39 ~ral~KRl~~--~n~~v~l~AL~-LLe~~vkNCG~~fh~evask~Fl~eL~kl~~~~~~~~Vk~kil~li~~W~~~f~-- 113 (144)
T cd03568 39 LKAIMKRLNH--KDPNVQLRALT-LLDACAENCGKRFHQEVASRDFTQELKKLINDRVHPTVKEKLREVVKQWADEFK-- 113 (144)
T ss_pred HHHHHHHHcC--CCHHHHHHHHH-HHHHHHHHCCHHHHHHHhhHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHhC--
Confidence 4666677642 22334455544 44555555556677776664555555555555 677899999998876544433
Q ss_pred HHHHHcCCC-HHHHHHHHHhcCCeec
Q 029202 137 DTALFLGMN-EDDAAYYVQQQGWTLD 161 (197)
Q Consensus 137 ~~a~~Lgls-~~e~~~~~~~~GW~~d 161 (197)
..-+++ -.++-+..+.+|..+-
T Consensus 114 ---~~~~l~~i~~~y~~L~~~G~~f~ 136 (144)
T cd03568 114 ---NDPSLSLMSDLYKKLKNEGPDLV 136 (144)
T ss_pred ---CCcccHHHHHHHHHHHHcCCCCC
Confidence 111232 3566677777888873
No 122
>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=33.54 E-value=1.1e+02 Score=21.53 Aligned_cols=33 Identities=12% Similarity=0.165 Sum_probs=25.9
Q ss_pred hhcccCHHHHHHHcCCCHH---HHHHHHHhcCCeec
Q 029202 129 AYSTISTQDTALFLGMNED---DAAYYVQQQGWTLD 161 (197)
Q Consensus 129 AY~sIs~~~~a~~Lgls~~---e~~~~~~~~GW~~d 161 (197)
.-..|+..++|+++|++.+ .+++-..++||-.-
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r 79 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFR 79 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 4678899999999999864 44555667899884
No 123
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=33.44 E-value=3.7e+02 Score=24.37 Aligned_cols=98 Identities=11% Similarity=0.165 Sum_probs=62.2
Q ss_pred hhcHHHHHHHHHHHHHHcCChHHHHHHhhCCCCc----HHHHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCH
Q 029202 71 DSRAEVVAAWKIGQHLWTRDYAGVYDAIRGFDWS----QEAQALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNE 146 (197)
Q Consensus 71 ~~~~~l~~~~~l~~~L~~~~y~~v~~~l~~~~ws----~~~~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~ 146 (197)
-..+-|..+-++.++--+|+...|=.++..+..- +-+..=...|-++.=+.=+.-|=-=|+.+.++++|+.+||+.
T Consensus 280 y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~hIA~~IGl~~ 359 (411)
T KOG1463|consen 280 YAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEISHIAEVIGLDV 359 (411)
T ss_pred ccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHHHHHHHHCCCc
Confidence 3467788899999999999888887777664211 112222234444444443444445799999999999999996
Q ss_pred HHH----HHHHHhc--CCeecCCCceEe
Q 029202 147 DDA----AYYVQQQ--GWTLDPASRMLT 168 (197)
Q Consensus 147 ~e~----~~~~~~~--GW~~d~~~~~~~ 168 (197)
..+ .+.+-.+ -=++|..+++++
T Consensus 360 ~~VEkKLsqMILDKkf~G~LDQg~g~Li 387 (411)
T KOG1463|consen 360 PQVEKKLSQMILDKKFYGTLDQGEGCLI 387 (411)
T ss_pred HHHHHHHHHHHHHHHhhcccccCCCeEE
Confidence 554 3444332 335665555544
No 124
>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=33.34 E-value=25 Score=25.14 Aligned_cols=29 Identities=24% Similarity=0.489 Sum_probs=27.3
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||++.|+.-+..|.|..+.+.+.+..+-.
T Consensus 46 mdl~~I~~kl~~~~Y~s~~ef~~D~~li~ 74 (102)
T cd05498 46 MDLSTIKKKLDNREYADAQEFAADVRLMF 74 (102)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999885
No 125
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=33.20 E-value=79 Score=26.29 Aligned_cols=44 Identities=14% Similarity=0.182 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHH
Q 029202 107 AQALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYY 152 (197)
Q Consensus 107 ~~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~ 152 (197)
...+++.+-...|++|++++++-= -.+...+.++|+++..+.+.
T Consensus 5 ~~~ildvLGNetRR~Il~lLt~~p--~yvsEiS~~lgvsqkAVl~H 48 (217)
T COG1777 5 IDKILDVLGNETRRRILQLLTRRP--CYVSEISRELGVSQKAVLKH 48 (217)
T ss_pred HHHHHHHHcCcHHHHHHHHHhcCc--hHHHHHHhhcCcCHHHHHHH
Confidence 456788888999999999998754 45667889999998776655
No 126
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=33.09 E-value=2.5e+02 Score=22.24 Aligned_cols=49 Identities=14% Similarity=0.185 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCH---HHHHHHHHhcCCee
Q 029202 112 AAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNE---DDAAYYVQQQGWTL 160 (197)
Q Consensus 112 ~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~---~e~~~~~~~~GW~~ 160 (197)
+.+.+.+|++|...-=+.=..|+..++|+.||+|- -|+.......|+-.
T Consensus 14 ~~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~ 65 (212)
T TIGR03338 14 TLVQDEIERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVR 65 (212)
T ss_pred HHHHHHHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEE
Confidence 45667888888887666777889999999999984 56666677789864
No 127
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=32.83 E-value=89 Score=25.83 Aligned_cols=48 Identities=15% Similarity=0.307 Sum_probs=39.2
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHHHHHHHhhcCHHHHHH
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIHLLGYYYVNDINSARF 60 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~Ll~~L~~ndl~~ar~ 60 (197)
||=+.|.++..+|+.+++..+||.-=+. + |.+||=.-++.+++....+
T Consensus 134 idGs~V~~~y~~g~i~~I~~YCe~DVl~----------T--~~lylR~~~~~G~l~~~~y 181 (209)
T PF10108_consen 134 IDGSQVAELYQEGDIDEIREYCEKDVLN----------T--YLLYLRFELLRGRLSPEDY 181 (209)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHH----------H--HHHHHHHHHhhCCCCHHHH
Confidence 4567899999999999999999987766 4 7888888888888776433
No 128
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=32.74 E-value=1e+02 Score=19.44 Aligned_cols=27 Identities=22% Similarity=0.224 Sum_probs=19.7
Q ss_pred HHHHhhcccCHHHHHHHcCCCHHHHHH
Q 029202 125 LLLSAYSTISTQDTALFLGMNEDDAAY 151 (197)
Q Consensus 125 lis~AY~sIs~~~~a~~Lgls~~e~~~ 151 (197)
+-..-...||-.++|.++|+++.++.+
T Consensus 21 l~~~G~~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 21 LKEEGVERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp HHHTT-SEE-HHHHHHHHTS-HHHHHH
T ss_pred HHHcCCeeECHHHHHHHHCCCHHHhcc
Confidence 344466799999999999999988865
No 129
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=32.27 E-value=94 Score=18.63 Aligned_cols=35 Identities=17% Similarity=0.245 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHH
Q 029202 117 LYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQ 154 (197)
Q Consensus 117 ~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~ 154 (197)
..|.+++.+... -.+..++|..||+|..-+..+.+
T Consensus 5 ~~R~~ii~l~~~---G~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 5 ERRAQIIRLLRE---GWSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp -----HHHHHHH---T--HHHHHHHHTS-HHHHHHHHT
T ss_pred hHHHHHHHHHHC---CCCHHHHHHHHCcCHHHHHHHHH
Confidence 345566666665 88999999999999988877765
No 130
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=32.08 E-value=52 Score=17.03 Aligned_cols=26 Identities=15% Similarity=0.304 Sum_probs=21.8
Q ss_pred HHHHHHHHHhhcCHHHHHHHHhcCCh
Q 029202 42 YVIHLLGYYYVNDINSARFLWKSIPS 67 (197)
Q Consensus 42 y~~~Ll~~L~~ndl~~ar~l~kRiP~ 67 (197)
|...+-.|--.+++..|.-++++++.
T Consensus 3 y~~li~~~~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 3 YNSLISGYCKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HHHHHHHHHccchHHHHHHHHHHHhH
Confidence 67788888888999999999888764
No 131
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=32.04 E-value=1.8e+02 Score=26.92 Aligned_cols=55 Identities=11% Similarity=0.193 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHhcCCeecCCCceEe
Q 029202 114 FSELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLT 168 (197)
Q Consensus 114 l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~ 168 (197)
+..--+..++..+.+.-.+|++++++...|+..+|++...+..|=-.--.|+.++
T Consensus 356 Y~~YW~~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l~~l~~~kg~~~i 410 (450)
T PLN00104 356 YRGYWTRVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSLNLIQYRKGQHVI 410 (450)
T ss_pred HHHHHHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCCCEEecCCcEEE
Confidence 4445556666666666679999999999999999999999988743322355444
No 132
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=32.03 E-value=1.1e+02 Score=24.48 Aligned_cols=43 Identities=12% Similarity=0.136 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHH---HHhcCCeec
Q 029202 118 YTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYY---VQQQGWTLD 161 (197)
Q Consensus 118 iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~d 161 (197)
.|++|+..+.+. ..++..++|..||++..-+... ..+.||-..
T Consensus 2 tr~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r 47 (203)
T TIGR02702 2 TKEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKDLETEGLIEY 47 (203)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 478889888764 7799999999999997655444 445799863
No 133
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=32.02 E-value=5.1e+02 Score=26.19 Aligned_cols=88 Identities=10% Similarity=0.077 Sum_probs=62.8
Q ss_pred HHccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHHHHH-----
Q 029202 9 ALASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAWKIG----- 83 (197)
Q Consensus 9 ~~~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~----- 83 (197)
++-.+++++-...|+...-+. +.....+...+++..--++.+.+|+..|+.+.+.--.-.+..+.+.-..|...
T Consensus 468 al~~~~~e~a~~lar~al~~L-~~~~~~~r~~~~sv~~~a~~~~G~~~~Al~~~~~a~~~a~~~~~~~l~~~~~~~~s~i 546 (894)
T COG2909 468 ALNRGDPEEAEDLARLALVQL-PEAAYRSRIVALSVLGEAAHIRGELTQALALMQQAEQMARQHDVYHLALWSLLQQSEI 546 (894)
T ss_pred HHhcCCHHHHHHHHHHHHHhc-ccccchhhhhhhhhhhHHHHHhchHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHH
Confidence 355678889889998888774 44444455566788888899999999999999987666666677766666544
Q ss_pred --------HHHHcCChHHHHHH
Q 029202 84 --------QHLWTRDYAGVYDA 97 (197)
Q Consensus 84 --------~~L~~~~y~~v~~~ 97 (197)
+.-+++.|+.++..
T Consensus 547 l~~qGq~~~a~~~~~~~~~~~q 568 (894)
T COG2909 547 LEAQGQVARAEQEKAFNLIREQ 568 (894)
T ss_pred HHHhhHHHHHHHHHHHHHHHHH
Confidence 44555555555543
No 134
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=31.94 E-value=1.4e+02 Score=21.43 Aligned_cols=37 Identities=11% Similarity=0.163 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh
Q 029202 119 TKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 119 R~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 155 (197)
|++..-...-.|--|+.+++..--|||++|+..+...
T Consensus 36 ~RKAaVV~aV~~Glis~~EA~~rY~Ls~eEf~~W~~a 72 (90)
T PF06627_consen 36 RRKAAVVRAVRGGLISVEEACRRYGLSEEEFESWQRA 72 (90)
T ss_dssp HHHHHHHHHHHCTTS-HHHHHHCTTSSHHHHHHHHHH
T ss_pred hHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 4555555566788999999999999999999988653
No 135
>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT). MAT alpha 1 is a transcription activator that activates mating-type alpha-specific genes with the help of the MADS-box containing MCM1 transcription factor, which together bind cooperatively to PQ elements upstream of alpha-specific genes. The MCM1-MATalpha1 complex is required for the proper DNA-bending that is needed for transcriptional activation []. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (IPR006742 from INTERPRO) response pathway [].; GO: 0000772 mating pheromone activity, 0003677 DNA binding, 0045895 positive regulation of transcription, mating-type specific, 0005634 nucleus
Probab=31.65 E-value=2.3e+02 Score=23.25 Aligned_cols=29 Identities=21% Similarity=0.480 Sum_probs=16.8
Q ss_pred HHHcCCCHHHHHHHHHhcCCeecCC--CceEee
Q 029202 139 ALFLGMNEDDAAYYVQQQGWTLDPA--SRMLTV 169 (197)
Q Consensus 139 a~~Lgls~~e~~~~~~~~GW~~d~~--~~~~~P 169 (197)
+.++|+-+ -..|....||++..+ |....-
T Consensus 116 ~p~~gi~~--p~~YL~~~Gw~l~~~~~g~~~l~ 146 (201)
T PF04769_consen 116 CPLIGIIP--PEDYLEQLGWQLSQNEEGTITLE 146 (201)
T ss_pred hhhcCCCC--HHHHHHHcCCeEeeCCCCCEEEE
Confidence 34445532 235777889999554 555443
No 136
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=31.52 E-value=1.6e+02 Score=19.44 Aligned_cols=25 Identities=16% Similarity=0.174 Sum_probs=18.4
Q ss_pred hcccCHHHHHHHcCCCHHHHHHHHH
Q 029202 130 YSTISTQDTALFLGMNEDDAAYYVQ 154 (197)
Q Consensus 130 Y~sIs~~~~a~~Lgls~~e~~~~~~ 154 (197)
=+.-+...+|..||++.+++.....
T Consensus 18 gr~Pt~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 18 GREPTDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp SS--BHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCHHHHHHHHcccHHHHHHHHH
Confidence 3677889999999999988877754
No 137
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=31.47 E-value=1e+02 Score=18.59 Aligned_cols=27 Identities=22% Similarity=0.484 Sum_probs=21.3
Q ss_pred cCHHHHHHHcCCCHHHHHHHHHhcCCee
Q 029202 133 ISTQDTALFLGMNEDDAAYYVQQQGWTL 160 (197)
Q Consensus 133 Is~~~~a~~Lgls~~e~~~~~~~~GW~~ 160 (197)
-|+.++|++||++..-+...+.. |+..
T Consensus 18 ~S~~eAa~~lg~~~~~I~~~~~~-~~~~ 44 (53)
T smart00497 18 SSIREAAKYLGISHSSISKYLNT-GKKF 44 (53)
T ss_pred cCHHHHHHHhCCCHHHHHHHHhC-CCcc
Confidence 37889999999998888777764 5554
No 138
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=31.38 E-value=2.8e+02 Score=22.31 Aligned_cols=23 Identities=17% Similarity=0.156 Sum_probs=17.8
Q ss_pred cccCHHHHHHHcCCCHHHHHHHH
Q 029202 131 STISTQDTALFLGMNEDDAAYYV 153 (197)
Q Consensus 131 ~sIs~~~~a~~Lgls~~e~~~~~ 153 (197)
...+...+|..||++.+++....
T Consensus 98 ~~~~~~ela~~l~~~~~~v~~~~ 120 (224)
T TIGR02479 98 REPTEEEIAEELGMDLKEYRQAL 120 (224)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 34567789999999988877764
No 139
>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=31.35 E-value=28 Score=25.43 Aligned_cols=30 Identities=17% Similarity=0.337 Sum_probs=28.2
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKVA 30 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~~ 30 (197)
||++-|+.=+..+.|..+.+++.+..|-..
T Consensus 41 MDL~tI~~kL~~~~Y~s~~ef~~D~~Lif~ 70 (102)
T cd05501 41 MWLNKVKERLNERVYHTVEGFVRDMRLIFH 70 (102)
T ss_pred CCHHHHHHHHcCCCCCCHHHHHHHHHHHHH
Confidence 999999999999999999999999999863
No 140
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=30.76 E-value=75 Score=20.47 Aligned_cols=22 Identities=14% Similarity=0.474 Sum_probs=18.8
Q ss_pred CHHHHHHHcCCCHHHHHHHHHh
Q 029202 134 STQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 134 s~~~~a~~Lgls~~e~~~~~~~ 155 (197)
++.++|+++|++..-+..+..+
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 6789999999999988877654
No 141
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=30.66 E-value=1.5e+02 Score=21.83 Aligned_cols=36 Identities=8% Similarity=0.094 Sum_probs=25.3
Q ss_pred HHHHHHHHHhh-cccCHHHHHHHcCCCHHHHHHHHHh
Q 029202 120 KRMFQLLLSAY-STISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 120 ~~i~~lis~AY-~sIs~~~~a~~Lgls~~e~~~~~~~ 155 (197)
.++...|...| ..++++++|+.+|+++.-+....++
T Consensus 12 ~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 12 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 35556666666 5689999999999998666554443
No 142
>PRK13239 alkylmercury lyase; Provisional
Probab=30.60 E-value=2.1e+02 Score=23.63 Aligned_cols=51 Identities=16% Similarity=0.180 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHhc-CCeecCCCceEe
Q 029202 117 LYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQQ-GWTLDPASRMLT 168 (197)
Q Consensus 117 ~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~~-GW~~d~~~~~~~ 168 (197)
.++..+++++. -=+.++++++|+-+|.+.+++.+..++. .=.+|++|+++-
T Consensus 22 ~~~~~llr~la-~G~pvt~~~lA~~~~~~~~~v~~~L~~l~~~~~d~~g~iv~ 73 (206)
T PRK13239 22 TLLVPLLRLLA-KGRPVSVTTLAAALGWPVEEVEAVLEAMPDTEYDEDGRIIG 73 (206)
T ss_pred HHHHHHHHHHH-cCCCCCHHHHHHHhCCCHHHHHHHHHhCCCeEECCCCCEEe
Confidence 46666777777 5578999999999999999999988875 456788887753
No 143
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=30.57 E-value=40 Score=19.16 Aligned_cols=21 Identities=10% Similarity=0.287 Sum_probs=17.5
Q ss_pred cCCCHHHHHHHHHhcCCeecC
Q 029202 142 LGMNEDDAAYYVQQQGWTLDP 162 (197)
Q Consensus 142 Lgls~~e~~~~~~~~GW~~d~ 162 (197)
+|++.+++.......||.++.
T Consensus 11 mGf~~~~a~~aL~~~~~d~~~ 31 (37)
T smart00165 11 MGFSREEALKALRAANGNVER 31 (37)
T ss_pred cCCCHHHHHHHHHHhCCCHHH
Confidence 389999999999999997653
No 144
>cd05520 Bromo_polybromo_III Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=30.49 E-value=28 Score=25.21 Aligned_cols=29 Identities=21% Similarity=0.421 Sum_probs=27.6
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
|||+.|+.=+..+.|..+.+.+.+.+|-.
T Consensus 47 mdL~tI~~kl~~~~Y~s~~~f~~D~~lm~ 75 (103)
T cd05520 47 ISLQQIRTKLKNGEYETLEELEADLNLMF 75 (103)
T ss_pred cCHHHHHHHHccCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999986
No 145
>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=30.37 E-value=36 Score=25.14 Aligned_cols=30 Identities=17% Similarity=0.440 Sum_probs=28.2
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKVA 30 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~~ 30 (197)
||++-|+.=|..|.|..+.+...+..|-..
T Consensus 47 mDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~ 76 (109)
T cd05492 47 LDVADIQEKINSEKYTSLEEFKADALLLLH 76 (109)
T ss_pred CcHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 899999999999999999999999998863
No 146
>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=30.06 E-value=29 Score=25.13 Aligned_cols=30 Identities=20% Similarity=0.389 Sum_probs=28.0
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKVA 30 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~~ 30 (197)
||++-|+.=+.+|.|..+-++..+..|-..
T Consensus 44 mDL~tI~~kl~~~~Y~s~~ef~~D~~li~~ 73 (104)
T cd05507 44 MDLSTIKKNIENGTIRSTAEFQRDVLLMFQ 73 (104)
T ss_pred cCHHHHHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 899999999999999999999999999863
No 147
>cd05506 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=29.98 E-value=29 Score=24.54 Aligned_cols=29 Identities=21% Similarity=0.405 Sum_probs=27.2
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
|||+.|+.-+..+.|..+.+...+..+-.
T Consensus 43 ~dl~tI~~kL~~~~Y~s~~ef~~D~~li~ 71 (99)
T cd05506 43 MDLGTVKKKLEKGEYSSPEEFAADVRLTF 71 (99)
T ss_pred CCHHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999885
No 148
>PRK09411 carbamate kinase; Reviewed
Probab=29.95 E-value=1.1e+02 Score=26.70 Aligned_cols=41 Identities=17% Similarity=0.362 Sum_probs=25.1
Q ss_pred CHHHHHHHHHhcCCeecCCCc---eEeecCCCCCCCCCCChHHHHHH
Q 029202 145 NEDDAAYYVQQQGWTLDPASR---MLTVKKQPLVTEQKLDPSKLQRL 188 (197)
Q Consensus 145 s~~e~~~~~~~~GW~~d~~~~---~~~P~~~~~~~~~~~~~~qL~~L 188 (197)
+++++.+...++||++-.+|+ .++|.|.+.. .++.+-|..|
T Consensus 129 ~~e~a~~l~~e~g~~~~~dg~g~rrVVpSP~P~~---iVe~~~I~~L 172 (297)
T PRK09411 129 QPEEQEALEAAYGWQMKRDGKYLRRVVASPQPRK---ILDSEAIELL 172 (297)
T ss_pred CHHHHHHHHHhcCCEEEecCCceEEEccCCCCcc---eECHHHHHHH
Confidence 578888888899998866653 3445543322 2244555444
No 149
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=29.80 E-value=54 Score=17.19 Aligned_cols=19 Identities=16% Similarity=0.067 Sum_probs=14.8
Q ss_pred HHHHHhhcCHHHHHHHHhc
Q 029202 46 LLGYYYVNDINSARFLWKS 64 (197)
Q Consensus 46 Ll~~L~~ndl~~ar~l~kR 64 (197)
=..|+-++|..+|+.+++|
T Consensus 8 a~~~~~~G~~~eA~~~l~~ 26 (26)
T PF07721_consen 8 ARALLAQGDPDEAERLLRR 26 (26)
T ss_pred HHHHHHcCCHHHHHHHHhC
Confidence 3456778999999988875
No 150
>cd05516 Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=29.68 E-value=30 Score=25.17 Aligned_cols=29 Identities=24% Similarity=0.580 Sum_probs=27.4
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||++.|+.=+..|.|..+.+++.+..|-.
T Consensus 48 mdl~tI~~kl~~~~Y~s~~ef~~D~~li~ 76 (107)
T cd05516 48 VDFKKIKERIRNHKYRSLEDLEKDVMLLC 76 (107)
T ss_pred CCHHHHHHHHccCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999886
No 151
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=29.30 E-value=1.4e+02 Score=18.41 Aligned_cols=34 Identities=9% Similarity=0.285 Sum_probs=25.0
Q ss_pred cCHHHHHHHcCCC-HHHHHHHHHhcCCee--cCCCce
Q 029202 133 ISTQDTALFLGMN-EDDAAYYVQQQGWTL--DPASRM 166 (197)
Q Consensus 133 Is~~~~a~~Lgls-~~e~~~~~~~~GW~~--d~~~~~ 166 (197)
++.+++..+.|.. ...-+++..+.||.+ +++|..
T Consensus 3 LT~~El~elTG~k~~~~Q~~~L~~~Gi~~~~~~~G~p 39 (47)
T PF13986_consen 3 LTDEELQELTGYKRPSKQIRWLRRNGIPFVVRADGRP 39 (47)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHCCCeeEECCCCCE
Confidence 5678888899986 666777888889987 344533
No 152
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=29.20 E-value=81 Score=20.41 Aligned_cols=52 Identities=13% Similarity=0.258 Sum_probs=33.9
Q ss_pred CHHHHHHHcCCCHHHHHHHHHhcCCeecCCCceEeecCCCCCCCCCC-ChHHHHHHHHHHHhh
Q 029202 134 STQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKLQRLTEYVFHL 195 (197)
Q Consensus 134 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~P~~~~~~~~~~~-~~~qL~~LT~~v~fL 195 (197)
++.++|+++|++..-+..+..+. +.+.|... ...-.. +.+++.+|-....+.
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~~~--------gl~~~~r~--~~g~R~yt~~di~~l~~i~~l~ 54 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWEREF--------GLLKPQRS--DGGHRLFNDADIDRILEIKRWI 54 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhc--------CCCCCCcC--CCCCcccCHHHHHHHHHHHHHH
Confidence 67899999999999998775432 23334322 222223 888888887766554
No 153
>PF13518 HTH_28: Helix-turn-helix domain
Probab=29.19 E-value=1.3e+02 Score=17.89 Aligned_cols=34 Identities=15% Similarity=0.288 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh
Q 029202 119 TKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 119 R~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 155 (197)
|.+++.++.. .-++..+|.-+|+|..-+..++..
T Consensus 2 r~~iv~~~~~---g~s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 2 RLQIVELYLE---GESVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred HHHHHHHHHc---CCCHHHHHHHHCCCHhHHHHHHHH
Confidence 4556666654 349999999999998888777653
No 154
>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=29.14 E-value=88 Score=17.92 Aligned_cols=17 Identities=29% Similarity=0.612 Sum_probs=11.4
Q ss_pred cCHHHHHHHcCCCHHHH
Q 029202 133 ISTQDTALFLGMNEDDA 149 (197)
Q Consensus 133 Is~~~~a~~Lgls~~e~ 149 (197)
++-.++|.++|++.+-+
T Consensus 3 mtr~diA~~lG~t~ETV 19 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETV 19 (32)
T ss_dssp --HHHHHHHHTS-HHHH
T ss_pred cCHHHHHHHhCCcHHHH
Confidence 56788999999996544
No 155
>cd05518 Bromo_polybromo_IV Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=29.11 E-value=32 Score=24.95 Aligned_cols=29 Identities=17% Similarity=0.442 Sum_probs=27.4
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
|||+.|+.-|..+.|..+.+.+.+.+|-.
T Consensus 47 mdl~tI~~kl~~~~Y~s~~ef~~D~~li~ 75 (103)
T cd05518 47 IDLKTIEHNIRNDKYATEEELMDDFKLMF 75 (103)
T ss_pred cCHHHHHHHHCCCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999886
No 156
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=29.07 E-value=2.3e+02 Score=23.65 Aligned_cols=24 Identities=21% Similarity=0.144 Sum_probs=19.0
Q ss_pred hcccCHHHHHHHcCCCHHHHHHHH
Q 029202 130 YSTISTQDTALFLGMNEDDAAYYV 153 (197)
Q Consensus 130 Y~sIs~~~~a~~Lgls~~e~~~~~ 153 (197)
-...+.+.+|..+|++.+++.+..
T Consensus 132 ~~~pt~~eia~~lg~~~~~v~~~~ 155 (268)
T PRK06288 132 GRTPSDEEIADELGISLEEYNSLL 155 (268)
T ss_pred CCCCCHHHHHHHcCCCHHHHHHHH
Confidence 345678899999999988876654
No 157
>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=29.03 E-value=31 Score=25.19 Aligned_cols=29 Identities=28% Similarity=0.419 Sum_probs=27.5
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||++.|+.=+..|.|..+.+.+.+..|-.
T Consensus 47 mDL~tI~~kL~~~~Y~s~~ef~~D~~li~ 75 (108)
T cd05495 47 MDLSTIRRKLDTGQYQDPWQYVDDVWLMF 75 (108)
T ss_pred CCHHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999986
No 158
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=28.99 E-value=2.2e+02 Score=20.37 Aligned_cols=49 Identities=10% Similarity=0.169 Sum_probs=30.9
Q ss_pred chHHHHHHHHHhhcC---HHHHHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCC
Q 029202 40 WPYVIHLLGYYYVND---INSARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRD 90 (197)
Q Consensus 40 ~py~~~Ll~~L~~nd---l~~ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~ 90 (197)
|++-..++-+...+. -.-++++|+||... ..+..++++.-|...+-+|.
T Consensus 18 ~~~i~~i~d~~~~~~~~~~~~~~~l~kRl~~~--~~~~~lkaL~lLe~lvkN~g 69 (115)
T cd00197 18 WPLIMEICDLINETNVGPKEAVDAIKKRINNK--NPHVVLKALTLLEYCVKNCG 69 (115)
T ss_pred HHHHHHHHHHHHCCCccHHHHHHHHHHHhcCC--cHHHHHHHHHHHHHHHHHcc
Confidence 555555666554431 23578999999754 33455777777776666664
No 159
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.
Probab=28.76 E-value=6.2e+02 Score=25.55 Aligned_cols=119 Identities=16% Similarity=0.165 Sum_probs=84.0
Q ss_pred ccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCC
Q 029202 11 ASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRD 90 (197)
Q Consensus 11 ~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~ 90 (197)
+..+...++..++.+-+. |+... ++ -+.||.+.-+...|..| +-+..+ +.....+|.|.-.+..|+
T Consensus 432 ~~~~~~rv~~~L~Al~~~--Pe~~~-~~---~~~yL~Lr~a~~rL~~a-----~~~~~l---~~v~~~LW~lAl~iEdG~ 497 (851)
T TIGR02302 432 DANQNSQVYDALDALLLA--PEETI-PN---AGHYLGLYTIRTRLERA-----RTDDAL---RDVADNLWSLALGIEDGD 497 (851)
T ss_pred CccccHHHHHHHHHHHhC--ccccc-CC---HHHHHHHHHHHHHHHhc-----CCHHHH---HHHHHHHHHHHHHhhcCC
Confidence 445667777777777665 34432 33 47888888887777776 222222 356788999999999999
Q ss_pred hHHHHHHhhC-----------CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhc--------------ccCHHHHHHHcC
Q 029202 91 YAGVYDAIRG-----------FDWSQEAQALVAAFSELYTKRMFQLLLSAYS--------------TISTQDTALFLG 143 (197)
Q Consensus 91 y~~v~~~l~~-----------~~ws~~~~~~i~~l~~~iR~~i~~lis~AY~--------------sIs~~~~a~~Lg 143 (197)
-+..-..++. ...-++++.+|+.|++++.+-+-.+-.++=. +++-+++..|+.
T Consensus 498 ls~A~~~Lr~AQ~aL~eAL~~gAsdeEI~~Lm~eLR~Am~~ym~~LAeq~~~~~~~~~~~~~~~~~~l~~~dLq~Mmd 575 (851)
T TIGR02302 498 LSDAERRLRAAQDALKDALERGASDEEIKQLTDKLRAAMQTYMRQLAQQLRNNPQQLARPLDPNTKVLRQQDLQNMMD 575 (851)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCcccccccCCccccccCHHHHHHHHH
Confidence 9987665543 3455789999999998888877776665554 377788888875
No 160
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=28.64 E-value=2.9e+02 Score=23.32 Aligned_cols=80 Identities=16% Similarity=0.163 Sum_probs=44.7
Q ss_pred HccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHHHH--HHHhhcCHHHHHHHHhcC----ChhhhhhcHHHHHHHHHH
Q 029202 10 LASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIHLL--GYYYVNDINSARFLWKSI----PSTIKDSRAEVVAAWKIG 83 (197)
Q Consensus 10 ~~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~Ll--~~L~~ndl~~ar~l~kRi----P~~~~~~~~~l~~~~~l~ 83 (197)
+..|+|++-+..++..--. -|++... |.+.|.+ +|+-++|...|...++++ |.+-+.. ..+++++
T Consensus 154 ~~~~~y~~Ai~af~~fl~~-yP~s~~a----~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~----dAl~klg 224 (263)
T PRK10803 154 QDKSRQDDAIVAFQNFVKK-YPDSTYQ----PNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAA----DAMFKVG 224 (263)
T ss_pred HhcCCHHHHHHHHHHHHHH-CcCCcch----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchh----HHHHHHH
Confidence 4567888777777665544 3444322 2344433 445668888888777766 4433332 2333444
Q ss_pred HHH-HcCChHHHHHHh
Q 029202 84 QHL-WTRDYAGVYDAI 98 (197)
Q Consensus 84 ~~L-~~~~y~~v~~~l 98 (197)
... ..|++.+.-..+
T Consensus 225 ~~~~~~g~~~~A~~~~ 240 (263)
T PRK10803 225 VIMQDKGDTAKAKAVY 240 (263)
T ss_pred HHHHHcCCHHHHHHHH
Confidence 444 456776654444
No 161
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=28.53 E-value=74 Score=20.53 Aligned_cols=24 Identities=21% Similarity=0.137 Sum_probs=19.6
Q ss_pred HHHHHHHcCCCHHHHHHHHHhcCC
Q 029202 135 TQDTALFLGMNEDDAAYYVQQQGW 158 (197)
Q Consensus 135 ~~~~a~~Lgls~~e~~~~~~~~GW 158 (197)
+...++-||++++++...+..-|=
T Consensus 23 v~ywa~~~gvt~~~L~~AV~~vG~ 46 (57)
T PF12244_consen 23 VRYWAKRFGVTEEQLREAVRAVGN 46 (57)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHCc
Confidence 456788999999999998887763
No 162
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=28.07 E-value=1.4e+02 Score=28.73 Aligned_cols=72 Identities=17% Similarity=0.191 Sum_probs=46.9
Q ss_pred HHHhHHhhhhhhCCCcCCC-cchHHHHH-----HHHHhhcCHHHHHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCChHH
Q 029202 20 DICDDLMLKVAAEGIVFQD-EWPYVIHL-----LGYYYVNDINSARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRDYAG 93 (197)
Q Consensus 20 ~~~e~~El~~~~~g~~~~~-~~py~~~L-----l~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~y~~ 93 (197)
..+|.+++- +..-+++.+ ..||+-.+ +..|=..++.++||+++-.. |..|-.+-..|+.+|+.=++.
T Consensus 438 r~~eaL~~G-avPviLg~~~~LPyqd~idWrraal~lPkaR~tE~HFllrs~~------dsDll~mRRqGRl~wEtYls~ 510 (907)
T KOG2264|consen 438 RFLEALQLG-AVPVILGNSQLLPYQDLIDWRRAALRLPKARLTEAHFLLRSFE------DSDLLEMRRQGRLFWETYLSD 510 (907)
T ss_pred HHHHHHhcC-CeeEEeccccccchHHHHHHHHHhhhCCccccchHHHHHHhcc------hhhHHHHHhhhhhhHHHHhhH
Confidence 345666655 333333322 37888773 55667799999999998764 455555668899999876655
Q ss_pred HHHHh
Q 029202 94 VYDAI 98 (197)
Q Consensus 94 v~~~l 98 (197)
.....
T Consensus 511 ~~~~~ 515 (907)
T KOG2264|consen 511 RHLLA 515 (907)
T ss_pred HHHHH
Confidence 54443
No 163
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=27.85 E-value=1.2e+02 Score=27.68 Aligned_cols=50 Identities=16% Similarity=0.129 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHhhcc-cCHHHHHHHcCCCHHHHHHHHHhcCCeecCCC
Q 029202 115 SELYTKRMFQLLLSAYST-ISTQDTALFLGMNEDDAAYYVQQQGWTLDPAS 164 (197)
Q Consensus 115 ~~~iR~~i~~lis~AY~s-Is~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~ 164 (197)
+.--+..++.++.+-=.+ |++++++...|+..+|++...+..||-.--.|
T Consensus 311 rsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~m~~y~k~ 361 (396)
T KOG2747|consen 311 RSYWRCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLNMIKYYKG 361 (396)
T ss_pred HHHHHHHHHHHHHhcCCCcccHHHHHHhhCCCHHHHHHHHHhhCCccccCC
Confidence 344455566655553322 99999999999999999999999888765343
No 164
>PHA02591 hypothetical protein; Provisional
Probab=27.81 E-value=83 Score=22.06 Aligned_cols=37 Identities=14% Similarity=0.231 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh
Q 029202 116 ELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 116 ~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 155 (197)
|..+.-.-.|.++- .+....|..||++.+.+.++..+
T Consensus 46 dd~~~vA~eL~eqG---lSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 46 DDLISVTHELARKG---FTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred chHHHHHHHHHHcC---CCHHHHHHHhCCCHHHHHHHHhc
Confidence 34444444555554 46889999999999999988764
No 165
>PF06262 DUF1025: Possibl zinc metallo-peptidase; InterPro: IPR010428 This is a family of bacterial protein with undetermined function.; PDB: 3E11_A.
Probab=27.81 E-value=42 Score=24.25 Aligned_cols=17 Identities=18% Similarity=0.434 Sum_probs=11.9
Q ss_pred HHHHHHHcCCCHHHHHH
Q 029202 135 TQDTALFLGMNEDDAAY 151 (197)
Q Consensus 135 ~~~~a~~Lgls~~e~~~ 151 (197)
+..+|.++|++++++..
T Consensus 78 vhEiah~fG~~~e~l~~ 94 (97)
T PF06262_consen 78 VHEIAHHFGISDEDLDA 94 (97)
T ss_dssp HHHHHHHTT--HHHHHC
T ss_pred HHHHHHHcCCCHHHhhh
Confidence 46778999999998764
No 166
>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=27.52 E-value=36 Score=24.39 Aligned_cols=29 Identities=34% Similarity=0.592 Sum_probs=27.4
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||++.|+.=+..+.|..+.+.+.+..|-.
T Consensus 42 mDL~tI~~kl~~~~Y~s~~ef~~D~~li~ 70 (98)
T cd05512 42 MDFSTMRKKLESQRYRTLEDFEADFNLII 70 (98)
T ss_pred cCHHHHHHHHhCCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999885
No 167
>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=27.50 E-value=34 Score=24.33 Aligned_cols=29 Identities=28% Similarity=0.480 Sum_probs=27.2
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||++.|+.-+..+.|..+.++..+..+-.
T Consensus 42 mdL~tI~~kl~~~~Y~s~~~f~~Dv~li~ 70 (101)
T cd05509 42 MDLSTMEEKLENGYYVTLEEFVADLKLIF 70 (101)
T ss_pred CCHHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999885
No 168
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=27.39 E-value=1.7e+02 Score=22.65 Aligned_cols=56 Identities=20% Similarity=0.201 Sum_probs=40.6
Q ss_pred hHHHHHccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHHHH--HHHhhcCHHHHHHHHhcC
Q 029202 5 PLTDALASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIHLL--GYYYVNDINSARFLWKSI 65 (197)
Q Consensus 5 ~i~~~~~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~Ll--~~L~~ndl~~ar~l~kRi 65 (197)
+=++++.+|+|++-+..+|+++-. =|.|...+. +++-+ +|.-+++...|....+|.
T Consensus 16 ~a~~~l~~~~Y~~A~~~le~L~~r-yP~g~ya~q----AqL~l~yayy~~~~y~~A~a~~~rF 73 (142)
T PF13512_consen 16 EAQEALQKGNYEEAIKQLEALDTR-YPFGEYAEQ----AQLDLAYAYYKQGDYEEAIAAYDRF 73 (142)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHhc-CCCCcccHH----HHHHHHHHHHHccCHHHHHHHHHHH
Confidence 346789999999999999999987 356665443 33433 455678888888777764
No 169
>PF12046 DUF3529: Protein of unknown function (DUF3529); InterPro: IPR021919 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 176 to 190 amino acids in length.
Probab=27.32 E-value=90 Score=25.09 Aligned_cols=26 Identities=12% Similarity=0.312 Sum_probs=20.1
Q ss_pred HHHHHHHHhcCCeecC---CCceEeecCC
Q 029202 147 DDAAYYVQQQGWTLDP---ASRMLTVKKQ 172 (197)
Q Consensus 147 ~e~~~~~~~~GW~~d~---~~~~~~P~~~ 172 (197)
+++.+|.++|||++.+ +++.+...-.
T Consensus 47 ~~l~~yf~~r~y~v~~~d~~~~~itFeG~ 75 (173)
T PF12046_consen 47 EQLKAYFEQRNYRVAEGDAEGEVITFEGF 75 (173)
T ss_pred HHHHHHHHhcCceecccCccccEEEEEEE
Confidence 5788999999999965 6777766543
No 170
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=27.17 E-value=2.7e+02 Score=23.29 Aligned_cols=50 Identities=8% Similarity=0.131 Sum_probs=33.6
Q ss_pred HHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHH---HHhcCCeecCCCceEee
Q 029202 119 TKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYY---VQQQGWTLDPASRMLTV 169 (197)
Q Consensus 119 R~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~d~~~~~~~P 169 (197)
|++|+.++.+ ...++++++|+.||+|+.=+..- ..++|--.-.-|+.+.+
T Consensus 7 ~~~Il~~L~~-~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~Gga~~~ 59 (256)
T PRK10434 7 QAAILEYLQK-QGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTYGGVVLN 59 (256)
T ss_pred HHHHHHHHHH-cCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEEcC
Confidence 5566666655 78899999999999997544332 34567654444666543
No 171
>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=27.13 E-value=36 Score=24.50 Aligned_cols=30 Identities=23% Similarity=0.317 Sum_probs=28.1
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKVA 30 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~~ 30 (197)
||++-|+.=+..|.|..+-++..+..|-..
T Consensus 43 mDL~tI~~kl~~~~Y~s~~ef~~Dv~LI~~ 72 (99)
T cd05508 43 MDLSTLEKNVRKKAYGSTDAFLADAKWILH 72 (99)
T ss_pred CCHHHHHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 899999999999999999999999999863
No 172
>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=27.11 E-value=35 Score=25.22 Aligned_cols=29 Identities=21% Similarity=0.413 Sum_probs=27.2
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
|||+.|+.-+..|.|..+.+++.+..|-.
T Consensus 53 mDL~tI~~kL~~~~Y~s~~~f~~Dv~LI~ 81 (115)
T cd05504 53 MDLGTIKEKLNMGEYKLAEEFLSDIQLVF 81 (115)
T ss_pred ccHHHHHHHHccCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999885
No 173
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=26.95 E-value=1.2e+02 Score=19.94 Aligned_cols=42 Identities=19% Similarity=0.392 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh---cCCee
Q 029202 119 TKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ---QGWTL 160 (197)
Q Consensus 119 R~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~---~GW~~ 160 (197)
.++|+.-|......++..++|.-+|+|.-.+..+... .|.-.
T Consensus 2 ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 2 KEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred cHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 3567777888899999999999999999888777553 46543
No 174
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=26.84 E-value=1.9e+02 Score=22.77 Aligned_cols=44 Identities=16% Similarity=0.188 Sum_probs=33.3
Q ss_pred HhhcccCHHHHHHHcCCCHHHHHHHHHhcCCee--cCCCceEeecC
Q 029202 128 SAYSTISTQDTALFLGMNEDDAAYYVQQQGWTL--DPASRMLTVKK 171 (197)
Q Consensus 128 ~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~--d~~~~~~~P~~ 171 (197)
..=..++.+++|+++|++++.+.+.-+++-=++ |..|+++-.+.
T Consensus 94 ~~~~~l~~dElA~sF~l~~e~i~qLr~~kiltVh~De~G~Ii~V~~ 139 (153)
T PRK14584 94 GHRPDLDDDELASSFALSPELIAQLKSGSCLTLYNDEHGHIIDVKE 139 (153)
T ss_pred CCCCCCChHHHHHHcCCCHHHHHHHHhCCeEEEEECCCCCEEEeec
Confidence 344678999999999999999988877665555 65676665544
No 175
>cd05519 Bromo_SNF2 Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=26.77 E-value=36 Score=24.42 Aligned_cols=29 Identities=10% Similarity=0.442 Sum_probs=27.4
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||++.|+.=|..+.|..+.+.+.+..+-.
T Consensus 47 mdl~~I~~kl~~~~Y~s~~~f~~D~~li~ 75 (103)
T cd05519 47 IALDQIKRRIEGRAYKSLEEFLEDFHLMF 75 (103)
T ss_pred cCHHHHHHHHccCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999886
No 176
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=26.73 E-value=68 Score=18.25 Aligned_cols=19 Identities=5% Similarity=0.170 Sum_probs=16.5
Q ss_pred CCCHHHHHHHHHhcCCeec
Q 029202 143 GMNEDDAAYYVQQQGWTLD 161 (197)
Q Consensus 143 gls~~e~~~~~~~~GW~~d 161 (197)
.|+.+++.++|.++|+...
T Consensus 3 ~l~~~~Lk~~l~~~gl~~~ 21 (35)
T smart00513 3 KLKVSELKDELKKRGLSTS 21 (35)
T ss_pred cCcHHHHHHHHHHcCCCCC
Confidence 4678999999999999975
No 177
>PF11193 DUF2812: Protein of unknown function (DUF2812); InterPro: IPR021359 This is a bacterial family of uncharacterised proteins, however some members of this family are annotated as membrane proteins.
Probab=26.61 E-value=2.1e+02 Score=20.55 Aligned_cols=44 Identities=11% Similarity=0.211 Sum_probs=28.6
Q ss_pred HHHHHHHHhcCCeec-C-CCceEeecCCCCCCCCCC---ChHHHHHHHH
Q 029202 147 DDAAYYVQQQGWTLD-P-ASRMLTVKKQPLVTEQKL---DPSKLQRLTE 190 (197)
Q Consensus 147 ~e~~~~~~~~GW~~d-~-~~~~~~P~~~~~~~~~~~---~~~qL~~LT~ 190 (197)
++-.+++++.||++= . .+...+..++.......+ .+.+++.+.+
T Consensus 54 ~~y~~~~e~~GW~~v~~~~~~~~if~~~~~~~~~~i~tD~~~~~~~~~~ 102 (115)
T PF11193_consen 54 KEYLEFFEEAGWEYVYSNFGGWQIFRKEEDDGPPEIYTDPESKIEMYKR 102 (115)
T ss_pred HHHHHHHHHCCCEEEeccCcEEEEEEEcCCCCCCCCcCCHHHHHHHHHH
Confidence 567888999999986 3 566777777665554333 4444444433
No 178
>PRK13500 transcriptional activator RhaR; Provisional
Probab=26.61 E-value=1.6e+02 Score=25.20 Aligned_cols=41 Identities=15% Similarity=0.123 Sum_probs=31.6
Q ss_pred HHHHHHHHHhhc-ccCHHHHHHHcCCCHHHHHHHHHhc-CCee
Q 029202 120 KRMFQLLLSAYS-TISTQDTALFLGMNEDDAAYYVQQQ-GWTL 160 (197)
Q Consensus 120 ~~i~~lis~AY~-sIs~~~~a~~Lgls~~e~~~~~~~~-GW~~ 160 (197)
.++.+.|..-|. .++++++|..+|+|+.-+....++. |=+.
T Consensus 209 ~~i~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~tG~T~ 251 (312)
T PRK13500 209 DKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTI 251 (312)
T ss_pred HHHHHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH
Confidence 456667777766 5899999999999998887777764 5443
No 179
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=26.60 E-value=74 Score=20.87 Aligned_cols=32 Identities=19% Similarity=0.369 Sum_probs=25.4
Q ss_pred hhcccCHHHHHHHcCC---------CHHHHHHHHHhcCCee
Q 029202 129 AYSTISTQDTALFLGM---------NEDDAAYYVQQQGWTL 160 (197)
Q Consensus 129 AY~sIs~~~~a~~Lgl---------s~~e~~~~~~~~GW~~ 160 (197)
.|.-|.++++.++|.. +...+.+||.++|=++
T Consensus 21 ~YePI~L~el~~~L~~~g~~~~~~~~~~~l~~~lD~~gIt~ 61 (64)
T PF09494_consen 21 MYEPINLEELHAWLKASGIGFDRKVDPSKLKEWLDSQGITF 61 (64)
T ss_pred cCCCccHHHHHHHHHHcCCCccceeCHHHHHHHHHHCCcee
Confidence 5889999999988862 4578999999888544
No 180
>PF13551 HTH_29: Winged helix-turn helix
Probab=26.55 E-value=1.5e+02 Score=20.53 Aligned_cols=33 Identities=18% Similarity=0.324 Sum_probs=22.6
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 155 (197)
+++.++..--+ ++..+|..+|++..=+..+.+.
T Consensus 3 ~~l~l~~~g~~--~~~~ia~~lg~s~~Tv~r~~~~ 35 (112)
T PF13551_consen 3 QILLLLAEGVS--TIAEIARRLGISRRTVYRWLKR 35 (112)
T ss_pred HHHHHHHcCCC--cHHHHHHHHCcCHHHHHHHHHH
Confidence 34444433333 5999999999998877777653
No 181
>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=26.48 E-value=37 Score=24.76 Aligned_cols=29 Identities=17% Similarity=0.292 Sum_probs=27.4
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||++.|+.=+..+.|..+-++..+.+|-.
T Consensus 48 mDL~tI~~kL~~~~Y~s~~ef~~D~~li~ 76 (107)
T cd05497 48 MDLGTIKKRLENNYYWSASECIQDFNTMF 76 (107)
T ss_pred ccHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999886
No 182
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=26.25 E-value=2.2e+02 Score=19.78 Aligned_cols=37 Identities=16% Similarity=0.244 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHhhcc-cCHHHHHHHcCCCHHHHHHHHH
Q 029202 117 LYTKRMFQLLLSAYST-ISTQDTALFLGMNEDDAAYYVQ 154 (197)
Q Consensus 117 ~iR~~i~~lis~AY~s-Is~~~~a~~Lgls~~e~~~~~~ 154 (197)
.++ ++...|...|.. ++++++|..+|+|..-+.....
T Consensus 21 ~~~-~~~~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~ 58 (127)
T COG2207 21 RLA-RALDYIEENLAEPLTLEDLARRLGMSRRTLSRLFK 58 (127)
T ss_pred HHH-HHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344 555555555554 8999999999999877766554
No 183
>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=25.66 E-value=38 Score=24.97 Aligned_cols=30 Identities=30% Similarity=0.433 Sum_probs=27.9
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKVA 30 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~~ 30 (197)
||++.|+.-+..+.|..+.++..+..|-..
T Consensus 49 mdL~tI~~kl~~~~Y~s~~ef~~D~~Li~~ 78 (112)
T cd05510 49 MDLGTMLKKLKNLQYKSKAEFVDDLNLIWK 78 (112)
T ss_pred cCHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Confidence 899999999999999999999999998863
No 184
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=25.23 E-value=48 Score=21.99 Aligned_cols=18 Identities=22% Similarity=0.394 Sum_probs=15.1
Q ss_pred HHHHHHHHhcCCeecCCC
Q 029202 147 DDAAYYVQQQGWTLDPAS 164 (197)
Q Consensus 147 ~e~~~~~~~~GW~~d~~~ 164 (197)
..+..+|.++||+++..|
T Consensus 13 r~lR~~A~~~g~~L~~~G 30 (64)
T PF14791_consen 13 RDLRQYAKKKGMKLSEYG 30 (64)
T ss_dssp HHHHHHHHHTTEEEESSE
T ss_pred HHHHHHHHHcCCeeCccc
Confidence 468889999999999655
No 185
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=24.84 E-value=3.6e+02 Score=21.53 Aligned_cols=53 Identities=4% Similarity=-0.105 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCH---HHHHHHHHhcCCee
Q 029202 108 QALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNE---DDAAYYVQQQGWTL 160 (197)
Q Consensus 108 ~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~---~e~~~~~~~~GW~~ 160 (197)
.++.+..-+.+|++|+..-=+.=..|+..++++.||+|- =|+.......|.-.
T Consensus 6 ~~~~~~vy~~i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~ 61 (224)
T PRK11534 6 QITALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVT 61 (224)
T ss_pred HhhhHHHHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 345667778888888887777778999999999999984 56666677778864
No 186
>PRK13501 transcriptional activator RhaR; Provisional
Probab=24.73 E-value=1.8e+02 Score=24.38 Aligned_cols=40 Identities=15% Similarity=0.153 Sum_probs=29.8
Q ss_pred HHHHHHHHhhcc-cCHHHHHHHcCCCHHHHHHHHHhc-CCee
Q 029202 121 RMFQLLLSAYST-ISTQDTALFLGMNEDDAAYYVQQQ-GWTL 160 (197)
Q Consensus 121 ~i~~lis~AY~s-Is~~~~a~~Lgls~~e~~~~~~~~-GW~~ 160 (197)
++.+.|..-|.. |+++++|..+|+|+.-+....++. |-+.
T Consensus 180 ~i~~~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~G~T~ 221 (290)
T PRK13501 180 LIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSI 221 (290)
T ss_pred HHHHHHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH
Confidence 455566666655 899999999999998887776653 6665
No 187
>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=24.67 E-value=41 Score=24.31 Aligned_cols=29 Identities=31% Similarity=0.511 Sum_probs=27.2
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||++.|+.-+..+.|..+.+++.+..|-.
T Consensus 47 mdL~tI~~kl~~~~Y~s~~~f~~D~~lm~ 75 (103)
T cd05517 47 IDLKTIAQRIQSGYYKSIEDMEKDLDLMV 75 (103)
T ss_pred cCHHHHHHHHCcCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999885
No 188
>PF10116 Host_attach: Protein required for attachment to host cells; InterPro: IPR019291 Members of this family of bacterial proteins are required for the attachment of the bacterium to host cells [, ].
Probab=24.55 E-value=74 Score=23.91 Aligned_cols=58 Identities=9% Similarity=0.062 Sum_probs=43.8
Q ss_pred HHHHHHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHc
Q 029202 81 KIGQHLWTRDYAGVYDAIRGFDWSQEAQALVAAFSELYTKRMFQLLLSAYSTISTQDTALFL 142 (197)
Q Consensus 81 ~l~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~L 142 (197)
.|.+..-++.|.+++-. ..+.-+-.+.+.|...++..+..-|.+-++..+..++.+.|
T Consensus 81 ~L~~~~~~~~~~~Lvlv----A~p~~LG~LR~~L~~~~~~~V~~ei~kDlt~~~~~ei~~~l 138 (138)
T PF10116_consen 81 RLEKARRAGKFDRLVLV----APPRFLGLLREHLSKAVRKRVVGEIDKDLTKLPADEIEKHL 138 (138)
T ss_pred HHHHHHHhCCCCeEEEE----ECHHHHHHHHHHhCHHHHHHHHHHHhhhhhcCCHHHHHhhC
Confidence 44455556666664443 23466778888899999999999999999999999887654
No 189
>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=24.51 E-value=1.2e+02 Score=18.67 Aligned_cols=38 Identities=16% Similarity=0.287 Sum_probs=26.4
Q ss_pred HHHHHHHhhcccCHHHHHHHcCCCHHH---HHHHHHhcCCee
Q 029202 122 MFQLLLSAYSTISTQDTALFLGMNEDD---AAYYVQQQGWTL 160 (197)
Q Consensus 122 i~~lis~AY~sIs~~~~a~~Lgls~~e---~~~~~~~~GW~~ 160 (197)
++.++. .+..++..++|..+|++..- +.+-..++||-.
T Consensus 8 iL~~l~-~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~ 48 (59)
T PF01047_consen 8 ILRILY-ENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIE 48 (59)
T ss_dssp HHHHHH-HHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHH-HcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEE
Confidence 344443 46779999999999999654 455555689975
No 190
>cd05525 Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=24.45 E-value=42 Score=24.46 Aligned_cols=29 Identities=14% Similarity=0.287 Sum_probs=27.3
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
|||+.|+.=|..|.|..+-+++.+.+|-.
T Consensus 49 ~dL~tI~~kl~~~~Y~s~~ef~~D~~l~f 77 (106)
T cd05525 49 VDLSTIEKQILTGYYKTPEAFDSDMLKVF 77 (106)
T ss_pred cCHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999886
No 191
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=24.44 E-value=2.3e+02 Score=20.33 Aligned_cols=44 Identities=9% Similarity=0.231 Sum_probs=26.0
Q ss_pred HHHHHHHHhcCCeecCCCceEeecCCCCCCCCCCChHHHHHHHHHHH
Q 029202 147 DDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKLQRLTEYVF 193 (197)
Q Consensus 147 ~e~~~~~~~~GW~~d~~~~~~~P~~~~~~~~~~~~~~qL~~LT~~v~ 193 (197)
+|+...+...||++- +.+ +.+...+.+..-.+.-+++.|.+.+.
T Consensus 11 ~El~~L~~t~g~~vv--~~~-~q~~~~~~p~~~iG~GK~eei~~~~~ 54 (95)
T PF13167_consen 11 EELEELAETAGYEVV--GTV-VQKRRKPDPKTYIGSGKVEEIKELIE 54 (95)
T ss_pred HHHHHHHHHCCCeEE--EEE-EecCCCCCcceeechhHHHHHHHHHh
Confidence 788888999999984 333 33332223323336666666666554
No 192
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=24.28 E-value=2.5e+02 Score=20.82 Aligned_cols=53 Identities=15% Similarity=0.174 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHH---HHHhcCCee
Q 029202 107 AQALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAY---YVQQQGWTL 160 (197)
Q Consensus 107 ~~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~ 160 (197)
...+...|.+..|.+|+.++... ...++.+++.-+|++..-+-. ..++.|+-.
T Consensus 6 ~~~~fkaLadptRl~IL~~L~~~-~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~ 61 (117)
T PRK10141 6 PLQLFKILSDETRLGIVLLLRES-GELCVCDLCTALDQSQPKISRHLALLRESGLLL 61 (117)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceE
Confidence 35667788889999999999753 368999999999999755544 455668875
No 193
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=24.13 E-value=2.2e+02 Score=18.71 Aligned_cols=26 Identities=15% Similarity=0.075 Sum_probs=18.2
Q ss_pred hcccCHHHHHHHcCCCHHHHHHHHHh
Q 029202 130 YSTISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 130 Y~sIs~~~~a~~Lgls~~e~~~~~~~ 155 (197)
-..-.-..+|..||++..++..+-.+
T Consensus 10 ~~~~~Wk~La~~Lg~~~~~i~~i~~~ 35 (83)
T PF00531_consen 10 DLGSDWKRLARKLGLSESEIENIEEE 35 (83)
T ss_dssp SHSTCHHHHHHHTTS-HHHHHHHHHH
T ss_pred cchhhHHHHHHHhCcCHHHHHHHHHh
Confidence 33445678899999998888777654
No 194
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=24.08 E-value=3e+02 Score=20.31 Aligned_cols=58 Identities=7% Similarity=0.022 Sum_probs=38.0
Q ss_pred chHHHHHccccHHHHHHHHhHHhhhhhhC-CCcCCCcchHHHHHHHHHhhcCHHHHHHHHh
Q 029202 4 SPLTDALASKSYEKIADICDDLMLKVAAE-GIVFQDEWPYVIHLLGYYYVNDINSARFLWK 63 (197)
Q Consensus 4 ~~i~~~~~~~~~~~l~~~~e~~El~~~~~-g~~~~~~~py~~~Ll~~L~~ndl~~ar~l~k 63 (197)
..|..+|..||++..+.+|++.--..-.. ..+.=.. +.+.++-++-.+|+.+|-..-+
T Consensus 6 ~~I~~~I~~g~i~~Ai~w~~~~~~~l~~~~~~L~f~L--~~q~fiell~~~~~~~Ai~y~r 64 (145)
T PF10607_consen 6 KKIRQAILNGDIDPAIEWLNENFPELLKRNSSLEFEL--RCQQFIELLREGDIMEAIEYAR 64 (145)
T ss_pred HHHHHHHHcCCHHHHHHHHHHcCHHHHhcCCchhHHH--HHHHHHHHHHHHhHHHHHHHHH
Confidence 47899999999999999999886443112 1211122 4555666667788887754333
No 195
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=24.03 E-value=4.8e+02 Score=22.61 Aligned_cols=53 Identities=17% Similarity=0.141 Sum_probs=39.1
Q ss_pred ccHHHHHHHHhHHhhhhhhCCCcCCCc---------chHHHHHHHHHhhcCHHHHHHHHhcCC
Q 029202 13 KSYEKIADICDDLMLKVAAEGIVFQDE---------WPYVIHLLGYYYVNDINSARFLWKSIP 66 (197)
Q Consensus 13 ~~~~~l~~~~e~~El~~~~~g~~~~~~---------~py~~~Ll~~L~~ndl~~ar~l~kRiP 66 (197)
+|...+.+.++.+.+- .++|.++.+. -+....|+-+++.+|...|+.+++++=
T Consensus 174 ~nl~~i~~Ei~KL~l~-~~~~~I~~~~V~~~v~~~~~~~~f~l~dail~g~~~~a~~~l~~L~ 235 (334)
T COG1466 174 GNLLAIAQEIEKLALY-AGDKEITLEDVEEVVSDVAEFNIFDLADALLKGDVKKALRLLRDLL 235 (334)
T ss_pred CcHHHHHHHHHHHHHh-CCCCcCCHHHHHHHHhccccCCHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 7888999999999988 4555443211 113455889999999999999998874
No 196
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=23.88 E-value=2.4e+02 Score=19.18 Aligned_cols=71 Identities=14% Similarity=0.163 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHH---hcCCeecCCCceEeecCCCC-CCCCC--CChHHHHHHHHH
Q 029202 118 YTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTLDPASRMLTVKKQPL-VTEQK--LDPSKLQRLTEY 191 (197)
Q Consensus 118 iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~d~~~~~~~P~~~~~-~~~~~--~~~~qL~~LT~~ 191 (197)
+|-.|+.++.. -..++.+++...||++..-+-+..+ +.|--- .-+.... -+... +++.-.+.+-+|
T Consensus 1 vRl~Il~~L~~-~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~-------~~k~~~~~~p~t~~~lT~~Gr~~~~~~ 72 (80)
T PF13601_consen 1 VRLAILALLYA-NEEATFSELKEELGLTDGNLSKHLKKLEEAGYVE-------VEKEFEGRRPRTWYSLTDKGREAFERY 72 (80)
T ss_dssp HHHHHHHHHHH-HSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEE-------EEEE-SSS--EEEEEE-HHHHHHHHHH
T ss_pred CHHHHHHHHhh-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEE-------EEEeccCCCCeEEEEECHHHHHHHHHH
Confidence 46666666665 5779999999999999866655544 334422 1111111 11111 277888888888
Q ss_pred HHhhc
Q 029202 192 VFHLE 196 (197)
Q Consensus 192 v~fLE 196 (197)
+.+|+
T Consensus 73 ~~~L~ 77 (80)
T PF13601_consen 73 VAALR 77 (80)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 87775
No 197
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=23.75 E-value=1.9e+02 Score=24.07 Aligned_cols=20 Identities=15% Similarity=0.087 Sum_probs=16.6
Q ss_pred cCHHHHHHHcCCCHHHHHHH
Q 029202 133 ISTQDTALFLGMNEDDAAYY 152 (197)
Q Consensus 133 Is~~~~a~~Lgls~~e~~~~ 152 (197)
-+...+|..||++.+++.+.
T Consensus 130 pt~~elA~~lgi~~~~v~~~ 149 (256)
T PRK07408 130 PTDQEIAQALDISLEEWQEI 149 (256)
T ss_pred CCHHHHHHHcCCCHHHHHHH
Confidence 35788999999999887765
No 198
>TIGR00400 mgtE Mg2+ transporter (mgtE). This family of prokaryotic proteins models a class of Mg++ transporter first described in Bacillus firmus. May form a homodimer.
Probab=23.74 E-value=2.4e+02 Score=25.76 Aligned_cols=100 Identities=11% Similarity=0.076 Sum_probs=47.3
Q ss_pred hHHHHHccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHHHHHHHhhcCHHHHHHHHhcCChhhhhh-----cHHHHHH
Q 029202 5 PLTDALASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIHLLGYYYVNDINSARFLWKSIPSTIKDS-----RAEVVAA 79 (197)
Q Consensus 5 ~i~~~~~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~-----~~~l~~~ 79 (197)
++.+++..++++.+...++++. | .=++-.|-+=+-.+...+|+.+|.+.... ++..+
T Consensus 10 ~~~~~~~~~~~~~l~~~l~~~~----------~------~dia~~l~~l~~~~~~~~~~~l~~~~~a~vl~~l~~~~~-- 71 (449)
T TIGR00400 10 RIRILLKEKSYSKIKEKFLKXQ----------P------XDIAEALKRLPGTELILLYRFLPKKIAVDTFSNLDQSTQ-- 71 (449)
T ss_pred HHHHHHHcCCHHHHHHHHhcCC----------H------HHHHHHHHhCCHHHHHHHHHhCChhhHHHHHHcCCHHHH--
Confidence 4556666777766655554321 1 11233333334455555666665443221 22222
Q ss_pred HHHHHHHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHHHHHHHHHHH
Q 029202 80 WKIGQHLWTRDYAGVYDAIRGFDWSQEAQALVAAFSELYTKRMFQLL 126 (197)
Q Consensus 80 ~~l~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~iR~~i~~li 126 (197)
..+.+.+-...-..+... --+++...+++.+.+..+++++..+
T Consensus 72 ~~ll~~l~~~~~~~~~~~----l~~dd~~~ll~~l~~~~~~~lL~~l 114 (449)
T TIGR00400 72 NKLLNSFTNKEISEMINE----MNLDDVIDLLEEVPANVVQQLLASS 114 (449)
T ss_pred HHHHHhCCHHHHHHHHHc----CChhHHHHHHHhCCHHHHHHHHHcC
Confidence 122333333333333333 3336777777777777666666543
No 199
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=23.51 E-value=1.2e+02 Score=21.01 Aligned_cols=27 Identities=19% Similarity=0.169 Sum_probs=22.3
Q ss_pred cCHHHHHHHcCCCHHHHHHHHHhcCCee
Q 029202 133 ISTQDTALFLGMNEDDAAYYVQQQGWTL 160 (197)
Q Consensus 133 Is~~~~a~~Lgls~~e~~~~~~~~GW~~ 160 (197)
|++++++...|++++.+..++. .||--
T Consensus 1 is~~e~~~~~~i~~~~l~~lve-~Gli~ 27 (84)
T PF13591_consen 1 ISLEEFCEACGIEPEFLRELVE-EGLIE 27 (84)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-CCCee
Confidence 6889999999999988888765 67754
No 200
>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=23.44 E-value=2e+02 Score=23.78 Aligned_cols=40 Identities=18% Similarity=0.230 Sum_probs=29.8
Q ss_pred HHHHHHHHHhh-cccCHHHHHHHcCCCHHHHHHHHHh-cCCe
Q 029202 120 KRMFQLLLSAY-STISTQDTALFLGMNEDDAAYYVQQ-QGWT 159 (197)
Q Consensus 120 ~~i~~lis~AY-~sIs~~~~a~~Lgls~~e~~~~~~~-~GW~ 159 (197)
.++...|..-| ..++++++|+.+|+|..-+...+++ -|=+
T Consensus 189 ~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t 230 (287)
T TIGR02297 189 NRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSALS 230 (287)
T ss_pred HHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhCCC
Confidence 45566665555 6799999999999999888777665 3533
No 201
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=23.24 E-value=2.9e+02 Score=22.62 Aligned_cols=59 Identities=10% Similarity=0.131 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccc-CHHHHHHHcCCCH---HHHHHHHHhcCCee-cCCCceEe
Q 029202 110 LVAAFSELYTKRMFQLLLSAYSTI-STQDTALFLGMNE---DDAAYYVQQQGWTL-DPASRMLT 168 (197)
Q Consensus 110 ~i~~l~~~iR~~i~~lis~AY~sI-s~~~~a~~Lgls~---~e~~~~~~~~GW~~-d~~~~~~~ 168 (197)
+.+.+.+.+|+.|...-=+.=..| +..++|+.||+|- =|+.......|+-. .+.++.++
T Consensus 11 ~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V 74 (254)
T PRK09464 11 LSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFV 74 (254)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCceeEE
Confidence 345566677777766544444778 7999999999984 56666677789975 43444444
No 202
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=23.08 E-value=79 Score=26.43 Aligned_cols=42 Identities=21% Similarity=0.180 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHhhcccCHHHHHHHcCCCHH----HHHHHHHhcCCee
Q 029202 117 LYTKRMFQLLLSAYSTISTQDTALFLGMNED----DAAYYVQQQGWTL 160 (197)
Q Consensus 117 ~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~----e~~~~~~~~GW~~ 160 (197)
.=|++|++.+.+ +..+++++++++||+|++ |+.. .++.|...
T Consensus 7 eR~~~I~~~l~~-~~~v~v~eLa~~~~VS~~TIRRDL~~-Le~~~~~~ 52 (252)
T PRK10681 7 ERIGQLLQALKR-SDKLHLKDAAALLGVSEMTIRRDLNA-HSAPVVLL 52 (252)
T ss_pred HHHHHHHHHHHH-cCCCcHHHHHHHhCCCHHHHHHHHHH-hhcCeEEE
Confidence 335566666655 899999999999999974 4443 22456543
No 203
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=23.05 E-value=77 Score=22.59 Aligned_cols=34 Identities=21% Similarity=0.359 Sum_probs=22.1
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 155 (197)
+|++++.. ...++-+++|..+|++..++.+.+..
T Consensus 17 ~Il~~L~~-~~~l~de~la~~~~l~~~~vRkiL~~ 50 (105)
T PF02002_consen 17 RILDALLR-KGELTDEDLAKKLGLKPKEVRKILYK 50 (105)
T ss_dssp HHHHHHHH-H--B-HHHHHHTT-S-HHHHHHHHHH
T ss_pred HHHHHHHH-cCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 55555553 45688999999999999999888653
No 204
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=22.94 E-value=1.7e+02 Score=20.03 Aligned_cols=36 Identities=17% Similarity=0.116 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHH
Q 029202 119 TKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQ 154 (197)
Q Consensus 119 R~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~ 154 (197)
|+++-+++...----.-..+|.-||++..++..|-.
T Consensus 2 ~~~v~~ll~~~nlG~dW~~LA~~LG~~~~~I~~i~~ 37 (77)
T cd08311 2 QEEVEKLLESGRPGRDWRSLAGELGYEDEAIDTFGR 37 (77)
T ss_pred hHHHHHHHhCCCCccCHHHHHHHcCCCHHHHHHHHc
Confidence 445555554442223356799999999988888754
No 205
>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=22.92 E-value=86 Score=23.02 Aligned_cols=30 Identities=20% Similarity=0.514 Sum_probs=27.9
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKVA 30 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~~ 30 (197)
|||+-|+.=+..+.|..+.+++.+..|-..
T Consensus 49 mdl~tI~~kl~~~~Y~s~~~f~~D~~lm~~ 78 (113)
T cd05524 49 IDLLKIQQKLKTEEYDDVDDLTADFELLIN 78 (113)
T ss_pred cCHHHHHHHhCcCCCCCHHHHHHHHHHHHH
Confidence 899999999999999999999999999863
No 206
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.89 E-value=2.9e+02 Score=19.74 Aligned_cols=48 Identities=17% Similarity=0.200 Sum_probs=30.9
Q ss_pred CHHHHHHHcCCCHHHHHHHHHhcCCeecCCCceEeecCCCCCCCCCC-ChHHHHHHHH
Q 029202 134 STQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKLQRLTE 190 (197)
Q Consensus 134 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~P~~~~~~~~~~~-~~~qL~~LT~ 190 (197)
++.++|+.+|++..-+.-|.. . +++.|........-.. +++++.+|..
T Consensus 2 ~i~eva~~~gis~~tlR~ye~--------~-GLi~p~~~~~~ngyR~Y~~~~i~~l~~ 50 (108)
T cd01107 2 TIGEFAKLSNLSIKALRYYDK--------I-GLLKPAYVDPDTGYRYYSAEQLERLNR 50 (108)
T ss_pred CHHHHHHHHCcCHHHHHHHHH--------c-CCCCCCcCCCCCCccccCHHHHHHHHH
Confidence 678999999999998887765 2 3555533222222233 7777777653
No 207
>PF01709 Transcrip_reg: Transcriptional regulator; InterPro: IPR002876 This entry represents the core region of several hypothetical proteins found in bacteria, plants, and yeast proteins. This core region can be subdivided into three domains: a 3-helical bundle domain, and two alpha+beta domains with different folds, where domain 3 (ferredoxin-like fold) is inserted within domain 2. This core region is found in the following hypothetical proteins: YebC from Escherichia coli, HP0162 from Helicobacter pylori (Campylobacter pylori) and aq1575 from Aquifex aeolicus []. The crystal structure of a conserved hypothetical protein, Aq1575, from Aquifex aeolicus has been determined. A structural homology search reveals that this protein has a new fold with no obvious similarity to those of other proteins of known three-dimensional structure. The protein reveals a monomer consisting of three domains arranged along a pseudo threefold symmetry axis. There is a large cleft with approximate dimensions of 10 A x 10 A x 20 A in the centre of the three domains along the symmetry axis. Two possible active sites are suggested based on the structure and multiple sequence alignment. There are several highly conserved residues in these putative active sites [].; PDB: 1LFP_A 1MW7_A 1KON_A.
Probab=22.82 E-value=93 Score=26.02 Aligned_cols=44 Identities=11% Similarity=0.217 Sum_probs=26.1
Q ss_pred HHHHHHhcCCeecCCCceEeecCCCCCCCCCCChHHHHHHHHHHHhhcC
Q 029202 149 AAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKLQRLTEYVFHLEH 197 (197)
Q Consensus 149 ~~~~~~~~GW~~d~~~~~~~P~~~~~~~~~~~~~~qL~~LT~~v~fLE~ 197 (197)
+.+...+.|+++...+-..+|.++.. ++++++.++.+++--||.
T Consensus 179 v~~~L~~~g~~i~~~e~~~~P~~~v~-----l~~e~~~~~~~lie~Lee 222 (234)
T PF01709_consen 179 VKKALEKKGYEIESAELEYIPNNPVE-----LSEEDAEKVEKLIEALEE 222 (234)
T ss_dssp HHHHHHHTT---SEEEEEEEESS-EE-------HHHHHHHHHHHHHHHT
T ss_pred HHHHHHHcCCCeeEEEEEEeCCCCcc-----cCHHHHHHHHHHHHHHhC
Confidence 34446667888875554556755422 277899999999988874
No 208
>PF12536 DUF3734: Patatin phospholipase ; InterPro: IPR021095 This entry represents bacterial proteins of approximately 110 amino acids in length. These proteins are found in association with PF01734 from PFAM. There are two completely conserved residues (F and G) that may be functionally important. The proteins in this family are frequently annotated as patatin family phospholipases however there is little accompanying literature to confirm this.
Probab=22.77 E-value=80 Score=23.08 Aligned_cols=34 Identities=21% Similarity=0.287 Sum_probs=24.0
Q ss_pred HHHHHhcCChhhhhhcHHHHHHHHHHHHHHcCChHHHH
Q 029202 58 ARFLWKSIPSTIKDSRAEVVAAWKIGQHLWTRDYAGVY 95 (197)
Q Consensus 58 ar~l~kRiP~~~~~~~~~l~~~~~l~~~L~~~~y~~v~ 95 (197)
.+.|.++||++.+. +|.++.+-.++. .+.++=|+
T Consensus 24 i~~Ll~~lP~~~r~-dp~~~~l~~~~~---~~~~~Ivh 57 (108)
T PF12536_consen 24 IRELLERLPEELRD-DPDVRELAELGC---GKRVNIVH 57 (108)
T ss_pred HHHHHHcCCHHHhC-CHHHHHHHHhcC---CCceEEEE
Confidence 46789999999996 799986666444 44444443
No 209
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=22.65 E-value=95 Score=21.91 Aligned_cols=27 Identities=7% Similarity=0.342 Sum_probs=19.2
Q ss_pred CCHHHHHHHHHhc--CCeecCCC-ceEeec
Q 029202 144 MNEDDAAYYVQQQ--GWTLDPAS-RMLTVK 170 (197)
Q Consensus 144 ls~~e~~~~~~~~--GW~~d~~~-~~~~P~ 170 (197)
++.+++..||.+. +|.+=+.| .+++|.
T Consensus 55 id~~~i~~fC~~~gy~~~iv~~g~~l~~PP 84 (86)
T PF11360_consen 55 IDPEEIEEFCRSAGYEYEIVPPGRDLLIPP 84 (86)
T ss_pred ECHHHHHHHHHHCCceEEEECCCCCeeCCC
Confidence 3568999999997 56665566 566664
No 210
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=22.58 E-value=2.9e+02 Score=22.02 Aligned_cols=37 Identities=8% Similarity=0.128 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHh
Q 029202 118 YTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 118 iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~ 155 (197)
.+.+++.++-+ -..++.+++|..||++..++.+.+..
T Consensus 23 ~~~~Vl~~L~~-~g~~tdeeLA~~Lgi~~~~VRk~L~~ 59 (178)
T PRK06266 23 EGFEVLKALIK-KGEVTDEEIAEQTGIKLNTVRKILYK 59 (178)
T ss_pred cHhHHHHHHHH-cCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 34556655442 12689999999999999998887553
No 211
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=22.54 E-value=1.5e+02 Score=21.87 Aligned_cols=50 Identities=6% Similarity=0.187 Sum_probs=30.0
Q ss_pred HHHHHHHHHcCChHHHHHHhhC-CCCcHHHHHHHHHHHHHHHHHHHHHHHH
Q 029202 79 AWKIGQHLWTRDYAGVYDAIRG-FDWSQEAQALVAAFSELYTKRMFQLLLS 128 (197)
Q Consensus 79 ~~~l~~~L~~~~y~~v~~~l~~-~~ws~~~~~~i~~l~~~iR~~i~~lis~ 128 (197)
+..+.+++-+||.+++...++. ..-+.+...++..+.+.+|+-..--...
T Consensus 18 i~~l~~ai~~~d~~~~l~~~~~l~~~G~d~~~~l~~L~~~~R~ll~~k~~~ 68 (143)
T PF12169_consen 18 IFELLDAILEGDAAEALELLNELLEQGKDPKQFLDDLIEYLRDLLLYKITG 68 (143)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHHTTSG
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhCC
Confidence 3466667777777777776664 1234566777777777777765544433
No 212
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=22.50 E-value=2.9e+02 Score=19.61 Aligned_cols=61 Identities=15% Similarity=0.213 Sum_probs=37.7
Q ss_pred HHHHHHhhCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHHhcC
Q 029202 92 AGVYDAIRGFDWSQEAQALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQQQG 157 (197)
Q Consensus 92 ~~v~~~l~~~~ws~~~~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~~~G 157 (197)
...|..+....+++.+...+..++..+ +...+.++ .=....+|+.||++..-+..-.++.|
T Consensus 33 ~~~~~~l~~~~~~~~~~~~l~~~Er~~---i~~aL~~~--~gn~s~AAr~LGIsRsTL~rKLkr~g 93 (95)
T PRK00430 33 KNYFAQLNGQDVNDLYELVLAEVEAPL---LDMVMQYT--RGNQTRAALMLGINRGTLRKKLKKYG 93 (95)
T ss_pred HHHHHHhcCCCchhHHHHHHHHHHHHH---HHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 345566666567777777777665433 22223222 24478899999999877666555433
No 213
>TIGR01033 DNA-binding regulatory protein, YebC/PmpR family. This model describes a minimally characterized protein family, restricted to bacteria excepting for some eukaryotic sequences that have possible transit peptides. YebC from E. coli is crystallized, and PA0964 from Pseudomonas aeruginosa has been shown to be a sequence-specific DNA-binding regulatory protein.
Probab=22.44 E-value=1.6e+02 Score=24.71 Aligned_cols=42 Identities=17% Similarity=0.241 Sum_probs=28.6
Q ss_pred HHHHHhcCCeecCCCceEeecCCCCCCCCCCChHHHHHHHHHHHhhc
Q 029202 150 AYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKLQRLTEYVFHLE 196 (197)
Q Consensus 150 ~~~~~~~GW~~d~~~~~~~P~~~~~~~~~~~~~~qL~~LT~~v~fLE 196 (197)
.+-..+.||++...+-..+|+.+.. +++++.+++.+++--||
T Consensus 184 ~~~L~~~g~~i~~sei~~~P~~~v~-----l~~e~~~~~~~li~~Le 225 (238)
T TIGR01033 184 KEALEAKGFPIESAEITMIPLTTVD-----LDDEQAEKLLKLIDALE 225 (238)
T ss_pred HHHHHHcCCCceeeEEEEecCCCcc-----cCHHHHHHHHHHHHHHh
Confidence 4445567998875555556764322 37788899999988776
No 214
>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=22.40 E-value=74 Score=22.94 Aligned_cols=29 Identities=17% Similarity=0.531 Sum_probs=27.1
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||++.|+.=+..+.|..+.+++.+..+-.
T Consensus 47 mdL~tI~~kl~~~~Y~s~~ef~~D~~l~~ 75 (105)
T cd05515 47 IDMEKIRSKIEGNQYQSLDDMVSDFVLMF 75 (105)
T ss_pred cCHHHHHHHHccCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999885
No 215
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=22.36 E-value=2.6e+02 Score=18.94 Aligned_cols=57 Identities=12% Similarity=0.031 Sum_probs=35.2
Q ss_pred HHHHHccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHHHHHHHhhcCHHHHHHHHhcC
Q 029202 6 LTDALASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIHLLGYYYVNDINSARFLWKSI 65 (197)
Q Consensus 6 i~~~~~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~Ll~~L~~ndl~~ar~l~kRi 65 (197)
...+...|+|+.-+..+++.--. .|++...+.. +-..-.+|.-.++..+|...++++
T Consensus 46 ~~~~~~~~~~~~A~~~~~~~~~~-~p~~~~~~~~--~~~~~~~~~~~~~~~~A~~~~~~~ 102 (119)
T TIGR02795 46 GEAYYAQGKYADAAKAFLAVVKK-YPKSPKAPDA--LLKLGMSLQELGDKEKAKATLQQV 102 (119)
T ss_pred HHHHHhhccHHHHHHHHHHHHHH-CCCCCcccHH--HHHHHHHHHHhCChHHHHHHHHHH
Confidence 34567788899888888876544 3344322222 222334555668888888777765
No 216
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=22.33 E-value=2.4e+02 Score=18.86 Aligned_cols=41 Identities=17% Similarity=0.249 Sum_probs=29.7
Q ss_pred HHHHHHHHhhcccCHHHHHHHcCCCHHHH---HHHHHhcCCeec
Q 029202 121 RMFQLLLSAYSTISTQDTALFLGMNEDDA---AYYVQQQGWTLD 161 (197)
Q Consensus 121 ~i~~lis~AY~sIs~~~~a~~Lgls~~e~---~~~~~~~GW~~d 161 (197)
+|+.++...=..+++.+++..+|++..-+ .+...+.||-..
T Consensus 9 ~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 9 AVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeee
Confidence 45666655425799999999999986544 444566899874
No 217
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=22.30 E-value=2e+02 Score=19.77 Aligned_cols=54 Identities=9% Similarity=0.102 Sum_probs=31.7
Q ss_pred cccCHHHHH-HHc-CCCHHHHHHHHHhcCCeecCCCceEeecCCCCCCCCCCChHHHHHHHHHH
Q 029202 131 STISTQDTA-LFL-GMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKLQRLTEYV 192 (197)
Q Consensus 131 ~sIs~~~~a-~~L-gls~~e~~~~~~~~GW~~d~~~~~~~P~~~~~~~~~~~~~~qL~~LT~~v 192 (197)
..|+++.++ .|+ |++++.+..-+.+ |.+-+|.-.-.......--..+..|++|+
T Consensus 13 ~~IpL~~v~~~yf~~lt~~~a~rk~~~--------g~lplPv~rl~~SqKs~~~V~v~dLA~yi 68 (76)
T PF11112_consen 13 PVIPLEEVCEDYFPHLTPKTAKRKANA--------GELPLPVFRLDDSQKSPKFVHVQDLAAYI 68 (76)
T ss_pred CCCcHHHHHHHHHccCCHHHHHHHHHC--------CCCCCceeecCCcccCCceeeHHHHHHHH
Confidence 468888866 888 9999888887763 33434433221111111345666666665
No 218
>PF07146 DUF1389: Protein of unknown function (DUF1389); InterPro: IPR010792 This family consists of several hypothetical bacterial proteins, which seem to be specific to Chlamydia pneumoniae (Chlamydophila pneumoniae). Members of this family are typically around 400 residues in length. The function of this family is unknown.
Probab=22.28 E-value=1.6e+02 Score=25.85 Aligned_cols=66 Identities=20% Similarity=0.365 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcCCCH
Q 029202 76 VVAAWKIGQHLWTRDYAGVYDAIRGFDWSQEAQALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLGMNE 146 (197)
Q Consensus 76 l~~~~~l~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~ 146 (197)
-...|-|.|-+.+.+|.......++..|... + .+...+|+|+..+++.-|....-.+-.....+.+
T Consensus 171 ~~~~~~l~~~vS~eey~~L~~hA~n~tW~~~-~----~~V~~i~~rl~~~l~~~~~~~~~~~~~~~~~~~~ 236 (314)
T PF07146_consen 171 HPHTWLLAQIVSEEEYSTLKNHARNNTWDQQ-Q----DIVSAIVDRLIACLGNYYQYSFENDKVILLSLTE 236 (314)
T ss_pred cchHHHHHHHccHHHHHHHHHHHhhCCccch-h----hHHHHHHHHHHhhhhhhhhhhhccchhHHHHhhh
Confidence 5678899999999999999888888799652 2 2445556666666666665555444444444433
No 219
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=22.17 E-value=1.5e+02 Score=18.10 Aligned_cols=27 Identities=4% Similarity=0.114 Sum_probs=23.4
Q ss_pred cchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 3 FSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 3 ~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
...|.+.|-.|+++..+.+|++.....
T Consensus 5 ~~~i~~~i~~g~~~~a~~~~~~~~~~l 31 (58)
T smart00668 5 RKRIRELILKGDWDEALEWLSSLKPPL 31 (58)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHcCHHH
Confidence 457899999999999999999887663
No 220
>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=22.16 E-value=50 Score=24.23 Aligned_cols=29 Identities=21% Similarity=0.479 Sum_probs=27.5
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||++.|+.-+..+.|..+.+...+..|-.
T Consensus 41 mdL~tI~~kl~~~~Y~s~~ef~~Dv~li~ 69 (112)
T cd05511 41 MDLQTIRKKISKHKYQSREEFLEDIELIV 69 (112)
T ss_pred CCHHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999986
No 221
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=21.94 E-value=3.6e+02 Score=22.84 Aligned_cols=36 Identities=11% Similarity=0.016 Sum_probs=25.1
Q ss_pred HHHHHHHhh-cccCHHHHHHHcCCCHHHHHHHHHhcC
Q 029202 122 MFQLLLSAY-STISTQDTALFLGMNEDDAAYYVQQQG 157 (197)
Q Consensus 122 i~~lis~AY-~sIs~~~~a~~Lgls~~e~~~~~~~~G 157 (197)
+.+.+...| ..++++++|..+|+|+.-+....++.|
T Consensus 139 v~~~I~~~~~~~~tl~~LA~~~gmS~s~l~R~FK~~G 175 (253)
T PRK09940 139 VRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQ 175 (253)
T ss_pred HHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHcC
Confidence 333333333 358999999999999987776666545
No 222
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=21.93 E-value=1e+02 Score=30.77 Aligned_cols=63 Identities=11% Similarity=0.183 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHcC-CCHHHHHHHHHh----c--CCeecCCCceEeec
Q 029202 108 QALVAAFSELYTKRMFQLLLSAYSTISTQDTALFLG-MNEDDAAYYVQQ----Q--GWTLDPASRMLTVK 170 (197)
Q Consensus 108 ~~~i~~l~~~iR~~i~~lis~AY~sIs~~~~a~~Lg-ls~~e~~~~~~~----~--GW~~d~~~~~~~P~ 170 (197)
...|..|.+-+--|.++-+|.-|.||+.+.+-++-- ++.-++.+++.+ . .=++|-..+.|.+.
T Consensus 423 ~QYI~sLq~v~~~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~v~iriDH~~~~v~Fg 492 (988)
T KOG2072|consen 423 SQYIPSLQDVIILRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLVEAAKHNDVSIRIDHESNSVSFG 492 (988)
T ss_pred cccchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccceeEEeccccceeeec
Confidence 456667778888899999999999999988665543 366666555332 2 33455444555544
No 223
>TIGR00746 arcC carbamate kinase. The seed alignment for this model includes experimentally confirmed examples from a set of phylogenetically distinct species. In a neighbor-joining tree constructed from an alignment of candidate carbamate kinases and several acetylglutamate kinases, the latter group forms a clear outgroup which roots the tree of carbamate kinase-like proteins. This analysis suggests that in E. coli, the ArcC paralog YqeA may be a second isozyme, while the paralog YahI branches as an outlier and is less likely to be an authentic carbamate kinase. The homolog from Mycoplasma pneumoniae likewise branches outside the set containing known carbamate kinases and also scores below the trusted cutoff.
Probab=21.92 E-value=1.6e+02 Score=25.76 Aligned_cols=20 Identities=20% Similarity=0.572 Sum_probs=16.9
Q ss_pred CCHHHHHHHHHhcCCeecCC
Q 029202 144 MNEDDAAYYVQQQGWTLDPA 163 (197)
Q Consensus 144 ls~~e~~~~~~~~GW~~d~~ 163 (197)
++.+|+.+..++.||++-+|
T Consensus 133 y~~~~a~~~~~~~~~~~~~d 152 (310)
T TIGR00746 133 YTEEEAKRLAAEKGWIVKED 152 (310)
T ss_pred cCHHHHHHHHHHcCCeEeec
Confidence 36789999999999999764
No 224
>PF08898 DUF1843: Domain of unknown function (DUF1843); InterPro: IPR014994 This domain is found in functionally uncharacterised proteins. It can be found independently or at the C terminus of the protein.
Probab=21.80 E-value=1.1e+02 Score=19.69 Aligned_cols=25 Identities=12% Similarity=0.254 Sum_probs=19.8
Q ss_pred hHHHHHccccHHHHHHHHhHHhhhh
Q 029202 5 PLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 5 ~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
.|+.++++||..+.-...-..|-+.
T Consensus 6 aiq~AiasGDLa~MK~l~~~aeq~L 30 (53)
T PF08898_consen 6 AIQQAIASGDLAQMKALAAQAEQQL 30 (53)
T ss_pred HHHHHHHcCcHHHHHHHHHHHHHHH
Confidence 6899999999988777766666554
No 225
>PF07304 SRA1: Steroid receptor RNA activator (SRA1); InterPro: IPR009917 This entry consists of several hypothetical mammalian steroid receptor RNA activator proteins. The SRA-RNAs encode stable proteins that are widely expressed and upregulated in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA. This domain is also found at the C terminus of Sec31, a component of the coat protein complex II (COPII, which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). COPII has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. ; PDB: 2YRU_A.
Probab=21.79 E-value=3.9e+02 Score=20.80 Aligned_cols=43 Identities=21% Similarity=0.271 Sum_probs=28.6
Q ss_pred cHHHHHHHHHHHHHHcCChHHH---HHHhhC------CCCcHHHHHHHHHHH
Q 029202 73 RAEVVAAWKIGQHLWTRDYAGV---YDAIRG------FDWSQEAQALVAAFS 115 (197)
Q Consensus 73 ~~~l~~~~~l~~~L~~~~y~~v---~~~l~~------~~ws~~~~~~i~~l~ 115 (197)
.+.+..+..|.++|-.|||... +..|-. ..|-.-++.+|...+
T Consensus 88 ~~v~~~L~~L~~aL~~~d~~~A~~Ih~~L~t~h~~E~~~WmvGVKRLI~~~r 139 (157)
T PF07304_consen 88 KPVVDKLHQLAQALQARDYDAADEIHVDLMTDHVDECGNWMVGVKRLIAMAR 139 (157)
T ss_dssp HHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHSSHHHHTTTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccHHHhhhHHHHHHHHHHHHH
Confidence 3667888899999999999984 444443 245556666665443
No 226
>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=21.74 E-value=1.5e+02 Score=18.87 Aligned_cols=22 Identities=18% Similarity=0.223 Sum_probs=17.2
Q ss_pred cccCHHHHHHHcCCCHHHHHHH
Q 029202 131 STISTQDTALFLGMNEDDAAYY 152 (197)
Q Consensus 131 ~sIs~~~~a~~Lgls~~e~~~~ 152 (197)
..+++.++|..||+|..-+...
T Consensus 22 R~~tl~elA~~lgis~st~~~~ 43 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEH 43 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHH
Confidence 3688999999999997655443
No 227
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=21.72 E-value=79 Score=19.90 Aligned_cols=24 Identities=17% Similarity=0.206 Sum_probs=14.1
Q ss_pred ccCHHHHHHHcCCCHHHHHHHHHh
Q 029202 132 TISTQDTALFLGMNEDDAAYYVQQ 155 (197)
Q Consensus 132 sIs~~~~a~~Lgls~~e~~~~~~~ 155 (197)
.|+..++|+..|++...+-.++..
T Consensus 10 ~it~~~La~~~gis~~tl~~~~~~ 33 (63)
T PF13443_consen 10 GITQKDLARKTGISRSTLSRILNG 33 (63)
T ss_dssp T--HHHHHHHHT--HHHHHHHHTT
T ss_pred CCCHHHHHHHHCcCHHHHHHHHhc
Confidence 457777777777777777776653
No 228
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=21.65 E-value=1.6e+02 Score=24.96 Aligned_cols=33 Identities=12% Similarity=0.308 Sum_probs=24.8
Q ss_pred hhcccCHHHHHHHcCCCHHH-----------HHHHHHhcCCeec
Q 029202 129 AYSTISTQDTALFLGMNEDD-----------AAYYVQQQGWTLD 161 (197)
Q Consensus 129 AY~sIs~~~~a~~Lgls~~e-----------~~~~~~~~GW~~d 161 (197)
-|...+...+|..||+|..- +.+...+.||.++
T Consensus 239 ~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~~~~ 282 (285)
T TIGR02394 239 GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGVDRE 282 (285)
T ss_pred CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 36889999999999999743 3444556688775
No 229
>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=21.64 E-value=3.7e+02 Score=20.47 Aligned_cols=38 Identities=11% Similarity=-0.004 Sum_probs=26.3
Q ss_pred ccCHHHHHHHcCCCHHHH---HHHHHhcCCeecCCCceEee
Q 029202 132 TISTQDTALFLGMNEDDA---AYYVQQQGWTLDPASRMLTV 169 (197)
Q Consensus 132 sIs~~~~a~~Lgls~~e~---~~~~~~~GW~~d~~~~~~~P 169 (197)
.++-.++|.++|++.+-+ .+-.++.|+---..+.+.++
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~ 183 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHKKKITVH 183 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEe
Confidence 478899999999996554 44555679865434555555
No 230
>cd05500 Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=21.53 E-value=52 Score=23.60 Aligned_cols=29 Identities=28% Similarity=0.500 Sum_probs=27.0
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
|||+.|+.=+..|.|..+.+++.+..+-.
T Consensus 47 ~dL~tI~~kl~~~~Y~s~~~f~~D~~li~ 75 (103)
T cd05500 47 MDLGTIERKLKSNVYTSVEEFTADFNLMV 75 (103)
T ss_pred CCHHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence 89999999999999999999999999885
No 231
>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=21.49 E-value=2e+02 Score=17.27 Aligned_cols=23 Identities=13% Similarity=0.281 Sum_probs=18.8
Q ss_pred hcccCHHHHHHHcCCCHHHHHHH
Q 029202 130 YSTISTQDTALFLGMNEDDAAYY 152 (197)
Q Consensus 130 Y~sIs~~~~a~~Lgls~~e~~~~ 152 (197)
|...+..++|..||+|.+-+...
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHH
Confidence 78999999999999998776554
No 232
>cd00256 VATPase_H VATPase_H, regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is that of a superhelical spiral, in part the geometry is similar to superhelices composed of armadillo repeat motifs, as found in importins for example.
Probab=21.35 E-value=3.4e+02 Score=24.99 Aligned_cols=83 Identities=7% Similarity=0.117 Sum_probs=58.1
Q ss_pred HHHHHHHHHHHHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhcccCH---------HHHHHHcCCC
Q 029202 75 EVVAAWKIGQHLWTRDYAGVYDAIRGFDWSQEAQALVAAFSELYTKRMFQLLLSAYSTIST---------QDTALFLGMN 145 (197)
Q Consensus 75 ~l~~~~~l~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~iR~~i~~lis~AY~sIs~---------~~~a~~Lgls 145 (197)
-++-.+.+.-++|.=.|..-...... -...+..+++.+....|+++.+++-..+.++-- ..+..|++..
T Consensus 200 ~~Ql~Y~~ll~lWlLSF~~~~~~~~~--~~~~i~~l~~i~k~s~KEKvvRv~l~~l~Nll~~~~~~~~~~~~~~~mv~~~ 277 (429)
T cd00256 200 GFQLQYQSIFCIWLLTFNPHAAEVLK--RLSLIQDLSDILKESTKEKVIRIVLAIFRNLISKRVDREVKKTAALQMVQCK 277 (429)
T ss_pred cHHHHHHHHHHHHHHhccHHHHHhhc--cccHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhcccccchhhhHHHHHHHcC
Confidence 46677788888888888765333222 136788899999999999999988777766654 2356667666
Q ss_pred HHHHHHHHHhcCCe
Q 029202 146 EDDAAYYVQQQGWT 159 (197)
Q Consensus 146 ~~e~~~~~~~~GW~ 159 (197)
--.+.+-..+|+|+
T Consensus 278 l~~~l~~L~~rk~~ 291 (429)
T cd00256 278 VLKTLQSLEQRKYD 291 (429)
T ss_pred hHHHHHHHhcCCCC
Confidence 55566666677773
No 233
>PF11084 DUF2621: Protein of unknown function (DUF2621); InterPro: IPR020203 This entry represents a group of uncharacterised proteins.
Probab=21.31 E-value=3.9e+02 Score=20.59 Aligned_cols=78 Identities=15% Similarity=0.257 Sum_probs=43.9
Q ss_pred HHHHHHHHHhhcCHHHHHHHHhcCChhhhhhcHHHH-HHHHHHHHHHcCChHHHHHHhhCCCCcHHHHHHHHHHHHHHHH
Q 029202 42 YVIHLLGYYYVNDINSARFLWKSIPSTIKDSRAEVV-AAWKIGQHLWTRDYAGVYDAIRGFDWSQEAQALVAAFSELYTK 120 (197)
Q Consensus 42 y~~~Ll~~L~~ndl~~ar~l~kRiP~~~~~~~~~l~-~~~~l~~~L~~~~y~~v~~~l~~~~ws~~~~~~i~~l~~~iR~ 120 (197)
++..|+.++.-+-.==||-.+||+|.+--.++-.-+ .-+.=.++||.-+...+...+= +|.=..|++-.|+
T Consensus 13 W~~vli~l~~IGGfFMFRKFLK~lPKeDGkS~LDWq~~yi~~trhlW~de~K~lL~eLV--------~PVPelFRdvAk~ 84 (141)
T PF11084_consen 13 WVVVLIGLMAIGGFFMFRKFLKRLPKEDGKSILDWQEYYIEKTRHLWTDEQKALLEELV--------SPVPELFRDVAKH 84 (141)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHhCCcccCcccccHHHHHHHHhHhhcCHHHHHHHHHHh--------hcCcHHHHHHHHH
Confidence 567788888889999999999999954332211111 1112233444444444433332 2222456666677
Q ss_pred HHHHHHH
Q 029202 121 RMFQLLL 127 (197)
Q Consensus 121 ~i~~lis 127 (197)
+|+.-|+
T Consensus 85 kIAgkIg 91 (141)
T PF11084_consen 85 KIAGKIG 91 (141)
T ss_pred HHHHHHH
Confidence 7766554
No 234
>cd04369 Bromodomain Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Probab=21.18 E-value=54 Score=22.13 Aligned_cols=29 Identities=24% Similarity=0.449 Sum_probs=26.4
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||+..|+.-+..+.|..+.+...+..+-.
T Consensus 43 ~~l~~I~~kl~~~~Y~s~~~f~~D~~li~ 71 (99)
T cd04369 43 MDLSTIKKKLKNGEYKSLEEFEADVRLIF 71 (99)
T ss_pred ccHHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence 78999999999999999999999998875
No 235
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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 is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. 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; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=21.15 E-value=1.2e+02 Score=17.68 Aligned_cols=21 Identities=24% Similarity=0.487 Sum_probs=16.4
Q ss_pred CHHHHHHHcCCCHHHHHHHHH
Q 029202 134 STQDTALFLGMNEDDAAYYVQ 154 (197)
Q Consensus 134 s~~~~a~~Lgls~~e~~~~~~ 154 (197)
++.++|+++|++..-+.-+-.
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467899999999988877655
No 236
>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=21.11 E-value=2.4e+02 Score=20.58 Aligned_cols=36 Identities=14% Similarity=0.119 Sum_probs=32.0
Q ss_pred HHhhcccCHHHHHHHcCCCHHHHHHHHHhcCCeecC
Q 029202 127 LSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDP 162 (197)
Q Consensus 127 s~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~ 162 (197)
-..+.-+.+.++|.-||++..-+..+....||+..-
T Consensus 66 v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t~KK 101 (119)
T PF01710_consen 66 VEENPDATLRELAERLGVSPSTIWRALKRLGITRKK 101 (119)
T ss_pred HHHCCCcCHHHHHHHcCCCHHHHHHHHHHcCchhcc
Confidence 345999999999999999999999999999999963
No 237
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=21.05 E-value=3.2e+02 Score=22.48 Aligned_cols=23 Identities=22% Similarity=0.427 Sum_probs=17.7
Q ss_pred ccCHHHHHHHcCCCHHHHHHHHH
Q 029202 132 TISTQDTALFLGMNEDDAAYYVQ 154 (197)
Q Consensus 132 sIs~~~~a~~Lgls~~e~~~~~~ 154 (197)
..+..++|..||++.+++.....
T Consensus 125 ~~~~~eia~~l~~~~~~v~~~~~ 147 (251)
T PRK07670 125 NVTPKEVAAELGMTEEEVEATMN 147 (251)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHH
Confidence 45677899999999888776643
No 238
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=20.99 E-value=3e+02 Score=19.19 Aligned_cols=40 Identities=18% Similarity=0.277 Sum_probs=29.6
Q ss_pred HHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHH---HhcCCee
Q 029202 120 KRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTL 160 (197)
Q Consensus 120 ~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~ 160 (197)
.+++.++..- ..++.+++|+.+|++...+.... .+.||-.
T Consensus 6 ~~il~~L~~~-~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 6 RKILEELQKD-ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 4666666653 67999999999999987665554 4578866
No 239
>PF11428 DUF3196: Protein of unknown function (DUF3196); InterPro: IPR024503 The entry comprises bacterial proteins of unknown function. One of the proteins in this entry, MPN330, is thought to involved in a cellular function that has yet to be characterised. The protein has 11 helices and a novel fold. No function is currently known for this protein.; PDB: 1TD6_A.
Probab=20.90 E-value=2.5e+02 Score=24.40 Aligned_cols=58 Identities=17% Similarity=0.236 Sum_probs=37.5
Q ss_pred HHHHHHHHHcCChHHHHHHhhCCCCcHHH-----HHHHHHHHHHHHHHHHHHHHHhhcccCHHH
Q 029202 79 AWKIGQHLWTRDYAGVYDAIRGFDWSQEA-----QALVAAFSELYTKRMFQLLLSAYSTISTQD 137 (197)
Q Consensus 79 ~~~l~~~L~~~~y~~v~~~l~~~~ws~~~-----~~~i~~l~~~iR~~i~~lis~AY~sIs~~~ 137 (197)
+-++.+.+-+++|..++..++. +.+.+| ......+...++.++..--++.+.++.-..
T Consensus 47 l~~i~~ll~~~~y~~A~~lI~~-EL~mPYIP~~~~~~fe~~l~~ik~~~~eq~~~~~~sLd~~~ 109 (286)
T PF11428_consen 47 LKKIKQLLDKKDYKEALELINE-ELSMPYIPLPLESKFESLLQEIKKDLYEQENKKYESLDKEK 109 (286)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHH-HTT-TTS-HHHHHHHHHHHHHHHHHHHHHH-GGGGG--HHH
T ss_pred HHHHHHHHHHhhHHHHHHHHHH-HhcCCCCChHHHHHHHHHHHHHHHHHHHHHhhHhccccHHH
Confidence 3478889999999999999988 655444 345566666777766666666666666433
No 240
>cd05528 Bromo_AAA Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver
Probab=20.82 E-value=62 Score=23.80 Aligned_cols=29 Identities=28% Similarity=0.434 Sum_probs=27.4
Q ss_pred CCcchHHHHHccccHHHHHHHHhHHhhhh
Q 029202 1 MDFSPLTDALASKSYEKIADICDDLMLKV 29 (197)
Q Consensus 1 ~~~~~i~~~~~~~~~~~l~~~~e~~El~~ 29 (197)
||++-|..=+..+.|..+-+.+.+..|-.
T Consensus 44 mdL~tI~~kl~~~~Y~s~~ef~~Dv~li~ 72 (112)
T cd05528 44 MDLQTILQKLDTHQYLTAKDFLKDIDLIV 72 (112)
T ss_pred CCHHHHHHHHcCCCcCCHHHHHHHHHHHH
Confidence 89999999999999999999999999986
No 241
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=20.62 E-value=3.5e+02 Score=19.76 Aligned_cols=58 Identities=9% Similarity=0.146 Sum_probs=39.3
Q ss_pred HHHHccccHHHHHHHHhHHhhhhhhCCCcCCCcchHHHHHHHHHhhcCHHHHHHHHhcCChhhh
Q 029202 7 TDALASKSYEKIADICDDLMLKVAAEGIVFQDEWPYVIHLLGYYYVNDINSARFLWKSIPSTIK 70 (197)
Q Consensus 7 ~~~~~~~~~~~l~~~~e~~El~~~~~g~~~~~~~py~~~Ll~~L~~ndl~~ar~l~kRiP~~~~ 70 (197)
..++..|++++.+..|+..--. .| ..+ ..|..++-+|.-.|+...|.-..++.-..+.
T Consensus 70 ~~~~~~~~~~~a~~~~~~~l~~-dP----~~E-~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~ 127 (146)
T PF03704_consen 70 EALLEAGDYEEALRLLQRALAL-DP----YDE-EAYRLLMRALAAQGRRAEALRVYERYRRRLR 127 (146)
T ss_dssp HHHHHTT-HHHHHHHHHHHHHH-ST----T-H-HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH
T ss_pred HHHHhccCHHHHHHHHHHHHhc-CC----CCH-HHHHHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3466788999999988877544 22 122 2388889999999999998887777654444
No 242
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=20.61 E-value=2.9e+02 Score=18.88 Aligned_cols=27 Identities=15% Similarity=0.103 Sum_probs=23.2
Q ss_pred HhhcccCHHHHHHHcCCCHHHHHHHHH
Q 029202 128 SAYSTISTQDTALFLGMNEDDAAYYVQ 154 (197)
Q Consensus 128 ~AY~sIs~~~~a~~Lgls~~e~~~~~~ 154 (197)
+-+.-.+..++|..||+|..-+.....
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~ 54 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLK 54 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 667999999999999999987777654
No 243
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=20.47 E-value=81 Score=21.28 Aligned_cols=21 Identities=14% Similarity=0.319 Sum_probs=18.8
Q ss_pred HHcCCCHHHHHHHHHhcCCee
Q 029202 140 LFLGMNEDDAAYYVQQQGWTL 160 (197)
Q Consensus 140 ~~Lgls~~e~~~~~~~~GW~~ 160 (197)
.++.++..|+++..+..||..
T Consensus 3 ~lp~~~~ke~ik~Le~~Gf~~ 23 (66)
T COG1724 3 KLPRMKAKEVIKALEKDGFQL 23 (66)
T ss_pred cCCcCCHHHHHHHHHhCCcEE
Confidence 467889999999999999998
No 244
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=20.46 E-value=4.1e+02 Score=20.49 Aligned_cols=38 Identities=8% Similarity=0.158 Sum_probs=25.6
Q ss_pred ccCHHHHHHHcCCCHHHHHH---HHHhcCCeecCCCceEee
Q 029202 132 TISTQDTALFLGMNEDDAAY---YVQQQGWTLDPASRMLTV 169 (197)
Q Consensus 132 sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~d~~~~~~~P 169 (197)
.++-.++|.+||++.+-+-. -.++.|+---..+.+.++
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~ 189 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREGYIRSGYGKIQLL 189 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEE
Confidence 46788999999999765444 344578887433444443
No 245
>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=20.38 E-value=2.3e+02 Score=17.61 Aligned_cols=32 Identities=16% Similarity=0.345 Sum_probs=24.0
Q ss_pred cccCHHHHHHHcCCCHHHHHH---HHHhcCCeecC
Q 029202 131 STISTQDTALFLGMNEDDAAY---YVQQQGWTLDP 162 (197)
Q Consensus 131 ~sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~d~ 162 (197)
..++..++|..+|++..-+.. -..+.||-.-.
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~ 58 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRR 58 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 468999999999999755544 44567998753
No 246
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=20.28 E-value=2.6e+02 Score=20.78 Aligned_cols=38 Identities=18% Similarity=0.279 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHhhcccCHHHHHHHcCCCHHHHHHHHH
Q 029202 116 ELYTKRMFQLLLSAYSTISTQDTALFLGMNEDDAAYYVQ 154 (197)
Q Consensus 116 ~~iR~~i~~lis~AY~sIs~~~~a~~Lgls~~e~~~~~~ 154 (197)
+.+-.+|+..+..--+ +|...+|..+|+|+..+..-++
T Consensus 7 D~~D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~ 44 (154)
T COG1522 7 DDIDRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIK 44 (154)
T ss_pred cHHHHHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHH
Confidence 4455677777766666 9999999999999877765544
No 247
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.22 E-value=1.4e+02 Score=20.63 Aligned_cols=26 Identities=19% Similarity=0.210 Sum_probs=21.1
Q ss_pred cCHHHHHHHcCCCHHHHHHHHHhcCCe
Q 029202 133 ISTQDTALFLGMNEDDAAYYVQQQGWT 159 (197)
Q Consensus 133 Is~~~~a~~Lgls~~e~~~~~~~~GW~ 159 (197)
.++.++|..+|++..-+..+.. .|+-
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~-~Gli 27 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER-LGLL 27 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH-CCCc
Confidence 4788999999999999988865 4554
No 248
>PF01329 Pterin_4a: Pterin 4 alpha carbinolamine dehydratase; InterPro: IPR001533 DCoH is the dimerisation cofactor of hepatocyte nuclear factor 1 (HNF-1) that functions as both a transcriptional coactivator and a pterin dehydratase []. X-ray crystallographic studies have shown that the ligand binds at four sites per tetrameric enzyme, with little apparent conformational change in the protein.; GO: 0008124 4-alpha-hydroxytetrahydrobiopterin dehydratase activity, 0006729 tetrahydrobiopterin biosynthetic process; PDB: 2V6T_B 2V6U_A 2V6S_B 2EBB_A 1USM_A 1F93_B 1DCP_C 1DCH_E 3HXA_E 1DCO_C ....
Probab=20.07 E-value=1.5e+02 Score=20.90 Aligned_cols=19 Identities=32% Similarity=0.686 Sum_probs=14.4
Q ss_pred CCHHHHHHHHHhc-CCeecC
Q 029202 144 MNEDDAAYYVQQQ-GWTLDP 162 (197)
Q Consensus 144 ls~~e~~~~~~~~-GW~~d~ 162 (197)
|+.+|+.....+. ||+++.
T Consensus 5 Ls~~ei~~~L~~l~~W~~~~ 24 (95)
T PF01329_consen 5 LSEEEIAEALAELPGWKLDG 24 (95)
T ss_dssp -THHHHHHHHHTSTTSEEET
T ss_pred CCHHHHHHhhhcCcCCEECC
Confidence 5678888877764 999986
No 249
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=20.00 E-value=1e+02 Score=17.51 Aligned_cols=17 Identities=24% Similarity=0.528 Sum_probs=13.0
Q ss_pred CHHHHHHHcCCCHHHHH
Q 029202 134 STQDTALFLGMNEDDAA 150 (197)
Q Consensus 134 s~~~~a~~Lgls~~e~~ 150 (197)
|+.++|+.||++..-+.
T Consensus 18 Si~eAa~~l~i~~~~I~ 34 (37)
T PF07453_consen 18 SIREAARYLGISHSTIS 34 (37)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 67889999999865543
Done!