Query 030647
Match_columns 174
No_of_seqs 163 out of 608
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 02:28:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030647.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030647hhsearch_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 4.8E-42 1E-46 275.1 14.8 127 2-129 1-130 (168)
2 KOG0871 Class 2 transcription 100.0 3E-28 6.5E-33 193.9 9.5 95 26-120 7-101 (156)
3 KOG0870 DNA polymerase epsilon 99.9 4.8E-27 1E-31 189.9 8.9 103 24-126 3-106 (172)
4 COG5150 Class 2 transcription 99.9 7.3E-23 1.6E-27 160.2 9.1 97 26-122 6-102 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 7.6E-19 1.7E-23 121.0 7.5 64 31-95 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.7 1.5E-17 3.2E-22 123.6 6.5 79 24-104 12-90 (91)
7 cd00076 H4 Histone H4, one of 99.2 9E-11 2E-15 86.3 8.2 71 31-103 13-83 (85)
8 PLN00035 histone H4; Provision 99.2 1.5E-10 3.3E-15 87.9 8.2 74 26-101 24-97 (103)
9 PTZ00015 histone H4; Provision 99.1 5.9E-10 1.3E-14 84.6 8.3 77 25-103 24-100 (102)
10 smart00428 H3 Histone H3. 99.0 1.9E-09 4.2E-14 82.1 6.7 73 26-98 24-101 (105)
11 smart00803 TAF TATA box bindin 99.0 3E-09 6.4E-14 74.4 7.2 64 31-96 2-65 (65)
12 smart00417 H4 Histone H4. 98.9 2.9E-09 6.3E-14 76.6 5.7 63 30-94 12-74 (74)
13 cd07981 TAF12 TATA Binding Pro 98.9 1.2E-08 2.6E-13 72.2 8.2 65 32-97 2-66 (72)
14 PF00125 Histone: Core histone 98.9 6E-09 1.3E-13 72.7 6.2 68 29-96 3-73 (75)
15 PLN00121 histone H3; Provision 98.6 7E-08 1.5E-12 76.6 5.8 71 26-96 57-130 (136)
16 PLN00160 histone H3; Provision 98.6 1.2E-07 2.7E-12 71.4 6.6 71 26-96 16-90 (97)
17 PLN00161 histone H3; Provision 98.6 1.8E-07 4E-12 74.1 7.5 71 26-96 50-124 (135)
18 COG5208 HAP5 CCAAT-binding fac 98.6 5.4E-08 1.2E-12 83.1 4.4 77 29-107 107-184 (286)
19 PTZ00018 histone H3; Provision 98.6 1.2E-07 2.5E-12 75.4 5.7 71 26-96 57-130 (136)
20 KOG1657 CCAAT-binding factor, 98.4 3.9E-07 8.4E-12 78.0 6.3 85 29-114 72-159 (236)
21 smart00576 BTP Bromodomain tra 98.4 2.9E-06 6.2E-11 60.5 8.0 66 34-101 9-74 (77)
22 cd00074 H2A Histone 2A; H2A is 98.3 2.7E-06 5.8E-11 65.8 6.7 68 29-97 18-85 (115)
23 cd07979 TAF9 TATA Binding Prot 98.0 5.2E-05 1.1E-09 58.5 9.3 79 35-115 5-84 (117)
24 cd08050 TAF6 TATA Binding Prot 97.9 4.3E-05 9.4E-10 68.0 8.0 67 33-101 1-67 (343)
25 PF15630 CENP-S: Kinetochore c 97.9 4.9E-05 1.1E-09 54.9 6.2 61 36-96 10-71 (76)
26 PF15511 CENP-T: Centromere ki 97.8 2.7E-05 5.9E-10 71.1 5.9 66 25-90 345-414 (414)
27 smart00427 H2B Histone H2B. 97.8 9.5E-05 2.1E-09 55.1 7.4 62 36-98 6-67 (89)
28 KOG1745 Histones H3 and H4 [Ch 97.8 1.2E-05 2.7E-10 63.9 2.7 74 26-99 58-134 (137)
29 PF03847 TFIID_20kDa: Transcri 97.7 0.00019 4.1E-09 50.7 6.9 63 34-97 2-64 (68)
30 PLN00158 histone H2B; Provisio 97.6 0.0003 6.5E-09 54.7 7.4 65 33-98 29-93 (116)
31 PF07524 Bromo_TP: Bromodomain 97.6 0.0006 1.3E-08 48.1 8.2 65 35-101 10-74 (77)
32 KOG3467 Histone H4 [Chromatin 97.6 0.00032 7E-09 52.5 6.9 69 31-101 29-97 (103)
33 PTZ00463 histone H2B; Provisio 97.6 0.00035 7.5E-09 54.4 7.3 62 36-98 33-94 (117)
34 PF09415 CENP-X: CENP-S associ 97.5 0.00013 2.9E-09 52.1 4.1 64 33-96 1-66 (72)
35 cd08048 TAF11 TATA Binding Pro 97.5 0.00073 1.6E-08 49.7 8.0 66 31-98 16-84 (85)
36 COG5262 HTA1 Histone H2A [Chro 97.3 0.00078 1.7E-08 52.8 6.8 68 28-96 23-90 (132)
37 KOG1142 Transcription initiati 97.3 0.0011 2.3E-08 57.8 7.9 68 28-96 151-218 (258)
38 PF04719 TAFII28: hTAFII28-lik 97.2 0.0016 3.5E-08 48.5 7.1 67 31-98 23-90 (90)
39 KOG1659 Class 2 transcription 97.2 0.00098 2.1E-08 56.7 6.6 81 30-111 12-92 (224)
40 PF02969 TAF: TATA box binding 97.2 0.0027 6E-08 44.7 7.5 64 31-96 3-66 (66)
41 smart00414 H2A Histone 2A. 97.1 0.0018 3.8E-08 49.5 6.0 68 29-97 7-74 (106)
42 PLN00154 histone H2A; Provisio 96.9 0.0079 1.7E-07 48.0 8.5 68 29-96 36-103 (136)
43 COG5247 BUR6 Class 2 transcrip 96.8 0.0031 6.8E-08 48.3 5.6 81 29-110 21-101 (113)
44 KOG1658 DNA polymerase epsilon 96.7 0.0011 2.5E-08 53.9 2.5 67 29-97 57-124 (162)
45 PTZ00017 histone H2A; Provisio 96.7 0.0038 8.3E-08 49.6 5.3 67 29-96 25-91 (134)
46 KOG1744 Histone H2B [Chromatin 96.6 0.0085 1.8E-07 47.3 6.7 61 37-98 43-103 (127)
47 PF02269 TFIID-18kDa: Transcri 96.4 0.004 8.8E-08 46.1 3.7 59 38-97 8-66 (93)
48 KOG1756 Histone 2A [Chromatin 96.4 0.0098 2.1E-07 47.1 5.8 68 28-96 24-91 (131)
49 PLN00157 histone H2A; Provisio 96.4 0.0071 1.5E-07 48.0 5.1 67 29-96 24-90 (132)
50 PF15510 CENP-W: Centromere ki 96.4 0.007 1.5E-07 45.7 4.8 67 30-97 15-95 (102)
51 PLN00153 histone H2A; Provisio 96.3 0.0085 1.8E-07 47.4 5.3 67 29-96 22-88 (129)
52 PLN00156 histone H2AX; Provisi 96.3 0.01 2.2E-07 47.6 5.6 67 29-96 27-93 (139)
53 cd07978 TAF13 The TATA Binding 95.2 0.11 2.4E-06 38.6 7.0 59 36-96 7-65 (92)
54 PTZ00252 histone H2A; Provisio 94.9 0.076 1.7E-06 42.3 5.9 67 29-96 23-91 (134)
55 KOG3219 Transcription initiati 94.9 0.037 8E-07 46.6 4.3 70 31-102 112-182 (195)
56 PF02291 TFIID-31kDa: Transcri 93.7 0.35 7.5E-06 38.2 7.2 85 28-114 7-94 (129)
57 KOG4336 TBP-associated transcr 92.8 0.65 1.4E-05 41.8 8.2 78 35-116 9-86 (323)
58 TIGR03015 pepcterm_ATPase puta 91.6 0.66 1.4E-05 38.3 6.6 70 32-101 192-269 (269)
59 KOG3423 Transcription initiati 91.4 1.1 2.3E-05 37.2 7.4 68 31-101 86-168 (176)
60 PRK00411 cdc6 cell division co 88.5 2.4 5.1E-05 37.2 7.8 70 34-103 209-287 (394)
61 KOG2549 Transcription initiati 87.9 2.3 4.9E-05 41.1 7.7 65 34-100 14-78 (576)
62 TIGR02928 orc1/cdc6 family rep 86.1 3 6.4E-05 36.1 6.9 75 34-108 201-284 (365)
63 KOG2389 Predicted bromodomain 85.0 2.7 5.8E-05 38.4 6.3 70 30-101 28-97 (353)
64 COG1067 LonB Predicted ATP-dep 79.2 1.8 3.8E-05 42.4 3.1 47 50-97 338-398 (647)
65 TIGR02902 spore_lonB ATP-depen 79.0 4.9 0.00011 37.9 5.9 63 34-97 265-331 (531)
66 PF13654 AAA_32: AAA domain; P 77.2 11 0.00023 35.8 7.6 60 37-98 436-506 (509)
67 TIGR00764 lon_rel lon-related 76.9 9.3 0.0002 36.9 7.2 49 50-98 330-391 (608)
68 cd08045 TAF4 TATA Binding Prot 75.7 14 0.0003 30.7 7.2 80 29-108 42-129 (212)
69 PF13335 Mg_chelatase_2: Magne 74.7 11 0.00024 27.8 5.7 48 49-96 41-94 (96)
70 COG1224 TIP49 DNA helicase TIP 74.5 14 0.0003 34.7 7.4 101 13-116 338-447 (450)
71 COG5095 TAF6 Transcription ini 73.6 7.7 0.00017 35.7 5.4 52 49-100 21-72 (450)
72 KOG3334 Transcription initiati 73.5 17 0.00036 29.6 6.7 65 51-115 31-96 (148)
73 KOG1757 Histone 2A [Chromatin 73.0 5.6 0.00012 31.3 3.8 65 28-96 27-95 (131)
74 KOG3901 Transcription initiati 68.2 14 0.0003 28.6 5.0 47 47-96 24-70 (109)
75 KOG2680 DNA helicase TIP49, TB 68.0 38 0.00083 31.4 8.6 61 36-96 362-427 (454)
76 PF00531 Death: Death domain; 67.0 8.3 0.00018 26.2 3.3 61 50-111 23-83 (83)
77 PF08369 PCP_red: Proto-chloro 61.5 11 0.00023 24.4 2.9 42 52-94 2-44 (45)
78 COG5248 TAF19 Transcription in 61.4 22 0.00048 27.9 5.0 48 47-96 24-71 (126)
79 PF02861 Clp_N: Clp amino term 59.6 7.6 0.00016 24.3 1.9 26 74-99 1-26 (53)
80 cd04752 Commd4 COMM_Domain con 59.6 28 0.00062 28.1 5.7 51 62-119 43-94 (174)
81 PRK09862 putative ATP-dependen 58.9 34 0.00074 32.6 6.9 59 49-107 437-501 (506)
82 PRK00080 ruvB Holliday junctio 58.7 42 0.0009 29.1 7.0 72 31-102 179-254 (328)
83 TIGR02442 Cob-chelat-sub cobal 56.1 40 0.00087 32.5 7.0 49 48-96 247-302 (633)
84 COG1474 CDC6 Cdc6-related prot 54.4 37 0.0008 30.8 6.1 74 35-108 193-275 (366)
85 TIGR00635 ruvB Holliday juncti 54.0 73 0.0016 26.9 7.5 70 32-101 159-232 (305)
86 TIGR02030 BchI-ChlI magnesium 53.0 58 0.0013 29.2 7.1 54 42-96 247-307 (337)
87 PRK13406 bchD magnesium chelat 53.0 31 0.00068 33.3 5.7 59 36-96 183-248 (584)
88 TIGR01052 top6b DNA topoisomer 52.0 17 0.00036 34.6 3.6 59 42-114 426-484 (488)
89 TIGR00368 Mg chelatase-related 51.7 35 0.00075 32.3 5.6 47 50-96 445-497 (499)
90 COG5162 Transcription initiati 51.5 94 0.002 26.1 7.4 50 52-101 107-189 (197)
91 TIGR01128 holA DNA polymerase 49.7 91 0.002 26.0 7.4 65 32-96 111-176 (302)
92 PRK13765 ATP-dependent proteas 48.3 29 0.00063 33.9 4.7 47 50-96 339-398 (637)
93 PF05236 TAF4: Transcription i 48.3 30 0.00065 29.6 4.3 76 27-102 39-122 (264)
94 PF00356 LacI: Bacterial regul 48.2 38 0.00082 21.9 3.8 32 31-66 10-41 (46)
95 PF09114 MotA_activ: Transcrip 47.7 27 0.00059 26.4 3.5 32 35-66 51-86 (96)
96 PRK12402 replication factor C 47.7 47 0.001 28.1 5.4 71 32-104 184-255 (337)
97 PRK07452 DNA polymerase III su 43.9 61 0.0013 27.8 5.6 65 37-101 135-202 (326)
98 CHL00081 chlI Mg-protoporyphyr 42.1 71 0.0015 29.0 5.9 54 42-96 260-320 (350)
99 PTZ00361 26 proteosome regulat 41.5 32 0.00069 32.1 3.7 32 67-98 393-424 (438)
100 TIGR02031 BchD-ChlD magnesium 41.2 88 0.0019 30.1 6.7 55 41-96 195-256 (589)
101 PRK03992 proteasome-activating 40.8 35 0.00075 30.8 3.7 34 66-99 340-373 (389)
102 cd00823 TopoIIB_Trans TopoIIB_ 40.3 50 0.0011 26.9 4.2 44 29-75 101-144 (151)
103 PF03540 TFIID_30kDa: Transcri 39.7 1.2E+02 0.0025 20.4 6.4 47 31-80 2-49 (51)
104 TIGR01242 26Sp45 26S proteasom 39.5 37 0.0008 30.0 3.7 33 66-98 331-363 (364)
105 PRK05574 holA DNA polymerase I 39.5 85 0.0018 26.7 5.8 65 31-96 145-211 (340)
106 smart00350 MCM minichromosome 38.9 1.4E+02 0.003 28.0 7.5 65 30-97 416-503 (509)
107 COG1389 DNA topoisomerase VI, 38.8 23 0.00049 34.0 2.3 46 42-87 434-479 (538)
108 PF08823 PG_binding_2: Putativ 37.5 50 0.0011 23.5 3.4 32 89-120 19-56 (74)
109 PF07647 SAM_2: SAM domain (St 37.5 35 0.00076 22.3 2.5 25 85-109 3-27 (66)
110 PLN00138 large subunit ribosom 37.3 97 0.0021 23.9 5.2 31 69-101 3-33 (113)
111 COG5624 TAF61 Transcription in 37.3 22 0.00048 33.6 1.9 79 30-108 382-463 (505)
112 PRK13407 bchI magnesium chelat 37.0 1.1E+02 0.0023 27.6 6.1 53 42-95 244-303 (334)
113 COG1222 RPT1 ATP-dependent 26S 36.9 55 0.0012 30.6 4.3 50 49-98 338-392 (406)
114 KOG1528 Salt-sensitive 3'-phos 36.8 95 0.0021 28.4 5.8 76 22-98 41-123 (351)
115 PRK09526 lacI lac repressor; R 36.8 32 0.0007 28.9 2.7 37 31-72 16-52 (342)
116 PTZ00373 60S Acidic ribosomal 35.6 1.1E+02 0.0024 23.6 5.3 32 68-101 4-35 (112)
117 PF12627 PolyA_pol_RNAbd: Prob 35.5 8 0.00017 25.5 -0.9 59 48-110 1-63 (64)
118 cd00166 SAM Sterile alpha moti 33.7 32 0.00069 21.8 1.8 24 87-110 3-26 (63)
119 PF07499 RuvA_C: RuvA, C-termi 33.4 28 0.0006 22.3 1.4 14 89-102 4-17 (47)
120 PTZ00454 26S protease regulato 33.3 53 0.0012 30.1 3.7 32 67-98 355-386 (398)
121 PF00536 SAM_1: SAM domain (St 32.9 43 0.00094 21.8 2.3 22 87-108 4-25 (64)
122 PRK12728 fliE flagellar hook-b 32.8 2E+02 0.0043 21.6 6.2 63 54-118 32-98 (102)
123 COG1724 Predicted RNA binding 30.9 30 0.00066 24.6 1.3 18 85-102 6-23 (66)
124 smart00354 HTH_LACI helix_turn 30.8 81 0.0018 21.3 3.5 32 31-66 11-42 (70)
125 PF12010 DUF3502: Domain of un 30.7 50 0.0011 25.5 2.7 61 53-117 72-132 (134)
126 COG1466 HolA DNA polymerase II 30.5 1.1E+02 0.0023 26.9 5.1 61 37-97 145-206 (334)
127 PRK04184 DNA topoisomerase VI 30.2 37 0.00081 32.7 2.2 56 42-97 431-488 (535)
128 PRK14867 DNA topoisomerase VI 29.8 59 0.0013 32.2 3.6 36 50-85 592-627 (659)
129 PRK10727 DNA-binding transcrip 29.4 48 0.001 28.1 2.6 37 32-73 13-49 (343)
130 PF13405 EF-hand_6: EF-hand do 29.4 50 0.0011 18.7 1.9 26 74-99 5-31 (31)
131 COG5251 TAF40 Transcription in 29.3 43 0.00092 28.2 2.2 61 31-95 115-178 (199)
132 PRK10423 transcriptional repre 28.6 33 0.00072 28.6 1.5 36 32-72 10-45 (327)
133 PF14434 Imm6: Immunity protei 28.1 1.8E+02 0.0039 22.5 5.4 49 57-105 8-62 (122)
134 PTZ00183 centrin; Provisional 27.7 2.1E+02 0.0045 21.0 5.6 17 80-96 64-80 (158)
135 PRK14975 bifunctional 3'-5' ex 27.5 3.6E+02 0.0078 25.7 8.3 89 29-120 161-269 (553)
136 PF09239 Topo-VIb_trans: Topoi 27.0 38 0.00081 27.9 1.5 34 42-75 120-153 (160)
137 PRK14987 gluconate operon tran 26.8 57 0.0012 27.4 2.6 37 31-72 16-52 (331)
138 PRK06585 holA DNA polymerase I 26.8 1.5E+02 0.0033 25.6 5.3 61 36-96 146-208 (343)
139 PRK14868 DNA topoisomerase VI 26.5 48 0.001 33.5 2.4 58 26-86 612-669 (795)
140 smart00454 SAM Sterile alpha m 26.5 47 0.001 21.1 1.6 26 85-110 3-28 (68)
141 cd05833 Ribosomal_P2 Ribosomal 26.1 2E+02 0.0044 21.9 5.3 31 69-101 3-33 (109)
142 TIGR01278 DPOR_BchB light-inde 24.9 1.3E+02 0.0028 28.3 4.8 52 47-99 459-511 (511)
143 PF11753 DUF3310: Protein of u 24.8 1.9E+02 0.0041 19.5 4.4 41 54-96 14-56 (60)
144 PRK02910 light-independent pro 24.7 1.3E+02 0.0028 28.4 4.8 52 47-99 466-518 (519)
145 PF08681 DUF1778: Protein of u 24.5 1.5E+02 0.0032 21.0 4.0 49 48-96 3-59 (80)
146 TIGR02903 spore_lon_C ATP-depe 24.3 1.4E+02 0.0031 28.9 5.0 72 34-105 355-437 (615)
147 smart00027 EH Eps15 homology d 24.3 1.4E+02 0.003 21.1 3.9 26 76-101 17-42 (96)
148 PRK00440 rfc replication facto 23.8 1.5E+02 0.0031 24.8 4.5 65 32-98 161-226 (319)
149 TIGR01481 ccpA catabolite cont 23.8 89 0.0019 26.0 3.2 35 32-71 13-47 (329)
150 PF10728 DUF2520: Domain of un 23.1 2.7E+02 0.0058 21.5 5.6 57 35-94 14-73 (132)
151 PF00403 HMA: Heavy-metal-asso 22.8 53 0.0011 21.1 1.3 16 86-101 47-62 (62)
152 PRK07914 hypothetical protein; 22.6 1.9E+02 0.0041 25.1 5.1 63 33-96 129-192 (320)
153 PRK05932 RNA polymerase factor 21.2 1.8E+02 0.004 27.2 5.0 40 77-120 407-446 (455)
154 PRK14971 DNA polymerase III su 21.1 1.7E+02 0.0036 28.5 4.8 63 32-95 180-243 (614)
155 TIGR03261 phnS2 putative 2-ami 20.5 2.6E+02 0.0056 23.9 5.5 60 61-120 261-331 (334)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=4.8e-42 Score=275.13 Aligned_cols=127 Identities=72% Similarity=1.155 Sum_probs=111.7
Q ss_pred CCCCCCCCCCCCCCC-CCCCC--CCCCccccccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHh
Q 030647 2 AAEAPASPGGGSHES-GEQSP--RSNVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKC 78 (174)
Q Consensus 2 ~~~~~~~~~~~~~~~-~~~~~--~~~~~~~D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~ 78 (174)
|.+++..+. +.|+. |.+++ ...++++|++||||||.||||+.||.+++|||||++++|+|++|||+|||+||+++|
T Consensus 1 m~~s~~~~~-~~~e~~g~~~~~~~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC 79 (168)
T KOG0869|consen 1 MAESDHDSG-GGDENGGNSSPQSSLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKC 79 (168)
T ss_pred CCCCcCCCC-ccccCCcccCCccccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence 344444443 34444 33333 358999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCCcCcchHHHHHHHcCCCchhHHHHHHHHHHHHHhcccCCCCCCCC
Q 030647 79 QREKRKTINGDDLLWAMATLGFEDYIDPLKIYLTRYREMEGDTKGNAKGGD 129 (174)
Q Consensus 79 ~~~kRKTI~~eDVl~AL~~LgF~~yv~~lk~~L~~yre~~~~kk~~~k~~~ 129 (174)
.+++|||||+|||||||..|||++|+++|+.||.+|||+++++....+.+.
T Consensus 80 ~~EkRKTIngdDllwAm~tLGFe~Y~eplkiyL~kYRe~e~e~~~~~~~~~ 130 (168)
T KOG0869|consen 80 QREKRKTINGDDLLWAMSTLGFENYAEPLKIYLQKYRELEGERGRSGKGGQ 130 (168)
T ss_pred HHHhcCcccHHHHHHHHHHcCcHhHHHHHHHHHHHHHHHhhhcccccccCc
Confidence 999999999999999999999999999999999999999999888777665
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.95 E-value=3e-28 Score=193.93 Aligned_cols=95 Identities=33% Similarity=0.642 Sum_probs=91.6
Q ss_pred ccccccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchhH
Q 030647 26 REQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYID 105 (174)
Q Consensus 26 ~~~D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv~ 105 (174)
..+|+.||+|+|.+|||+.||.+++|.+||+++|+.||.+||++|+++||++|..+.||||+++||++||+.|||.+|++
T Consensus 7 ~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYie 86 (156)
T KOG0871|consen 7 EDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIE 86 (156)
T ss_pred ccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHH
Confidence 56789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcc
Q 030647 106 PLKIYLTRYREMEGD 120 (174)
Q Consensus 106 ~lk~~L~~yre~~~~ 120 (174)
.+...|++|+.....
T Consensus 87 e~~~vl~~~K~~~~~ 101 (156)
T KOG0871|consen 87 EAEEVLENCKEEAKK 101 (156)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999987664
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.94 E-value=4.8e-27 Score=189.90 Aligned_cols=103 Identities=32% Similarity=0.527 Sum_probs=98.4
Q ss_pred CCccccccCchhHHHHHHHhhCCCC-CccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCc
Q 030647 24 NVREQDRYLPIANISRIMKKALPAN-GKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFED 102 (174)
Q Consensus 24 ~~~~~D~~LP~A~V~RImK~~LP~~-~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~ 102 (174)
..+++|+.||+|+|.||+|++||+. +.|||||+.+|+++|++||+||++.|+++|+.++||||+++||+.||++|+|..
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 4688999999999999999999987 899999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHhcccCCCCC
Q 030647 103 YIDPLKIYLTRYREMEGDTKGNAK 126 (174)
Q Consensus 103 yv~~lk~~L~~yre~~~~kk~~~k 126 (174)
|+.+|+..|+.||...++||.++.
T Consensus 83 f~~plk~~Le~yk~~~k~Kk~~~~ 106 (172)
T KOG0870|consen 83 FVNPLKSALEAYKKAVKQKKLAKA 106 (172)
T ss_pred HhhHHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999999998886554
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.88 E-value=7.3e-23 Score=160.21 Aligned_cols=97 Identities=27% Similarity=0.516 Sum_probs=92.8
Q ss_pred ccccccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchhH
Q 030647 26 REQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYID 105 (174)
Q Consensus 26 ~~~D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv~ 105 (174)
..++..||+|+|.+.+.+.||.+..++|||++.++.||.+||+.|+++||++|..+.+|||.++||++||+.|+|.+|++
T Consensus 6 ~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~ 85 (148)
T COG5150 6 NDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIE 85 (148)
T ss_pred ccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHH
Confidence 46778999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcccC
Q 030647 106 PLKIYLTRYREMEGDTK 122 (174)
Q Consensus 106 ~lk~~L~~yre~~~~kk 122 (174)
.+...+.+|+..+++|.
T Consensus 86 ~~~e~~~n~k~~qK~ke 102 (148)
T COG5150 86 SCMEEHENYKSYQKQKE 102 (148)
T ss_pred HHHHHHHHHHHHHhhch
Confidence 99999999998877643
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=7.6e-19 Score=120.97 Aligned_cols=64 Identities=39% Similarity=0.639 Sum_probs=59.4
Q ss_pred cCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHH
Q 030647 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAM 95 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL 95 (174)
.||++.|.||||.. |++.+||+||.++|++|+++||.||+.+|++.|..++||||+++||..||
T Consensus 2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 69999999999999 88899999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.71 E-value=1.5e-17 Score=123.61 Aligned_cols=79 Identities=32% Similarity=0.479 Sum_probs=74.7
Q ss_pred CCccccccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCch
Q 030647 24 NVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDY 103 (174)
Q Consensus 24 ~~~~~D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y 103 (174)
..+..|..||+++|.||||++.++ +||.+|+++|++|+++|+..|+..|++.|.++|||||+++||..|++.+||..|
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 457789999999999999999986 999999999999999999999999999999999999999999999999999766
Q ss_pred h
Q 030647 104 I 104 (174)
Q Consensus 104 v 104 (174)
.
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=99.19 E-value=9e-11 Score=86.32 Aligned_cols=71 Identities=18% Similarity=0.320 Sum_probs=66.2
Q ss_pred cCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCch
Q 030647 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDY 103 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y 103 (174)
.||++.|.||++... ..+||.|+.+.+.++..+|+..|..+|...|++.+||||+++||..||+..|-.-|
T Consensus 13 gi~k~~I~RLarr~G--vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 13 GITKPAIRRLARRGG--VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred cCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 599999999999985 46899999999999999999999999999999999999999999999999885433
No 8
>PLN00035 histone H4; Provisional
Probab=99.16 E-value=1.5e-10 Score=87.90 Aligned_cols=74 Identities=18% Similarity=0.274 Sum_probs=67.2
Q ss_pred ccccccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCC
Q 030647 26 REQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (174)
Q Consensus 26 ~~~D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 101 (174)
++....||++.|.||++..- ..+||.|+.+.+.+..++|+.-|..+|...|++.+||||+++||..||+..|-.
T Consensus 24 ~d~i~~ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ 97 (103)
T PLN00035 24 RDNIQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred HhhhccCCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCc
Confidence 33445599999999999995 468999999999999999999999999999999999999999999999987754
No 9
>PTZ00015 histone H4; Provisional
Probab=99.08 E-value=5.9e-10 Score=84.58 Aligned_cols=77 Identities=21% Similarity=0.362 Sum_probs=69.2
Q ss_pred CccccccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCch
Q 030647 25 VREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDY 103 (174)
Q Consensus 25 ~~~~D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y 103 (174)
.++....||++.|.||++... ..+||.|+.+.+.++.++|+..|..+|...|++.+||||+++||..||+..|-.-|
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 345556799999999999985 46899999999999999999999999999999999999999999999998876433
No 10
>smart00428 H3 Histone H3.
Probab=98.95 E-value=1.9e-09 Score=82.10 Aligned_cols=73 Identities=16% Similarity=0.183 Sum_probs=66.8
Q ss_pred ccccccCchhHHHHHHHhhCCC-----CCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHc
Q 030647 26 REQDRYLPIANISRIMKKALPA-----NGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (174)
Q Consensus 26 ~~~D~~LP~A~V~RImK~~LP~-----~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~L 98 (174)
+..++.+|+....|++++...+ +.+++.+|..+||++++.|+.-+...|+..+.+.||+||.++|+.-|..-.
T Consensus 24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir 101 (105)
T smart00428 24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIR 101 (105)
T ss_pred cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHh
Confidence 5678999999999999998864 679999999999999999999999999999999999999999998886533
No 11
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=98.95 E-value=3e-09 Score=74.39 Aligned_cols=64 Identities=25% Similarity=0.285 Sum_probs=60.2
Q ss_pred cCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.||+++|.||++...- .+||.|+..+|.+-++.|+.-|..+|...+++.+||||+++||-.||+
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 12
>smart00417 H4 Histone H4.
Probab=98.90 E-value=2.9e-09 Score=76.57 Aligned_cols=63 Identities=16% Similarity=0.301 Sum_probs=58.5
Q ss_pred ccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHH
Q 030647 30 RYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWA 94 (174)
Q Consensus 30 ~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~A 94 (174)
..||++.|.||+|... --+||.|+.+.+.+..++|+..|..+|...|++.+||||+++||..|
T Consensus 12 ~gI~k~~IrRLaRr~G--vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 12 QGITKPAIRRLARRGG--VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred cCCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 4699999999999985 35899999999999999999999999999999999999999999753
No 13
>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=98.88 E-value=1.2e-08 Score=72.22 Aligned_cols=65 Identities=17% Similarity=0.328 Sum_probs=61.6
Q ss_pred CchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHH
Q 030647 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (174)
Q Consensus 32 LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~ 97 (174)
|++..+..++|+.-| ..+++.||.++|++.+.+|+.-++..|...|++.+|+||.++||.-+|+.
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 678899999999987 58999999999999999999999999999999999999999999999975
No 14
>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=98.87 E-value=6e-09 Score=72.73 Aligned_cols=68 Identities=25% Similarity=0.336 Sum_probs=62.6
Q ss_pred cccCchhHHHHHHHhhCCC---CCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 29 DRYLPIANISRIMKKALPA---NGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~---~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
+..+|+..|.|+.|+..++ ..+||++|..+|+..++.|+.-|..+|...|.+.||+||++.||..|+.
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 4578999999999998874 2699999999999999999999999999999999999999999999985
No 15
>PLN00121 histone H3; Provisional
Probab=98.62 E-value=7e-08 Score=76.62 Aligned_cols=71 Identities=14% Similarity=0.171 Sum_probs=65.7
Q ss_pred ccccccCchhHHHHHHHhhCCC---CCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 26 REQDRYLPIANISRIMKKALPA---NGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 26 ~~~D~~LP~A~V~RImK~~LP~---~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
+..++.+|+....||+++...+ +.+++.+|.++||++++.|+.-|...++-.+.+.+|.||.+.|+.-|..
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 4568999999999999999864 6899999999999999999999999999999999999999999987764
No 16
>PLN00160 histone H3; Provisional
Probab=98.60 E-value=1.2e-07 Score=71.35 Aligned_cols=71 Identities=15% Similarity=0.116 Sum_probs=65.1
Q ss_pred ccccccCchhHHHHHHHhhCC----CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 26 REQDRYLPIANISRIMKKALP----ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 26 ~~~D~~LP~A~V~RImK~~LP----~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
+..++.+|++...|++++... ++.+++.+|..+||++++.|+.-+...++-.|.+.||.||.+.|+.-|..
T Consensus 16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 456899999999999999864 35899999999999999999999999999999999999999999987764
No 17
>PLN00161 histone H3; Provisional
Probab=98.59 E-value=1.8e-07 Score=74.15 Aligned_cols=71 Identities=15% Similarity=0.192 Sum_probs=65.2
Q ss_pred ccccccCchhHHHHHHHhhCC----CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 26 REQDRYLPIANISRIMKKALP----ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 26 ~~~D~~LP~A~V~RImK~~LP----~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
+..++.+|+....||+++... .+.+++.+|.++||++++.|+.-|...|+-.|.+.||.||.+.|+.-|..
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 566889999999999999864 36899999999999999999999999999999999999999999988764
No 18
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.57 E-value=5.4e-08 Score=83.05 Aligned_cols=77 Identities=26% Similarity=0.361 Sum_probs=69.4
Q ss_pred cccCchhHHHHHHHhhCCCCCc-cchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchhHHH
Q 030647 29 DRYLPIANISRIMKKALPANGK-IAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPL 107 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~r-ISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~l 107 (174)
+..||+|.|.|+||-. ++++ ||.||-.++.++|+.||..||..|.-.+++.+|+|+.-.||-.|+++-+.-+|+-.+
T Consensus 107 ~h~LPlARIkkvMKtd--edVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLidi 184 (286)
T COG5208 107 DHNLPLARIKKVMKTD--EDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLIDI 184 (286)
T ss_pred hccCcHHHHHHHHhcc--cchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhhh
Confidence 5679999999999965 4454 999999999999999999999999999999999999999999999998887776544
No 19
>PTZ00018 histone H3; Provisional
Probab=98.56 E-value=1.2e-07 Score=75.37 Aligned_cols=71 Identities=14% Similarity=0.175 Sum_probs=65.3
Q ss_pred ccccccCchhHHHHHHHhhCC---CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 26 REQDRYLPIANISRIMKKALP---ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 26 ~~~D~~LP~A~V~RImK~~LP---~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
+..|+.+|+..+.||+++... .+.+++.+|.++||++++.|+..|...++-.|.+.+|.||.+.|+.-|..
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 456899999999999999874 36899999999999999999999999999999999999999999987764
No 20
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.44 E-value=3.9e-07 Score=78.04 Aligned_cols=85 Identities=27% Similarity=0.374 Sum_probs=71.6
Q ss_pred cccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHH---cCCCchhH
Q 030647 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT---LGFEDYID 105 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~---LgF~~yv~ 105 (174)
...||++.|.+|||..- +.-.|+.||..++.+||+.||..|+..|+..+...+|+|+...|+..|+.. .+|.-.+-
T Consensus 72 ~~~lPlaRiKkimK~de-dv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~Div 150 (236)
T KOG1657|consen 72 NHILPLARIKKIMKSDE-DVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRDIV 150 (236)
T ss_pred hccCcHhhccccccccc-cccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceeccc
Confidence 45799999999999773 233799999999999999999999999999999999999999999999984 45555555
Q ss_pred HHHHHHHHH
Q 030647 106 PLKIYLTRY 114 (174)
Q Consensus 106 ~lk~~L~~y 114 (174)
+.+...++|
T Consensus 151 P~~~~~~~~ 159 (236)
T KOG1657|consen 151 PRKILAEKY 159 (236)
T ss_pred cchhccccc
Confidence 556666655
No 21
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.35 E-value=2.9e-06 Score=60.49 Aligned_cols=66 Identities=20% Similarity=0.265 Sum_probs=59.5
Q ss_pred hhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCC
Q 030647 34 IANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (174)
Q Consensus 34 ~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 101 (174)
+-.|.+|+|.+.= -+++.+|.++|.+....|+..|+..+...|...+|++++..||..||+++|+.
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 4467788887742 48999999999999999999999999999999999999999999999999873
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=98.27 E-value=2.7e-06 Score=65.80 Aligned_cols=68 Identities=18% Similarity=0.238 Sum_probs=62.3
Q ss_pred cccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHH
Q 030647 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~ 97 (174)
.+.||.+.|.|+||+.-- ..||+.+|...|..+.+.+..-|...|...|+..+|++|+++||..|+..
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 36999999999999999999999999999999999999999999999874
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=98.02 E-value=5.2e-05 Score=58.48 Aligned_cols=79 Identities=14% Similarity=0.158 Sum_probs=65.9
Q ss_pred hHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchhHH-HHHHHHH
Q 030647 35 ANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDP-LKIYLTR 113 (174)
Q Consensus 35 A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~-lk~~L~~ 113 (174)
..|.+|+|+.. ..+++.+++..|.+.+..++.-|..+|...|++.+|+||+.+||.-|++...-..|..+ -+++|..
T Consensus 5 ~~v~~iLk~~G--v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~ 82 (117)
T cd07979 5 RVIAAILKSMG--ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLE 82 (117)
T ss_pred HHHHHHHHHCC--CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHH
Confidence 35788888863 35899999999999999999999999999999999999999999999996665455444 6666655
Q ss_pred HH
Q 030647 114 YR 115 (174)
Q Consensus 114 yr 115 (174)
.-
T Consensus 83 ~a 84 (117)
T cd07979 83 LA 84 (117)
T ss_pred HH
Confidence 54
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=97.90 E-value=4.3e-05 Score=68.00 Aligned_cols=67 Identities=19% Similarity=0.206 Sum_probs=58.5
Q ss_pred chhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCC
Q 030647 33 PIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (174)
Q Consensus 33 P~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 101 (174)
|..+|.-|++... -.++++||..+|.+.++.++.-|..+|...+++.+|||++++||-.||+.++.+
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 4566777777663 238999999999999999999999999999999999999999999999966553
No 25
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.86 E-value=4.9e-05 Score=54.85 Aligned_cols=61 Identities=15% Similarity=0.199 Sum_probs=52.1
Q ss_pred HHHHHHHhhC-CCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 36 NISRIMKKAL-PANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 36 ~V~RImK~~L-P~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.|.||+.+.. +.+..+|+++..+|.+.+-.++..++..---.|++.||+||+.+||+-...
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
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.85 E-value=2.7e-05 Score=71.12 Aligned_cols=66 Identities=21% Similarity=0.261 Sum_probs=48.2
Q ss_pred CccccccCchhHHHHHHHhhCC----CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcch
Q 030647 25 VREQDRYLPIANISRIMKKALP----ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDD 90 (174)
Q Consensus 25 ~~~~D~~LP~A~V~RImK~~LP----~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eD 90 (174)
..+.--.||.+.|.|++..... .+++|+|||..+|.+|...|...|+..-.-.|++.|||||..+|
T Consensus 345 hgi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 345 HGIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp -------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4455567999999999888864 46899999999999999999999999999999999999999876
No 27
>smart00427 H2B Histone H2B.
Probab=97.82 E-value=9.5e-05 Score=55.06 Aligned_cols=62 Identities=21% Similarity=0.336 Sum_probs=57.5
Q ss_pred HHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHc
Q 030647 36 NISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (174)
Q Consensus 36 ~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~L 98 (174)
-|.|++|++-|+ .-||..|...++--+..+..-|+.||...|...+|+||+..+|..|.+-+
T Consensus 6 Yi~kvLKqVhpd-~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 6 YIYKVLKQVHPD-TGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHHhCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 489999999995 68999999999999999999999999999999999999999999998644
No 28
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=97.81 E-value=1.2e-05 Score=63.93 Aligned_cols=74 Identities=16% Similarity=0.205 Sum_probs=65.5
Q ss_pred ccccccCchhHHHHHHHhhCC---CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcC
Q 030647 26 REQDRYLPIANISRIMKKALP---ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLG 99 (174)
Q Consensus 26 ~~~D~~LP~A~V~RImK~~LP---~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~Lg 99 (174)
+..|+.+++....|++++..+ .+.++...|+.+||++++.|+.-|.-.+|-.+.+.||.||.+.||--|....|
T Consensus 58 kstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg 134 (137)
T KOG1745|consen 58 KSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 134 (137)
T ss_pred hhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence 356889999999999995554 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=97.69 E-value=0.00019 Score=50.74 Aligned_cols=63 Identities=21% Similarity=0.311 Sum_probs=51.6
Q ss_pred hhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHH
Q 030647 34 IANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (174)
Q Consensus 34 ~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~ 97 (174)
+..+..++++.=| +.++..|+.++|.+.|.+||.-++..|-..|++-+-.||...||.-.|++
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 4567889999866 78999999999999999999999999999999999999999999998874
No 30
>PLN00158 histone H2B; Provisional
Probab=97.60 E-value=0.0003 Score=54.71 Aligned_cols=65 Identities=17% Similarity=0.277 Sum_probs=59.1
Q ss_pred chhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHc
Q 030647 33 PIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (174)
Q Consensus 33 P~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~L 98 (174)
-..-|.|++|++-|+ .-||..+...|+-.+..+..-|+.||...|.-.+|+||+..+|..|.+-+
T Consensus 29 y~~YI~kVLKQVhPd-~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 29 YKIYIYKVLKQVHPD-TGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred HHHHHHHHHHHhCCC-CCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 345699999999994 68999999999999999999999999999999999999999999998644
No 31
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=97.58 E-value=0.0006 Score=48.14 Aligned_cols=65 Identities=17% Similarity=0.257 Sum_probs=56.6
Q ss_pred hHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCC
Q 030647 35 ANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (174)
Q Consensus 35 A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 101 (174)
-.|.+|++.+. =-.++..|.+.|.+.+..||..|+..+...|...+|...+..||..||+++|+.
T Consensus 10 ~~va~il~~~G--F~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 10 RSVAQILKHAG--FDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 34566666552 126999999999999999999999999999999999999999999999999984
No 32
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=97.57 E-value=0.00032 Score=52.50 Aligned_cols=69 Identities=19% Similarity=0.272 Sum_probs=61.0
Q ss_pred cCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCC
Q 030647 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 101 (174)
-+-+-+|.||.+... .-+|+--.-+.+..++.+||.-+-+.|...+.+.+||||++-||+-+|+..|.-
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 366778999999874 347888888889999999999999999999999999999999999999998753
No 33
>PTZ00463 histone H2B; Provisional
Probab=97.57 E-value=0.00035 Score=54.39 Aligned_cols=62 Identities=19% Similarity=0.367 Sum_probs=57.3
Q ss_pred HHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHc
Q 030647 36 NISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (174)
Q Consensus 36 ~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~L 98 (174)
-|.|++|++-|+ .-||..|...|+-.+..+..-|+.||...|.-.+|+||+..+|..|.+-+
T Consensus 33 YI~KVLKqVhPd-~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 33 YIFKVLKQVHPD-TGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred HHHHHHHhhCCC-CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 499999999984 68999999999999999999999999999999999999999999998644
No 34
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=97.51 E-value=0.00013 Score=52.09 Aligned_cols=64 Identities=20% Similarity=0.305 Sum_probs=53.4
Q ss_pred chhHHHHHHHhhCC-CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCC-cCcchHHHHHH
Q 030647 33 PIANISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKT-INGDDLLWAMA 96 (174)
Q Consensus 33 P~A~V~RImK~~LP-~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKT-I~~eDVl~AL~ 96 (174)
|..+|.||++.... ++.+|++||..++.+....||.--...|.+.++.++..+ |..+|+-+.+-
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~p 66 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILP 66 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 88999999998774 568999999999999999999999999999999999888 99999877654
No 35
>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=97.50 E-value=0.00073 Score=49.66 Aligned_cols=66 Identities=20% Similarity=0.213 Sum_probs=61.3
Q ss_pred cCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCC---CCcCcchHHHHHHHc
Q 030647 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKR---KTINGDDLLWAMATL 98 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kR---KTI~~eDVl~AL~~L 98 (174)
.||++.|.|||...++ ..++.+...+|.-.+.+||--|.-+|.++..+.+. .-|.++||-.|...|
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 4999999999999986 78999999999999999999999999999988765 789999999999876
No 36
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.34 E-value=0.00078 Score=52.80 Aligned_cols=68 Identities=19% Similarity=0.240 Sum_probs=61.0
Q ss_pred ccccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 28 QDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 28 ~D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.-+.+|...|.||+|..- -.+||+++|...+.-|.+-.+..|+.-|-..|+..++|.|.+.|+-.|+.
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 357899999999999443 36899999999999999988999998999999999999999999999986
No 37
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.30 E-value=0.0011 Score=57.76 Aligned_cols=68 Identities=15% Similarity=0.277 Sum_probs=62.7
Q ss_pred ccccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 28 QDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 28 ~D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.+..|=+-.|.-+++++-+ +.+|-+|+.++|.+.|..||..|+..|-..|++-|..||-..||...|+
T Consensus 151 ~~~il~k~kl~dLvqqId~-~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLE 218 (258)
T KOG1142|consen 151 NNPILSKRKLDDLVQQIDG-TTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLE 218 (258)
T ss_pred CCccccccchhHHHHhhcC-cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeee
Confidence 3566788889999999954 6899999999999999999999999999999999999999999999998
No 38
>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=97.22 E-value=0.0016 Score=48.48 Aligned_cols=67 Identities=21% Similarity=0.231 Sum_probs=52.3
Q ss_pred cCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCC-CCcCcchHHHHHHHc
Q 030647 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKR-KTINGDDLLWAMATL 98 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kR-KTI~~eDVl~AL~~L 98 (174)
.||++.|.|||...+. |..|+.....+|.-.+.+||--|-.+|.+++...+. .-|.+.|+-.|..+|
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 578999999999999999999999999999986653 479999999998765
No 39
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.22 E-value=0.00098 Score=56.74 Aligned_cols=81 Identities=17% Similarity=0.234 Sum_probs=69.9
Q ss_pred ccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchhHHHHH
Q 030647 30 RYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLKI 109 (174)
Q Consensus 30 ~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~lk~ 109 (174)
..||.+.|.|||...- +-.+|..-.-..+.++.+.|+.-|...+.++++..+-|||+++|+..|+..-.--+|+..+-.
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 4699999999998664 246899999999999999999999999999999999999999999999997776677766444
Q ss_pred HH
Q 030647 110 YL 111 (174)
Q Consensus 110 ~L 111 (174)
..
T Consensus 91 ~v 92 (224)
T KOG1659|consen 91 KV 92 (224)
T ss_pred hc
Confidence 33
No 40
>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=97.17 E-value=0.0027 Score=44.71 Aligned_cols=64 Identities=19% Similarity=0.194 Sum_probs=49.0
Q ss_pred cCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.+|..+|.-+..... -..++.|+..+|.+=++--|..|..+|....++.+|++++.+||-.||+
T Consensus 3 ~~~~esvk~iAes~G--i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESLG--ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHTT-----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHcC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 467777766665552 2379999999999999999999999999999999999999999999985
No 41
>smart00414 H2A Histone 2A.
Probab=97.06 E-value=0.0018 Score=49.50 Aligned_cols=68 Identities=15% Similarity=0.258 Sum_probs=59.6
Q ss_pred cccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHH
Q 030647 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~ 97 (174)
.+.||.+.|.|++|+.-- ..+|+..|...|.-|.+-+...|...|-..|+..+++.|+++||..|+..
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 35999999999999888888888878888899999999999999999864
No 42
>PLN00154 histone H2A; Provisional
Probab=96.87 E-value=0.0079 Score=48.00 Aligned_cols=68 Identities=19% Similarity=0.256 Sum_probs=57.6
Q ss_pred cccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.+.||.+.|.|++|+-..-..||+..|-..|.-+.+-+..-|...|-..|+..+++-|++.||..|+.
T Consensus 36 gL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred CccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 68999999999999986435699999999888777666666666677788899999999999999985
No 43
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=96.82 E-value=0.0031 Score=48.34 Aligned_cols=81 Identities=16% Similarity=0.281 Sum_probs=68.5
Q ss_pred cccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchhHHHH
Q 030647 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLK 108 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~lk 108 (174)
-..+|+|.|.|||.-.- +-.+|+.-+-....++.+.|+..|-.+..+.++..+-|.|+.+++..|.+.-+=-+|+..+.
T Consensus 21 ktrFP~ar~KkIMQ~de-DiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~ 99 (113)
T COG5247 21 KTRFPIARLKKIMQLDE-DIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNME 99 (113)
T ss_pred hhcCCHHHHHHHHHhhh-hhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHH
Confidence 45699999999998653 24689999999999999999999999999999999999999999999998766556665554
Q ss_pred HH
Q 030647 109 IY 110 (174)
Q Consensus 109 ~~ 110 (174)
.+
T Consensus 100 ~~ 101 (113)
T COG5247 100 QF 101 (113)
T ss_pred Hh
Confidence 43
No 44
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=96.69 E-value=0.0011 Score=53.91 Aligned_cols=67 Identities=25% Similarity=0.305 Sum_probs=57.9
Q ss_pred cccCchhHHHHHHHhhCCCCCc-cchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHH
Q 030647 29 DRYLPIANISRIMKKALPANGK-IAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~r-ISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~ 97 (174)
-..||++.|..++| ++++.+ ..+|++.++.+++..||.+|+..++..+...+|||+.-.|+=.|++.
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 35799999999999 556776 56778999999999999999999999999999999998888777653
No 45
>PTZ00017 histone H2A; Provisional
Probab=96.67 E-value=0.0038 Score=49.65 Aligned_cols=67 Identities=15% Similarity=0.232 Sum_probs=59.5
Q ss_pred cccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.+.||.+.|.|++|+.-- ..||+..|...|.-+.+-+..-|...|-..|+..+++-|++.||..|+.
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 689999999999998643 3599999999999988888888888888889999999999999999985
No 46
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.58 E-value=0.0085 Score=47.34 Aligned_cols=61 Identities=25% Similarity=0.339 Sum_probs=56.0
Q ss_pred HHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHc
Q 030647 37 ISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (174)
Q Consensus 37 V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~L 98 (174)
|.|++|++-|+ .-|+.++...++--.-.|+-.|+.+|+..+.-.+|.||+..+|..|..-|
T Consensus 43 v~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 43 VYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred hhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 66799999997 66999999999999999999999999999999999999999999998543
No 47
>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=96.41 E-value=0.004 Score=46.14 Aligned_cols=59 Identities=24% Similarity=0.293 Sum_probs=28.8
Q ss_pred HHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHH
Q 030647 38 SRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (174)
Q Consensus 38 ~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~ 97 (174)
..+|-.-. +.-.-..|+..+|-+.+.+||..|..+|.+.|...++++|+.+|++.+|+.
T Consensus 8 ~~mMy~fG-D~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 8 RQMMYGFG-DVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp HHHHHCTT-S-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHcC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 34444433 445788999999999999999999999999999999999999999999984
No 48
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.37 E-value=0.0098 Score=47.08 Aligned_cols=68 Identities=16% Similarity=0.246 Sum_probs=54.9
Q ss_pred ccccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 28 QDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 28 ~D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
..+.+|...|.|++|+.- --.+|+.+|-..+.-|.+-....|+.-|-..++..++.-|++.||..|+.
T Consensus 24 agl~fPvgri~r~Lr~~~-~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 24 AGLQFPVGRIHRLLRKGR-YAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred cccccCHHHHHHHHHccc-hhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 358899999999999932 24689999999999776655556666666667778899999999999986
No 49
>PLN00157 histone H2A; Provisional
Probab=96.37 E-value=0.0071 Score=48.03 Aligned_cols=67 Identities=13% Similarity=0.191 Sum_probs=58.4
Q ss_pred cccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.+.||...|.|++|+.-- ..||+..|-..|.-+.+-+..-|...|-..|...+++-|++.||..|+.
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 689999999999999643 3699999999999887777777777788888999999999999999985
No 50
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.36 E-value=0.007 Score=45.65 Aligned_cols=67 Identities=21% Similarity=0.257 Sum_probs=55.8
Q ss_pred ccCchhHHHHHHHhhCCCCCccchHHHHH--------------HHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHH
Q 030647 30 RYLPIANISRIMKKALPANGKIAKDAKET--------------VQECVSEFISFITSEASDKCQREKRKTINGDDLLWAM 95 (174)
Q Consensus 30 ~~LP~A~V~RImK~~LP~~~rISkDA~~a--------------l~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL 95 (174)
..-|++.+.|++|..-| ..++....-.+ +.--|-.||+-|+-||...+-.++-.||..+||+.|-
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 45799999999998877 56666655455 5667889999999999988888889999999999997
Q ss_pred HH
Q 030647 96 AT 97 (174)
Q Consensus 96 ~~ 97 (174)
+.
T Consensus 94 Kv 95 (102)
T PF15510_consen 94 KV 95 (102)
T ss_pred HH
Confidence 64
No 51
>PLN00153 histone H2A; Provisional
Probab=96.34 E-value=0.0085 Score=47.44 Aligned_cols=67 Identities=16% Similarity=0.224 Sum_probs=58.9
Q ss_pred cccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.+.||...|.|++|+.-- ..||+..|-..|.-|.+-++.-|...|-..|...+++-|++.||..|+.
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 689999999999998654 3599999999999888877777777788888999999999999999985
No 52
>PLN00156 histone H2AX; Provisional
Probab=96.29 E-value=0.01 Score=47.57 Aligned_cols=67 Identities=13% Similarity=0.206 Sum_probs=57.3
Q ss_pred cccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.+.||.+.|.|++|+.-- ..||+..|-..|.-|.+-...-|...|-..|...+++-|+++||..|+.
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 688999999999998643 3599999999998887766667777777788889999999999999985
No 53
>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=95.18 E-value=0.11 Score=38.63 Aligned_cols=59 Identities=17% Similarity=0.288 Sum_probs=48.5
Q ss_pred HHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 36 NISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 36 ~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
-|..+|.-.. +...-..|+..+|-+++.+||.-|+.+|.+.|. .+|.-|+.||++-+|.
T Consensus 7 ei~~mmy~~G-D~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR 65 (92)
T cd07978 7 EIRQMMYGFG-DVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR 65 (92)
T ss_pred HHHHHHHHcC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence 4566666554 345678999999999999999999999999998 4444459999999996
No 54
>PTZ00252 histone H2A; Provisional
Probab=94.94 E-value=0.076 Score=42.34 Aligned_cols=67 Identities=7% Similarity=0.173 Sum_probs=49.5
Q ss_pred cccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHh--cCCCCcCcchHHHHHH
Q 030647 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQR--EKRKTINGDDLLWAMA 96 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~--~kRKTI~~eDVl~AL~ 96 (174)
.+.||.+.|.|++|+.-- ..||+.-|-..|.-+.+-...-|...|-..|.. .+++-|+++||..|+.
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 359999988887766544444444444444433 4678999999999985
No 55
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=94.92 E-value=0.037 Score=46.57 Aligned_cols=70 Identities=14% Similarity=0.187 Sum_probs=61.2
Q ss_pred cCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCC-CCcCcchHHHHHHHcCCCc
Q 030647 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKR-KTINGDDLLWAMATLGFED 102 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kR-KTI~~eDVl~AL~~LgF~~ 102 (174)
.||+++|.|||..... ..|+..+..+++-.+.+||--|--+|.++|..-+. --|.+.||-.|...|....
T Consensus 112 ~f~Ka~iKkL~~~itg--~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~qg 182 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITG--QSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQG 182 (195)
T ss_pred cCCHHHHHHHHHHHhC--CccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhcC
Confidence 4999999999999985 34999999999999999999999999999987764 4699999999988876643
No 56
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=93.71 E-value=0.35 Score=38.15 Aligned_cols=85 Identities=21% Similarity=0.219 Sum_probs=47.1
Q ss_pred ccccCchh--HHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH-HcCCCchh
Q 030647 28 QDRYLPIA--NISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA-TLGFEDYI 104 (174)
Q Consensus 28 ~D~~LP~A--~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~-~LgF~~yv 104 (174)
....+|+. .|.-|+|+.. -......+...|-+.+-.|+.-|-..|...+.+.+|++|+.+||..|++ .+++.-..
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 34456663 3445555542 2247778888999999999999999999999999999999999999999 67777666
Q ss_pred HHHHHHHHHH
Q 030647 105 DPLKIYLTRY 114 (174)
Q Consensus 105 ~~lk~~L~~y 114 (174)
.+-+++|.+.
T Consensus 85 pppre~llel 94 (129)
T PF02291_consen 85 PPPREFLLEL 94 (129)
T ss_dssp ----------
T ss_pred CCChHHHHHH
Confidence 7766776654
No 57
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=92.81 E-value=0.65 Score=41.75 Aligned_cols=78 Identities=18% Similarity=0.273 Sum_probs=65.2
Q ss_pred hHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchhHHHHHHHHHH
Q 030647 35 ANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLKIYLTRY 114 (174)
Q Consensus 35 A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~lk~~L~~y 114 (174)
..|..|.++.+=+ .|++-|++.|.+....+|.-|...+...|...+|...+.-||..+|-++||. +..|..+++++
T Consensus 9 ~VV~~Ll~~~gfd--~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~ 84 (323)
T KOG4336|consen 9 PVVSNLLKTKGFD--SISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQ 84 (323)
T ss_pred HHHHHHHHHhCch--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhc
Confidence 3455566655432 4999999999999999999999999999999999999999999999999996 56677776665
Q ss_pred HH
Q 030647 115 RE 116 (174)
Q Consensus 115 re 116 (174)
..
T Consensus 85 ~~ 86 (323)
T KOG4336|consen 85 EF 86 (323)
T ss_pred cc
Confidence 43
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=91.61 E-value=0.66 Score=38.26 Aligned_cols=70 Identities=14% Similarity=0.247 Sum_probs=55.1
Q ss_pred CchhHHHHHHHhhCC-----CCCccchHHHHHHHHHHHH---HHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCC
Q 030647 32 LPIANISRIMKKALP-----ANGKIAKDAKETVQECVSE---FISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (174)
Q Consensus 32 LP~A~V~RImK~~LP-----~~~rISkDA~~al~~~ate---FI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 101 (174)
|....+..++...+. ....+++++.+.|.+.+.= .|+.+...|...+-..+.++|+.++|..++.++.|+
T Consensus 192 l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~~ 269 (269)
T TIGR03015 192 LDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDFE 269 (269)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhcC
Confidence 444556666655442 2346999999999988875 799999999988888889999999999999998753
No 59
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=91.42 E-value=1.1 Score=37.23 Aligned_cols=68 Identities=25% Similarity=0.252 Sum_probs=55.2
Q ss_pred cCchhHHHHHHHhhCCCCCc-cchHHHHHHHHHHHHHHHHHHHHHHHHhHhcC--------------CCCcCcchHHHHH
Q 030647 31 YLPIANISRIMKKALPANGK-IAKDAKETVQECVSEFISFITSEASDKCQREK--------------RKTINGDDLLWAM 95 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~r-ISkDA~~al~~~ateFI~~LtseA~e~~~~~k--------------RKTI~~eDVl~AL 95 (174)
.||=+.+.-+++.+. +. ...-.+-+|.=++-.||+-|+..|.+.|+-.. |-|++-+|+-.||
T Consensus 86 ~IPDavt~~yL~~aG---f~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL 162 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKAG---FQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPAL 162 (176)
T ss_pred CCcHHHHHHHHHhcC---CCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHH
Confidence 588888888888774 33 33456778999999999999999999996433 4589999999999
Q ss_pred HHcCCC
Q 030647 96 ATLGFE 101 (174)
Q Consensus 96 ~~LgF~ 101 (174)
++.|..
T Consensus 163 ~EyGin 168 (176)
T KOG3423|consen 163 AEYGIN 168 (176)
T ss_pred HHhCcc
Confidence 998874
No 60
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=88.45 E-value=2.4 Score=37.22 Aligned_cols=70 Identities=13% Similarity=0.171 Sum_probs=51.0
Q ss_pred hhHHHHHHHhhCCC---CCccchHHHHHHHHHH------HHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCch
Q 030647 34 IANISRIMKKALPA---NGKIAKDAKETVQECV------SEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDY 103 (174)
Q Consensus 34 ~A~V~RImK~~LP~---~~rISkDA~~al~~~a------teFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y 103 (174)
...+..|++..+-. ...++.++.+.+.+.+ -..+..+...|.+.|...++.+|+.+||.+|++.+....+
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 45566666655421 2358999988888777 3345566678888898899999999999999998854333
No 61
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=87.93 E-value=2.3 Score=41.08 Aligned_cols=65 Identities=20% Similarity=0.245 Sum_probs=54.0
Q ss_pred hhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCC
Q 030647 34 IANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGF 100 (174)
Q Consensus 34 ~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF 100 (174)
.-.+. .+-+.+. -..|++|+..+|.+=++.=|.-|+.+|.+.-.+.||.+++.+||..||+.+..
T Consensus 14 ~Es~k-~vAEslG-i~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nV 78 (576)
T KOG2549|consen 14 KESVK-VVAESLG-ITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNV 78 (576)
T ss_pred HHHHH-HHHHHhC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhccc
Confidence 44444 4444443 34699999999999999999999999999999999999999999999996543
No 62
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=86.07 E-value=3 Score=36.14 Aligned_cols=75 Identities=9% Similarity=0.135 Sum_probs=51.1
Q ss_pred hhHHHHHHHhhCC---CCCccchHHHHHHHHHHH------HHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchh
Q 030647 34 IANISRIMKKALP---ANGKIAKDAKETVQECVS------EFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYI 104 (174)
Q Consensus 34 ~A~V~RImK~~LP---~~~rISkDA~~al~~~at------eFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv 104 (174)
...+..|++..+. ....+++|+...+.+.+. -.+..+...|.+.|..+++.+|+.+||..|++.+....+.
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 3446666665543 123588888877766543 2344455677788888899999999999999988655555
Q ss_pred HHHH
Q 030647 105 DPLK 108 (174)
Q Consensus 105 ~~lk 108 (174)
..++
T Consensus 281 ~~i~ 284 (365)
T TIGR02928 281 ELIR 284 (365)
T ss_pred HHHH
Confidence 4444
No 63
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=84.98 E-value=2.7 Score=38.39 Aligned_cols=70 Identities=16% Similarity=0.162 Sum_probs=58.8
Q ss_pred ccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCC
Q 030647 30 RYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (174)
Q Consensus 30 ~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 101 (174)
..|-+..|..|+...-=. ....-|.+.|+..+..||.-|+..|...+...+|.-.|..||+.||+.|+..
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 357777888888766432 3444499999999999999999999999999999999999999999987763
No 64
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=79.18 E-value=1.8 Score=42.36 Aligned_cols=47 Identities=28% Similarity=0.348 Sum_probs=36.7
Q ss_pred ccchHHHHHHHHHHH--------------HHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHH
Q 030647 50 KIAKDAKETVQECVS--------------EFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (174)
Q Consensus 50 rISkDA~~al~~~at--------------eFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~ 97 (174)
.++++|..-|.+-+. .....|. +|.++|..++++-|+++||.+|++.
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~-~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVR-EAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHH-HhhHHHhcCCcccCcHHHHHHHHHh
Confidence 477777766655544 3344444 9999999999999999999999987
No 65
>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=78.96 E-value=4.9 Score=37.92 Aligned_cols=63 Identities=25% Similarity=0.311 Sum_probs=44.3
Q ss_pred hhHHHHHHHhhCC-CCCccchHHHHHHHHHHH---HHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHH
Q 030647 34 IANISRIMKKALP-ANGKIAKDAKETVQECVS---EFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (174)
Q Consensus 34 ~A~V~RImK~~LP-~~~rISkDA~~al~~~at---eFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~ 97 (174)
...+.+|++..+. .+..|++++.+.|.+.+. +.++.| ..|..+|..++|++|+.+||.|++..
T Consensus 265 ~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll-~~Aa~~A~~~~~~~It~~dI~~vl~~ 331 (531)
T TIGR02902 265 DEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIV-QLAAGIALGEGRKRILAEDIEWVAEN 331 (531)
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHH-HHHHHHHhhCCCcEEcHHHHHHHhCC
Confidence 3446666666654 246799999998877765 333333 34556777788999999999999754
No 66
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=77.18 E-value=11 Score=35.82 Aligned_cols=60 Identities=18% Similarity=0.184 Sum_probs=43.0
Q ss_pred HHHHHHhhCCCCCccchHHHHHHHHHHHH-----------HHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHc
Q 030647 37 ISRIMKKALPANGKIAKDAKETVQECVSE-----------FISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (174)
Q Consensus 37 V~RImK~~LP~~~rISkDA~~al~~~ate-----------FI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~L 98 (174)
|.+++++.- --.++++|+..|-+.+.. -|.-|-.+|+..|+.+++++|+++||..|++.-
T Consensus 436 i~~~~~~~~--L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 436 IASICQKEG--LPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHS--S--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHhCC--CCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 445554441 125899998888877653 566777899999999999999999999999853
No 67
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=76.89 E-value=9.3 Score=36.85 Aligned_cols=49 Identities=14% Similarity=0.160 Sum_probs=39.3
Q ss_pred ccchHHHHHHHHHHH-------------HHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHc
Q 030647 50 KIAKDAKETVQECVS-------------EFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (174)
Q Consensus 50 rISkDA~~al~~~at-------------eFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~L 98 (174)
.++++|...|.+-++ -=|.-|..+|+.+|+.+++.+|+.+||.+|++.-
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 699999998876544 2345566788889989999999999999999754
No 68
>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=75.67 E-value=14 Score=30.73 Aligned_cols=80 Identities=10% Similarity=0.141 Sum_probs=59.3
Q ss_pred cccCchhHHHHHHHhhCCCCC--ccchHHHHHHHHHHHHHHHHHHHHHHHHhHhc------CCCCcCcchHHHHHHHcCC
Q 030647 29 DRYLPIANISRIMKKALPANG--KIAKDAKETVQECVSEFISFITSEASDKCQRE------KRKTINGDDLLWAMATLGF 100 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~--rISkDA~~al~~~ateFI~~LtseA~e~~~~~------kRKTI~~eDVl~AL~~LgF 100 (174)
..+|....|.+.|...+.... .|+.|...+|.-||.+++..|-......|++- ...++-..||-..|..|+-
T Consensus 42 ~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~~ 121 (212)
T cd08045 42 PSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLEQ 121 (212)
T ss_pred hhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHHH
Confidence 356777777777776665432 69999999999999999999999999888764 3456777888887776655
Q ss_pred CchhHHHH
Q 030647 101 EDYIDPLK 108 (174)
Q Consensus 101 ~~yv~~lk 108 (174)
-+..+.-+
T Consensus 122 ~ek~e~er 129 (212)
T cd08045 122 LEREEEEK 129 (212)
T ss_pred HHHHHHHh
Confidence 44444333
No 69
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=74.73 E-value=11 Score=27.78 Aligned_cols=48 Identities=15% Similarity=0.197 Sum_probs=40.6
Q ss_pred CccchHHHHHHHHHHHHH------HHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 49 GKIAKDAKETVQECVSEF------ISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 49 ~rISkDA~~al~~~ateF------I~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
..+++++..+|.+++..| ++-|..-|..+|--++...|..+||..||.
T Consensus 41 ~~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 41 CPLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred cCCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 358888888888888776 455667889999999999999999999984
No 70
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=74.52 E-value=14 Score=34.65 Aligned_cols=101 Identities=20% Similarity=0.214 Sum_probs=67.1
Q ss_pred CCCCCCCCCCC----CCccccccCchhHHHHHHHhhCC-CCCccchHHHHHHHHHHHH----HHHHHHHHHHHHhHhcCC
Q 030647 13 SHESGEQSPRS----NVREQDRYLPIANISRIMKKALP-ANGKIAKDAKETVQECVSE----FISFITSEASDKCQREKR 83 (174)
Q Consensus 13 ~~~~~~~~~~~----~~~~~D~~LP~A~V~RImK~~LP-~~~rISkDA~~al~~~ate----FI~~LtseA~e~~~~~kR 83 (174)
.-++|+..|.+ .+-+.-+..+..-|.-|++--.. .++.+++||.+.|....++ +..-|..-|+.+|++.++
T Consensus 338 d~~sPhGIP~DlLDRllII~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~ 417 (450)
T COG1224 338 DIESPHGIPLDLLDRLLIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGS 417 (450)
T ss_pred CCcCCCCCCHhhhhheeEEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCC
Confidence 44455555543 22233344566677777775544 3678999999999887655 444455678899999999
Q ss_pred CCcCcchHHHHHHHcCCCchhHHHHHHHHHHHH
Q 030647 84 KTINGDDLLWAMATLGFEDYIDPLKIYLTRYRE 116 (174)
Q Consensus 84 KTI~~eDVl~AL~~LgF~~yv~~lk~~L~~yre 116 (174)
++|..+||-.|-+ =|.|-....+ |++.|++
T Consensus 418 ~~V~~~dVe~a~~--lF~D~krSv~-~v~~~~~ 447 (450)
T COG1224 418 KRVEVEDVERAKE--LFLDVKRSVE-YVEKYEG 447 (450)
T ss_pred CeeehhHHHHHHH--HHhhHHHHHH-HHHHHHh
Confidence 9999999999843 2444444433 6666654
No 71
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=73.55 E-value=7.7 Score=35.70 Aligned_cols=52 Identities=25% Similarity=0.273 Sum_probs=48.4
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCC
Q 030647 49 GKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGF 100 (174)
Q Consensus 49 ~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF 100 (174)
..|.+|+..+|..-.+-=|+-+..+|...-.+.||..++-+||-.||..|..
T Consensus 21 ~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNV 72 (450)
T COG5095 21 SNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNV 72 (450)
T ss_pred cccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCC
Confidence 4699999999999999999999999999999999999999999999998754
No 72
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=73.54 E-value=17 Score=29.61 Aligned_cols=65 Identities=14% Similarity=0.201 Sum_probs=49.8
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchhH-HHHHHHHHHH
Q 030647 51 IAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYID-PLKIYLTRYR 115 (174)
Q Consensus 51 ISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv~-~lk~~L~~yr 115 (174)
...-...-|-+-+--++.-|...|.-.+.+.+|.||.++||..|++...-..|.. +=+++|-++-
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 4444555666777777778888999999999999999999999999776666666 5556655543
No 73
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=72.97 E-value=5.6 Score=31.26 Aligned_cols=65 Identities=18% Similarity=0.313 Sum_probs=49.7
Q ss_pred ccccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcC----CCCcCcchHHHHHH
Q 030647 28 QDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREK----RKTINGDDLLWAMA 96 (174)
Q Consensus 28 ~D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~k----RKTI~~eDVl~AL~ 96 (174)
.-+.||...|.|.+|.....+.++..-+..- ....+.|||.|-.+.+.... -|.|++.|+-.|+.
T Consensus 27 aGlqFpVgRihr~LK~r~t~h~rVGataavy----~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 27 AGLQFPVGRIHRHLKTRTTSHGRVGATAAVY----SAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred cccccchHHHHHHHHHhcccccccchHHHHH----HHHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 3578999999999999988777776543322 33467899999888876654 48899999888765
No 74
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=68.22 E-value=14 Score=28.57 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=38.3
Q ss_pred CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 47 ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 47 ~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
++..=-.|++++|-..+.+||.-++..|.++. +|=.+..||++-+|+
T Consensus 24 Dd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 24 DDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred CCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 34455678999999999999999988777777 444578899999997
No 75
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=68.04 E-value=38 Score=31.40 Aligned_cols=61 Identities=18% Similarity=0.287 Sum_probs=46.8
Q ss_pred HHHHHHHhhCC-CCCccchHHHHHHHHHHHH----HHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 36 NISRIMKKALP-ANGKIAKDAKETVQECVSE----FISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 36 ~V~RImK~~LP-~~~rISkDA~~al~~~ate----FI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
-|..|++-... +++.++.||++.|.+...+ +-.+|-+.|+.+|.+.|-+++..+||-.+-+
T Consensus 362 d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 362 DIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred HHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 35555554443 4678999999999876543 5556667788999999999999999999864
No 76
>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=67.05 E-value=8.3 Score=26.23 Aligned_cols=61 Identities=16% Similarity=0.257 Sum_probs=38.0
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchhHHHHHHH
Q 030647 50 KIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLKIYL 111 (174)
Q Consensus 50 rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~lk~~L 111 (174)
-++.+-.+.|..+... ..-=+.+............-+.++++.||.++|..+.++.++.+|
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 222222333444444456778899999999999999999988764
No 77
>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=61.47 E-value=11 Score=24.43 Aligned_cols=42 Identities=12% Similarity=0.068 Sum_probs=26.3
Q ss_pred chHHHHHHHHHHHHHHHHHH-HHHHHHhHhcCCCCcCcchHHHH
Q 030647 52 AKDAKETVQECVSEFISFIT-SEASDKCQREKRKTINGDDLLWA 94 (174)
Q Consensus 52 SkDA~~al~~~ateFI~~Lt-seA~e~~~~~kRKTI~~eDVl~A 94 (174)
+.||...|.+. =.|+.--. ..+-..|+..|...||.++|..|
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 56777777765 44555333 34456778889999999998776
No 78
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=61.37 E-value=22 Score=27.85 Aligned_cols=48 Identities=21% Similarity=0.334 Sum_probs=40.6
Q ss_pred CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 47 ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 47 ~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
+...=..|+.++|.+.+.-+++.+...|...|+ .|-.+..||+.-||+
T Consensus 24 Dvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr 71 (126)
T COG5248 24 DVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALR 71 (126)
T ss_pred CCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHh
Confidence 345667889999999999999999999999998 344567799999997
No 79
>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=59.62 E-value=7.6 Score=24.29 Aligned_cols=26 Identities=19% Similarity=0.221 Sum_probs=21.0
Q ss_pred HHHHhHhcCCCCcCcchHHHHHHHcC
Q 030647 74 ASDKCQREKRKTINGDDLLWAMATLG 99 (174)
Q Consensus 74 A~e~~~~~kRKTI~~eDVl~AL~~Lg 99 (174)
|.+.|+..+...|+.+||+.||=+-+
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 56789999999999999999975544
No 80
>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=59.57 E-value=28 Score=28.12 Aligned_cols=51 Identities=20% Similarity=0.260 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCC-chhHHHHHHHHHHHHHhc
Q 030647 62 CVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE-DYIDPLKIYLTRYREMEG 119 (174)
Q Consensus 62 ~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~-~yv~~lk~~L~~yre~~~ 119 (174)
.+.+.+.||-.+|. |.-++.+++..-|+.|||+ +.++.+...+..+|+...
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l~ 94 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKLQ 94 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH
Confidence 55666777776665 5569999999999999997 566666666666665443
No 81
>PRK09862 putative ATP-dependent protease; Provisional
Probab=58.86 E-value=34 Score=32.55 Aligned_cols=59 Identities=12% Similarity=0.113 Sum_probs=45.2
Q ss_pred CccchHHHHHHHHHHHHH------HHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchhHHH
Q 030647 49 GKIAKDAKETVQECVSEF------ISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPL 107 (174)
Q Consensus 49 ~rISkDA~~al~~~ateF------I~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~l 107 (174)
..+++++...+.+++..+ ...|..-|..+|--++|..|+.+||..|+.=-+++...-.+
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~~~~~~ 501 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDRLLIHL 501 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccHHHHHH
Confidence 467888888887765544 56677788999999999999999999999855555444333
No 82
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=58.72 E-value=42 Score=29.14 Aligned_cols=72 Identities=13% Similarity=0.198 Sum_probs=49.3
Q ss_pred cCchhHHHHHHHhhCC-CCCccchHHHHHHHHHHH---HHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCc
Q 030647 31 YLPIANISRIMKKALP-ANGKIAKDAKETVQECVS---EFISFITSEASDKCQREKRKTINGDDLLWAMATLGFED 102 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP-~~~rISkDA~~al~~~at---eFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~ 102 (174)
.++...+..|++.... .++.++.|+...|.+.+. -++..+...+.+.+...+.+.|+.++|..+++.++...
T Consensus 179 ~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~ 254 (328)
T PRK00080 179 FYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDE 254 (328)
T ss_pred CCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCc
Confidence 3555666666665543 357899999888877663 22444444555666666677999999999999887754
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=56.11 E-value=40 Score=32.55 Aligned_cols=49 Identities=16% Similarity=0.188 Sum_probs=41.8
Q ss_pred CCccchHHHHHHHHHHHHHH-------HHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 48 NGKIAKDAKETVQECVSEFI-------SFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 48 ~~rISkDA~~al~~~ateFI-------~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.+.|+.++++.|.+.+..+- .++...|..+|.-++|.+|+.+||..|++
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
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=54.38 E-value=37 Score=30.77 Aligned_cols=74 Identities=18% Similarity=0.215 Sum_probs=51.2
Q ss_pred hHHHHHHHhhCCC---CCccchHHHHHHHHHHH------HHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchhH
Q 030647 35 ANISRIMKKALPA---NGKIAKDAKETVQECVS------EFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYID 105 (174)
Q Consensus 35 A~V~RImK~~LP~---~~rISkDA~~al~~~at------eFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv~ 105 (174)
.-|.-|+++-.-. ...++.++...+..-+. .+..-|...|.++|+++++.+|+.+||..|-+..+..-+.+
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 4456666655431 34678877776664332 34456667889999999999999999999977777665555
Q ss_pred HHH
Q 030647 106 PLK 108 (174)
Q Consensus 106 ~lk 108 (174)
.++
T Consensus 273 ~~~ 275 (366)
T COG1474 273 VLK 275 (366)
T ss_pred HHH
Confidence 443
No 85
>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=53.99 E-value=73 Score=26.86 Aligned_cols=70 Identities=19% Similarity=0.204 Sum_probs=46.2
Q ss_pred CchhHHHHHHHhhCC-CCCccchHHHHHHHHHHH---HHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCC
Q 030647 32 LPIANISRIMKKALP-ANGKIAKDAKETVQECVS---EFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (174)
Q Consensus 32 LP~A~V~RImK~~LP-~~~rISkDA~~al~~~at---eFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 101 (174)
++...+..|++.... .+..++.|+...|.+.+. -++.-+...+.+.+...+...|+.++|..++..++++
T Consensus 159 l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~ 232 (305)
T TIGR00635 159 YTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMID 232 (305)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCC
Confidence 444556666665543 246799999888777643 1233344445566655666789999999999987665
No 86
>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=53.04 E-value=58 Score=29.19 Aligned_cols=54 Identities=22% Similarity=0.205 Sum_probs=41.3
Q ss_pred HhhCCCCCccchHHHHHHHHHHHHHH-------HHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 42 KKALPANGKIAKDAKETVQECVSEFI-------SFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 42 K~~LP~~~rISkDA~~al~~~ateFI-------~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
++.++ .+.|+++.+..+.+.+..+= .++...|...|.-++|..|+++||..+..
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 44454 57899999888888776652 34556777888899999999999998764
No 87
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=53.03 E-value=31 Score=33.30 Aligned_cols=59 Identities=15% Similarity=0.166 Sum_probs=47.7
Q ss_pred HHHHHHHhhCCCCCccchHHHHHHHHHHHHHH-------HHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 36 NISRIMKKALPANGKIAKDAKETVQECVSEFI-------SFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 36 ~V~RImK~~LP~~~rISkDA~~al~~~ateFI-------~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.|.+. ++.++ ++.|+.+.+..+.++|..|- .+|...|..+|--++|.+|+.+||..|+.
T Consensus 183 ~I~~A-R~rl~-~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 183 DIAAA-RARLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHHHH-HHHHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 34433 33454 78999999999888888774 47788899999999999999999999986
No 88
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=51.97 E-value=17 Score=34.61 Aligned_cols=59 Identities=17% Similarity=0.310 Sum_probs=40.4
Q ss_pred HhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchhHHHHHHHHHH
Q 030647 42 KKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLKIYLTRY 114 (174)
Q Consensus 42 K~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~lk~~L~~y 114 (174)
|+++.+.--|-+|.+.||++||.+.=.||...-...-+++++++ |..|++.+-..|...
T Consensus 426 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~~ 484 (488)
T TIGR01052 426 KQSVADIPEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAYI 484 (488)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHH
Confidence 34443334688999999999999999999987665555555444 445666666655543
No 89
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=51.74 E-value=35 Score=32.31 Aligned_cols=47 Identities=15% Similarity=0.181 Sum_probs=41.1
Q ss_pred ccchHHHHHHHHHHHHH------HHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 50 KIAKDAKETVQECVSEF------ISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 50 rISkDA~~al~~~ateF------I~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.++++++..|.+++..| ++-|..-|..+|.-+++..|..+||..|+.
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 56889999999998887 566777899999999999999999999984
No 90
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=51.47 E-value=94 Score=26.07 Aligned_cols=50 Identities=20% Similarity=0.230 Sum_probs=38.0
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhHh-------------------c--------------CCCCcCcchHHHHHHHc
Q 030647 52 AKDAKETVQECVSEFISFITSEASDKCQR-------------------E--------------KRKTINGDDLLWAMATL 98 (174)
Q Consensus 52 SkDA~~al~~~ateFI~~LtseA~e~~~~-------------------~--------------kRKTI~~eDVl~AL~~L 98 (174)
..-.+-+|.-.+..||+-|+..|.+..+- . ++.+++..|+-.||++.
T Consensus 107 D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~~dr~K~vltv~DLs~Al~Ey 186 (197)
T COG5162 107 DQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTVVDLSKALEEY 186 (197)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccccccCCceeeehHHHHHHHHh
Confidence 34457788889999999999877754421 1 45678999999999988
Q ss_pred CCC
Q 030647 99 GFE 101 (174)
Q Consensus 99 gF~ 101 (174)
|+.
T Consensus 187 Gin 189 (197)
T COG5162 187 GIN 189 (197)
T ss_pred ccc
Confidence 873
No 91
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=49.72 E-value=91 Score=25.97 Aligned_cols=65 Identities=18% Similarity=0.130 Sum_probs=45.9
Q ss_pred CchhHHHHHHHhhCCC-CCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 32 LPIANISRIMKKALPA-NGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 32 LP~A~V~RImK~~LP~-~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
+....+.+++++.+.. +..|+.++...|.+.+.-=+..+-.+-...|.-.+.++|+.+||...+.
T Consensus 111 ~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~ 176 (302)
T TIGR01128 111 PKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVS 176 (302)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHh
Confidence 4566666667666543 5689999999998877665566666666666554445799999987765
No 92
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=48.33 E-value=29 Score=33.93 Aligned_cols=47 Identities=17% Similarity=0.160 Sum_probs=38.4
Q ss_pred ccchHHHHHHHHHHHHH-------------HHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 50 KIAKDAKETVQECVSEF-------------ISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 50 rISkDA~~al~~~ateF-------------I~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
.|+++|...|.+-++.- |.-|-.+|..+|+.++++.|+.+||..|+.
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 58999988887766632 233677899999999999999999999984
No 93
>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=48.31 E-value=30 Score=29.59 Aligned_cols=76 Identities=11% Similarity=0.121 Sum_probs=35.9
Q ss_pred cccccCchhHHHHHHHhhCCCC--CccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCC------CCcCcchHHHHHHHc
Q 030647 27 EQDRYLPIANISRIMKKALPAN--GKIAKDAKETVQECVSEFISFITSEASDKCQREKR------KTINGDDLLWAMATL 98 (174)
Q Consensus 27 ~~D~~LP~A~V~RImK~~LP~~--~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kR------KTI~~eDVl~AL~~L 98 (174)
.++.+|-...+.+-|.+....+ ..|..|...+|.-||.+.|..|-..+..+|++-.. .+....||-..|..|
T Consensus 39 ~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~l 118 (264)
T PF05236_consen 39 KEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRFL 118 (264)
T ss_dssp -----S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH-----------------------------
T ss_pred ccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHHH
Confidence 4567888888888888776443 46999999999999999999999999988865422 233467777777655
Q ss_pred CCCc
Q 030647 99 GFED 102 (174)
Q Consensus 99 gF~~ 102 (174)
.--+
T Consensus 119 ~~~e 122 (264)
T PF05236_consen 119 EQLE 122 (264)
T ss_dssp ----
T ss_pred HHHH
Confidence 5433
No 94
>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=48.17 E-value=38 Score=21.87 Aligned_cols=32 Identities=16% Similarity=0.428 Sum_probs=26.3
Q ss_pred cCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHH
Q 030647 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEF 66 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateF 66 (174)
-+-+++|.|++... .+||.++++-|.+++.+.
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 46688999998866 489999999999988764
No 95
>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=47.68 E-value=27 Score=26.41 Aligned_cols=32 Identities=19% Similarity=0.315 Sum_probs=26.7
Q ss_pred hHHHHHHHhhC----CCCCccchHHHHHHHHHHHHH
Q 030647 35 ANISRIMKKAL----PANGKIAKDAKETVQECVSEF 66 (174)
Q Consensus 35 A~V~RImK~~L----P~~~rISkDA~~al~~~ateF 66 (174)
++|.+|+|+-| .|+..++.++.+.|+++++.|
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~ 86 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELW 86 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHH
Confidence 56888999887 356789999999999999998
No 96
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=47.67 E-value=47 Score=28.14 Aligned_cols=71 Identities=8% Similarity=0.037 Sum_probs=43.2
Q ss_pred CchhHHHHHHHhhCC-CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchh
Q 030647 32 LPIANISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYI 104 (174)
Q Consensus 32 LP~A~V~RImK~~LP-~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv 104 (174)
++...+.+++++.+. .+..|+.++.+.|.+.+.-=+..+-......|. ..++|+.+||..++.....++.+
T Consensus 184 ~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~~~i 255 (337)
T PRK12402 184 PTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTDEVI 255 (337)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCHHHH
Confidence 445566666666554 356799999999888773223333333333332 23479999999988765544333
No 97
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=43.85 E-value=61 Score=27.81 Aligned_cols=65 Identities=12% Similarity=0.157 Sum_probs=47.0
Q ss_pred HHHHHHhhCC-CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHh--cCCCCcCcchHHHHHHHcCCC
Q 030647 37 ISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQR--EKRKTINGDDLLWAMATLGFE 101 (174)
Q Consensus 37 V~RImK~~LP-~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~--~kRKTI~~eDVl~AL~~LgF~ 101 (174)
+.++|++.+- .+..|+.+|...|.+++.-=+..+..|-...|.- .++.+|+.+||...+....+.
T Consensus 135 l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~ 202 (326)
T PRK07452 135 LKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQN 202 (326)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCc
Confidence 4454544443 3578999999999999887666677776666654 457789999999887765543
No 98
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=42.11 E-value=71 Score=28.99 Aligned_cols=54 Identities=19% Similarity=0.245 Sum_probs=43.8
Q ss_pred HhhCCCCCccchHHHHHHHHHHHHHH-------HHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 42 KKALPANGKIAKDAKETVQECVSEFI-------SFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 42 K~~LP~~~rISkDA~~al~~~ateFI-------~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
++.++ .+.|+++.+..|.+.|..+= .++...|.-.|--++|..|+++||..+..
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 57899999999988888763 36667788888999999999999998875
No 99
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=41.45 E-value=32 Score=32.07 Aligned_cols=32 Identities=28% Similarity=0.279 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhHhcCCCCcCcchHHHHHHHc
Q 030647 67 ISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (174)
Q Consensus 67 I~~LtseA~e~~~~~kRKTI~~eDVl~AL~~L 98 (174)
|..|..+|...|.+++|..|+.+||..|+++.
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 66778889999999999999999999999763
No 100
>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=41.21 E-value=88 Score=30.08 Aligned_cols=55 Identities=16% Similarity=0.235 Sum_probs=40.8
Q ss_pred HHhhCCCCCccchHHHHHHHHHHHHH-------HHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 41 MKKALPANGKIAKDAKETVQECVSEF-------ISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 41 mK~~LP~~~rISkDA~~al~~~ateF-------I~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
+++.++ .+.|+.+.++.|.+.+..+ -.++...|.-.|.-++|.+|+.+||..|..
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 124556677788889999999999999986
No 101
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=40.79 E-value=35 Score=30.79 Aligned_cols=34 Identities=24% Similarity=0.254 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcC
Q 030647 66 FISFITSEASDKCQREKRKTINGDDLLWAMATLG 99 (174)
Q Consensus 66 FI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~Lg 99 (174)
=|..|..+|...|.+++++.|+.+|+..|++..-
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~ 373 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVM 373 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence 4556777888888899999999999999997653
No 102
>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=40.25 E-value=50 Score=26.93 Aligned_cols=44 Identities=16% Similarity=0.315 Sum_probs=31.0
Q ss_pred cccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHH
Q 030647 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEAS 75 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~ 75 (174)
...+|-.... |+++.+.--|-+|.+.||++||...=.||...-.
T Consensus 101 St~VPfts~~---KeaIadvpEI~~EIrlAl~~~~R~L~~~l~kk~~ 144 (151)
T cd00823 101 STKVPFTSEG---KEAIADIPEIEEEIKLALQEVARKLKRYLSKKRK 144 (151)
T ss_pred ecCCCcCCcc---hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445544443 4555444468899999999999999999987533
No 103
>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=39.72 E-value=1.2e+02 Score=20.44 Aligned_cols=47 Identities=19% Similarity=0.217 Sum_probs=35.2
Q ss_pred cCchhHHHHHHHhhCCCCCcc-chHHHHHHHHHHHHHHHHHHHHHHHHhHh
Q 030647 31 YLPIANISRIMKKALPANGKI-AKDAKETVQECVSEFISFITSEASDKCQR 80 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rI-SkDA~~al~~~ateFI~~LtseA~e~~~~ 80 (174)
.+|-+.+.-+++.+. ... ..-.+-+|.=++..||+-|+..|.+.|+-
T Consensus 2 ~IPD~v~~~yL~~~G---~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSG---FQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCC---CCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 467788888888774 222 23345688889999999999999998863
No 104
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=39.53 E-value=37 Score=29.97 Aligned_cols=33 Identities=27% Similarity=0.298 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHc
Q 030647 66 FISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (174)
Q Consensus 66 FI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~L 98 (174)
-|..|..+|...|.+.++..|+.+|+..|++..
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~~ 363 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEKV 363 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHh
Confidence 355777888889999999999999999999763
No 105
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=39.50 E-value=85 Score=26.71 Aligned_cols=65 Identities=17% Similarity=0.083 Sum_probs=46.6
Q ss_pred cCchhHHHHHHHhhCC-CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhc-CCCCcCcchHHHHHH
Q 030647 31 YLPIANISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQRE-KRKTINGDDLLWAMA 96 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP-~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~-kRKTI~~eDVl~AL~ 96 (174)
.+....+.+.|++.+- .+..|+.+|...|.+.+..=+..+..|....|.-. +++ |+.+||-..+.
T Consensus 145 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~ 211 (340)
T PRK05574 145 PPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVP 211 (340)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHh
Confidence 3556666666666654 35689999999999988876777777777776543 333 99999876655
No 106
>smart00350 MCM minichromosome maintenance proteins.
Probab=38.94 E-value=1.4e+02 Score=27.98 Aligned_cols=65 Identities=12% Similarity=0.173 Sum_probs=45.7
Q ss_pred ccCchhHHHHHHHhh----CCCCCccchHHHHHHHHHHHHH-------------------HHHHHHHHHHHhHhcCCCCc
Q 030647 30 RYLPIANISRIMKKA----LPANGKIAKDAKETVQECVSEF-------------------ISFITSEASDKCQREKRKTI 86 (174)
Q Consensus 30 ~~LP~A~V~RImK~~----LP~~~rISkDA~~al~~~ateF-------------------I~~LtseA~e~~~~~kRKTI 86 (174)
..++...+.+.+.-+ .| +||+++.+.|.+...+. +..|-..|.-.|+-..|.+|
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 356777777766433 34 58999999887654442 23445566677888899999
Q ss_pred CcchHHHHHHH
Q 030647 87 NGDDLLWAMAT 97 (174)
Q Consensus 87 ~~eDVl~AL~~ 97 (174)
+.+||..|++-
T Consensus 493 ~~~Dv~~ai~l 503 (509)
T smart00350 493 EEADVEEAIRL 503 (509)
T ss_pred CHHHHHHHHHH
Confidence 99999999764
No 107
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=38.82 E-value=23 Score=34.03 Aligned_cols=46 Identities=20% Similarity=0.367 Sum_probs=36.6
Q ss_pred HhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcC
Q 030647 42 KKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTIN 87 (174)
Q Consensus 42 K~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~ 87 (174)
|+++.+.--|-+|.+.|+++||.+.=+||+....+.-+.+++++|.
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 3344333458899999999999999999999988888887777753
No 108
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=37.50 E-value=50 Score=23.47 Aligned_cols=32 Identities=16% Similarity=0.178 Sum_probs=26.7
Q ss_pred chHHHHHHHcCC------CchhHHHHHHHHHHHHHhcc
Q 030647 89 DDLLWAMATLGF------EDYIDPLKIYLTRYREMEGD 120 (174)
Q Consensus 89 eDVl~AL~~LgF------~~yv~~lk~~L~~yre~~~~ 120 (174)
+.|..+|..||| +.+-+.++..|..|..+++-
T Consensus 19 ~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~ENf 56 (74)
T PF08823_consen 19 REVQEALKRLGYYKGEADGVWDEATEDALRAWAGTENF 56 (74)
T ss_pred HHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhhH
Confidence 467889999999 78888999999999877654
No 109
>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=37.47 E-value=35 Score=22.33 Aligned_cols=25 Identities=28% Similarity=0.453 Sum_probs=20.7
Q ss_pred CcCcchHHHHHHHcCCCchhHHHHH
Q 030647 85 TINGDDLLWAMATLGFEDYIDPLKI 109 (174)
Q Consensus 85 TI~~eDVl~AL~~LgF~~yv~~lk~ 109 (174)
+=+++||..-|+.+||++|.+..+.
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 3467899999999999999887764
No 110
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=37.32 E-value=97 Score=23.85 Aligned_cols=31 Identities=13% Similarity=0.096 Sum_probs=26.7
Q ss_pred HHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCC
Q 030647 69 FITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (174)
Q Consensus 69 ~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 101 (174)
||+ |+-.|.-.++..||.+||...|+..|.+
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 6778888899999999999999999875
No 111
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=37.29 E-value=22 Score=33.58 Aligned_cols=79 Identities=13% Similarity=0.205 Sum_probs=65.5
Q ss_pred ccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH---HcCCCchhHH
Q 030647 30 RYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA---TLGFEDYIDP 106 (174)
Q Consensus 30 ~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~---~LgF~~yv~~ 106 (174)
+.+-+-.+.-+.+..+....+|-.|.-+++-..+-.|+.-++..+-..+++-+-+||-+.|+---|+ .+-++.|+..
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 4566777788888888777899999999999999999999999988889999999999999977776 3445677765
Q ss_pred HH
Q 030647 107 LK 108 (174)
Q Consensus 107 lk 108 (174)
.-
T Consensus 462 ~I 463 (505)
T COG5624 462 II 463 (505)
T ss_pred HH
Confidence 54
No 112
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=36.98 E-value=1.1e+02 Score=27.57 Aligned_cols=53 Identities=11% Similarity=0.031 Sum_probs=41.4
Q ss_pred HhhCCCCCccchHHHHHHHHHHHHHH-------HHHHHHHHHHhHhcCCCCcCcchHHHHH
Q 030647 42 KKALPANGKIAKDAKETVQECVSEFI-------SFITSEASDKCQREKRKTINGDDLLWAM 95 (174)
Q Consensus 42 K~~LP~~~rISkDA~~al~~~ateFI-------~~LtseA~e~~~~~kRKTI~~eDVl~AL 95 (174)
++.++ .+.|+++.+..+.+.|..+= .+|...|...|.-++|..|+++||..+.
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 44454 57899999998888887764 2366778888999999999999996654
No 113
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=36.86 E-value=55 Score=30.62 Aligned_cols=50 Identities=26% Similarity=0.343 Sum_probs=38.6
Q ss_pred CccchHH-HHHHHHHHHHH----HHHHHHHHHHHhHhcCCCCcCcchHHHHHHHc
Q 030647 49 GKIAKDA-KETVQECVSEF----ISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (174)
Q Consensus 49 ~rISkDA-~~al~~~ateF----I~~LtseA~e~~~~~kRKTI~~eDVl~AL~~L 98 (174)
+++++|. .+.|.+++.-| |.-|..||--.|.++.|..|+-+|.+.|.++.
T Consensus 338 M~l~~dvd~e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~KV 392 (406)
T COG1222 338 MNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEKV 392 (406)
T ss_pred ccCccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHHHHHHHH
Confidence 4555554 45555555544 77889999999999999999999999998753
No 114
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=36.83 E-value=95 Score=28.39 Aligned_cols=76 Identities=20% Similarity=0.256 Sum_probs=51.1
Q ss_pred CCCCccccccCchhHHHHHHHhhCCCCC--ccchHHHHHHHHH-HHHHHHHHHHHHHH-HhHhc--CC-CCcCcchHHHH
Q 030647 22 RSNVREQDRYLPIANISRIMKKALPANG--KIAKDAKETVQEC-VSEFISFITSEASD-KCQRE--KR-KTINGDDLLWA 94 (174)
Q Consensus 22 ~~~~~~~D~~LP~A~V~RImK~~LP~~~--rISkDA~~al~~~-ateFI~~LtseA~e-~~~~~--kR-KTI~~eDVl~A 94 (174)
.++|+..|+- -.|.|.-.+++.+|+.- .+..|-...|.+. ++.|+.-|+..-|+ ++..+ +- +.++.+||++|
T Consensus 41 ~SPVTvaDyG-~QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~a 119 (351)
T KOG1528|consen 41 KSPVTVADYG-SQAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLKA 119 (351)
T ss_pred CCCcchhhhh-HHHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHHH
Confidence 3567777765 36889999999999654 4666655555554 56677777764443 22222 23 78999999999
Q ss_pred HHHc
Q 030647 95 MATL 98 (174)
Q Consensus 95 L~~L 98 (174)
++.-
T Consensus 120 ID~G 123 (351)
T KOG1528|consen 120 IDRG 123 (351)
T ss_pred Hhcc
Confidence 9854
No 115
>PRK09526 lacI lac repressor; Reviewed
Probab=36.82 E-value=32 Score=28.90 Aligned_cols=37 Identities=16% Similarity=0.501 Sum_probs=29.7
Q ss_pred cCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHH
Q 030647 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITS 72 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~Lts 72 (174)
-.-++||.|.+... .+||+++++-+.+++.+ +.|.-.
T Consensus 16 GVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn 52 (342)
T PRK09526 16 GVSYQTVSRVLNQA----SHVSAKTREKVEAAMAE-LNYVPN 52 (342)
T ss_pred CCCHHHHHHHhcCC----CCCCHHHHHHHHHHHHH-HCCCcC
Confidence 46688999999753 47999999999999999 567544
No 116
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=35.62 E-value=1.1e+02 Score=23.63 Aligned_cols=32 Identities=6% Similarity=0.160 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCC
Q 030647 68 SFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (174)
Q Consensus 68 ~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 101 (174)
.||+ |+-.|.-.++.+||.+||...|+..|.+
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 5678888899999999999999988875
No 117
>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=35.53 E-value=8 Score=25.48 Aligned_cols=59 Identities=25% Similarity=0.376 Sum_probs=33.5
Q ss_pred CCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCc---CcchHHHHHHHcCCCchh-HHHHHH
Q 030647 48 NGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTI---NGDDLLWAMATLGFEDYI-DPLKIY 110 (174)
Q Consensus 48 ~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI---~~eDVl~AL~~LgF~~yv-~~lk~~ 110 (174)
+.+|.+++..+|.+++. .+..|+.+ .-..+=.|.+ .+...+..|.++|+-+++ +.+..+
T Consensus 1 gF~ie~~t~~ai~~~~~-~L~~is~E---Ri~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~a 63 (64)
T PF12627_consen 1 GFKIEPETEEAIKENAE-LLSKISKE---RIREELEKILSSPNPSRAFKLLDELGLLEYIFPELDAA 63 (64)
T ss_dssp T-EE-HHHHHHHHHHGG-GGGGS-HH---HHHHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT-
T ss_pred CCccCHHHHHHHHHHHH-HHhcCCHH---HHHHHHHHHHcCCCHHHHHHHHHHcCCHHHHCcccccc
Confidence 35788899999988877 55555544 2222223333 445566677788876653 555443
No 118
>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=33.68 E-value=32 Score=21.75 Aligned_cols=24 Identities=21% Similarity=0.387 Sum_probs=20.0
Q ss_pred CcchHHHHHHHcCCCchhHHHHHH
Q 030647 87 NGDDLLWAMATLGFEDYIDPLKIY 110 (174)
Q Consensus 87 ~~eDVl~AL~~LgF~~yv~~lk~~ 110 (174)
+.++|..-|+.+|+++|++.++..
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 578999999999998888887653
No 119
>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=33.43 E-value=28 Score=22.28 Aligned_cols=14 Identities=36% Similarity=0.672 Sum_probs=11.8
Q ss_pred chHHHHHHHcCCCc
Q 030647 89 DDLLWAMATLGFED 102 (174)
Q Consensus 89 eDVl~AL~~LgF~~ 102 (174)
+|++.||..|||..
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 120
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=33.35 E-value=53 Score=30.05 Aligned_cols=32 Identities=28% Similarity=0.254 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHhHhcCCCCcCcchHHHHHHHc
Q 030647 67 ISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (174)
Q Consensus 67 I~~LtseA~e~~~~~kRKTI~~eDVl~AL~~L 98 (174)
|..|..+|...|.+++|+.|+.+|+..|++..
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 66788889999999999999999999998753
No 121
>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=32.92 E-value=43 Score=21.82 Aligned_cols=22 Identities=23% Similarity=0.453 Sum_probs=19.3
Q ss_pred CcchHHHHHHHcCCCchhHHHH
Q 030647 87 NGDDLLWAMATLGFEDYIDPLK 108 (174)
Q Consensus 87 ~~eDVl~AL~~LgF~~yv~~lk 108 (174)
++++|..-|+.+|++.|++..+
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 5789999999999999998773
No 122
>PRK12728 fliE flagellar hook-basal body protein FliE; Provisional
Probab=32.83 E-value=2e+02 Score=21.64 Aligned_cols=63 Identities=11% Similarity=0.183 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh--HhcCCCCcCcchHHHHHHHcCC--CchhHHHHHHHHHHHHHh
Q 030647 54 DAKETVQECVSEFISFITSEASDKC--QREKRKTINGDDLLWAMATLGF--EDYIDPLKIYLTRYREME 118 (174)
Q Consensus 54 DA~~al~~~ateFI~~LtseA~e~~--~~~kRKTI~~eDVl~AL~~LgF--~~yv~~lk~~L~~yre~~ 118 (174)
.+.+.|.++... ++-.-.+|.+.. -..|. +++..||+-|+++.+. .-.+.-=...++.|+|+-
T Consensus 32 sF~~~L~~ai~~-vn~~q~~a~~~~~~~~~G~-~~~lhevmiA~~kA~lslq~~vqVRNKlv~AYqEIM 98 (102)
T PRK12728 32 SFSDFLKEALNK-VNELQVEADNSTEKLVKGE-IVDLHDVMIAAQKASISLQLTVQIRNKVVEAYQEIM 98 (102)
T ss_pred CHHHHHHHHHHH-HHHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455566555555 333333333222 22343 8899999999995554 444444456778999874
No 123
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=30.88 E-value=30 Score=24.57 Aligned_cols=18 Identities=17% Similarity=0.381 Sum_probs=15.7
Q ss_pred CcCcchHHHHHHHcCCCc
Q 030647 85 TINGDDLLWAMATLGFED 102 (174)
Q Consensus 85 TI~~eDVl~AL~~LgF~~ 102 (174)
.+++.+|+++|+.+||..
T Consensus 6 ~~~~ke~ik~Le~~Gf~~ 23 (66)
T COG1724 6 RMKAKEVIKALEKDGFQL 23 (66)
T ss_pred cCCHHHHHHHHHhCCcEE
Confidence 478899999999999963
No 124
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=30.82 E-value=81 Score=21.35 Aligned_cols=32 Identities=22% Similarity=0.505 Sum_probs=23.9
Q ss_pred cCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHH
Q 030647 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEF 66 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateF 66 (174)
-+..++|.|++... ..|+.+.++.|.+++.++
T Consensus 11 gvS~~TVSr~ln~~----~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 11 GVSKATVSRVLNGN----GRVSEETREKVLAAMEEL 42 (70)
T ss_pred CCCHHHHHHHHCCC----CCCCHHHHHHHHHHHHHh
Confidence 46778888877543 457888888888887776
No 125
>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=30.73 E-value=50 Score=25.51 Aligned_cols=61 Identities=10% Similarity=0.163 Sum_probs=40.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCCchhHHHHHHHHHHHHH
Q 030647 53 KDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLKIYLTRYREM 117 (174)
Q Consensus 53 kDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~lk~~L~~yre~ 117 (174)
...+.-|..|..+.-.|......=.. ----.-..++..|+..|++..+.++..-|++|++.
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 44556666677666666543222111 01123456788899999999999999999999743
No 126
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=30.52 E-value=1.1e+02 Score=26.90 Aligned_cols=61 Identities=18% Similarity=0.150 Sum_probs=44.9
Q ss_pred HHHHHHhhCC-CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHH
Q 030647 37 ISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (174)
Q Consensus 37 V~RImK~~LP-~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~ 97 (174)
+.+.|++.+- .+.+|++||.+.|..+..-=+..|.+|-...|--..-++|+.+||..++-.
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 4444444443 257899999999999998777777777776665555559999999988763
No 127
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=30.17 E-value=37 Score=32.66 Aligned_cols=56 Identities=18% Similarity=0.315 Sum_probs=40.3
Q ss_pred HhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcC--cchHHHHHHH
Q 030647 42 KKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTIN--GDDLLWAMAT 97 (174)
Q Consensus 42 K~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~--~eDVl~AL~~ 97 (174)
|+++.+.--|-+|.+.||++||...=.||...-...-++++++++. ..+|.++|..
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 4444444468999999999999999999999777666666665543 3455666653
No 128
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=29.84 E-value=59 Score=32.17 Aligned_cols=36 Identities=22% Similarity=0.426 Sum_probs=28.8
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCC
Q 030647 50 KIAKDAKETVQECVSEFISFITSEASDKCQREKRKT 85 (174)
Q Consensus 50 rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKT 85 (174)
-|-+|.+.||++||.+.=.||...-...-+++++++
T Consensus 592 eI~~Ei~lAl~~~~r~L~~~l~~~~~~~~~~~k~~~ 627 (659)
T PRK14867 592 EIFNEIRQALMICARELEKYISRIRREKEEEQKRKY 627 (659)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 477888899999999999999987665555555555
No 129
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=29.43 E-value=48 Score=28.09 Aligned_cols=37 Identities=16% Similarity=0.418 Sum_probs=28.8
Q ss_pred CchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHH
Q 030647 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSE 73 (174)
Q Consensus 32 LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~Ltse 73 (174)
+-++||.|.+... .+||.++++-|.+++.+. .|.-..
T Consensus 13 VS~~TVSrvLn~~----~~Vs~~tr~rV~~~a~el-gY~pn~ 49 (343)
T PRK10727 13 VSVATVSRVINNS----PKASEASRLAVHSAMESL-SYHPNA 49 (343)
T ss_pred CCHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCCCH
Confidence 5578999998653 479999999999999984 554443
No 130
>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=29.37 E-value=50 Score=18.71 Aligned_cols=26 Identities=19% Similarity=0.227 Sum_probs=19.5
Q ss_pred HHHHhHhcCCCCcCcchHHHHHH-HcC
Q 030647 74 ASDKCQREKRKTINGDDLLWAMA-TLG 99 (174)
Q Consensus 74 A~e~~~~~kRKTI~~eDVl~AL~-~Lg 99 (174)
+....-.++.-+|+.+++..+|+ .||
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 34556667778999999999998 576
No 131
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=29.27 E-value=43 Score=28.21 Aligned_cols=61 Identities=11% Similarity=-0.019 Sum_probs=45.7
Q ss_pred cCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCC---CcCcchHHHHH
Q 030647 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRK---TINGDDLLWAM 95 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRK---TI~~eDVl~AL 95 (174)
.||++.|.+++..++. -.|+...+.+|+-.+.+|+--|--.|..+- +++. -+.+.|+-.|.
T Consensus 115 ~lnKt~VKKlastV~n--QtVspNi~I~l~g~~KVfvGEiIElA~~Vq--~~w~~sgpl~p~h~reay 178 (199)
T COG5251 115 SLNKTQVKKLASTVAN--QTVSPNIRIFLQGVGKVFVGEIIELAMIVQ--NKWLTSGPLIPFHKREAY 178 (199)
T ss_pred CCCHHHHHHHHHHHhc--cccCCCeeeeeechhHHHHHHHHHHHHHHH--HHhcccCCCChHHHHHHH
Confidence 5999999999999984 578888888999999999887765554322 2222 37777777664
No 132
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=28.57 E-value=33 Score=28.55 Aligned_cols=36 Identities=14% Similarity=0.376 Sum_probs=28.3
Q ss_pred CchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHH
Q 030647 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITS 72 (174)
Q Consensus 32 LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~Lts 72 (174)
.-++||.|.+... .+||.++++-+.+++.+. .|.-.
T Consensus 10 VS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l-gY~pn 45 (327)
T PRK10423 10 VSTSTVSHVINKD----RFVSEAITAKVEAAIKEL-NYAPS 45 (327)
T ss_pred CcHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCcc
Confidence 4578999999643 379999999999999886 45443
No 133
>PF14434 Imm6: Immunity protein Imm6
Probab=28.14 E-value=1.8e+02 Score=22.55 Aligned_cols=49 Identities=20% Similarity=0.281 Sum_probs=34.4
Q ss_pred HHHHHHHHHHH-----HHHHHHHHHHhHhc-CCCCcCcchHHHHHHHcCCCchhH
Q 030647 57 ETVQECVSEFI-----SFITSEASDKCQRE-KRKTINGDDLLWAMATLGFEDYID 105 (174)
Q Consensus 57 ~al~~~ateFI-----~~LtseA~e~~~~~-kRKTI~~eDVl~AL~~LgF~~yv~ 105 (174)
..|.++...+| .++..+|.+.|..- ..+.++++++..-|+..+|.+...
T Consensus 8 l~iae~~~~~I~~~~~~~~~~~aL~~cw~wle~~~~~~D~LY~lldn~D~~gi~~ 62 (122)
T PF14434_consen 8 LAIAEKLVDYIKKSEYGEFVREALDACWKWLEGKEVTGDELYSLLDNEDENGIFI 62 (122)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHcCCCCHHHHHHHHhCcccccHHH
Confidence 44555555555 34448889999764 348999999999999877765443
No 134
>PTZ00183 centrin; Provisional
Probab=27.68 E-value=2.1e+02 Score=21.04 Aligned_cols=17 Identities=18% Similarity=0.284 Sum_probs=9.5
Q ss_pred hcCCCCcCcchHHHHHH
Q 030647 80 REKRKTINGDDLLWAMA 96 (174)
Q Consensus 80 ~~kRKTI~~eDVl~AL~ 96 (174)
.++...|+.++++.++.
T Consensus 64 ~~~~g~i~~~eF~~~~~ 80 (158)
T PTZ00183 64 KDGSGKIDFEEFLDIMT 80 (158)
T ss_pred CCCCCcEeHHHHHHHHH
Confidence 34455566666665554
No 135
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=27.53 E-value=3.6e+02 Score=25.65 Aligned_cols=89 Identities=17% Similarity=0.113 Sum_probs=52.8
Q ss_pred cccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHH----------HHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHc
Q 030647 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVS----------EFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (174)
Q Consensus 29 D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~at----------eFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~L 98 (174)
++++|.+.|---|... ++.|..+....+..-.. .-+.-|..+..+......=--=++.+|.++|+.+
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 4456666666656554 57888887766665554 5556666666555422111224568999999998
Q ss_pred CCC----------chhHHHHHHHHHHHHHhcc
Q 030647 99 GFE----------DYIDPLKIYLTRYREMEGD 120 (174)
Q Consensus 99 gF~----------~yv~~lk~~L~~yre~~~~ 120 (174)
|+. .-..|+-..+-+||+..+.
T Consensus 238 g~~~~~t~~~~L~~~~hp~~~~ile~r~~~kl 269 (553)
T PRK14975 238 GIELPSTRKWELREIDHPAVEPLLEYRKLSKL 269 (553)
T ss_pred CCCCCCCcHHHhccCCCchHHHHHHHHHHHHH
Confidence 884 1112344456677766544
No 136
>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=27.01 E-value=38 Score=27.91 Aligned_cols=34 Identities=21% Similarity=0.464 Sum_probs=25.1
Q ss_pred HhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHH
Q 030647 42 KKALPANGKIAKDAKETVQECVSEFISFITSEAS 75 (174)
Q Consensus 42 K~~LP~~~rISkDA~~al~~~ateFI~~LtseA~ 75 (174)
|+++.+.--|-+|.+.||++||...=.||.....
T Consensus 120 KeaIa~~pEI~~Ei~lAl~e~~R~L~~yl~rk~~ 153 (160)
T PF09239_consen 120 KEAIADVPEIEKEIRLALQECARKLKKYLSRKRK 153 (160)
T ss_dssp SSSB---HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444468899999999999999999987543
No 137
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=26.84 E-value=57 Score=27.38 Aligned_cols=37 Identities=11% Similarity=0.357 Sum_probs=28.3
Q ss_pred cCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHH
Q 030647 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITS 72 (174)
Q Consensus 31 ~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~Lts 72 (174)
-.-++||.|++... .+||.++++-+.+++.+ +.|.-.
T Consensus 16 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn 52 (331)
T PRK14987 16 GVTKMTVSRFLRNP----EQVSVALRGKIAAALDE-LGYIPN 52 (331)
T ss_pred CCCHHHhhhhhCCC----CCCCHHHHHHHHHHHHH-hCCCcc
Confidence 35678999988643 47999999999999988 456543
No 138
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=26.80 E-value=1.5e+02 Score=25.58 Aligned_cols=61 Identities=16% Similarity=0.165 Sum_probs=40.6
Q ss_pred HHHHHHHhhCC-CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHh-cCCCCcCcchHHHHHH
Q 030647 36 NISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQR-EKRKTINGDDLLWAMA 96 (174)
Q Consensus 36 ~V~RImK~~LP-~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~-~kRKTI~~eDVl~AL~ 96 (174)
.+.+++++.+- .+.+|+.||...|.+++.-=...+..|-...+.- .+.++|+.+||...+.
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 33444444433 3578999999999998876555566665555554 3456899999877654
No 139
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=26.51 E-value=48 Score=33.54 Aligned_cols=58 Identities=21% Similarity=0.339 Sum_probs=40.7
Q ss_pred ccccccCchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCc
Q 030647 26 REQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTI 86 (174)
Q Consensus 26 ~~~D~~LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI 86 (174)
-+-...+|-.... |+++.+.--|-+|.+.||++||.+.=.||...-...-++++++++
T Consensus 612 hvaST~VPfts~s---KeaIA~vpEI~~EI~lAl~~~aR~Lk~yl~k~~~~~~~~~k~~~~ 669 (795)
T PRK14868 612 HVASTNVPFTSES---KDAIANVPEIEDEIELAIREAARELKSYLNKRRSMQKRREKQDVL 669 (795)
T ss_pred EEeecCCCCCCcc---hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334555655443 455544446999999999999999999999876666666666554
No 140
>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=26.51 E-value=47 Score=21.09 Aligned_cols=26 Identities=15% Similarity=0.318 Sum_probs=20.6
Q ss_pred CcCcchHHHHHHHcCCCchhHHHHHH
Q 030647 85 TINGDDLLWAMATLGFEDYIDPLKIY 110 (174)
Q Consensus 85 TI~~eDVl~AL~~LgF~~yv~~lk~~ 110 (174)
.-+.++|..-|+.+||++|++.+...
T Consensus 3 ~w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 3 QWSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCCHHHHHHHHHHCChHHHHHHHHHC
Confidence 34678899999999999888877654
No 141
>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=26.06 E-value=2e+02 Score=21.88 Aligned_cols=31 Identities=13% Similarity=0.163 Sum_probs=26.1
Q ss_pred HHHHHHHHHhHhcCCCCcCcchHHHHHHHcCCC
Q 030647 69 FITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (174)
Q Consensus 69 ~LtseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 101 (174)
||+ |+-.|.-.++.+||.+||...|+..|.+
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 454 5678888888899999999999988875
No 142
>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=24.85 E-value=1.3e+02 Score=28.28 Aligned_cols=52 Identities=12% Similarity=0.151 Sum_probs=38.6
Q ss_pred CCCccchHHHHHHHHHHHHHHH-HHHHHHHHHhHhcCCCCcCcchHHHHHHHcC
Q 030647 47 ANGKIAKDAKETVQECVSEFIS-FITSEASDKCQREKRKTINGDDLLWAMATLG 99 (174)
Q Consensus 47 ~~~rISkDA~~al~~~ateFI~-~LtseA~e~~~~~kRKTI~~eDVl~AL~~Lg 99 (174)
+.+.++.||...|.+ .=-|+. -+-..+-+.|+..+...|+.+.|..|=..+|
T Consensus 459 ~~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 511 (511)
T TIGR01278 459 GELGWTAEAEAELKK-VPFFVRGKVRRNTENFARERGYSVITLEVIYAAKEHFG 511 (511)
T ss_pred CCCCcCHHHHHHHhh-CChhhhHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhcC
Confidence 356899999999965 344444 3444555778889999999999999876654
No 143
>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=24.77 E-value=1.9e+02 Score=19.51 Aligned_cols=41 Identities=22% Similarity=0.173 Sum_probs=31.4
Q ss_pred HHHHHHHHH--HHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 54 DAKETVQEC--VSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 54 DA~~al~~~--ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
|+.+.+ +. ...|+.|....|...+-+.++|.- -+|+.+|..
T Consensus 14 e~id~~-~~~~~~~~~~f~~gnaiKY~~R~~~K~~-~eDl~KA~~ 56 (60)
T PF11753_consen 14 ECIDFI-EQFTEEQFLGFCLGNAIKYLWRAGKKNG-IEDLKKAKW 56 (60)
T ss_pred cHHHHH-HHhcchhhhhHHHHHHHHHHHHHcccCc-HHHHHHHHH
Confidence 455555 44 348999999999999999999943 788888875
No 144
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=24.71 E-value=1.3e+02 Score=28.36 Aligned_cols=52 Identities=13% Similarity=0.142 Sum_probs=39.1
Q ss_pred CCCccchHHHHHHHHHHHHHHH-HHHHHHHHHhHhcCCCCcCcchHHHHHHHcC
Q 030647 47 ANGKIAKDAKETVQECVSEFIS-FITSEASDKCQREKRKTINGDDLLWAMATLG 99 (174)
Q Consensus 47 ~~~rISkDA~~al~~~ateFI~-~LtseA~e~~~~~kRKTI~~eDVl~AL~~Lg 99 (174)
+.+.++.||...|.+ .=-|+. -+-..+-+.|+..+...|+.+.|..|-..+|
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 457899999999965 444554 3344455678888999999999999977654
No 145
>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=24.53 E-value=1.5e+02 Score=20.95 Aligned_cols=49 Identities=20% Similarity=0.334 Sum_probs=26.5
Q ss_pred CCccchHHHHHHHHHHH-------HHHHHHHHHHHHHhHh-cCCCCcCcchHHHHHH
Q 030647 48 NGKIAKDAKETVQECVS-------EFISFITSEASDKCQR-EKRKTINGDDLLWAMA 96 (174)
Q Consensus 48 ~~rISkDA~~al~~~at-------eFI~~LtseA~e~~~~-~kRKTI~~eDVl~AL~ 96 (174)
++|++.+.++.|.++|. .||.-.+.++.+.... +..-+++.+|.-.-++
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~ 59 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMA 59 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHH
Confidence 36899999999999975 4555444443333222 2334555555443333
No 146
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
Probab=24.33 E-value=1.4e+02 Score=28.87 Aligned_cols=72 Identities=15% Similarity=0.194 Sum_probs=45.0
Q ss_pred hhHHHHHHHhhCCC-CCccchHHHHHHHHHH---HHHHHHHHHHH----HH---HhHhcCCCCcCcchHHHHHHHcCCCc
Q 030647 34 IANISRIMKKALPA-NGKIAKDAKETVQECV---SEFISFITSEA----SD---KCQREKRKTINGDDLLWAMATLGFED 102 (174)
Q Consensus 34 ~A~V~RImK~~LP~-~~rISkDA~~al~~~a---teFI~~LtseA----~e---~~~~~kRKTI~~eDVl~AL~~LgF~~ 102 (174)
..-+..|++..+.. +..++.++..+|.+++ ...++.|.... +. .+...++.+|+.+||.+++..--|..
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 35577777776543 3568999999988765 34444443221 11 12233456899999999998766665
Q ss_pred hhH
Q 030647 103 YID 105 (174)
Q Consensus 103 yv~ 105 (174)
|..
T Consensus 435 ~~~ 437 (615)
T TIGR02903 435 YEK 437 (615)
T ss_pred chh
Confidence 543
No 147
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=24.26 E-value=1.4e+02 Score=21.13 Aligned_cols=26 Identities=12% Similarity=0.192 Sum_probs=20.0
Q ss_pred HHhHhcCCCCcCcchHHHHHHHcCCC
Q 030647 76 DKCQREKRKTINGDDLLWAMATLGFE 101 (174)
Q Consensus 76 e~~~~~kRKTI~~eDVl~AL~~LgF~ 101 (174)
..+-.++.-.|+.++|..+|..+|+.
T Consensus 17 ~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 17 RSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 55556677788888888888888764
No 148
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=23.82 E-value=1.5e+02 Score=24.84 Aligned_cols=65 Identities=11% Similarity=0.059 Sum_probs=38.8
Q ss_pred CchhHHHHHHHhhCC-CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHHHc
Q 030647 32 LPIANISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (174)
Q Consensus 32 LP~A~V~RImK~~LP-~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~~L 98 (174)
++...+.++++..+. .+..|+.++.+.|.+.+.--+..+-.+-...+. . .++|+.+||..++...
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 445555566655543 256799999998888765333333222222222 2 3689999998887543
No 149
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=23.77 E-value=89 Score=26.05 Aligned_cols=35 Identities=14% Similarity=0.397 Sum_probs=27.6
Q ss_pred CchhHHHHHHHhhCCCCCccchHHHHHHHHHHHHHHHHHH
Q 030647 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFIT 71 (174)
Q Consensus 32 LP~A~V~RImK~~LP~~~rISkDA~~al~~~ateFI~~Lt 71 (174)
+-++||.|++... .+||+++++-|.+++.+. .|.-
T Consensus 13 vS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l-gY~p 47 (329)
T TIGR01481 13 VSMATVSRVVNGN----PNVKPATRKKVLEVIKRL-DYRP 47 (329)
T ss_pred CCHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCC
Confidence 5578999998753 479999999999999885 4433
No 150
>PF10728 DUF2520: Domain of unknown function (DUF2520); InterPro: IPR018931 This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases. ; PDB: 3D1L_A 2I76_A 3DFU_A.
Probab=23.12 E-value=2.7e+02 Score=21.54 Aligned_cols=57 Identities=14% Similarity=0.144 Sum_probs=37.6
Q ss_pred hHHHHHHHhhCCCCCccchHHHHHHHHHH---HHHHHHHHHHHHHHhHhcCCCCcCcchHHHH
Q 030647 35 ANISRIMKKALPANGKIAKDAKETVQECV---SEFISFITSEASDKCQREKRKTINGDDLLWA 94 (174)
Q Consensus 35 A~V~RImK~~LP~~~rISkDA~~al~~~a---teFI~~LtseA~e~~~~~kRKTI~~eDVl~A 94 (174)
..+.+|+++.-.....|..+-|....-++ +-|+.+|...|.+++... -|..++.+.+
T Consensus 14 ~~l~~l~~~lg~~~~~i~~~~r~~yHaAav~asNf~~~L~~~a~~ll~~~---gi~~~~a~~~ 73 (132)
T PF10728_consen 14 EVLQELAKELGGRPFEIDSEQRALYHAAAVFASNFLVALYALAAELLEQA---GIDFEEALEA 73 (132)
T ss_dssp HHHHHHHHHTTSEEEE--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHT---T-SHHH--HH
T ss_pred HHHHHHHHHhCCceEEeCHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHc---CCCchhHHHH
Confidence 45677777776666789999999888765 468888888888888766 3444443333
No 151
>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=22.82 E-value=53 Score=21.13 Aligned_cols=16 Identities=19% Similarity=0.406 Sum_probs=13.7
Q ss_pred cCcchHHHHHHHcCCC
Q 030647 86 INGDDLLWAMATLGFE 101 (174)
Q Consensus 86 I~~eDVl~AL~~LgF~ 101 (174)
++.++|..+++++||+
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 152
>PRK07914 hypothetical protein; Reviewed
Probab=22.58 E-value=1.9e+02 Score=25.06 Aligned_cols=63 Identities=11% Similarity=0.127 Sum_probs=42.7
Q ss_pred chhHHHHHHHhhCC-CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHHH
Q 030647 33 PIANISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (174)
Q Consensus 33 P~A~V~RImK~~LP-~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL~ 96 (174)
+-..+.+.|++.+- .+.+|+.||...|.+++..=+..|..|-...+-..+ .+|+.+||...+.
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 44555555555544 256899999999999997666666666655554333 5798888877654
No 153
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=21.24 E-value=1.8e+02 Score=27.19 Aligned_cols=40 Identities=15% Similarity=0.239 Sum_probs=32.7
Q ss_pred HhHhcCCCCcCcchHHHHHHHcCCCchhHHHHHHHHHHHHHhcc
Q 030647 77 KCQREKRKTINGDDLLWAMATLGFEDYIDPLKIYLTRYREMEGD 120 (174)
Q Consensus 77 ~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~lk~~L~~yre~~~~ 120 (174)
+...+++|-++-+.|...|++-|+ ..-+..+.+||+..+=
T Consensus 407 I~~Ed~~~PlSD~~I~~~L~~~Gi----~IaRRTVaKYRe~L~I 446 (455)
T PRK05932 407 IAAENPKKPLSDSKIAELLKEQGI----DVARRTVAKYREALNI 446 (455)
T ss_pred HHhcCCCCCCCHHHHHHHHHHcCC----CeehHHHHHHHHHcCC
Confidence 556777899999999999999887 4567788899987654
No 154
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=21.08 E-value=1.7e+02 Score=28.47 Aligned_cols=63 Identities=8% Similarity=0.004 Sum_probs=32.0
Q ss_pred CchhHHHHHHHhhCC-CCCccchHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCcCcchHHHHH
Q 030647 32 LPIANISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAM 95 (174)
Q Consensus 32 LP~A~V~RImK~~LP-~~~rISkDA~~al~~~ateFI~~LtseA~e~~~~~kRKTI~~eDVl~AL 95 (174)
|+...+.+.+++.+- .+..|+.++...|.+.+.-=+..+-.+....+.-.+++ |+.++|...+
T Consensus 180 ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l 243 (614)
T PRK14971 180 IQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENL 243 (614)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHh
Confidence 444555555554432 25778998888877655433333333332322222322 6666665544
No 155
>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=20.48 E-value=2.6e+02 Score=23.90 Aligned_cols=60 Identities=7% Similarity=0.048 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHHHHHh-HhcCCCCcC----------cchHHHHHHHcCCCchhHHHHHHHHHHHHHhcc
Q 030647 61 ECVSEFISFITSEASDKC-QREKRKTIN----------GDDLLWAMATLGFEDYIDPLKIYLTRYREMEGD 120 (174)
Q Consensus 61 ~~ateFI~~LtseA~e~~-~~~kRKTI~----------~eDVl~AL~~LgF~~yv~~lk~~L~~yre~~~~ 120 (174)
++|..||.|+.+...... .+.....++ ++++...+-.+.+..+.+.....+++|.+..+.
T Consensus 261 e~A~~fidfllS~e~Q~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~rw~~~~~~ 331 (334)
T TIGR03261 261 DAAKKLVDWSISDEAMELYAKNYAVVATPGVAKPDAGFPKNVEDLLIKNDFVWAAANRDKILEEWSKRYGA 331 (334)
T ss_pred HHHHHHHHHHcCHHHHHHHHhcCcccccCCcccCcccCCcchhhhcccCCHHHHHHhHHHHHHHHHHHhhc
Confidence 789999999976533222 222221111 124444444566666788888888999876654
Done!