Query 031569
Match_columns 157
No_of_seqs 165 out of 534
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 15:58:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031569.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031569hhsearch_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 4E-51 8.6E-56 317.5 14.9 139 6-145 3-142 (156)
2 COG5150 Class 2 transcription 100.0 2.7E-43 5.9E-48 268.6 14.4 136 8-144 4-139 (148)
3 KOG0869 CCAAT-binding factor, 100.0 4.6E-32 9.9E-37 212.9 10.3 94 10-103 27-120 (168)
4 KOG0870 DNA polymerase epsilon 99.9 7.1E-27 1.5E-31 184.8 10.4 103 10-112 5-108 (172)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 1.4E-18 3.1E-23 117.3 7.7 64 15-79 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.6 5.2E-16 1.1E-20 112.9 6.0 76 10-87 14-89 (91)
7 cd00076 H4 Histone H4, one of 99.1 2.3E-10 5E-15 82.3 7.6 71 15-87 13-83 (85)
8 PLN00035 histone H4; Provision 99.1 6.3E-10 1.4E-14 82.7 7.7 70 14-85 28-97 (103)
9 PTZ00015 histone H4; Provision 99.0 1.3E-09 2.9E-14 80.8 7.6 72 14-87 29-100 (102)
10 smart00803 TAF TATA box bindin 98.9 1.1E-08 2.4E-13 70.0 7.2 64 15-80 2-65 (65)
11 smart00417 H4 Histone H4. 98.8 1.1E-08 2.4E-13 71.9 6.4 62 15-78 13-74 (74)
12 cd07981 TAF12 TATA Binding Pro 98.8 4E-08 8.6E-13 68.2 8.0 65 16-81 2-66 (72)
13 PF00125 Histone: Core histone 98.8 2.2E-08 4.7E-13 68.6 6.1 68 13-80 3-73 (75)
14 smart00428 H3 Histone H3. 98.5 2.7E-07 5.9E-12 68.8 5.9 69 11-79 25-98 (105)
15 COG5208 HAP5 CCAAT-binding fac 98.5 1.4E-07 3E-12 78.8 4.7 78 12-91 106-184 (286)
16 smart00576 BTP Bromodomain tra 98.3 6.7E-06 1.4E-10 57.4 7.8 66 18-85 9-74 (77)
17 cd00074 H2A Histone 2A; H2A is 98.2 6.4E-06 1.4E-10 62.3 6.7 69 12-81 17-85 (115)
18 KOG1657 CCAAT-binding factor, 98.0 6E-06 1.3E-10 69.3 4.5 78 11-90 70-148 (236)
19 PLN00161 histone H3; Provision 97.9 3.5E-05 7.6E-10 59.9 6.3 69 11-79 51-123 (135)
20 PLN00160 histone H3; Provision 97.9 3E-05 6.4E-10 57.2 5.7 69 11-79 17-89 (97)
21 PLN00121 histone H3; Provision 97.9 2.1E-05 4.5E-10 61.3 4.8 69 11-79 58-129 (136)
22 cd07979 TAF9 TATA Binding Prot 97.8 7.9E-05 1.7E-09 56.2 7.1 77 19-97 5-82 (117)
23 cd08048 TAF11 TATA Binding Pro 97.8 0.00011 2.4E-09 52.9 7.4 66 15-82 16-84 (85)
24 PTZ00018 histone H3; Provision 97.8 3.4E-05 7.4E-10 60.0 5.0 68 12-79 59-129 (136)
25 smart00427 H2B Histone H2B. 97.8 0.00012 2.6E-09 53.3 7.1 64 19-83 5-68 (89)
26 PF15630 CENP-S: Kinetochore c 97.7 0.00013 2.8E-09 51.5 6.7 61 20-80 10-71 (76)
27 cd08050 TAF6 TATA Binding Prot 97.7 0.00017 3.7E-09 62.9 7.6 67 17-85 1-67 (343)
28 PF15511 CENP-T: Centromere ki 97.6 0.00012 2.5E-09 65.7 6.1 64 11-74 347-414 (414)
29 PF03847 TFIID_20kDa: Transcri 97.6 0.00036 7.8E-09 48.2 7.0 63 18-81 2-64 (68)
30 PF07524 Bromo_TP: Bromodomain 97.6 0.00053 1.1E-08 47.5 7.8 64 20-85 11-74 (77)
31 PLN00158 histone H2B; Provisio 97.6 0.00035 7.6E-09 53.1 7.2 68 15-83 27-94 (116)
32 PF09415 CENP-X: CENP-S associ 97.5 0.00013 2.7E-09 51.1 4.3 66 17-82 1-68 (72)
33 PTZ00463 histone H2B; Provisio 97.5 0.00043 9.4E-09 52.6 7.2 63 20-83 33-95 (117)
34 KOG1659 Class 2 transcription 97.5 0.00048 1E-08 57.3 7.7 113 14-129 12-127 (224)
35 PF04719 TAFII28: hTAFII28-lik 97.5 0.00052 1.1E-08 50.0 6.7 67 15-82 23-90 (90)
36 KOG3467 Histone H4 [Chromatin 97.3 0.001 2.2E-08 48.6 6.7 68 16-85 30-97 (103)
37 PF15510 CENP-W: Centromere ki 97.0 0.0011 2.4E-08 48.7 4.5 67 14-81 15-95 (102)
38 COG5262 HTA1 Histone H2A [Chro 96.8 0.0035 7.5E-08 48.1 5.7 68 13-81 24-91 (132)
39 smart00414 H2A Histone 2A. 96.8 0.0046 1E-07 46.2 6.2 68 13-81 7-74 (106)
40 COG5247 BUR6 Class 2 transcrip 96.7 0.0063 1.4E-07 45.6 6.2 78 14-93 22-100 (113)
41 PF02969 TAF: TATA box binding 96.7 0.014 3.1E-07 40.2 7.5 63 16-80 4-66 (66)
42 PLN00154 histone H2A; Provisio 96.5 0.0081 1.8E-07 46.8 6.1 69 13-81 36-104 (136)
43 PTZ00017 histone H2A; Provisio 96.3 0.0093 2E-07 46.4 5.5 72 13-85 25-97 (134)
44 KOG1744 Histone H2B [Chromatin 96.3 0.014 3E-07 45.1 6.4 61 21-82 43-103 (127)
45 PF02269 TFIID-18kDa: Transcri 96.2 0.0063 1.4E-07 44.1 3.8 60 21-81 7-66 (93)
46 KOG1756 Histone 2A [Chromatin 96.2 0.015 3.2E-07 45.0 5.8 68 12-80 24-91 (131)
47 KOG1745 Histones H3 and H4 [Ch 96.0 0.0048 1E-07 48.2 2.6 71 11-81 59-132 (137)
48 KOG3219 Transcription initiati 96.0 0.0071 1.5E-07 49.7 3.7 70 14-85 111-181 (195)
49 PLN00157 histone H2A; Provisio 96.0 0.017 3.6E-07 44.9 5.3 73 13-86 24-97 (132)
50 PLN00153 histone H2A; Provisio 96.0 0.018 3.8E-07 44.6 5.4 73 13-86 22-95 (129)
51 PLN00156 histone H2AX; Provisi 95.9 0.021 4.5E-07 44.7 5.8 68 13-81 27-94 (139)
52 KOG1142 Transcription initiati 95.8 0.02 4.3E-07 48.9 5.7 70 11-81 150-219 (258)
53 KOG1658 DNA polymerase epsilon 95.8 0.011 2.3E-07 47.2 3.5 73 14-88 58-131 (162)
54 cd07978 TAF13 The TATA Binding 94.6 0.22 4.9E-06 36.1 7.2 60 20-81 7-66 (92)
55 PTZ00252 histone H2A; Provisio 94.1 0.18 3.8E-06 39.4 6.1 70 12-86 22-98 (134)
56 PF02291 TFIID-31kDa: Transcri 93.9 0.35 7.6E-06 37.3 7.4 89 8-98 3-94 (129)
57 TIGR03015 pepcterm_ATPase puta 91.3 0.66 1.4E-05 37.5 6.2 69 16-84 192-268 (269)
58 KOG3423 Transcription initiati 90.0 1.8 3.8E-05 35.1 7.3 68 15-85 86-168 (176)
59 PRK00411 cdc6 cell division co 89.0 2.6 5.6E-05 36.3 8.2 72 18-89 209-289 (394)
60 cd08045 TAF4 TATA Binding Prot 89.0 6.4 0.00014 32.1 10.1 79 12-90 41-127 (212)
61 PF07499 RuvA_C: RuvA, C-termi 86.9 2.1 4.6E-05 26.9 4.9 38 73-126 4-41 (47)
62 TIGR02928 orc1/cdc6 family rep 86.0 4.2 9E-05 34.5 7.7 75 18-92 201-284 (365)
63 KOG2549 Transcription initiati 82.8 5.6 0.00012 37.6 7.5 65 17-83 13-77 (576)
64 KOG4336 TBP-associated transcr 82.5 5.4 0.00012 35.2 6.9 72 21-96 11-82 (323)
65 KOG2389 Predicted bromodomain 82.2 3.4 7.4E-05 36.9 5.7 71 13-85 27-97 (353)
66 COG1067 LonB Predicted ATP-dep 79.8 1.8 3.8E-05 41.5 3.3 46 35-81 339-398 (647)
67 PF13654 AAA_32: AAA domain; P 79.0 8.5 0.00018 35.7 7.4 48 34-81 447-505 (509)
68 TIGR00764 lon_rel lon-related 76.5 9.1 0.0002 36.1 6.9 51 34-84 330-393 (608)
69 PF13335 Mg_chelatase_2: Magne 75.1 10 0.00022 27.3 5.5 48 33-80 41-94 (96)
70 PF02861 Clp_N: Clp amino term 73.4 3 6.5E-05 25.6 2.0 26 58-83 1-26 (53)
71 TIGR02902 spore_lonB ATP-depen 71.8 13 0.00027 34.5 6.5 63 21-84 268-334 (531)
72 KOG1757 Histone 2A [Chromatin 68.9 14 0.0003 28.3 5.1 64 13-80 28-95 (131)
73 PRK12402 replication factor C 63.5 25 0.00055 29.2 6.2 76 15-92 183-259 (337)
74 TIGR01128 holA DNA polymerase 62.7 40 0.00086 27.6 7.2 67 15-81 110-177 (302)
75 PRK00080 ruvB Holliday junctio 60.7 32 0.0007 29.2 6.5 70 16-85 180-253 (328)
76 TIGR02442 Cob-chelat-sub cobal 59.5 25 0.00055 33.2 6.1 53 27-80 243-302 (633)
77 PF09114 MotA_activ: Transcrip 59.3 17 0.00038 26.8 3.9 34 19-52 51-88 (96)
78 PF08369 PCP_red: Proto-chloro 59.1 14 0.0003 23.3 3.0 41 37-78 3-44 (45)
79 TIGR00635 ruvB Holliday juncti 58.4 36 0.00077 28.2 6.2 70 16-85 159-232 (305)
80 PF08621 RPAP1_N: RPAP1-like, 56.7 11 0.00024 24.4 2.3 18 116-133 13-30 (49)
81 PRK13406 bchD magnesium chelat 55.7 24 0.00053 33.3 5.3 59 20-80 183-248 (584)
82 PF07647 SAM_2: SAM domain (St 55.3 15 0.00032 23.7 2.8 25 69-93 3-27 (66)
83 PF12010 DUF3502: Domain of un 55.3 16 0.00035 27.6 3.4 62 37-102 72-133 (134)
84 TIGR02030 BchI-ChlI magnesium 55.2 47 0.001 29.1 6.7 53 26-79 247-306 (337)
85 PF00531 Death: Death domain; 55.2 46 0.001 21.9 5.4 29 67-95 55-83 (83)
86 PF00536 SAM_1: SAM domain (St 54.1 17 0.00036 23.3 2.9 22 71-92 4-25 (64)
87 PRK07452 DNA polymerase III su 52.5 50 0.0011 27.7 6.3 67 21-87 135-204 (326)
88 cd00166 SAM Sterile alpha moti 52.1 16 0.00035 22.7 2.6 24 70-93 2-25 (63)
89 PRK09862 putative ATP-dependen 51.5 56 0.0012 30.5 6.9 56 33-88 437-498 (506)
90 KOG3334 Transcription initiati 49.9 34 0.00074 27.1 4.5 64 35-98 31-95 (148)
91 CHL00081 chlI Mg-protoporyphyr 49.7 42 0.00092 29.7 5.6 53 26-79 260-319 (350)
92 COG5251 TAF40 Transcription in 49.7 21 0.00045 29.3 3.3 63 15-79 115-178 (199)
93 PRK13765 ATP-dependent proteas 49.1 25 0.00055 33.6 4.3 47 34-80 339-398 (637)
94 TIGR00368 Mg chelatase-related 48.4 41 0.00088 31.2 5.5 47 34-80 445-497 (499)
95 PRK09526 lacI lac repressor; R 47.7 24 0.00051 29.2 3.5 38 14-56 15-52 (342)
96 PF00356 LacI: Bacterial regul 46.8 48 0.001 20.8 4.1 32 14-49 9-40 (46)
97 TIGR02031 BchD-ChlD magnesium 46.8 60 0.0013 30.5 6.4 55 25-80 195-256 (589)
98 smart00454 SAM Sterile alpha m 45.1 24 0.00052 22.0 2.5 25 70-94 4-28 (68)
99 PRK14987 gluconate operon tran 43.4 25 0.00054 29.0 3.0 38 15-57 16-53 (331)
100 PRK05574 holA DNA polymerase I 42.4 80 0.0017 26.3 5.9 67 15-81 145-212 (340)
101 KOG2680 DNA helicase TIP49, TB 42.0 51 0.0011 29.9 4.8 67 13-79 339-426 (454)
102 COG5095 TAF6 Transcription ini 41.2 85 0.0018 28.4 6.0 65 19-85 9-73 (450)
103 COG1224 TIP49 DNA helicase TIP 40.9 68 0.0015 29.5 5.5 49 31-79 377-429 (450)
104 PRK10423 transcriptional repre 40.9 37 0.0008 27.7 3.6 38 14-56 8-45 (327)
105 PRK13407 bchI magnesium chelat 40.6 82 0.0018 27.6 5.9 53 26-79 244-303 (334)
106 KOG3901 Transcription initiati 39.4 1.6E+02 0.0035 22.3 6.4 48 30-80 23-70 (109)
107 PRK10727 DNA-binding transcrip 39.3 36 0.00078 28.3 3.4 38 15-57 12-49 (343)
108 COG1474 CDC6 Cdc6-related prot 39.0 49 0.0011 29.3 4.3 74 19-92 193-275 (366)
109 TIGR01052 top6b DNA topoisomer 38.5 51 0.0011 30.7 4.5 51 34-98 434-484 (488)
110 PRK00440 rfc replication facto 37.6 1.2E+02 0.0025 24.9 6.1 66 16-83 161-227 (319)
111 PF12627 PolyA_pol_RNAbd: Prob 37.5 12 0.00026 24.1 0.1 59 32-94 1-63 (64)
112 PRK07914 hypothetical protein; 37.4 83 0.0018 26.7 5.4 64 17-81 129-193 (320)
113 PF09339 HTH_IclR: IclR helix- 36.9 19 0.00042 22.5 1.1 17 12-28 26-42 (52)
114 COG1500 Predicted exosome subu 36.1 1.3E+02 0.0027 25.7 6.1 70 21-93 72-144 (234)
115 COG5162 Transcription initiati 35.8 2E+02 0.0044 23.5 6.9 51 35-85 106-189 (197)
116 cd04752 Commd4 COMM_Domain con 35.3 2.2E+02 0.0048 22.4 8.9 49 46-101 43-92 (174)
117 smart00354 HTH_LACI helix_turn 34.5 78 0.0017 20.9 3.8 33 14-50 10-42 (70)
118 PRK14971 DNA polymerase III su 34.4 1.1E+02 0.0025 29.0 6.2 71 16-87 180-251 (614)
119 PF03540 TFIID_30kDa: Transcri 34.3 1.4E+02 0.0029 19.6 6.1 47 15-64 2-49 (51)
120 PF13405 EF-hand_6: EF-hand do 33.6 39 0.00084 18.7 1.9 26 58-83 5-31 (31)
121 smart00350 MCM minichromosome 32.7 1.8E+02 0.0038 26.7 7.0 65 14-81 416-503 (509)
122 PF05236 TAF4: Transcription i 32.6 59 0.0013 27.2 3.6 74 11-84 39-120 (264)
123 PF10728 DUF2520: Domain of un 32.3 1.5E+02 0.0033 22.4 5.6 69 19-98 14-85 (132)
124 COG1724 Predicted RNA binding 31.3 31 0.00067 23.9 1.4 17 69-85 6-22 (66)
125 PTZ00361 26 proteosome regulat 31.2 53 0.0011 30.0 3.3 31 51-81 393-423 (438)
126 TIGR01242 26Sp45 26S proteasom 30.4 59 0.0013 28.1 3.4 32 50-81 331-362 (364)
127 PRK06585 holA DNA polymerase I 30.1 1.2E+02 0.0025 25.8 5.1 64 18-81 144-209 (343)
128 TIGR02454 CbiQ_TIGR cobalt ABC 29.9 94 0.002 24.1 4.2 37 68-104 112-159 (198)
129 PRK09492 treR trehalose repres 29.8 67 0.0015 26.1 3.5 38 14-56 14-51 (315)
130 cd01392 HTH_LacI Helix-turn-he 29.7 1E+02 0.0022 18.5 3.5 33 14-50 7-39 (52)
131 PRK03992 proteasome-activating 29.4 62 0.0013 28.6 3.4 33 50-82 340-372 (389)
132 smart00027 EH Eps15 homology d 29.4 1E+02 0.0022 21.3 3.9 72 57-147 14-85 (96)
133 TIGR02903 spore_lon_C ATP-depe 28.7 1.2E+02 0.0026 28.7 5.3 71 19-89 356-437 (615)
134 PF00403 HMA: Heavy-metal-asso 27.6 38 0.00083 21.3 1.3 16 70-85 47-62 (62)
135 PF13690 CheX: Chemotaxis phos 27.5 1.3E+02 0.0028 20.9 4.2 46 13-62 16-61 (94)
136 PF12022 DUF3510: Domain of un 27.4 2.6E+02 0.0057 20.8 6.9 47 84-130 72-123 (125)
137 KOG1792 Reticulon [Intracellul 27.4 97 0.0021 26.0 4.0 63 28-90 110-174 (230)
138 PRK11303 DNA-binding transcrip 27.2 84 0.0018 25.7 3.6 36 14-50 10-45 (328)
139 PF03130 HEAT_PBS: PBS lyase H 27.2 1E+02 0.0022 16.8 2.9 23 75-97 5-27 (27)
140 PF08681 DUF1778: Protein of u 27.2 22 0.00048 24.7 0.1 61 32-93 3-63 (80)
141 COG1239 ChlI Mg-chelatase subu 26.7 1E+02 0.0022 28.4 4.3 53 27-80 261-320 (423)
142 TIGR02397 dnaX_nterm DNA polym 26.7 2.4E+02 0.0051 23.6 6.3 62 18-80 178-240 (355)
143 COG1422 Predicted membrane pro 26.6 41 0.0009 27.9 1.6 18 86-103 76-93 (201)
144 PF07580 Peptidase_M26_C: M26 26.6 2.4E+02 0.0052 27.9 7.0 60 29-88 588-649 (737)
145 COG5248 TAF19 Transcription in 26.5 2.2E+02 0.0048 21.8 5.4 50 30-81 23-72 (126)
146 PRK14961 DNA polymerase III su 26.4 2E+02 0.0043 25.0 5.9 65 16-81 178-243 (363)
147 TIGR02417 fruct_sucro_rep D-fr 26.1 92 0.002 25.5 3.7 39 15-55 10-48 (327)
148 cd00083 HLH Helix-loop-helix d 26.1 1E+02 0.0023 19.0 3.2 34 24-57 25-58 (60)
149 PF02361 CbiQ: Cobalt transpor 25.7 1.1E+02 0.0023 23.8 3.8 37 68-104 123-171 (224)
150 PTZ00454 26S protease regulato 24.5 81 0.0018 28.3 3.2 31 51-81 355-385 (398)
151 KOG0188 Alanyl-tRNA synthetase 24.4 6.7E+02 0.014 25.3 9.4 67 20-86 338-408 (895)
152 PRK09111 DNA polymerase III su 24.1 2.2E+02 0.0047 27.1 6.1 64 16-80 191-255 (598)
153 COG5340 Predicted transcriptio 23.9 1.3E+02 0.0028 26.0 4.1 53 10-62 149-207 (269)
154 PRK07764 DNA polymerase III su 23.7 2.4E+02 0.0052 28.0 6.5 61 16-76 179-240 (824)
155 PRK08487 DNA polymerase III su 23.7 2.8E+02 0.006 23.6 6.3 60 20-81 139-199 (328)
156 KOG0784 Isocitrate dehydrogena 23.4 51 0.0011 29.8 1.7 46 52-98 187-232 (375)
157 COG3311 AlpA Predicted transcr 23.1 1.5E+02 0.0033 20.6 3.7 24 14-37 23-47 (70)
158 PF11625 DUF3253: Protein of u 22.3 1.6E+02 0.0034 21.2 3.8 36 64-99 19-54 (83)
159 PRK14964 DNA polymerase III su 22.0 2.4E+02 0.0053 26.2 5.9 64 16-80 175-239 (491)
160 PRK05907 hypothetical protein; 21.9 1.9E+02 0.004 25.0 4.9 54 32-85 151-207 (311)
161 PRK10401 DNA-binding transcrip 21.9 1.1E+02 0.0024 25.4 3.4 37 14-55 11-47 (346)
162 cd04750 Commd2 COMM_Domain con 21.8 4E+02 0.0086 20.9 7.1 34 67-100 49-83 (166)
163 KOG0093 GTPase Rab3, small G p 21.5 53 0.0011 26.8 1.3 52 37-88 106-162 (193)
164 PRK05629 hypothetical protein; 21.4 2.6E+02 0.0056 23.6 5.6 50 31-81 142-191 (318)
165 PF03484 B5: tRNA synthetase B 21.2 52 0.0011 21.9 1.1 17 69-85 18-34 (70)
166 COG1466 HolA DNA polymerase II 21.1 2.5E+02 0.0053 24.1 5.5 51 32-82 157-207 (334)
167 PF06782 UPF0236: Uncharacteri 21.1 1.7E+02 0.0036 26.8 4.6 59 29-89 112-170 (470)
168 PRK14970 DNA polymerase III su 21.1 3E+02 0.0065 23.5 6.0 66 18-84 169-235 (367)
169 PRK14958 DNA polymerase III su 20.9 3.3E+02 0.0071 25.2 6.6 64 16-84 178-246 (509)
170 KOG1775 U6 snRNA-associated Sm 20.7 65 0.0014 23.1 1.5 23 81-103 34-56 (84)
171 PRK04184 DNA topoisomerase VI 20.7 1.5E+02 0.0033 27.9 4.4 37 33-69 438-474 (535)
172 TIGR01481 ccpA catabolite cont 20.6 1.3E+02 0.0028 24.6 3.5 37 15-56 12-48 (329)
173 PRK10339 DNA-binding transcrip 20.3 1.2E+02 0.0026 24.9 3.3 40 14-56 11-50 (327)
174 PF05225 HTH_psq: helix-turn-h 20.2 78 0.0017 19.6 1.7 19 12-30 24-42 (45)
No 1
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=100.00 E-value=4e-51 Score=317.51 Aligned_cols=139 Identities=53% Similarity=0.815 Sum_probs=131.0
Q ss_pred CCCCCcccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCch
Q 031569 6 IVGKSKEDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (157)
Q Consensus 6 ~~g~~~dd~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~ 85 (157)
..|..+|+++||+|||+||||+.||.+++|++|+|++|++||++||++|||+||++|.++.||||++|||++||+.|||+
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 hhHHHHHHHHHHHHHHhhhhhccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH-hCCCCCC
Q 031569 86 EYIEEVYAAYEQHKLETMQDSLKGGKWSNGAEMTEEEAAAEQQRMFAEARARM-NGGAAGP 145 (157)
Q Consensus 86 ~yv~~l~~~l~~~k~~~k~~r~kk~~k~~~~g~~eEel~~~Q~eLF~~ar~~~-~~~~~~~ 145 (157)
+|++.+.++|++||..++ +|+++.+|++++|||+|||++||++||++||+|+ +++.+.+
T Consensus 83 eYiee~~~vl~~~K~~~~-~~~~kssk~e~~Gi~eEEL~~qQqeLf~~ARar~~~~~~sv~ 142 (156)
T KOG0871|consen 83 EYIEEAEEVLENCKEEAK-KRRRKSSKFEKSGIPEEELLRQQQELFAKARARLMQQAASVA 142 (156)
T ss_pred HHHHHHHHHHHHHHHHHH-HhhhhhhhHHhcCCCHHHHHHHHHHHHHHHHHHHHhcccccc
Confidence 999999999999999999 5888889999999999999999999999999994 5544333
No 2
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=100.00 E-value=2.7e-43 Score=268.63 Aligned_cols=136 Identities=38% Similarity=0.582 Sum_probs=131.0
Q ss_pred CCCcccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhh
Q 031569 8 GKSKEDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEY 87 (157)
Q Consensus 8 g~~~dd~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~y 87 (157)
|..+|+++||+|||+|+|.++||.+..++||||+++++||.+||++||++||++|+++.+|||+++||++||+.|||.+|
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 45689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhhhccCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHhCCCCC
Q 031569 88 IEEVYAAYEQHKLETMQDSLKGGKWSNGAEMTEEEAAAEQQRMFAEARARMNGGAAG 144 (157)
Q Consensus 88 v~~l~~~l~~~k~~~k~~r~kk~~k~~~~g~~eEel~~~Q~eLF~~ar~~~~~~~~~ 144 (157)
++.+.+.+.+|+..+| .|++|.+|+++||+|+|||+|||++||.+||.||++....
T Consensus 84 i~~~~e~~~n~k~~qK-~ke~k~sKFk~SGls~eELlrQQeeLf~~ar~rf~h~~~~ 139 (148)
T COG5150 84 IESCMEEHENYKSYQK-QKESKISKFKDSGLSMEELLRQQEELFQNARLRFEHSFED 139 (148)
T ss_pred HHHHHHHHHHHHHHHh-hchhhhhHHHhcCCCHHHHHHHHHHHHHHHHHHhcccccc
Confidence 9999999999999999 6889999999999999999999999999999999887633
No 3
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=99.97 E-value=4.6e-32 Score=212.87 Aligned_cols=94 Identities=33% Similarity=0.614 Sum_probs=91.6
Q ss_pred CcccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHH
Q 031569 10 SKEDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIE 89 (157)
Q Consensus 10 ~~dd~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~ 89 (157)
.+.|..||+|+|.||||..||.+.+|||||++.+++|++|||+|||++|+++|..++||||++|||+|||..|||++|++
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 46799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhh
Q 031569 90 EVYAAYEQHKLETM 103 (157)
Q Consensus 90 ~l~~~l~~~k~~~k 103 (157)
+|+.+|..||+...
T Consensus 107 plkiyL~kYRe~e~ 120 (168)
T KOG0869|consen 107 PLKIYLQKYRELEG 120 (168)
T ss_pred HHHHHHHHHHHHhh
Confidence 99999999999865
No 4
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.94 E-value=7.1e-27 Score=184.75 Aligned_cols=103 Identities=29% Similarity=0.503 Sum_probs=97.1
Q ss_pred CcccccCcHHHHHHHHHhhCCCC-ccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhH
Q 031569 10 SKEDASLPKATMTKIIKEMLPAD-VRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYI 88 (157)
Q Consensus 10 ~~dd~~LP~A~V~riiKe~LP~~-~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv 88 (157)
.++++.||+|+|.||||+.||.. +.|+|||+.+|++++++||+||++.|+++|...+||||+++||++||++|||.+|+
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 HHHHHHHHHHHHHhhhhhccCCCC
Q 031569 89 EEVYAAYEQHKLETMQDSLKGGKW 112 (157)
Q Consensus 89 ~~l~~~l~~~k~~~k~~r~kk~~k 112 (157)
++|+..|+.||..++++|..+.++
T Consensus 85 ~plk~~Le~yk~~~k~Kk~~~~~~ 108 (172)
T KOG0870|consen 85 NPLKSALEAYKKAVKQKKLAKANK 108 (172)
T ss_pred hHHHHHHHHHHHHHHHHHHhcccc
Confidence 999999999999988776555443
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=117.35 Aligned_cols=64 Identities=36% Similarity=0.603 Sum_probs=59.3
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhh
Q 031569 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL 79 (157)
.||.+.|.||||.. |+..+||+||..+|.+|+++||.||+.+|+++|..++||||+++||..||
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=5.2e-16 Score=112.87 Aligned_cols=76 Identities=26% Similarity=0.417 Sum_probs=72.3
Q ss_pred CcccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhh
Q 031569 10 SKEDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEY 87 (157)
Q Consensus 10 ~~dd~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~y 87 (157)
...+..||+++|.||||+..++ +||.+|.++|++|..+|+..|+..|++.|.+.|||||+++||..|++.+||..|
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=2.3e-10 Score=82.35 Aligned_cols=71 Identities=14% Similarity=0.202 Sum_probs=66.4
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhh
Q 031569 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEY 87 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~y 87 (157)
.||+++|.||++... -.+||.|+.+.+.++..+|+..|...|...|++.+||||+++||.-||+..|-.-|
T Consensus 13 gi~k~~I~RLarr~G--vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 13 GITKPAIRRLARRGG--VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred cCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 599999999999975 67899999999999999999999999999999999999999999999999985533
No 8
>PLN00035 histone H4; Provisional
Probab=99.06 E-value=6.3e-10 Score=82.71 Aligned_cols=70 Identities=13% Similarity=0.121 Sum_probs=65.6
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCch
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~ 85 (157)
..||+++|.||++... ..+||.|+.+.+.+...+|+.-|...|..+|++.+||||+++||.-||+..|=.
T Consensus 28 ~~ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ 97 (103)
T PLN00035 28 QGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred ccCCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCc
Confidence 3599999999999985 678999999999999999999999999999999999999999999999988754
No 9
>PTZ00015 histone H4; Provisional
Probab=99.01 E-value=1.3e-09 Score=80.82 Aligned_cols=72 Identities=17% Similarity=0.217 Sum_probs=66.7
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhh
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEY 87 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~y 87 (157)
..||+++|.||++... -.+||.|+.+.+.++..+|+..|...|..+|++.+||||+++||.-||+..|-.-|
T Consensus 29 ~gI~k~~IrRLarr~G--vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 29 RGITKGAIRRLARRGG--VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred cCCCHHHHHHHHHHcC--CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 4699999999999975 57899999999999999999999999999999999999999999999998886433
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=98.86 E-value=1.1e-08 Score=69.96 Aligned_cols=64 Identities=20% Similarity=0.225 Sum_probs=59.9
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
.||+++|.||++... --+||.|+...|.+-...|+.-|..+|...+++.+|||++++||-.||+
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 3579999999999999999999999999999999999999999999984
No 11
>smart00417 H4 Histone H4.
Probab=98.83 E-value=1.1e-08 Score=71.94 Aligned_cols=62 Identities=13% Similarity=0.156 Sum_probs=58.3
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhh
Q 031569 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKA 78 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~A 78 (157)
.||+++|.||++... --+||.++.+.+.+...+|+..|...|..+|++.+||||+++||..|
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 699999999999975 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=98.78 E-value=4e-08 Score=68.16 Aligned_cols=65 Identities=23% Similarity=0.404 Sum_probs=61.8
Q ss_pred CcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 16 LPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 16 LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
+++..+..++++.=| +.+++.||.++|++.+.+|+.-|+..|...|++.||+||.++||.-+|+.
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=98.76 E-value=2.2e-08 Score=68.58 Aligned_cols=68 Identities=16% Similarity=0.308 Sum_probs=62.4
Q ss_pred cccCcHHHHHHHHHhhCCC---CccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 13 DASLPKATMTKIIKEMLPA---DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 13 d~~LP~A~V~riiKe~LP~---~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
...+|+..|.|+.++..++ ..+||++|.++|+..+..|+.-|...|..+|...+|+||++.||..|+.
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 3568999999999998763 2799999999999999999999999999999999999999999999875
No 14
>smart00428 H3 Histone H3.
Probab=98.50 E-value=2.7e-07 Score=68.83 Aligned_cols=69 Identities=20% Similarity=0.298 Sum_probs=63.7
Q ss_pred cccccCcHHHHHHHHHhhCCC-----CccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhh
Q 031569 11 KEDASLPKATMTKIIKEMLPA-----DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (157)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP~-----~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL 79 (157)
..++.+|+.+..|+++++..+ +++++.+|..+|++++..|+.-+...|+..|.+.+|+||.+.|+.-|.
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 457899999999999998753 789999999999999999999999999999999999999999997665
No 15
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.50 E-value=1.4e-07 Score=78.75 Aligned_cols=78 Identities=19% Similarity=0.341 Sum_probs=71.4
Q ss_pred ccccCcHHHHHHHHHhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHHH
Q 031569 12 EDASLPKATMTKIIKEMLPADVR-VARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEE 90 (157)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~~~~-iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~~ 90 (157)
.+++||.|.|.|+||- .++++ ||.||..++.+.|..||..||..|.-.+++++|+|+--.||-.|++.-++.+|+=.
T Consensus 106 k~h~LPlARIkkvMKt--dedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLid 183 (286)
T COG5208 106 KDHNLPLARIKKVMKT--DEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLID 183 (286)
T ss_pred HhccCcHHHHHHHHhc--ccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhh
Confidence 4678999999999995 45666 99999999999999999999999999999999999999999999999999888755
Q ss_pred H
Q 031569 91 V 91 (157)
Q Consensus 91 l 91 (157)
+
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=98.25 E-value=6.7e-06 Score=57.41 Aligned_cols=66 Identities=15% Similarity=0.181 Sum_probs=59.2
Q ss_pred HHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCch
Q 031569 18 KATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (157)
Q Consensus 18 ~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~ 85 (157)
+-.|.+|++... --+++..|.+.|.+....|+..|+..+...|+..||+++++.||..||+++|..
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 445777777663 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=98.17 E-value=6.4e-06 Score=62.30 Aligned_cols=69 Identities=17% Similarity=0.185 Sum_probs=63.1
Q ss_pred ccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 12 EDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
-.+.||.+.|.|+|++.-. ..||+.+|...|..+...+..-|...|...|...+|++|+|+||..|+..
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 3689999999999998433 58999999999999999999999999999999999999999999999865
No 18
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.03 E-value=6e-06 Score=69.29 Aligned_cols=78 Identities=22% Similarity=0.316 Sum_probs=68.9
Q ss_pred cccccCcHHHHHHHHHhhCCCCc-cccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHH
Q 031569 11 KEDASLPKATMTKIIKEMLPADV-RVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIE 89 (157)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP~~~-~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~ 89 (157)
.....||++.|.||||.- +++ .|+.||..++.+||..||..|+..|...++..+|+|+...|+-.|+..-.-.+|+-
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 346699999999999954 244 59999999999999999999999999999999999999999999999877766654
Q ss_pred H
Q 031569 90 E 90 (157)
Q Consensus 90 ~ 90 (157)
.
T Consensus 148 D 148 (236)
T KOG1657|consen 148 D 148 (236)
T ss_pred c
Confidence 4
No 19
>PLN00161 histone H3; Provisional
Probab=97.89 E-value=3.5e-05 Score=59.88 Aligned_cols=69 Identities=17% Similarity=0.237 Sum_probs=62.9
Q ss_pred cccccCcHHHHHHHHHhhC----CCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhh
Q 031569 11 KEDASLPKATMTKIIKEML----PADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (157)
Q Consensus 11 ~dd~~LP~A~V~riiKe~L----P~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL 79 (157)
..++.+|+....|+|+++. +.++++..+|..+|+++++.|+.-+...||-.|.+.+|.||.+.|+.-|.
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 3578899999999999985 34699999999999999999999999999999999999999999997664
No 20
>PLN00160 histone H3; Provisional
Probab=97.89 E-value=3e-05 Score=57.23 Aligned_cols=69 Identities=17% Similarity=0.169 Sum_probs=62.9
Q ss_pred cccccCcHHHHHHHHHhhCC----CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhh
Q 031569 11 KEDASLPKATMTKIIKEMLP----ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (157)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP----~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL 79 (157)
..++-+|+++..|+++++.. .++++..+|..+|++++.-|+.-+...+|-.|.+.+|.||.+.|+--|.
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 45789999999999999863 4599999999999999999999999999999999999999999996664
No 21
>PLN00121 histone H3; Provisional
Probab=97.88 E-value=2.1e-05 Score=61.25 Aligned_cols=69 Identities=17% Similarity=0.260 Sum_probs=63.4
Q ss_pred cccccCcHHHHHHHHHhhCCC---CccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhh
Q 031569 11 KEDASLPKATMTKIIKEMLPA---DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (157)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP~---~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL 79 (157)
..++-+|+....|+|+++..+ ++++..+|..+|+++++.|+.-+...++-.|.+.+|.||.+.|+.-|.
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 357899999999999998753 799999999999999999999999999999999999999999996664
No 22
>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=97.82 E-value=7.9e-05 Score=56.24 Aligned_cols=77 Identities=13% Similarity=0.082 Sum_probs=64.3
Q ss_pred HHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHHH-HHHHHHH
Q 031569 19 ATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEE-VYAAYEQ 97 (157)
Q Consensus 19 A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~~-l~~~l~~ 97 (157)
..|.+|+|+.. ..+++.+++..|.+.+..++.-|..+|...|.+.||+||+++||.-|++..+-..|.+. -++.+-+
T Consensus 5 ~~v~~iLk~~G--v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~ 82 (117)
T cd07979 5 RVIAAILKSMG--ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLE 82 (117)
T ss_pred HHHHHHHHHCC--CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHH
Confidence 35788888763 46899999999999999999999999999999999999999999999988766555444 4455444
No 23
>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=97.82 E-value=0.00011 Score=52.86 Aligned_cols=66 Identities=20% Similarity=0.326 Sum_probs=61.5
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCC---CccChhhHHhhhhhc
Q 031569 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDK---RTIAPEHVLKALEVL 82 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~R---KTI~~edVl~AL~~L 82 (157)
+||++.|.|||...++ ..++.+...+|.-.+.+||.-|..+|.++..+.+. ..|.|+||-.|...|
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 5999999999999985 89999999999999999999999999999998776 789999999998776
No 24
>PTZ00018 histone H3; Provisional
Probab=97.81 E-value=3.4e-05 Score=60.02 Aligned_cols=68 Identities=18% Similarity=0.267 Sum_probs=62.8
Q ss_pred ccccCcHHHHHHHHHhhCC---CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhh
Q 031569 12 EDASLPKATMTKIIKEMLP---ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (157)
Q Consensus 12 dd~~LP~A~V~riiKe~LP---~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL 79 (157)
.++-+|+....|+++++.. .++++..+|..+|+++++.|+.-+...+|-.|.+.+|.||.+.|+.-|.
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 5788999999999999863 4799999999999999999999999999999999999999999996664
No 25
>smart00427 H2B Histone H2B.
Probab=97.78 E-value=0.00012 Score=53.30 Aligned_cols=64 Identities=14% Similarity=0.332 Sum_probs=58.6
Q ss_pred HHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcC
Q 031569 19 ATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLG 83 (157)
Q Consensus 19 A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~Lg 83 (157)
.-|+|++|++-| +..||..+...+.-...-+..-|+.+|...|...+|+||++.+|-.|..-+=
T Consensus 5 ~Yi~kvLKqVhp-d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~L 68 (89)
T smart00427 5 IYIYKVLKQVHP-DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLIL 68 (89)
T ss_pred HHHHHHHHHhCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHc
Confidence 358999999998 7899999999999999999999999999999999999999999999986543
No 26
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.75 E-value=0.00013 Score=51.55 Aligned_cols=61 Identities=18% Similarity=0.182 Sum_probs=52.1
Q ss_pred HHHHHHHhhC-CCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 20 TMTKIIKEML-PADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 20 ~V~riiKe~L-P~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
+|.||+.+.. +.++.+|+.+..+|.+.+-.++..++..---.|.+.||+||+++||+-...
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 6889998875 568999999999999999999999999999999999999999999986543
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=97.65 E-value=0.00017 Score=62.92 Aligned_cols=67 Identities=15% Similarity=0.198 Sum_probs=58.7
Q ss_pred cHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCch
Q 031569 17 PKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (157)
Q Consensus 17 P~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~ 85 (157)
|..+|.-|++... --++++||..+|.+....++.-|+.+|...+.+.+|||++++||-.||+.++.+
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 4566777777652 349999999999999999999999999999999999999999999999887654
No 28
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.61 E-value=0.00012 Score=65.67 Aligned_cols=64 Identities=16% Similarity=0.297 Sum_probs=48.0
Q ss_pred cccccCcHHHHHHHHHhhCC----CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhh
Q 031569 11 KEDASLPKATMTKIIKEMLP----ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEH 74 (157)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP----~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~ed 74 (157)
+.--.||.+.|.|++....- .+++|++||..+|.+|...|..-|+.---.+|.+.|||||..+|
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 45567999999999887743 57999999999999999999999999999999999999999876
No 29
>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=97.60 E-value=0.00036 Score=48.23 Aligned_cols=63 Identities=22% Similarity=0.381 Sum_probs=51.6
Q ss_pred HHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 18 KATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 18 ~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
+..++.+|+++-| +..+..|+.++|.+.+.+||.-+.+.|-.+|++.+-.||...||.-.|+.
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 4568889999866 89999999999999999999999999999999999999999999888864
No 30
>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=97.58 E-value=0.00053 Score=47.45 Aligned_cols=64 Identities=16% Similarity=0.215 Sum_probs=55.4
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCch
Q 031569 20 TMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (157)
Q Consensus 20 ~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~ 85 (157)
.|.+|.+... =-.++..|.+.|.+.+..||..|++.+...|+..+|...++.||..||.++|+.
T Consensus 11 ~va~il~~~G--F~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 11 SVAQILKHAG--FDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 4555555432 136999999999999999999999999999999999999999999999999984
No 31
>PLN00158 histone H2B; Provisional
Probab=97.56 E-value=0.00035 Score=53.08 Aligned_cols=68 Identities=15% Similarity=0.298 Sum_probs=60.7
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcC
Q 031569 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLG 83 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~Lg 83 (157)
+--..-|+|++|++-| +..||..+...|.-....+..-|++||...|...+|+||++.+|-.|+.-+=
T Consensus 27 esy~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvL 94 (116)
T PLN00158 27 ETYKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLIL 94 (116)
T ss_pred ccHHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhc
Confidence 3345569999999998 7899999999999999999999999999999999999999999999986543
No 32
>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=97.55 E-value=0.00013 Score=51.05 Aligned_cols=66 Identities=21% Similarity=0.344 Sum_probs=55.1
Q ss_pred cHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCc-cChhhHHhhhhhc
Q 031569 17 PKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRT-IAPEHVLKALEVL 82 (157)
Q Consensus 17 P~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKT-I~~edVl~AL~~L 82 (157)
|+.+|.||++...- ++.+|++||..++.+....||.--...|.+.+..++..+ |..+|+-+.+-.|
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pqL 68 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQL 68 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHCH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence 88999999998774 679999999999999999999999999999999999998 9999998766443
No 33
>PTZ00463 histone H2B; Provisional
Probab=97.52 E-value=0.00043 Score=52.62 Aligned_cols=63 Identities=16% Similarity=0.418 Sum_probs=57.8
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcC
Q 031569 20 TMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLG 83 (157)
Q Consensus 20 ~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~Lg 83 (157)
-|+|++|++-| +..||..+...|.-...-...-|++||...|...+|+||++.+|-.|+.-+=
T Consensus 33 YI~KVLKqVhP-d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLlL 95 (117)
T PTZ00463 33 YIFKVLKQVHP-DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVL 95 (117)
T ss_pred HHHHHHHhhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhcc
Confidence 49999999998 7899999999999988888889999999999999999999999999986543
No 34
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.49 E-value=0.00048 Score=57.27 Aligned_cols=113 Identities=14% Similarity=0.185 Sum_probs=85.8
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHHHHHH
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYA 93 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~ 93 (157)
--+|.+.|.|||...= +--+|+.-+..++.++...|+.-|-..+-+++...+-|||+++|+..|+..-.-.+|+.++-+
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 3689999999998432 124799999999999999999999999999999999999999999999999988899888655
Q ss_pred HHHHHHHHh---hhhhccCCCCCCCCCCCHHHHHHHHHH
Q 031569 94 AYEQHKLET---MQDSLKGGKWSNGAEMTEEEAAAEQQR 129 (157)
Q Consensus 94 ~l~~~k~~~---k~~r~kk~~k~~~~g~~eEel~~~Q~e 129 (157)
.....-... .-.++++ ...+.+.+.|.....+++
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 444332221 1112222 456677777777665333
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=97.46 E-value=0.00052 Score=49.98 Aligned_cols=67 Identities=21% Similarity=0.338 Sum_probs=52.0
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCC-ccChhhHHhhhhhc
Q 031569 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKR-TIAPEHVLKALEVL 82 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RK-TI~~edVl~AL~~L 82 (157)
.||+++|.|||...+. +..|+.-...+|.-.+..||--|-.+|.+++...+.. .|.|.|+-.|...|
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 6899999999999999999999999999999966654 79999999998765
No 36
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=97.32 E-value=0.001 Score=48.65 Aligned_cols=68 Identities=13% Similarity=0.131 Sum_probs=59.6
Q ss_pred CcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCch
Q 031569 16 LPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (157)
Q Consensus 16 LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~ 85 (157)
+.+-+|.||.+... --+|+--.-+.+.....+||.-+-+.|...+++.+||||++-||+-+|+..|--
T Consensus 30 itKpaIRRlARr~G--VkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 30 ITKPAIRRLARRGG--VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred cchHHHHHHHHhcC--cchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 55778899988763 346888888889999999999999999999999999999999999999998753
No 37
>PF15510 CENP-W: Centromere kinetochore component W
Probab=97.02 E-value=0.0011 Score=48.69 Aligned_cols=67 Identities=24% Similarity=0.409 Sum_probs=57.5
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHH--------------HHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhh
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDL--------------LIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~--------------l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL 79 (157)
..-|++.+.|++|..-| .+++....-.+ +.--|-.|+|-|+-||...|=.++-.||.++||+.|-
T Consensus 15 rkaPrgfLkrv~Kr~Kp-hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~Aaa 93 (102)
T PF15510_consen 15 RKAPRGFLKRVFKRQKP-HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAA 93 (102)
T ss_pred HhCchHHHHHHHHhcCC-ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHH
Confidence 45799999999998887 78877666555 6667899999999999999989999999999999986
Q ss_pred hh
Q 031569 80 EV 81 (157)
Q Consensus 80 ~~ 81 (157)
+.
T Consensus 94 Kv 95 (102)
T PF15510_consen 94 KV 95 (102)
T ss_pred HH
Confidence 54
No 38
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=96.80 E-value=0.0035 Score=48.07 Aligned_cols=68 Identities=15% Similarity=0.215 Sum_probs=59.0
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
-+.+|...|.|++|.. .-.+||+++|...+.-|..-.+..|..-|-..|...++|.|.|.|+-.|+..
T Consensus 24 gl~fpvgrvkr~lk~~-~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrn 91 (132)
T COG5262 24 GLIFPVGRVKRLLKKG-NYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRN 91 (132)
T ss_pred CccccHHHHHHHHHcC-ccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcC
Confidence 4789999999999933 3479999999999999988888888888888889999999999999988753
No 39
>smart00414 H2A Histone 2A.
Probab=96.78 E-value=0.0046 Score=46.16 Aligned_cols=68 Identities=18% Similarity=0.222 Sum_probs=58.9
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
.+.+|.+-|.|++++.-. ..+|+..|...|.-+..-+...|-.-|-..|...+++.|+|+||..|+..
T Consensus 7 gL~fPVgRi~r~Lk~~~~-~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 7 GLQFPVGRIHRLLRKGTY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred CccCchHHHHHHHHcCcc-ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 578999999999998643 56999999999999888777777777888888999999999999999865
No 40
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=96.69 E-value=0.0063 Score=45.58 Aligned_cols=78 Identities=14% Similarity=0.209 Sum_probs=68.4
Q ss_pred ccCcHHHHHHHHHhhCCCC-ccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHHHHH
Q 031569 14 ASLPKATMTKIIKEMLPAD-VRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVY 92 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~-~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~~l~ 92 (157)
-.+|.|.|.|||.- ..+ -+|+.-+.....++..-|+..|-..+-..+...+-|.|+.+++..|...-.=.+|+..+.
T Consensus 22 trFP~ar~KkIMQ~--deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~ 99 (113)
T COG5247 22 TRFPIARLKKIMQL--DEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNME 99 (113)
T ss_pred hcCCHHHHHHHHHh--hhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHH
Confidence 37999999999973 334 469999999999999999999999999999999999999999999998887777876654
Q ss_pred H
Q 031569 93 A 93 (157)
Q Consensus 93 ~ 93 (157)
.
T Consensus 100 ~ 100 (113)
T COG5247 100 Q 100 (113)
T ss_pred H
Confidence 4
No 41
>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=96.67 E-value=0.014 Score=40.17 Aligned_cols=63 Identities=14% Similarity=0.186 Sum_probs=48.5
Q ss_pred CcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 16 LPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 16 LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
+|..+|.-+. +.++ --.++.|+...|.+-++--|..|-.+|.....+.+|++++++||-.||+
T Consensus 4 ~~~esvk~iA-es~G-i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 4 FSQESVKDIA-ESLG-ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp --HHHHHHHH-HHTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred CCHHHHHHHH-HHcC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 6777776555 4553 2379999999999999999999999999999999999999999999985
No 42
>PLN00154 histone H2A; Provisional
Probab=96.51 E-value=0.0081 Score=46.85 Aligned_cols=69 Identities=16% Similarity=0.161 Sum_probs=56.2
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
.+.||.+.|.|++|+...-..||+..|...|.-...-+..-|-.-|-..|...+++.|+|.||..|+..
T Consensus 36 gL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred CccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 689999999999999764467999999999888765555555555666788889999999999999854
No 43
>PTZ00017 histone H2A; Provisional
Probab=96.34 E-value=0.0093 Score=46.40 Aligned_cols=72 Identities=17% Similarity=0.181 Sum_probs=60.6
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh-cCch
Q 031569 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV-LGFG 85 (157)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~-LgF~ 85 (157)
.+.||.+.|.|++++.-- ..||+..|...|.-+..-+..-|-.-|-..|...+++-|+|.||..|+.. -+|.
T Consensus 25 gL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~nDeEL~ 97 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELN 97 (134)
T ss_pred CcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccCcHHHH
Confidence 689999999999998643 56999999999999888777777777888888999999999999999853 3343
No 44
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.34 E-value=0.014 Score=45.05 Aligned_cols=61 Identities=16% Similarity=0.366 Sum_probs=56.1
Q ss_pred HHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhc
Q 031569 21 MTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVL 82 (157)
Q Consensus 21 V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~L 82 (157)
|+|++|++-|+ .-|+..+..+++-....++--|+++|+..+...+|.||+..+|-.|..-|
T Consensus 43 v~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 43 VYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred hhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 78899999985 88999999999999999999999999999999999999999999987433
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=96.22 E-value=0.0063 Score=44.13 Aligned_cols=60 Identities=20% Similarity=0.247 Sum_probs=29.7
Q ss_pred HHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 21 MTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 21 V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
|..||-. .++.-.-..|+..+|-+...+||..+...|..+|...|+++|+.+|++-+|..
T Consensus 7 I~~mMy~-fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 7 IRQMMYG-FGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp CHHHHHC-TTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHH-cCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 3445554 33456788999999999999999999999999999999999999999999975
No 46
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.18 E-value=0.015 Score=45.00 Aligned_cols=68 Identities=15% Similarity=0.215 Sum_probs=53.0
Q ss_pred ccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 12 EDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
-.+.+|...|.|++|+. --..+|+.+|...+.-|..-.+..|..-|-..+..++|.-|+|.||..|+.
T Consensus 24 agl~fPvgri~r~Lr~~-~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 24 AGLQFPVGRIHRLLRKG-RYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred cccccCHHHHHHHHHcc-chhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 35789999999999993 236889999999999665544444455555556677888899999999986
No 47
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=96.05 E-value=0.0048 Score=48.16 Aligned_cols=71 Identities=18% Similarity=0.298 Sum_probs=62.3
Q ss_pred cccccCcHHHHHHHHHhhCC---CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 11 KEDASLPKATMTKIIKEMLP---ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP---~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
..|+.+++....|++++..+ .++++...|..+|++++.-|+.-|--.+|-.|.+.+|-||.|.||--|..-
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 35788889999999996554 489999999999999999999999999999999999999999999776543
No 48
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=96.04 E-value=0.0071 Score=49.67 Aligned_cols=70 Identities=19% Similarity=0.303 Sum_probs=61.7
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCC-ccChhhHHhhhhhcCch
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKR-TIAPEHVLKALEVLGFG 85 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RK-TI~~edVl~AL~~LgF~ 85 (157)
-.||+++|.|||..+.. -.|+.-+..++.-.+.+||--|--+|.++|..-+.. .|-|.||-.|...|+..
T Consensus 111 s~f~Ka~iKkL~~~itg--~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~q 181 (195)
T KOG3219|consen 111 SAFPKAQIKKLMSSITG--QSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQ 181 (195)
T ss_pred hcCCHHHHHHHHHHHhC--CccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhc
Confidence 36999999999999985 339999999999999999999999999999977763 59999999998887654
No 49
>PLN00157 histone H2A; Provisional
Probab=95.99 E-value=0.017 Score=44.91 Aligned_cols=73 Identities=16% Similarity=0.172 Sum_probs=59.3
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh-cCchh
Q 031569 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV-LGFGE 86 (157)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~-LgF~~ 86 (157)
-+.||.+.|.|++++.-- ..||+..|...|.-+..-+..-|-.-|-..|...+++-|+|+||..|+.. -+|..
T Consensus 24 gL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~nDeEL~~ 97 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRNDEELSK 97 (132)
T ss_pred CcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccCcHHHHH
Confidence 689999999999998643 57999999999988777666666666777788889999999999999854 44433
No 50
>PLN00153 histone H2A; Provisional
Probab=95.98 E-value=0.018 Score=44.62 Aligned_cols=73 Identities=16% Similarity=0.204 Sum_probs=59.9
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh-cCchh
Q 031569 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV-LGFGE 86 (157)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~-LgF~~ 86 (157)
.+.+|.+.|.|++++.-. ..||+..|...|.-+..-++.-|-.-|-..|...+++-|+|.||..|+.. -+|..
T Consensus 22 gL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~nDeEL~~ 95 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGK 95 (129)
T ss_pred CcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccCcHHHHH
Confidence 689999999999998654 57999999999988877666666667777788889999999999999854 44443
No 51
>PLN00156 histone H2AX; Provisional
Probab=95.95 E-value=0.021 Score=44.71 Aligned_cols=68 Identities=18% Similarity=0.181 Sum_probs=56.0
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
.+.+|.+.|.|++++.-- ..||+..|...|.-+..-...-|-.-|-..|...+++-|+|+||..|+..
T Consensus 27 gL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrn 94 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN 94 (139)
T ss_pred CcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccC
Confidence 689999999999998643 56999999999888776555555566666788889999999999999854
No 52
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.85 E-value=0.02 Score=48.88 Aligned_cols=70 Identities=17% Similarity=0.335 Sum_probs=63.0
Q ss_pred cccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 11 KEDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
.....|-+--|..+++++-+ +..+-+|+.++|.+.|-.||.-|+..|-..|++.+..||-+-||.-.|+.
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 34556777788999998854 88999999999999999999999999999999999999999999999875
No 53
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=95.75 E-value=0.011 Score=47.19 Aligned_cols=73 Identities=18% Similarity=0.297 Sum_probs=60.5
Q ss_pred ccCcHHHHHHHHHhhCCCCcccc-HHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhH
Q 031569 14 ASLPKATMTKIIKEMLPADVRVA-RDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYI 88 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~is-kdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv 88 (157)
..||.+.|..+++ ++++++++ +++..++.+++.-||..|+..+...+...+|||+.--|+=.|.+.-+=..|.
T Consensus 58 ~rLpL~rik~vvk--l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~de~~fl 131 (162)
T KOG1658|consen 58 SRLPLARIKQVVK--LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVDEFAFL 131 (162)
T ss_pred hhccHHHHHhhcc--CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchHHHHHH
Confidence 5689999999997 67788855 6788999999999999999999999999999999988887776654433333
No 54
>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=94.60 E-value=0.22 Score=36.13 Aligned_cols=60 Identities=17% Similarity=0.222 Sum_probs=48.8
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 20 TMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 20 ~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
-|..+|.... +.-.-..|+..+|-+..++||.-+..+|.++|. .++.-|+.||++-+|..
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 3666776544 345678999999999999999999999999999 44444699999999964
No 55
>PTZ00252 histone H2A; Provisional
Probab=94.12 E-value=0.18 Score=39.35 Aligned_cols=70 Identities=11% Similarity=0.208 Sum_probs=51.9
Q ss_pred ccccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhh------cCCCccChhhHHhhhhh-cCc
Q 031569 12 EDASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSR------EDKRTIAPEHVLKALEV-LGF 84 (157)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~------~~RKTI~~edVl~AL~~-LgF 84 (157)
-.+.||.+.|.|++++.-- ..||+.-|...|.-+. .||++|-.+.+-+ .+++-|+|+||..|+.. -+|
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 3689999999999998754 5799999988887754 4566665555432 46678999999999854 444
Q ss_pred hh
Q 031569 85 GE 86 (157)
Q Consensus 85 ~~ 86 (157)
..
T Consensus 97 ~~ 98 (134)
T PTZ00252 97 GS 98 (134)
T ss_pred HH
Confidence 33
No 56
>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=93.90 E-value=0.35 Score=37.27 Aligned_cols=89 Identities=17% Similarity=0.175 Sum_probs=47.5
Q ss_pred CCCcccccCcHH--HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhh-hcCc
Q 031569 8 GKSKEDASLPKA--TMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE-VLGF 84 (157)
Q Consensus 8 g~~~dd~~LP~A--~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~-~LgF 84 (157)
|.....-.+|+. +|.-|+++.. -......+...|.+.+-.|+.-|-..|...+.+.+|++|+.+||--|++ .+++
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 444556678873 3455555542 2247788889999999999999999999999999999999999999998 5677
Q ss_pred hhhHHHHHHHHHHH
Q 031569 85 GEYIEEVYAAYEQH 98 (157)
Q Consensus 85 ~~yv~~l~~~l~~~ 98 (157)
.-.-++=++.|.+.
T Consensus 81 ~f~~pppre~llel 94 (129)
T PF02291_consen 81 SFTQPPPREFLLEL 94 (129)
T ss_dssp --------------
T ss_pred hccCCCChHHHHHH
Confidence 65556655666544
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=91.30 E-value=0.66 Score=37.54 Aligned_cols=69 Identities=20% Similarity=0.229 Sum_probs=54.6
Q ss_pred CcHHHHHHHHHhhC-----CCCccccHHHHHHHHHHHHH---HHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCc
Q 031569 16 LPKATMTKIIKEML-----PADVRVARDAQDLLIECCVE---FINLVSSESNEVCSREDKRTIAPEHVLKALEVLGF 84 (157)
Q Consensus 16 LP~A~V~riiKe~L-----P~~~~iskdA~~~l~~c~~e---FI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF 84 (157)
|...-+..++...+ .....++.++.+.|.+.+.= .|+.+...|...+-..+.++|+.++|-.++.++.|
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 34445555555433 12356999999999998875 79999999999988899999999999999998875
No 58
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=89.96 E-value=1.8 Score=35.14 Aligned_cols=68 Identities=16% Similarity=0.246 Sum_probs=54.5
Q ss_pred cCcHHHHHHHHHhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcC--------------CCccChhhHHhhh
Q 031569 15 SLPKATMTKIIKEMLPADVR-VARDAQDLLIECCVEFINLVSSESNEVCSRED--------------KRTIAPEHVLKAL 79 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~-iskdA~~~l~~c~~eFI~~lsseAneia~~~~--------------RKTI~~edVl~AL 79 (157)
.||-+.+--.++.+. +. ...-.+-+|.=++-.||.-|+..|.+.|+-.. |-|++-+|+-.||
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 677787777777653 33 44556778999999999999999999997444 4589999999999
Q ss_pred hhcCch
Q 031569 80 EVLGFG 85 (157)
Q Consensus 80 ~~LgF~ 85 (157)
.+.|..
T Consensus 163 ~EyGin 168 (176)
T KOG3423|consen 163 AEYGIN 168 (176)
T ss_pred HHhCcc
Confidence 999874
No 59
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=89.02 E-value=2.6 Score=36.27 Aligned_cols=72 Identities=19% Similarity=0.202 Sum_probs=52.1
Q ss_pred HHHHHHHHHhhCCC---CccccHHHHHHHHHHH------HHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhH
Q 031569 18 KATMTKIIKEMLPA---DVRVARDAQDLLIECC------VEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYI 88 (157)
Q Consensus 18 ~A~V~riiKe~LP~---~~~iskdA~~~l~~c~------~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv 88 (157)
..-+..|++..+-. ...++.++.+.+.+.+ ...+..+...|.+.|...++.+|+.+||..|+..+....+.
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 031569 89 E 89 (157)
Q Consensus 89 ~ 89 (157)
.
T Consensus 289 ~ 289 (394)
T PRK00411 289 E 289 (394)
T ss_pred H
Confidence 3
No 60
>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=88.98 E-value=6.4 Score=32.06 Aligned_cols=79 Identities=24% Similarity=0.220 Sum_probs=56.7
Q ss_pred ccccCcHHHHHHHHHhhCCC-Cc-cccHHHHHHHHHHHHHHHHHHHhhhHHHhhhc------CCCccChhhHHhhhhhcC
Q 031569 12 EDASLPKATMTKIIKEMLPA-DV-RVARDAQDLLIECCVEFINLVSSESNEVCSRE------DKRTIAPEHVLKALEVLG 83 (157)
Q Consensus 12 dd~~LP~A~V~riiKe~LP~-~~-~iskdA~~~l~~c~~eFI~~lsseAneia~~~------~RKTI~~edVl~AL~~Lg 83 (157)
+...|....|.+.|...+.. ++ .|+.|+..+|..||.+++..|-.....+|++- ...++-..||-.-|..|+
T Consensus 41 ~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~ 120 (212)
T cd08045 41 DPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLE 120 (212)
T ss_pred hhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHH
Confidence 34556666666666665542 23 79999999999999999999999999998854 335666778877776665
Q ss_pred chhhHHH
Q 031569 84 FGEYIEE 90 (157)
Q Consensus 84 F~~yv~~ 90 (157)
--+..+.
T Consensus 121 ~~ek~e~ 127 (212)
T cd08045 121 QLEREEE 127 (212)
T ss_pred HHHHHHH
Confidence 5444443
No 61
>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=86.93 E-value=2.1 Score=26.94 Aligned_cols=38 Identities=29% Similarity=0.303 Sum_probs=23.8
Q ss_pred hhHHhhhhhcCchhhHHHHHHHHHHHHHHhhhhhccCCCCCCCCCCCHHHHHHH
Q 031569 73 EHVLKALEVLGFGEYIEEVYAAYEQHKLETMQDSLKGGKWSNGAEMTEEEAAAE 126 (157)
Q Consensus 73 edVl~AL~~LgF~~yv~~l~~~l~~~k~~~k~~r~kk~~k~~~~g~~eEel~~~ 126 (157)
+|++.||..|||.. .++..++..... ..+++.|+++++
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 68999999999985 334444433221 256778888875
No 62
>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=85.98 E-value=4.2 Score=34.54 Aligned_cols=75 Identities=16% Similarity=0.143 Sum_probs=52.0
Q ss_pred HHHHHHHHHhhCC---CCccccHHHHHHHHHHHH------HHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhH
Q 031569 18 KATMTKIIKEMLP---ADVRVARDAQDLLIECCV------EFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYI 88 (157)
Q Consensus 18 ~A~V~riiKe~LP---~~~~iskdA~~~l~~c~~------eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv 88 (157)
...+..|++..+. ....++.++.+.+.+.+. -.+..+-..|.+.|..+++.+|+.+||..|+..+....++
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 4446666665442 133588888877766442 2344455677888888899999999999999999766666
Q ss_pred HHHH
Q 031569 89 EEVY 92 (157)
Q Consensus 89 ~~l~ 92 (157)
..+.
T Consensus 281 ~~i~ 284 (365)
T TIGR02928 281 ELIR 284 (365)
T ss_pred HHHH
Confidence 5554
No 63
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=82.84 E-value=5.6 Score=37.64 Aligned_cols=65 Identities=20% Similarity=0.212 Sum_probs=54.6
Q ss_pred cHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcC
Q 031569 17 PKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLG 83 (157)
Q Consensus 17 P~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~Lg 83 (157)
|+-++.-++ +.+. -..++.|+-.+|..=...=|.-|..+|...-.+.+|.+++.+||..||..+.
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 455554444 5553 3449999999999999999999999999999999999999999999998764
No 64
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=82.49 E-value=5.4 Score=35.20 Aligned_cols=72 Identities=14% Similarity=0.251 Sum_probs=58.8
Q ss_pred HHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHHHHHHHHH
Q 031569 21 MTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYAAYE 96 (157)
Q Consensus 21 V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~~l~ 96 (157)
|.-|.+..+ --.|++-|++-|.+....+|.-|...+...|+..||...+.-||.-+|-.+|+. +..|...++
T Consensus 11 V~~Ll~~~g--fd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q 82 (323)
T KOG4336|consen 11 VSNLLKTKG--FDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQ 82 (323)
T ss_pred HHHHHHHhC--chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHH
Confidence 444444443 234999999999999999999999999999999999999999999999999997 344444443
No 65
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=82.24 E-value=3.4 Score=36.88 Aligned_cols=71 Identities=11% Similarity=0.163 Sum_probs=59.9
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCch
Q 031569 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (157)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~ 85 (157)
.+.|-+..|..|.....-. ....-|.+.|..-...||.-|+..|...+...||--.+.-||+.||++|+-.
T Consensus 27 a~sla~~avaQIcqslg~~--~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 27 AFSLARVAVAQICQSLGYS--STQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHHHhcCCc--ccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 4577788888888754322 2334499999999999999999999999999999999999999999998875
No 66
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=79.85 E-value=1.8 Score=41.47 Aligned_cols=46 Identities=30% Similarity=0.435 Sum_probs=36.1
Q ss_pred ccHHHHHHHHHHH--------------HHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 35 VARDAQDLLIECC--------------VEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 35 iskdA~~~l~~c~--------------~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
++++|..-|.+-+ ..-...|. +|+++|..++++-|+++||.+|++.
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 6666666555544 44555565 9999999999999999999999987
No 67
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=79.02 E-value=8.5 Score=35.73 Aligned_cols=48 Identities=29% Similarity=0.359 Sum_probs=38.6
Q ss_pred cccHHHHHHHHHHHHH-----------HHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 34 RVARDAQDLLIECCVE-----------FINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 34 ~iskdA~~~l~~c~~e-----------FI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
-++.+|...|.+.+.. .|.-|-.+|+-+|...++++|+++||..|++.
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 4788888888887653 56667799999999999999999999999975
No 68
>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=76.50 E-value=9.1 Score=36.13 Aligned_cols=51 Identities=20% Similarity=0.263 Sum_probs=40.6
Q ss_pred cccHHHHHHHHHHHHH-------------HHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCc
Q 031569 34 RVARDAQDLLIECCVE-------------FINLVSSESNEVCSREDKRTIAPEHVLKALEVLGF 84 (157)
Q Consensus 34 ~iskdA~~~l~~c~~e-------------FI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF 84 (157)
.++.+|...|.+.++. =|.-|-.+|+.+|..+++.+|+.+||.+|++.-.+
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~~ 393 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAKT 393 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHHH
Confidence 6899999999875552 34455678899999999999999999999876543
No 69
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=75.10 E-value=10 Score=27.34 Aligned_cols=48 Identities=19% Similarity=0.318 Sum_probs=40.1
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 33 VRVARDAQDLLIECCVEF------INLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 33 ~~iskdA~~~l~~c~~eF------I~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
..+++++..+|..++..| ++-|-.-|-.||.-++...|..+||..||.
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 457888888888887765 455667899999999999999999999984
No 70
>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=73.43 E-value=3 Score=25.65 Aligned_cols=26 Identities=31% Similarity=0.395 Sum_probs=20.7
Q ss_pred hHHHhhhcCCCccChhhHHhhhhhcC
Q 031569 58 SNEVCSREDKRTIAPEHVLKALEVLG 83 (157)
Q Consensus 58 Aneia~~~~RKTI~~edVl~AL~~Lg 83 (157)
|.++|...+...|+++|++.||=.-+
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 56788999999999999999975443
No 71
>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=71.76 E-value=13 Score=34.48 Aligned_cols=63 Identities=17% Similarity=0.300 Sum_probs=43.0
Q ss_pred HHHHHHhhCC-CCccccHHHHHHHHHHHH---HHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCc
Q 031569 21 MTKIIKEMLP-ADVRVARDAQDLLIECCV---EFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGF 84 (157)
Q Consensus 21 V~riiKe~LP-~~~~iskdA~~~l~~c~~---eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF 84 (157)
+..|++..+. .++.+++++.+.|...+. +.++.+ ..|..+|..++|++|+.+||.+++..-.|
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 4444444432 257899999998887765 333333 44556788889999999999999754433
No 72
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=68.92 E-value=14 Score=28.34 Aligned_cols=64 Identities=19% Similarity=0.327 Sum_probs=49.2
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCC----CccChhhHHhhhh
Q 031569 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDK----RTIAPEHVLKALE 80 (157)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~R----KTI~~edVl~AL~ 80 (157)
-+.+|...|.|.+|.......+|..-+..- ..-.+.||+.|-.+.|.+..+ |.|+|.|+--|+.
T Consensus 28 GlqFpVgRihr~LK~r~t~h~rVGataavy----~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 28 GLQFPVGRIHRHLKTRTTSHGRVGATAAVY----SAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred ccccchHHHHHHHHHhcccccccchHHHHH----HHHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 468999999999999887777776544332 233568999999999887665 7899999877764
No 73
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=63.46 E-value=25 Score=29.18 Aligned_cols=76 Identities=14% Similarity=0.145 Sum_probs=47.9
Q ss_pred cCcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHHHHH
Q 031569 15 SLPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVY 92 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~~l~ 92 (157)
.++...+.++++..+. .++.++.++.+.|.+.+.-=+..+-......|. +..+|+.+||-.++.....++.+-.+-
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 4555666777776554 367799999999998873323333333333342 234799999999888766554444433
No 74
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=62.71 E-value=40 Score=27.61 Aligned_cols=67 Identities=19% Similarity=0.207 Sum_probs=49.5
Q ss_pred cCcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 15 SLPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
.+....+.+.|++.+- .++.|+.++...|...+.-=...+-++-..+|.-.+.++|+.+||...+..
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 4556666666766554 368899999999998887666677777777776555557999999877653
No 75
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=60.74 E-value=32 Score=29.23 Aligned_cols=70 Identities=17% Similarity=0.200 Sum_probs=48.2
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHH---HHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCch
Q 031569 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCV---EFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (157)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~---eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~ 85 (157)
++...+..|++.... .++.++.++...|.+.|. -.+..+-..+.+.|...+...|+.++|..++..++..
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 444555555554432 367899999988888773 2344444556666666667789999999999987665
No 76
>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=59.47 E-value=25 Score=33.17 Aligned_cols=53 Identities=25% Similarity=0.500 Sum_probs=43.7
Q ss_pred hhCCCCccccHHHHHHHHHHHHHHH-------HHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 27 EMLPADVRVARDAQDLLIECCVEFI-------NLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 27 e~LP~~~~iskdA~~~l~~c~~eFI-------~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
..+| .+.|+.++.+.|...|..+- .++...|..+|.-++|.+|+.+||..|+.
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 3344 78999999999999998762 35667788889999999999999998874
No 77
>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=59.26 E-value=17 Score=26.77 Aligned_cols=34 Identities=15% Similarity=0.326 Sum_probs=27.7
Q ss_pred HHHHHHHHhhC----CCCccccHHHHHHHHHHHHHHHH
Q 031569 19 ATMTKIIKEML----PADVRVARDAQDLLIECCVEFIN 52 (157)
Q Consensus 19 A~V~riiKe~L----P~~~~iskdA~~~l~~c~~eFI~ 52 (157)
++|.++||..| .++..++.++.++|++++..|-.
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 46899999999999999998853
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=59.08 E-value=14 Score=23.34 Aligned_cols=41 Identities=17% Similarity=0.122 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHH-HHHhhhHHHhhhcCCCccChhhHHhh
Q 031569 37 RDAQDLLIECCVEFIN-LVSSESNEVCSREDKRTIAPEHVLKA 78 (157)
Q Consensus 37 kdA~~~l~~c~~eFI~-~lsseAneia~~~~RKTI~~edVl~A 78 (157)
.||...|.+. =.|+. .|=..+-..|...|...|+.++|..|
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 4455555443 23443 33345556688999999999999765
No 79
>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=58.37 E-value=36 Score=28.17 Aligned_cols=70 Identities=16% Similarity=0.195 Sum_probs=46.8
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHH---HHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCch
Q 031569 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCV---EFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (157)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~---eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~ 85 (157)
++...+..+++.... .++.++.++.+.|.+.|. -++..+...+.+.+...+...|+.++|..++..++++
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 344455555554432 357899999988888763 2334444456666666666779999999999987654
No 80
>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=56.66 E-value=11 Score=24.39 Aligned_cols=18 Identities=28% Similarity=0.492 Sum_probs=16.2
Q ss_pred CCCCHHHHHHHHHHHHHH
Q 031569 116 AEMTEEEAAAEQQRMFAE 133 (157)
Q Consensus 116 ~g~~eEel~~~Q~eLF~~ 133 (157)
++||.+|....|++|++.
T Consensus 13 ~~MS~eEI~~er~eL~~~ 30 (49)
T PF08621_consen 13 ASMSPEEIEEEREELLES 30 (49)
T ss_pred HhCCHHHHHHHHHHHHHh
Confidence 579999999999999875
No 81
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=55.75 E-value=24 Score=33.31 Aligned_cols=59 Identities=14% Similarity=0.126 Sum_probs=48.1
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHH-------HHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 20 TMTKIIKEMLPADVRVARDAQDLLIECCVEFI-------NLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 20 ~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI-------~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
.|.+.- +.++ ++.|+.+....+.+.|..|- .++...|..+|--++|.+|+++||..|+.
T Consensus 183 ~I~~AR-~rl~-~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 183 DIAAAR-ARLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHHHHH-HHHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 344433 3455 89999999999998888874 47778899999999999999999999974
No 82
>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=55.33 E-value=15 Score=23.65 Aligned_cols=25 Identities=32% Similarity=0.531 Sum_probs=21.3
Q ss_pred ccChhhHHhhhhhcCchhhHHHHHH
Q 031569 69 TIAPEHVLKALEVLGFGEYIEEVYA 93 (157)
Q Consensus 69 TI~~edVl~AL~~LgF~~yv~~l~~ 93 (157)
+=++++|..-|..+||..|++.+..
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 3478999999999999999987654
No 83
>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=55.30 E-value=16 Score=27.62 Aligned_cols=62 Identities=10% Similarity=0.132 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHHHHHHHHHHHHHHh
Q 031569 37 RDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYAAYEQHKLET 102 (157)
Q Consensus 37 kdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~~l~~~k~~~ 102 (157)
..++.-|..|..+.-.|...-..-... ---.-...+..|+..|++..+.++.+.+++|+..+
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 456667777777766665543332221 00124567788999999999999999999998654
No 84
>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=55.19 E-value=47 Score=29.13 Aligned_cols=53 Identities=15% Similarity=0.323 Sum_probs=41.3
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHHH-------HHHHhhhHHHhhhcCCCccChhhHHhhh
Q 031569 26 KEMLPADVRVARDAQDLLIECCVEFI-------NLVSSESNEVCSREDKRTIAPEHVLKAL 79 (157)
Q Consensus 26 Ke~LP~~~~iskdA~~~l~~c~~eFI-------~~lsseAneia~~~~RKTI~~edVl~AL 79 (157)
++.+| .+.|+.+....+.+.|..+= .++...|-..|--+||..|+++||..+.
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 79999999999999887653 2344667778888999999999997764
No 85
>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=55.17 E-value=46 Score=21.92 Aligned_cols=29 Identities=14% Similarity=0.268 Sum_probs=23.6
Q ss_pred CCccChhhHHhhhhhcCchhhHHHHHHHH
Q 031569 67 KRTIAPEHVLKALEVLGFGEYIEEVYAAY 95 (157)
Q Consensus 67 RKTI~~edVl~AL~~LgF~~yv~~l~~~l 95 (157)
...-+..+++.||..+|..+-+..|...|
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 44567889999999999999988887643
No 86
>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=54.09 E-value=17 Score=23.35 Aligned_cols=22 Identities=32% Similarity=0.437 Sum_probs=19.5
Q ss_pred ChhhHHhhhhhcCchhhHHHHH
Q 031569 71 APEHVLKALEVLGFGEYIEEVY 92 (157)
Q Consensus 71 ~~edVl~AL~~LgF~~yv~~l~ 92 (157)
++++|..-|+.+|++.|++...
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 6889999999999999997763
No 87
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=52.51 E-value=50 Score=27.73 Aligned_cols=67 Identities=13% Similarity=0.183 Sum_probs=49.8
Q ss_pred HHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhh--cCCCccChhhHHhhhhhcCchhh
Q 031569 21 MTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSR--EDKRTIAPEHVLKALEVLGFGEY 87 (157)
Q Consensus 21 V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~--~~RKTI~~edVl~AL~~LgF~~y 87 (157)
+.+.|++.+- .+..|+.+|...|..++.-=...+..+-..+|.- .++.+|+.+||...+....+.-|
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 3789999999999999987677777777777775 45778999999988777665433
No 88
>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=52.11 E-value=16 Score=22.66 Aligned_cols=24 Identities=38% Similarity=0.655 Sum_probs=20.4
Q ss_pred cChhhHHhhhhhcCchhhHHHHHH
Q 031569 70 IAPEHVLKALEVLGFGEYIEEVYA 93 (157)
Q Consensus 70 I~~edVl~AL~~LgF~~yv~~l~~ 93 (157)
-++++|..-|..+|+++|++.+.+
T Consensus 2 w~~~~V~~wL~~~~~~~y~~~f~~ 25 (63)
T cd00166 2 WSPEDVAEWLESLGLGQYADNFRE 25 (63)
T ss_pred CCHHHHHHHHHHcChHHHHHHHHH
Confidence 367899999999999999987754
No 89
>PRK09862 putative ATP-dependent protease; Provisional
Probab=51.49 E-value=56 Score=30.47 Aligned_cols=56 Identities=9% Similarity=0.198 Sum_probs=43.5
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhH
Q 031569 33 VRVARDAQDLLIECCVEF------INLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYI 88 (157)
Q Consensus 33 ~~iskdA~~~l~~c~~eF------I~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv 88 (157)
+.++.++..++...+..+ .+.|-.-|..+|.-+++..|+++||..|+.=-+++..+
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~~~ 498 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDRLL 498 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccHHH
Confidence 467888888777765544 56677789999999999999999999999755555433
No 90
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=49.91 E-value=34 Score=27.15 Aligned_cols=64 Identities=16% Similarity=0.109 Sum_probs=50.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHH-HHHHHHHHH
Q 031569 35 VARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIE-EVYAAYEQH 98 (157)
Q Consensus 35 iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~-~l~~~l~~~ 98 (157)
...-+.--|.+.+--++.-|-..|.-.+.+.+|.||.++||.-|+...+=.+|.+ +=++++-++
T Consensus 31 yEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~l 95 (148)
T KOG3334|consen 31 YEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLEL 95 (148)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHH
Confidence 4555666777777778888888999999999999999999999999888777776 334444443
No 91
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=49.71 E-value=42 Score=29.74 Aligned_cols=53 Identities=17% Similarity=0.429 Sum_probs=44.0
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHHH-------HHHHhhhHHHhhhcCCCccChhhHHhhh
Q 031569 26 KEMLPADVRVARDAQDLLIECCVEFI-------NLVSSESNEVCSREDKRTIAPEHVLKAL 79 (157)
Q Consensus 26 Ke~LP~~~~iskdA~~~l~~c~~eFI-------~~lsseAneia~~~~RKTI~~edVl~AL 79 (157)
++.++ .+.|+.+....|.+.|..+= .++...|.-.|--+||..|+++||..+.
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 45566 79999999999999988874 3566778888899999999999998775
No 92
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=49.67 E-value=21 Score=29.31 Aligned_cols=63 Identities=17% Similarity=0.144 Sum_probs=46.9
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCC-CccChhhHHhhh
Q 031569 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDK-RTIAPEHVLKAL 79 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~R-KTI~~edVl~AL 79 (157)
.||++.|.|++..++ +-.|+...+.+|+-.+.+|+--|---|.-+-.+-+- -.+.|.|+-.|.
T Consensus 115 ~lnKt~VKKlastV~--nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p~h~reay 178 (199)
T COG5251 115 SLNKTQVKKLASTVA--NQTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIPFHKREAY 178 (199)
T ss_pred CCCHHHHHHHHHHHh--ccccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCChHHHHHHH
Confidence 799999999999998 577888888889999999988776555544332221 237778877664
No 93
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=49.08 E-value=25 Score=33.62 Aligned_cols=47 Identities=21% Similarity=0.246 Sum_probs=38.7
Q ss_pred cccHHHHHHHHHHHHHHH-------------HHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 34 RVARDAQDLLIECCVEFI-------------NLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 34 ~iskdA~~~l~~c~~eFI-------------~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
.|+.+|...|.+.++.-. .-|-.+|+.+|..++++.|+.+||..|+.
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 589999988888776332 22667899999999999999999999974
No 94
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=48.44 E-value=41 Score=31.15 Aligned_cols=47 Identities=13% Similarity=0.235 Sum_probs=40.8
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 34 RVARDAQDLLIECCVEF------INLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 34 ~iskdA~~~l~~c~~eF------I~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
.++++++.+|.+++..| .+-|-.-|..+|.-++...|..+||..|+.
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 46889999999998886 556667899999999999999999999984
No 95
>PRK09526 lacI lac repressor; Reviewed
Probab=47.73 E-value=24 Score=29.15 Aligned_cols=38 Identities=16% Similarity=0.348 Sum_probs=30.8
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHh
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSS 56 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lss 56 (157)
...-++||.|++.. .-+||.++++-|.+++.+ +.|.-.
T Consensus 15 aGVS~~TVSrvLn~----~~~vs~~tr~rV~~~a~e-lgY~pn 52 (342)
T PRK09526 15 AGVSYQTVSRVLNQ----ASHVSAKTREKVEAAMAE-LNYVPN 52 (342)
T ss_pred hCCCHHHHHHHhcC----CCCCCHHHHHHHHHHHHH-HCCCcC
Confidence 35678999999975 246999999999999999 567544
No 96
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=46.80 E-value=48 Score=20.84 Aligned_cols=32 Identities=22% Similarity=0.481 Sum_probs=26.5
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHH
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVE 49 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~e 49 (157)
..+..+||.|++... -+||.++++-|.+.+.+
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 97
>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=46.78 E-value=60 Score=30.53 Aligned_cols=55 Identities=15% Similarity=0.251 Sum_probs=41.8
Q ss_pred HHhhCCCCccccHHHHHHHHHHHHHHH-------HHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 25 IKEMLPADVRVARDAQDLLIECCVEFI-------NLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 25 iKe~LP~~~~iskdA~~~l~~c~~eFI-------~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
+++.+| .+.|+.+..+.|.+.|..+= .++...|--.|.-++|.+|+++||..|..
T Consensus 195 ar~~~~-~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 195 ARELLP-QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred HHHhcC-CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 344565 78999999988888776542 23446677778889999999999988863
No 98
>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=45.13 E-value=24 Score=22.03 Aligned_cols=25 Identities=28% Similarity=0.488 Sum_probs=21.0
Q ss_pred cChhhHHhhhhhcCchhhHHHHHHH
Q 031569 70 IAPEHVLKALEVLGFGEYIEEVYAA 94 (157)
Q Consensus 70 I~~edVl~AL~~LgF~~yv~~l~~~ 94 (157)
-++++|..-|..+||+.|++.+.+.
T Consensus 4 w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 4 WSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCHHHHHHHHHHCChHHHHHHHHHC
Confidence 4678999999999999999887653
No 99
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=43.39 E-value=25 Score=29.01 Aligned_cols=38 Identities=11% Similarity=0.246 Sum_probs=30.1
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhh
Q 031569 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSE 57 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsse 57 (157)
..-++||.|++... -+||.+++.-+.+.+.+ +.|.-..
T Consensus 16 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn~ 53 (331)
T PRK14987 16 GVTKMTVSRFLRNP----EQVSVALRGKIAAALDE-LGYIPNR 53 (331)
T ss_pred CCCHHHhhhhhCCC----CCCCHHHHHHHHHHHHH-hCCCccH
Confidence 56789999999642 47999999999999998 5565443
No 100
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=42.36 E-value=80 Score=26.34 Aligned_cols=67 Identities=18% Similarity=0.154 Sum_probs=48.0
Q ss_pred cCcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 15 SLPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
.++...+.+.|+..+- .++.|+.+|...|.+.+..=...+.++-..+|.-.+.+.|+.+||-..+..
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 4555666666655553 468999999999999988767777788888776443233999998766544
No 101
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=41.99 E-value=51 Score=29.90 Aligned_cols=67 Identities=18% Similarity=0.374 Sum_probs=50.4
Q ss_pred cccCcHHHHHHHH------------HhhCC-----CCccccHHHHHHHHHHHHH----HHHHHHhhhHHHhhhcCCCccC
Q 031569 13 DASLPKATMTKII------------KEMLP-----ADVRVARDAQDLLIECCVE----FINLVSSESNEVCSREDKRTIA 71 (157)
Q Consensus 13 d~~LP~A~V~rii------------Ke~LP-----~~~~iskdA~~~l~~c~~e----FI~~lsseAneia~~~~RKTI~ 71 (157)
...+|..-+.|++ ++.|. +++.++.||.++|...... |...|-+.|+.+|.+.+-+++.
T Consensus 339 phGiP~D~lDR~lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~ 418 (454)
T KOG2680|consen 339 PHGIPIDLLDRMLIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVE 418 (454)
T ss_pred CCCCcHHHhhhhheeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceee
Confidence 4567777776653 22322 4788999999999876543 4455556799999999999999
Q ss_pred hhhHHhhh
Q 031569 72 PEHVLKAL 79 (157)
Q Consensus 72 ~edVl~AL 79 (157)
.+||-.+.
T Consensus 419 ~~di~r~y 426 (454)
T KOG2680|consen 419 VDDIERVY 426 (454)
T ss_pred hhHHHHHH
Confidence 99998885
No 102
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=41.20 E-value=85 Score=28.43 Aligned_cols=65 Identities=18% Similarity=0.157 Sum_probs=53.4
Q ss_pred HHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCch
Q 031569 19 ATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG 85 (157)
Q Consensus 19 A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~ 85 (157)
.+|.-+. +.|. --.|.+|+..+|..-..-=|+-+-.+|...-.+.+|..++-+||-.||..|..+
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 4453 345899999999999999999999999999999999999999999999998654
No 103
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=40.93 E-value=68 Score=29.55 Aligned_cols=49 Identities=18% Similarity=0.305 Sum_probs=40.8
Q ss_pred CCccccHHHHHHHHHHHHH----HHHHHHhhhHHHhhhcCCCccChhhHHhhh
Q 031569 31 ADVRVARDAQDLLIECCVE----FINLVSSESNEVCSREDKRTIAPEHVLKAL 79 (157)
Q Consensus 31 ~~~~iskdA~~~l~~c~~e----FI~~lsseAneia~~~~RKTI~~edVl~AL 79 (157)
.++.+++||.+.|....++ |..-|-+-|+.+|...|+++|..+||-.|-
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 4789999999999887665 444455678999999999999999999884
No 104
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=40.89 E-value=37 Score=27.72 Aligned_cols=38 Identities=18% Similarity=0.209 Sum_probs=29.6
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHh
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSS 56 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lss 56 (157)
..+-++||.|.+... -.||.++++-|.+++.+. .|.-+
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 346689999999752 469999999999999875 45443
No 105
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=40.59 E-value=82 Score=27.63 Aligned_cols=53 Identities=9% Similarity=0.218 Sum_probs=42.6
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHHHH-------HHHhhhHHHhhhcCCCccChhhHHhhh
Q 031569 26 KEMLPADVRVARDAQDLLIECCVEFIN-------LVSSESNEVCSREDKRTIAPEHVLKAL 79 (157)
Q Consensus 26 Ke~LP~~~~iskdA~~~l~~c~~eFI~-------~lsseAneia~~~~RKTI~~edVl~AL 79 (157)
++.++ .+.|+.+....|.+.|..+=. ++...|.-.|--+||-.|+++||..+.
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 44565 799999999999999887642 366778888999999999999995543
No 106
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=39.35 E-value=1.6e+02 Score=22.26 Aligned_cols=48 Identities=21% Similarity=0.273 Sum_probs=38.4
Q ss_pred CCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 30 PADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 30 P~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
.++..=-.|+.++|-....+||..++..|..+. .|-.+..||++-+|.
T Consensus 23 GDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 23 GDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred CCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 456667789999999999999999988888887 333467788887774
No 107
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=39.30 E-value=36 Score=28.29 Aligned_cols=38 Identities=8% Similarity=0.171 Sum_probs=30.1
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhh
Q 031569 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSE 57 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsse 57 (157)
.+-++||.|++... -+||.++|+-|.+++.+ +.|.-..
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 46689999999753 46999999999999998 5565443
No 108
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=38.98 E-value=49 Score=29.34 Aligned_cols=74 Identities=18% Similarity=0.210 Sum_probs=48.8
Q ss_pred HHHHHHHHhhCC---CCccccHHHHHHHHHHH------HHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHH
Q 031569 19 ATMTKIIKEMLP---ADVRVARDAQDLLIECC------VEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIE 89 (157)
Q Consensus 19 A~V~riiKe~LP---~~~~iskdA~~~l~~c~------~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~ 89 (157)
.-+.-|+++-.- ..-.++.++.+++..-+ ..+..-+...|.++|+.+++.+|+.+||..|-+..+..-+..
T Consensus 193 ~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~ 272 (366)
T COG1474 193 EELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEE 272 (366)
T ss_pred HHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHH
Confidence 344555554332 13456666666555322 234455667899999999999999999999977777765555
Q ss_pred HHH
Q 031569 90 EVY 92 (157)
Q Consensus 90 ~l~ 92 (157)
.+.
T Consensus 273 ~~~ 275 (366)
T COG1474 273 VLK 275 (366)
T ss_pred HHH
Confidence 543
No 109
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=38.45 E-value=51 Score=30.69 Aligned_cols=51 Identities=14% Similarity=0.204 Sum_probs=38.4
Q ss_pred cccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHHHHHHHHHHH
Q 031569 34 RVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYAAYEQH 98 (157)
Q Consensus 34 ~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~~l~~~ 98 (157)
-|-+|.+.+|++||...=.||+..-...-...++++ |..|++++-..+...
T Consensus 434 ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~~ 484 (488)
T TIGR01052 434 EIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAYI 484 (488)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHH
Confidence 477889999999999999999976555544444443 677888887776543
No 110
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=37.65 E-value=1.2e+02 Score=24.93 Aligned_cols=66 Identities=11% Similarity=0.139 Sum_probs=40.0
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcC
Q 031569 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLG 83 (157)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~Lg 83 (157)
++..-+.++++..+. .++.|+.++.+.|.+.+.--+..+-.+-...+.. .++|+.+||..++....
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 445555555555442 3678999999999887753333332222223322 36799999988876543
No 111
>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=37.46 E-value=12 Score=24.12 Aligned_cols=59 Identities=27% Similarity=0.414 Sum_probs=32.1
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCcc---ChhhHHhhhhhcCchhhH-HHHHHH
Q 031569 32 DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTI---APEHVLKALEVLGFGEYI-EEVYAA 94 (157)
Q Consensus 32 ~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI---~~edVl~AL~~LgF~~yv-~~l~~~ 94 (157)
+.+|.+++..+|.+++. . |..-+.+.-..+=.|.+ .+...+..|.++|+-+|+ |.+...
T Consensus 1 gF~ie~~t~~ai~~~~~-~---L~~is~ERi~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~a 63 (64)
T PF12627_consen 1 GFKIEPETEEAIKENAE-L---LSKISKERIREELEKILSSPNPSRAFKLLDELGLLEYIFPELDAA 63 (64)
T ss_dssp T-EE-HHHHHHHHHHGG-G---GGGS-HHHHHHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT-
T ss_pred CCccCHHHHHHHHHHHH-H---HhcCCHHHHHHHHHHHHcCCCHHHHHHHHHHcCCHHHHCcccccc
Confidence 35677888888877765 3 33333333333333332 456677788888877664 655443
No 112
>PRK07914 hypothetical protein; Reviewed
Probab=37.41 E-value=83 Score=26.70 Aligned_cols=64 Identities=11% Similarity=0.156 Sum_probs=44.7
Q ss_pred cHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 17 PKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 17 P~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
+..-+.+.|++.+- .+.+|+.+|...|.+++..=...+.+|-...+...+ .+|+.+||-..+..
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 34444444444442 368899999999999997666667777666665444 56999999887654
No 113
>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=36.95 E-value=19 Score=22.48 Aligned_cols=17 Identities=24% Similarity=0.618 Sum_probs=13.2
Q ss_pred ccccCcHHHHHHHHHhh
Q 031569 12 EDASLPKATMTKIIKEM 28 (157)
Q Consensus 12 dd~~LP~A~V~riiKe~ 28 (157)
+.+.+|+++|+|+++.-
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 114
>COG1500 Predicted exosome subunit [Translation, ribosomal structure and biogenesis]
Probab=36.08 E-value=1.3e+02 Score=25.70 Aligned_cols=70 Identities=17% Similarity=0.289 Sum_probs=50.1
Q ss_pred HHHHHHhhCC-CCccccHHHHHHHHHHHH-HHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCch-hhHHHHHH
Q 031569 21 MTKIIKEMLP-ADVRVARDAQDLLIECCV-EFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG-EYIEEVYA 93 (157)
Q Consensus 21 V~riiKe~LP-~~~~iskdA~~~l~~c~~-eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~-~yv~~l~~ 93 (157)
+.+|+.++|- +.+.+|.+-|..+.+.-. ..|++|+..|.+- ..+....|.-|-+||++++|. ++..++++
T Consensus 72 ~~eI~~eIl~kGeiQlTaeqR~~m~e~k~rqIi~~IsRn~IdP---~t~~P~Pp~rIe~Ameeakv~id~~K~ae~ 144 (234)
T COG1500 72 PDEIAEEILKKGEIQLTAEQRREMLEEKKRQIINIISRNAIDP---QTKAPHPPARIEKAMEEAKVHIDPFKSAEE 144 (234)
T ss_pred HHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHhccCC---CCCCCCCHHHHHHHHHhcCcccCCCCCHHH
Confidence 4555555554 368899999888777654 5666888765543 455789999999999999997 55555544
No 115
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=35.85 E-value=2e+02 Score=23.54 Aligned_cols=51 Identities=18% Similarity=0.270 Sum_probs=37.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHHhhhHHHhh-------------------hc--------------CCCccChhhHHhhhhh
Q 031569 35 VARDAQDLLIECCVEFINLVSSESNEVCS-------------------RE--------------DKRTIAPEHVLKALEV 81 (157)
Q Consensus 35 iskdA~~~l~~c~~eFI~~lsseAneia~-------------------~~--------------~RKTI~~edVl~AL~~ 81 (157)
...-.+-+|.-.+..||.-|+-.|-+... +. +|-+++..|+-.||++
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 44457788888999999999866554432 01 4557888999999998
Q ss_pred cCch
Q 031569 82 LGFG 85 (157)
Q Consensus 82 LgF~ 85 (157)
.|..
T Consensus 186 yGin 189 (197)
T COG5162 186 YGIN 189 (197)
T ss_pred hccc
Confidence 8874
No 116
>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=35.27 E-value=2.2e+02 Score=22.38 Aligned_cols=49 Identities=18% Similarity=0.355 Sum_probs=36.3
Q ss_pred HHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCch-hhHHHHHHHHHHHHHH
Q 031569 46 CCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFG-EYIEEVYAAYEQHKLE 101 (157)
Q Consensus 46 c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~-~yv~~l~~~l~~~k~~ 101 (157)
.+.+.++||-..|. |..++++++..-|..|||+ +.++.+..++.+++..
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~ 92 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSK 92 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 45566667666553 4559999999999999998 6777777777777654
No 117
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=34.53 E-value=78 Score=20.95 Aligned_cols=33 Identities=21% Similarity=0.472 Sum_probs=23.3
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHH
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEF 50 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eF 50 (157)
..+..+||.|++.. .-.|+.++++.|.+++.++
T Consensus 10 ~gvS~~TVSr~ln~----~~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 10 AGVSKATVSRVLNG----NGRVSEETREKVLAAMEEL 42 (70)
T ss_pred HCCCHHHHHHHHCC----CCCCCHHHHHHHHHHHHHh
Confidence 45777888887764 3446888888887777664
No 118
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=34.41 E-value=1.1e+02 Score=28.98 Aligned_cols=71 Identities=14% Similarity=0.190 Sum_probs=42.0
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhh
Q 031569 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEY 87 (157)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~y 87 (157)
++..-+.+.++..+- .++.++.++..+|.+.+.-=+..+-++....+.-.+++ |+.++|...+..+..+.|
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 36889999988888776544444444444444334444 888888777665544433
No 119
>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=34.32 E-value=1.4e+02 Score=19.60 Aligned_cols=47 Identities=11% Similarity=0.252 Sum_probs=36.1
Q ss_pred cCcHHHHHHHHHhhCCCCccc-cHHHHHHHHHHHHHHHHHHHhhhHHHhhh
Q 031569 15 SLPKATMTKIIKEMLPADVRV-ARDAQDLLIECCVEFINLVSSESNEVCSR 64 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~i-skdA~~~l~~c~~eFI~~lsseAneia~~ 64 (157)
.+|-+.+.-+++.+. +.. ..-..-+|.=++-.||.-|+..|.+.|+-
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 478888888888774 322 23345688889999999999999998863
No 120
>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=33.64 E-value=39 Score=18.72 Aligned_cols=26 Identities=19% Similarity=0.253 Sum_probs=19.9
Q ss_pred hHHHhhhcCCCccChhhHHhhhh-hcC
Q 031569 58 SNEVCSREDKRTIAPEHVLKALE-VLG 83 (157)
Q Consensus 58 Aneia~~~~RKTI~~edVl~AL~-~Lg 83 (157)
+....-.++.-+|+.+++..+|. .||
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 44555667788999999999998 676
No 121
>smart00350 MCM minichromosome maintenance proteins.
Probab=32.73 E-value=1.8e+02 Score=26.73 Aligned_cols=65 Identities=14% Similarity=0.232 Sum_probs=47.7
Q ss_pred ccCcHHHHHHHHHhh----CCCCccccHHHHHHHHHHHHHHH-------------------HHHHhhhHHHhhhcCCCcc
Q 031569 14 ASLPKATMTKIIKEM----LPADVRVARDAQDLLIECCVEFI-------------------NLVSSESNEVCSREDKRTI 70 (157)
Q Consensus 14 ~~LP~A~V~riiKe~----LP~~~~iskdA~~~l~~c~~eFI-------------------~~lsseAneia~~~~RKTI 70 (157)
..++...+.+.|.-+ .| .+|+++.+.|.+.....= ..|-.-|--.|.-..|.+|
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 457888888877533 34 489999999987665532 3344556677888999999
Q ss_pred ChhhHHhhhhh
Q 031569 71 APEHVLKALEV 81 (157)
Q Consensus 71 ~~edVl~AL~~ 81 (157)
+++||..|++-
T Consensus 493 ~~~Dv~~ai~l 503 (509)
T smart00350 493 EEADVEEAIRL 503 (509)
T ss_pred CHHHHHHHHHH
Confidence 99999998754
No 122
>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=32.58 E-value=59 Score=27.23 Aligned_cols=74 Identities=19% Similarity=0.141 Sum_probs=34.7
Q ss_pred cccccCcHHHHHHHHHhhCCC--CccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCC------ccChhhHHhhhhhc
Q 031569 11 KEDASLPKATMTKIIKEMLPA--DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKR------TIAPEHVLKALEVL 82 (157)
Q Consensus 11 ~dd~~LP~A~V~riiKe~LP~--~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RK------TI~~edVl~AL~~L 82 (157)
.++..|....+.+-|..+... ...|..|...+|.-||.+.+..|-..+..+|.+-..- +....||-..|..|
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 456678887788777776532 3579999999999999999999999999998753322 22355666665554
Q ss_pred Cc
Q 031569 83 GF 84 (157)
Q Consensus 83 gF 84 (157)
.-
T Consensus 119 ~~ 120 (264)
T PF05236_consen 119 EQ 120 (264)
T ss_dssp --
T ss_pred HH
Confidence 43
No 123
>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=32.25 E-value=1.5e+02 Score=22.40 Aligned_cols=69 Identities=17% Similarity=0.255 Sum_probs=45.2
Q ss_pred HHHHHHHHhhCCCCccccHHHHHHHHHHHH---HHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHHHHHHHH
Q 031569 19 ATMTKIIKEMLPADVRVARDAQDLLIECCV---EFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYAAY 95 (157)
Q Consensus 19 A~V~riiKe~LP~~~~iskdA~~~l~~c~~---eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~~l 95 (157)
..+..+++......+.|+.+-|....-+|+ .|+..|...|.+++...| |..++.+.+| .|-++..+
T Consensus 14 ~~l~~l~~~lg~~~~~i~~~~r~~yHaAav~asNf~~~L~~~a~~ll~~~g---i~~~~a~~~L--------~PLi~~t~ 82 (132)
T PF10728_consen 14 EVLQELAKELGGRPFEIDSEQRALYHAAAVFASNFLVALYALAAELLEQAG---IDFEEALEAL--------LPLIRETL 82 (132)
T ss_dssp HHHHHHHHHTTSEEEE--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SHHH--HHH--------HHHHHHHH
T ss_pred HHHHHHHHHhCCceEEeCHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHcC---CCchhHHHHH--------HHHHHHHH
Confidence 457788887766667899999988887765 788888888888887763 5555544443 34555555
Q ss_pred HHH
Q 031569 96 EQH 98 (157)
Q Consensus 96 ~~~ 98 (157)
+..
T Consensus 83 ~n~ 85 (132)
T PF10728_consen 83 ENI 85 (132)
T ss_dssp HHH
T ss_pred HHH
Confidence 554
No 124
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=31.28 E-value=31 Score=23.91 Aligned_cols=17 Identities=41% Similarity=0.591 Sum_probs=15.2
Q ss_pred ccChhhHHhhhhhcCch
Q 031569 69 TIAPEHVLKALEVLGFG 85 (157)
Q Consensus 69 TI~~edVl~AL~~LgF~ 85 (157)
.+++.+|+++|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 47889999999999995
No 125
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=31.21 E-value=53 Score=29.98 Aligned_cols=31 Identities=23% Similarity=0.293 Sum_probs=27.1
Q ss_pred HHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 51 INLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 51 I~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
|..|..+|-..|...+|..|+.+||..|++.
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~ 423 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEK 423 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHH
Confidence 5567788999999999999999999999865
No 126
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=30.41 E-value=59 Score=28.11 Aligned_cols=32 Identities=19% Similarity=0.341 Sum_probs=27.1
Q ss_pred HHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 50 FINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 50 FI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
-|..|..+|...|...++..|+.+|+..|++.
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 34567778888888999999999999999875
No 127
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=30.14 E-value=1.2e+02 Score=25.76 Aligned_cols=64 Identities=19% Similarity=0.215 Sum_probs=44.2
Q ss_pred HHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhh-cCCCccChhhHHhhhhh
Q 031569 18 KATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSR-EDKRTIAPEHVLKALEV 81 (157)
Q Consensus 18 ~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~-~~RKTI~~edVl~AL~~ 81 (157)
...+.+.|.+.+- .+.+|+.+|...|.+++.-=...+.++-..++.- .+.++|+.+||...+..
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 3333444443332 3789999999999999886555666666666664 44578999999877654
No 128
>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=29.85 E-value=94 Score=24.06 Aligned_cols=37 Identities=22% Similarity=0.217 Sum_probs=30.6
Q ss_pred CccChhhHHhhhhhcCch-----------hhHHHHHHHHHHHHHHhhh
Q 031569 68 RTIAPEHVLKALEVLGFG-----------EYIEEVYAAYEQHKLETMQ 104 (157)
Q Consensus 68 KTI~~edVl~AL~~LgF~-----------~yv~~l~~~l~~~k~~~k~ 104 (157)
-|.++.|++.+|+.+|++ .|+|.+.+..+.-+++++.
T Consensus 112 ~TT~~~~l~~~l~~l~~P~~~~~~~~l~~Rfip~l~~e~~~i~~Aq~a 159 (198)
T TIGR02454 112 LTTPFPELLSALRRLGVPPLLVEILLLTYRYLFVLLEELRRMLLAQRS 159 (198)
T ss_pred HcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999986 4788888888888888774
No 129
>PRK09492 treR trehalose repressor; Provisional
Probab=29.77 E-value=67 Score=26.09 Aligned_cols=38 Identities=11% Similarity=0.302 Sum_probs=30.0
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHh
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSS 56 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lss 56 (157)
..+-++||.|++.. .-+||.++++-|.+++.+. .|.-.
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 46778999999975 2479999999999998884 46543
No 130
>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=29.68 E-value=1e+02 Score=18.53 Aligned_cols=33 Identities=18% Similarity=0.433 Sum_probs=21.4
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHH
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEF 50 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eF 50 (157)
+.+..+||.++++. ...|+.+.+..|.+++.++
T Consensus 7 ~gvs~~tvs~~l~g----~~~vs~~~~~~i~~~~~~l 39 (52)
T cd01392 7 AGVSVATVSRVLNG----KPRVSEETRERVLAAAEEL 39 (52)
T ss_pred HCcCHHHHHHHHcC----CCCCCHHHHHHHHHHHHHh
Confidence 45677777777763 2357777777776666554
No 131
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=29.38 E-value=62 Score=28.56 Aligned_cols=33 Identities=24% Similarity=0.410 Sum_probs=26.7
Q ss_pred HHHHHHhhhHHHhhhcCCCccChhhHHhhhhhc
Q 031569 50 FINLVSSESNEVCSREDKRTIAPEHVLKALEVL 82 (157)
Q Consensus 50 FI~~lsseAneia~~~~RKTI~~edVl~AL~~L 82 (157)
=|.-|..+|...|..+++..|+.+|+..|++..
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~ 372 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKV 372 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 345566778888888899999999999998765
No 132
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=29.37 E-value=1e+02 Score=21.29 Aligned_cols=72 Identities=14% Similarity=0.135 Sum_probs=43.8
Q ss_pred hhHHHhhhcCCCccChhhHHhhhhhcCchhhHHHHHHHHHHHHHHhhhhhccCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q 031569 57 ESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYAAYEQHKLETMQDSLKGGKWSNGAEMTEEEAAAEQQRMFAEARA 136 (157)
Q Consensus 57 eAneia~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~~l~~~k~~~k~~r~kk~~k~~~~g~~eEel~~~Q~eLF~~ar~ 136 (157)
.+...+..++.-+|+.++|..+|..+|+.. +.+...+..+ .. -.+..++-+|.+.. =....
T Consensus 14 ~~F~~~D~d~~G~Is~~el~~~l~~~~~~~--~ev~~i~~~~---d~---------~~~g~I~~~eF~~~-----~~~~~ 74 (96)
T smart00027 14 QIFRSLDKNQDGTVTGAQAKPILLKSGLPQ--TLLAKIWNLA---DI---------DNDGELDKDEFALA-----MHLIY 74 (96)
T ss_pred HHHHHhCCCCCCeEeHHHHHHHHHHcCCCH--HHHHHHHHHh---cC---------CCCCCcCHHHHHHH-----HHHHH
Confidence 455666778888999999999999999863 2344433322 11 13345787777643 23344
Q ss_pred HHhCCCCCCCC
Q 031569 137 RMNGGAAGPPK 147 (157)
Q Consensus 137 ~~~~~~~~~~~ 147 (157)
++..|-..|+.
T Consensus 75 ~~~~g~~~~~~ 85 (96)
T smart00027 75 RKLNGYPIPAS 85 (96)
T ss_pred HHHcCCCCCcc
Confidence 55556655443
No 133
>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=28.72 E-value=1.2e+02 Score=28.75 Aligned_cols=71 Identities=17% Similarity=0.326 Sum_probs=44.5
Q ss_pred HHHHHHHHhhCCC-CccccHHHHHHHHHHH---HHHHHHHHhh-------hHHHhhhcCCCccChhhHHhhhhhcCchhh
Q 031569 19 ATMTKIIKEMLPA-DVRVARDAQDLLIECC---VEFINLVSSE-------SNEVCSREDKRTIAPEHVLKALEVLGFGEY 87 (157)
Q Consensus 19 A~V~riiKe~LP~-~~~iskdA~~~l~~c~---~eFI~~lsse-------Aneia~~~~RKTI~~edVl~AL~~LgF~~y 87 (157)
.-+..|++..+.. ++.++.++.++|.+++ ...++.|... +...+...++.+|+.+||.+++..--|..|
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 4578899999988765 3444444322 111233445668999999999988777766
Q ss_pred HH
Q 031569 88 IE 89 (157)
Q Consensus 88 v~ 89 (157)
..
T Consensus 436 ~~ 437 (615)
T TIGR02903 436 EK 437 (615)
T ss_pred hh
Confidence 53
No 134
>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=27.63 E-value=38 Score=21.31 Aligned_cols=16 Identities=25% Similarity=0.542 Sum_probs=14.1
Q ss_pred cChhhHHhhhhhcCch
Q 031569 70 IAPEHVLKALEVLGFG 85 (157)
Q Consensus 70 I~~edVl~AL~~LgF~ 85 (157)
+++++|..+++.+||+
T Consensus 47 ~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 47 TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp SCHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHhCcC
Confidence 6779999999999984
No 135
>PF13690 CheX: Chemotaxis phosphatase CheX; PDB: 3HM4_B 3H4Y_A 3H2D_A 3IIC_B.
Probab=27.55 E-value=1.3e+02 Score=20.88 Aligned_cols=46 Identities=9% Similarity=0.220 Sum_probs=34.6
Q ss_pred cccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHh
Q 031569 13 DASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSESNEVC 62 (157)
Q Consensus 13 d~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia 62 (157)
-+.+|+.+..++++. +..+ ..|.-+.+..+..||.+.|+.-+....
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 467899999999997 4433 344778889999999999998777554
No 136
>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=27.44 E-value=2.6e+02 Score=20.83 Aligned_cols=47 Identities=15% Similarity=0.119 Sum_probs=25.5
Q ss_pred chhhHHHHHHHHHHHHHHhhh-hhccCC----CCCCCCCCCHHHHHHHHHHH
Q 031569 84 FGEYIEEVYAAYEQHKLETMQ-DSLKGG----KWSNGAEMTEEEAAAEQQRM 130 (157)
Q Consensus 84 F~~yv~~l~~~l~~~k~~~k~-~r~kk~----~k~~~~g~~eEel~~~Q~eL 130 (157)
++.|...+.++|.--+..... +|-|+. ......|++.++-++.|--|
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 446666666666543322111 222222 12223689999999999654
No 137
>KOG1792 consensus Reticulon [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.38 E-value=97 Score=26.04 Aligned_cols=63 Identities=19% Similarity=0.187 Sum_probs=50.8
Q ss_pred hCCCCccccHHHHHHHHHHHHHHHHHHHhhhHHH-hhhcCCCccChhhHHhhhhhcC-chhhHHH
Q 031569 28 MLPADVRVARDAQDLLIECCVEFINLVSSESNEV-CSREDKRTIAPEHVLKALEVLG-FGEYIEE 90 (157)
Q Consensus 28 ~LP~~~~iskdA~~~l~~c~~eFI~~lsseAnei-a~~~~RKTI~~edVl~AL~~Lg-F~~yv~~ 90 (157)
.+|.++.++++....+..++++-|+..+++.+++ |.++-+.-+...=.++.+.-+| +-+++.-
T Consensus 110 ~lp~~i~ipee~~~~~a~~~~~~in~~l~~l~~ia~~~d~~~~lk~~v~lw~lS~vGs~fn~lTl 174 (230)
T KOG1792|consen 110 YLPVEITIPEEFVLALASSLRVEINQALSELRDIALGRDLKDFLKVAVGLWILSYVGSLFNFLTL 174 (230)
T ss_pred cCCceeecCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhhhHHHH
Confidence 5777899999999999999999999999999999 5566666566666788888888 4444433
No 138
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=27.25 E-value=84 Score=25.68 Aligned_cols=36 Identities=17% Similarity=0.278 Sum_probs=28.0
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHH
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEF 50 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eF 50 (157)
...-++||.|++... |...+||.++++-|.+++.+.
T Consensus 10 aGVS~~TVSrvLn~~-~~~~~Vs~~tr~rV~~~a~el 45 (328)
T PRK11303 10 AGVSRTTASYVINGK-AKQYRVSDKTVEKVMAVVREH 45 (328)
T ss_pred hCCCHHHHHHHHcCC-CCCCCcCHHHHHHHHHHHHHh
Confidence 356789999999753 111379999999999999884
No 139
>PF03130 HEAT_PBS: PBS lyase HEAT-like repeat; InterPro: IPR004155 These proteins contain a short bi-helical repeat that is related to HEAT. Cyanobacteria and red algae harvest light energy using macromolecular complexes known as phycobilisomes (PBS), peripherally attached to the photosynthetic membrane. The major components of PBS are the phycobiliproteins. These heterodimeric proteins are covalently attached to phycobilins: open-chain tetrapyrrole chromophores, which function as the photosynthetic light-harvesting pigments. Phycobiliproteins differ in sequence and in the nature and number of attached phycobilins to each of their subunits. These proteins include the lyase enzymes that specifically attach particular phycobilins to apophycobiliprotein subunits. The most comprehensively studied of these is the CpcE/Flyase P31967 from SWISSPROT, P31968 from SWISSPROT, which attaches phycocyanobilin (PCB) to the alpha subunit of apophycocyanin []. Similarly, MpeU/V attaches phycoerythrobilin to phycoerythrin II, while CpeY/Z is thought to be involved in phycoerythrobilin (PEB) attachment to phycoerythrin (PE) I (PEs I and II differ in sequence and in the number of attached molecules of PEB: PE I has five, PE II has six) []. All the reactions of the above lyases involve an apoprotein cysteine SH addition to a terminal delta 3,3'-double bond. Such a reaction is not possible in the case of phycoviolobilin (PVB), the phycobilin of alpha-phycoerythrocyanin (alpha-PEC). It is thought that in this case, PCB, not PVB, is first added to apo-alpha-PEC, and is then isomerized to PVB. The addition reaction has been shown to occur in the presence of either of the components of alpha-PEC-PVB lyase PecE or PecF (or both). The isomerisation reaction occurs only when both PecE and PecF components are present, i.e. the PecE/F phycobiliprotein lyase is also a phycobilin isomerase []. Another member of this family is the NblB protein, whose similarity to the phycobiliprotein lyases was previously noted []. This constitutively expressed protein is not known to have any lyase activity. It is thought to be involved in the coordination of PBS degradation with environmental nutrient limitation. It has been suggested that the similarity of NblB to the phycobiliprotein lyases is due to the ability to bind tetrapyrrole phycobilins via the common repeated motif [].; PDB: 1TE4_A.
Probab=27.24 E-value=1e+02 Score=16.77 Aligned_cols=23 Identities=26% Similarity=0.273 Sum_probs=18.4
Q ss_pred HHhhhhhcCchhhHHHHHHHHHH
Q 031569 75 VLKALEVLGFGEYIEEVYAAYEQ 97 (157)
Q Consensus 75 Vl~AL~~LgF~~yv~~l~~~l~~ 97 (157)
...||-.+|-...++.|.+.|++
T Consensus 5 Aa~aLg~igd~~ai~~L~~~L~d 27 (27)
T PF03130_consen 5 AARALGQIGDPRAIPALIEALED 27 (27)
T ss_dssp HHHHHGGG-SHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCHHHHHHHHHHhcC
Confidence 46789999999999999888764
No 140
>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=27.20 E-value=22 Score=24.68 Aligned_cols=61 Identities=11% Similarity=0.120 Sum_probs=29.0
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHHHHHH
Q 031569 32 DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYA 93 (157)
Q Consensus 32 ~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~ 93 (157)
++|++.+.+++|.+++..--.-+|.-....+...-+.+|.-..+ --|..-+|..|+.-|..
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~-~~Ls~~~~~~f~~aLd~ 63 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHER-IRLSAEDFEAFMAALDN 63 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHH-HHHCCHHHHHHHHHHH-
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcce-eEcCHHHHHHHHHHHhC
Confidence 47899999999999986432222222222222222333332222 33455555555555443
No 141
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=26.68 E-value=1e+02 Score=28.41 Aligned_cols=53 Identities=19% Similarity=0.381 Sum_probs=44.3
Q ss_pred hhCCCCccccHHHHHHHHHHHHHHHH-------HHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 27 EMLPADVRVARDAQDLLIECCVEFIN-------LVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 27 e~LP~~~~iskdA~~~l~~c~~eFI~-------~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
+.|| .+.++.++...+.+.|..+-. .+...|..++.-.||.+++.+||-.|+.
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 4677888899999999999999988864
No 142
>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=26.68 E-value=2.4e+02 Score=23.64 Aligned_cols=62 Identities=16% Similarity=0.195 Sum_probs=34.1
Q ss_pred HHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 18 KATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 18 ~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
...+..+++..+- .++.|+.++...|.+.+.--...+-.+....+...+ +.|+.+||-.++.
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 257788888888877664433333333333333223 3488887765543
No 143
>COG1422 Predicted membrane protein [Function unknown]
Probab=26.58 E-value=41 Score=27.94 Aligned_cols=18 Identities=6% Similarity=-0.051 Sum_probs=9.7
Q ss_pred hhHHHHHHHHHHHHHHhh
Q 031569 86 EYIEEVYAAYEQHKLETM 103 (157)
Q Consensus 86 ~yv~~l~~~l~~~k~~~k 103 (157)
.+-..+++.-++++++++
T Consensus 76 ~~qk~m~efq~e~~eA~~ 93 (201)
T COG1422 76 ELQKMMKEFQKEFREAQE 93 (201)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 444455555555665544
No 144
>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=26.56 E-value=2.4e+02 Score=27.86 Aligned_cols=60 Identities=18% Similarity=0.272 Sum_probs=50.1
Q ss_pred CCCCccccHHHHHHHHHHHH--HHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhH
Q 031569 29 LPADVRVARDAQDLLIECCV--EFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYI 88 (157)
Q Consensus 29 LP~~~~iskdA~~~l~~c~~--eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv 88 (157)
.|+++.+-+-|=+++..-.= =||-|+|..=...|..+|+.+++-+-|++.+-.=.|.++.
T Consensus 588 ~pG~~~Frr~afeLlg~~GYe~Gfv~Y~SNkyk~~A~~~g~~~l~D~~ii~Ki~~g~y~s~~ 649 (737)
T PF07580_consen 588 APGDLMFRRNAFELLGYYGYEDGFVPYASNKYKKEAKAEGKKILSDDYIIKKIFNGQYNSWE 649 (737)
T ss_pred CCccchhhHHHHHHHHHhcccccchHhhhhhHHHHHHhcCCCcccHHHHHHHHhcCccCCHH
Confidence 45677788888888877653 4999999999999999999999999999999877776643
No 145
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=26.55 E-value=2.2e+02 Score=21.78 Aligned_cols=50 Identities=14% Similarity=0.230 Sum_probs=41.8
Q ss_pred CCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 30 PADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 30 P~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
.+.+.=..|+.++|.+...-+++.+-..|..+|...+ .+..||..-||+.
T Consensus 23 GDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~rn--K~k~eDfkfaLr~ 72 (126)
T COG5248 23 GDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRN--KTKTEDFKFALRR 72 (126)
T ss_pred CCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcc--cchHHHHHHHHhh
Confidence 4566778899999999999999999999999998444 3677899988865
No 146
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=26.36 E-value=2e+02 Score=25.02 Aligned_cols=65 Identities=12% Similarity=0.093 Sum_probs=34.7
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
++...+..+++..+. .++.++.++...|.+.+.-=+..+-......+.. ++..|+.++|.+++..
T Consensus 178 l~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s~G~~R~al~~l~~~~~~-~~~~It~~~v~~~l~~ 243 (363)
T PRK14961 178 ISEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLEHAINL-GKGNINIKNVTDMLGL 243 (363)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh-cCCCCCHHHHHHHHCC
Confidence 334445555544332 2577888888887766532111111111112222 4667999999886653
No 147
>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=26.09 E-value=92 Score=25.50 Aligned_cols=39 Identities=13% Similarity=0.265 Sum_probs=28.7
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHH
Q 031569 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVS 55 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~ls 55 (157)
..-++||.|++... |...+||.++++-|.+++.+ +.|.-
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 35689999999753 11137999999999999887 34443
No 148
>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=26.06 E-value=1e+02 Score=19.02 Aligned_cols=34 Identities=12% Similarity=0.248 Sum_probs=24.7
Q ss_pred HHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhh
Q 031569 24 IIKEMLPADVRVARDAQDLLIECCVEFINLVSSE 57 (157)
Q Consensus 24 iiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsse 57 (157)
.++..+|......+-.+..|...+..||.+|...
T Consensus 25 ~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~ 58 (60)
T cd00083 25 ELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQEL 58 (60)
T ss_pred HHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 3456677654466666788888889999998754
No 149
>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=25.66 E-value=1.1e+02 Score=23.77 Aligned_cols=37 Identities=16% Similarity=0.266 Sum_probs=30.9
Q ss_pred CccChhhHHhhhhhcCchh------------hHHHHHHHHHHHHHHhhh
Q 031569 68 RTIAPEHVLKALEVLGFGE------------YIEEVYAAYEQHKLETMQ 104 (157)
Q Consensus 68 KTI~~edVl~AL~~LgF~~------------yv~~l~~~l~~~k~~~k~ 104 (157)
.|.+++|++.+|+.++++. |+|.+.+....-+++++.
T Consensus 123 ~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A~~~ 171 (224)
T PF02361_consen 123 LTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREAQRL 171 (224)
T ss_pred HHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999887 888888888877777663
No 150
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=24.53 E-value=81 Score=28.25 Aligned_cols=31 Identities=19% Similarity=0.326 Sum_probs=26.3
Q ss_pred HHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 51 INLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 51 I~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
|..|..+|...|...++..|+.+|+..|++.
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~ 385 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKT 385 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHH
Confidence 5667788888888999999999999999765
No 151
>KOG0188 consensus Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=24.38 E-value=6.7e+02 Score=25.31 Aligned_cols=67 Identities=15% Similarity=0.278 Sum_probs=48.1
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHhh---hHHHhhh-cCCCccChhhHHhhhhhcCchh
Q 031569 20 TMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSSE---SNEVCSR-EDKRTIAPEHVLKALEVLGFGE 86 (157)
Q Consensus 20 ~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lsse---Aneia~~-~~RKTI~~edVl~AL~~LgF~~ 86 (157)
+|.-.|.++.|+=-+=+...+++|.+==..|..-|.+- -...+.. .+-+||.++++..--+..||+-
T Consensus 338 vvv~~lgd~fPEl~~~~~~v~diineEE~~F~ktl~rg~~~f~r~~~~~~~s~tipGd~~w~LydTyGfPv 408 (895)
T KOG0188|consen 338 VVVETLGDAFPELKRDPQHVIDIINEEEAQFLKTLDRGRKLFDRVARELGSSKTIPGDVAWRLYDTYGFPV 408 (895)
T ss_pred HHHHHHhhhchhhhcCHHHHHHHhcHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchHHHHHHHhhcCCcH
Confidence 45556667777555566777888888888888888765 2222333 3358999999999999999983
No 152
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=24.06 E-value=2.2e+02 Score=27.10 Aligned_cols=64 Identities=13% Similarity=0.132 Sum_probs=40.3
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
++...+.+.++..+. .++.|+.++..+|.+.+.--+..+.++....+.. +...|+.+||...+.
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 444455555554433 3688999999999888765555555554443333 345699998876653
No 153
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=23.87 E-value=1.3e+02 Score=25.97 Aligned_cols=53 Identities=21% Similarity=0.272 Sum_probs=43.9
Q ss_pred CcccccCcHHHHHHHHHhhCCC-----Ccc-ccHHHHHHHHHHHHHHHHHHHhhhHHHh
Q 031569 10 SKEDASLPKATMTKIIKEMLPA-----DVR-VARDAQDLLIECCVEFINLVSSESNEVC 62 (157)
Q Consensus 10 ~~dd~~LP~A~V~riiKe~LP~-----~~~-iskdA~~~l~~c~~eFI~~lsseAneia 62 (157)
+++.+..|.+++.|-|.+.+.. +++ ++|-.+.+....|.+|..|+-.-+|-.+
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 4677789999999999999864 444 8999999999999999999887766543
No 154
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=23.74 E-value=2.4e+02 Score=27.95 Aligned_cols=61 Identities=13% Similarity=0.144 Sum_probs=34.6
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHH
Q 031569 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVL 76 (157)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl 76 (157)
|+...|.+++++.+- .++.|++++..+|.+.+.-=+..+-++...++...+...|+.+||.
T Consensus 179 l~~~~l~~~L~~il~~EGv~id~eal~lLa~~sgGdlR~Al~eLEKLia~~~~~~IT~e~V~ 240 (824)
T PRK07764 179 VPPEVMRGYLERICAQEGVPVEPGVLPLVIRAGGGSVRDSLSVLDQLLAGAGPEGVTYERAV 240 (824)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCCHHHHH
Confidence 456666666666553 3678888888887776544333333333333333334457666544
No 155
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=23.70 E-value=2.8e+02 Score=23.65 Aligned_cols=60 Identities=12% Similarity=0.127 Sum_probs=41.4
Q ss_pred HHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 20 TMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 20 ~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
-+.+.|.+.+- .+..|+.+|...|...+.-=...+.+|--..+.-.+ +|+.+||-..+..
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 33444443332 378999999999999887656666666666665533 7999999887643
No 156
>KOG0784 consensus Isocitrate dehydrogenase, gamma subunit [Amino acid transport and metabolism]
Probab=23.40 E-value=51 Score=29.77 Aligned_cols=46 Identities=13% Similarity=0.246 Sum_probs=36.7
Q ss_pred HHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHHHHHHHHHHH
Q 031569 52 NLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIEEVYAAYEQH 98 (157)
Q Consensus 52 ~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~~l~~~l~~~ 98 (157)
.-|+..|.+.|.+.+||.+++=|=-. .-.||=+-|++.+.++...|
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 34667899999999999999988766 34688888998888876544
No 157
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=23.11 E-value=1.5e+02 Score=20.57 Aligned_cols=24 Identities=25% Similarity=0.558 Sum_probs=18.5
Q ss_pred ccCcHHHHHHHHHhh-CCCCccccH
Q 031569 14 ASLPKATMTKIIKEM-LPADVRVAR 37 (157)
Q Consensus 14 ~~LP~A~V~riiKe~-LP~~~~isk 37 (157)
+.|-++||+|+|++. +|..+++.-
T Consensus 23 ~GlSrstiYr~i~~~~FPkpvklG~ 47 (70)
T COG3311 23 TGLSRSTIYRLIKDGTFPKPVKLGG 47 (70)
T ss_pred HCccHHHHHHHHccCCCCCCeecCc
Confidence 467899999999965 677666663
No 158
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=22.35 E-value=1.6e+02 Score=21.16 Aligned_cols=36 Identities=28% Similarity=0.329 Sum_probs=24.9
Q ss_pred hcCCCccChhhHHhhhhhcCchhhHHHHHHHHHHHH
Q 031569 64 REDKRTIAPEHVLKALEVLGFGEYIEEVYAAYEQHK 99 (157)
Q Consensus 64 ~~~RKTI~~edVl~AL~~LgF~~yv~~l~~~l~~~k 99 (157)
...-|||-|.+|-.||..-+|-++.+.+......--
T Consensus 19 R~~~ktiCPSevARal~~~~WR~lm~~vR~~A~~L~ 54 (83)
T PF11625_consen 19 RGPGKTICPSEVARALGPDDWRDLMPPVRAAARRLA 54 (83)
T ss_dssp S-TT--B-HHHHHHHH-TTS-GGGHHHHHHHHHHHH
T ss_pred cCCCCccCHHHHHHHHCchhhHHHHHHHHHHHHHHH
Confidence 445699999999999988889999999988776543
No 159
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=21.96 E-value=2.4e+02 Score=26.19 Aligned_cols=64 Identities=9% Similarity=0.149 Sum_probs=37.6
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhh
Q 031569 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALE 80 (157)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~ 80 (157)
++...+.+.++..+- .++.|+.++..+|.+.+.-=+..+-+.-...+...+ .+|+.++|...|.
T Consensus 175 l~~~el~~~L~~ia~~Egi~i~~eAL~lIa~~s~GslR~alslLdqli~y~~-~~It~e~V~~llg 239 (491)
T PRK14964 175 IPTDKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNALFLLEQAAIYSN-NKISEKSVRDLLG 239 (491)
T ss_pred ccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcC-CCCCHHHHHHHHc
Confidence 344444444444332 478899999999988774333333333333333333 4799999877653
No 160
>PRK05907 hypothetical protein; Provisional
Probab=21.94 E-value=1.9e+02 Score=25.04 Aligned_cols=54 Identities=7% Similarity=0.041 Sum_probs=39.7
Q ss_pred CccccHHHHHHHHHHHH-HHHHHHHhhhHHHhhh-cCCCccChhhHHhhhh-hcCch
Q 031569 32 DVRVARDAQDLLIECCV-EFINLVSSESNEVCSR-EDKRTIAPEHVLKALE-VLGFG 85 (157)
Q Consensus 32 ~~~iskdA~~~l~~c~~-eFI~~lsseAneia~~-~~RKTI~~edVl~AL~-~LgF~ 85 (157)
+.+|+.+|...+.+.+. -=+..+..|-...|.- ..+++|+.+||-..+. .+.+.
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 78999999999998773 3445666666666665 6688999999987743 34544
No 161
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=21.93 E-value=1.1e+02 Score=25.38 Aligned_cols=37 Identities=16% Similarity=0.359 Sum_probs=29.5
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHH
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVS 55 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~ls 55 (157)
...-++||.|++... -.||.++++-|.+++.+. .|.-
T Consensus 11 aGVS~~TVSrvLn~~----~~Vs~~tr~kV~~~a~el-gY~p 47 (346)
T PRK10401 11 AGVSVATVSRVLNNS----ALVSADTREAVMKAVSEL-GYRP 47 (346)
T ss_pred hCCCHHHHHHHHCCC----CCCCHHHHHHHHHHHHHH-CCCC
Confidence 356789999999752 369999999999999885 4653
No 162
>cd04750 Commd2 COMM_Domain containing protein 2. 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=21.80 E-value=4e+02 Score=20.88 Aligned_cols=34 Identities=24% Similarity=0.437 Sum_probs=25.2
Q ss_pred CCccChhhHHhhhhhcCch-hhHHHHHHHHHHHHH
Q 031569 67 KRTIAPEHVLKALEVLGFG-EYIEEVYAAYEQHKL 100 (157)
Q Consensus 67 RKTI~~edVl~AL~~LgF~-~yv~~l~~~l~~~k~ 100 (157)
|..++.+++..-|..|||+ +.+..+...+.+++.
T Consensus 49 K~~l~~~~~~~~L~~l~~~~e~~~~l~~~y~~~~~ 83 (166)
T cd04750 49 KLKLSERDFQDSIEFLGFSDDLNEILLQLYESNRK 83 (166)
T ss_pred hccCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 4459999999999999998 455556666655553
No 163
>KOG0093 consensus GTPase Rab3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.53 E-value=53 Score=26.76 Aligned_cols=52 Identities=13% Similarity=0.213 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHHHHHHh-----hhHHHhhhcCCCccChhhHHhhhhhcCchhhH
Q 031569 37 RDAQDLLIECCVEFINLVSS-----ESNEVCSREDKRTIAPEHVLKALEVLGFGEYI 88 (157)
Q Consensus 37 kdA~~~l~~c~~eFI~~lss-----eAneia~~~~RKTI~~edVl~AL~~LgF~~yv 88 (157)
.+.-..++.-++..-+|-=. -+-..|.-+..++|+.|.+..-.++|||+-|-
T Consensus 106 eeSf~svqdw~tqIktysw~naqvilvgnKCDmd~eRvis~e~g~~l~~~LGfefFE 162 (193)
T KOG0093|consen 106 EESFNSVQDWITQIKTYSWDNAQVILVGNKCDMDSERVISHERGRQLADQLGFEFFE 162 (193)
T ss_pred HHHHHHHHHHHHHheeeeccCceEEEEecccCCccceeeeHHHHHHHHHHhChHHhh
Confidence 44555666666554444111 12346888889999999999999999995443
No 164
>PRK05629 hypothetical protein; Validated
Probab=21.35 E-value=2.6e+02 Score=23.63 Aligned_cols=50 Identities=16% Similarity=0.115 Sum_probs=37.9
Q ss_pred CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhh
Q 031569 31 ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEV 81 (157)
Q Consensus 31 ~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~ 81 (157)
.+.+|+.+|.+.|..++..=...+.++--..|... ..+|+.+||-..+..
T Consensus 142 ~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~-~~~It~e~V~~~v~~ 191 (318)
T PRK05629 142 HGVRPTPDVVHALLEGVGSDLRELASAISQLVEDT-QGNVTVEKVRAYYVG 191 (318)
T ss_pred cCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcC-CCCcCHHHHHHHhCC
Confidence 37899999999999988776666777666666543 457999999776443
No 165
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=21.23 E-value=52 Score=21.94 Aligned_cols=17 Identities=47% Similarity=0.876 Sum_probs=12.3
Q ss_pred ccChhhHHhhhhhcCch
Q 031569 69 TIAPEHVLKALEVLGFG 85 (157)
Q Consensus 69 TI~~edVl~AL~~LgF~ 85 (157)
.|+.++|...|+.|||.
T Consensus 18 ~i~~~~i~~~L~~lg~~ 34 (70)
T PF03484_consen 18 DISPEEIIKILKRLGFK 34 (70)
T ss_dssp ---HHHHHHHHHHTT-E
T ss_pred CCCHHHHHHHHHHCCCE
Confidence 68999999999999996
No 166
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=21.14 E-value=2.5e+02 Score=24.12 Aligned_cols=51 Identities=16% Similarity=0.242 Sum_probs=41.3
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhc
Q 031569 32 DVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVL 82 (157)
Q Consensus 32 ~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~L 82 (157)
+++|++||.+.|..+..-=...+.++-+..+--.+-++|+.+||..++-.-
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 167
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=21.14 E-value=1.7e+02 Score=26.82 Aligned_cols=59 Identities=17% Similarity=0.246 Sum_probs=44.2
Q ss_pred CCCCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCchhhHH
Q 031569 29 LPADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGFGEYIE 89 (157)
Q Consensus 29 LP~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF~~yv~ 89 (157)
|++..++|.+++..|.+.|++ ..|= ..|..+-...+...||.+-|..+++.+|+....+
T Consensus 112 l~~~~R~S~~~~~~i~~~a~~-~sYr-~aa~~l~~~~~~~~iS~~tV~~~v~~~g~~~~~~ 170 (470)
T PF06782_consen 112 LKKYQRISPELKEKIVELATE-MSYR-KAAEILEELLGNVSISKQTVWNIVKEAGFEEIKE 170 (470)
T ss_pred CCcccchhHHHHHHHHHHHhh-cCHH-HHHHHHhhccCCCccCHHHHHHHHHhccchhhhc
Confidence 456789999999999999888 4443 2233333556778999999999999999754433
No 168
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=21.09 E-value=3e+02 Score=23.54 Aligned_cols=66 Identities=14% Similarity=0.171 Sum_probs=36.8
Q ss_pred HHHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCc
Q 031569 18 KATMTKIIKEMLP-ADVRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRTIAPEHVLKALEVLGF 84 (157)
Q Consensus 18 ~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF 84 (157)
...+..++.+.+- .++.|+.++.+.|.+-+.-=+..+-.+-...+.-.++. |+.+||...+.....
T Consensus 169 ~~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~gdlr~~~~~lekl~~y~~~~-it~~~v~~~~~~~~~ 235 (367)
T PRK14970 169 IKDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFDRVVTFCGKN-ITRQAVTENLNILDY 235 (367)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHhCCCCH
Confidence 4555555544332 36789999999887755432333333333333332333 888887777665543
No 169
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.94 E-value=3.3e+02 Score=25.23 Aligned_cols=64 Identities=19% Similarity=0.252 Sum_probs=36.6
Q ss_pred CcHHHHHHHHHhhCC-CCccccHHHHHHHHHHHHH----HHHHHHhhhHHHhhhcCCCccChhhHHhhhhhcCc
Q 031569 16 LPKATMTKIIKEMLP-ADVRVARDAQDLLIECCVE----FINLVSSESNEVCSREDKRTIAPEHVLKALEVLGF 84 (157)
Q Consensus 16 LP~A~V~riiKe~LP-~~~~iskdA~~~l~~c~~e----FI~~lsseAneia~~~~RKTI~~edVl~AL~~LgF 84 (157)
||...|.+.++..+- .++.+++++...|.+.+.- .+++|-. + ++- +...|+.+||...+....-
T Consensus 178 l~~~~i~~~l~~il~~egi~~~~~al~~ia~~s~GslR~al~lLdq-~--ia~--~~~~It~~~V~~~lg~~~~ 246 (509)
T PRK14958 178 LPPLQIAAHCQHLLKEENVEFENAALDLLARAANGSVRDALSLLDQ-S--IAY--GNGKVLIADVKTMLGTIEP 246 (509)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHH-H--Hhc--CCCCcCHHHHHHHHCCCCH
Confidence 555555554444442 3678999998888776542 3333321 1 122 3456888888776644443
No 170
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=20.73 E-value=65 Score=23.07 Aligned_cols=23 Identities=13% Similarity=0.443 Sum_probs=17.8
Q ss_pred hcCchhhHHHHHHHHHHHHHHhh
Q 031569 81 VLGFGEYIEEVYAAYEQHKLETM 103 (157)
Q Consensus 81 ~LgF~~yv~~l~~~l~~~k~~~k 103 (157)
-+||++|+.-+.+-.-+|.....
T Consensus 34 L~GFDd~VNmvLeDvtEye~~~e 56 (84)
T KOG1775|consen 34 LVGFDDFVNMVLEDVTEYEITPE 56 (84)
T ss_pred EechHHHHHHHHHhhhheeeCCC
Confidence 47999999998888777764433
No 171
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=20.70 E-value=1.5e+02 Score=27.93 Aligned_cols=37 Identities=14% Similarity=0.212 Sum_probs=28.9
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHhhhHHHhhhcCCCc
Q 031569 33 VRVARDAQDLLIECCVEFINLVSSESNEVCSREDKRT 69 (157)
Q Consensus 33 ~~iskdA~~~l~~c~~eFI~~lsseAneia~~~~RKT 69 (157)
--|-+|.+.+|++||...=.||+..-...-...++++
T Consensus 438 ~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~k~~~ 474 (535)
T PRK04184 438 PEIEKEIRLALQEVARKLKKYLSRKRKEEEAKKKAKT 474 (535)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3478899999999999999999986665555555544
No 172
>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=20.64 E-value=1.3e+02 Score=24.58 Aligned_cols=37 Identities=11% Similarity=0.236 Sum_probs=29.2
Q ss_pred cCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHh
Q 031569 15 SLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSS 56 (157)
Q Consensus 15 ~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lss 56 (157)
.+-.+||.|++... -+||.++++-|.+++.+. .|.-.
T Consensus 12 gvS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l-gY~pn 48 (329)
T TIGR01481 12 GVSMATVSRVVNGN----PNVKPATRKKVLEVIKRL-DYRPN 48 (329)
T ss_pred CCCHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCCC
Confidence 56789999999753 479999999999999884 45443
No 173
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=20.26 E-value=1.2e+02 Score=24.90 Aligned_cols=40 Identities=18% Similarity=0.409 Sum_probs=30.5
Q ss_pred ccCcHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHh
Q 031569 14 ASLPKATMTKIIKEMLPADVRVARDAQDLLIECCVEFINLVSS 56 (157)
Q Consensus 14 ~~LP~A~V~riiKe~LP~~~~iskdA~~~l~~c~~eFI~~lss 56 (157)
..+-++||.|++... | ..+||.++++-|.+++.+. .|.-+
T Consensus 11 agVS~~TVSrvln~~-~-~~~vs~~tr~rV~~~a~~l-gY~pn 50 (327)
T PRK10339 11 AGVSLATVSRVLNDD-P-TLNVKEETKHRILEIAEKL-EYKTS 50 (327)
T ss_pred hCCCHHhhhhhhcCC-C-CCCcCHHHHHHHHHHHHHh-CCCCc
Confidence 356789999999753 3 3579999999999999885 44433
No 174
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=20.23 E-value=78 Score=19.61 Aligned_cols=19 Identities=11% Similarity=0.350 Sum_probs=14.0
Q ss_pred ccccCcHHHHHHHHHhhCC
Q 031569 12 EDASLPKATMTKIIKEMLP 30 (157)
Q Consensus 12 dd~~LP~A~V~riiKe~LP 30 (157)
..+.+|++|+.+-++...|
T Consensus 24 ~~ygVp~sTL~~r~~g~~~ 42 (45)
T PF05225_consen 24 KKYGVPRSTLRRRLRGKPS 42 (45)
T ss_dssp HHHT--HHHHHHHHHHTTT
T ss_pred HHHCcCHHHHHHHHcCCCC
Confidence 4678999999999987655
Done!