Query 030812
Match_columns 171
No_of_seqs 163 out of 596
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 04:56:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030812.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030812hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0869 CCAAT-binding factor, 100.0 1.1E-42 2.3E-47 279.1 15.7 129 1-130 1-130 (168)
2 KOG0871 Class 2 transcription 100.0 2.9E-28 6.2E-33 194.2 9.6 96 26-121 6-101 (156)
3 KOG0870 DNA polymerase epsilon 99.9 5.8E-26 1.3E-30 183.7 9.0 103 25-127 3-106 (172)
4 COG5150 Class 2 transcription 99.9 2E-22 4.3E-27 158.0 9.8 97 26-122 5-101 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 8.4E-19 1.8E-23 120.5 7.9 64 32-96 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.7 1.2E-17 2.5E-22 124.2 6.8 79 25-105 12-90 (91)
7 cd00076 H4 Histone H4, one of 99.2 4.2E-11 9.2E-16 88.0 8.5 72 31-104 12-83 (85)
8 PLN00035 histone H4; Provision 99.2 7E-11 1.5E-15 89.7 8.6 77 26-104 23-99 (103)
9 PTZ00015 histone H4; Provision 99.2 2.2E-10 4.7E-15 86.9 8.6 77 26-104 24-100 (102)
10 smart00803 TAF TATA box bindin 99.0 1.5E-09 3.2E-14 75.9 7.6 64 32-97 2-65 (65)
11 smart00417 H4 Histone H4. 99.0 1.4E-09 3E-14 78.2 6.0 63 31-95 12-74 (74)
12 smart00428 H3 Histone H3. 99.0 2.3E-09 5E-14 81.6 7.2 74 26-99 23-101 (105)
13 PF00125 Histone: Core histone 98.9 3.9E-09 8.5E-14 73.5 6.6 68 30-97 3-73 (75)
14 cd07981 TAF12 TATA Binding Pro 98.9 1.3E-08 2.7E-13 72.1 8.5 65 33-98 2-66 (72)
15 COG5208 HAP5 CCAAT-binding fac 98.8 2.7E-09 5.7E-14 91.0 4.2 78 28-107 105-183 (286)
16 PLN00160 histone H3; Provision 98.6 1.3E-07 2.7E-12 71.3 6.7 72 26-97 15-90 (97)
17 KOG1657 CCAAT-binding factor, 98.6 6.6E-08 1.4E-12 82.6 5.8 86 29-115 71-159 (236)
18 PLN00161 histone H3; Provision 98.6 1.7E-07 3.7E-12 74.3 7.6 71 27-97 50-124 (135)
19 PLN00121 histone H3; Provision 98.6 1E-07 2.2E-12 75.7 6.1 71 27-97 57-130 (136)
20 PTZ00018 histone H3; Provision 98.6 1.3E-07 2.8E-12 75.1 6.0 71 27-97 57-130 (136)
21 smart00576 BTP Bromodomain tra 98.4 2.8E-06 6.1E-11 60.4 8.3 66 35-102 9-74 (77)
22 cd00074 H2A Histone 2A; H2A is 98.4 1.4E-06 3E-11 67.3 7.0 68 30-98 18-85 (115)
23 cd07979 TAF9 TATA Binding Prot 98.2 2.6E-05 5.7E-10 60.0 10.3 79 37-117 6-85 (117)
24 cd08050 TAF6 TATA Binding Prot 97.9 5.5E-05 1.2E-09 67.2 8.4 67 34-102 1-67 (343)
25 PF15630 CENP-S: Kinetochore c 97.9 5.5E-05 1.2E-09 54.6 6.7 61 37-97 10-71 (76)
26 smart00427 H2B Histone H2B. 97.9 7.8E-05 1.7E-09 55.5 7.7 62 37-99 6-67 (89)
27 PF15511 CENP-T: Centromere ki 97.8 3.2E-05 7E-10 70.5 6.3 65 27-91 346-414 (414)
28 KOG1745 Histones H3 and H4 [Ch 97.8 1.3E-05 2.8E-10 63.8 2.6 75 26-100 57-134 (137)
29 PF03847 TFIID_20kDa: Transcri 97.7 0.00027 5.8E-09 49.9 7.3 63 35-98 2-64 (68)
30 PLN00158 histone H2B; Provisio 97.6 0.00027 5.8E-09 55.0 7.7 65 34-99 29-93 (116)
31 KOG1142 Transcription initiati 97.6 0.00029 6.2E-09 61.3 8.2 70 28-98 150-219 (258)
32 PTZ00463 histone H2B; Provisio 97.6 0.00034 7.4E-09 54.5 7.7 62 37-99 33-94 (117)
33 PF07524 Bromo_TP: Bromodomain 97.6 0.00067 1.5E-08 47.8 8.5 64 37-102 11-74 (77)
34 KOG3467 Histone H4 [Chromatin 97.6 0.00037 8E-09 52.3 7.3 69 32-102 29-97 (103)
35 KOG1659 Class 2 transcription 97.5 0.00028 6E-09 60.0 6.8 84 31-115 12-95 (224)
36 cd08048 TAF11 TATA Binding Pro 97.5 0.00074 1.6E-08 49.6 8.0 66 32-99 16-84 (85)
37 PF09415 CENP-X: CENP-S associ 97.5 0.00018 3.8E-09 51.4 4.2 65 34-98 1-67 (72)
38 COG5262 HTA1 Histone H2A [Chro 97.3 0.00048 1E-08 54.1 5.5 68 29-97 23-90 (132)
39 COG5247 BUR6 Class 2 transcrip 97.3 0.0011 2.5E-08 50.8 7.2 81 29-110 20-100 (113)
40 PF04719 TAFII28: hTAFII28-lik 97.2 0.0022 4.8E-08 47.8 7.3 67 32-99 23-90 (90)
41 PF02969 TAF: TATA box binding 97.2 0.0033 7.1E-08 44.3 7.8 64 32-97 3-66 (66)
42 smart00414 H2A Histone 2A. 97.1 0.0015 3.2E-08 49.9 6.2 68 30-98 7-74 (106)
43 PLN00154 histone H2A; Provisio 97.0 0.0048 1E-07 49.2 7.9 69 30-98 36-104 (136)
44 KOG1658 DNA polymerase epsilon 96.8 0.00075 1.6E-08 55.0 2.0 67 30-98 57-124 (162)
45 PTZ00017 histone H2A; Provisio 96.7 0.0035 7.7E-08 49.8 5.6 67 30-97 25-91 (134)
46 KOG1744 Histone H2B [Chromatin 96.6 0.0085 1.8E-07 47.3 6.9 69 26-98 34-102 (127)
47 PF15510 CENP-W: Centromere ki 96.4 0.0067 1.5E-07 45.8 5.0 67 31-98 15-95 (102)
48 PLN00157 histone H2A; Provisio 96.4 0.0072 1.6E-07 48.0 5.2 67 30-97 24-90 (132)
49 PLN00153 histone H2A; Provisio 96.3 0.0087 1.9E-07 47.4 5.5 67 30-97 22-88 (129)
50 KOG1756 Histone 2A [Chromatin 96.3 0.011 2.4E-07 46.9 6.0 69 28-97 23-91 (131)
51 PLN00156 histone H2AX; Provisi 96.3 0.0099 2.2E-07 47.6 5.8 67 30-97 27-93 (139)
52 PF02269 TFIID-18kDa: Transcri 96.2 0.0067 1.5E-07 44.9 3.8 59 39-98 8-66 (93)
53 KOG3219 Transcription initiati 94.9 0.04 8.7E-07 46.4 4.3 69 32-102 112-181 (195)
54 PF02291 TFIID-31kDa: Transcri 94.9 0.18 3.8E-06 39.8 7.7 86 29-116 7-95 (129)
55 PTZ00252 histone H2A; Provisio 94.8 0.089 1.9E-06 42.0 6.1 67 30-97 23-91 (134)
56 cd07978 TAF13 The TATA Binding 94.4 0.24 5.2E-06 36.8 7.1 60 37-98 7-66 (92)
57 KOG4336 TBP-associated transcr 93.6 0.47 1E-05 42.6 8.6 76 38-117 11-86 (323)
58 TIGR03015 pepcterm_ATPase puta 91.8 0.69 1.5E-05 38.0 6.9 69 33-101 192-268 (269)
59 KOG2549 Transcription initiati 90.2 1.4 3E-05 42.5 7.9 66 34-101 13-78 (576)
60 KOG3423 Transcription initiati 90.2 1.9 4E-05 35.9 7.7 69 32-102 86-168 (176)
61 PRK00411 cdc6 cell division co 88.0 2.8 6.2E-05 36.6 7.9 70 35-104 209-287 (394)
62 KOG2389 Predicted bromodomain 85.7 2.6 5.6E-05 38.5 6.5 70 31-102 28-97 (353)
63 TIGR02928 orc1/cdc6 family rep 85.6 3.4 7.4E-05 35.6 7.0 75 35-109 201-284 (365)
64 TIGR02902 spore_lonB ATP-depen 81.4 4.2 9.1E-05 38.3 6.3 64 35-99 265-332 (531)
65 COG5095 TAF6 Transcription ini 78.5 5.1 0.00011 36.8 5.6 53 50-102 21-73 (450)
66 PF13654 AAA_32: AAA domain; P 77.4 12 0.00026 35.4 8.0 49 51-99 447-506 (509)
67 KOG3334 Transcription initiati 76.8 11 0.00025 30.6 6.6 65 52-116 31-96 (148)
68 TIGR00764 lon_rel lon-related 76.3 11 0.00024 36.2 7.6 49 51-99 330-391 (608)
69 COG1067 LonB Predicted ATP-dep 74.2 3.2 6.9E-05 40.6 3.3 47 51-98 338-398 (647)
70 KOG2680 DNA helicase TIP49, TB 70.1 19 0.00042 33.3 7.1 78 20-97 338-427 (454)
71 PF13335 Mg_chelatase_2: Magne 69.5 20 0.00043 26.4 6.0 47 51-97 42-94 (96)
72 cd08045 TAF4 TATA Binding Prot 68.4 25 0.00053 29.2 7.0 79 29-107 41-127 (212)
73 PF00531 Death: Death domain; 68.4 8.5 0.00018 26.1 3.6 61 51-112 23-83 (83)
74 PF08369 PCP_red: Proto-chloro 67.1 9.1 0.0002 24.8 3.3 42 53-95 2-44 (45)
75 KOG3901 Transcription initiati 67.0 17 0.00037 28.2 5.3 49 47-98 23-71 (109)
76 COG5248 TAF19 Transcription in 65.3 19 0.00042 28.2 5.3 50 47-98 23-72 (126)
77 KOG1757 Histone 2A [Chromatin 65.2 10 0.00022 29.9 3.8 64 30-97 28-95 (131)
78 PF02861 Clp_N: Clp amino term 63.8 6.8 0.00015 24.5 2.2 26 75-100 1-26 (53)
79 PRK00080 ruvB Holliday junctio 62.9 36 0.00079 29.4 7.3 84 32-115 179-268 (328)
80 TIGR00635 ruvB Holliday juncti 62.1 43 0.00093 28.2 7.4 71 33-103 159-233 (305)
81 cd04752 Commd4 COMM_Domain con 59.8 34 0.00073 27.7 6.1 50 63-119 43-93 (174)
82 PRK09862 putative ATP-dependen 57.2 41 0.0009 32.0 7.1 56 50-105 437-498 (506)
83 TIGR02442 Cob-chelat-sub cobal 57.0 43 0.00093 32.3 7.3 49 49-97 247-302 (633)
84 TIGR02030 BchI-ChlI magnesium 55.1 58 0.0013 29.1 7.4 54 43-97 247-307 (337)
85 TIGR01128 holA DNA polymerase 53.3 71 0.0015 26.5 7.3 66 32-97 110-176 (302)
86 PRK13406 bchD magnesium chelat 52.9 36 0.00077 32.9 6.0 59 37-97 183-248 (584)
87 COG5162 Transcription initiati 51.3 1E+02 0.0022 25.9 7.6 51 52-102 106-189 (197)
88 PRK12402 replication factor C 51.3 37 0.0008 28.7 5.3 68 33-102 184-252 (337)
89 PRK13765 ATP-dependent proteas 50.8 46 0.00099 32.6 6.4 47 51-97 339-398 (637)
90 COG1474 CDC6 Cdc6-related prot 49.4 53 0.0011 29.7 6.2 72 36-107 193-273 (366)
91 TIGR01052 top6b DNA topoisomer 48.5 21 0.00045 33.9 3.6 44 43-86 426-469 (488)
92 TIGR00368 Mg chelatase-related 46.9 51 0.0011 31.2 5.9 47 51-97 445-497 (499)
93 smart00350 MCM minichromosome 44.7 1.1E+02 0.0025 28.5 7.9 65 31-98 416-503 (509)
94 CHL00081 chlI Mg-protoporyphyr 43.3 92 0.002 28.2 6.8 54 43-97 260-320 (350)
95 TIGR02031 BchD-ChlD magnesium 42.8 91 0.002 29.9 7.0 55 42-97 195-256 (589)
96 COG1224 TIP49 DNA helicase TIP 42.5 89 0.0019 29.5 6.6 95 20-117 341-447 (450)
97 COG5624 TAF61 Transcription in 42.4 13 0.00028 35.1 1.2 77 31-107 382-461 (505)
98 PF00356 LacI: Bacterial regul 41.8 54 0.0012 21.1 3.8 32 32-67 10-41 (46)
99 PTZ00361 26 proteosome regulat 41.5 36 0.00077 31.7 4.0 32 68-99 393-424 (438)
100 PRK07452 DNA polymerase III su 41.5 74 0.0016 27.2 5.7 64 38-101 135-201 (326)
101 COG1222 RPT1 ATP-dependent 26S 41.0 40 0.00086 31.5 4.1 74 26-99 314-392 (406)
102 PF09114 MotA_activ: Transcrip 40.8 42 0.0009 25.5 3.5 33 36-68 51-87 (96)
103 PF07647 SAM_2: SAM domain (St 40.7 34 0.00074 22.4 2.8 25 86-110 3-27 (66)
104 PRK03992 proteasome-activating 40.7 39 0.00085 30.4 4.0 34 67-100 340-373 (389)
105 PF05236 TAF4: Transcription i 40.5 44 0.00096 28.5 4.2 76 27-102 38-121 (264)
106 PLN00138 large subunit ribosom 40.0 97 0.0021 23.9 5.6 31 70-102 3-33 (113)
107 TIGR01242 26Sp45 26S proteasom 39.7 42 0.00091 29.5 4.0 33 67-99 331-363 (364)
108 PRK05574 holA DNA polymerase I 39.4 96 0.0021 26.3 6.1 66 32-98 145-212 (340)
109 PRK13407 bchI magnesium chelat 39.0 1.1E+02 0.0023 27.5 6.5 53 43-96 244-303 (334)
110 PF08681 DUF1778: Protein of u 38.2 27 0.00059 24.7 2.2 51 49-99 3-61 (80)
111 PTZ00373 60S Acidic ribosomal 37.3 1.2E+02 0.0025 23.5 5.6 32 69-102 4-35 (112)
112 PF08823 PG_binding_2: Putativ 37.1 61 0.0013 23.0 3.8 32 89-120 18-55 (74)
113 cd00166 SAM Sterile alpha moti 36.7 28 0.00062 21.9 1.9 24 88-111 3-26 (63)
114 cd00823 TopoIIB_Trans TopoIIB_ 35.4 68 0.0015 26.2 4.2 42 31-75 102-143 (151)
115 KOG1528 Salt-sensitive 3'-phos 35.1 1.1E+02 0.0025 27.9 6.0 75 25-100 43-124 (351)
116 PF00536 SAM_1: SAM domain (St 34.6 46 0.00099 21.7 2.7 22 88-109 4-25 (64)
117 PF12010 DUF3502: Domain of un 34.5 39 0.00085 26.1 2.7 61 54-118 72-132 (134)
118 PTZ00454 26S protease regulato 34.3 56 0.0012 29.8 4.0 32 68-99 355-386 (398)
119 COG1389 DNA topoisomerase VI, 34.1 32 0.0007 33.1 2.5 46 43-88 434-479 (538)
120 COG5251 TAF40 Transcription in 33.2 64 0.0014 27.2 3.8 61 32-96 115-178 (199)
121 PF13405 EF-hand_6: EF-hand do 33.2 49 0.0011 18.8 2.3 26 75-100 5-31 (31)
122 COG1724 Predicted RNA binding 32.8 31 0.00066 24.6 1.6 18 86-103 6-23 (66)
123 PF07499 RuvA_C: RuvA, C-termi 32.7 32 0.00068 22.0 1.6 14 90-103 4-17 (47)
124 COG1466 HolA DNA polymerase II 32.5 1.1E+02 0.0023 26.9 5.4 61 38-98 145-206 (334)
125 PF12627 PolyA_pol_RNAbd: Prob 32.3 8.7 0.00019 25.3 -1.2 58 49-110 1-62 (64)
126 PRK07914 hypothetical protein; 31.1 1E+02 0.0022 26.6 5.0 63 34-97 129-192 (320)
127 PTZ00183 centrin; Provisional 30.0 2E+02 0.0044 21.0 5.9 21 78-98 61-81 (158)
128 cd05833 Ribosomal_P2 Ribosomal 29.9 1.7E+02 0.0038 22.3 5.5 31 70-102 3-33 (109)
129 smart00454 SAM Sterile alpha m 29.9 40 0.00088 21.3 1.8 26 86-111 3-28 (68)
130 TIGR01278 DPOR_BchB light-inde 29.3 1.1E+02 0.0024 28.7 5.2 51 49-100 460-511 (511)
131 PF03540 TFIID_30kDa: Transcri 28.9 1.8E+02 0.004 19.5 6.3 48 32-81 2-49 (51)
132 PRK02910 light-independent pro 28.8 1.1E+02 0.0024 28.7 5.2 52 48-100 466-518 (519)
133 PRK04184 DNA topoisomerase VI 27.9 46 0.001 32.0 2.4 56 43-98 431-488 (535)
134 PRK00440 rfc replication facto 27.8 1.3E+02 0.0027 25.1 4.8 65 33-99 161-226 (319)
135 smart00027 EH Eps15 homology d 27.7 1.2E+02 0.0026 21.4 4.1 28 75-102 15-42 (96)
136 PRK14975 bifunctional 3'-5' ex 27.3 4E+02 0.0086 25.3 8.5 89 30-121 161-269 (553)
137 PHA03328 nuclear egress lamina 25.6 81 0.0018 28.6 3.4 79 28-116 229-307 (316)
138 PRK06585 holA DNA polymerase I 25.5 1.9E+02 0.0041 25.0 5.6 61 37-97 146-208 (343)
139 TIGR02903 spore_lon_C ATP-depe 25.2 1.5E+02 0.0032 28.7 5.4 72 35-106 355-437 (615)
140 PTZ00183 centrin; Provisional 24.9 2.8E+02 0.0061 20.2 6.0 29 74-102 94-122 (158)
141 PRK09526 lacI lac repressor; R 24.4 72 0.0016 26.7 2.8 36 32-72 16-51 (342)
142 PF11753 DUF3310: Protein of u 24.2 2.3E+02 0.0049 19.2 4.7 42 55-98 14-57 (60)
143 PRK14868 DNA topoisomerase VI 23.9 61 0.0013 32.8 2.5 69 26-97 611-681 (795)
144 PF09239 Topo-VIb_trans: Topoi 23.8 83 0.0018 25.9 2.9 33 43-75 120-152 (160)
145 PF00403 HMA: Heavy-metal-asso 23.0 60 0.0013 20.8 1.6 16 87-102 47-62 (62)
146 smart00354 HTH_LACI helix_turn 22.6 1.4E+02 0.003 20.1 3.5 32 32-67 11-42 (70)
147 CHL00076 chlB photochlorophyll 22.5 1.8E+02 0.004 27.4 5.3 51 49-100 461-512 (513)
148 KOG0739 AAA+-type ATPase [Post 22.3 4.3E+02 0.0093 24.8 7.4 64 41-114 13-77 (439)
149 PRK14971 DNA polymerase III su 22.0 1.7E+02 0.0037 28.4 5.1 64 33-97 180-244 (614)
150 PTZ00184 calmodulin; Provision 22.0 2.8E+02 0.0061 19.8 5.3 38 74-111 88-125 (149)
151 TIGR02639 ClpA ATP-dependent C 21.8 1.2E+02 0.0027 29.6 4.2 33 52-96 1-33 (731)
152 PRK12728 fliE flagellar hook-b 21.3 3.6E+02 0.0078 20.2 6.3 38 81-119 59-98 (102)
153 cd08779 Death_PIDD Death Domai 21.1 2.5E+02 0.0054 20.1 4.7 33 79-111 53-85 (86)
154 COG1239 ChlI Mg-chelatase subu 21.0 1.8E+02 0.0039 27.4 4.8 52 45-97 262-320 (423)
155 PF02361 CbiQ: Cobalt transpor 21.0 4.1E+02 0.009 20.8 7.7 65 51-121 95-171 (224)
156 PRK05932 RNA polymerase factor 20.9 1.6E+02 0.0035 27.5 4.6 39 78-120 407-445 (455)
157 TIGR03261 phnS2 putative 2-ami 20.5 2.5E+02 0.0055 23.9 5.4 60 62-121 261-331 (334)
158 PRK10423 transcriptional repre 20.5 51 0.0011 27.3 1.1 35 33-72 10-44 (327)
159 PRK14867 DNA topoisomerase VI 20.1 83 0.0018 31.1 2.6 37 51-87 592-628 (659)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=1.1e-42 Score=279.06 Aligned_cols=129 Identities=70% Similarity=1.143 Sum_probs=115.7
Q ss_pred CCCCCCCCCCCCCCCCCCCCC-CCCCCCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 030812 1 MAEAPTSPAGGSHESGGEQSP-HAGGVREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKC 79 (171)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~ 79 (171)
|++++..+ +++++.|+.+.+ .+..++++|++||||||.||||+.||.++||||||++.||+|++|||+|||++|+++|
T Consensus 1 m~~s~~~~-~~~~e~~g~~~~~~~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC 79 (168)
T KOG0869|consen 1 MAESDHDS-GGGDENGGNSSPQSSLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKC 79 (168)
T ss_pred CCCCcCCC-CccccCCcccCCccccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence 66777666 456666655444 4457999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCccChhhHHHHHHhcCCCcchHHHHHHHHHHHHHhhcccCCCCCCC
Q 030812 80 QKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEGDTKGSARGGD 130 (171)
Q Consensus 80 ~~~kRKTI~~eDVl~AL~~LgF~dyv~~Lk~~L~~yre~~~~kk~~~k~~~ 130 (171)
++++|||||+|||||||..|||++|+++|+.||.+|||+++++....+.+.
T Consensus 80 ~~EkRKTIngdDllwAm~tLGFe~Y~eplkiyL~kYRe~e~e~~~~~~~~~ 130 (168)
T KOG0869|consen 80 QREKRKTINGDDLLWAMSTLGFENYAEPLKIYLQKYRELEGERGRSGKGGQ 130 (168)
T ss_pred HHHhcCcccHHHHHHHHHHcCcHhHHHHHHHHHHHHHHHhhhcccccccCc
Confidence 999999999999999999999999999999999999999988877666554
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.95 E-value=2.9e-28 Score=194.18 Aligned_cols=96 Identities=32% Similarity=0.631 Sum_probs=92.4
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcch
Q 030812 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (171)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv 105 (171)
...+|+.||+|+|.+|||+.||.+++|.+||+++|.+||.+||+.|+++|+++|.++.||||++|||++||+.|||.+|+
T Consensus 6 ~~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYi 85 (156)
T KOG0871|consen 6 KEDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYI 85 (156)
T ss_pred cccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHH
Confidence 46788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhc
Q 030812 106 DPLKAYLMRYREMEGD 121 (171)
Q Consensus 106 ~~Lk~~L~~yre~~~~ 121 (171)
+.+...|+.|+...+.
T Consensus 86 ee~~~vl~~~K~~~~~ 101 (156)
T KOG0871|consen 86 EEAEEVLENCKEEAKK 101 (156)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999987653
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.93 E-value=5.8e-26 Score=183.65 Aligned_cols=103 Identities=32% Similarity=0.526 Sum_probs=98.0
Q ss_pred CCCcccccCchhHHHHHHHhhCCCC-CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCc
Q 030812 25 GVREQDRYLPIANISRIMKKALPAN-GKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (171)
Q Consensus 25 ~~~~~d~~LP~A~V~RImK~~LP~~-~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~d 103 (171)
..+++|+.||+|+|.||+|+.||+. +.|+|||+.+|+++|++||+|||+.|+++|+.++||||+++|||.||++++|..
T Consensus 3 ~eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~ 82 (172)
T KOG0870|consen 3 DERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSS 82 (172)
T ss_pred chhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHH
Confidence 4678999999999999999999986 899999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHhhcccCCCC
Q 030812 104 YIDPLKAYLMRYREMEGDTKGSAR 127 (171)
Q Consensus 104 yv~~Lk~~L~~yre~~~~kk~~~k 127 (171)
|+.+|+..|+.||...++||.++.
T Consensus 83 f~~plk~~Le~yk~~~k~Kk~~~~ 106 (172)
T KOG0870|consen 83 FVNPLKSALEAYKKAVKQKKLAKA 106 (172)
T ss_pred HhhHHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999999888877544
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.88 E-value=2e-22 Score=157.98 Aligned_cols=97 Identities=26% Similarity=0.508 Sum_probs=93.2
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcch
Q 030812 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (171)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv 105 (171)
...++..||+|+|.+++-+.||.+..+.|||++.++.||.+||+.|+++|++.|..+.+|||.++||++||+.|+|.+|+
T Consensus 5 ~~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi 84 (148)
T COG5150 5 KNDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYI 84 (148)
T ss_pred cccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHH
Confidence 45678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhcc
Q 030812 106 DPLKAYLMRYREMEGDT 122 (171)
Q Consensus 106 ~~Lk~~L~~yre~~~~k 122 (171)
+.+.+.+..|+..++.|
T Consensus 85 ~~~~e~~~n~k~~qK~k 101 (148)
T COG5150 85 ESCMEEHENYKSYQKQK 101 (148)
T ss_pred HHHHHHHHHHHHHHhhc
Confidence 99999999999987655
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=99.78 E-value=8.4e-19 Score=120.51 Aligned_cols=64 Identities=36% Similarity=0.624 Sum_probs=59.3
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHH
Q 030812 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (171)
.||++.|.||||.. |++.+||+||.++|++|+++||.||+.+|++.|.+++||||+++||..||
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 88889999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.72 E-value=1.2e-17 Score=124.15 Aligned_cols=79 Identities=30% Similarity=0.465 Sum_probs=75.1
Q ss_pred CCCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcc
Q 030812 25 GVREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (171)
Q Consensus 25 ~~~~~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dy 104 (171)
..+..+..||+++|.||||++.++ |||.+|+++|++|+++|+..|+..|+++|.++|||||+++||..|++.+||..|
T Consensus 12 ~~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~~ 89 (91)
T COG2036 12 YQRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIY 89 (91)
T ss_pred hhhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccccc
Confidence 467889999999999999999985 999999999999999999999999999999999999999999999999999866
Q ss_pred h
Q 030812 105 I 105 (171)
Q Consensus 105 v 105 (171)
.
T Consensus 90 ~ 90 (91)
T COG2036 90 G 90 (91)
T ss_pred c
Confidence 3
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=99.24 E-value=4.2e-11 Score=88.02 Aligned_cols=72 Identities=19% Similarity=0.337 Sum_probs=66.7
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcc
Q 030812 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (171)
Q Consensus 31 ~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dy 104 (171)
-.||++.|.||++... ..+||.|+.+.+.++.++|+..|..+|...|++.+||||+++||..||+..|-.-|
T Consensus 12 ~gi~k~~I~RLarr~G--vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 12 KGITKPAIRRLARRGG--VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred ccCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 3599999999999986 46899999999999999999999999999999999999999999999999886544
No 8
>PLN00035 histone H4; Provisional
Probab=99.21 E-value=7e-11 Score=89.75 Aligned_cols=77 Identities=17% Similarity=0.284 Sum_probs=68.7
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcc
Q 030812 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (171)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dy 104 (171)
.++.-..||++.|.||++..- ..+||.|+.+.+.+..++|+..|..+|..+|++.+||||+++||..||+..|-.-|
T Consensus 23 ~~d~i~~ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ly 99 (103)
T PLN00035 23 LRDNIQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLY 99 (103)
T ss_pred HHhhhccCCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcCC
Confidence 344445699999999999986 46899999999999999999999999999999999999999999999998775433
No 9
>PTZ00015 histone H4; Provisional
Probab=99.15 E-value=2.2e-10 Score=86.92 Aligned_cols=77 Identities=19% Similarity=0.357 Sum_probs=69.4
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcc
Q 030812 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (171)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dy 104 (171)
.++....||++.|.||++..- ..+||.|+.+.+.++.++|+..|..+|..+|++.+||||+++||..||+..|-.-|
T Consensus 24 ~r~~i~gI~k~~IrRLarr~G--vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 24 LRDNIRGITKGAIRRLARRGG--VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred HhhcccCCCHHHHHHHHHHcC--CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 345556799999999999986 35899999999999999999999999999999999999999999999998876544
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=99.02 E-value=1.5e-09 Score=75.88 Aligned_cols=64 Identities=25% Similarity=0.281 Sum_probs=60.1
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.||+++|.||++...- .+||.|+...|.+-++.|+.-|..+|...+++.+||||+++||-.||+
T Consensus 2 ~~p~~~i~ria~~~Gi--~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLGI--GNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCCC--ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 5899999999998853 479999999999999999999999999999999999999999999984
No 11
>smart00417 H4 Histone H4.
Probab=98.97 E-value=1.4e-09 Score=78.21 Aligned_cols=63 Identities=17% Similarity=0.314 Sum_probs=58.6
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHH
Q 030812 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWA 95 (171)
Q Consensus 31 ~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~A 95 (171)
..||++.|.||+|...- -+||.++.+.+.+..++|+..|..+|..+|++.+||||+++||..|
T Consensus 12 ~gI~k~~IrRLaRr~Gv--kRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 12 QGITKPAIRRLARRGGV--KRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred cCCCHHHHHHHHHHcCc--chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 46999999999999863 5899999999999999999999999999999999999999999753
No 12
>smart00428 H3 Histone H3.
Probab=98.95 E-value=2.3e-09 Score=81.65 Aligned_cols=74 Identities=16% Similarity=0.170 Sum_probs=67.4
Q ss_pred CCcccccCchhHHHHHHHhhCCC-----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhc
Q 030812 26 VREQDRYLPIANISRIMKKALPA-----NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~-----~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (171)
.+..++.+|+.+..|++++...+ +.+|+.+|..+||++++.|+.-+...|+..+.+.||+||.++||..|..-.
T Consensus 23 Qkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir 101 (105)
T smart00428 23 QKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIR 101 (105)
T ss_pred ccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHh
Confidence 46678999999999999998864 679999999999999999999999999999999999999999998887543
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=98.91 E-value=3.9e-09 Score=73.47 Aligned_cols=68 Identities=25% Similarity=0.331 Sum_probs=62.5
Q ss_pred cccCchhHHHHHHHhhCCC---CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 30 DRYLPIANISRIMKKALPA---NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 30 d~~LP~A~V~RImK~~LP~---~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
+..+|+..|.|+.|+..++ ..+|+++|...|+..++.|+.-|...|...|.+.||+||+++||..|++
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 4578899999999988874 2699999999999999999999999999999999999999999999985
No 14
>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=98.89 E-value=1.3e-08 Score=72.08 Aligned_cols=65 Identities=15% Similarity=0.324 Sum_probs=61.4
Q ss_pred CchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 33 LPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 33 LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
|++..+..++|+.-| ..+|+.||.++|++.+++|+.-++..|...|++.||+||.++||..+|+.
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 677889999999977 58999999999999999999999999999999999999999999999975
No 15
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.84 E-value=2.7e-09 Score=91.05 Aligned_cols=78 Identities=24% Similarity=0.319 Sum_probs=70.2
Q ss_pred cccccCchhHHHHHHHhhCCCCC-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcchH
Q 030812 28 EQDRYLPIANISRIMKKALPANG-KIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID 106 (171)
Q Consensus 28 ~~d~~LP~A~V~RImK~~LP~~~-rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv~ 106 (171)
..+..||+|.|.|+||-. +++ .||.||..++.+.|+.||..||-.|+-.+++++|+|+-..||..|+++-++.||+-
T Consensus 105 ~k~h~LPlARIkkvMKtd--edVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLi 182 (286)
T COG5208 105 LKDHNLPLARIKKVMKTD--EDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLI 182 (286)
T ss_pred HHhccCcHHHHHHHHhcc--cchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHh
Confidence 345689999999999955 455 49999999999999999999999999999999999999999999999998888864
Q ss_pred H
Q 030812 107 P 107 (171)
Q Consensus 107 ~ 107 (171)
.
T Consensus 183 d 183 (286)
T COG5208 183 D 183 (286)
T ss_pred h
Confidence 3
No 16
>PLN00160 histone H3; Provisional
Probab=98.61 E-value=1.3e-07 Score=71.34 Aligned_cols=72 Identities=15% Similarity=0.102 Sum_probs=65.5
Q ss_pred CCcccccCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 26 VREQDRYLPIANISRIMKKALP----ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP----~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.+..++.+|++...|++++... ++.+++.+|..+||++++.|+.-+...++-.|.+.||.||.+.|+..|..
T Consensus 15 Qkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 15 QKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred ccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 3567889999999999999864 35899999999999999999999999999999999999999999988764
No 17
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.60 E-value=6.6e-08 Score=82.64 Aligned_cols=86 Identities=26% Similarity=0.333 Sum_probs=73.0
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhc---CCCcch
Q 030812 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL---GFEDYI 105 (171)
Q Consensus 29 ~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L---gF~dyv 105 (171)
....||++.|.+|||..= +.-.|+.||...+.+||+.||..||..|+..+...+|+|+...||..|+..- +|.-.+
T Consensus 71 ~~~~lPlaRiKkimK~de-dv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~Di 149 (236)
T KOG1657|consen 71 KNHILPLARIKKIMKSDE-DVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRDI 149 (236)
T ss_pred hhccCcHhhccccccccc-cccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceecc
Confidence 345799999999999763 2347999999999999999999999999999999999999999999999864 444445
Q ss_pred HHHHHHHHHH
Q 030812 106 DPLKAYLMRY 115 (171)
Q Consensus 106 ~~Lk~~L~~y 115 (171)
-+.+..++.|
T Consensus 150 vP~~~~~~~~ 159 (236)
T KOG1657|consen 150 VPRKILAEKY 159 (236)
T ss_pred ccchhccccc
Confidence 5667777777
No 18
>PLN00161 histone H3; Provisional
Probab=98.60 E-value=1.7e-07 Score=74.31 Aligned_cols=71 Identities=15% Similarity=0.186 Sum_probs=65.2
Q ss_pred CcccccCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 27 REQDRYLPIANISRIMKKALP----ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 27 ~~~d~~LP~A~V~RImK~~LP----~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
+..++.+|++.+.|++++... .+.+++.+|.++||++++.|+.-+...|+-.|.+.||.||.+.|+..|..
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 567889999999999999864 36899999999999999999999999999999999999999999988864
No 19
>PLN00121 histone H3; Provisional
Probab=98.59 E-value=1e-07 Score=75.65 Aligned_cols=71 Identities=14% Similarity=0.165 Sum_probs=65.8
Q ss_pred CcccccCchhHHHHHHHhhCCC---CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 27 REQDRYLPIANISRIMKKALPA---NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 27 ~~~d~~LP~A~V~RImK~~LP~---~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
+..++.||+..+.|++++...+ +.+++.+|.++||++++.|+.-+...++..+.+.||.||.+.|+..|+.
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 5568899999999999998865 6899999999999999999999999999999999999999999988864
No 20
>PTZ00018 histone H3; Provisional
Probab=98.56 E-value=1.3e-07 Score=75.07 Aligned_cols=71 Identities=14% Similarity=0.169 Sum_probs=65.3
Q ss_pred CcccccCchhHHHHHHHhhCC---CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 27 REQDRYLPIANISRIMKKALP---ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 27 ~~~d~~LP~A~V~RImK~~LP---~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
+..|+.||+..+.|++++... .+.++..+|.++||++++.|+.-|...++..|.+.||.||.+.|+..|..
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence 556889999999999999874 36899999999999999999999999999999999999999999988864
No 21
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.37 E-value=2.8e-06 Score=60.44 Aligned_cols=66 Identities=18% Similarity=0.261 Sum_probs=58.9
Q ss_pred hhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCC
Q 030812 35 IANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (171)
Q Consensus 35 ~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (171)
+-.|.+|+|.+.= -+++.+|.++|.+....|+..|+..+...|++.+|++++..||..||+++|+.
T Consensus 9 ~~~Vaqil~~~Gf--~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESAGF--DSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHcCc--cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 3457777877642 38999999999999999999999999999999999999999999999999974
No 22
>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=98.36 E-value=1.4e-06 Score=67.32 Aligned_cols=68 Identities=18% Similarity=0.237 Sum_probs=62.3
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
.+.||.+.|.|+||+.-- ..||+.+|...|..+.+-+...|...|...|++.+|++|+++||..|+..
T Consensus 18 gL~fPV~ri~R~Lk~~~~-a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 18 GLQFPVGRIHRYLKKGRY-AERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred CccCcHHHHHHHHHcCcc-ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 589999999999998432 36999999999999999999999999999999999999999999999864
No 23
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=98.17 E-value=2.6e-05 Score=60.03 Aligned_cols=79 Identities=14% Similarity=0.199 Sum_probs=66.9
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcchH-HHHHHHHHH
Q 030812 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID-PLKAYLMRY 115 (171)
Q Consensus 37 ~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv~-~Lk~~L~~y 115 (171)
.|.+|+|+.. ..+++.+++..|.+.+..++.-|..+|...+++.+|+||+.+||..|++...-..|.. +-+++|.++
T Consensus 6 ~v~~iLk~~G--v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~~ 83 (117)
T cd07979 6 VIAAILKSMG--ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLEL 83 (117)
T ss_pred HHHHHHHHCC--CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHHH
Confidence 5788888763 3489999999999999999999999999999999999999999999999766655554 467777665
Q ss_pred HH
Q 030812 116 RE 117 (171)
Q Consensus 116 re 117 (171)
-.
T Consensus 84 a~ 85 (117)
T cd07979 84 AR 85 (117)
T ss_pred HH
Confidence 44
No 24
>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=97.89 E-value=5.5e-05 Score=67.16 Aligned_cols=67 Identities=19% Similarity=0.202 Sum_probs=58.0
Q ss_pred chhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCC
Q 030812 34 PIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (171)
Q Consensus 34 P~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (171)
|..+|.-|++... -.++++||..+|.+.++.++..|..+|...+++.||||++++||-.||+.++.+
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 3456666776653 238999999999999999999999999999999999999999999999966553
No 25
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.88 E-value=5.5e-05 Score=54.61 Aligned_cols=61 Identities=15% Similarity=0.198 Sum_probs=52.1
Q ss_pred HHHHHHHhhC-CCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 37 NISRIMKKAL-PANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 37 ~V~RImK~~L-P~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.|.||+.+.. +.++.+|+++.-+|.+.+-.++..++..-.-.|++.||+||+.+||+...+
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 5789999885 457889999999999999999999999999999999999999999987654
No 26
>smart00427 H2B Histone H2B.
Probab=97.88 E-value=7.8e-05 Score=55.53 Aligned_cols=62 Identities=21% Similarity=0.350 Sum_probs=57.5
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhc
Q 030812 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 37 ~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (171)
-|+|+.|+.-| +.-||..|...|+-.+..+..-|+.||...|.-.+|+||+..+|..|++-+
T Consensus 6 Yi~kvLKqVhp-d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 6 YIYKVLKQVHP-DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHHhCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 48999999999 568999999999999999999999999999999999999999999998654
No 27
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.85 E-value=3.2e-05 Score=70.49 Aligned_cols=65 Identities=20% Similarity=0.271 Sum_probs=48.1
Q ss_pred CcccccCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhh
Q 030812 27 REQDRYLPIANISRIMKKALP----ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDD 91 (171)
Q Consensus 27 ~~~d~~LP~A~V~RImK~~LP----~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eD 91 (171)
++.--.||.+.|+|++..... .+++|+|||..+|.+|...|...|...-..+|.|.|||||..+|
T Consensus 346 gi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 346 GIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 444457999999999888764 46899999999999999999999999999999999999999876
No 28
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=97.80 E-value=1.3e-05 Score=63.81 Aligned_cols=75 Identities=16% Similarity=0.194 Sum_probs=65.7
Q ss_pred CCcccccCchhHHHHHHHhhCC---CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcC
Q 030812 26 VREQDRYLPIANISRIMKKALP---ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (171)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP---~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (171)
.+..|+.+++....|++++..+ .+.++...|..+||++++.|+.-|.-.++-.+.+.||.||.+.||--|..-.|
T Consensus 57 QkstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg 134 (137)
T KOG1745|consen 57 QKSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 134 (137)
T ss_pred HhhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence 3467888999999999995544 47899999999999999999999999999999999999999999998876443
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=97.66 E-value=0.00027 Score=49.95 Aligned_cols=63 Identities=19% Similarity=0.306 Sum_probs=51.3
Q ss_pred hhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 35 IANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 35 ~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
+..+.-++++.-| +.++.+|+.++|.+.|.+||.-++..|...|++-+-.||...||...|++
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 3467788998866 78999999999999999999999999999999999999999999999874
No 30
>PLN00158 histone H2B; Provisional
Probab=97.65 E-value=0.00027 Score=54.97 Aligned_cols=65 Identities=17% Similarity=0.290 Sum_probs=58.9
Q ss_pred chhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhc
Q 030812 34 PIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 34 P~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (171)
-..-|+|++|+.-| +.-||..+...|+-.+..+..-|+.||...|.-.+|+||+..+|..|++-+
T Consensus 29 y~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 29 YKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred HHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 34559999999999 568999999999999999999999999999999999999999999998644
No 31
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.61 E-value=0.00029 Score=61.27 Aligned_cols=70 Identities=16% Similarity=0.274 Sum_probs=62.8
Q ss_pred cccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 28 EQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 28 ~~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
..+..|=+-.|.-++++.-+ +.+|-+|+.+.|.+.|..||..|+..|-..|++-|..||-+.||...|++
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 33456777788999999855 77999999999999999999999999999999999999999999999983
No 32
>PTZ00463 histone H2B; Provisional
Probab=97.60 E-value=0.00034 Score=54.47 Aligned_cols=62 Identities=19% Similarity=0.386 Sum_probs=57.2
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhc
Q 030812 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 37 ~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (171)
-|+|++|+.-| +.-||..|...|+-.+.....-|+.||...|.-.+|+||+..+|..|++-+
T Consensus 33 YI~KVLKqVhP-d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 33 YIFKVLKQVHP-DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred HHHHHHHhhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 49999999999 567999999999999999999999999999999999999999999998644
No 33
>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=97.59 E-value=0.00067 Score=47.81 Aligned_cols=64 Identities=19% Similarity=0.274 Sum_probs=55.6
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCC
Q 030812 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (171)
Q Consensus 37 ~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (171)
.|.+|++... =-.++..|.+.|...+..||..|+..+...|...+|...+..||..||+++|+.
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 4555555442 127999999999999999999999999999999999999999999999999984
No 34
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=97.57 E-value=0.00037 Score=52.28 Aligned_cols=69 Identities=17% Similarity=0.268 Sum_probs=60.9
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCC
Q 030812 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (171)
-+-+-+|.||.+..- .-+|+--.-+.+..++.+||.-+-+.|...+++.|||||++-||+-+|+..|.-
T Consensus 29 gitKpaIRRlARr~G--VkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 29 GITKPAIRRLARRGG--VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred ccchHHHHHHHHhcC--cchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 366778999999875 347888888889999999999999999999999999999999999999988753
No 35
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.52 E-value=0.00028 Score=60.03 Aligned_cols=84 Identities=17% Similarity=0.216 Sum_probs=72.4
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcchHHHHH
Q 030812 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKA 110 (171)
Q Consensus 31 ~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv~~Lk~ 110 (171)
..+|.+.|.|||...= +-.||+.-+...+.++.+.|+.-|-..+.+++...+-|||+++|+..|+..-.-.||+..+-.
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 4689999999998653 256999999999999999999999999999999999999999999999998888888776544
Q ss_pred HHHHH
Q 030812 111 YLMRY 115 (171)
Q Consensus 111 ~L~~y 115 (171)
.+..+
T Consensus 91 ~vpd~ 95 (224)
T KOG1659|consen 91 KVPDR 95 (224)
T ss_pred hcCCC
Confidence 44433
No 36
>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=97.51 E-value=0.00074 Score=49.63 Aligned_cols=66 Identities=20% Similarity=0.211 Sum_probs=61.2
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CccChhhHHHHHHhc
Q 030812 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKR---KTINGDDLLWAMATL 99 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kR---KTI~~eDVl~AL~~L 99 (171)
.||++.|.|||...++ ..++.+...+|.-.+.+||-.|.-+|.++..+.+. .-|.++||..|...|
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 4999999999999996 78999999999999999999999999999987765 789999999999876
No 37
>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=97.46 E-value=0.00018 Score=51.43 Aligned_cols=65 Identities=20% Similarity=0.297 Sum_probs=53.9
Q ss_pred chhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-cChhhHHHHHHh
Q 030812 34 PIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKT-INGDDLLWAMAT 98 (171)
Q Consensus 34 P~A~V~RImK~~LP-~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKT-I~~eDVl~AL~~ 98 (171)
|..+|.||++.... +..||++||..++.+....||..-...|.+.+..++..+ |..+|+-+.+-.
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq 67 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ 67 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 78899999998774 478999999999999999999999999999999999888 999999876543
No 38
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.33 E-value=0.00048 Score=54.08 Aligned_cols=68 Identities=19% Similarity=0.239 Sum_probs=60.8
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 29 ~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.-+.+|...|.||||..- -.+||+++|...+.-|.+-.+..|+..|-..|...|+|-|.+.|+-.|+.
T Consensus 23 agl~fpvgrvkr~lk~~~-~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 23 AGLIFPVGRVKRLLKKGN-YRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred cCccccHHHHHHHHHcCc-cceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 347899999999999443 36899999999999999988888988899999999999999999999986
No 39
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=97.30 E-value=0.0011 Score=50.81 Aligned_cols=81 Identities=17% Similarity=0.271 Sum_probs=68.3
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcchHHH
Q 030812 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPL 108 (171)
Q Consensus 29 ~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv~~L 108 (171)
.-..+|+|.|.|||.-.- +-.+|+.-......++.+.|+..|-.+..+.++..+-|-|+.+++..|.+.-+=.||+..+
T Consensus 20 ~ktrFP~ar~KkIMQ~de-DiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~ 98 (113)
T COG5247 20 KKTRFPIARLKKIMQLDE-DIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNM 98 (113)
T ss_pred hhhcCCHHHHHHHHHhhh-hhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHH
Confidence 345799999999998543 2458999999999999999999999999999999999999999999999876666665544
Q ss_pred HH
Q 030812 109 KA 110 (171)
Q Consensus 109 k~ 110 (171)
..
T Consensus 99 ~~ 100 (113)
T COG5247 99 EQ 100 (113)
T ss_pred HH
Confidence 43
No 40
>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=97.17 E-value=0.0022 Score=47.75 Aligned_cols=67 Identities=21% Similarity=0.229 Sum_probs=52.2
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CccChhhHHHHHHhc
Q 030812 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKR-KTINGDDLLWAMATL 99 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kR-KTI~~eDVl~AL~~L 99 (171)
.||++.|.|||...+. +..|+.-...+|.-.+..||-.|-.+|.+++.+.+. .-|.+.|+-.|...|
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 4999999999999995 578999999999999999999999999999986553 379999999998765
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=97.16 E-value=0.0033 Score=44.34 Aligned_cols=64 Identities=20% Similarity=0.237 Sum_probs=48.4
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.+|..+|.-+.. .+. -..++.|+...|.+=++--|..|..+|.....+.+|++++.+||-.||+
T Consensus 3 ~~~~esvk~iAe-s~G-i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAE-SLG-ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHH-HTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHH-HcC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 367777765554 443 2379999999999999999999999999999999999999999999985
No 42
>smart00414 H2A Histone 2A.
Probab=97.13 E-value=0.0015 Score=49.88 Aligned_cols=68 Identities=15% Similarity=0.257 Sum_probs=59.5
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
.+.||.+.|.|+||+.-- ..||+..|...|.-+.+=+...|-..|...|...+++.|+++||..|+..
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 478999999999998743 35999999999999888888888777888899999999999999999865
No 43
>PLN00154 histone H2A; Provisional
Probab=96.96 E-value=0.0048 Score=49.23 Aligned_cols=69 Identities=19% Similarity=0.246 Sum_probs=57.3
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
.+.||...|.|++|+...-..||+..|...|.-+.+=+...|-..|-..|...+++-|++.||..|+..
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 588999999999999764346999999988887776666666666777889999999999999999853
No 44
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=96.77 E-value=0.00075 Score=54.97 Aligned_cols=67 Identities=25% Similarity=0.302 Sum_probs=58.5
Q ss_pred cccCchhHHHHHHHhhCCCCCc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 30 DRYLPIANISRIMKKALPANGK-IAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~r-ISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
-..||++.|..+|| ++++.+ ..+|++.++.+++..||.+|...++..+...+|||+.-.|+=.|++.
T Consensus 57 l~rLpL~rik~vvk--l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~ 124 (162)
T KOG1658|consen 57 LSRLPLARIKQVVK--LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEA 124 (162)
T ss_pred hhhccHHHHHhhcc--CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccc
Confidence 36799999999998 666776 56778999999999999999999999999999999999888777654
No 45
>PTZ00017 histone H2A; Provisional
Probab=96.73 E-value=0.0035 Score=49.84 Aligned_cols=67 Identities=15% Similarity=0.231 Sum_probs=59.3
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.+.||...|.|++|+.-- ..||+..|...|.-+.+-+...|-..|...|...+++-|+++||..|+.
T Consensus 25 gL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 589999999999998643 3599999999999988888888888888899999999999999999985
No 46
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.62 E-value=0.0085 Score=47.35 Aligned_cols=69 Identities=22% Similarity=0.266 Sum_probs=59.5
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
.+.+.+..+ |+|++|++-|+ .-|+.++...|+-....|+--|+.+|...+.-.+|.||+..+|..|.+-
T Consensus 34 ~~~e~~s~y---v~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rL 102 (127)
T KOG1744|consen 34 RRKESYSEY---VYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRL 102 (127)
T ss_pred cccCceeee---hhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHH
Confidence 334444444 67799999996 6699999999999999999999999999999999999999999999854
No 47
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.43 E-value=0.0067 Score=45.82 Aligned_cols=67 Identities=21% Similarity=0.255 Sum_probs=55.1
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHH
Q 030812 31 RYLPIANISRIMKKALPANGKIAKDAKDT--------------VQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (171)
Q Consensus 31 ~~LP~A~V~RImK~~LP~~~rISkDA~~a--------------l~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (171)
+.-|++.+.|++|..-| ..++....-.+ +.--|-.||+-|+-||...|-++|-.||..+||+.|-
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 56665544444 5666889999999999988888889999999999987
Q ss_pred Hh
Q 030812 97 AT 98 (171)
Q Consensus 97 ~~ 98 (171)
+.
T Consensus 94 Kv 95 (102)
T PF15510_consen 94 KV 95 (102)
T ss_pred HH
Confidence 53
No 48
>PLN00157 histone H2A; Provisional
Probab=96.39 E-value=0.0072 Score=48.00 Aligned_cols=67 Identities=13% Similarity=0.190 Sum_probs=58.1
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.+.||...|.|++|+.-- ..||+..|...|.-+.+-++..|-..|...|...+++-|+++||..|+.
T Consensus 24 gL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred CcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 589999999999998643 3599999999998887777777777788889999999999999999985
No 49
>PLN00153 histone H2A; Provisional
Probab=96.34 E-value=0.0087 Score=47.37 Aligned_cols=67 Identities=16% Similarity=0.223 Sum_probs=58.5
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.+.+|...|.|++|+.-- ..||+..|...|.-+.+-++..|-..|...|...+++-|+++||..|+.
T Consensus 22 gL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred CcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 589999999999998654 3599999999999888877777777788889999999999999999985
No 50
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.34 E-value=0.011 Score=46.85 Aligned_cols=69 Identities=16% Similarity=0.244 Sum_probs=55.0
Q ss_pred cccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 28 EQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 28 ~~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
-..+.+|...|.|++|+.- --.+|+.+|...|.-|.+-....|+..|-..+..+++.-|+++||..|+.
T Consensus 23 ~agl~fPvgri~r~Lr~~~-~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 23 RAGLQFPVGRIHRLLRKGR-YAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred hcccccCHHHHHHHHHccc-hhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 3457899999999999932 24689999999999766655555555566667788999999999999986
No 51
>PLN00156 histone H2AX; Provisional
Probab=96.33 E-value=0.0099 Score=47.60 Aligned_cols=67 Identities=13% Similarity=0.205 Sum_probs=56.9
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.+.||...|.|++|+.-- ..||+..|...|.-+.+=....|-..|...|...+++-|+++||.+|+.
T Consensus 27 gL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred CcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 578999999999998643 3599999999888887766666666777788999999999999999985
No 52
>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=96.17 E-value=0.0067 Score=44.92 Aligned_cols=59 Identities=24% Similarity=0.309 Sum_probs=28.7
Q ss_pred HHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 39 SRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 39 ~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
..+|-.- .+...-..|+..+|-+.+.+||..|..+|...|...++++|+.+|++.+|+.
T Consensus 8 ~~mMy~f-GD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 8 RQMMYGF-GDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp HHHHHCT-TS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHc-CCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 3444433 3455788999999999999999999999999999999999999999999985
No 53
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=94.87 E-value=0.04 Score=46.37 Aligned_cols=69 Identities=14% Similarity=0.185 Sum_probs=60.3
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCccChhhHHHHHHhcCCC
Q 030812 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEK-RKTINGDDLLWAMATLGFE 102 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~k-RKTI~~eDVl~AL~~LgF~ 102 (171)
.||+++|.|||..... ..|+.-+..+|+-.+.+||-.|--+|.++|..-+ ---|-+.||-.|...|...
T Consensus 112 ~f~Ka~iKkL~~~itg--~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~q 181 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITG--QSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQ 181 (195)
T ss_pred cCCHHHHHHHHHHHhC--CccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhc
Confidence 5999999999999986 3499999999999999999999999999998655 4468999999998877654
No 54
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=94.85 E-value=0.18 Score=39.79 Aligned_cols=86 Identities=21% Similarity=0.245 Sum_probs=46.0
Q ss_pred ccccCchh--HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH-hcCCCcch
Q 030812 29 QDRYLPIA--NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA-TLGFEDYI 105 (171)
Q Consensus 29 ~d~~LP~A--~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~-~LgF~dyv 105 (171)
..-.+|+. .|.-|+|+.. -......+...|.+.+-.|+.-|-..|..++.+.+|++|+.+||..|++ .+++.-..
T Consensus 7 ~~~~~PrDa~~i~~iL~~~G--v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~ 84 (129)
T PF02291_consen 7 QSKSLPRDARVIHLILKSMG--VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQ 84 (129)
T ss_dssp ------HHHHHHHHHHHHTT-----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-------
T ss_pred CCccCChHHHHHHHHHHHcC--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccC
Confidence 34566762 2444444432 2246778888899999999999999999999999999999999999999 56776566
Q ss_pred HHHHHHHHHHH
Q 030812 106 DPLKAYLMRYR 116 (171)
Q Consensus 106 ~~Lk~~L~~yr 116 (171)
.+-+++|.+.-
T Consensus 85 pppre~llelA 95 (129)
T PF02291_consen 85 PPPREFLLELA 95 (129)
T ss_dssp -----------
T ss_pred CCChHHHHHHH
Confidence 67677776543
No 55
>PTZ00252 histone H2A; Provisional
Probab=94.85 E-value=0.089 Score=41.97 Aligned_cols=67 Identities=7% Similarity=0.168 Sum_probs=49.0
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccChhhHHHHHH
Q 030812 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQK--EKRKTINGDDLLWAMA 97 (171)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~--~kRKTI~~eDVl~AL~ 97 (171)
.+.||...|.|++|+.-- ..||+.-|...|.-+.+=....|-..|...|.+ .+++-|+++||..|+.
T Consensus 23 GL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred CccCchHHHHHHHHcCCc-ccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 589999999999998764 359999988887765543333333334444433 5778999999999985
No 56
>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=94.38 E-value=0.24 Score=36.77 Aligned_cols=60 Identities=18% Similarity=0.295 Sum_probs=48.6
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 37 ~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
-|..+|--.. +...-..|...+|-+.+.+||.-|+.+|.+.|. .+|.-|+.||++-+|+.
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 4566666444 355678899999999999999999999999999 44444599999999974
No 57
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=93.59 E-value=0.47 Score=42.62 Aligned_cols=76 Identities=18% Similarity=0.295 Sum_probs=63.4
Q ss_pred HHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcchHHHHHHHHHHHH
Q 030812 38 ISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYRE 117 (171)
Q Consensus 38 V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv~~Lk~~L~~yre 117 (171)
|.-|.++..=+ .|++-|++.|.+....+|.-|...+...|...+|...+.-||...|-.+||. +..|..+++.+..
T Consensus 11 V~~Ll~~~gfd--~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~~ 86 (323)
T KOG4336|consen 11 VSNLLKTKGFD--SISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQEF 86 (323)
T ss_pred HHHHHHHhCch--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhccc
Confidence 34444444322 5999999999999999999999999999999999999999999999999997 5777777776544
No 58
>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=91.80 E-value=0.69 Score=37.99 Aligned_cols=69 Identities=14% Similarity=0.243 Sum_probs=54.4
Q ss_pred CchhHHHHHHHhhCC-----CCCcccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCC
Q 030812 33 LPIANISRIMKKALP-----ANGKIAKDAKDTVQECVSE---FISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (171)
Q Consensus 33 LP~A~V~RImK~~LP-----~~~rISkDA~~al~~case---FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF 101 (171)
|....+..++...+. ....+++++.+.|.+.+.= .|+.+...|...+-..+.++|+.++|..++.++.|
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 444555555554431 2346999999999998875 79999999999888888999999999999998875
No 59
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=90.21 E-value=1.4 Score=42.52 Aligned_cols=66 Identities=21% Similarity=0.286 Sum_probs=54.8
Q ss_pred chhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCC
Q 030812 34 PIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (171)
Q Consensus 34 P~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF 101 (171)
|.-.+ +.+-+.+. -..|+.|+..+|.+=++.=|..|+.+|.++-.+.||.+++.+||..||+.+..
T Consensus 13 ~~Es~-k~vAEslG-i~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nV 78 (576)
T KOG2549|consen 13 PKESV-KVVAESLG-ITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNV 78 (576)
T ss_pred cHHHH-HHHHHHhC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhccc
Confidence 34444 44445553 34699999999999999999999999999999999999999999999996543
No 60
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=90.18 E-value=1.9 Score=35.90 Aligned_cols=69 Identities=26% Similarity=0.257 Sum_probs=55.1
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--------------CCCccChhhHHHHHH
Q 030812 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKE--------------KRKTINGDDLLWAMA 97 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~--------------kRKTI~~eDVl~AL~ 97 (171)
.||=+.+.-+++.+.= .....-.+.+|.=++-.||+-|+..|.+.|+-. +|-|++-+|+-.||+
T Consensus 86 ~IPDavt~~yL~~aGf--~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~ 163 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKAGF--QTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALA 163 (176)
T ss_pred CCcHHHHHHHHHhcCC--CcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHH
Confidence 5888888888887641 234455678899999999999999999999743 355899999999999
Q ss_pred hcCCC
Q 030812 98 TLGFE 102 (171)
Q Consensus 98 ~LgF~ 102 (171)
+.|+.
T Consensus 164 EyGin 168 (176)
T KOG3423|consen 164 EYGIN 168 (176)
T ss_pred HhCcc
Confidence 98874
No 61
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=87.95 E-value=2.8 Score=36.58 Aligned_cols=70 Identities=13% Similarity=0.171 Sum_probs=50.9
Q ss_pred hhHHHHHHHhhCCC---CCcccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcc
Q 030812 35 IANISRIMKKALPA---NGKIAKDAKDTVQECV------SEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (171)
Q Consensus 35 ~A~V~RImK~~LP~---~~rISkDA~~al~~ca------seFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dy 104 (171)
...+..|++..+.. ...++.++.+.+.+.+ -.++..+...|.+.|...++.+|+.+||..|++.+....+
T Consensus 209 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~ 287 (394)
T PRK00411 209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHL 287 (394)
T ss_pred HHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHH
Confidence 45566666655422 2358999988888776 3345566678888898899999999999999998844333
No 62
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=85.70 E-value=2.6 Score=38.49 Aligned_cols=70 Identities=14% Similarity=0.159 Sum_probs=59.0
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCC
Q 030812 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (171)
Q Consensus 31 ~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (171)
+.|-+..|..|+...-=. ....-|.+.|+..+..||.-|+..|..++...+|.-.+..||+.||+.|+..
T Consensus 28 ~sla~~avaQIcqslg~~--~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 28 FSLARVAVAQICQSLGYS--STQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHHhcCCc--ccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 357777888888755432 3444499999999999999999999999999999999999999999987763
No 63
>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=85.56 E-value=3.4 Score=35.63 Aligned_cols=75 Identities=8% Similarity=0.125 Sum_probs=51.0
Q ss_pred hhHHHHHHHhhCC---CCCcccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcch
Q 030812 35 IANISRIMKKALP---ANGKIAKDAKDTVQECVS------EFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (171)
Q Consensus 35 ~A~V~RImK~~LP---~~~rISkDA~~al~~cas------eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv 105 (171)
...+..|++..+. ....+.+|+.+.+.+.+. -.+..+...|.+.|..+++.+|+.+||..|++.+....+.
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 3446667765543 123588888877766443 2344456677888888899999999999999988655554
Q ss_pred HHHH
Q 030812 106 DPLK 109 (171)
Q Consensus 106 ~~Lk 109 (171)
..++
T Consensus 281 ~~i~ 284 (365)
T TIGR02928 281 ELIR 284 (365)
T ss_pred HHHH
Confidence 4443
No 64
>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=81.44 E-value=4.2 Score=38.28 Aligned_cols=64 Identities=23% Similarity=0.280 Sum_probs=45.2
Q ss_pred hhHHHHHHHhhCCC-CCcccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhc
Q 030812 35 IANISRIMKKALPA-NGKIAKDAKDTVQECVS---EFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 35 ~A~V~RImK~~LP~-~~rISkDA~~al~~cas---eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (171)
...+.+|++..+.. +..|++++.+.|.+.+. +.++.+ ..|...|..++|++|+.+||.|++..-
T Consensus 265 ~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll-~~Aa~~A~~~~~~~It~~dI~~vl~~~ 332 (531)
T TIGR02902 265 DEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIV-QLAAGIALGEGRKRILAEDIEWVAENG 332 (531)
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHH-HHHHHHHhhCCCcEEcHHHHHHHhCCc
Confidence 44566677776643 46799999998877665 333333 345567777889999999999997543
No 65
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=78.48 E-value=5.1 Score=36.84 Aligned_cols=53 Identities=26% Similarity=0.286 Sum_probs=49.0
Q ss_pred CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCC
Q 030812 50 GKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (171)
Q Consensus 50 ~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (171)
..|.+|+..++..-.+-=|+.+..+|...-.+.||..++-+||-.||+.|..+
T Consensus 21 ~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 21 SNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred cccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 47999999999999999999999999999999999999999999999987653
No 66
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=77.43 E-value=12 Score=35.44 Aligned_cols=49 Identities=18% Similarity=0.201 Sum_probs=38.8
Q ss_pred cccHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhcCCCccChhhHHHHHHhc
Q 030812 51 KIAKDAKDTVQECVSE-----------FISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 51 rISkDA~~al~~case-----------FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (171)
.++.+|...|-+.+.. .|.-|-.+|+..|..+++++|+++||..|++.-
T Consensus 447 ~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 447 PFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp -BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred CCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 5889998888877653 566777899999999999999999999999853
No 67
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=76.81 E-value=11 Score=30.57 Aligned_cols=65 Identities=14% Similarity=0.242 Sum_probs=51.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcchH-HHHHHHHHHH
Q 030812 52 IAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID-PLKAYLMRYR 116 (171)
Q Consensus 52 ISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv~-~Lk~~L~~yr 116 (171)
...-...-|-+.+--++.-|-..|.-++.+.++.||.++||..|+....=..|.. +=+++|-++-
T Consensus 31 yEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~lA 96 (148)
T KOG3334|consen 31 YEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLELA 96 (148)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHHH
Confidence 4455556677777777777888999999999999999999999999877777776 5556665543
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=76.32 E-value=11 Score=36.22 Aligned_cols=49 Identities=12% Similarity=0.156 Sum_probs=39.3
Q ss_pred cccHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhc
Q 030812 51 KIAKDAKDTVQECVS-------------EFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 51 rISkDA~~al~~cas-------------eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (171)
.++++|.+.|.+.++ .=|.-|-.+|..+|..+++.+|+.+||.+|++.-
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 699999988876544 2345566788888988999999999999999754
No 69
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=74.16 E-value=3.2 Score=40.56 Aligned_cols=47 Identities=26% Similarity=0.327 Sum_probs=36.5
Q ss_pred cccHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 51 KIAKDAKDTVQECVSE--------------FISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 51 rISkDA~~al~~case--------------FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
-++++|..-|.+-+.. ....| .+|.++|..++++-|+++||.+|++.
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv-~~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLV-REAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHH-HHhhHHHhcCCcccCcHHHHHHHHHh
Confidence 4777777666655443 33444 49999999999999999999999987
No 70
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=70.08 E-value=19 Score=33.33 Aligned_cols=78 Identities=26% Similarity=0.332 Sum_probs=54.6
Q ss_pred CCCCCCCCcccccCchhH-------HHHHHHhhCC-CCCcccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCcc
Q 030812 20 SPHAGGVREQDRYLPIAN-------ISRIMKKALP-ANGKIAKDAKDTVQECVSE----FISFITSEASDKCQKEKRKTI 87 (171)
Q Consensus 20 ~~~~~~~~~~d~~LP~A~-------V~RImK~~LP-~~~rISkDA~~al~~case----FI~~LtseA~~~~~~~kRKTI 87 (171)
+|+.-+++--|+.|=+.+ |..|++--.. +++.++.||++.|.+...+ |...|-+.|+.+|.+.|-+++
T Consensus 338 SphGiP~D~lDR~lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v 417 (454)
T KOG2680|consen 338 SPHGIPIDLLDRMLIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVV 417 (454)
T ss_pred CCCCCcHHHhhhhheeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCcee
Confidence 445545555555544433 4555554333 4778999999999876543 555566678889999999999
Q ss_pred ChhhHHHHHH
Q 030812 88 NGDDLLWAMA 97 (171)
Q Consensus 88 ~~eDVl~AL~ 97 (171)
..+||-.+.+
T Consensus 418 ~~~di~r~y~ 427 (454)
T KOG2680|consen 418 EVDDIERVYR 427 (454)
T ss_pred ehhHHHHHHH
Confidence 9999999974
No 71
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=69.53 E-value=20 Score=26.39 Aligned_cols=47 Identities=15% Similarity=0.211 Sum_probs=39.3
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 51 KIAKDAKDTVQECVSEF------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 51 rISkDA~~al~~caseF------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.+++++...|..++..| ++-|..-|..+|--++...|..+||..||.
T Consensus 42 ~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 42 PLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred CCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 58888888888888776 345566788999999999999999999984
No 72
>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=68.43 E-value=25 Score=29.19 Aligned_cols=79 Identities=10% Similarity=0.153 Sum_probs=58.4
Q ss_pred ccccCchhHHHHHHHhhCCCCC--cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCccChhhHHHHHHhcC
Q 030812 29 QDRYLPIANISRIMKKALPANG--KIAKDAKDTVQECVSEFISFITSEASDKCQKE------KRKTINGDDLLWAMATLG 100 (171)
Q Consensus 29 ~d~~LP~A~V~RImK~~LP~~~--rISkDA~~al~~caseFI~~LtseA~~~~~~~------kRKTI~~eDVl~AL~~Lg 100 (171)
+..+|....|.+.|...+.... .|+.|+..+|.-||.+++..|-......|++- ...++-..||-..|..|+
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 3456777777777776665432 69999999999999999999999888888753 345666788887776665
Q ss_pred CCcchHH
Q 030812 101 FEDYIDP 107 (171)
Q Consensus 101 F~dyv~~ 107 (171)
--+..+.
T Consensus 121 ~~ek~e~ 127 (212)
T cd08045 121 QLEREEE 127 (212)
T ss_pred HHHHHHH
Confidence 5444443
No 73
>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=68.39 E-value=8.5 Score=26.10 Aligned_cols=61 Identities=15% Similarity=0.262 Sum_probs=38.2
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcchHHHHHHH
Q 030812 51 KIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYL 112 (171)
Q Consensus 51 rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv~~Lk~~L 112 (171)
-++..-.+.|..+... ...=+.+............-+.++++.||+++|..+.++.++.+|
T Consensus 23 g~~~~~i~~i~~~~~~-~~~~~~~~L~~W~~~~~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 23 GLSESEIENIEEENPD-LREQTYEMLQRWRQREGPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp TS-HHHHHHHHHHSTS-HHHHHHHHHHHHHHHHGSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred CcCHHHHHHHHHhCCC-hHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 3555555555554422 222233334444444556778899999999999999999888765
No 74
>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=67.07 E-value=9.1 Score=24.79 Aligned_cols=42 Identities=12% Similarity=0.120 Sum_probs=26.5
Q ss_pred cHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCccChhhHHHH
Q 030812 53 AKDAKDTVQECVSEFIS-FITSEASDKCQKEKRKTINGDDLLWA 95 (171)
Q Consensus 53 SkDA~~al~~caseFI~-~LtseA~~~~~~~kRKTI~~eDVl~A 95 (171)
+.||...|.+. =.|+. -|-..+-..|...|...||.++|..|
T Consensus 2 ~~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 2 TDEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp -HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred CHHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 45666666664 33544 33345557888999999999999876
No 75
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=66.95 E-value=17 Score=28.16 Aligned_cols=49 Identities=18% Similarity=0.262 Sum_probs=39.3
Q ss_pred CCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 47 PANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 47 P~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
.++..=-.|..++|...+.+||..++..|..+. +|--+..||++-+|+.
T Consensus 23 GDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRk 71 (109)
T KOG3901|consen 23 GDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRK 71 (109)
T ss_pred CCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHh
Confidence 344556678899999999999999988777776 4556788999999974
No 76
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=65.27 E-value=19 Score=28.24 Aligned_cols=50 Identities=18% Similarity=0.303 Sum_probs=42.2
Q ss_pred CCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 47 PANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 47 P~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
.+.+.=..|..++|.+.+..+++.+...|...|+ .|-.+..||...||++
T Consensus 23 GDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~ 72 (126)
T COG5248 23 GDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRR 72 (126)
T ss_pred CCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhh
Confidence 3455677899999999999999999999999998 4445678999999974
No 77
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=65.22 E-value=10 Score=29.92 Aligned_cols=64 Identities=22% Similarity=0.366 Sum_probs=48.0
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc----CCCccChhhHHHHHH
Q 030812 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKE----KRKTINGDDLLWAMA 97 (171)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~----kRKTI~~eDVl~AL~ 97 (171)
-+.+|...|.|.+|.-.....++-.-+. +- ....+.|||.|-.+.+.+. |-|-|++.|+..|++
T Consensus 28 GlqFpVgRihr~LK~r~t~h~rVGataa--vy--~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 28 GLQFPVGRIHRHLKTRTTSHGRVGATAA--VY--SAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred ccccchHHHHHHHHHhcccccccchHHH--HH--HHHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 4789999999999999887777765443 22 2235678999888877544 457899999988875
No 78
>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=63.84 E-value=6.8 Score=24.47 Aligned_cols=26 Identities=19% Similarity=0.231 Sum_probs=21.0
Q ss_pred HHHHHHhcCCCccChhhHHHHHHhcC
Q 030812 75 ASDKCQKEKRKTINGDDLLWAMATLG 100 (171)
Q Consensus 75 A~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (171)
|.+.|...+...|+.+|++.||=+-.
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 56789999999999999999975543
No 79
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=62.90 E-value=36 Score=29.43 Aligned_cols=84 Identities=13% Similarity=0.178 Sum_probs=54.3
Q ss_pred cCchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcc--h
Q 030812 32 YLPIANISRIMKKALP-ANGKIAKDAKDTVQECVSE---FISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY--I 105 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP-~~~rISkDA~~al~~case---FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dy--v 105 (171)
.++...+..|++.... .++.++.|+...|.+.|.= ++..+-..+.+.+...+.+.|+.++|..+++.++.... -
T Consensus 179 ~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~~~l~ 258 (328)
T PRK00080 179 FYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDELGLD 258 (328)
T ss_pred CCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCcCCCC
Confidence 3555667777765543 2568999998888877632 23334444556666666678999999999998877643 2
Q ss_pred HHHHHHHHHH
Q 030812 106 DPLKAYLMRY 115 (171)
Q Consensus 106 ~~Lk~~L~~y 115 (171)
+.-..+|..+
T Consensus 259 ~~~~~~l~~~ 268 (328)
T PRK00080 259 EMDRKYLRTI 268 (328)
T ss_pred HHHHHHHHHH
Confidence 2333455433
No 80
>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=62.15 E-value=43 Score=28.19 Aligned_cols=71 Identities=18% Similarity=0.204 Sum_probs=47.5
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCc
Q 030812 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSE---FISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (171)
Q Consensus 33 LP~A~V~RImK~~LP-~~~rISkDA~~al~~case---FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~d 103 (171)
++...+..|++.... .+..++.|+...|.+.+.= ++.-+...+.+.+...+...|+.++|..++..++++.
T Consensus 159 l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~~ 233 (305)
T TIGR00635 159 YTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMIDE 233 (305)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCCC
Confidence 445556666665543 2467999998888776532 2344444555666656667899999999999876653
No 81
>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=59.77 E-value=34 Score=27.66 Aligned_cols=50 Identities=20% Similarity=0.272 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCC-cchHHHHHHHHHHHHHh
Q 030812 63 CVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE-DYIDPLKAYLMRYREME 119 (171)
Q Consensus 63 caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~-dyv~~Lk~~L~~yre~~ 119 (171)
.+.+.+.||-.+|. |.-++.+++..-|+.|||+ +.++.+......+|+..
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l 93 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKL 93 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 45566777776666 5569999999999999997 56666666666666543
No 82
>PRK09862 putative ATP-dependent protease; Provisional
Probab=57.25 E-value=41 Score=31.97 Aligned_cols=56 Identities=11% Similarity=0.122 Sum_probs=43.3
Q ss_pred CcccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcch
Q 030812 50 GKIAKDAKDTVQECVSEF------ISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (171)
Q Consensus 50 ~rISkDA~~al~~caseF------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv 105 (171)
..+++++...+.+++..+ ..+|...|..+|.-++|..|+.+||..|+.--+++...
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 55677788999999999999999999999765555433
No 83
>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=57.03 E-value=43 Score=32.28 Aligned_cols=49 Identities=16% Similarity=0.184 Sum_probs=41.5
Q ss_pred CCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 49 NGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 49 ~~rISkDA~~al~~caseFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.+.|+.++.+.|.+.+..+- .++...|..+|.-++|.+|+.+||..|++
T Consensus 247 ~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~ 302 (633)
T TIGR02442 247 SVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAE 302 (633)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence 57899999999999887762 45667788889999999999999999886
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=55.14 E-value=58 Score=29.14 Aligned_cols=54 Identities=22% Similarity=0.198 Sum_probs=40.7
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 43 KKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 43 K~~LP~~~rISkDA~~al~~caseFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
++.++ .+.|+++.+..+.+.|..+= .++...|...|--++|..|+++||..+..
T Consensus 247 ~~~~~-~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 247 QNLLP-QVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred HHHhc-cCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 44455 67899999888888776652 24556677788889999999999998764
No 85
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=53.26 E-value=71 Score=26.53 Aligned_cols=66 Identities=18% Similarity=0.113 Sum_probs=45.9
Q ss_pred cCchhHHHHHHHhhCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 32 YLPIANISRIMKKALPA-NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~-~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.+....+.+++++.+.. +..|+.++...|...+.-=+..+-.+-...|.-.+.++|+.+||...+.
T Consensus 110 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~ 176 (302)
T TIGR01128 110 TPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVS 176 (302)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHh
Confidence 35566677777776654 5679999999998877654555555666555544444799999987765
No 86
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=52.92 E-value=36 Score=32.89 Aligned_cols=59 Identities=15% Similarity=0.141 Sum_probs=47.6
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 37 ~V~RImK~~LP~~~rISkDA~~al~~caseFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.|.+.-+ .++ ++.|+.+....+.++|..|= .++...|..+|-=++|.+|+.+||..|+.
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 DIAAARA-RLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHHHHHH-HHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 4444433 444 78999999999888888774 47778889999999999999999999986
No 87
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=51.34 E-value=1e+02 Score=25.90 Aligned_cols=51 Identities=20% Similarity=0.259 Sum_probs=38.9
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHH-hc--------------------------------CCCccChhhHHHHHHh
Q 030812 52 IAKDAKDTVQECVSEFISFITSEASDKCQ-KE--------------------------------KRKTINGDDLLWAMAT 98 (171)
Q Consensus 52 ISkDA~~al~~caseFI~~LtseA~~~~~-~~--------------------------------kRKTI~~eDVl~AL~~ 98 (171)
...-.+.+|.-.+..||+-|+..|.++.+ +. ++.+++..|+-.||++
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 34456778888999999999988776543 11 5667899999999998
Q ss_pred cCCC
Q 030812 99 LGFE 102 (171)
Q Consensus 99 LgF~ 102 (171)
.|+.
T Consensus 186 yGin 189 (197)
T COG5162 186 YGIN 189 (197)
T ss_pred hccc
Confidence 8873
No 88
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=51.30 E-value=37 Score=28.68 Aligned_cols=68 Identities=7% Similarity=0.018 Sum_probs=42.2
Q ss_pred CchhHHHHHHHhhCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCC
Q 030812 33 LPIANISRIMKKALPA-NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (171)
Q Consensus 33 LP~A~V~RImK~~LP~-~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (171)
++...+..++++.+.. +..++.++.+.|.+.+.-=+..+-......|. ...+|+.+||..++.....+
T Consensus 184 ~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~ 252 (337)
T PRK12402 184 PTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTD 252 (337)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCH
Confidence 4455667777665543 55799999999988773222222222233332 23479999999988765544
No 89
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=50.76 E-value=46 Score=32.56 Aligned_cols=47 Identities=15% Similarity=0.155 Sum_probs=38.2
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 51 KIAKDAKDTVQECVSEF-------------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 51 rISkDA~~al~~caseF-------------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.|+++|...|.+-++.- |.-|-.+|..+|+.++++.|+.+||..|+.
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 68999988887766532 233677899999999999999999999984
No 90
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=49.36 E-value=53 Score=29.72 Aligned_cols=72 Identities=14% Similarity=0.176 Sum_probs=49.1
Q ss_pred hHHHHHHHhhCCC---CCcccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcchH
Q 030812 36 ANISRIMKKALPA---NGKIAKDAKDTVQECV------SEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID 106 (171)
Q Consensus 36 A~V~RImK~~LP~---~~rISkDA~~al~~ca------seFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv~ 106 (171)
..|.-|+++-... ...++.++.+.+..-+ ..+..-|...|.++|+++++.+|+.+||..|-+..+..-+.+
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 3456666554432 3467777776665332 234456677899999999999999999999977666654444
Q ss_pred H
Q 030812 107 P 107 (171)
Q Consensus 107 ~ 107 (171)
.
T Consensus 273 ~ 273 (366)
T COG1474 273 V 273 (366)
T ss_pred H
Confidence 3
No 91
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=48.48 E-value=21 Score=33.93 Aligned_cols=44 Identities=16% Similarity=0.288 Sum_probs=32.2
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc
Q 030812 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKT 86 (171)
Q Consensus 43 K~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKT 86 (171)
|+++.+.--|-+|.+.||++||...=.||...-...-.++++++
T Consensus 426 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~ 469 (488)
T TIGR01052 426 KQSVADIPEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT 469 (488)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444688999999999999999999886665555554444
No 92
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=46.94 E-value=51 Score=31.15 Aligned_cols=47 Identities=15% Similarity=0.191 Sum_probs=40.4
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 51 KIAKDAKDTVQECVSEF------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 51 rISkDA~~al~~caseF------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.++++++..|.+++..| .+-|..-|..+|.-+++..|..+||..|+.
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 56889999999888876 556667889999999999999999999984
No 93
>smart00350 MCM minichromosome maintenance proteins.
Probab=44.74 E-value=1.1e+02 Score=28.51 Aligned_cols=65 Identities=11% Similarity=0.170 Sum_probs=46.4
Q ss_pred ccCchhHHHHHHHhh----CCCCCcccHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhcCCCcc
Q 030812 31 RYLPIANISRIMKKA----LPANGKIAKDAKDTVQECVSEF-------------------ISFITSEASDKCQKEKRKTI 87 (171)
Q Consensus 31 ~~LP~A~V~RImK~~----LP~~~rISkDA~~al~~caseF-------------------I~~LtseA~~~~~~~kRKTI 87 (171)
..++...+.+.+.-+ .| +|++++.+.|.+...+. +..|-..|...|+-..|.+|
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 457777777766433 34 68999999887654442 24455667777888899999
Q ss_pred ChhhHHHHHHh
Q 030812 88 NGDDLLWAMAT 98 (171)
Q Consensus 88 ~~eDVl~AL~~ 98 (171)
+.+||..|++-
T Consensus 493 ~~~Dv~~ai~l 503 (509)
T smart00350 493 EEADVEEAIRL 503 (509)
T ss_pred CHHHHHHHHHH
Confidence 99999999764
No 94
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=43.27 E-value=92 Score=28.21 Aligned_cols=54 Identities=19% Similarity=0.238 Sum_probs=43.4
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 43 KKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 43 K~~LP~~~rISkDA~~al~~caseFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
++.++ .+.|+++....+.+.|..+= .++...|.-.|--++|..|+++||..+..
T Consensus 260 r~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 260 QNLLP-KVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred HHhcC-CCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 44555 57899999999988887763 35666777888899999999999998875
No 95
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=42.78 E-value=91 Score=29.92 Aligned_cols=55 Identities=16% Similarity=0.232 Sum_probs=40.4
Q ss_pred HHhhCCCCCcccHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 42 MKKALPANGKIAKDAKDTVQECVSEF-------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 42 mK~~LP~~~rISkDA~~al~~caseF-------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
+++.++ .+.|+.+..+.|.+.|..+ -.++...|...|.-++|.+|+.+||..|..
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 344454 5789999987777766543 124455677778889999999999999986
No 96
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=42.54 E-value=89 Score=29.49 Aligned_cols=95 Identities=20% Similarity=0.239 Sum_probs=64.0
Q ss_pred CCCCCCCCccccc-------CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCcc
Q 030812 20 SPHAGGVREQDRY-------LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSE----FISFITSEASDKCQKEKRKTI 87 (171)
Q Consensus 20 ~~~~~~~~~~d~~-------LP~A~V~RImK~~LP-~~~rISkDA~~al~~case----FI~~LtseA~~~~~~~kRKTI 87 (171)
+|+.-+.+.-|+. .+..-|.-|++--.. +++.+++||.+.|....++ |..-|-.-|+.+|++.++++|
T Consensus 341 sPhGIP~DlLDRllII~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V 420 (450)
T COG1224 341 SPHGIPLDLLDRLLIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRV 420 (450)
T ss_pred CCCCCCHhhhhheeEEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCee
Confidence 4555455555554 345557777765443 3678999999999876654 445555678899999999999
Q ss_pred ChhhHHHHHHhcCCCcchHHHHHHHHHHHH
Q 030812 88 NGDDLLWAMATLGFEDYIDPLKAYLMRYRE 117 (171)
Q Consensus 88 ~~eDVl~AL~~LgF~dyv~~Lk~~L~~yre 117 (171)
..+||-.|-+ =|.|-.. --+|++.|++
T Consensus 421 ~~~dVe~a~~--lF~D~kr-Sv~~v~~~~~ 447 (450)
T COG1224 421 EVEDVERAKE--LFLDVKR-SVEYVEKYEG 447 (450)
T ss_pred ehhHHHHHHH--HHhhHHH-HHHHHHHHHh
Confidence 9999999953 2333322 2356666654
No 97
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=42.38 E-value=13 Score=35.12 Aligned_cols=77 Identities=12% Similarity=0.201 Sum_probs=62.7
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh---cCCCcchHH
Q 030812 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT---LGFEDYIDP 107 (171)
Q Consensus 31 ~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~---LgF~dyv~~ 107 (171)
+.+-+-.+.-+.+..+....+|-.|.-+.+-..+-.|+--+|.-+-..+++-+-+||-+.||-.-|+. +-++.|+..
T Consensus 382 Rl~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhlErnwnIr~pGf~~d 461 (505)
T COG5624 382 RLDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHLERNWNIRCPGFVDD 461 (505)
T ss_pred hhhhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeeeccccceecCcchHH
Confidence 45566667777777777778999999999999999999999988888899999999999999877763 334666654
No 98
>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=41.80 E-value=54 Score=21.14 Aligned_cols=32 Identities=13% Similarity=0.419 Sum_probs=26.0
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHH
Q 030812 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEF 67 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseF 67 (171)
.+-+++|.|++... .+|+.+.++-|.+++.+.
T Consensus 10 gvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~l 41 (46)
T PF00356_consen 10 GVSKSTVSRVLNGP----PRVSEETRERILEAAEEL 41 (46)
T ss_dssp TSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHHH
Confidence 46688999998755 489999999999888763
No 99
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=41.54 E-value=36 Score=31.71 Aligned_cols=32 Identities=25% Similarity=0.258 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHhcCCCccChhhHHHHHHhc
Q 030812 68 ISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 68 I~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (171)
|..|..+|...|.+++|..|+.+||..|++..
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v 424 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEKV 424 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence 56778889999999999999999999999763
No 100
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=41.52 E-value=74 Score=27.18 Aligned_cols=64 Identities=11% Similarity=0.149 Sum_probs=45.7
Q ss_pred HHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccChhhHHHHHHhcCC
Q 030812 38 ISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQK--EKRKTINGDDLLWAMATLGF 101 (171)
Q Consensus 38 V~RImK~~LP-~~~rISkDA~~al~~caseFI~~LtseA~~~~~~--~kRKTI~~eDVl~AL~~LgF 101 (171)
+.++|++.+. .+..|+.+|...|.+++.-=...+..|-...|.- .++.+|+.+||...+....+
T Consensus 135 l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~ 201 (326)
T PRK07452 135 LKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQ 201 (326)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcC
Confidence 4455544443 3568999999999998886556666666666654 45778999999988776554
No 101
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=40.99 E-value=40 Score=31.51 Aligned_cols=74 Identities=20% Similarity=0.217 Sum_probs=47.5
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHH-HHHHHHHHHHH----HHHHHHHHHHHHHhcCCCccChhhHHHHHHhc
Q 030812 26 VREQDRYLPIANISRIMKKALPANGKIAKDA-KDTVQECVSEF----ISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~~rISkDA-~~al~~caseF----I~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (171)
-|.-++.||-..=.+-|=+..-..+.+++|. .+.|.+++.-| |.-|..||--.|.++.|..|+-+|++.|.++.
T Consensus 314 DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~KV 392 (406)
T COG1222 314 DRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEKV 392 (406)
T ss_pred cceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHHHHHHHH
Confidence 3444455663332222222222234566655 45566655554 77889999999999999999999999998753
No 102
>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=40.78 E-value=42 Score=25.48 Aligned_cols=33 Identities=21% Similarity=0.318 Sum_probs=26.8
Q ss_pred hHHHHHHHhhC----CCCCcccHHHHHHHHHHHHHHH
Q 030812 36 ANISRIMKKAL----PANGKIAKDAKDTVQECVSEFI 68 (171)
Q Consensus 36 A~V~RImK~~L----P~~~rISkDA~~al~~caseFI 68 (171)
++|.+++|+.| .|+..++.++.+.|+++++.|-
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~a 87 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELWA 87 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHHH
Confidence 56788999887 3466899999999999999983
No 103
>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=40.69 E-value=34 Score=22.36 Aligned_cols=25 Identities=28% Similarity=0.489 Sum_probs=20.8
Q ss_pred ccChhhHHHHHHhcCCCcchHHHHH
Q 030812 86 TINGDDLLWAMATLGFEDYIDPLKA 110 (171)
Q Consensus 86 TI~~eDVl~AL~~LgF~dyv~~Lk~ 110 (171)
+=+++||..-|+.+||.+|.+..+.
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 3468899999999999999887664
No 104
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=40.65 E-value=39 Score=30.40 Aligned_cols=34 Identities=21% Similarity=0.234 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcC
Q 030812 67 FISFITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (171)
Q Consensus 67 FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (171)
=|..|..+|...|.+++++.|+.+|+..|++..-
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~ 373 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVM 373 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence 3556777888888899999999999999997653
No 105
>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=40.47 E-value=44 Score=28.52 Aligned_cols=76 Identities=9% Similarity=0.107 Sum_probs=35.6
Q ss_pred CcccccCchhHHHHHHHhhCCCC--CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CccChhhHHHHHHh
Q 030812 27 REQDRYLPIANISRIMKKALPAN--GKIAKDAKDTVQECVSEFISFITSEASDKCQKEKR------KTINGDDLLWAMAT 98 (171)
Q Consensus 27 ~~~d~~LP~A~V~RImK~~LP~~--~rISkDA~~al~~caseFI~~LtseA~~~~~~~kR------KTI~~eDVl~AL~~ 98 (171)
..++.+|....+.+-|.+....+ ..|..|...+|.-||.+++..|-..+..+|++-.. .+....||-..|..
T Consensus 38 ~~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~ 117 (264)
T PF05236_consen 38 EKEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRF 117 (264)
T ss_dssp ------S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH----------------------------
T ss_pred cccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHH
Confidence 35567888888888887776443 46999999999999999999999988888764321 13346677666665
Q ss_pred cCCC
Q 030812 99 LGFE 102 (171)
Q Consensus 99 LgF~ 102 (171)
|.--
T Consensus 118 l~~~ 121 (264)
T PF05236_consen 118 LEQL 121 (264)
T ss_dssp ----
T ss_pred HHHH
Confidence 5443
No 106
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=40.01 E-value=97 Score=23.87 Aligned_cols=31 Identities=13% Similarity=0.097 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhcCCCccChhhHHHHHHhcCCC
Q 030812 70 FITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (171)
Q Consensus 70 ~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (171)
||+ |+-.|.-.+...+|.+||...|+..|.+
T Consensus 3 yva--Ayll~~l~g~~~pta~dI~~IL~AaGve 33 (113)
T PLN00138 3 VVA--AYLLAVLGGNTCPSAEDLKDILGSVGAD 33 (113)
T ss_pred HHH--HHHHHHhcCCCCCCHHHHHHHHHHcCCc
Confidence 554 6778888899999999999999998875
No 107
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=39.68 E-value=42 Score=29.53 Aligned_cols=33 Identities=24% Similarity=0.277 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHhcCCCccChhhHHHHHHhc
Q 030812 67 FISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 67 FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (171)
-|..|..+|...|.+.+|..|+.+|+..|++..
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~~ 363 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEKV 363 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHh
Confidence 355677788889999999999999999999763
No 108
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=39.37 E-value=96 Score=26.30 Aligned_cols=66 Identities=17% Similarity=0.078 Sum_probs=46.7
Q ss_pred cCchhHHHHHHHhhCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCccChhhHHHHHHh
Q 030812 32 YLPIANISRIMKKALPA-NGKIAKDAKDTVQECVSEFISFITSEASDKCQKE-KRKTINGDDLLWAMAT 98 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~-~~rISkDA~~al~~caseFI~~LtseA~~~~~~~-kRKTI~~eDVl~AL~~ 98 (171)
.+....+.+.|+..+.. +..|+.+|...|.+.+..=...+..|-...|.-. +++ |+.+||-..+..
T Consensus 145 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~ 212 (340)
T PRK05574 145 PPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPD 212 (340)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhh
Confidence 35566667767666643 5689999999999988766667777777666533 233 999998776553
No 109
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=39.04 E-value=1.1e+02 Score=27.49 Aligned_cols=53 Identities=11% Similarity=0.031 Sum_probs=41.2
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhhHHHHH
Q 030812 43 KKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAM 96 (171)
Q Consensus 43 K~~LP~~~rISkDA~~al~~caseFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (171)
++.++ .+.|+++....+.+.|..+= .+|...|...|--++|..|+++||..+.
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 34454 57899999998888887763 2366778888999999999999996654
No 110
>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=38.20 E-value=27 Score=24.75 Aligned_cols=51 Identities=20% Similarity=0.374 Sum_probs=28.5
Q ss_pred CCcccHHHHHHHHHHHH-------HHHHHHHHHHHHHH-HhcCCCccChhhHHHHHHhc
Q 030812 49 NGKIAKDAKDTVQECVS-------EFISFITSEASDKC-QKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 49 ~~rISkDA~~al~~cas-------eFI~~LtseA~~~~-~~~kRKTI~~eDVl~AL~~L 99 (171)
++|++.+.++.|.+++. .||.-.+.++.+.. ..+..-+++.+|.-.-++.|
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~aL 61 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMAAL 61 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHHHH
Confidence 36899999999999875 56555544444322 23334456666644444433
No 111
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=37.33 E-value=1.2e+02 Score=23.51 Aligned_cols=32 Identities=6% Similarity=0.161 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCC
Q 030812 69 SFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (171)
Q Consensus 69 ~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (171)
.||+ |+-.|.-.++.++|.+||...|+..|.+
T Consensus 4 kyva--AYlL~~lgG~~~pTaddI~kIL~AaGve 35 (112)
T PTZ00373 4 KYVA--AYLMCVLGGNENPTKKEVKNVLSAVNAD 35 (112)
T ss_pred HHHH--HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 3554 6778888999999999999999998875
No 112
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=37.15 E-value=61 Score=23.01 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=26.2
Q ss_pred hhhHHHHHHhcCC------CcchHHHHHHHHHHHHHhh
Q 030812 89 GDDLLWAMATLGF------EDYIDPLKAYLMRYREMEG 120 (171)
Q Consensus 89 ~eDVl~AL~~LgF------~dyv~~Lk~~L~~yre~~~ 120 (171)
++.|..+|..||| +.|-+.++..|..|..+++
T Consensus 18 ~~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~EN 55 (74)
T PF08823_consen 18 AREVQEALKRLGYYKGEADGVWDEATEDALRAWAGTEN 55 (74)
T ss_pred HHHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhh
Confidence 3567889999999 6788889999999887654
No 113
>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=36.71 E-value=28 Score=21.94 Aligned_cols=24 Identities=21% Similarity=0.425 Sum_probs=19.9
Q ss_pred ChhhHHHHHHhcCCCcchHHHHHH
Q 030812 88 NGDDLLWAMATLGFEDYIDPLKAY 111 (171)
Q Consensus 88 ~~eDVl~AL~~LgF~dyv~~Lk~~ 111 (171)
+.++|..-|+.+|+++|++.++..
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 678999999999998888877654
No 114
>cd00823 TopoIIB_Trans TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB family is topo VI. Topo VI enzymes are heterotetramers found in archaea and plants. S. shibatae topoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Probab=35.38 E-value=68 Score=26.19 Aligned_cols=42 Identities=17% Similarity=0.316 Sum_probs=30.4
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHH
Q 030812 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEA 75 (171)
Q Consensus 31 ~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA 75 (171)
..+|..... |+++.+.--|-+|.+.||++||...=.||...-
T Consensus 102 t~VPfts~~---KeaIadvpEI~~EIrlAl~~~~R~L~~~l~kk~ 143 (151)
T cd00823 102 TKVPFTSEG---KEAIADIPEIEEEIKLALQEVARKLKRYLSKKR 143 (151)
T ss_pred cCCCcCCcc---hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345544442 455555446889999999999999999997643
No 115
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=35.14 E-value=1.1e+02 Score=27.93 Aligned_cols=75 Identities=17% Similarity=0.221 Sum_probs=48.9
Q ss_pred CCCcccccCchhHHHHHHHhhCCCCC--cccHHHHHHHHHH-HHHHHHHHHHHHHH-HH--HhcCC-CccChhhHHHHHH
Q 030812 25 GVREQDRYLPIANISRIMKKALPANG--KIAKDAKDTVQEC-VSEFISFITSEASD-KC--QKEKR-KTINGDDLLWAMA 97 (171)
Q Consensus 25 ~~~~~d~~LP~A~V~RImK~~LP~~~--rISkDA~~al~~c-aseFI~~LtseA~~-~~--~~~kR-KTI~~eDVl~AL~ 97 (171)
++..-|+- --|.|.-.+++.+|+.- .+..|--..|.+. ++.|+.-|+..-++ ++ ..=+- .+++.+||++|+.
T Consensus 43 PVTvaDyG-~QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~aID 121 (351)
T KOG1528|consen 43 PVTVADYG-SQAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLKAID 121 (351)
T ss_pred Ccchhhhh-HHHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHHHHh
Confidence 45555554 35788899999999754 5666666666554 56677777763333 22 22222 7899999999997
Q ss_pred hcC
Q 030812 98 TLG 100 (171)
Q Consensus 98 ~Lg 100 (171)
.-+
T Consensus 122 ~G~ 124 (351)
T KOG1528|consen 122 RGN 124 (351)
T ss_pred ccc
Confidence 543
No 116
>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=34.59 E-value=46 Score=21.67 Aligned_cols=22 Identities=23% Similarity=0.453 Sum_probs=19.2
Q ss_pred ChhhHHHHHHhcCCCcchHHHH
Q 030812 88 NGDDLLWAMATLGFEDYIDPLK 109 (171)
Q Consensus 88 ~~eDVl~AL~~LgF~dyv~~Lk 109 (171)
++++|..-|+.+|++.|++...
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 6789999999999999988763
No 117
>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=34.51 E-value=39 Score=26.07 Aligned_cols=61 Identities=10% Similarity=0.163 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcchHHHHHHHHHHHHH
Q 030812 54 KDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREM 118 (171)
Q Consensus 54 kDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv~~Lk~~L~~yre~ 118 (171)
..++.-|..|..+.-.|......=.. ----.-..++..|+..|++.++.+++..|.+|+..
T Consensus 72 s~Vk~Eiaa~~~v~~~Y~~~L~~G~v----d~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~ 132 (134)
T PF12010_consen 72 SPVKNEIAACSNVWSEYYPPLETGLV----DPEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAA 132 (134)
T ss_pred chhHHHHHHHHHHHHHHHHHHHccCC----CHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHh
Confidence 34556666666666666543222111 01123456788899999999999999999999853
No 118
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=34.31 E-value=56 Score=29.84 Aligned_cols=32 Identities=25% Similarity=0.233 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHhcCCCccChhhHHHHHHhc
Q 030812 68 ISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 68 I~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (171)
|..|..+|...|.+++|..|+.+|+..|++..
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 66778889999999999999999999998753
No 119
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=34.07 E-value=32 Score=33.07 Aligned_cols=46 Identities=17% Similarity=0.344 Sum_probs=36.8
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC
Q 030812 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTIN 88 (171)
Q Consensus 43 K~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~ 88 (171)
|+++.+.--|-+|.+.|+++||.+.=+||.....+.-..+++++|.
T Consensus 434 KqsIa~vpeIe~Eir~Al~evaRkL~~yLsrk~r~~e~~~K~~~i~ 479 (538)
T COG1389 434 KQSIADVPEIENEIRLALMEVARKLKLYLSRKRREMEERKKRKTIE 479 (538)
T ss_pred chhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444434468899999999999999999999988887787777764
No 120
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=33.21 E-value=64 Score=27.21 Aligned_cols=61 Identities=11% Similarity=-0.004 Sum_probs=45.6
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ccChhhHHHHH
Q 030812 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRK---TINGDDLLWAM 96 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRK---TI~~eDVl~AL 96 (171)
.||+++|.+++...+. -.|+...+.+|+-.+.+|+-.|--.|..+ .+++. -+.+.|+-.|.
T Consensus 115 ~lnKt~VKKlastV~n--QtVspNi~I~l~g~~KVfvGEiIElA~~V--q~~w~~sgpl~p~h~reay 178 (199)
T COG5251 115 SLNKTQVKKLASTVAN--QTVSPNIRIFLQGVGKVFVGEIIELAMIV--QNKWLTSGPLIPFHKREAY 178 (199)
T ss_pred CCCHHHHHHHHHHHhc--cccCCCeeeeeechhHHHHHHHHHHHHHH--HHHhcccCCCChHHHHHHH
Confidence 6999999999999984 56888888899999999988876555432 23333 36677776665
No 121
>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=33.17 E-value=49 Score=18.76 Aligned_cols=26 Identities=23% Similarity=0.234 Sum_probs=20.0
Q ss_pred HHHHHHhcCCCccChhhHHHHHH-hcC
Q 030812 75 ASDKCQKEKRKTINGDDLLWAMA-TLG 100 (171)
Q Consensus 75 A~~~~~~~kRKTI~~eDVl~AL~-~Lg 100 (171)
+....-.++.-+|+.+++..+|+ .||
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 45566677788999999999999 576
No 122
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=32.78 E-value=31 Score=24.58 Aligned_cols=18 Identities=17% Similarity=0.381 Sum_probs=15.8
Q ss_pred ccChhhHHHHHHhcCCCc
Q 030812 86 TINGDDLLWAMATLGFED 103 (171)
Q Consensus 86 TI~~eDVl~AL~~LgF~d 103 (171)
.+++.+|+++|+.+||..
T Consensus 6 ~~~~ke~ik~Le~~Gf~~ 23 (66)
T COG1724 6 RMKAKEVIKALEKDGFQL 23 (66)
T ss_pred cCCHHHHHHHHHhCCcEE
Confidence 478999999999999963
No 123
>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=32.69 E-value=32 Score=22.01 Aligned_cols=14 Identities=36% Similarity=0.672 Sum_probs=11.8
Q ss_pred hhHHHHHHhcCCCc
Q 030812 90 DDLLWAMATLGFED 103 (171)
Q Consensus 90 eDVl~AL~~LgF~d 103 (171)
+|++.||..|||..
T Consensus 4 ~d~~~AL~~LGy~~ 17 (47)
T PF07499_consen 4 EDALEALISLGYSK 17 (47)
T ss_dssp HHHHHHHHHTTS-H
T ss_pred HHHHHHHHHcCCCH
Confidence 68999999999973
No 124
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=32.51 E-value=1.1e+02 Score=26.86 Aligned_cols=61 Identities=18% Similarity=0.150 Sum_probs=45.1
Q ss_pred HHHHHHhhCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 38 ISRIMKKALPA-NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 38 V~RImK~~LP~-~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
+.+.+++.+.. +.+|++||.+.|..+..-=...|..|-...|--..-++|+.+||..++..
T Consensus 145 l~~~i~~~~~~~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~ 206 (334)
T COG1466 145 LPQWIKKRAKELGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSD 206 (334)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhc
Confidence 44444444432 57899999999999998767777777776666444449999999998874
No 125
>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=32.28 E-value=8.7 Score=25.27 Aligned_cols=58 Identities=26% Similarity=0.413 Sum_probs=32.3
Q ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc---ChhhHHHHHHhcCCCcch-HHHHH
Q 030812 49 NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTI---NGDDLLWAMATLGFEDYI-DPLKA 110 (171)
Q Consensus 49 ~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI---~~eDVl~AL~~LgF~dyv-~~Lk~ 110 (171)
+.+|.+++..+|.+++. .+..|+.+ +-..+=.|.+ .+...+..|.++|+.+|+ +.+..
T Consensus 1 gF~ie~~t~~ai~~~~~-~L~~is~E---Ri~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~ 62 (64)
T PF12627_consen 1 GFKIEPETEEAIKENAE-LLSKISKE---RIREELEKILSSPNPSRAFKLLDELGLLEYIFPELDA 62 (64)
T ss_dssp T-EE-HHHHHHHHHHGG-GGGGS-HH---HHHHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT
T ss_pred CCccCHHHHHHHHHHHH-HHhcCCHH---HHHHHHHHHHcCCCHHHHHHHHHHcCCHHHHCccccc
Confidence 35788888888888777 44555443 2222223333 345566677788877664 54443
No 126
>PRK07914 hypothetical protein; Reviewed
Probab=31.10 E-value=1e+02 Score=26.61 Aligned_cols=63 Identities=11% Similarity=0.144 Sum_probs=43.0
Q ss_pred chhHHHHHHHhhCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 34 PIANISRIMKKALPA-NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 34 P~A~V~RImK~~LP~-~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
+-..+.+.|++.+.. +..|+.||...|.+++..=+..+..|-...+-..+ .+|+.+||...+.
T Consensus 129 ~~~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 192 (320)
T PRK07914 129 KAAERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHS 192 (320)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcC
Confidence 345555555555543 56899999999999986656666666555554333 5799999887755
No 127
>PTZ00183 centrin; Provisional
Probab=30.01 E-value=2e+02 Score=21.02 Aligned_cols=21 Identities=19% Similarity=0.262 Sum_probs=12.6
Q ss_pred HHHhcCCCccChhhHHHHHHh
Q 030812 78 KCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 78 ~~~~~kRKTI~~eDVl~AL~~ 98 (171)
.+..++...|+.++.+.++..
T Consensus 61 ~~d~~~~g~i~~~eF~~~~~~ 81 (158)
T PTZ00183 61 DVDKDGSGKIDFEEFLDIMTK 81 (158)
T ss_pred HhCCCCCCcEeHHHHHHHHHH
Confidence 334455666777777766654
No 128
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=29.94 E-value=1.7e+02 Score=22.25 Aligned_cols=31 Identities=13% Similarity=0.164 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHhcCCCccChhhHHHHHHhcCCC
Q 030812 70 FITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (171)
Q Consensus 70 ~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (171)
||+ |+-.|.-.++..||.+||...|+..|.+
T Consensus 3 yva--AylL~~l~g~~~pTa~dI~~IL~AaGve 33 (109)
T cd05833 3 YVA--AYLLAVLGGNASPSAADVKKILGSVGVE 33 (109)
T ss_pred HHH--HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 554 5778888888899999999999998874
No 129
>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=29.85 E-value=40 Score=21.34 Aligned_cols=26 Identities=15% Similarity=0.340 Sum_probs=20.6
Q ss_pred ccChhhHHHHHHhcCCCcchHHHHHH
Q 030812 86 TINGDDLLWAMATLGFEDYIDPLKAY 111 (171)
Q Consensus 86 TI~~eDVl~AL~~LgF~dyv~~Lk~~ 111 (171)
.-+.++|..-|..+||.+|++.+...
T Consensus 3 ~w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 3 QWSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCCHHHHHHHHHHCChHHHHHHHHHC
Confidence 34678899999999999888776654
No 130
>TIGR01278 DPOR_BchB light-independent protochlorophyllide reductase, B subunit. This enzyme describes the B subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme. This subunit shows homology to the nitrogenase molybdenum-iron protein. It catalyzes a step in bacteriochlorophyll biosynthesis.
Probab=29.32 E-value=1.1e+02 Score=28.67 Aligned_cols=51 Identities=12% Similarity=0.158 Sum_probs=39.0
Q ss_pred CCcccHHHHHHHHHHHHHHH-HHHHHHHHHHHHhcCCCccChhhHHHHHHhcC
Q 030812 49 NGKIAKDAKDTVQECVSEFI-SFITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (171)
Q Consensus 49 ~~rISkDA~~al~~caseFI-~~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (171)
.+.++.||...|.+ .=-|+ .-+-..+-+.|+..+...||.+.|..|-..+|
T Consensus 460 ~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 511 (511)
T TIGR01278 460 ELGWTAEAEAELKK-VPFFVRGKVRRNTENFARERGYSVITLEVIYAAKEHFG 511 (511)
T ss_pred CCCcCHHHHHHHhh-CChhhhHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhcC
Confidence 46799999999965 33444 34445566788999999999999999976654
No 131
>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=28.92 E-value=1.8e+02 Score=19.50 Aligned_cols=48 Identities=19% Similarity=0.200 Sum_probs=33.8
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 030812 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQK 81 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~ 81 (171)
.+|=+.+.-+++.+.=+ .-..-.+-+|.=++..||.-|+..|.+.|+-
T Consensus 2 ~IPD~v~~~yL~~~G~~--~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSGFQ--TSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCCCC--CCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35667777777766421 1223345678888999999999999998863
No 132
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=28.81 E-value=1.1e+02 Score=28.71 Aligned_cols=52 Identities=13% Similarity=0.145 Sum_probs=39.8
Q ss_pred CCCcccHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCccChhhHHHHHHhcC
Q 030812 48 ANGKIAKDAKDTVQECVSEFIS-FITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (171)
Q Consensus 48 ~~~rISkDA~~al~~caseFI~-~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (171)
+.+.++.||...|.+ .=-|+. -+-..+-+.|+..+...|+.+.|..|-..+|
T Consensus 466 ~~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 518 (519)
T PRK02910 466 SELVWTPEAEAELKK-IPFFVRGKVRRNTEKFARERGLPEITLEVLYDAKAHFG 518 (519)
T ss_pred CCCCCCHHHHHHHhh-CChhhHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhc
Confidence 456899999999965 444554 3444556788999999999999999977654
No 133
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=27.87 E-value=46 Score=32.01 Aligned_cols=56 Identities=20% Similarity=0.311 Sum_probs=41.0
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC--hhhHHHHHHh
Q 030812 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTIN--GDDLLWAMAT 98 (171)
Q Consensus 43 K~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~--~eDVl~AL~~ 98 (171)
|+++.+.--|-+|.+.||++||...=.||...-...-.+++++++. -.+|..+|..
T Consensus 431 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~k~~~~~~y~p~~a~~~~~ 488 (535)
T PRK04184 431 KEAIADVPEIEKEIRLALQEVARKLKKYLSRKRKEEEAKKKAKTFEKYIPEIARKLAE 488 (535)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555544468999999999999999999998776666666665543 3566666654
No 134
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=27.77 E-value=1.3e+02 Score=25.12 Aligned_cols=65 Identities=9% Similarity=0.053 Sum_probs=39.1
Q ss_pred CchhHHHHHHHhhCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhc
Q 030812 33 LPIANISRIMKKALPA-NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 33 LP~A~V~RImK~~LP~-~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (171)
++...+.++++..+.. +..|+.++.+.+.+.+.--+..+-.+-...+. . .++|+.+||..++...
T Consensus 161 l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~-~-~~~it~~~v~~~~~~~ 226 (319)
T PRK00440 161 LKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAA-T-GKEVTEEAVYKITGTA 226 (319)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH-c-CCCCCHHHHHHHhCCC
Confidence 4455566666655532 56799999999888765332222222222222 2 3689999998887543
No 135
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=27.71 E-value=1.2e+02 Score=21.38 Aligned_cols=28 Identities=14% Similarity=0.141 Sum_probs=21.2
Q ss_pred HHHHHHhcCCCccChhhHHHHHHhcCCC
Q 030812 75 ASDKCQKEKRKTINGDDLLWAMATLGFE 102 (171)
Q Consensus 75 A~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (171)
+...+-.++.-+|+.++|..+|..+|+.
T Consensus 15 ~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 15 IFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 4455566777788899998888888764
No 136
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=27.30 E-value=4e+02 Score=25.31 Aligned_cols=89 Identities=15% Similarity=0.128 Sum_probs=53.2
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHH----------HHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhc
Q 030812 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVS----------EFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (171)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~cas----------eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (171)
++++|.+.|---|... ++.|..+....+..-.. .-+.-|..+..+......=-.=++.+|..+|+.+
T Consensus 161 ~~E~~~~~~l~~me~~---Gi~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~g~~~~n~~S~~ql~~~L~~~ 237 (553)
T PRK14975 161 AAESAGALAAAEMELA---GLPWDTDVHEALLAELLGPRPAAGGRPARLAELAAEIREALGRPRLNPDSPQQVLRALRRA 237 (553)
T ss_pred HHHhhHHHHHHHHHHh---CeEeCHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHC
Confidence 4466766666666544 46788887766665544 4555666555544422111234678999999988
Q ss_pred CCC----------cchHHHHHHHHHHHHHhhc
Q 030812 100 GFE----------DYIDPLKAYLMRYREMEGD 121 (171)
Q Consensus 100 gF~----------dyv~~Lk~~L~~yre~~~~ 121 (171)
|+. .-..|+-..|-+||+..+.
T Consensus 238 g~~~~~t~~~~L~~~~hp~~~~ile~r~~~kl 269 (553)
T PRK14975 238 GIELPSTRKWELREIDHPAVEPLLEYRKLSKL 269 (553)
T ss_pred CCCCCCCcHHHhccCCCchHHHHHHHHHHHHH
Confidence 884 1112344556678876543
No 137
>PHA03328 nuclear egress lamina protein UL31; Provisional
Probab=25.62 E-value=81 Score=28.62 Aligned_cols=79 Identities=19% Similarity=0.336 Sum_probs=48.9
Q ss_pred cccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcchHH
Q 030812 28 EQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDP 107 (171)
Q Consensus 28 ~~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv~~ 107 (171)
.+++-||=.-|.+|+- ++| +.+|+-|... .-||+.+...+--....+..-||+++||..++.+|+|++ +-
T Consensus 229 ~~slHL~~~~L~~Ll~-n~~-gY~i~adv~~------~~fvL~v~~~~~~~~~~~~~~~V~~~dIy~k~~dL~f~d--El 298 (316)
T PHA03328 229 GKSLHLHYRLIDRLLT-ACP-GYRIIAHVWQ------TTFVLVVRRDAERQTTDADVPAVSAEDIYCKMCDLNFDG--EL 298 (316)
T ss_pred CCcccchHHHHHHHHH-hCC-CCeEEEEEec------ceEEEEEeeCCCCCCccccccccCHHHHHHHHhCCCCCh--HH
Confidence 3445566665655554 455 5666554422 345555554433345677788999999999999999985 23
Q ss_pred HHHHHHHHH
Q 030812 108 LKAYLMRYR 116 (171)
Q Consensus 108 Lk~~L~~yr 116 (171)
+.+|..-|.
T Consensus 299 ~~Ey~kly~ 307 (316)
T PHA03328 299 LLEYKRLYA 307 (316)
T ss_pred HHHHHHHHH
Confidence 334444443
No 138
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=25.45 E-value=1.9e+02 Score=24.96 Aligned_cols=61 Identities=16% Similarity=0.162 Sum_probs=40.2
Q ss_pred HHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCccChhhHHHHHH
Q 030812 37 NISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQK-EKRKTINGDDLLWAMA 97 (171)
Q Consensus 37 ~V~RImK~~LP-~~~rISkDA~~al~~caseFI~~LtseA~~~~~~-~kRKTI~~eDVl~AL~ 97 (171)
.+.+++++.+. .+.+|+.||...|.+++.-=...+..+-...+.- ...++|+.+||...+.
T Consensus 146 ~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 146 DLARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 34444444443 3568999999999998876444555555555543 3456899999977654
No 139
>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=25.24 E-value=1.5e+02 Score=28.65 Aligned_cols=72 Identities=14% Similarity=0.193 Sum_probs=45.7
Q ss_pred hhHHHHHHHhhCCC-CCcccHHHHHHHHHHH---HHHHHHHHHHH----HH---HHHhcCCCccChhhHHHHHHhcCCCc
Q 030812 35 IANISRIMKKALPA-NGKIAKDAKDTVQECV---SEFISFITSEA----SD---KCQKEKRKTINGDDLLWAMATLGFED 103 (171)
Q Consensus 35 ~A~V~RImK~~LP~-~~rISkDA~~al~~ca---seFI~~LtseA----~~---~~~~~kRKTI~~eDVl~AL~~LgF~d 103 (171)
...+..|++..+.. +..++.++.++|.+++ ...++.|.... .. .+...++.+|+.+||.+++..--|..
T Consensus 355 ~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r~~~ 434 (615)
T TIGR02903 355 PEDIALIVLNAAEKINVHLAAGVEELIARYTIEGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQISRLSP 434 (615)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCCcCcc
Confidence 35577777776653 3468999999988765 33444443221 11 12233456899999999998777765
Q ss_pred chH
Q 030812 104 YID 106 (171)
Q Consensus 104 yv~ 106 (171)
|..
T Consensus 435 ~~~ 437 (615)
T TIGR02903 435 YEK 437 (615)
T ss_pred chh
Confidence 543
No 140
>PTZ00183 centrin; Provisional
Probab=24.86 E-value=2.8e+02 Score=20.25 Aligned_cols=29 Identities=21% Similarity=0.148 Sum_probs=22.2
Q ss_pred HHHHHHHhcCCCccChhhHHHHHHhcCCC
Q 030812 74 EASDKCQKEKRKTINGDDLLWAMATLGFE 102 (171)
Q Consensus 74 eA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (171)
.+...+-.++.-.|+.+++..+|..+|..
T Consensus 94 ~~F~~~D~~~~G~i~~~e~~~~l~~~~~~ 122 (158)
T PTZ00183 94 KAFRLFDDDKTGKISLKNLKRVAKELGET 122 (158)
T ss_pred HHHHHhCCCCCCcCcHHHHHHHHHHhCCC
Confidence 34556666777789999999999988854
No 141
>PRK09526 lacI lac repressor; Reviewed
Probab=24.41 E-value=72 Score=26.69 Aligned_cols=36 Identities=14% Similarity=0.498 Sum_probs=29.0
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHH
Q 030812 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFIT 72 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~Lt 72 (171)
-.-++||.|++... .+||++.++-+.+++.+ +.|.-
T Consensus 16 GVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~p 51 (342)
T PRK09526 16 GVSYQTVSRVLNQA----SHVSAKTREKVEAAMAE-LNYVP 51 (342)
T ss_pred CCCHHHHHHHhcCC----CCCCHHHHHHHHHHHHH-HCCCc
Confidence 46688999999642 37999999999999999 56654
No 142
>PF11753 DUF3310: Protein of unknwon function (DUF3310); InterPro: IPR021739 This entry is represented by Bacteriophage T7, Gp1.7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=24.21 E-value=2.3e+02 Score=19.15 Aligned_cols=42 Identities=21% Similarity=0.192 Sum_probs=31.4
Q ss_pred HHHHHHHHH--HHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHh
Q 030812 55 DAKDTVQEC--VSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (171)
Q Consensus 55 DA~~al~~c--aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (171)
|+.+.+ +. ...|..|....|...+-+.++|. .-+|+.+|..=
T Consensus 14 e~id~~-~~~~~~~~~~f~~gnaiKY~~R~~~K~-~~eDl~KA~~Y 57 (60)
T PF11753_consen 14 ECIDFI-EQFTEEQFLGFCLGNAIKYLWRAGKKN-GIEDLKKAKWY 57 (60)
T ss_pred cHHHHH-HHhcchhhhhHHHHHHHHHHHHHcccC-cHHHHHHHHHH
Confidence 344444 33 45899999999999999999994 48888888743
No 143
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=23.93 E-value=61 Score=32.80 Aligned_cols=69 Identities=19% Similarity=0.285 Sum_probs=46.2
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC--hhhHHHHHH
Q 030812 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTIN--GDDLLWAMA 97 (171)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~--~eDVl~AL~ 97 (171)
+-.-...+|..... |+++.+.--|-+|.+.||++||.+.=.||...-...-++++++++. .-+|..+|.
T Consensus 611 VhvaST~VPfts~s---KeaIA~vpEI~~EI~lAl~~~aR~Lk~yl~k~~~~~~~~~k~~~~~kylp~~a~~l~ 681 (795)
T PRK14868 611 VHVASTNVPFTSES---KDAIANVPEIEDEIELAIREAARELKSYLNKRRSMQKRREKQDVLGTILPEMATKVA 681 (795)
T ss_pred EEEeecCCCCCCcc---hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444556665543 4555544469999999999999999999998776666666665543 234444444
No 144
>PF09239 Topo-VIb_trans: Topoisomerase VI B subunit, transducer; InterPro: IPR015320 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. This entry represents subunit B of topoisomerase VI, an ATP-dependent type IIB enzyme. Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A 2Q2E_B.
Probab=23.83 E-value=83 Score=25.93 Aligned_cols=33 Identities=21% Similarity=0.465 Sum_probs=24.7
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHH
Q 030812 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEA 75 (171)
Q Consensus 43 K~~LP~~~rISkDA~~al~~caseFI~~LtseA 75 (171)
|+++.+.--|-+|.+.+|++||...=.||....
T Consensus 120 KeaIa~~pEI~~Ei~lAl~e~~R~L~~yl~rk~ 152 (160)
T PF09239_consen 120 KEAIADVPEIEKEIRLALQECARKLKKYLSRKR 152 (160)
T ss_dssp SSSB---HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444544446889999999999999999997644
No 145
>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=23.03 E-value=60 Score=20.82 Aligned_cols=16 Identities=19% Similarity=0.406 Sum_probs=13.7
Q ss_pred cChhhHHHHHHhcCCC
Q 030812 87 INGDDLLWAMATLGFE 102 (171)
Q Consensus 87 I~~eDVl~AL~~LgF~ 102 (171)
++.++|..+++.+||+
T Consensus 47 ~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 47 TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp SCHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHhCcC
Confidence 6678999999999984
No 146
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=22.62 E-value=1.4e+02 Score=20.13 Aligned_cols=32 Identities=22% Similarity=0.538 Sum_probs=21.9
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHH
Q 030812 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEF 67 (171)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~caseF 67 (171)
.+.+++|.|++.. ...|+.+.++.+.+++.++
T Consensus 11 gvS~~TVSr~ln~----~~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 11 GVSKATVSRVLNG----NGRVSEETREKVLAAMEEL 42 (70)
T ss_pred CCCHHHHHHHHCC----CCCCCHHHHHHHHHHHHHh
Confidence 4667778777753 2357788887777777665
No 147
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=22.55 E-value=1.8e+02 Score=27.40 Aligned_cols=51 Identities=8% Similarity=0.090 Sum_probs=40.0
Q ss_pred CCcccHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCccChhhHHHHHHhcC
Q 030812 49 NGKIAKDAKDTVQECVSEFIS-FITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (171)
Q Consensus 49 ~~rISkDA~~al~~caseFI~-~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (171)
...++.||...|.+. =-|+. -+-..+-..|+..+...||.+.|..|=..+|
T Consensus 461 ~~~w~~ea~~~l~~i-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 512 (513)
T CHL00076 461 DLIWSPESQLELSKI-PGFVRGKVKRNTEKFARQNGITNITVEVMYAAKEALS 512 (513)
T ss_pred CCCCCHHHHHHHHhC-CHHhHHHHHHHHHHHHHHcCCCeEcHHHHHHHHHhhC
Confidence 457999999999987 44443 3444566788999999999999999977765
No 148
>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=22.31 E-value=4.3e+02 Score=24.75 Aligned_cols=64 Identities=30% Similarity=0.382 Sum_probs=40.5
Q ss_pred HHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCcchHHHHHHHHH
Q 030812 41 IMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR 114 (171)
Q Consensus 41 ImK~~LP-~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv~~Lk~~L~~ 114 (171)
++++++. ++..==.||..+.+.+.+=|.++|-=||+.. .+.|.+.| +-.++.+=.+.|+.||..
T Consensus 13 lv~kA~~eD~a~nY~eA~~lY~~aleYF~~~lKYE~~~~---------kaKd~Ira-K~~EYLdRAEkLK~yL~~ 77 (439)
T KOG0739|consen 13 LVKKAIDEDNAKNYEEALRLYQNALEYFLHALKYEANNK---------KAKDSIRA-KFTEYLDRAEKLKAYLKE 77 (439)
T ss_pred HHHHHhhhcchhchHHHHHHHHHHHHHHHHHHHhhhcCh---------hHHHHHHH-HHHHHHHHHHHHHHHHHh
Confidence 4444443 2456678999999999999999997766522 12345555 233344445677777764
No 149
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=22.03 E-value=1.7e+02 Score=28.38 Aligned_cols=64 Identities=8% Similarity=0.009 Sum_probs=33.0
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 33 LP~A~V~RImK~~LP-~~~rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
|+...+.+.+++.+. .+..++.++...|.+.+.-=+..+-.+....+.-.+++ |+.++|...+.
T Consensus 180 ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~ 244 (614)
T PRK14971 180 IQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLN 244 (614)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhC
Confidence 445555555554433 25678998888877755433333333333322222322 66666655443
No 150
>PTZ00184 calmodulin; Provisional
Probab=21.99 E-value=2.8e+02 Score=19.83 Aligned_cols=38 Identities=18% Similarity=0.179 Sum_probs=26.2
Q ss_pred HHHHHHHhcCCCccChhhHHHHHHhcCCCcchHHHHHH
Q 030812 74 EASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAY 111 (171)
Q Consensus 74 eA~~~~~~~kRKTI~~eDVl~AL~~LgF~dyv~~Lk~~ 111 (171)
.+...+-.+++-.|+.+|+..+|..+|+.--.+.++..
T Consensus 88 ~~F~~~D~~~~g~i~~~e~~~~l~~~~~~~~~~~~~~~ 125 (149)
T PTZ00184 88 EAFKVFDRDGNGFISAAELRHVMTNLGEKLTDEEVDEM 125 (149)
T ss_pred HHHHhhCCCCCCeEeHHHHHHHHHHHCCCCCHHHHHHH
Confidence 34455556677789999999999998875433444433
No 151
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=21.76 E-value=1.2e+02 Score=29.59 Aligned_cols=33 Identities=15% Similarity=0.370 Sum_probs=24.9
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHH
Q 030812 52 IAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (171)
Q Consensus 52 ISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (171)
|+++++.+|. .|...|..-+..-|+++|+|.||
T Consensus 1 ~~~~a~~~L~------------~A~~~A~~~~h~~V~~EHLLlaL 33 (731)
T TIGR02639 1 ISEELERILD------------AALEEAKKRRHEFVTLEHILLAL 33 (731)
T ss_pred CCHHHHHHHH------------HHHHHHHHhCCCcCcHHHHHHHH
Confidence 4556666665 36778888888889999999886
No 152
>PRK12728 fliE flagellar hook-basal body protein FliE; Provisional
Probab=21.34 E-value=3.6e+02 Score=20.23 Aligned_cols=38 Identities=11% Similarity=0.149 Sum_probs=26.7
Q ss_pred hcCCCccChhhHHHHHHhcC--CCcchHHHHHHHHHHHHHh
Q 030812 81 KEKRKTINGDDLLWAMATLG--FEDYIDPLKAYLMRYREME 119 (171)
Q Consensus 81 ~~kRKTI~~eDVl~AL~~Lg--F~dyv~~Lk~~L~~yre~~ 119 (171)
..|. +++..||+-|+++-. |.-.+..=...++.|+|+.
T Consensus 59 ~~G~-~~~lhevmiA~~kA~lslq~~vqVRNKlv~AYqEIM 98 (102)
T PRK12728 59 VKGE-IVDLHDVMIAAQKASISLQLTVQIRNKVVEAYQEIM 98 (102)
T ss_pred HcCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344 789999999999644 4444444446799999875
No 153
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=21.15 E-value=2.5e+02 Score=20.07 Aligned_cols=33 Identities=21% Similarity=0.247 Sum_probs=24.7
Q ss_pred HHhcCCCccChhhHHHHHHhcCCCcchHHHHHH
Q 030812 79 CQKEKRKTINGDDLLWAMATLGFEDYIDPLKAY 111 (171)
Q Consensus 79 ~~~~kRKTI~~eDVl~AL~~LgF~dyv~~Lk~~ 111 (171)
.+.++...-+.+.+..||..+|..+.++.+++.
T Consensus 53 ~~~~~~~~atv~~L~~AL~~~gr~dlae~l~~~ 85 (86)
T cd08779 53 AQRQAGDPDAVGKLVTALEESGRQDLADEVRAV 85 (86)
T ss_pred HHhcCCCchHHHHHHHHHHHcCHHHHHHHHHhh
Confidence 344444444578899999999999999888764
No 154
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=21.05 E-value=1.8e+02 Score=27.45 Aligned_cols=52 Identities=15% Similarity=0.220 Sum_probs=42.2
Q ss_pred hCCCCCcccHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030812 45 ALPANGKIAKDAKDTVQECVSEFIS-------FITSEASDKCQKEKRKTINGDDLLWAMA 97 (171)
Q Consensus 45 ~LP~~~rISkDA~~al~~caseFI~-------~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (171)
.|| .+.++.++...+.+.|..+-. .++..|..++.=.+|.+++.+||-.|++
T Consensus 262 ~l~-~V~l~~~~~~~ia~~~~~~~v~g~radi~~~r~a~a~aa~~Gr~~v~~~Di~~a~~ 320 (423)
T COG1239 262 LLS-EVELDDDAETKIAELCARLAVDGHRADIVVVRAAKALAALRGRTEVEEEDIREAAE 320 (423)
T ss_pred ccc-cccCcHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHhcCceeeehhhHHHHHh
Confidence 344 567899999999888887743 4667778888999999999999999976
No 155
>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=20.98 E-value=4.1e+02 Score=20.78 Aligned_cols=65 Identities=17% Similarity=0.118 Sum_probs=41.5
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHhcCCCc------------chHHHHHHHHHHHHH
Q 030812 51 KIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED------------YIDPLKAYLMRYREM 118 (171)
Q Consensus 51 rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~d------------yv~~Lk~~L~~yre~ 118 (171)
.+..+. +..++..++..+..-..-..- -.|.+.+|++.+++.+.+.. |++.+.+.+++-++.
T Consensus 95 ~i~~~g---~~~~~~~~lr~~~~~~~~~~~---~~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A 168 (224)
T PF02361_consen 95 SITQEG---LIYAALLALRILAILLASLLF---ILTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREA 168 (224)
T ss_pred hhhHHH---HHHHHHHHHHHHHHHHHHHHH---HHHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344443 445555555444443333222 23889999999999999987 777777777776665
Q ss_pred hhc
Q 030812 119 EGD 121 (171)
Q Consensus 119 ~~~ 121 (171)
++-
T Consensus 169 ~~~ 171 (224)
T PF02361_consen 169 QRL 171 (224)
T ss_pred HHH
Confidence 543
No 156
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=20.90 E-value=1.6e+02 Score=27.51 Aligned_cols=39 Identities=13% Similarity=0.272 Sum_probs=32.7
Q ss_pred HHHhcCCCccChhhHHHHHHhcCCCcchHHHHHHHHHHHHHhh
Q 030812 78 KCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEG 120 (171)
Q Consensus 78 ~~~~~kRKTI~~eDVl~AL~~LgF~dyv~~Lk~~L~~yre~~~ 120 (171)
+...++++-++.+.|...|+.-|+. .-+.-+.+||+..+
T Consensus 407 I~~Ed~~~PlSD~~I~~~L~~~Gi~----IaRRTVaKYRe~L~ 445 (455)
T PRK05932 407 IAAENPKKPLSDSKIAELLKEQGID----VARRTVAKYREALN 445 (455)
T ss_pred HHhcCCCCCCCHHHHHHHHHHcCCC----eehHHHHHHHHHcC
Confidence 6677888999999999999998883 55788999999654
No 157
>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate-binding protein. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=20.53 E-value=2.5e+02 Score=23.88 Aligned_cols=60 Identities=8% Similarity=0.069 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHH-HHHHhcCCCccC----------hhhHHHHHHhcCCCcchHHHHHHHHHHHHHhhc
Q 030812 62 ECVSEFISFITSEAS-DKCQKEKRKTIN----------GDDLLWAMATLGFEDYIDPLKAYLMRYREMEGD 121 (171)
Q Consensus 62 ~caseFI~~LtseA~-~~~~~~kRKTI~----------~eDVl~AL~~LgF~dyv~~Lk~~L~~yre~~~~ 121 (171)
++|..||.|+.+... ..-.+.....++ ++++...+-..++..+.+.....+++|....+.
T Consensus 261 e~A~~fidfllS~e~Q~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~rw~~~~~~ 331 (334)
T TIGR03261 261 DAAKKLVDWSISDEAMELYAKNYAVVATPGVAKPDAGFPKNVEDLLIKNDFVWAAANRDKILEEWSKRYGA 331 (334)
T ss_pred HHHHHHHHHHcCHHHHHHHHhcCcccccCCcccCcccCCcchhhhcccCCHHHHHHhHHHHHHHHHHHhhc
Confidence 779999999976533 332222222211 123444444566666778888889999887653
No 158
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=20.50 E-value=51 Score=27.32 Aligned_cols=35 Identities=11% Similarity=0.363 Sum_probs=27.8
Q ss_pred CchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHH
Q 030812 33 LPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFIT 72 (171)
Q Consensus 33 LP~A~V~RImK~~LP~~~rISkDA~~al~~caseFI~~Lt 72 (171)
.-++||.|.+... .+||+++++-+.+++.+. .|.-
T Consensus 10 VS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l-gY~p 44 (327)
T PRK10423 10 VSTSTVSHVINKD----RFVSEAITAKVEAAIKEL-NYAP 44 (327)
T ss_pred CcHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCc
Confidence 4578999999643 379999999999999885 5544
No 159
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=20.06 E-value=83 Score=31.13 Aligned_cols=37 Identities=22% Similarity=0.442 Sum_probs=28.8
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc
Q 030812 51 KIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTI 87 (171)
Q Consensus 51 rISkDA~~al~~caseFI~~LtseA~~~~~~~kRKTI 87 (171)
-|-+|.+.||++||.+.=.||...-...-++++++++
T Consensus 592 eI~~Ei~lAl~~~~r~L~~~l~~~~~~~~~~~k~~~~ 628 (659)
T PRK14867 592 EIFNEIRQALMICARELEKYISRIRREKEEEQKRKYV 628 (659)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4778888999999999999999866655555555553
Done!