Query 031627
Match_columns 156
No_of_seqs 166 out of 538
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 03:09:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031627.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031627hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0871 Class 2 transcription 100.0 5.3E-51 1.2E-55 316.5 15.1 136 6-141 3-139 (156)
2 COG5150 Class 2 transcription 100.0 6.7E-43 1.5E-47 266.2 14.6 134 8-141 4-137 (148)
3 KOG0869 CCAAT-binding factor, 100.0 7.3E-32 1.6E-36 211.5 10.4 99 10-108 27-125 (168)
4 KOG0870 DNA polymerase epsilon 99.9 1.4E-26 3.1E-31 182.9 9.6 97 10-106 5-102 (172)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 1.4E-18 3E-23 117.3 7.8 64 15-79 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.6 4.8E-16 1E-20 112.9 6.2 76 10-87 14-89 (91)
7 cd00076 H4 Histone H4, one of 99.1 2.4E-10 5.1E-15 82.2 7.8 69 15-85 13-81 (85)
8 PLN00035 histone H4; Provision 99.1 6.5E-10 1.4E-14 82.5 7.8 69 15-85 29-97 (103)
9 PTZ00015 histone H4; Provision 99.0 1.5E-09 3.2E-14 80.5 7.7 70 14-85 29-98 (102)
10 smart00803 TAF TATA box bindin 98.9 1E-08 2.2E-13 70.1 7.5 64 15-80 2-65 (65)
11 smart00417 H4 Histone H4. 98.8 1E-08 2.2E-13 72.1 6.8 62 15-78 13-74 (74)
12 cd07981 TAF12 TATA Binding Pro 98.8 4.1E-08 8.9E-13 68.0 8.1 65 16-81 2-66 (72)
13 PF00125 Histone: Core histone 98.8 2E-08 4.4E-13 68.6 6.3 68 13-80 3-73 (75)
14 smart00428 H3 Histone H3. 98.5 2.2E-07 4.7E-12 69.3 6.1 69 11-79 25-98 (105)
15 COG5208 HAP5 CCAAT-binding fac 98.5 1.1E-07 2.4E-12 79.2 4.6 78 12-91 106-184 (286)
16 smart00576 BTP Bromodomain tra 98.3 6.6E-06 1.4E-10 57.4 7.9 66 18-85 9-74 (77)
17 cd00074 H2A Histone 2A; H2A is 98.2 7E-06 1.5E-10 62.0 6.9 69 12-81 17-85 (115)
18 KOG1657 CCAAT-binding factor, 98.0 5.7E-06 1.2E-10 69.3 4.4 77 11-89 70-147 (236)
19 PLN00161 histone H3; Provision 97.9 2.9E-05 6.2E-10 60.3 6.6 69 11-79 51-123 (135)
20 PLN00121 histone H3; Provision 97.9 1.5E-05 3.2E-10 62.0 4.9 69 11-79 58-129 (136)
21 PLN00160 histone H3; Provision 97.9 2.3E-05 5E-10 57.8 5.7 69 11-79 17-89 (97)
22 cd08048 TAF11 TATA Binding Pro 97.9 9.2E-05 2E-09 53.2 7.5 66 15-82 16-84 (85)
23 cd07979 TAF9 TATA Binding Prot 97.9 7E-05 1.5E-09 56.5 7.2 76 20-97 6-82 (117)
24 PF15630 CENP-S: Kinetochore c 97.9 7.3E-05 1.6E-09 52.7 6.8 61 20-80 10-71 (76)
25 smart00427 H2B Histone H2B. 97.8 8.6E-05 1.9E-09 54.0 7.3 63 20-83 6-68 (89)
26 PTZ00018 histone H3; Provision 97.8 3.9E-05 8.4E-10 59.7 5.3 68 12-79 59-129 (136)
27 cd08050 TAF6 TATA Binding Prot 97.8 8.8E-05 1.9E-09 64.7 7.6 67 17-85 1-67 (343)
28 PLN00158 histone H2B; Provisio 97.6 0.00025 5.4E-09 53.8 7.3 71 15-86 27-97 (116)
29 KOG1659 Class 2 transcription 97.6 0.00028 6E-09 58.6 8.0 113 14-128 12-127 (224)
30 PF15511 CENP-T: Centromere ki 97.6 0.00012 2.5E-09 65.6 6.3 64 11-74 347-414 (414)
31 PF07524 Bromo_TP: Bromodomain 97.6 0.0005 1.1E-08 47.5 7.9 63 20-85 11-74 (77)
32 PTZ00463 histone H2B; Provisio 97.6 0.0003 6.6E-09 53.4 7.3 66 20-86 33-98 (117)
33 PF03847 TFIID_20kDa: Transcri 97.6 0.00042 9E-09 47.8 7.1 63 18-81 2-64 (68)
34 PF09415 CENP-X: CENP-S associ 97.6 0.00013 2.9E-09 50.9 4.6 65 17-81 1-67 (72)
35 PF04719 TAFII28: hTAFII28-lik 97.5 0.00046 9.9E-09 50.2 6.9 67 15-82 23-90 (90)
36 KOG3467 Histone H4 [Chromatin 97.4 0.00072 1.6E-08 49.4 6.8 67 16-84 30-96 (103)
37 PF15510 CENP-W: Centromere ki 97.1 0.001 2.2E-08 48.9 4.6 66 15-81 16-95 (102)
38 COG5262 HTA1 Histone H2A [Chro 97.0 0.0019 4.2E-08 49.4 5.7 68 13-81 24-91 (132)
39 PF02969 TAF: TATA box binding 97.0 0.0065 1.4E-07 41.8 7.6 63 15-80 3-66 (66)
40 COG5247 BUR6 Class 2 transcrip 96.9 0.0037 7.9E-08 46.8 6.5 79 14-94 22-101 (113)
41 smart00414 H2A Histone 2A. 96.8 0.0045 9.8E-08 46.1 6.5 69 12-81 6-74 (106)
42 PLN00154 histone H2A; Provisio 96.6 0.0077 1.7E-07 46.9 6.4 70 12-81 35-104 (136)
43 KOG1744 Histone H2B [Chromatin 96.5 0.0096 2.1E-07 45.9 6.5 62 20-82 42-103 (127)
44 PTZ00017 histone H2A; Provisio 96.4 0.0092 2E-07 46.4 5.8 76 12-88 24-100 (134)
45 PF02269 TFIID-18kDa: Transcri 96.3 0.0061 1.3E-07 44.2 4.0 60 21-81 7-66 (93)
46 KOG1756 Histone 2A [Chromatin 96.3 0.014 2.9E-07 45.2 6.0 68 12-80 24-91 (131)
47 KOG3219 Transcription initiati 96.2 0.0054 1.2E-07 50.3 3.9 69 15-85 112-181 (195)
48 KOG1745 Histones H3 and H4 [Ch 96.1 0.0049 1.1E-07 48.0 2.9 71 11-81 59-132 (137)
49 PLN00157 histone H2A; Provisio 96.0 0.018 3.9E-07 44.7 5.6 75 13-88 24-99 (132)
50 PLN00153 histone H2A; Provisio 96.0 0.019 4.1E-07 44.4 5.7 76 12-88 21-97 (129)
51 PLN00156 histone H2AX; Provisi 96.0 0.022 4.7E-07 44.6 6.1 76 12-88 26-102 (139)
52 KOG1658 DNA polymerase epsilon 95.9 0.0082 1.8E-07 47.8 3.5 74 14-89 58-132 (162)
53 KOG1142 Transcription initiati 95.8 0.025 5.5E-07 48.2 6.1 70 11-81 150-219 (258)
54 PF02291 TFIID-31kDa: Transcri 95.1 0.13 2.8E-06 39.6 7.5 89 8-98 3-94 (129)
55 cd07978 TAF13 The TATA Binding 94.7 0.22 4.8E-06 36.1 7.4 60 20-81 7-66 (92)
56 PTZ00252 histone H2A; Provisio 94.2 0.19 4.1E-06 39.1 6.4 72 12-88 22-100 (134)
57 TIGR03015 pepcterm_ATPase puta 91.8 0.57 1.2E-05 37.9 6.3 69 16-84 192-268 (269)
58 PRK00411 cdc6 cell division co 89.4 2.6 5.5E-05 36.2 8.5 72 18-89 209-289 (394)
59 KOG3423 Transcription initiati 89.2 2.3 4.9E-05 34.5 7.4 68 15-85 86-168 (176)
60 KOG4336 TBP-associated transcr 88.0 3.1 6.6E-05 36.6 7.9 73 20-96 10-82 (323)
61 TIGR02928 orc1/cdc6 family rep 86.5 4.3 9.3E-05 34.4 8.0 75 18-92 201-284 (365)
62 cd08045 TAF4 TATA Binding Prot 84.9 19 0.00042 29.2 11.2 77 13-89 42-126 (212)
63 KOG2549 Transcription initiati 84.0 5 0.00011 37.9 7.6 65 17-83 13-77 (576)
64 PF13654 AAA_32: AAA domain; P 82.9 5.4 0.00012 36.9 7.5 48 34-81 447-505 (509)
65 KOG2389 Predicted bromodomain 82.3 3.4 7.3E-05 36.9 5.6 71 13-85 27-97 (353)
66 COG1067 LonB Predicted ATP-dep 81.0 1.6 3.4E-05 41.7 3.4 46 35-81 339-398 (647)
67 TIGR00764 lon_rel lon-related 77.2 8.8 0.00019 36.2 7.0 50 34-83 330-392 (608)
68 PF13335 Mg_chelatase_2: Magne 75.3 11 0.00023 27.2 5.6 48 33-80 41-94 (96)
69 TIGR02902 spore_lonB ATP-depen 73.0 12 0.00027 34.5 6.8 63 21-84 268-334 (531)
70 KOG1757 Histone 2A [Chromatin 72.6 12 0.00026 28.7 5.4 64 13-80 28-95 (131)
71 PF07499 RuvA_C: RuvA, C-termi 72.1 12 0.00027 23.3 4.7 38 73-125 4-41 (47)
72 PF02861 Clp_N: Clp amino term 71.7 3.3 7.1E-05 25.4 1.9 26 58-83 1-26 (53)
73 KOG3334 Transcription initiati 65.2 61 0.0013 25.7 8.2 82 13-97 9-94 (148)
74 PRK12402 replication factor C 64.4 27 0.00058 29.0 6.5 76 15-92 183-259 (337)
75 TIGR01128 holA DNA polymerase 63.1 46 0.001 27.2 7.6 67 15-81 110-177 (302)
76 PRK00080 ruvB Holliday junctio 60.5 36 0.00078 28.9 6.7 70 16-85 180-253 (328)
77 TIGR02442 Cob-chelat-sub cobal 60.1 26 0.00056 33.1 6.3 53 27-80 243-302 (633)
78 PF08369 PCP_red: Proto-chloro 59.8 14 0.00031 23.3 3.1 41 37-78 3-44 (45)
79 PF08621 RPAP1_N: RPAP1-like, 59.3 9.4 0.0002 24.7 2.3 18 115-132 13-30 (49)
80 TIGR02030 BchI-ChlI magnesium 57.4 44 0.00095 29.3 6.9 53 26-79 247-306 (337)
81 COG5251 TAF40 Transcription in 57.4 13 0.00029 30.3 3.4 62 15-78 115-177 (199)
82 TIGR00635 ruvB Holliday juncti 57.3 40 0.00087 27.8 6.4 70 16-85 159-232 (305)
83 PF00531 Death: Death domain; 57.1 45 0.00098 22.0 5.5 29 67-95 55-83 (83)
84 PRK07452 DNA polymerase III su 55.9 45 0.00098 28.0 6.5 67 21-87 135-204 (326)
85 PRK13406 bchD magnesium chelat 55.8 26 0.00056 33.1 5.5 58 20-79 183-247 (584)
86 PF09114 MotA_activ: Transcrip 53.9 24 0.00053 26.0 3.9 34 19-52 51-88 (96)
87 PF12627 PolyA_pol_RNAbd: Prob 53.8 6.3 0.00014 25.4 0.8 58 32-93 1-62 (64)
88 KOG3901 Transcription initiati 53.2 39 0.00085 25.5 5.0 47 30-79 23-69 (109)
89 PRK09862 putative ATP-dependen 53.0 54 0.0012 30.5 7.0 57 33-89 437-499 (506)
90 PF07647 SAM_2: SAM domain (St 51.8 16 0.00035 23.4 2.6 25 69-93 3-27 (66)
91 CHL00081 chlI Mg-protoporyphyr 51.4 40 0.00086 29.9 5.7 53 26-79 260-319 (350)
92 PF00536 SAM_1: SAM domain (St 50.2 19 0.00042 23.0 2.7 22 71-92 4-25 (64)
93 TIGR00368 Mg chelatase-related 48.9 42 0.00091 31.0 5.6 47 34-80 445-497 (499)
94 PRK13765 ATP-dependent proteas 48.5 28 0.0006 33.3 4.5 47 34-80 339-398 (637)
95 TIGR02031 BchD-ChlD magnesium 48.1 59 0.0013 30.6 6.5 54 25-79 195-255 (589)
96 PF12010 DUF3502: Domain of un 48.1 24 0.00052 26.7 3.3 62 37-102 72-133 (134)
97 COG5095 TAF6 Transcription ini 48.1 39 0.00084 30.5 5.0 65 19-85 9-73 (450)
98 cd00166 SAM Sterile alpha moti 47.9 20 0.00043 22.2 2.4 24 70-93 2-25 (63)
99 PF05236 TAF4: Transcription i 46.7 30 0.00064 29.0 4.0 74 11-84 39-120 (264)
100 PRK09526 lacI lac repressor; R 46.2 31 0.00067 28.4 4.0 38 14-56 15-52 (342)
101 PF00356 LacI: Bacterial regul 45.7 51 0.0011 20.7 4.0 32 14-49 9-40 (46)
102 PRK05574 holA DNA polymerase I 43.7 81 0.0018 26.3 6.2 67 15-81 145-212 (340)
103 smart00454 SAM Sterile alpha m 43.2 26 0.00056 21.8 2.5 26 69-94 3-28 (68)
104 PRK13407 bchI magnesium chelat 43.0 74 0.0016 27.9 6.0 53 26-79 244-303 (334)
105 PRK14987 gluconate operon tran 41.7 33 0.00071 28.3 3.5 39 14-57 15-53 (331)
106 KOG2680 DNA helicase TIP49, TB 40.8 57 0.0012 29.6 4.9 49 31-79 374-426 (454)
107 PRK00440 rfc replication facto 40.8 1.1E+02 0.0025 24.9 6.6 66 16-83 161-227 (319)
108 COG1474 CDC6 Cdc6-related prot 40.2 50 0.0011 29.2 4.5 73 20-92 194-275 (366)
109 PRK07914 hypothetical protein; 39.3 81 0.0018 26.7 5.6 64 17-81 129-193 (320)
110 PF12022 DUF3510: Domain of un 38.7 1.7E+02 0.0036 21.9 7.0 46 84-129 72-123 (125)
111 PRK10423 transcriptional repre 37.5 54 0.0012 26.7 4.1 38 14-56 8-45 (327)
112 PF09339 HTH_IclR: IclR helix- 37.3 19 0.00041 22.5 1.1 17 12-28 26-42 (52)
113 PRK10727 DNA-binding transcrip 36.7 48 0.001 27.5 3.7 38 15-57 12-49 (343)
114 PRK14971 DNA polymerase III su 35.6 1.2E+02 0.0027 28.7 6.6 71 16-87 180-251 (614)
115 smart00350 MCM minichromosome 35.4 1.6E+02 0.0035 27.0 7.2 65 14-81 416-503 (509)
116 PF13405 EF-hand_6: EF-hand do 34.8 37 0.00081 18.8 2.0 26 58-83 5-31 (31)
117 PF03540 TFIID_30kDa: Transcri 33.9 1.4E+02 0.003 19.5 6.4 47 15-64 2-49 (51)
118 COG5162 Transcription initiati 33.9 2.4E+02 0.0051 23.1 7.0 51 35-85 106-189 (197)
119 TIGR01242 26Sp45 26S proteasom 33.7 51 0.0011 28.5 3.5 32 50-81 331-362 (364)
120 smart00354 HTH_LACI helix_turn 33.7 81 0.0018 20.8 3.8 33 14-50 10-42 (70)
121 cd04752 Commd4 COMM_Domain con 33.4 2.4E+02 0.0052 22.2 8.9 51 46-103 43-94 (174)
122 PRK03992 proteasome-activating 33.0 52 0.0011 29.0 3.5 33 50-82 340-372 (389)
123 PTZ00361 26 proteosome regulat 33.0 50 0.0011 30.1 3.4 31 51-81 393-423 (438)
124 TIGR01052 top6b DNA topoisomer 32.8 78 0.0017 29.5 4.7 50 34-97 434-483 (488)
125 PF07580 Peptidase_M26_C: M26 32.7 1.6E+02 0.0036 28.9 7.0 59 30-88 589-649 (737)
126 TIGR02454 CbiQ_TIGR cobalt ABC 32.5 73 0.0016 24.6 4.0 38 68-105 112-160 (198)
127 COG1224 TIP49 DNA helicase TIP 32.4 96 0.0021 28.6 5.1 49 31-79 377-429 (450)
128 PF10728 DUF2520: Domain of un 32.2 1.7E+02 0.0037 22.1 5.8 58 19-79 14-74 (132)
129 cd00083 HLH Helix-loop-helix d 32.0 75 0.0016 19.7 3.3 34 24-57 25-58 (60)
130 PF08681 DUF1778: Protein of u 31.8 18 0.00038 25.1 0.3 61 32-93 3-63 (80)
131 COG5340 Predicted transcriptio 31.7 71 0.0015 27.4 3.9 53 10-62 149-207 (269)
132 COG5248 TAF19 Transcription in 31.4 1.3E+02 0.0029 22.9 5.0 49 31-81 24-72 (126)
133 PRK06585 holA DNA polymerase I 31.1 1.2E+02 0.0026 25.6 5.3 64 18-81 144-209 (343)
134 cd01392 HTH_LacI Helix-turn-he 29.8 1E+02 0.0022 18.5 3.5 34 13-50 6-39 (52)
135 COG1724 Predicted RNA binding 29.8 31 0.00068 23.8 1.2 17 69-85 6-22 (66)
136 smart00027 EH Eps15 homology d 29.6 1E+02 0.0023 21.3 4.0 56 57-125 14-69 (96)
137 KOG0784 Isocitrate dehydrogena 29.5 41 0.00089 30.3 2.2 46 52-98 187-232 (375)
138 TIGR02397 dnaX_nterm DNA polym 29.3 2.3E+02 0.0051 23.6 6.8 62 18-80 178-240 (355)
139 KOG1792 Reticulon [Intracellul 29.0 89 0.0019 26.2 4.1 62 28-89 110-173 (230)
140 COG1500 Predicted exosome subu 28.3 1.6E+02 0.0036 25.0 5.5 70 21-93 72-144 (234)
141 PRK14961 DNA polymerase III su 27.9 2.1E+02 0.0045 24.8 6.3 66 16-82 178-244 (363)
142 PF08863 YolD: YolD-like prote 27.3 98 0.0021 21.0 3.5 22 112-133 18-39 (92)
143 PTZ00454 26S protease regulato 27.1 71 0.0015 28.6 3.4 31 51-81 355-385 (398)
144 COG1239 ChlI Mg-chelatase subu 27.1 1E+02 0.0023 28.3 4.4 53 27-80 261-320 (423)
145 PRK09492 treR trehalose repres 26.7 94 0.002 25.2 3.8 38 14-56 14-51 (315)
146 TIGR02903 spore_lon_C ATP-depe 26.3 1.4E+02 0.0031 28.2 5.4 71 19-89 356-437 (615)
147 PF13690 CheX: Chemotaxis phos 26.2 1.6E+02 0.0034 20.4 4.4 46 13-62 16-61 (94)
148 PRK09111 DNA polymerase III su 25.8 2.2E+02 0.0048 27.0 6.5 64 16-80 191-255 (598)
149 KOG0605 NDR and related serine 25.5 83 0.0018 29.9 3.6 76 14-94 390-470 (550)
150 PRK07764 DNA polymerase III su 25.4 2.5E+02 0.0054 27.8 7.0 62 16-77 179-241 (824)
151 PRK11303 DNA-binding transcrip 25.3 1.1E+02 0.0023 25.0 3.9 36 14-50 10-45 (328)
152 PRK08487 DNA polymerase III su 25.0 2.7E+02 0.0059 23.7 6.5 60 20-81 139-199 (328)
153 PF00403 HMA: Heavy-metal-asso 24.5 43 0.00092 21.1 1.1 16 70-85 47-62 (62)
154 PRK14964 DNA polymerase III su 24.1 2.4E+02 0.0052 26.2 6.3 66 16-82 175-241 (491)
155 TIGR02417 fruct_sucro_rep D-fr 23.9 1.2E+02 0.0027 24.7 4.0 39 15-55 10-48 (327)
156 PRK05907 hypothetical protein; 23.9 1.7E+02 0.0037 25.2 5.0 54 32-85 151-207 (311)
157 PRK14958 DNA polymerase III su 23.2 3.3E+02 0.0071 25.2 7.0 71 15-86 177-248 (509)
158 PF02361 CbiQ: Cobalt transpor 22.8 1.2E+02 0.0027 23.4 3.7 38 68-105 123-172 (224)
159 PRK14970 DNA polymerase III su 22.4 3.2E+02 0.0069 23.4 6.4 67 18-85 169-236 (367)
160 COG1466 HolA DNA polymerase II 22.2 2.5E+02 0.0053 24.1 5.7 51 32-82 157-207 (334)
161 PRK05629 hypothetical protein; 21.5 2.8E+02 0.006 23.4 5.8 49 31-80 142-190 (318)
162 PF06782 UPF0236: Uncharacteri 21.4 1.7E+02 0.0037 26.7 4.7 58 29-88 112-169 (470)
163 PF14434 Imm6: Immunity protei 21.3 3.4E+02 0.0074 20.5 5.7 36 53-89 25-62 (122)
164 PRK08691 DNA polymerase III su 21.1 3.6E+02 0.0077 26.5 7.0 67 16-83 178-245 (709)
165 TIGR02639 ClpA ATP-dependent C 20.8 1.2E+02 0.0026 29.1 3.8 23 57-79 11-33 (731)
166 TIGR01481 ccpA catabolite cont 20.5 1.3E+02 0.0028 24.5 3.5 38 14-56 11-48 (329)
167 KOG1528 Salt-sensitive 3'-phos 20.4 2.6E+02 0.0057 25.0 5.5 66 18-83 52-124 (351)
No 1
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=100.00 E-value=5.3e-51 Score=316.48 Aligned_cols=136 Identities=54% Similarity=0.837 Sum_probs=130.6
Q ss_pred cCCCCcccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh
Q 031627 6 IVGKSKEDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (156)
Q Consensus 6 ~~g~~~dd~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~ 85 (156)
..|..+|+++||+|||+||||+.||.+++|++|+|++|++||++||++||++||++|.++.||||+||||++||+.|||+
T Consensus 3 ~~~~~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~ 82 (156)
T KOG0871|consen 3 NDGKEDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFG 82 (156)
T ss_pred CCccccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchH
Confidence 45678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH-hCCC
Q 031627 86 EYIEEVYAAYEQHKLETMDSLKGGKWSNGAEMTEEEAAAEQQRMFAEARARM-NGGA 141 (156)
Q Consensus 86 ~yv~~l~~~l~~~k~~~~~r~k~~~k~~~~g~~eEel~~~Q~eLf~~ar~~~-~~~~ 141 (156)
+|++++.+++++||..+++|++++.|++++|||+|||++|||+||++||+|+ +++.
T Consensus 83 eYiee~~~vl~~~K~~~~~~~~kssk~e~~Gi~eEEL~~qQqeLf~~ARar~~~~~~ 139 (156)
T KOG0871|consen 83 EYIEEAEEVLENCKEEAKKRRRKSSKFEKSGIPEEELLRQQQELFAKARARLMQQAA 139 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhHHhcCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 9999999999999999999999999999999999999999999999999995 4443
No 2
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=100.00 E-value=6.7e-43 Score=266.20 Aligned_cols=134 Identities=38% Similarity=0.590 Sum_probs=130.7
Q ss_pred CCCcccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhh
Q 031627 8 GKSKEDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEY 87 (156)
Q Consensus 8 g~~~dd~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~y 87 (156)
|..+|+++||+|||+|+|.++||.+..++||||+++++||.+||++||++||++|+++.+|||+++||++||+.|||.+|
T Consensus 4 ~~~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~ey 83 (148)
T COG5150 4 EKNDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEY 83 (148)
T ss_pred ccccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHH
Confidence 56789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhcccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhCCC
Q 031627 88 IEEVYAAYEQHKLETMDSLKGGKWSNGAEMTEEEAAAEQQRMFAEARARMNGGA 141 (156)
Q Consensus 88 v~~l~~~l~~~k~~~~~r~k~~~k~~~~g~~eEel~~~Q~eLf~~ar~~~~~~~ 141 (156)
++.+.+.+.+|+..+|.|++|..||++||+|+|||+|||++||.+||.||+-.-
T Consensus 84 i~~~~e~~~n~k~~qK~ke~k~sKFk~SGls~eELlrQQeeLf~~ar~rf~h~~ 137 (148)
T COG5150 84 IESCMEEHENYKSYQKQKESKISKFKDSGLSMEELLRQQEELFQNARLRFEHSF 137 (148)
T ss_pred HHHHHHHHHHHHHHHhhchhhhhHHHhcCCCHHHHHHHHHHHHHHHHHHhcccc
Confidence 999999999999999999999999999999999999999999999999997665
No 3
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=99.97 E-value=7.3e-32 Score=211.50 Aligned_cols=99 Identities=31% Similarity=0.587 Sum_probs=93.9
Q ss_pred CcccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHH
Q 031627 10 SKEDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIE 89 (156)
Q Consensus 10 ~~dd~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~ 89 (156)
.+.|..||+|+|.||||..||++.+|||||++.+++|++|||.|||++|+++|..++||||++|||+|||..|||++|++
T Consensus 27 reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe~Y~e 106 (168)
T KOG0869|consen 27 REQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFENYAE 106 (168)
T ss_pred chhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcHhHHH
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhcccC
Q 031627 90 EVYAAYEQHKLETMDSLKG 108 (156)
Q Consensus 90 ~l~~~l~~~k~~~~~r~k~ 108 (156)
+|+.+|..||+....|...
T Consensus 107 plkiyL~kYRe~e~e~~~~ 125 (168)
T KOG0869|consen 107 PLKIYLQKYRELEGERGRS 125 (168)
T ss_pred HHHHHHHHHHHHhhhcccc
Confidence 9999999999987655443
No 4
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.94 E-value=1.4e-26 Score=182.88 Aligned_cols=97 Identities=29% Similarity=0.518 Sum_probs=93.1
Q ss_pred CcccccCcHHHHHHHHHhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhH
Q 031627 10 SKEDASLPKATMTKIIKEMLPAD-VRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYI 88 (156)
Q Consensus 10 ~~dd~~LP~A~V~riiKe~LP~~-~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv 88 (156)
.++++.||+|+|.||||+.||+. +.|||||+.+|+++|++||+|||+.|+++|...+||||+++||++||++|||.+|+
T Consensus 5 ri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f~ 84 (172)
T KOG0870|consen 5 RIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSFV 84 (172)
T ss_pred hHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHHh
Confidence 47899999999999999999987 99999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhcc
Q 031627 89 EEVYAAYEQHKLETMDSL 106 (156)
Q Consensus 89 ~~l~~~l~~~k~~~~~r~ 106 (156)
++|+..|+.|+..++.|+
T Consensus 85 ~plk~~Le~yk~~~k~Kk 102 (172)
T KOG0870|consen 85 NPLKSALEAYKKAVKQKK 102 (172)
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 999999999998887544
No 5
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=99.77 E-value=1.4e-18 Score=117.29 Aligned_cols=64 Identities=36% Similarity=0.603 Sum_probs=59.2
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
.||.+.|.||||.. |+..+||+||..+|.+|+++||.||+.+|+++|..++||||+++||..||
T Consensus 2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 69999999999999 88899999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.63 E-value=4.8e-16 Score=112.95 Aligned_cols=76 Identities=26% Similarity=0.417 Sum_probs=72.3
Q ss_pred CcccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhh
Q 031627 10 SKEDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEY 87 (156)
Q Consensus 10 ~~dd~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~y 87 (156)
...+..||+++|.||||+..++ +||.+|.+.+++|..+|+..|+..|+++|.+.|||||+++||..|++.+||..|
T Consensus 14 ~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~~ 89 (91)
T COG2036 14 RSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIY 89 (91)
T ss_pred hhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccccc
Confidence 3567899999999999999985 999999999999999999999999999999999999999999999999999866
No 7
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=99.13 E-value=2.4e-10 Score=82.21 Aligned_cols=69 Identities=13% Similarity=0.184 Sum_probs=65.4
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh
Q 031627 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~ 85 (156)
.||++.|.||++... -.+||.|+.+.+.++..+|+..|...|..+|++.+||||+++||.-||+..|-.
T Consensus 13 gi~k~~I~RLarr~G--vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~ 81 (85)
T cd00076 13 GITKPAIRRLARRGG--VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 81 (85)
T ss_pred cCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCC
Confidence 599999999999985 678999999999999999999999999999999999999999999999998854
No 8
>PLN00035 histone H4; Provisional
Probab=99.06 E-value=6.5e-10 Score=82.55 Aligned_cols=69 Identities=13% Similarity=0.123 Sum_probs=65.1
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh
Q 031627 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~ 85 (156)
.||+++|.||++... ..+||.|+.+.+.+...+|+.-|...|..+|++.+||||+++||.-||+..|=.
T Consensus 29 ~ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ 97 (103)
T PLN00035 29 GITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred cCCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCc
Confidence 599999999999985 678999999999999999999999999999999999999999999999987753
No 9
>PTZ00015 histone H4; Provisional
Probab=99.01 E-value=1.5e-09 Score=80.54 Aligned_cols=70 Identities=16% Similarity=0.199 Sum_probs=65.7
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh
Q 031627 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (156)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~ 85 (156)
..||+++|.||++... -.+||.|+.+.+.++..+|+..|...|..+|++.+||||+++||.-||+..|-.
T Consensus 29 ~gI~k~~IrRLarr~G--vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~ 98 (102)
T PTZ00015 29 RGITKGAIRRLARRGG--VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRT 98 (102)
T ss_pred cCCCHHHHHHHHHHcC--CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCC
Confidence 4699999999999985 578999999999999999999999999999999999999999999999988754
No 10
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=98.88 E-value=1e-08 Score=70.14 Aligned_cols=64 Identities=20% Similarity=0.225 Sum_probs=60.0
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
.||+++|.||++... --+||.|+...|.+-.+.|+.-|..+|..++++.+|||++++||-.||+
T Consensus 2 ~~p~~~i~ria~~~G--i~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLG--IGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCC--CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 589999999999874 3579999999999999999999999999999999999999999999985
No 11
>smart00417 H4 Histone H4.
Probab=98.85 E-value=1e-08 Score=72.11 Aligned_cols=62 Identities=13% Similarity=0.156 Sum_probs=58.2
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhh
Q 031627 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKA 78 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~A 78 (156)
.||+++|.||++... --+||.++.+.+.+...+|+..|...|..+|++.+||||+++||..|
T Consensus 13 gI~k~~IrRLaRr~G--vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 13 GITKPAIRRLARRGG--VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred CCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 599999999999985 57899999999999999999999999999999999999999999754
No 12
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=98.79 E-value=4.1e-08 Score=68.01 Aligned_cols=65 Identities=23% Similarity=0.404 Sum_probs=61.7
Q ss_pred CcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 16 LPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 16 LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
+++..+..++++.-| +.+++.|+.++|++.+.+|+.-++..|...|.+.||+||.++||.-+|+.
T Consensus 2 ~~k~~l~~lv~~id~-~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 2 LTKRKLQELLKEIDP-REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred CcHHHHHHHHHhhCC-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 678899999999877 79999999999999999999999999999999999999999999999875
No 13
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=98.78 E-value=2e-08 Score=68.65 Aligned_cols=68 Identities=16% Similarity=0.308 Sum_probs=62.4
Q ss_pred cccCcHHHHHHHHHhhCCC---CccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 13 DASLPKATMTKIIKEMLPA---DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 13 d~~LP~A~V~riiKe~LP~---~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
...+|+..|.|+.++..++ ..+||++|.++|+..+..|+.-|...|..+|...+|+||++.||..|+.
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 3568999999999998873 2799999999999999999999999999999999999999999999874
No 14
>smart00428 H3 Histone H3.
Probab=98.53 E-value=2.2e-07 Score=69.31 Aligned_cols=69 Identities=20% Similarity=0.298 Sum_probs=63.9
Q ss_pred cccccCcHHHHHHHHHhhCCC-----CccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 11 KEDASLPKATMTKIIKEMLPA-----DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP~-----~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
..++.+|+....|+++++..+ +++++.+|..+|+++++.|+.-+...|+..|.+.+|+||.+.|+.-|.
T Consensus 25 st~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ 98 (105)
T smart00428 25 STDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLAR 98 (105)
T ss_pred CcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHH
Confidence 467899999999999998753 789999999999999999999999999999999999999999997765
No 15
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.52 E-value=1.1e-07 Score=79.24 Aligned_cols=78 Identities=19% Similarity=0.331 Sum_probs=71.4
Q ss_pred ccccCcHHHHHHHHHhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHHH
Q 031627 12 EDASLPKATMTKIIKEMLPADVR-VARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEE 90 (156)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~~~~-iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~~ 90 (156)
.+++||.|.|.|+||-- ++++ ||.||..++.+.|..||..||-.|.-.+++++|+|+--.||-.|++.-++.||+=.
T Consensus 106 k~h~LPlARIkkvMKtd--edVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLid 183 (286)
T COG5208 106 KDHNLPLARIKKVMKTD--EDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLID 183 (286)
T ss_pred HhccCcHHHHHHHHhcc--cchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhh
Confidence 46789999999999953 5676 99999999999999999999999999999999999999999999999999888754
Q ss_pred H
Q 031627 91 V 91 (156)
Q Consensus 91 l 91 (156)
+
T Consensus 184 i 184 (286)
T COG5208 184 I 184 (286)
T ss_pred h
Confidence 4
No 16
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.26 E-value=6.6e-06 Score=57.36 Aligned_cols=66 Identities=15% Similarity=0.181 Sum_probs=59.3
Q ss_pred HHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh
Q 031627 18 KATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (156)
Q Consensus 18 ~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~ 85 (156)
+-.|.+|++... --+++..|.+.|.+....|+..|+..+..+|+..||+++++.||..||.++|+.
T Consensus 9 ~~~Vaqil~~~G--f~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESAG--FDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 446777787763 357999999999999999999999999999999999999999999999999974
No 17
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=98.16 E-value=7e-06 Score=62.04 Aligned_cols=69 Identities=17% Similarity=0.185 Sum_probs=63.1
Q ss_pred ccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 12 EDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
-.+.||.+.|.|+|++.-. ..||+.+|...|..+.+.+..-|...|...|...+|++|+|+||..|+..
T Consensus 17 agL~fPV~ri~R~Lk~~~~-a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 17 AGLQFPVGRIHRYLKKGRY-AERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred cCccCcHHHHHHHHHcCcc-ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 4689999999999998432 58999999999999999999999999999999999999999999999865
No 18
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.03 E-value=5.7e-06 Score=69.35 Aligned_cols=77 Identities=22% Similarity=0.308 Sum_probs=68.5
Q ss_pred cccccCcHHHHHHHHHhhCCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHH
Q 031627 11 KEDASLPKATMTKIIKEMLPADV-RVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIE 89 (156)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP~~~-~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~ 89 (156)
.....||++.|.||||.. +++ .|+.||..++.+||..||..|+..|...++..+|+|+...|+-.|+..-.-.+|+-
T Consensus 70 ~~~~~lPlaRiKkimK~d--edv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~ 147 (236)
T KOG1657|consen 70 FKNHILPLARIKKIMKSD--EDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLR 147 (236)
T ss_pred hhhccCcHhhcccccccc--ccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCcccee
Confidence 345699999999999964 344 59999999999999999999999999999999999999999999999877766664
No 19
>PLN00161 histone H3; Provisional
Probab=97.94 E-value=2.9e-05 Score=60.30 Aligned_cols=69 Identities=17% Similarity=0.237 Sum_probs=62.9
Q ss_pred cccccCcHHHHHHHHHhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 11 KEDASLPKATMTKIIKEMLP----ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP----~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
..++.+|++...|+++++.. .++++..+|..+|+++++.|+.-+-..||-.|.+.+|.||.+.|+.-|.
T Consensus 51 st~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ 123 (135)
T PLN00161 51 STELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLAR 123 (135)
T ss_pred ccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHH
Confidence 35788999999999999863 4699999999999999999999999999999999999999999997664
No 20
>PLN00121 histone H3; Provisional
Probab=97.94 E-value=1.5e-05 Score=61.99 Aligned_cols=69 Identities=17% Similarity=0.260 Sum_probs=63.6
Q ss_pred cccccCcHHHHHHHHHhhCCC---CccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 11 KEDASLPKATMTKIIKEMLPA---DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP~---~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
..++.+|+....|+++++..+ ++++..+|..+|+++++.|+.-+-..+|-.|.+.+|.||.+.|+.-+.
T Consensus 58 st~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 58 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred ccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 358899999999999998863 799999999999999999999999999999999999999999997664
No 21
>PLN00160 histone H3; Provisional
Probab=97.94 E-value=2.3e-05 Score=57.76 Aligned_cols=69 Identities=17% Similarity=0.169 Sum_probs=62.9
Q ss_pred cccccCcHHHHHHHHHhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 11 KEDASLPKATMTKIIKEMLP----ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP----~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
..++.+|++...|+++++.. .++++..+|..+|++++.-|+.-+-..+|-.|.+.+|.||.+.|+.-|.
T Consensus 17 st~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ 89 (97)
T PLN00160 17 STDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLAR 89 (97)
T ss_pred chhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHH
Confidence 45789999999999999864 3599999999999999999999999999999999999999999997664
No 22
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=97.85 E-value=9.2e-05 Score=53.19 Aligned_cols=66 Identities=20% Similarity=0.326 Sum_probs=61.4
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC---CccChhhhhhhhhhc
Q 031627 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDK---RTIAPEHVLKALEVL 82 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~R---KTI~~edVl~AL~~L 82 (156)
.||++.|.|||...++ .+++.+...+|.-.+.+||.-|..+|.++..+.+. ..|.|+||-.|...|
T Consensus 16 ~f~k~~iKr~~~~~~~--~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 16 SFPKAAIKRLIQSVTG--QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hccHHHHHHHHHHHcC--CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 5999999999999995 89999999999999999999999999999998766 789999999998766
No 23
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=97.85 E-value=7e-05 Score=56.48 Aligned_cols=76 Identities=13% Similarity=0.086 Sum_probs=63.6
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHHH-HHHHHHH
Q 031627 20 TMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEE-VYAAYEQ 97 (156)
Q Consensus 20 ~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~~-l~~~l~~ 97 (156)
.|.+|+|+.. ..+++.+++..|.+.+..++.-|...|...|.+.||+||+++||.-|++..+-..|.+. -++.+-+
T Consensus 6 ~v~~iLk~~G--v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~ 82 (117)
T cd07979 6 VIAAILKSMG--ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLE 82 (117)
T ss_pred HHHHHHHHCC--CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHH
Confidence 6888888873 46899999999999999999999999999999999999999999999988766555443 3444433
No 24
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.85 E-value=7.3e-05 Score=52.72 Aligned_cols=61 Identities=18% Similarity=0.182 Sum_probs=52.5
Q ss_pred HHHHHHHhhC-CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 20 TMTKIIKEML-PADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 20 ~V~riiKe~L-P~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
+|.||+.+.. +.++.+|+.+..+|.+.+-.++..++..---.|.+.||+||+++||+-...
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 6889999875 568999999999999999999999999999999999999999999986553
No 25
>smart00427 H2B Histone H2B.
Probab=97.84 E-value=8.6e-05 Score=53.97 Aligned_cols=63 Identities=14% Similarity=0.342 Sum_probs=58.4
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcC
Q 031627 20 TMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLG 83 (156)
Q Consensus 20 ~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~Lg 83 (156)
-|+|++|++-| +..||..+...+.-...-+..-|+.+|...|...+|+||++.+|..|.+-+=
T Consensus 6 Yi~kvLKqVhp-d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~L 68 (89)
T smart00427 6 YIYKVLKQVHP-DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLIL 68 (89)
T ss_pred HHHHHHHHhCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHc
Confidence 58999999998 7899999999999999999999999999999999999999999999986553
No 26
>PTZ00018 histone H3; Provisional
Probab=97.81 E-value=3.9e-05 Score=59.67 Aligned_cols=68 Identities=18% Similarity=0.267 Sum_probs=62.9
Q ss_pred ccccCcHHHHHHHHHhhCC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 12 EDASLPKATMTKIIKEMLP---ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 12 dd~~LP~A~V~riiKe~LP---~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
.++.+|+....|+++++.. .++++..+|..+|+++++.|+.-+-..+|-.|.+.+|.||.+.|+.-|.
T Consensus 59 t~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 59 TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred chhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 5789999999999999864 4799999999999999999999999999999999999999999997664
No 27
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=97.77 E-value=8.8e-05 Score=64.65 Aligned_cols=67 Identities=15% Similarity=0.198 Sum_probs=58.9
Q ss_pred cHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh
Q 031627 17 PKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (156)
Q Consensus 17 P~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~ 85 (156)
|..+|.-|++... --++++|+..+|.+....++.-|+.+|...+.+.+|||++++||-.||+.++.+
T Consensus 1 ~~~~i~~ia~~~G--i~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 1 PQESIKLIAESLG--IDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred ChhHHHHHHHHcC--CCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 4567777777652 339999999999999999999999999999999999999999999999887655
No 28
>PLN00158 histone H2B; Provisional
Probab=97.64 E-value=0.00025 Score=53.83 Aligned_cols=71 Identities=17% Similarity=0.316 Sum_probs=62.0
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhh
Q 031627 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGE 86 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~ 86 (156)
.--..-|+|++|++-| +..||..+...+.-....+..-|+.||...|...+|+||++.+|..|..-+==++
T Consensus 27 esy~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvLpgE 97 (116)
T PLN00158 27 ETYKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGE 97 (116)
T ss_pred ccHHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhccHH
Confidence 3344569999999998 7899999999999999999999999999999999999999999999986553333
No 29
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.63 E-value=0.00028 Score=58.60 Aligned_cols=113 Identities=14% Similarity=0.181 Sum_probs=85.8
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHHHHHH
Q 031627 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYA 93 (156)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~ 93 (156)
-.+|.+.|.|||...= +--+|+.-+..+|.++...|+.-|-..+-+++...+-|||+++|+..++..-.-.||+.++-.
T Consensus 12 trfp~aRiKKIMQ~dE-dIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~v~ 90 (224)
T KOG1659|consen 12 TRFPPARIKKIMQSDE-DIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEVVE 90 (224)
T ss_pred ccCCHHHHHHHHhhhh-hhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHHHH
Confidence 3689999999998542 124799999999999999999999999999999999999999999999999998899988655
Q ss_pred HHHHHHHH--h-hhcccCCCCCCCCCCCHHHHHHHHHH
Q 031627 94 AYEQHKLE--T-MDSLKGGKWSNGAEMTEEEAAAEQQR 128 (156)
Q Consensus 94 ~l~~~k~~--~-~~r~k~~~k~~~~g~~eEel~~~Q~e 128 (156)
.....-.. . +-.+++. ...+.+.+.|.....+++
T Consensus 91 ~vpd~~~~~ee~s~t~rr~-~~~~~~~sdes~~~~~a~ 127 (224)
T KOG1659|consen 91 KVPDRQQAEEESSMTKRRK-MLDEQQDSDESSAKLTAQ 127 (224)
T ss_pred hcCCCccchhhcccccccc-ccccccccCHHHHHHHHh
Confidence 44332211 1 1111111 456677777777665433
No 30
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.63 E-value=0.00012 Score=65.59 Aligned_cols=64 Identities=16% Similarity=0.297 Sum_probs=48.1
Q ss_pred cccccCcHHHHHHHHHhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhh
Q 031627 11 KEDASLPKATMTKIIKEMLP----ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEH 74 (156)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP----~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~ed 74 (156)
+.--.||.+.|.|++....- .+++|+|||..+|.+|...|...|+.---.+|.+.|||||..+|
T Consensus 347 i~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 347 IPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp -----S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 45568999999999887753 57999999999999999999999999999999999999999876
No 31
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=97.61 E-value=0.0005 Score=47.53 Aligned_cols=63 Identities=16% Similarity=0.282 Sum_probs=55.9
Q ss_pred HHHHHHHhhCCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh
Q 031627 20 TMTKIIKEMLPADV-RVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (156)
Q Consensus 20 ~V~riiKe~LP~~~-~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~ 85 (156)
.|.+|++.. +. .++..|.+.|.+.+..||..|++.+...|+..+|...++.||..||.++|+.
T Consensus 11 ~va~il~~~---GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 11 SVAQILKHA---GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHc---CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 455555554 34 6999999999999999999999999999999999999999999999999984
No 32
>PTZ00463 histone H2B; Provisional
Probab=97.61 E-value=0.0003 Score=53.40 Aligned_cols=66 Identities=18% Similarity=0.431 Sum_probs=59.3
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhh
Q 031627 20 TMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGE 86 (156)
Q Consensus 20 ~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~ 86 (156)
-|+|++|++-| +..||..+...|+-...-...-|++||...|...+|+||++.+|..|..-+==++
T Consensus 33 YI~KVLKqVhP-d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLlLpGE 98 (117)
T PTZ00463 33 YIFKVLKQVHP-DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGE 98 (117)
T ss_pred HHHHHHHhhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhcccHH
Confidence 49999999998 7899999999999999999999999999999999999999999999986553333
No 33
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=97.58 E-value=0.00042 Score=47.85 Aligned_cols=63 Identities=22% Similarity=0.381 Sum_probs=51.4
Q ss_pred HHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 18 KATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 18 ~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
+..++.+|+++-| +..+..|+.++|.+.+.+||.-+.+.|-..|++.+-.||...||.-.|+.
T Consensus 2 K~~l~~Lv~~iDp-~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 2 KRKLQELVKQIDP-NEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHHHHCC-S-S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred hHHHHHHHHHcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 4568889999876 89999999999999999999999999999999999999999999888764
No 34
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=97.57 E-value=0.00013 Score=50.87 Aligned_cols=65 Identities=20% Similarity=0.329 Sum_probs=54.7
Q ss_pred cHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCc-cChhhhhhhhhh
Q 031627 17 PKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRT-IAPEHVLKALEV 81 (156)
Q Consensus 17 P~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKT-I~~edVl~AL~~ 81 (156)
|+.+|.||++.... +..+|++||..++.+....||.--...|.+.+..++..+ |..+|+-+.+-.
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq 67 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ 67 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 88999999998774 579999999999999999999999999999999999998 999999876644
No 35
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=97.51 E-value=0.00046 Score=50.21 Aligned_cols=67 Identities=21% Similarity=0.338 Sum_probs=51.9
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC-ccChhhhhhhhhhc
Q 031627 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKR-TIAPEHVLKALEVL 82 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RK-TI~~edVl~AL~~L 82 (156)
.||+++|.|||...+. +..|+.-...+|.-.+..||--|-.+|.+++...+.. .|.|.|+-.|...|
T Consensus 23 ~~~k~~ikkli~~~~~-~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 23 SFNKAAIKKLINQVLG-NQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp ---HHHHHHHHHHHHS--S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcC-CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 6999999999999995 5899999999999999999999999999999975544 79999999997765
No 36
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=97.41 E-value=0.00072 Score=49.39 Aligned_cols=67 Identities=13% Similarity=0.138 Sum_probs=59.2
Q ss_pred CcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcCh
Q 031627 16 LPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGF 84 (156)
Q Consensus 16 LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF 84 (156)
+.+-+|.||.+... --+|+--.-+.+.....+||.-+-+-|...+++.+||||++-||+-+|+..|-
T Consensus 30 itKpaIRRlARr~G--VkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~ 96 (103)
T KOG3467|consen 30 ITKPAIRRLARRGG--VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred cchHHHHHHHHhcC--cchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCc
Confidence 55778899988764 34688888888999999999999999999999999999999999999999875
No 37
>PF15510 CENP-W: Centromere kinetochore component W
Probab=97.07 E-value=0.001 Score=48.90 Aligned_cols=66 Identities=24% Similarity=0.418 Sum_probs=57.2
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHH--------------HHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 15 SLPKATMTKIIKEMLPADVRVARDAQDL--------------LIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskda~~~--------------i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
.-|++.+.|++|..-| .+++....-.+ +.--|-.||+-|+-||...|-.++-.||.++||+.|-+
T Consensus 16 kaPrgfLkrv~Kr~Kp-hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaK 94 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKP-HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAAK 94 (102)
T ss_pred hCchHHHHHHHHhcCC-ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHH
Confidence 5699999999998887 78877766656 66778999999999999999999999999999999865
Q ss_pred h
Q 031627 81 V 81 (156)
Q Consensus 81 ~ 81 (156)
.
T Consensus 95 v 95 (102)
T PF15510_consen 95 V 95 (102)
T ss_pred H
Confidence 3
No 38
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.00 E-value=0.0019 Score=49.40 Aligned_cols=68 Identities=15% Similarity=0.210 Sum_probs=59.2
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
-+.+|...|.|++|. -.-.+||+++|...+.-|..-.+..|..-|-..|...++|.|.|.|+-.|+..
T Consensus 24 gl~fpvgrvkr~lk~-~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrn 91 (132)
T COG5262 24 GLIFPVGRVKRLLKK-GNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRN 91 (132)
T ss_pred CccccHHHHHHHHHc-CccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcC
Confidence 478999999999993 33479999999999999988778888888888899999999999999999753
No 39
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=96.97 E-value=0.0065 Score=41.80 Aligned_cols=63 Identities=13% Similarity=0.218 Sum_probs=48.6
Q ss_pred cCcHHHHHHHHHhhCCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 15 SLPKATMTKIIKEMLPADV-RVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~-~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
.+|..+|.-+.. ++ ++ .++.|+...|.+=++--|..|-.+|.....+.+|++++++||-.||+
T Consensus 3 ~~~~esvk~iAe-s~--Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAE-SL--GISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHH-HT--T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHH-Hc--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 367777765554 55 35 79999999999999999999999999999999999999999999985
No 40
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=96.92 E-value=0.0037 Score=46.78 Aligned_cols=79 Identities=14% Similarity=0.187 Sum_probs=69.6
Q ss_pred ccCcHHHHHHHHHhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHHHHH
Q 031627 14 ASLPKATMTKIIKEMLPAD-VRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVY 92 (156)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~-~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~~l~ 92 (156)
-.+|.|.|.|||.-. ++ -+|+.-+.....++...|+..|-..+-..+...+-|.|+.+++..|...-.=.||+..+.
T Consensus 22 trFP~ar~KkIMQ~d--eDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~ 99 (113)
T COG5247 22 TRFPIARLKKIMQLD--EDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNME 99 (113)
T ss_pred hcCCHHHHHHHHHhh--hhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHH
Confidence 379999999999843 34 469999999999999999999999999999999999999999999998888778887765
Q ss_pred HH
Q 031627 93 AA 94 (156)
Q Consensus 93 ~~ 94 (156)
.+
T Consensus 100 ~~ 101 (113)
T COG5247 100 QF 101 (113)
T ss_pred Hh
Confidence 53
No 41
>smart00414 H2A Histone 2A.
Probab=96.84 E-value=0.0045 Score=46.15 Aligned_cols=69 Identities=17% Similarity=0.219 Sum_probs=59.1
Q ss_pred ccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 12 EDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
-.+.||.+.|.|++|+.-. ..||+..|...|.-+..-+...|-.-|-..|...+++.|+|+|+..|+..
T Consensus 6 agL~fPVgRi~r~Lk~~~~-~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 6 AGLQFPVGRIHRLLRKGTY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred CCccCchHHHHHHHHcCcc-ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 3589999999999998643 56999999999998887777777777888888899999999999999865
No 42
>PLN00154 histone H2A; Provisional
Probab=96.58 E-value=0.0077 Score=46.93 Aligned_cols=70 Identities=16% Similarity=0.159 Sum_probs=56.6
Q ss_pred ccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 12 EDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
-.+.||.+.|.|++|+...-..||+..|...|.-..+-+..-|-.-|-..|...+++-|+|.||..|+..
T Consensus 35 AgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 35 AGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred cCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 3689999999999999764457999999999888765555555555666788889999999999999854
No 43
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.53 E-value=0.0096 Score=45.91 Aligned_cols=62 Identities=16% Similarity=0.350 Sum_probs=56.7
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhc
Q 031627 20 TMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVL 82 (156)
Q Consensus 20 ~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~L 82 (156)
.|.|++|++-|+ .-|+..+..+++-....++-.|+++|+..+...+|.||+..+|..|..-|
T Consensus 42 yv~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 42 YVYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred ehhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 378899999985 88999999999999999999999999999999999999999999987543
No 44
>PTZ00017 histone H2A; Provisional
Probab=96.39 E-value=0.0092 Score=46.38 Aligned_cols=76 Identities=16% Similarity=0.189 Sum_probs=62.3
Q ss_pred ccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh-cChhhhH
Q 031627 12 EDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV-LGFGEYI 88 (156)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~-LgF~~yv 88 (156)
-.+.||.+.|.|++++.-- ..||+..|...|.-+..-+..-|-.-|-..|...+++-|+|.||..|+.. -+|..++
T Consensus 24 agL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~nDeEL~~Ll 100 (134)
T PTZ00017 24 AGLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKLL 100 (134)
T ss_pred CCcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccCcHHHHHHH
Confidence 3689999999999998643 56999999999999888777777777888888999999999999999853 4444433
No 45
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=96.28 E-value=0.0061 Score=44.16 Aligned_cols=60 Identities=20% Similarity=0.245 Sum_probs=29.7
Q ss_pred HHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 21 MTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 21 V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
|..+|-.- ++.-.-..|+..+|-+...+||..+...|..+|...|+++|+.+|++-+|..
T Consensus 7 I~~mMy~f-GD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 7 IRQMMYGF-GDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp CHHHHHCT-TS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHHc-CCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 34555543 3456788999999999999999999999999999999999999999999864
No 46
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.27 E-value=0.014 Score=45.18 Aligned_cols=68 Identities=15% Similarity=0.211 Sum_probs=52.4
Q ss_pred ccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 12 EDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
-.+.+|...|.|++|+ .--..+|+.+|...+.-|..-....|..-|-..+..++|.-|+|.||..|+.
T Consensus 24 agl~fPvgri~r~Lr~-~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 24 AGLQFPVGRIHRLLRK-GRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred cccccCHHHHHHHHHc-cchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 3578999999999999 3336899999999999554444444444455556677888899999999985
No 47
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=96.23 E-value=0.0054 Score=50.34 Aligned_cols=69 Identities=19% Similarity=0.302 Sum_probs=61.1
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC-ccChhhhhhhhhhcChh
Q 031627 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKR-TIAPEHVLKALEVLGFG 85 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RK-TI~~edVl~AL~~LgF~ 85 (156)
.||+++|.|||..+.. -.|+.-+..++.=.+.+||--|--+|.++|..-+.. .|.|.||-.|...|+..
T Consensus 112 ~f~Ka~iKkL~~~itg--~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~q 181 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITG--QSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQ 181 (195)
T ss_pred cCCHHHHHHHHHHHhC--CccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhc
Confidence 6999999999999985 339999999999999999999999999999987664 59999999998777654
No 48
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=96.09 E-value=0.0049 Score=48.04 Aligned_cols=71 Identities=18% Similarity=0.298 Sum_probs=62.1
Q ss_pred cccccCcHHHHHHHHHhhCC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 11 KEDASLPKATMTKIIKEMLP---ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP---~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
..|+.+++....|++++.-+ .++++...|..+|++++.-|+.-|--.+|-.|.+.+|-||.|.||--|..-
T Consensus 59 stdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArri 132 (137)
T KOG1745|consen 59 STDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 132 (137)
T ss_pred hhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhc
Confidence 35778888888888885554 489999999999999999999999999999999999999999999877643
No 49
>PLN00157 histone H2A; Provisional
Probab=96.01 E-value=0.018 Score=44.68 Aligned_cols=75 Identities=16% Similarity=0.180 Sum_probs=60.0
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh-cChhhhH
Q 031627 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV-LGFGEYI 88 (156)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~-LgF~~yv 88 (156)
.+.||...|.|++++.-- ..||+..|...|.-+..-+..-|-.-|-..|...+++-|+|.||..|+.. -+|..++
T Consensus 24 gL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~nDeEL~~Ll 99 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRNDEELSKLL 99 (132)
T ss_pred CcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccCcHHHHHHH
Confidence 689999999999998543 57999999999988776666666666777788889999999999999854 4444443
No 50
>PLN00153 histone H2A; Provisional
Probab=96.00 E-value=0.019 Score=44.38 Aligned_cols=76 Identities=16% Similarity=0.208 Sum_probs=61.0
Q ss_pred ccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh-cChhhhH
Q 031627 12 EDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV-LGFGEYI 88 (156)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~-LgF~~yv 88 (156)
-.+.+|...|.|++++.-. ..||+..|...+.-+..-++.-|-.-|-..|...+++-|+|.||..|+.. -+|..++
T Consensus 21 agL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~nDeEL~~Ll 97 (129)
T PLN00153 21 AGLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLL 97 (129)
T ss_pred cCcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccCcHHHHHHH
Confidence 3689999999999998654 57999999999988877666666666777788889999999999999854 4444443
No 51
>PLN00156 histone H2AX; Provisional
Probab=96.00 E-value=0.022 Score=44.58 Aligned_cols=76 Identities=16% Similarity=0.175 Sum_probs=59.0
Q ss_pred ccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh-cChhhhH
Q 031627 12 EDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV-LGFGEYI 88 (156)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~-LgF~~yv 88 (156)
-.+.+|...|.|++++.-- ..||+..|...+.-+..-...-|-.-|-..|...+++-|+|+||..|+.. -+|..++
T Consensus 26 AgL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrnDeEL~~Ll 102 (139)
T PLN00156 26 AGLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLL 102 (139)
T ss_pred cCcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccCcHHHHHHH
Confidence 3689999999999998643 56999999999888766555555556666788889999999999999854 4444333
No 52
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=95.94 E-value=0.0082 Score=47.79 Aligned_cols=74 Identities=19% Similarity=0.313 Sum_probs=61.7
Q ss_pred ccCcHHHHHHHHHhhCCCCccc-cHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHH
Q 031627 14 ASLPKATMTKIIKEMLPADVRV-ARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIE 89 (156)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~i-skda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~ 89 (156)
..||.+.|..+++ +++++++ .+|+..+|.+++.-||..|+..+...+...+|||+.--|+=.|++.-+=..|..
T Consensus 58 ~rLpL~rik~vvk--l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~de~~fle 132 (162)
T KOG1658|consen 58 SRLPLARIKQVVK--LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVDEFAFLE 132 (162)
T ss_pred hhccHHHHHhhcc--CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchHHHHHHh
Confidence 5789999999988 6678885 567889999999999999999999999999999999988888776654444443
No 53
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.80 E-value=0.025 Score=48.19 Aligned_cols=70 Identities=17% Similarity=0.335 Sum_probs=62.7
Q ss_pred cccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 11 KEDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
.....|-+--|..+++.+-+ +..|-+|+.++|.+.|-.||..|+..|-..|++.+..||-+-||.-.|+.
T Consensus 150 ~~~~il~k~kl~dLvqqId~-~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr 219 (258)
T KOG1142|consen 150 GNNPILSKRKLDDLVQQIDG-TTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLER 219 (258)
T ss_pred CCCccccccchhHHHHhhcC-cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeec
Confidence 34556667788999998854 78999999999999999999999999999999999999999999999875
No 54
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=95.11 E-value=0.13 Score=39.62 Aligned_cols=89 Identities=17% Similarity=0.175 Sum_probs=49.2
Q ss_pred CCCcccccCcHH--HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhh-hcCh
Q 031627 8 GKSKEDASLPKA--TMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE-VLGF 84 (156)
Q Consensus 8 g~~~dd~~LP~A--~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~-~LgF 84 (156)
|.....-.+|+. +|.-|+++.. -......+...|.+.+-.|+.-|-..|..+|.+.+|++|+.+||--|++ .+++
T Consensus 3 ~~~~~~~~~PrDa~~i~~iL~~~G--v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~ 80 (129)
T PF02291_consen 3 GIDSQSKSLPRDARVIHLILKSMG--VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDH 80 (129)
T ss_dssp ----------HHHHHHHHHHHHTT-----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT---
T ss_pred CcCCCCccCChHHHHHHHHHHHcC--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhh
Confidence 444566778885 5666777652 2247788899999999999999999999999999999999999999998 5666
Q ss_pred hhhHHHHHHHHHHH
Q 031627 85 GEYIEEVYAAYEQH 98 (156)
Q Consensus 85 ~~yv~~l~~~l~~~ 98 (156)
.-.-+.=+++|-+.
T Consensus 81 ~f~~pppre~llel 94 (129)
T PF02291_consen 81 SFTQPPPREFLLEL 94 (129)
T ss_dssp --------------
T ss_pred hccCCCChHHHHHH
Confidence 65555555555443
No 55
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=94.71 E-value=0.22 Score=36.12 Aligned_cols=60 Identities=17% Similarity=0.222 Sum_probs=48.9
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 20 TMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 20 ~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
-|..+|-... +.-.-..|+..+|-+...+||.-+..+|.++|. .++.-|+.||++-+|..
T Consensus 7 ei~~mmy~~G-D~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~ 66 (92)
T cd07978 7 EIRQMMYGFG-DVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK 66 (92)
T ss_pred HHHHHHHHcC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence 4667777554 345678999999999999999999999999999 44444699999999854
No 56
>PTZ00252 histone H2A; Provisional
Probab=94.18 E-value=0.19 Score=39.13 Aligned_cols=72 Identities=11% Similarity=0.216 Sum_probs=53.1
Q ss_pred ccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhh------cCCCccChhhhhhhhhh-cCh
Q 031627 12 EDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSR------EDKRTIAPEHVLKALEV-LGF 84 (156)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~------~~RKTI~~edVl~AL~~-LgF 84 (156)
-.+.||...|.|++++.-- ..||+.-|...|.-+. .||++|-.+.+-+ .+++-|+|+||..|+.. -+|
T Consensus 22 AGL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAVL----EYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrNDeEL 96 (134)
T PTZ00252 22 AGLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAVL----EYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRHDDDL 96 (134)
T ss_pred cCccCchHHHHHHHHcCCc-ccccCCccHHHHHHHH----HHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccChHHH
Confidence 4689999999999998754 5799999988887754 4666665555432 46678999999999854 444
Q ss_pred hhhH
Q 031627 85 GEYI 88 (156)
Q Consensus 85 ~~yv 88 (156)
..++
T Consensus 97 ~~Ll 100 (134)
T PTZ00252 97 GSLL 100 (134)
T ss_pred HHHH
Confidence 4443
No 57
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=91.81 E-value=0.57 Score=37.90 Aligned_cols=69 Identities=20% Similarity=0.231 Sum_probs=54.7
Q ss_pred CcHHHHHHHHHhhCC-----CCccccHHHHHHHHHHHHH---HHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcCh
Q 031627 16 LPKATMTKIIKEMLP-----ADVRVARDAQDLLIECCVE---FINLVSSESNEVCSREDKRTIAPEHVLKALEVLGF 84 (156)
Q Consensus 16 LP~A~V~riiKe~LP-----~~~~iskda~~~i~~c~~e---FI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF 84 (156)
|...-+..++...+. ....++.++.+.|.+.+.= .|+.+...+...+-..+.++|+.++|-.++.++.|
T Consensus 192 l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~ 268 (269)
T TIGR03015 192 LDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF 268 (269)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence 344455555554431 2356999999999998875 79999999999988899999999999999998875
No 58
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=89.41 E-value=2.6 Score=36.24 Aligned_cols=72 Identities=19% Similarity=0.202 Sum_probs=52.1
Q ss_pred HHHHHHHHHhhCCC---CccccHHHHHHHHHHH------HHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhH
Q 031627 18 KATMTKIIKEMLPA---DVRVARDAQDLLIECC------VEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYI 88 (156)
Q Consensus 18 ~A~V~riiKe~LP~---~~~iskda~~~i~~c~------~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv 88 (156)
..-+..|++..+-. ...++.++.+.+.+.+ .-.+..+...|.+.|...++.+|+.+||..|+..+....+.
T Consensus 209 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~~ 288 (394)
T PRK00411 209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHLS 288 (394)
T ss_pred HHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHHH
Confidence 45566666654421 2358899988888877 34455666788889999999999999999999998544444
Q ss_pred H
Q 031627 89 E 89 (156)
Q Consensus 89 ~ 89 (156)
.
T Consensus 289 ~ 289 (394)
T PRK00411 289 E 289 (394)
T ss_pred H
Confidence 3
No 59
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=89.17 E-value=2.3 Score=34.49 Aligned_cols=68 Identities=16% Similarity=0.246 Sum_probs=54.8
Q ss_pred cCcHHHHHHHHHhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC--------------CCccChhhhhhhh
Q 031627 15 SLPKATMTKIIKEMLPADVR-VARDAQDLLIECCVEFINLVSSESNEVCSRED--------------KRTIAPEHVLKAL 79 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~-iskda~~~i~~c~~eFI~~lsseAn~~a~~~~--------------RKTI~~edVl~AL 79 (156)
.||-+.+--.++.+. +. ...-.+-+|.=++-.||.-|+.-|.+.|+-.+ |-|++-+|+-.||
T Consensus 86 ~IPDavt~~yL~~aG---f~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL 162 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKAG---FQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPAL 162 (176)
T ss_pred CCcHHHHHHHHHhcC---CCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHH
Confidence 678887777777663 33 44556778999999999999999999998544 4489999999999
Q ss_pred hhcChh
Q 031627 80 EVLGFG 85 (156)
Q Consensus 80 ~~LgF~ 85 (156)
.+.|..
T Consensus 163 ~EyGin 168 (176)
T KOG3423|consen 163 AEYGIN 168 (176)
T ss_pred HHhCcc
Confidence 999875
No 60
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=87.96 E-value=3.1 Score=36.65 Aligned_cols=73 Identities=14% Similarity=0.247 Sum_probs=59.9
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHHHHHHHHH
Q 031627 20 TMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYAAYE 96 (156)
Q Consensus 20 ~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~~l~ 96 (156)
.|.-|.+..+ --.|++-|++-|.+....+|.-|...+...|+..||.-.+.-||.-+|-.+|+. ++.|..+++
T Consensus 10 VV~~Ll~~~g--fd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q 82 (323)
T KOG4336|consen 10 VVSNLLKTKG--FDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQ 82 (323)
T ss_pred HHHHHHHHhC--chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHH
Confidence 3444555443 234999999999999999999999999999999999999999999999999997 444444443
No 61
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=86.46 E-value=4.3 Score=34.40 Aligned_cols=75 Identities=16% Similarity=0.143 Sum_probs=52.0
Q ss_pred HHHHHHHHHhhCC---CCccccHHHHHHHHHHHH------HHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhH
Q 031627 18 KATMTKIIKEMLP---ADVRVARDAQDLLIECCV------EFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYI 88 (156)
Q Consensus 18 ~A~V~riiKe~LP---~~~~iskda~~~i~~c~~------eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv 88 (156)
..-+..|++..+. ....++.++...+.+.+. -.+..+-..|.+.|...++.+|+.+||..|+..+..+.++
T Consensus 201 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~~ 280 (365)
T TIGR02928 201 AEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLL 280 (365)
T ss_pred HHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 3456666665543 133488888877766442 2344455677888888899999999999999999766666
Q ss_pred HHHH
Q 031627 89 EEVY 92 (156)
Q Consensus 89 ~~l~ 92 (156)
..+.
T Consensus 281 ~~i~ 284 (365)
T TIGR02928 281 ELIR 284 (365)
T ss_pred HHHH
Confidence 5554
No 62
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=84.89 E-value=19 Score=29.19 Aligned_cols=77 Identities=23% Similarity=0.199 Sum_probs=55.3
Q ss_pred cccCcHHHHHHHHHhhCCC-Cc-cccHHHHHHHHHHHHHHHHHHHHHHHHHhhhc------CCCccChhhhhhhhhhcCh
Q 031627 13 DASLPKATMTKIIKEMLPA-DV-RVARDAQDLLIECCVEFINLVSSESNEVCSRE------DKRTIAPEHVLKALEVLGF 84 (156)
Q Consensus 13 d~~LP~A~V~riiKe~LP~-~~-~iskda~~~i~~c~~eFI~~lsseAn~~a~~~------~RKTI~~edVl~AL~~LgF 84 (156)
...|....|.+.|...+.. ++ .|+.|...+|.-||.+++..|-.....+|++- ...++-..||-.-|..|+-
T Consensus 42 ~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~~ 121 (212)
T cd08045 42 PSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLEQ 121 (212)
T ss_pred hhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHHH
Confidence 3455666666665555542 23 79999999999999999999999999998864 3456667788777766655
Q ss_pred hhhHH
Q 031627 85 GEYIE 89 (156)
Q Consensus 85 ~~yv~ 89 (156)
-+..+
T Consensus 122 ~ek~e 126 (212)
T cd08045 122 LEREE 126 (212)
T ss_pred HHHHH
Confidence 44443
No 63
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=83.96 E-value=5 Score=37.92 Aligned_cols=65 Identities=20% Similarity=0.212 Sum_probs=54.6
Q ss_pred cHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcC
Q 031627 17 PKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLG 83 (156)
Q Consensus 17 P~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~Lg 83 (156)
|+-+|.-++ +++. -..++.|+..+|.+=...=|.-|..+|..+-.+.+|.+++.+||..||+.+.
T Consensus 13 ~~Es~k~vA-EslG-i~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 13 PKESVKVVA-ESLG-ITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred cHHHHHHHH-HHhC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 455555444 4552 3449999999999999999999999999999999999999999999998764
No 64
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=82.89 E-value=5.4 Score=36.95 Aligned_cols=48 Identities=29% Similarity=0.359 Sum_probs=38.8
Q ss_pred cccHHHHHHHHHHHHH-----------HHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 34 RVARDAQDLLIECCVE-----------FINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 34 ~iskda~~~i~~c~~e-----------FI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
.++.+|...|.+.+.. .|.-|-.+|+.+|...++++|+++||..|++.
T Consensus 447 ~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~ 505 (509)
T PF13654_consen 447 PFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEE 505 (509)
T ss_dssp -BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHc
Confidence 4888888888887653 56777799999999999999999999999875
No 65
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=82.31 E-value=3.4 Score=36.88 Aligned_cols=71 Identities=11% Similarity=0.166 Sum_probs=59.7
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh
Q 031627 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (156)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~ 85 (156)
.+.|-+..|..|.....-.. ...-|.+.|..-...||+-|+..|..++...||--.+.-||+.||++|+..
T Consensus 27 a~sla~~avaQIcqslg~~~--~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 27 AFSLARVAVAQICQSLGYSS--TQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHHHhcCCcc--cccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 34677778888887553222 333499999999999999999999999999999999999999999999876
No 66
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=81.00 E-value=1.6 Score=41.73 Aligned_cols=46 Identities=30% Similarity=0.435 Sum_probs=36.0
Q ss_pred ccHHHHHHHHHHH--------------HHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 35 VARDAQDLLIECC--------------VEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 35 iskda~~~i~~c~--------------~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
++++|..-|.+-+ ..-...|. +|+.+|..++++-|+++||.+|++.
T Consensus 339 ~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~-~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 339 LDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVR-EAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred CCHHHHHHHHHHHHHhccccceeccCHHHHHHHHH-HhhHHHhcCCcccCcHHHHHHHHHh
Confidence 6666666655544 34455555 9999999999999999999999977
No 67
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=77.22 E-value=8.8 Score=36.18 Aligned_cols=50 Identities=20% Similarity=0.283 Sum_probs=40.5
Q ss_pred cccHHHHHHHHHHHH-------------HHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcC
Q 031627 34 RVARDAQDLLIECCV-------------EFINLVSSESNEVCSREDKRTIAPEHVLKALEVLG 83 (156)
Q Consensus 34 ~iskda~~~i~~c~~-------------eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~Lg 83 (156)
.++.+|...|.+.++ -=|.-|-.+|+.+|..+++.+|+.+||.+|++.-.
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~ 392 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAK 392 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence 689999999987554 33555667889999999999999999999987543
No 68
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=75.25 E-value=11 Score=27.17 Aligned_cols=48 Identities=19% Similarity=0.318 Sum_probs=40.3
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 33 VRVARDAQDLLIECCVEF------INLVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 33 ~~iskda~~~i~~c~~eF------I~~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
..+++++..+|..++..| ++-|-.-|-.||.-++...|..+||..||.
T Consensus 41 ~~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 41 CPLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred cCCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 457888888888888766 455667899999999999999999999974
No 69
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=72.99 E-value=12 Score=34.48 Aligned_cols=63 Identities=17% Similarity=0.300 Sum_probs=43.4
Q ss_pred HHHHHHhhCC-CCccccHHHHHHHHHHHH---HHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcCh
Q 031627 21 MTKIIKEMLP-ADVRVARDAQDLLIECCV---EFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGF 84 (156)
Q Consensus 21 V~riiKe~LP-~~~~iskda~~~i~~c~~---eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF 84 (156)
+..|++..+. .++.+++++.+.|.+.+. +.++.+ ..|..+|..++|++|+.+||.+++..-.|
T Consensus 268 i~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll-~~Aa~~A~~~~~~~It~~dI~~vl~~~~~ 334 (531)
T TIGR02902 268 IKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIV-QLAAGIALGEGRKRILAEDIEWVAENGNY 334 (531)
T ss_pred HHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHH-HHHHHHHhhCCCcEEcHHHHHHHhCCccc
Confidence 4445554443 257899999998887765 333333 44556788889999999999999754433
No 70
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=72.55 E-value=12 Score=28.71 Aligned_cols=64 Identities=19% Similarity=0.327 Sum_probs=49.6
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC----CccChhhhhhhhh
Q 031627 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDK----RTIAPEHVLKALE 80 (156)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~R----KTI~~edVl~AL~ 80 (156)
-+.+|...|.|.+|.......++..-+... . .-.+.||+.|-.+.|.+..+ |.|+|.|+--|+.
T Consensus 28 GlqFpVgRihr~LK~r~t~h~rVGataavy--~--aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 28 GLQFPVGRIHRHLKTRTTSHGRVGATAAVY--S--AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred ccccchHHHHHHHHHhcccccccchHHHHH--H--HHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 478999999999999888778876544432 2 33568999999998876554 6799999987764
No 71
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=72.05 E-value=12 Score=23.34 Aligned_cols=38 Identities=29% Similarity=0.303 Sum_probs=22.8
Q ss_pred hhhhhhhhhcChhhhHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCHHHHHHH
Q 031627 73 EHVLKALEVLGFGEYIEEVYAAYEQHKLETMDSLKGGKWSNGAEMTEEEAAAE 125 (156)
Q Consensus 73 edVl~AL~~LgF~~yv~~l~~~l~~~k~~~~~r~k~~~k~~~~g~~eEel~~~ 125 (156)
+|++.||..|||.. .++..++..... ..+++.|+++++
T Consensus 4 ~d~~~AL~~LGy~~--~e~~~av~~~~~-------------~~~~~~e~~ik~ 41 (47)
T PF07499_consen 4 EDALEALISLGYSK--AEAQKAVSKLLE-------------KPGMDVEELIKQ 41 (47)
T ss_dssp HHHHHHHHHTTS-H--HHHHHHHHHHHH-------------STTS-HHHHHHH
T ss_pred HHHHHHHHHcCCCH--HHHHHHHHHhhc-------------CCCCCHHHHHHH
Confidence 68999999999973 233333322211 356778888875
No 72
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=71.74 E-value=3.3 Score=25.43 Aligned_cols=26 Identities=31% Similarity=0.395 Sum_probs=20.6
Q ss_pred HHHHhhhcCCCccChhhhhhhhhhcC
Q 031627 58 SNEVCSREDKRTIAPEHVLKALEVLG 83 (156)
Q Consensus 58 An~~a~~~~RKTI~~edVl~AL~~Lg 83 (156)
|.++|...+...|+++|++.||=.-+
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~~ 26 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLEDP 26 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHHT
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhhh
Confidence 56788999999999999999964443
No 73
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=65.19 E-value=61 Score=25.70 Aligned_cols=82 Identities=17% Similarity=0.223 Sum_probs=58.9
Q ss_pred cccCcHH--HHHHHHHhhCCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHH
Q 031627 13 DASLPKA--TMTKIIKEMLPADV-RVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIE 89 (156)
Q Consensus 13 d~~LP~A--~V~riiKe~LP~~~-~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~ 89 (156)
.-.-|+. .|.-|+++. ++ -...-..-.|.+.+--++.-|-..|.-++.+.+|.||.++||.-|+.-.+=.+|.+
T Consensus 9 ~~~~pkDa~~i~~iL~s~---GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~ 85 (148)
T KOG3334|consen 9 TKGVPKDARVIASILKSL---GIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTP 85 (148)
T ss_pred ccCCcHHHHHHHHHHHHc---CccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCC
Confidence 3445665 344444443 23 25566677778888888888889999999999999999999999999887777776
Q ss_pred -HHHHHHHH
Q 031627 90 -EVYAAYEQ 97 (156)
Q Consensus 90 -~l~~~l~~ 97 (156)
+=++++-+
T Consensus 86 pPpRe~lL~ 94 (148)
T KOG3334|consen 86 PPPREFLLE 94 (148)
T ss_pred CCchHHHHH
Confidence 33344433
No 74
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=64.42 E-value=27 Score=29.01 Aligned_cols=76 Identities=14% Similarity=0.145 Sum_probs=48.0
Q ss_pred cCcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHHHHH
Q 031627 15 SLPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVY 92 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~~l~ 92 (156)
.++...+.++++..+. .++.++.++...|.+.+.-=+..+-......|. +..+|+.+||..++.....++.+-.+-
T Consensus 183 ~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~~~i~~l~ 259 (337)
T PRK12402 183 APTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTDEVIESLL 259 (337)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCHHHHHHHH
Confidence 4455666777776554 367899999999998874333333333333442 234799999999888766554444333
No 75
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=63.13 E-value=46 Score=27.19 Aligned_cols=67 Identities=19% Similarity=0.207 Sum_probs=49.7
Q ss_pred cCcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 15 SLPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
.+....+.+.|++.+. .++.|+.++...|...+.-=+..+-++-..+|.-.+.++|+.+||...+..
T Consensus 110 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~ 177 (302)
T TIGR01128 110 TPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSD 177 (302)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhh
Confidence 4556667777766654 368899999999998887666777777777776555557999999877653
No 76
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=60.51 E-value=36 Score=28.91 Aligned_cols=70 Identities=17% Similarity=0.195 Sum_probs=48.3
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHH---HHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh
Q 031627 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVE---FINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (156)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskda~~~i~~c~~e---FI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~ 85 (156)
++...+..|++.... .++.++.++...|.+.|.= .+..+-..+.++|...+...|+.++|..++..++..
T Consensus 180 ~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~ 253 (328)
T PRK00080 180 YTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVD 253 (328)
T ss_pred CCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 344455555554432 3678999999988887732 344444556667766677789999999999887665
No 77
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=60.12 E-value=26 Score=33.09 Aligned_cols=53 Identities=25% Similarity=0.500 Sum_probs=43.8
Q ss_pred hhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 27 EMLPADVRVARDAQDLLIECCVEFI-------NLVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 27 e~LP~~~~iskda~~~i~~c~~eFI-------~~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
..+| .+.|+.+....|...|..+- .++...|..+|.-++|.+|+++||..|+.
T Consensus 243 ~~~~-~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~ 302 (633)
T TIGR02442 243 SLLP-SVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAE 302 (633)
T ss_pred HhCC-CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence 3444 78999999999999998763 45667788889999999999999998863
No 78
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=59.78 E-value=14 Score=23.26 Aligned_cols=41 Identities=17% Similarity=0.122 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHhhhcCCCccChhhhhhh
Q 031627 37 RDAQDLLIECCVEFIN-LVSSESNEVCSREDKRTIAPEHVLKA 78 (156)
Q Consensus 37 kda~~~i~~c~~eFI~-~lsseAn~~a~~~~RKTI~~edVl~A 78 (156)
.||...|.+. =.|+. .+=..+-..|...|...|+.++|..|
T Consensus 3 ~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 3 DEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred HHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 3444444443 23443 33355566788899999999999765
No 79
>PF08621 RPAP1_N: RPAP1-like, N-terminal; InterPro: IPR013930 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.
Probab=59.30 E-value=9.4 Score=24.70 Aligned_cols=18 Identities=28% Similarity=0.492 Sum_probs=16.2
Q ss_pred CCCCHHHHHHHHHHHHHH
Q 031627 115 AEMTEEEAAAEQQRMFAE 132 (156)
Q Consensus 115 ~g~~eEel~~~Q~eLf~~ 132 (156)
++||.+|....|++|++.
T Consensus 13 ~~MS~eEI~~er~eL~~~ 30 (49)
T PF08621_consen 13 ASMSPEEIEEEREELLES 30 (49)
T ss_pred HhCCHHHHHHHHHHHHHh
Confidence 579999999999999875
No 80
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=57.41 E-value=44 Score=29.29 Aligned_cols=53 Identities=15% Similarity=0.323 Sum_probs=42.2
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 26 KEMLPADVRVARDAQDLLIECCVEFI-------NLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 26 Ke~LP~~~~iskda~~~i~~c~~eFI-------~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
++.+| .+.|+.+....|.+.|..+= .++...|-..|--+||..|+++||..+.
T Consensus 247 ~~~~~-~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a 306 (337)
T TIGR02030 247 QNLLP-QVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVA 306 (337)
T ss_pred HHHhc-cCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 44565 79999999999999887763 2355677888889999999999998764
No 81
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=57.36 E-value=13 Score=30.35 Aligned_cols=62 Identities=18% Similarity=0.146 Sum_probs=47.7
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC-CccChhhhhhh
Q 031627 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDK-RTIAPEHVLKA 78 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~R-KTI~~edVl~A 78 (156)
.||++.|.|++..++ +-.|+...+.+|+-.+.+|+--|---|..+-.+-+- -.+.|.|+-.|
T Consensus 115 ~lnKt~VKKlastV~--nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p~h~rea 177 (199)
T COG5251 115 SLNKTQVKKLASTVA--NQTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIPFHKREA 177 (199)
T ss_pred CCCHHHHHHHHHHHh--ccccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCChHHHHHH
Confidence 799999999999998 577888888899999999998777666555433221 14778888776
No 82
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=57.29 E-value=40 Score=27.82 Aligned_cols=70 Identities=16% Similarity=0.189 Sum_probs=46.8
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHH---HHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh
Q 031627 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVE---FINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (156)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskda~~~i~~c~~e---FI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~ 85 (156)
++...+..+++.... .++.++.++.+.|.+.|.= ++..+...+.+.+...+...|+.++|..++..++++
T Consensus 159 l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~ 232 (305)
T TIGR00635 159 YTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMID 232 (305)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCC
Confidence 334455555554442 3578999999888887632 334444456667666666779999999999987654
No 83
>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=57.07 E-value=45 Score=21.95 Aligned_cols=29 Identities=14% Similarity=0.268 Sum_probs=23.7
Q ss_pred CCccChhhhhhhhhhcChhhhHHHHHHHH
Q 031627 67 KRTIAPEHVLKALEVLGFGEYIEEVYAAY 95 (156)
Q Consensus 67 RKTI~~edVl~AL~~LgF~~yv~~l~~~l 95 (156)
...-+..+++.||..+|..+-+..|...+
T Consensus 55 ~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 55 GPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp GSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred CCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 34567889999999999999998887653
No 84
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=55.92 E-value=45 Score=27.98 Aligned_cols=67 Identities=13% Similarity=0.183 Sum_probs=50.2
Q ss_pred HHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCCCccChhhhhhhhhhcChhhh
Q 031627 21 MTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSR--EDKRTIAPEHVLKALEVLGFGEY 87 (156)
Q Consensus 21 V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~--~~RKTI~~edVl~AL~~LgF~~y 87 (156)
+.+.|++.+- .+..|+.+|...|..++.-=...+..+-...|.- .++.+|+.+||...+....+.-|
T Consensus 135 l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~if 204 (326)
T PRK07452 135 LKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQNSL 204 (326)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCcHH
Confidence 4444444332 3789999999999999987677777788887775 45778999999998877665433
No 85
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=55.85 E-value=26 Score=33.12 Aligned_cols=58 Identities=14% Similarity=0.126 Sum_probs=47.9
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 20 TMTKIIKEMLPADVRVARDAQDLLIECCVEFI-------NLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 20 ~V~riiKe~LP~~~~iskda~~~i~~c~~eFI-------~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
.|.+.- +.++ ++.|+.+....+.+.|..|- .++...|..+|--+||.+|+++||..|+
T Consensus 183 ~I~~AR-~rl~-~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa 247 (584)
T PRK13406 183 DIAAAR-ARLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAA 247 (584)
T ss_pred HHHHHH-HHHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 444433 3555 89999999999999888874 4778889999999999999999999996
No 86
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=53.87 E-value=24 Score=25.97 Aligned_cols=34 Identities=15% Similarity=0.326 Sum_probs=27.6
Q ss_pred HHHHHHHHhhC----CCCccccHHHHHHHHHHHHHHHH
Q 031627 19 ATMTKIIKEML----PADVRVARDAQDLLIECCVEFIN 52 (156)
Q Consensus 19 A~V~riiKe~L----P~~~~iskda~~~i~~c~~eFI~ 52 (156)
++|.++||..| .++..++.++.++|++++..|-.
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~a~ 88 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELWAQ 88 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHHHh
Confidence 45777999887 36799999999999999998853
No 87
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=53.77 E-value=6.3 Score=25.39 Aligned_cols=58 Identities=24% Similarity=0.422 Sum_probs=31.4
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCcc---ChhhhhhhhhhcChhhhH-HHHHH
Q 031627 32 DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTI---APEHVLKALEVLGFGEYI-EEVYA 93 (156)
Q Consensus 32 ~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI---~~edVl~AL~~LgF~~yv-~~l~~ 93 (156)
+.+|.+++..+|.+++. .+..|+.+ .-..+=.|.+ .+...+..|.++|+-+|+ |++..
T Consensus 1 gF~ie~~t~~ai~~~~~-~L~~is~E---Ri~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~ 62 (64)
T PF12627_consen 1 GFKIEPETEEAIKENAE-LLSKISKE---RIREELEKILSSPNPSRAFKLLDELGLLEYIFPELDA 62 (64)
T ss_dssp T-EE-HHHHHHHHHHGG-GGGGS-HH---HHHHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT
T ss_pred CCccCHHHHHHHHHHHH-HHhcCCHH---HHHHHHHHHHcCCCHHHHHHHHHHcCCHHHHCccccc
Confidence 35677788888877666 34444322 2222222222 456677788888876664 65544
No 88
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=53.16 E-value=39 Score=25.47 Aligned_cols=47 Identities=21% Similarity=0.275 Sum_probs=37.7
Q ss_pred CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 30 PADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 30 P~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
.++..=-.|+.+++-..+.+||.-++..|..+. .|-.+..||++-+|
T Consensus 23 GDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~l 69 (109)
T KOG3901|consen 23 GDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLL 69 (109)
T ss_pred CCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHH
Confidence 345666789999999999999999988888887 44447788888876
No 89
>PRK09862 putative ATP-dependent protease; Provisional
Probab=52.98 E-value=54 Score=30.52 Aligned_cols=57 Identities=9% Similarity=0.179 Sum_probs=44.0
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHH
Q 031627 33 VRVARDAQDLLIECCVEF------INLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIE 89 (156)
Q Consensus 33 ~~iskda~~~i~~c~~eF------I~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~ 89 (156)
+.++.++..++...+..+ .+.|-.-|..+|.-+++..|+++||..|+.=-+++..+-
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~~~~ 499 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDRLLI 499 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccHHHH
Confidence 467888888877765554 566778899999999999999999999997555554433
No 90
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=51.76 E-value=16 Score=23.43 Aligned_cols=25 Identities=32% Similarity=0.531 Sum_probs=21.4
Q ss_pred ccChhhhhhhhhhcChhhhHHHHHH
Q 031627 69 TIAPEHVLKALEVLGFGEYIEEVYA 93 (156)
Q Consensus 69 TI~~edVl~AL~~LgF~~yv~~l~~ 93 (156)
+=++++|..-|..+||..|.+....
T Consensus 3 ~w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 3 TWSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp GHCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCCHHHHHHHHHHCCcHHHHHHHHH
Confidence 3478999999999999999987765
No 91
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=51.43 E-value=40 Score=29.88 Aligned_cols=53 Identities=17% Similarity=0.429 Sum_probs=44.4
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 26 KEMLPADVRVARDAQDLLIECCVEFI-------NLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 26 Ke~LP~~~~iskda~~~i~~c~~eFI-------~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
++.++ .+.|+.+....|.+.|..+= .++...|.-.|--+||..|+++||..+.
T Consensus 260 r~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a 319 (350)
T CHL00081 260 QNLLP-KVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVI 319 (350)
T ss_pred HHhcC-CCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 45565 79999999999999998874 3666778888899999999999998774
No 92
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=50.22 E-value=19 Score=22.97 Aligned_cols=22 Identities=32% Similarity=0.437 Sum_probs=19.6
Q ss_pred ChhhhhhhhhhcChhhhHHHHH
Q 031627 71 APEHVLKALEVLGFGEYIEEVY 92 (156)
Q Consensus 71 ~~edVl~AL~~LgF~~yv~~l~ 92 (156)
++++|..-|+.+|++.|++...
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F~ 25 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENFE 25 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHH
Confidence 6889999999999999998773
No 93
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=48.94 E-value=42 Score=31.04 Aligned_cols=47 Identities=13% Similarity=0.235 Sum_probs=41.1
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 34 RVARDAQDLLIECCVEF------INLVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 34 ~iskda~~~i~~c~~eF------I~~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
.++++++.++.+++..| .+-|-.-|..+|.-++...|..+||..|+.
T Consensus 445 ~l~~~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 445 KLSAIDANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred CCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 46889999999998887 566778899999999999999999999974
No 94
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=48.54 E-value=28 Score=33.32 Aligned_cols=47 Identities=21% Similarity=0.272 Sum_probs=38.7
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 34 RVARDAQDLLIECCVEF-------------INLVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 34 ~iskda~~~i~~c~~eF-------------I~~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
.|+.+|...|.+-++.- |.-|-.+|+.+|..++++.|+.+||..|+.
T Consensus 339 ~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~ 398 (637)
T PRK13765 339 HFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKK 398 (637)
T ss_pred CCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHH
Confidence 58999998888876632 223668899999999999999999999974
No 95
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=48.11 E-value=59 Score=30.56 Aligned_cols=54 Identities=13% Similarity=0.233 Sum_probs=41.8
Q ss_pred HHhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 25 IKEMLPADVRVARDAQDLLIECCVEFI-------NLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 25 iKe~LP~~~~iskda~~~i~~c~~eFI-------~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
+++.+| .+.|+.+....|.+.|..+= .++...|-..|.-++|.+|+++||..|.
T Consensus 195 ar~~~~-~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~ 255 (589)
T TIGR02031 195 ARELLP-QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAV 255 (589)
T ss_pred HHHhcC-CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHH
Confidence 344565 78999999988888776542 2445667777888999999999999886
No 96
>PF12010 DUF3502: Domain of unknown function (DUF3502); InterPro: IPR022627 This domain is about 140 amino acids in length and is functionally uncharacterised. It is found in bacteria C-terminal to PF01547 from PFAM.
Probab=48.10 E-value=24 Score=26.67 Aligned_cols=62 Identities=10% Similarity=0.132 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHHHHHHHHHHHHHHh
Q 031627 37 RDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYAAYEQHKLET 102 (156)
Q Consensus 37 kda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~~l~~~k~~~ 102 (156)
..++.-|..|..+.-.|...-..-... ---.-..+...|+..|++..+.++...+++|+..+
T Consensus 72 s~Vk~Eiaa~~~v~~~Y~~~L~~G~vd----~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~~ 133 (134)
T PF12010_consen 72 SPVKNEIAACSNVWSEYYPPLETGLVD----PEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAAN 133 (134)
T ss_pred chhHHHHHHHHHHHHHHHHHHHccCCC----HHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhc
Confidence 456666777777766665543322211 00123567788999999999999999999998764
No 97
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=48.08 E-value=39 Score=30.50 Aligned_cols=65 Identities=18% Similarity=0.157 Sum_probs=53.4
Q ss_pred HHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh
Q 031627 19 ATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (156)
Q Consensus 19 A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~ 85 (156)
.+|.-+. ++|. --.|..|+..+|..-..-=|+-+-.+|...-.+.+|..++-+||-.||..|..+
T Consensus 9 et~KdvA-eslG-i~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 9 ETLKDVA-ESLG-ISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred HHHHHHH-HHcC-CcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 3444433 3442 345899999999999988999999999999999999999999999999998654
No 98
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=47.89 E-value=20 Score=22.24 Aligned_cols=24 Identities=38% Similarity=0.655 Sum_probs=20.4
Q ss_pred cChhhhhhhhhhcChhhhHHHHHH
Q 031627 70 IAPEHVLKALEVLGFGEYIEEVYA 93 (156)
Q Consensus 70 I~~edVl~AL~~LgF~~yv~~l~~ 93 (156)
-++++|..-|..+|+++|++.+.+
T Consensus 2 w~~~~V~~wL~~~~~~~y~~~f~~ 25 (63)
T cd00166 2 WSPEDVAEWLESLGLGQYADNFRE 25 (63)
T ss_pred CCHHHHHHHHHHcChHHHHHHHHH
Confidence 367899999999999999987755
No 99
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=46.71 E-value=30 Score=28.98 Aligned_cols=74 Identities=19% Similarity=0.141 Sum_probs=34.3
Q ss_pred cccccCcHHHHHHHHHhhCCC--CccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC------ccChhhhhhhhhhc
Q 031627 11 KEDASLPKATMTKIIKEMLPA--DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKR------TIAPEHVLKALEVL 82 (156)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP~--~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RK------TI~~edVl~AL~~L 82 (156)
.++..|....+.+.|..+... ...+..|...+|.-||.+++..|-..+..+|.+-..- +....||-..|..|
T Consensus 39 ~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~l 118 (264)
T PF05236_consen 39 KEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRFL 118 (264)
T ss_dssp -----S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH-----------------------------
T ss_pred ccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHHH
Confidence 456677777777777766532 3569999999999999999999999999998753221 23355666665544
Q ss_pred Ch
Q 031627 83 GF 84 (156)
Q Consensus 83 gF 84 (156)
.-
T Consensus 119 ~~ 120 (264)
T PF05236_consen 119 EQ 120 (264)
T ss_dssp --
T ss_pred HH
Confidence 43
No 100
>PRK09526 lacI lac repressor; Reviewed
Probab=46.18 E-value=31 Score=28.42 Aligned_cols=38 Identities=16% Similarity=0.344 Sum_probs=31.1
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHH
Q 031627 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSS 56 (156)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lss 56 (156)
...-++||.|++... -+||.+++.-|.+++.+ +.|.-.
T Consensus 15 aGVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn 52 (342)
T PRK09526 15 AGVSYQTVSRVLNQA----SHVSAKTREKVEAAMAE-LNYVPN 52 (342)
T ss_pred hCCCHHHHHHHhcCC----CCCCHHHHHHHHHHHHH-HCCCcC
Confidence 367789999999753 46999999999999999 567654
No 101
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=45.69 E-value=51 Score=20.70 Aligned_cols=32 Identities=22% Similarity=0.481 Sum_probs=26.7
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHH
Q 031627 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVE 49 (156)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~e 49 (156)
..+..+||.|++... -+||.++++-|.+++.+
T Consensus 9 agvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 9 AGVSKSTVSRVLNGP----PRVSEETRERILEAAEE 40 (46)
T ss_dssp HTSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHH
T ss_pred HCcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHH
Confidence 457789999999864 58999999999988765
No 102
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=43.66 E-value=81 Score=26.27 Aligned_cols=67 Identities=18% Similarity=0.154 Sum_probs=48.5
Q ss_pred cCcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 15 SLPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
.++...+.+.|+..+- .++.|+.++...|.+.+..=...+.+|-..+|.-.+.+.|+.+||-..+..
T Consensus 145 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~ 212 (340)
T PRK05574 145 PPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPD 212 (340)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhh
Confidence 4555666666665553 468999999999999988767777788888876543233999998766544
No 103
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=43.19 E-value=26 Score=21.85 Aligned_cols=26 Identities=27% Similarity=0.469 Sum_probs=21.3
Q ss_pred ccChhhhhhhhhhcChhhhHHHHHHH
Q 031627 69 TIAPEHVLKALEVLGFGEYIEEVYAA 94 (156)
Q Consensus 69 TI~~edVl~AL~~LgF~~yv~~l~~~ 94 (156)
.-++++|..-|..+||+.|++.+.+.
T Consensus 3 ~w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 3 QWSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCCHHHHHHHHHHCChHHHHHHHHHC
Confidence 34678999999999999999877653
No 104
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=42.98 E-value=74 Score=27.88 Aligned_cols=53 Identities=9% Similarity=0.193 Sum_probs=42.9
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 26 KEMLPADVRVARDAQDLLIECCVEFI-------NLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 26 Ke~LP~~~~iskda~~~i~~c~~eFI-------~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
++.++ .+.|+.+....|.+.|..+= .++...|.-.|--+||-.|+++||..+.
T Consensus 244 ~~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 244 RARLP-QLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred HHhcC-CcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 45565 79999999999999988764 2366778888999999999999996553
No 105
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=41.73 E-value=33 Score=28.27 Aligned_cols=39 Identities=10% Similarity=0.241 Sum_probs=30.6
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHH
Q 031627 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSE 57 (156)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsse 57 (156)
...-++||.|++... -+||.+++.-+.+.+.+ +.|.-..
T Consensus 15 agVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn~ 53 (331)
T PRK14987 15 VGVTKMTVSRFLRNP----EQVSVALRGKIAAALDE-LGYIPNR 53 (331)
T ss_pred hCCCHHHhhhhhCCC----CCCCHHHHHHHHHHHHH-hCCCccH
Confidence 356789999999653 47999999999999998 5675443
No 106
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=40.81 E-value=57 Score=29.57 Aligned_cols=49 Identities=18% Similarity=0.331 Sum_probs=40.6
Q ss_pred CCccccHHHHHHHHHHHHH----HHHHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 31 ADVRVARDAQDLLIECCVE----FINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 31 ~~~~iskda~~~i~~c~~e----FI~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
+++.++.||.++|...... |-.+|-+.|+.+|.+.+-+++..+||-.+.
T Consensus 374 Edv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y 426 (454)
T KOG2680|consen 374 EDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVY 426 (454)
T ss_pred hccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHH
Confidence 4788999999999876543 555566679999999999999999998884
No 107
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=40.79 E-value=1.1e+02 Score=24.92 Aligned_cols=66 Identities=11% Similarity=0.139 Sum_probs=40.7
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcC
Q 031627 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLG 83 (156)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~Lg 83 (156)
++..-+.++++..+. .++.|+.++.+.|.+.+.--+..+-.+-...+.. .++|+.+||..++....
T Consensus 161 l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~--~~~it~~~v~~~~~~~~ 227 (319)
T PRK00440 161 LKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAAT--GKEVTEEAVYKITGTAR 227 (319)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc--CCCCCHHHHHHHhCCCC
Confidence 444555555555443 3678999999999888753333333333233332 36899999988876553
No 108
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=40.17 E-value=50 Score=29.24 Aligned_cols=73 Identities=18% Similarity=0.213 Sum_probs=48.4
Q ss_pred HHHHHHHhhCC---CCccccHHHHHHHHHHH------HHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHHH
Q 031627 20 TMTKIIKEMLP---ADVRVARDAQDLLIECC------VEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEE 90 (156)
Q Consensus 20 ~V~riiKe~LP---~~~~iskda~~~i~~c~------~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~~ 90 (156)
-+.-|+++-.- ..-.++.++..++..-+ ..+..-+...|.++|+.+++.+|+.+||..|-+..+..-+...
T Consensus 194 el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~~ 273 (366)
T COG1474 194 ELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEEV 273 (366)
T ss_pred HHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHHH
Confidence 45555554432 13456666666555322 2344556677999999999999999999999777777655554
Q ss_pred HH
Q 031627 91 VY 92 (156)
Q Consensus 91 l~ 92 (156)
+.
T Consensus 274 ~~ 275 (366)
T COG1474 274 LK 275 (366)
T ss_pred HH
Confidence 43
No 109
>PRK07914 hypothetical protein; Reviewed
Probab=39.27 E-value=81 Score=26.75 Aligned_cols=64 Identities=11% Similarity=0.156 Sum_probs=45.3
Q ss_pred cHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 17 PKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 17 P~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
+..-+.+.|++.+- .+.+|+.+|...|.+++..=...+.+|-...+...+ .+|+.+||-..+..
T Consensus 129 ~~~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~~ 193 (320)
T PRK07914 129 KAAERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHSG 193 (320)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcCC
Confidence 34444555554443 368899999999999997666777777666665444 57999999887654
No 110
>PF12022 DUF3510: Domain of unknown function (DUF3510); InterPro: IPR024603 The COG complex comprises eight proteins (COG1-8) and plays critical roles in Golgi structure and function []. This uncharacterised domain is found in the C-terminal of COG complex subunit 2 proteins.
Probab=38.73 E-value=1.7e+02 Score=21.92 Aligned_cols=46 Identities=15% Similarity=0.120 Sum_probs=25.6
Q ss_pred hhhhHHHHHHHHHHHHHHhh--hcccCC----CCCCCCCCCHHHHHHHHHHH
Q 031627 84 FGEYIEEVYAAYEQHKLETM--DSLKGG----KWSNGAEMTEEEAAAEQQRM 129 (156)
Q Consensus 84 F~~yv~~l~~~l~~~k~~~~--~r~k~~----~k~~~~g~~eEel~~~Q~eL 129 (156)
++.|...+.++|.-.+.... +|-|+. .-....|+|.++-++.|--|
T Consensus 72 ~~~y~~~~~evL~sv~KtEeSL~rlkk~~~~~~~~~~~~~sD~dKIr~QL~L 123 (125)
T PF12022_consen 72 TERYYEIASEVLTSVRKTEESLKRLKKRRKRTSGSSSGGMSDDDKIRLQLYL 123 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccCCCCCcHHHHHHHHHc
Confidence 34677666666654442221 222221 12223689999999999654
No 111
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=37.48 E-value=54 Score=26.70 Aligned_cols=38 Identities=18% Similarity=0.209 Sum_probs=29.8
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHH
Q 031627 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSS 56 (156)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lss 56 (156)
..+-++||.|.+... -+||.++++-|.+++.+. .|.-+
T Consensus 8 agVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l-gY~pn 45 (327)
T PRK10423 8 AGVSTSTVSHVINKD----RFVSEAITAKVEAAIKEL-NYAPS 45 (327)
T ss_pred hCCcHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCcc
Confidence 356789999999753 469999999999999875 45443
No 112
>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=37.30 E-value=19 Score=22.49 Aligned_cols=17 Identities=24% Similarity=0.618 Sum_probs=13.3
Q ss_pred ccccCcHHHHHHHHHhh
Q 031627 12 EDASLPKATMTKIIKEM 28 (156)
Q Consensus 12 dd~~LP~A~V~riiKe~ 28 (156)
+.+.+|+++|+|+++.-
T Consensus 26 ~~~gl~~stv~r~L~tL 42 (52)
T PF09339_consen 26 RALGLPKSTVHRLLQTL 42 (52)
T ss_dssp HHHTS-HHHHHHHHHHH
T ss_pred HHHCcCHHHHHHHHHHH
Confidence 45689999999999854
No 113
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=36.69 E-value=48 Score=27.50 Aligned_cols=38 Identities=8% Similarity=0.171 Sum_probs=30.2
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHH
Q 031627 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSE 57 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsse 57 (156)
.+-.+||.|++... -+||.++++-|.+++.+ +.|.-..
T Consensus 12 GVS~~TVSrvLn~~----~~Vs~~tr~rV~~~a~e-lgY~pn~ 49 (343)
T PRK10727 12 GVSVATVSRVINNS----PKASEASRLAVHSAMES-LSYHPNA 49 (343)
T ss_pred CCCHHHHHHHhCCC----CCCCHHHHHHHHHHHHH-HCCCCCH
Confidence 56789999999753 46999999999999998 5565443
No 114
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=35.56 E-value=1.2e+02 Score=28.72 Aligned_cols=71 Identities=14% Similarity=0.190 Sum_probs=43.2
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhh
Q 031627 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEY 87 (156)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~y 87 (156)
++..-+.+.++..+- .++.++.++..+|.+.+.-=+..+-++....+.-.+++ |+.++|...+..+..+.|
T Consensus 180 ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~~~~~~~i 251 (614)
T PRK14971 180 IQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLNILDYDYY 251 (614)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhCCCCHHHH
Confidence 445555555554332 36889999988888776544444444444444434444 888888877765555444
No 115
>smart00350 MCM minichromosome maintenance proteins.
Probab=35.37 E-value=1.6e+02 Score=26.98 Aligned_cols=65 Identities=14% Similarity=0.232 Sum_probs=48.2
Q ss_pred ccCcHHHHHHHHHhh----CCCCccccHHHHHHHHHHHHHHH-------------------HHHHHHHHHHhhhcCCCcc
Q 031627 14 ASLPKATMTKIIKEM----LPADVRVARDAQDLLIECCVEFI-------------------NLVSSESNEVCSREDKRTI 70 (156)
Q Consensus 14 ~~LP~A~V~riiKe~----LP~~~~iskda~~~i~~c~~eFI-------------------~~lsseAn~~a~~~~RKTI 70 (156)
..++...+.+.|.-+ .| .+|+++.+.|.+...+.= ..|-.-|-..|.-.+|.+|
T Consensus 416 ~~~~~~~l~~yi~~ar~~~~P---~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V 492 (509)
T smart00350 416 VPISQEFLRKYIAYAREKIKP---KLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVV 492 (509)
T ss_pred ccCCHHHHHHHHHHHHhcCCC---CCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCcc
Confidence 457888888877433 34 489999999987665532 3444667777888999999
Q ss_pred Chhhhhhhhhh
Q 031627 71 APEHVLKALEV 81 (156)
Q Consensus 71 ~~edVl~AL~~ 81 (156)
+++||..|++-
T Consensus 493 ~~~Dv~~ai~l 503 (509)
T smart00350 493 EEADVEEAIRL 503 (509)
T ss_pred CHHHHHHHHHH
Confidence 99999999754
No 116
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=34.85 E-value=37 Score=18.76 Aligned_cols=26 Identities=19% Similarity=0.253 Sum_probs=20.0
Q ss_pred HHHHhhhcCCCccChhhhhhhhh-hcC
Q 031627 58 SNEVCSREDKRTIAPEHVLKALE-VLG 83 (156)
Q Consensus 58 An~~a~~~~RKTI~~edVl~AL~-~Lg 83 (156)
+....-.++.-+|+.+++..+|+ .||
T Consensus 5 ~F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 5 AFKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 44556677888999999999998 576
No 117
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=33.87 E-value=1.4e+02 Score=19.55 Aligned_cols=47 Identities=11% Similarity=0.252 Sum_probs=36.4
Q ss_pred cCcHHHHHHHHHhhCCCCccc-cHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 031627 15 SLPKATMTKIIKEMLPADVRV-ARDAQDLLIECCVEFINLVSSESNEVCSR 64 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~i-skda~~~i~~c~~eFI~~lsseAn~~a~~ 64 (156)
.+|-+.+.-+++.+. +.. ..-..-+|.=++-.||.-|+..|.+.|+-
T Consensus 2 ~IPD~v~~~yL~~~G---~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSG---FQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCC---CCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 478888888888875 332 23345688889999999999999998863
No 118
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=33.86 E-value=2.4e+02 Score=23.12 Aligned_cols=51 Identities=18% Similarity=0.236 Sum_probs=37.7
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHhhh-------------------c--------------CCCccChhhhhhhhhh
Q 031627 35 VARDAQDLLIECCVEFINLVSSESNEVCSR-------------------E--------------DKRTIAPEHVLKALEV 81 (156)
Q Consensus 35 iskda~~~i~~c~~eFI~~lsseAn~~a~~-------------------~--------------~RKTI~~edVl~AL~~ 81 (156)
...-.+-++.-.+-.||.-|+-.|-++.+= . +|-+++..|+-.||.+
T Consensus 106 ~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~~dr~K~vltv~DLs~Al~E 185 (197)
T COG5162 106 SDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTVVDLSKALEE 185 (197)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccccccCCceeeehHHHHHHHH
Confidence 344567788889999999998777655431 1 4557888999999998
Q ss_pred cChh
Q 031627 82 LGFG 85 (156)
Q Consensus 82 LgF~ 85 (156)
.|+.
T Consensus 186 yGin 189 (197)
T COG5162 186 YGIN 189 (197)
T ss_pred hccc
Confidence 8874
No 119
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=33.68 E-value=51 Score=28.47 Aligned_cols=32 Identities=19% Similarity=0.341 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 50 FINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 50 FI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
-|..|..+|...|...++..|+.+|+..|++.
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 35567788889999999999999999999875
No 120
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=33.67 E-value=81 Score=20.82 Aligned_cols=33 Identities=21% Similarity=0.472 Sum_probs=23.7
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHH
Q 031627 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEF 50 (156)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eF 50 (156)
..+..+||.|++.. .-.|+.+++..|.+++.++
T Consensus 10 ~gvS~~TVSr~ln~----~~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 10 AGVSKATVSRVLNG----NGRVSEETREKVLAAMEEL 42 (70)
T ss_pred HCCCHHHHHHHHCC----CCCCCHHHHHHHHHHHHHh
Confidence 45778888887764 3446888888888877765
No 121
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=33.39 E-value=2.4e+02 Score=22.17 Aligned_cols=51 Identities=18% Similarity=0.326 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh-hhHHHHHHHHHHHHHHhh
Q 031627 46 CCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG-EYIEEVYAAYEQHKLETM 103 (156)
Q Consensus 46 c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~-~yv~~l~~~l~~~k~~~~ 103 (156)
.+.+.++||-..|. |..++++++..=|..|||+ +.++.+..++.+++....
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l~ 94 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKLQ 94 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH
Confidence 45566667666554 4459999999999999998 677777777777775543
No 122
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=33.01 E-value=52 Score=28.99 Aligned_cols=33 Identities=24% Similarity=0.410 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHhhhcCCCccChhhhhhhhhhc
Q 031627 50 FINLVSSESNEVCSREDKRTIAPEHVLKALEVL 82 (156)
Q Consensus 50 FI~~lsseAn~~a~~~~RKTI~~edVl~AL~~L 82 (156)
=|..|..+|...|.+++++.|+.+|+..|++..
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~ 372 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKV 372 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 355677888888888999999999999998654
No 123
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=33.00 E-value=50 Score=30.11 Aligned_cols=31 Identities=23% Similarity=0.293 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 51 INLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 51 I~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
|..|..+|-..|...+|..|+.+||..|++.
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~ 423 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEK 423 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHH
Confidence 5567788999999999999999999999754
No 124
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=32.77 E-value=78 Score=29.47 Aligned_cols=50 Identities=14% Similarity=0.222 Sum_probs=37.6
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHHHHHHHHHH
Q 031627 34 RVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYAAYEQ 97 (156)
Q Consensus 34 ~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~~l~~ 97 (156)
-|-+|.+.+|++||...=.||+..-...-...++++ |..|++++-..+..
T Consensus 434 ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~ 483 (488)
T TIGR01052 434 EIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAY 483 (488)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHH
Confidence 477889999999999999999976655555444444 56788887776654
No 125
>PF07580 Peptidase_M26_C: M26 IgA1-specific Metallo-endopeptidase C-terminal region; InterPro: IPR011505 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry represents metallopeptidases belonging to MEROPS peptidase family M26 (IgA1-specific metallopeptidase, clan MA). They are extracellular enzymes, which cleave mammalian IgA. They are only found in Gram-positive bacteria and are often found associated with IPR001899 from INTERPRO; they may be attached to the cell wall. This entry also contains the metallopeptidases ZmpB and ZmpC from Streptococcus pneumoniae. These metallopeptidases are thought to contribute to the inflammatory response to Streptococcal infection [, ].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0005576 extracellular region, 0005618 cell wall
Probab=32.66 E-value=1.6e+02 Score=28.91 Aligned_cols=59 Identities=19% Similarity=0.273 Sum_probs=47.9
Q ss_pred CCCccccHHHHHHHHHHH--HHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhH
Q 031627 30 PADVRVARDAQDLLIECC--VEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYI 88 (156)
Q Consensus 30 P~~~~iskda~~~i~~c~--~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv 88 (156)
|+++.+-+-|=+++..-. .=||-|+|..=...|..+|+.+++-+-|++.+-.=.|.++.
T Consensus 589 pG~~~Frr~afeLlg~~GYe~Gfv~Y~SNkyk~~A~~~g~~~l~D~~ii~Ki~~g~y~s~~ 649 (737)
T PF07580_consen 589 PGDLMFRRNAFELLGYYGYEDGFVPYASNKYKKEAKAEGKKILSDDYIIKKIFNGQYNSWE 649 (737)
T ss_pred CccchhhHHHHHHHHHhcccccchHhhhhhHHHHHHhcCCCcccHHHHHHHHhcCccCCHH
Confidence 456667777777776654 34999999999999999999999999999999877776543
No 126
>TIGR02454 CbiQ_TIGR cobalt ABC transporter, permease protein CbiQ. This model represents the permease component of the cobalt-specific ABC transporter. This model finds permeases which are generally next to the other subunits of the complex (CbiN and CbiO) or the cobalamin biosynthesis protein CbiM which is a transmembrane protein which likely interacts with the complex in some manner. In genomes which possess all of these subunits the ATPase is most likely running in the direction of import (for the biosynthesis of coenzyme B12). In other genomes, this subunit may be involved in the export of cobalt and/or other closely related heavy metals.
Probab=32.52 E-value=73 Score=24.64 Aligned_cols=38 Identities=21% Similarity=0.204 Sum_probs=30.8
Q ss_pred CccChhhhhhhhhhcChhh-----------hHHHHHHHHHHHHHHhhhc
Q 031627 68 RTIAPEHVLKALEVLGFGE-----------YIEEVYAAYEQHKLETMDS 105 (156)
Q Consensus 68 KTI~~edVl~AL~~LgF~~-----------yv~~l~~~l~~~k~~~~~r 105 (156)
-|.++.|++.+|+.+|++. |++.+.+..+.-++.++-|
T Consensus 112 ~TT~~~~l~~~l~~l~~P~~~~~~~~l~~Rfip~l~~e~~~i~~Aq~aR 160 (198)
T TIGR02454 112 LTTPFPELLSALRRLGVPPLLVEILLLTYRYLFVLLEELRRMLLAQRSR 160 (198)
T ss_pred HcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4789999999999999864 7777877777777777765
No 127
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=32.43 E-value=96 Score=28.57 Aligned_cols=49 Identities=18% Similarity=0.305 Sum_probs=40.3
Q ss_pred CCccccHHHHHHHHHHHHH----HHHHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 31 ADVRVARDAQDLLIECCVE----FINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 31 ~~~~iskda~~~i~~c~~e----FI~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
.++.+++||.+.|....++ |..-|-+-|+.+|...|+++|..+||-.|-
T Consensus 377 e~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~ 429 (450)
T COG1224 377 EDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAK 429 (450)
T ss_pred hccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHH
Confidence 4788999999999877655 444444568999999999999999999883
No 128
>PF10728 DUF2520: Domain of unknown function (DUF2520); InterPro: IPR018931 This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases. ; PDB: 3D1L_A 2I76_A 3DFU_A.
Probab=32.15 E-value=1.7e+02 Score=22.07 Aligned_cols=58 Identities=19% Similarity=0.283 Sum_probs=40.3
Q ss_pred HHHHHHHHhhCCCCccccHHHHHHHHHHHH---HHHHHHHHHHHHHhhhcCCCccChhhhhhhh
Q 031627 19 ATMTKIIKEMLPADVRVARDAQDLLIECCV---EFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 19 A~V~riiKe~LP~~~~iskda~~~i~~c~~---eFI~~lsseAn~~a~~~~RKTI~~edVl~AL 79 (156)
..+..|++......+.|+.+-|....-+|+ .|+..|...|.+++...| |..++.+.+|
T Consensus 14 ~~l~~l~~~lg~~~~~i~~~~r~~yHaAav~asNf~~~L~~~a~~ll~~~g---i~~~~a~~~L 74 (132)
T PF10728_consen 14 EVLQELAKELGGRPFEIDSEQRALYHAAAVFASNFLVALYALAAELLEQAG---IDFEEALEAL 74 (132)
T ss_dssp HHHHHHHHHTTSEEEE--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SHHH--HHH
T ss_pred HHHHHHHHHhCCceEEeCHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHcC---CCchhHHHHH
Confidence 457788887776668899999998887765 788888899999887764 5555544443
No 129
>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and
Probab=32.00 E-value=75 Score=19.69 Aligned_cols=34 Identities=12% Similarity=0.248 Sum_probs=25.4
Q ss_pred HHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHH
Q 031627 24 IIKEMLPADVRVARDAQDLLIECCVEFINLVSSE 57 (156)
Q Consensus 24 iiKe~LP~~~~iskda~~~i~~c~~eFI~~lsse 57 (156)
.++..+|......+-.+..|...+..||.+|...
T Consensus 25 ~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~ 58 (60)
T cd00083 25 ELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQEL 58 (60)
T ss_pred HHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 4566778654566667788888999999998764
No 130
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=31.85 E-value=18 Score=25.12 Aligned_cols=61 Identities=11% Similarity=0.119 Sum_probs=30.9
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHHHHHH
Q 031627 32 DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYA 93 (156)
Q Consensus 32 ~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~ 93 (156)
++|++.+.+++|.+++..--.-+|.--...+...-+.+|.-.+ .--|..=+|..|+..|..
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~-~~~Ls~~~~~~f~~aLd~ 63 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHE-RIRLSAEDFEAFMAALDN 63 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHH-HHHHCCHHHHHHHHHHH-
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcc-eeEcCHHHHHHHHHHHhC
Confidence 4789999999999998653332332222222222233333332 334555666666665554
No 131
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=31.74 E-value=71 Score=27.44 Aligned_cols=53 Identities=21% Similarity=0.272 Sum_probs=44.3
Q ss_pred CcccccCcHHHHHHHHHhhCCC-----Ccc-ccHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 031627 10 SKEDASLPKATMTKIIKEMLPA-----DVR-VARDAQDLLIECCVEFINLVSSESNEVC 62 (156)
Q Consensus 10 ~~dd~~LP~A~V~riiKe~LP~-----~~~-iskda~~~i~~c~~eFI~~lsseAn~~a 62 (156)
+++.+..|.+++.|-|.+.+.. +++ +.|-.+.+....|.+|..|+-.-+|-.+
T Consensus 149 ~Ie~~~VpvttlaKTi~DC~~kP~YCGG~~~~akAl~aa~e~a~~e~t~Yl~R~~n~Aa 207 (269)
T COG5340 149 SIEGTVVPVTTLAKTIVDCADKPEYCGGIRELAKALVAADEQACSEATEYLQRLDNGAA 207 (269)
T ss_pred ceeeeeeehHHHHHHHHHHhcCccccCCHHHHHHHHHHhHHHHHHHHHHHHHhccchHH
Confidence 4778889999999999999964 444 8999999999999999999887766544
No 132
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=31.42 E-value=1.3e+02 Score=22.94 Aligned_cols=49 Identities=14% Similarity=0.248 Sum_probs=41.0
Q ss_pred CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 31 ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 31 ~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
+.+.=..|+..++.+.+.-+++.+-..|..+|.. |-.+..||..-||+.
T Consensus 24 Dvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~--rnK~k~eDfkfaLr~ 72 (126)
T COG5248 24 DVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQV--RNKTKTEDFKFALRR 72 (126)
T ss_pred CCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHh--cccchHHHHHHHHhh
Confidence 4566778999999999999999999999999984 444677899888864
No 133
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=31.08 E-value=1.2e+02 Score=25.64 Aligned_cols=64 Identities=19% Similarity=0.215 Sum_probs=45.2
Q ss_pred HHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhh-cCCCccChhhhhhhhhh
Q 031627 18 KATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSR-EDKRTIAPEHVLKALEV 81 (156)
Q Consensus 18 ~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~-~~RKTI~~edVl~AL~~ 81 (156)
...+.+.|.+.+- .+.+|+.+|...|.+++.-=...+.++-..++.- .+.++|+.+||...+..
T Consensus 144 ~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~ 209 (343)
T PRK06585 144 ERDLARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGD 209 (343)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC
Confidence 3344444444432 3789999999999999887566666777777665 44678999999877654
No 134
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=29.81 E-value=1e+02 Score=18.54 Aligned_cols=34 Identities=18% Similarity=0.399 Sum_probs=21.8
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHH
Q 031627 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEF 50 (156)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eF 50 (156)
.+.+..++|.++++.. ..|+.+.+..|.+++.++
T Consensus 6 ~~gvs~~tvs~~l~g~----~~vs~~~~~~i~~~~~~l 39 (52)
T cd01392 6 AAGVSVATVSRVLNGK----PRVSEETRERVLAAAEEL 39 (52)
T ss_pred HHCcCHHHHHHHHcCC----CCCCHHHHHHHHHHHHHh
Confidence 3456777777777642 357777777776666554
No 135
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=29.77 E-value=31 Score=23.85 Aligned_cols=17 Identities=41% Similarity=0.591 Sum_probs=15.2
Q ss_pred ccChhhhhhhhhhcChh
Q 031627 69 TIAPEHVLKALEVLGFG 85 (156)
Q Consensus 69 TI~~edVl~AL~~LgF~ 85 (156)
.+++.+|+++|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 47889999999999996
No 136
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=29.59 E-value=1e+02 Score=21.25 Aligned_cols=56 Identities=13% Similarity=0.134 Sum_probs=36.5
Q ss_pred HHHHHhhhcCCCccChhhhhhhhhhcChhhhHHHHHHHHHHHHHHhhhcccCCCCCCCCCCCHHHHHHH
Q 031627 57 ESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYAAYEQHKLETMDSLKGGKWSNGAEMTEEEAAAE 125 (156)
Q Consensus 57 eAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~~l~~~k~~~~~r~k~~~k~~~~g~~eEel~~~ 125 (156)
.+...+..++.-+|+.++|..+|..+|+.. +.+...+..+. .-.+..++-+|.+..
T Consensus 14 ~~F~~~D~d~~G~Is~~el~~~l~~~~~~~--~ev~~i~~~~d-----------~~~~g~I~~~eF~~~ 69 (96)
T smart00027 14 QIFRSLDKNQDGTVTGAQAKPILLKSGLPQ--TLLAKIWNLAD-----------IDNDGELDKDEFALA 69 (96)
T ss_pred HHHHHhCCCCCCeEeHHHHHHHHHHcCCCH--HHHHHHHHHhc-----------CCCCCCcCHHHHHHH
Confidence 456667778888999999999999999853 23444433221 112345788877643
No 137
>KOG0784 consensus Isocitrate dehydrogenase, gamma subunit [Amino acid transport and metabolism]
Probab=29.47 E-value=41 Score=30.29 Aligned_cols=46 Identities=13% Similarity=0.246 Sum_probs=36.9
Q ss_pred HHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhHHHHHHHHHHH
Q 031627 52 NLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYAAYEQH 98 (156)
Q Consensus 52 ~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~~l~~~ 98 (156)
.-|+.-|.+.|.+.|||.+++=|=-. +-.||=+-|++.+.++...|
T Consensus 187 eRIaryAF~yA~k~gRKkVTaVHKAn-imKL~DGlFle~~~eva~~Y 232 (375)
T KOG0784|consen 187 ERIARYAFEYAKKNGRKKVTAVHKAN-IMKLGDGLFLESCQEVAKKY 232 (375)
T ss_pred HHHHHHHHHHHHHhCCceEEEEeccC-ceecchhhHHHHHHHHHhcC
Confidence 35677899999999999999988666 45688788999888876443
No 138
>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
Probab=29.34 E-value=2.3e+02 Score=23.64 Aligned_cols=62 Identities=16% Similarity=0.195 Sum_probs=35.0
Q ss_pred HHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 18 KATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 18 ~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
...+..+++..+- .++.|+.++...|.+.+.--+..+-.+....+...+ +.|+.+||-.++.
T Consensus 178 ~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~~-~~it~~~v~~~~~ 240 (355)
T TIGR02397 178 LEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLLDQLISFGN-GNITYEDVNELLG 240 (355)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCChHHHHHHHHHHHhhcC-CCCCHHHHHHHhC
Confidence 4445555554332 257789898888877665433344343333333333 3488887766554
No 139
>KOG1792 consensus Reticulon [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.98 E-value=89 Score=26.24 Aligned_cols=62 Identities=19% Similarity=0.205 Sum_probs=49.7
Q ss_pred hCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHH-hhhcCCCccChhhhhhhhhhcC-hhhhHH
Q 031627 28 MLPADVRVARDAQDLLIECCVEFINLVSSESNEV-CSREDKRTIAPEHVLKALEVLG-FGEYIE 89 (156)
Q Consensus 28 ~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~-a~~~~RKTI~~edVl~AL~~Lg-F~~yv~ 89 (156)
-+|.++.+++|....+..++++-|+..+++.+++ |.++-+.-+...=.++.+.-+| +.+++.
T Consensus 110 ~lp~~i~ipee~~~~~a~~~~~~in~~l~~l~~ia~~~d~~~~lk~~v~lw~lS~vGs~fn~lT 173 (230)
T KOG1792|consen 110 YLPVEITIPEEFVLALASSLRVEINQALSELRDIALGRDLKDFLKVAVGLWILSYVGSLFNFLT 173 (230)
T ss_pred cCCceeecCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhhhHHH
Confidence 5677899999999999999999999999999999 5556555566666788888887 444443
No 140
>COG1500 Predicted exosome subunit [Translation, ribosomal structure and biogenesis]
Probab=28.27 E-value=1.6e+02 Score=24.97 Aligned_cols=70 Identities=17% Similarity=0.293 Sum_probs=50.3
Q ss_pred HHHHHHhhCC-CCccccHHHHHHHHHHHH-HHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh-hhHHHHHH
Q 031627 21 MTKIIKEMLP-ADVRVARDAQDLLIECCV-EFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG-EYIEEVYA 93 (156)
Q Consensus 21 V~riiKe~LP-~~~~iskda~~~i~~c~~-eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~-~yv~~l~~ 93 (156)
+.+|+.+.|- +.+.++.+-|..+.+--. ..|++|+..|.+ -..+....|.-|-+||++++|. ++..+.++
T Consensus 72 ~~eI~~eIl~kGeiQlTaeqR~~m~e~k~rqIi~~IsRn~Id---P~t~~P~Pp~rIe~Ameeakv~id~~K~ae~ 144 (234)
T COG1500 72 PDEIAEEILKKGEIQLTAEQRREMLEEKKRQIINIISRNAID---PQTKAPHPPARIEKAMEEAKVHIDPFKSAEE 144 (234)
T ss_pred HHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHhccC---CCCCCCCCHHHHHHHHHhcCcccCCCCCHHH
Confidence 4555555554 357899998887776654 566688776544 3456789999999999999997 66666554
No 141
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=27.86 E-value=2.1e+02 Score=24.84 Aligned_cols=66 Identities=14% Similarity=0.111 Sum_probs=35.7
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhc
Q 031627 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVL 82 (156)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~L 82 (156)
++...+..+++..+. .++.++.++...|.+.+.-=+..+-......+.. ++..|+.++|.+++...
T Consensus 178 l~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s~G~~R~al~~l~~~~~~-~~~~It~~~v~~~l~~~ 244 (363)
T PRK14961 178 ISEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLEHAINL-GKGNINIKNVTDMLGLL 244 (363)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh-cCCCCCHHHHHHHHCCC
Confidence 334445555554332 2577899988887766532111111111112222 46779999998876533
No 142
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=27.28 E-value=98 Score=20.98 Aligned_cols=22 Identities=9% Similarity=0.176 Sum_probs=16.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHHH
Q 031627 112 SNGAEMTEEEAAAEQQRMFAEA 133 (156)
Q Consensus 112 ~~~~g~~eEel~~~Q~eLf~~a 133 (156)
.....++++++....+.|...-
T Consensus 18 ~~kp~Lde~~leei~~~l~~a~ 39 (92)
T PF08863_consen 18 VEKPELDEQQLEEINEKLSEAY 39 (92)
T ss_pred cCCCCCcHHHHHHHHHHHHHHh
Confidence 3456689999999988886553
No 143
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=27.09 E-value=71 Score=28.55 Aligned_cols=31 Identities=19% Similarity=0.326 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 51 INLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 51 I~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
|..|..+|...|...+|..|+.+|+..|++.
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~ 385 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKT 385 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHH
Confidence 6677888999999999999999999999754
No 144
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=27.05 E-value=1e+02 Score=28.29 Aligned_cols=53 Identities=19% Similarity=0.381 Sum_probs=44.5
Q ss_pred hhCCCCccccHHHHHHHHHHHHHHHH-------HHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 27 EMLPADVRVARDAQDLLIECCVEFIN-------LVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 27 e~LP~~~~iskda~~~i~~c~~eFI~-------~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
+.|| .+.++.++...|.+.|..+-. .+...|..++.-.||.+++.+||-.|+.
T Consensus 261 ~~l~-~V~l~~~~~~~ia~~~~~~~v~g~radi~~~r~a~a~aa~~Gr~~v~~~Di~~a~~ 320 (423)
T COG1239 261 SLLS-EVELDDDAETKIAELCARLAVDGHRADIVVVRAAKALAALRGRTEVEEEDIREAAE 320 (423)
T ss_pred hccc-cccCcHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHhcCceeeehhhHHHHHh
Confidence 4455 789999999999999988754 4778888899999999999999988863
No 145
>PRK09492 treR trehalose repressor; Provisional
Probab=26.74 E-value=94 Score=25.20 Aligned_cols=38 Identities=11% Similarity=0.302 Sum_probs=30.1
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHH
Q 031627 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSS 56 (156)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lss 56 (156)
..+-++||.|++.. .-+||.++++-|.+++.+. .|.-.
T Consensus 14 agVS~~TVSrvLn~----~~~vs~~tr~rV~~~a~el-gY~pn 51 (315)
T PRK09492 14 SGVGKSTVSRVLNN----ESGVSEETRERVEAVINQH-GFSPS 51 (315)
T ss_pred hCCCHHHHhHHhCC----CCCCCHHHHHHHHHHHHHH-CCCcC
Confidence 46778999999985 2479999999999998884 46544
No 146
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
Probab=26.32 E-value=1.4e+02 Score=28.17 Aligned_cols=71 Identities=17% Similarity=0.326 Sum_probs=44.5
Q ss_pred HHHHHHHHhhCCC-CccccHHHHHHHHHHH---HHHHHHHHHH-------HHHHhhhcCCCccChhhhhhhhhhcChhhh
Q 031627 19 ATMTKIIKEMLPA-DVRVARDAQDLLIECC---VEFINLVSSE-------SNEVCSREDKRTIAPEHVLKALEVLGFGEY 87 (156)
Q Consensus 19 A~V~riiKe~LP~-~~~iskda~~~i~~c~---~eFI~~lsse-------An~~a~~~~RKTI~~edVl~AL~~LgF~~y 87 (156)
.-+..|++..+.. ++.++.++.++|.+++ ...++.|... +...+...++.+|+.+||.+++..--|..|
T Consensus 356 edi~~Il~~~a~~~~v~ls~eal~~L~~ys~~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r~~~~ 435 (615)
T TIGR02903 356 EDIALIVLNAAEKINVHLAAGVEELIARYTIEGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQISRLSPY 435 (615)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCCcCccc
Confidence 3455555555432 4678899999988865 3344444322 111223445668999999999988777665
Q ss_pred HH
Q 031627 88 IE 89 (156)
Q Consensus 88 v~ 89 (156)
..
T Consensus 436 ~~ 437 (615)
T TIGR02903 436 EK 437 (615)
T ss_pred hh
Confidence 53
No 147
>PF13690 CheX: Chemotaxis phosphatase CheX; PDB: 3HM4_B 3H4Y_A 3H2D_A 3IIC_B.
Probab=26.15 E-value=1.6e+02 Score=20.38 Aligned_cols=46 Identities=9% Similarity=0.220 Sum_probs=34.5
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 031627 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVC 62 (156)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a 62 (156)
-+.+|+.+..++++. +..+ ..|.-+.+..+..||.+.|+.-+....
T Consensus 16 ~l~~~~~~a~~la~~-mg~~---~~~~~e~~~da~~El~NiI~G~~~~~l 61 (94)
T PF13690_consen 16 ILSFDEELAKKLASA-MGEE---EEEDDEMVQDALGELANIIAGNAKSEL 61 (94)
T ss_dssp EEEE-HHHHHHHHHH-HSSS----SSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEEECHHHHHHHHHH-hCCC---CcchhHHHHHHHHHHHHHHHHHHHHHc
Confidence 367899999999997 4433 444778889999999999998777555
No 148
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=25.85 E-value=2.2e+02 Score=27.00 Aligned_cols=64 Identities=13% Similarity=0.132 Sum_probs=41.0
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
++..-+.+.++..+. .++.|+.++..+|.+.+.--+..+.++....+.. +...|+.+||...+.
T Consensus 191 l~~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~-g~g~It~e~V~~llg 255 (598)
T PRK09111 191 IEADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLLDQAIAH-GAGEVTAEAVRDMLG 255 (598)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhh-cCCCcCHHHHHHHhC
Confidence 334445555554443 4688999999999988775555555555444333 345799999887653
No 149
>KOG0605 consensus NDR and related serine/threonine kinases [General function prediction only]
Probab=25.47 E-value=83 Score=29.86 Aligned_cols=76 Identities=17% Similarity=0.291 Sum_probs=52.9
Q ss_pred ccCcHHHHHHHHHhh----CCCCccccHHHHHHHHHHHHHHHHHHH-HHHHHHhhhcCCCccChhhhhhhhhhcChhhhH
Q 031627 14 ASLPKATMTKIIKEM----LPADVRVARDAQDLLIECCVEFINLVS-SESNEVCSREDKRTIAPEHVLKALEVLGFGEYI 88 (156)
Q Consensus 14 ~~LP~A~V~riiKe~----LP~~~~iskda~~~i~~c~~eFI~~ls-seAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv 88 (156)
-+-|.+|-.||+.-. .|..+.+|.||+++|.+|+..=.+-|. .-+.+|=.+-==++|.=+||... . .-|+
T Consensus 390 s~tp~~T~rkI~nwr~~l~fP~~~~~s~eA~DLI~rll~d~~~RLG~~G~~EIK~HPfF~~v~W~~l~~~----~-apfv 464 (550)
T KOG0605|consen 390 SETPQETYRKIVNWRETLKFPEEVDLSDEAKDLITRLLCDPENRLGSKGAEEIKKHPFFKGVDWDHLREM----P-APFV 464 (550)
T ss_pred CCCHHHHHHHHHHHhhhccCCCcCcccHHHHHHHHHHhcCHHHhcCcccHHHHhcCCccccCCcchhhcC----C-CCCC
Confidence 367999999999754 378999999999999999987777766 23444444444456777766543 1 4456
Q ss_pred HHHHHH
Q 031627 89 EEVYAA 94 (156)
Q Consensus 89 ~~l~~~ 94 (156)
|.+...
T Consensus 465 P~v~~~ 470 (550)
T KOG0605|consen 465 PQVNSE 470 (550)
T ss_pred CCCCCc
Confidence 555543
No 150
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=25.35 E-value=2.5e+02 Score=27.82 Aligned_cols=62 Identities=13% Similarity=0.139 Sum_probs=35.9
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhh
Q 031627 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLK 77 (156)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~ 77 (156)
|+...|.+++++.+- .++.|++++..+|.+.+.-=+..+-++....+...+...|+.+||..
T Consensus 179 l~~~~l~~~L~~il~~EGv~id~eal~lLa~~sgGdlR~Al~eLEKLia~~~~~~IT~e~V~a 241 (824)
T PRK07764 179 VPPEVMRGYLERICAQEGVPVEPGVLPLVIRAGGGSVRDSLSVLDQLLAGAGPEGVTYERAVA 241 (824)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCCHHHHHH
Confidence 456666666666653 36788999888877765543333333333444333344577765543
No 151
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=25.33 E-value=1.1e+02 Score=25.01 Aligned_cols=36 Identities=17% Similarity=0.264 Sum_probs=28.2
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHH
Q 031627 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEF 50 (156)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eF 50 (156)
...-++||.|++...- ...+||.++++-|.+++.+.
T Consensus 10 aGVS~~TVSrvLn~~~-~~~~Vs~~tr~rV~~~a~el 45 (328)
T PRK11303 10 AGVSRTTASYVINGKA-KQYRVSDKTVEKVMAVVREH 45 (328)
T ss_pred hCCCHHHHHHHHcCCC-CCCCcCHHHHHHHHHHHHHh
Confidence 3567899999997642 11379999999999999884
No 152
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=25.02 E-value=2.7e+02 Score=23.67 Aligned_cols=60 Identities=12% Similarity=0.127 Sum_probs=42.1
Q ss_pred HHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhh
Q 031627 20 TMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (156)
Q Consensus 20 ~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~ 81 (156)
-+.+.|.+.+- .+.+|+.+|...|...+.-=...+.+|--..+.-.+ +|+.+||...+..
T Consensus 139 ~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v~~ 199 (328)
T PRK08487 139 EALELLQERAKELGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELVFG 199 (328)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHhcc
Confidence 34444444432 378999999999999888666666666666666533 7999999887633
No 153
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=24.47 E-value=43 Score=21.06 Aligned_cols=16 Identities=25% Similarity=0.542 Sum_probs=13.7
Q ss_pred cChhhhhhhhhhcChh
Q 031627 70 IAPEHVLKALEVLGFG 85 (156)
Q Consensus 70 I~~edVl~AL~~LgF~ 85 (156)
+++++|..+++.+||+
T Consensus 47 ~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 47 TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp SCHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHhCcC
Confidence 6778999999999984
No 154
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=24.15 E-value=2.4e+02 Score=26.20 Aligned_cols=66 Identities=9% Similarity=0.154 Sum_probs=38.7
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhc
Q 031627 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVL 82 (156)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~L 82 (156)
++...+.+.++..+- .++.|+.++..+|.+.+.-=+..+-+.-...+...+ .+|+.++|...|...
T Consensus 175 l~~~el~~~L~~ia~~Egi~i~~eAL~lIa~~s~GslR~alslLdqli~y~~-~~It~e~V~~llg~~ 241 (491)
T PRK14964 175 IPTDKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNALFLLEQAAIYSN-NKISEKSVRDLLGCV 241 (491)
T ss_pred ccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcC-CCCCHHHHHHHHccC
Confidence 344444444444332 478899999999998774333333333333333333 479999997765333
No 155
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=23.90 E-value=1.2e+02 Score=24.70 Aligned_cols=39 Identities=13% Similarity=0.265 Sum_probs=28.9
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHH
Q 031627 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVS 55 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~ls 55 (156)
..-.+||.|++... +...+||.+++.-|.+++.+ +.|.-
T Consensus 10 GVS~~TVSrvLn~~-~~~~~vs~~tr~rV~~~a~~-lgY~p 48 (327)
T TIGR02417 10 GVSKTTASYVINGK-AKEYRISQETVERVMAVVRE-QGYQP 48 (327)
T ss_pred CCCHHHHHHHHcCC-CCCCccCHHHHHHHHHHHHH-hCCCC
Confidence 45689999999763 11137999999999999887 34443
No 156
>PRK05907 hypothetical protein; Provisional
Probab=23.89 E-value=1.7e+02 Score=25.24 Aligned_cols=54 Identities=7% Similarity=0.041 Sum_probs=39.9
Q ss_pred CccccHHHHHHHHHHHH-HHHHHHHHHHHHHhhh-cCCCccChhhhhhhhh-hcChh
Q 031627 32 DVRVARDAQDLLIECCV-EFINLVSSESNEVCSR-EDKRTIAPEHVLKALE-VLGFG 85 (156)
Q Consensus 32 ~~~iskda~~~i~~c~~-eFI~~lsseAn~~a~~-~~RKTI~~edVl~AL~-~LgF~ 85 (156)
+.+|+.+|...+.+.+. -=+..+..|-...|.- ..+++|+.+||-..+. .+.+.
T Consensus 151 g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~~s~e~n 207 (311)
T PRK05907 151 GISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVVKKEAAS 207 (311)
T ss_pred CCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhcCccccc
Confidence 78999999999988773 4445666777777665 6688999999987743 34444
No 157
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=23.19 E-value=3.3e+02 Score=25.23 Aligned_cols=71 Identities=15% Similarity=0.103 Sum_probs=38.9
Q ss_pred cCcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhh
Q 031627 15 SLPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGE 86 (156)
Q Consensus 15 ~LP~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~ 86 (156)
.||...|.+.++..+- .++.++.++...|.+.+.-=+..+-+.--..+. -+...|+.+||...+....-..
T Consensus 177 ~l~~~~i~~~l~~il~~egi~~~~~al~~ia~~s~GslR~al~lLdq~ia-~~~~~It~~~V~~~lg~~~~~~ 248 (509)
T PRK14958 177 QLPPLQIAAHCQHLLKEENVEFENAALDLLARAANGSVRDALSLLDQSIA-YGNGKVLIADVKTMLGTIEPLL 248 (509)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHh-cCCCCcCHHHHHHHHCCCCHHH
Confidence 3555555555444443 368899999988887764212222111111111 2455688888887765544443
No 158
>PF02361 CbiQ: Cobalt transport protein; InterPro: IPR003339 Cobalt transport proteins are most often found in cobalamin (vitamin B12) biosynthesis operons. Salmonella typhimurium synthesizes cobalamin (vitamin B12) de novo under anaerobic conditions. Not all Salmonella and Pseudomonas cobalamin synthetic genes have apparent homologs in the other species suggesting that the cobalamin biosynthetic pathways differ between the two organisms [].; GO: 0015087 cobalt ion transmembrane transporter activity, 0006824 cobalt ion transport, 0009236 cobalamin biosynthetic process
Probab=22.84 E-value=1.2e+02 Score=23.36 Aligned_cols=38 Identities=16% Similarity=0.236 Sum_probs=31.0
Q ss_pred CccChhhhhhhhhhcChhh------------hHHHHHHHHHHHHHHhhhc
Q 031627 68 RTIAPEHVLKALEVLGFGE------------YIEEVYAAYEQHKLETMDS 105 (156)
Q Consensus 68 KTI~~edVl~AL~~LgF~~------------yv~~l~~~l~~~k~~~~~r 105 (156)
.|.+++|++.+|+.+++.. |++.+.+....-++.++-|
T Consensus 123 ~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A~~~R 172 (224)
T PF02361_consen 123 LTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREAQRLR 172 (224)
T ss_pred HHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4789999999999999887 7788887777777777644
No 159
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=22.36 E-value=3.2e+02 Score=23.36 Aligned_cols=67 Identities=13% Similarity=0.169 Sum_probs=38.1
Q ss_pred HHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChh
Q 031627 18 KATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (156)
Q Consensus 18 ~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~ 85 (156)
...+..++...+- .++.|+.++...|.+-+.-=+..+-.+-...+.-.++. |+.+||...+.....+
T Consensus 169 ~~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~gdlr~~~~~lekl~~y~~~~-it~~~v~~~~~~~~~~ 236 (367)
T PRK14970 169 IKDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFDRVVTFCGKN-ITRQAVTENLNILDYD 236 (367)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHhCCCCHH
Confidence 3555555544332 36789999999887755432333333333333333333 8888887776655443
No 160
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=22.20 E-value=2.5e+02 Score=24.09 Aligned_cols=51 Identities=16% Similarity=0.242 Sum_probs=41.4
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhc
Q 031627 32 DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVL 82 (156)
Q Consensus 32 ~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~L 82 (156)
+++|++||.+.|..+..-=...+.+|-+..+--.+-++|+.+||..++-.-
T Consensus 157 ~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~~ 207 (334)
T COG1466 157 GLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSDV 207 (334)
T ss_pred CCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhcc
Confidence 789999999999999886667777777777775555599999998887653
No 161
>PRK05629 hypothetical protein; Validated
Probab=21.48 E-value=2.8e+02 Score=23.40 Aligned_cols=49 Identities=16% Similarity=0.140 Sum_probs=37.7
Q ss_pred CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhh
Q 031627 31 ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (156)
Q Consensus 31 ~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~ 80 (156)
.+.+|+.+|.+.|..++..=...+.+|--..|... ..+|+.+||-..+.
T Consensus 142 ~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~-~~~It~e~V~~~v~ 190 (318)
T PRK05629 142 HGVRPTPDVVHALLEGVGSDLRELASAISQLVEDT-QGNVTVEKVRAYYV 190 (318)
T ss_pred cCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcC-CCCcCHHHHHHHhC
Confidence 37899999999999988776666777766666543 45799999977644
No 162
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=21.42 E-value=1.7e+02 Score=26.74 Aligned_cols=58 Identities=16% Similarity=0.230 Sum_probs=43.9
Q ss_pred CCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcChhhhH
Q 031627 29 LPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYI 88 (156)
Q Consensus 29 LP~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~LgF~~yv 88 (156)
|++..++|.+....|.+.|++ ..|= ..|..+-...+...||.+-|..+++.+|+....
T Consensus 112 l~~~~R~S~~~~~~i~~~a~~-~sYr-~aa~~l~~~~~~~~iS~~tV~~~v~~~g~~~~~ 169 (470)
T PF06782_consen 112 LKKYQRISPELKEKIVELATE-MSYR-KAAEILEELLGNVSISKQTVWNIVKEAGFEEIK 169 (470)
T ss_pred CCcccchhHHHHHHHHHHHhh-cCHH-HHHHHHhhccCCCccCHHHHHHHHHhccchhhh
Confidence 345689999999999999888 4443 223344355678899999999999999975443
No 163
>PF14434 Imm6: Immunity protein Imm6
Probab=21.31 E-value=3.4e+02 Score=20.45 Aligned_cols=36 Identities=11% Similarity=0.176 Sum_probs=27.7
Q ss_pred HHHHHHHHHhhh--cCCCccChhhhhhhhhhcChhhhHH
Q 031627 53 LVSSESNEVCSR--EDKRTIAPEHVLKALEVLGFGEYIE 89 (156)
Q Consensus 53 ~lsseAn~~a~~--~~RKTI~~edVl~AL~~LgF~~yv~ 89 (156)
+...+|.+.|.+ +| +.++++++..-|++.+|.+...
T Consensus 25 ~~~~~aL~~cw~wle~-~~~~~D~LY~lldn~D~~gi~~ 62 (122)
T PF14434_consen 25 EFVREALDACWKWLEG-KEVTGDELYSLLDNEDENGIFI 62 (122)
T ss_pred HHHHHHHHHHHHHHHc-CCCCHHHHHHHHhCcccccHHH
Confidence 333888888886 55 7899999999998877765443
No 164
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=21.12 E-value=3.6e+02 Score=26.52 Aligned_cols=67 Identities=10% Similarity=0.109 Sum_probs=37.7
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCccChhhhhhhhhhcC
Q 031627 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLG 83 (156)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskda~~~i~~c~~eFI~~lsseAn~~a~~~~RKTI~~edVl~AL~~Lg 83 (156)
|+..-|...++..+. .++.|+.++...|.+.+.-=+..+-+.--..+.. +...|+.++|...|...+
T Consensus 178 Ls~eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A~GslRdAlnLLDqaia~-g~g~It~e~V~~lLG~~d 245 (709)
T PRK08691 178 MTAQQVADHLAHVLDSEKIAYEPPALQLLGRAAAGSMRDALSLLDQAIAL-GSGKVAENDVRQMIGAVD 245 (709)
T ss_pred CCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHHh-cCCCcCHHHHHHHHcccC
Confidence 344444444544443 3688999999999988752222222211111111 344688888877766655
No 165
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=20.84 E-value=1.2e+02 Score=29.06 Aligned_cols=23 Identities=26% Similarity=0.355 Sum_probs=19.1
Q ss_pred HHHHHhhhcCCCccChhhhhhhh
Q 031627 57 ESNEVCSREDKRTIAPEHVLKAL 79 (156)
Q Consensus 57 eAn~~a~~~~RKTI~~edVl~AL 79 (156)
.|...|..-+..-|.++|++.||
T Consensus 11 ~A~~~A~~~~h~~V~~EHLLlaL 33 (731)
T TIGR02639 11 AALEEAKKRRHEFVTLEHILLAL 33 (731)
T ss_pred HHHHHHHHhCCCcCcHHHHHHHH
Confidence 46778888888889999998876
No 166
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=20.53 E-value=1.3e+02 Score=24.53 Aligned_cols=38 Identities=13% Similarity=0.251 Sum_probs=29.7
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHH
Q 031627 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSS 56 (156)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskda~~~i~~c~~eFI~~lss 56 (156)
..+-.+||.|++... -+||.++++-|.+++.+. .|.-.
T Consensus 11 agvS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l-gY~pn 48 (329)
T TIGR01481 11 AGVSMATVSRVVNGN----PNVKPATRKKVLEVIKRL-DYRPN 48 (329)
T ss_pred hCCCHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCCC
Confidence 356789999999863 479999999999999884 45443
No 167
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=20.40 E-value=2.6e+02 Score=25.01 Aligned_cols=66 Identities=21% Similarity=0.350 Sum_probs=43.6
Q ss_pred HHHHHHHHHhhCCCCc--cccHHHHHHHHHH-HHHHHHHHHHHHHH-Hhhhc--CC-CccChhhhhhhhhhcC
Q 031627 18 KATMTKIIKEMLPADV--RVARDAQDLLIEC-CVEFINLVSSESNE-VCSRE--DK-RTIAPEHVLKALEVLG 83 (156)
Q Consensus 18 ~A~V~riiKe~LP~~~--~iskda~~~i~~c-~~eFI~~lsseAn~-~a~~~--~R-KTI~~edVl~AL~~Lg 83 (156)
.|.|.-.+++.+|++- .+..|-..-+.+. ++.|+.-|+.--|+ ++..+ +- .+.+.+||++|++.=+
T Consensus 52 QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~aID~G~ 124 (351)
T KOG1528|consen 52 QAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLKAIDRGN 124 (351)
T ss_pred HHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHHHHhccc
Confidence 5788889999999653 4555555555544 56677777774444 33322 22 7799999999986543
Done!