Query 026469
Match_columns 238
No_of_seqs 158 out of 631
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 08:24:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026469.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026469hhsearch_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 7.7E-37 1.7E-41 258.5 11.5 106 51-156 21-126 (168)
2 KOG0871 Class 2 transcription 99.9 5.5E-26 1.2E-30 191.0 9.5 103 57-159 7-111 (156)
3 KOG0870 DNA polymerase epsilon 99.9 7E-24 1.5E-28 180.9 9.0 104 56-159 4-108 (172)
4 COG5150 Class 2 transcription 99.8 6.6E-21 1.4E-25 157.8 8.9 95 58-152 7-101 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.7 8.5E-18 1.8E-22 121.1 7.7 64 62-126 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.7 1.3E-17 2.8E-22 130.6 6.4 80 54-135 11-90 (91)
7 cd00076 H4 Histone H4, one of 99.4 2.1E-12 4.5E-17 100.1 8.2 72 61-134 12-83 (85)
8 PLN00035 histone H4; Provision 99.3 4.8E-12 1E-16 101.3 8.2 75 58-134 25-99 (103)
9 PTZ00015 histone H4; Provision 99.3 9.7E-12 2.1E-16 99.4 8.1 76 57-134 25-100 (102)
10 smart00417 H4 Histone H4. 99.2 7.1E-11 1.5E-15 89.6 6.2 64 60-125 11-74 (74)
11 smart00803 TAF TATA box bindin 99.2 1.4E-10 3E-15 85.4 7.4 64 62-127 2-65 (65)
12 smart00428 H3 Histone H3. 99.0 1.5E-09 3.3E-14 87.1 6.6 72 57-128 24-100 (105)
13 cd07981 TAF12 TATA Binding Pro 98.9 5.9E-09 1.3E-13 77.6 8.1 66 63-129 2-67 (72)
14 PF00125 Histone: Core histone 98.9 3.7E-09 7.9E-14 77.2 6.3 68 60-127 3-73 (75)
15 COG5208 HAP5 CCAAT-binding fac 98.7 1.5E-08 3.2E-13 91.4 3.9 79 57-136 104-182 (286)
16 PLN00161 histone H3; Provision 98.6 1.5E-07 3.2E-12 78.8 7.2 71 57-127 50-124 (135)
17 PLN00121 histone H3; Provision 98.6 8.7E-08 1.9E-12 80.2 5.8 71 57-127 57-130 (136)
18 PLN00160 histone H3; Provision 98.6 1.3E-07 2.8E-12 75.3 6.4 71 57-127 16-90 (97)
19 PTZ00018 histone H3; Provision 98.5 1.4E-07 2.9E-12 79.1 5.6 71 57-127 57-130 (136)
20 smart00576 BTP Bromodomain tra 98.5 8.6E-07 1.9E-11 66.4 8.0 66 65-132 9-74 (77)
21 KOG3467 Histone H4 [Chromatin 98.4 1.1E-06 2.5E-11 69.6 6.8 69 62-132 29-97 (103)
22 cd00074 H2A Histone 2A; H2A is 98.4 1E-06 2.2E-11 71.8 6.7 69 59-128 17-85 (115)
23 KOG1657 CCAAT-binding factor, 98.3 5.5E-07 1.2E-11 81.1 4.7 91 54-145 66-159 (236)
24 cd07979 TAF9 TATA Binding Prot 98.3 3.3E-06 7.1E-11 68.5 7.8 77 66-144 5-82 (117)
25 cd08050 TAF6 TATA Binding Prot 98.1 1.1E-05 2.4E-10 75.2 8.0 67 64-132 1-67 (343)
26 KOG1745 Histones H3 and H4 [Ch 97.9 6.5E-06 1.4E-10 69.2 2.8 73 57-129 58-133 (137)
27 PF15511 CENP-T: Centromere ki 97.9 2.2E-05 4.7E-10 75.3 6.1 65 57-121 346-414 (414)
28 PF15630 CENP-S: Kinetochore c 97.8 7E-05 1.5E-09 57.1 6.8 62 67-128 10-72 (76)
29 PF07524 Bromo_TP: Bromodomain 97.7 0.00024 5.3E-09 52.7 8.1 64 67-132 11-74 (77)
30 PF03847 TFIID_20kDa: Transcri 97.7 0.0002 4.3E-09 53.5 7.0 63 65-128 2-64 (68)
31 smart00427 H2B Histone H2B. 97.6 0.00031 6.7E-09 55.4 7.1 62 67-129 6-67 (89)
32 cd08048 TAF11 TATA Binding Pro 97.5 0.00047 1E-08 53.5 7.7 66 62-129 16-84 (85)
33 PF02969 TAF: TATA box binding 97.5 0.00058 1.2E-08 50.9 7.4 64 62-127 3-66 (66)
34 KOG1659 Class 2 transcription 97.4 0.00025 5.4E-09 63.7 5.5 79 61-140 12-90 (224)
35 PF09415 CENP-X: CENP-S associ 97.4 0.00028 6E-09 53.3 4.4 65 64-128 1-67 (72)
36 PLN00158 histone H2B; Provisio 97.3 0.001 2.2E-08 54.8 7.1 65 64-129 29-93 (116)
37 PTZ00463 histone H2B; Provisio 97.2 0.0012 2.6E-08 54.4 7.1 62 67-129 33-94 (117)
38 PF04719 TAFII28: hTAFII28-lik 97.0 0.0025 5.4E-08 50.2 6.9 67 62-129 23-90 (90)
39 COG5262 HTA1 Histone H2A [Chro 97.0 0.0014 3.1E-08 54.5 5.5 68 59-127 23-90 (132)
40 smart00414 H2A Histone 2A. 97.0 0.0023 5E-08 51.6 6.3 69 59-128 6-74 (106)
41 COG5247 BUR6 Class 2 transcrip 96.9 0.0022 4.8E-08 52.2 5.4 77 61-138 22-98 (113)
42 KOG1142 Transcription initiati 96.8 0.0027 5.9E-08 58.4 5.7 70 58-128 150-219 (258)
43 PLN00154 histone H2A; Provisio 96.7 0.0051 1.1E-07 51.9 6.3 69 59-127 35-103 (136)
44 PTZ00017 histone H2A; Provisio 96.5 0.0058 1.3E-07 51.4 5.5 68 59-127 24-91 (134)
45 KOG1744 Histone H2B [Chromatin 96.2 0.014 3E-07 48.9 6.4 62 67-129 42-103 (127)
46 PF15510 CENP-W: Centromere ki 96.2 0.0084 1.8E-07 48.1 4.6 67 61-128 15-95 (102)
47 PF02291 TFIID-31kDa: Transcri 96.2 0.022 4.8E-07 47.4 7.2 85 57-143 5-92 (129)
48 PF02269 TFIID-18kDa: Transcri 96.1 0.0071 1.5E-07 47.3 3.9 59 69-128 8-66 (93)
49 PLN00157 histone H2A; Provisio 96.1 0.012 2.5E-07 49.6 5.3 68 59-127 23-90 (132)
50 PLN00153 histone H2A; Provisio 96.1 0.014 3E-07 48.9 5.5 68 59-127 21-88 (129)
51 KOG1756 Histone 2A [Chromatin 96.0 0.016 3.5E-07 48.7 5.8 68 59-127 24-91 (131)
52 PLN00156 histone H2AX; Provisi 96.0 0.016 3.4E-07 49.1 5.8 68 59-127 26-93 (139)
53 KOG1658 DNA polymerase epsilon 95.8 0.005 1.1E-07 53.2 2.0 70 58-129 55-125 (162)
54 cd07978 TAF13 The TATA Binding 95.6 0.15 3.2E-06 40.1 9.4 60 67-128 7-66 (92)
55 KOG3219 Transcription initiati 95.3 0.021 4.5E-07 50.8 4.0 69 62-132 112-181 (195)
56 PTZ00252 histone H2A; Provisio 94.4 0.11 2.5E-06 43.8 6.0 68 59-127 22-91 (134)
57 KOG4336 TBP-associated transcr 93.5 0.82 1.8E-05 43.5 10.5 77 67-147 10-86 (323)
58 KOG2549 Transcription initiati 92.9 0.35 7.6E-06 49.0 7.5 66 64-131 13-78 (576)
59 KOG3423 Transcription initiati 92.7 0.53 1.2E-05 41.4 7.4 69 62-132 86-168 (176)
60 TIGR03015 pepcterm_ATPase puta 91.3 0.64 1.4E-05 40.1 6.4 70 62-131 191-268 (269)
61 PRK00411 cdc6 cell division co 86.6 2.8 6E-05 38.5 7.4 71 64-134 208-287 (394)
62 KOG3334 Transcription initiati 86.2 4.3 9.4E-05 35.0 7.7 64 81-144 30-94 (148)
63 TIGR02928 orc1/cdc6 family rep 83.4 3.7 8E-05 37.2 6.6 75 65-139 201-284 (365)
64 KOG2389 Predicted bromodomain 82.8 3.5 7.5E-05 39.9 6.3 69 62-132 29-97 (353)
65 COG5095 TAF6 Transcription ini 78.9 6.9 0.00015 38.2 6.9 53 80-132 21-73 (450)
66 TIGR02902 spore_lonB ATP-depen 77.9 5.6 0.00012 39.5 6.3 68 64-131 264-334 (531)
67 PF13654 AAA_32: AAA domain; P 76.9 8.8 0.00019 38.4 7.3 49 81-129 447-506 (509)
68 cd08045 TAF4 TATA Binding Prot 73.7 17 0.00036 31.9 7.5 80 58-137 40-127 (212)
69 COG1067 LonB Predicted ATP-dep 72.9 3 6.4E-05 43.1 2.9 47 81-128 338-398 (647)
70 TIGR00764 lon_rel lon-related 71.8 13 0.00028 37.9 7.1 50 81-130 330-392 (608)
71 COG5162 Transcription initiati 69.5 26 0.00056 31.2 7.6 69 62-132 88-189 (197)
72 PF03540 TFIID_30kDa: Transcri 69.4 27 0.00059 25.1 6.4 48 62-111 2-49 (51)
73 PF00531 Death: Death domain; 68.5 9.9 0.00022 27.2 4.1 61 81-142 23-83 (83)
74 KOG3901 Transcription initiati 66.3 13 0.00028 30.6 4.8 48 78-128 24-71 (109)
75 KOG1757 Histone 2A [Chromatin 65.7 9.7 0.00021 31.9 4.0 65 59-127 27-95 (131)
76 PF13335 Mg_chelatase_2: Magne 65.4 20 0.00043 28.0 5.5 48 80-127 41-94 (96)
77 COG5248 TAF19 Transcription in 59.2 22 0.00047 29.8 4.9 49 78-128 24-72 (126)
78 PRK00080 ruvB Holliday junctio 55.7 45 0.00098 30.4 6.9 73 62-134 179-255 (328)
79 TIGR00635 ruvB Holliday juncti 54.7 54 0.0012 29.1 7.1 71 63-133 159-233 (305)
80 PRK09862 putative ATP-dependen 53.7 38 0.00083 34.0 6.6 57 80-136 437-499 (506)
81 TIGR01128 holA DNA polymerase 52.9 50 0.0011 28.9 6.6 65 63-127 111-176 (302)
82 PF08369 PCP_red: Proto-chloro 51.3 18 0.00039 24.9 2.8 42 83-125 2-44 (45)
83 KOG2680 DNA helicase TIP49, TB 50.1 45 0.00098 32.8 6.2 50 78-127 374-427 (454)
84 TIGR02030 BchI-ChlI magnesium 49.7 59 0.0013 30.8 6.9 54 73-127 247-307 (337)
85 PRK07452 DNA polymerase III su 48.5 40 0.00086 30.4 5.3 65 68-132 135-202 (326)
86 COG1224 TIP49 DNA helicase TIP 48.4 63 0.0014 32.3 7.0 62 65-126 363-429 (450)
87 TIGR02442 Cob-chelat-sub cobal 48.3 46 0.00099 33.9 6.2 50 78-127 246-302 (633)
88 PF02861 Clp_N: Clp amino term 47.7 14 0.00031 24.3 1.8 26 105-130 1-26 (53)
89 COG4187 RocB Arginine degradat 47.3 17 0.00037 36.9 3.0 102 86-189 318-430 (553)
90 PRK13406 bchD magnesium chelat 45.9 41 0.00088 34.3 5.5 52 75-127 190-248 (584)
91 PRK12402 replication factor C 45.4 44 0.00095 29.7 5.1 71 63-135 184-255 (337)
92 PRK13765 ATP-dependent proteas 44.3 48 0.001 34.3 5.7 48 81-128 339-399 (637)
93 PF05236 TAF4: Transcription i 44.2 35 0.00075 30.8 4.3 76 58-133 39-122 (264)
94 CHL00081 chlI Mg-protoporyphyr 41.6 76 0.0016 30.4 6.3 54 73-127 260-320 (350)
95 PF00356 LacI: Bacterial regul 41.3 57 0.0012 22.4 4.0 31 62-96 10-40 (46)
96 TIGR00368 Mg chelatase-related 41.1 55 0.0012 32.7 5.5 48 80-127 444-497 (499)
97 PRK13407 bchI magnesium chelat 40.5 75 0.0016 30.1 6.0 48 79-126 249-303 (334)
98 smart00350 MCM minichromosome 39.5 1.2E+02 0.0026 29.9 7.5 65 61-128 416-503 (509)
99 PRK05574 holA DNA polymerase I 38.2 1.1E+02 0.0024 27.3 6.5 65 63-128 146-212 (340)
100 TIGR01052 top6b DNA topoisomer 37.4 35 0.00077 34.3 3.5 59 73-145 426-484 (488)
101 PF08681 DUF1778: Protein of u 36.8 26 0.00057 26.4 2.0 47 79-125 3-57 (80)
102 PF09114 MotA_activ: Transcrip 35.3 51 0.0011 26.7 3.4 34 66-99 51-88 (96)
103 COG1474 CDC6 Cdc6-related prot 35.1 1.1E+02 0.0024 29.3 6.3 74 66-139 193-275 (366)
104 TIGR02031 BchD-ChlD magnesium 34.4 1.1E+02 0.0024 31.0 6.5 49 79-127 201-256 (589)
105 PTZ00361 26 proteosome regulat 33.6 44 0.00096 32.9 3.4 31 98-128 393-423 (438)
106 PRK06585 holA DNA polymerase I 32.5 1.1E+02 0.0024 27.8 5.7 50 78-127 158-208 (343)
107 PF09123 DUF1931: Domain of un 31.8 45 0.00097 28.6 2.7 69 68-148 1-69 (138)
108 PRK03992 proteasome-activating 30.4 56 0.0012 31.1 3.5 34 96-129 339-372 (389)
109 COG5251 TAF40 Transcription in 30.3 64 0.0014 28.9 3.6 60 62-125 115-177 (199)
110 PF02361 CbiQ: Cobalt transpor 29.8 63 0.0014 26.9 3.4 63 90-155 101-175 (224)
111 TIGR01242 26Sp45 26S proteasom 29.5 61 0.0013 30.1 3.5 32 97-128 331-362 (364)
112 PRK10423 transcriptional repre 29.2 43 0.00094 29.2 2.4 37 62-103 9-45 (327)
113 COG1466 HolA DNA polymerase II 29.2 1.1E+02 0.0023 28.4 5.0 64 68-131 145-209 (334)
114 cd08316 Death_FAS_TNFRSF6 Deat 29.2 2.6E+02 0.0057 22.1 6.5 73 62-144 17-94 (97)
115 PRK04184 DNA topoisomerase VI 28.5 57 0.0012 33.2 3.3 56 73-128 431-488 (535)
116 PF12010 DUF3502: Domain of un 27.6 45 0.00097 27.3 2.0 62 83-148 71-132 (134)
117 KOG1528 Salt-sensitive 3'-phos 27.0 1.5E+02 0.0033 28.9 5.6 81 50-131 38-125 (351)
118 PF11753 DUF3310: Protein of u 26.9 1.4E+02 0.0029 21.6 4.2 41 85-127 14-56 (60)
119 PF07647 SAM_2: SAM domain (St 26.6 56 0.0012 22.6 2.1 24 117-140 4-27 (66)
120 PTZ00454 26S protease regulato 26.5 71 0.0015 30.8 3.5 33 96-128 353-385 (398)
121 PRK14971 DNA polymerase III su 26.5 1.1E+02 0.0023 31.4 4.9 65 63-128 180-245 (614)
122 PRK00440 rfc replication facto 26.5 1.2E+02 0.0026 26.7 4.6 65 63-129 161-226 (319)
123 PRK09526 lacI lac repressor; R 26.1 45 0.00097 29.4 1.9 37 62-103 16-52 (342)
124 PRK07914 hypothetical protein; 25.9 1.2E+02 0.0027 27.6 4.8 62 65-127 130-192 (320)
125 COG1389 DNA topoisomerase VI, 25.6 52 0.0011 33.5 2.4 46 73-118 434-479 (538)
126 COG5094 TAF9 Transcription ini 25.3 4.4E+02 0.0095 22.7 7.8 65 81-145 31-99 (145)
127 PRK02910 light-independent pro 25.1 1.1E+02 0.0024 30.3 4.6 52 78-130 466-518 (519)
128 TIGR01278 DPOR_BchB light-inde 24.3 1.2E+02 0.0025 30.1 4.6 52 78-130 459-511 (511)
129 PF08823 PG_binding_2: Putativ 23.6 1.1E+02 0.0023 23.2 3.3 33 119-151 18-56 (74)
130 cd00166 SAM Sterile alpha moti 23.4 48 0.001 22.1 1.2 23 118-140 3-25 (63)
131 TIGR02903 spore_lon_C ATP-depe 23.3 1.5E+02 0.0032 30.3 5.2 71 64-135 354-436 (615)
132 PRK06130 3-hydroxybutyryl-CoA 22.9 1.2E+02 0.0025 27.3 3.9 60 66-132 162-223 (311)
133 cd00823 TopoIIB_Trans TopoIIB_ 22.7 1.4E+02 0.003 25.9 4.2 45 58-105 99-143 (151)
134 PF12627 PolyA_pol_RNAbd: Prob 22.6 16 0.00034 25.4 -1.3 57 80-140 2-62 (64)
135 PF00536 SAM_1: SAM domain (St 22.2 72 0.0016 22.0 2.0 22 118-139 4-25 (64)
136 KOG0093 GTPase Rab3, small G p 21.7 78 0.0017 28.2 2.5 53 83-135 105-162 (193)
137 PRK14987 gluconate operon tran 21.5 58 0.0013 28.7 1.7 37 62-103 16-52 (331)
138 PF07499 RuvA_C: RuvA, C-termi 21.1 53 0.0012 22.3 1.1 14 120-133 4-17 (47)
139 cd04752 Commd4 COMM_Domain con 21.0 5.3E+02 0.011 22.0 9.0 50 94-150 44-94 (174)
140 PF13405 EF-hand_6: EF-hand do 20.7 82 0.0018 19.0 1.8 27 104-130 4-31 (31)
141 CHL00076 chlB photochlorophyll 20.7 1.6E+02 0.0036 29.3 4.8 52 78-130 460-512 (513)
142 TIGR02454 CbiQ_TIGR cobalt ABC 20.4 1.3E+02 0.0027 25.1 3.4 38 115-152 112-160 (198)
143 PRK09492 treR trehalose repres 20.2 82 0.0018 27.4 2.3 36 62-102 15-50 (315)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=7.7e-37 Score=258.52 Aligned_cols=106 Identities=67% Similarity=1.153 Sum_probs=101.3
Q ss_pred CCcccccccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcC
Q 026469 51 DNECTVREQDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLG 130 (238)
Q Consensus 51 ~~e~~v~e~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LG 130 (238)
...+.++++|++||+|+|.||||+.||.+.+||||||+.+|+|++|||+|||++|+++|++++||||++|||||||..||
T Consensus 21 ~~~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 21 QSSLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred ccccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 34688999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcchHHHHHHHHHHHHHHhhhcCCC
Q 026469 131 FDDYIEPLTVYLHRYREMEGERGSIR 156 (238)
Q Consensus 131 F~dyve~Lk~~L~~yRE~~~~rks~k 156 (238)
|++|+++|+.||.+|||.+.+|+...
T Consensus 101 Fe~Y~eplkiyL~kYRe~e~e~~~~~ 126 (168)
T KOG0869|consen 101 FENYAEPLKIYLQKYRELEGERGRSG 126 (168)
T ss_pred cHhHHHHHHHHHHHHHHHhhhccccc
Confidence 99999999999999999988876543
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.93 E-value=5.5e-26 Score=190.99 Aligned_cols=103 Identities=34% Similarity=0.623 Sum_probs=94.4
Q ss_pred cccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchH
Q 026469 57 REQDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIE 136 (238)
Q Consensus 57 ~e~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve 136 (238)
..+|+.||+|+|.+|||+.||.++||.+||+++|.+||.+||+.|+++|+++|..+.||||.+|||++||+.|||.+|++
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 34678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHh--hhcCCCCCC
Q 026469 137 PLTVYLHRYREMEG--ERGSIRGEP 159 (238)
Q Consensus 137 ~Lk~~L~~yRE~~~--~rks~k~~~ 159 (238)
.+...|+.|+...+ .+++.|.++
T Consensus 87 e~~~vl~~~K~~~~~~~~kssk~e~ 111 (156)
T KOG0871|consen 87 EAEEVLENCKEEAKKRRRKSSKFEK 111 (156)
T ss_pred HHHHHHHHHHHHHHHhhhhhhhHHh
Confidence 99999999998765 344444444
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.90 E-value=7e-24 Score=180.89 Aligned_cols=104 Identities=28% Similarity=0.530 Sum_probs=99.2
Q ss_pred ccccccCCchhHHHHHHHhhCCCC-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcc
Q 026469 56 VREQDRFMPIANVIRIMRKILPQH-AKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDY 134 (238)
Q Consensus 56 v~e~D~~LPkA~I~RImKeaLp~~-~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dy 134 (238)
.+++|+.||+|+|.||+|++||+. +.|+|||+.+|++++++||+||++.|+++|+.++||||+++|||.||++++|..|
T Consensus 4 eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f 83 (172)
T KOG0870|consen 4 ERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSF 83 (172)
T ss_pred hhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHH
Confidence 478999999999999999999987 9999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHhhhcCCCCCC
Q 026469 135 IEPLTVYLHRYREMEGERGSIRGEP 159 (238)
Q Consensus 135 ve~Lk~~L~~yRE~~~~rks~k~~~ 159 (238)
+.+|+..|+.|+...+.||-.+..+
T Consensus 84 ~~plk~~Le~yk~~~k~Kk~~~~~~ 108 (172)
T KOG0870|consen 84 VNPLKSALEAYKKAVKQKKLAKANK 108 (172)
T ss_pred hhHHHHHHHHHHHHHHHHHHhcccc
Confidence 9999999999999999888766554
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.84 E-value=6.6e-21 Score=157.76 Aligned_cols=95 Identities=29% Similarity=0.572 Sum_probs=91.3
Q ss_pred ccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHH
Q 026469 58 EQDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIEP 137 (238)
Q Consensus 58 e~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve~ 137 (238)
.++..||+|+|.+++.+.||.+..+.|||++.+++||.+||+.|+++|++.|+.+.+|||.+|||++||+.|+|.+|++.
T Consensus 7 dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~~ 86 (148)
T COG5150 7 DDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIES 86 (148)
T ss_pred cccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHHH
Confidence 46679999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhh
Q 026469 138 LTVYLHRYREMEGER 152 (238)
Q Consensus 138 Lk~~L~~yRE~~~~r 152 (238)
+.+.+..|+..++.|
T Consensus 87 ~~e~~~n~k~~qK~k 101 (148)
T COG5150 87 CMEEHENYKSYQKQK 101 (148)
T ss_pred HHHHHHHHHHHHhhc
Confidence 999999999988654
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=99.73 E-value=8.5e-18 Score=121.08 Aligned_cols=64 Identities=44% Similarity=0.642 Sum_probs=59.4
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHH
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAM 126 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~AL 126 (238)
.||++.|.||||.. |+..+||+||.++|++|+++||.+|+.+|++.|..++||||+++||..||
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=1.3e-17 Score=130.57 Aligned_cols=80 Identities=36% Similarity=0.490 Sum_probs=75.4
Q ss_pred ccccccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCc
Q 026469 54 CTVREQDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDD 133 (238)
Q Consensus 54 ~~v~e~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~d 133 (238)
...+..|..||+++|.||||+++++ |||.+|+++|++|+++|+..|+..|+++|.++|||||+++||..|++.+||..
T Consensus 11 ~~~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~ 88 (91)
T COG2036 11 RYQRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRI 88 (91)
T ss_pred hhhhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcccc
Confidence 4557889999999999999999994 99999999999999999999999999999999999999999999999999976
Q ss_pred ch
Q 026469 134 YI 135 (238)
Q Consensus 134 yv 135 (238)
|.
T Consensus 89 ~~ 90 (91)
T COG2036 89 YG 90 (91)
T ss_pred cc
Confidence 63
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=99.37 E-value=2.1e-12 Score=100.07 Aligned_cols=72 Identities=22% Similarity=0.350 Sum_probs=67.5
Q ss_pred cCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcc
Q 026469 61 RFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDY 134 (238)
Q Consensus 61 ~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dy 134 (238)
..||++.|.||+|.... .|||+|+.+.+.++.++|+..|..+|..+|++++||||+++||..||++.|-.-|
T Consensus 12 ~gi~k~~I~RLarr~Gv--kRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 12 KGITKPAIRRLARRGGV--KRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred ccCCHHHHHHHHHHcCc--chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 35999999999999986 8999999999999999999999999999999999999999999999999985443
No 8
>PLN00035 histone H4; Provisional
Probab=99.33 E-value=4.8e-12 Score=101.31 Aligned_cols=75 Identities=21% Similarity=0.268 Sum_probs=68.3
Q ss_pred ccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcc
Q 026469 58 EQDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDY 134 (238)
Q Consensus 58 e~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dy 134 (238)
.....||++.|.||+|+... .|||.|+.+.+.+..++|+..|+.+|..+|++++||||+++||..||+++|=.-|
T Consensus 25 d~i~~ipk~~IrRLARr~Gv--kRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ly 99 (103)
T PLN00035 25 DNIQGITKPAIRRLARRGGV--KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLY 99 (103)
T ss_pred hhhccCCHHHHHHHHHHcCc--ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcCC
Confidence 33445999999999999986 8999999999999999999999999999999999999999999999998875433
No 9
>PTZ00015 histone H4; Provisional
Probab=99.29 E-value=9.7e-12 Score=99.38 Aligned_cols=76 Identities=24% Similarity=0.364 Sum_probs=69.7
Q ss_pred cccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcc
Q 026469 57 REQDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDY 134 (238)
Q Consensus 57 ~e~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dy 134 (238)
+.-...||++.|.||+|.... .|||.|+.+.+.++.++|+..|..+|..+|++++||||+++||..||+.+|-.-|
T Consensus 25 r~~i~gI~k~~IrRLarr~Gv--kRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 25 RDNIRGITKGAIRRLARRGGV--KRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred hhcccCCCHHHHHHHHHHcCC--ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 344457999999999999987 8999999999999999999999999999999999999999999999999886443
No 10
>smart00417 H4 Histone H4.
Probab=99.15 E-value=7.1e-11 Score=89.58 Aligned_cols=64 Identities=20% Similarity=0.260 Sum_probs=60.2
Q ss_pred ccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHH
Q 026469 60 DRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWA 125 (238)
Q Consensus 60 D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~A 125 (238)
-..||++.|.||+|.... .|||.|+.+.+.+..++|+..|..+|..+|++++||||+++||..|
T Consensus 11 i~gI~k~~IrRLaRr~Gv--kRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 11 IQGITKPAIRRLARRGGV--KRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred hcCCCHHHHHHHHHHcCc--chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 346999999999999986 8999999999999999999999999999999999999999999754
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=99.15 E-value=1.4e-10 Score=85.42 Aligned_cols=64 Identities=23% Similarity=0.291 Sum_probs=61.3
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
.||+++|.||++...- .+||+|+.+.|.+-++.|+..|..+|..++++.+||||+++||-.||+
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 6899999999999876 689999999999999999999999999999999999999999999985
No 12
>smart00428 H3 Histone H3.
Probab=98.96 E-value=1.5e-09 Score=87.12 Aligned_cols=72 Identities=21% Similarity=0.279 Sum_probs=66.6
Q ss_pred cccccCCchhHHHHHHHhhCCC-----CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 57 REQDRFMPIANVIRIMRKILPQ-----HAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 57 ~e~D~~LPkA~I~RImKeaLp~-----~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
+.+++.+|+....|++++...+ +.|++.+|.++||++++.|+.-+..+|+..|.++||+||.++||..|..-
T Consensus 24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ri 100 (105)
T smart00428 24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRI 100 (105)
T ss_pred cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHH
Confidence 6788999999999999998764 67999999999999999999999999999999999999999999888643
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=98.92 E-value=5.9e-09 Score=77.59 Aligned_cols=66 Identities=14% Similarity=0.332 Sum_probs=62.0
Q ss_pred CchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 026469 63 MPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKL 129 (238)
Q Consensus 63 LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~L 129 (238)
|++..+..++|+.-| ..+|+.||.++|++.+++|+.-|+..|...|++.||+||.++||..+|++.
T Consensus 2 ~~k~~l~~lv~~id~-~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~ 67 (72)
T cd07981 2 LTKRKLQELLKEIDP-REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67 (72)
T ss_pred CcHHHHHHHHHhhCC-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 678889999999876 699999999999999999999999999999999999999999999999863
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=98.90 E-value=3.7e-09 Score=77.20 Aligned_cols=68 Identities=28% Similarity=0.378 Sum_probs=63.0
Q ss_pred ccCCchhHHHHHHHhhCCC---CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 60 DRFMPIANVIRIMRKILPQ---HAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 60 D~~LPkA~I~RImKeaLp~---~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
+..+|+..|.|+.|+..++ ..+||++|.+.|+.+++.|+..|..+|..+|.+.||+||+++||..|++
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 2699999999999999999999999999999999999999999999986
No 15
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.67 E-value=1.5e-08 Score=91.35 Aligned_cols=79 Identities=20% Similarity=0.250 Sum_probs=71.3
Q ss_pred cccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchH
Q 026469 57 REQDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIE 136 (238)
Q Consensus 57 ~e~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve 136 (238)
-..+..||.|.|+|+||..-. .-.||.||..++.+.|+.||..||-.|+-.+++.||+|+...||..|+++-++.||+-
T Consensus 104 ~~k~h~LPlARIkkvMKtded-VkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLi 182 (286)
T COG5208 104 LLKDHNLPLARIKKVMKTDED-VKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLI 182 (286)
T ss_pred HHHhccCcHHHHHHHHhcccc-hhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHh
Confidence 345678999999999997643 2359999999999999999999999999999999999999999999999999988864
No 16
>PLN00161 histone H3; Provisional
Probab=98.59 E-value=1.5e-07 Score=78.82 Aligned_cols=71 Identities=17% Similarity=0.265 Sum_probs=65.8
Q ss_pred cccccCCchhHHHHHHHhhCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 57 REQDRFMPIANVIRIMRKILP----QHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 57 ~e~D~~LPkA~I~RImKeaLp----~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
+.+++.||+....||+++... .+.|+..+|.++||++++.|+.-+..+|+-.|.+.||.||.+.||..|..
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 678899999999999999854 35899999999999999999999999999999999999999999988864
No 17
>PLN00121 histone H3; Provisional
Probab=98.58 E-value=8.7e-08 Score=80.24 Aligned_cols=71 Identities=18% Similarity=0.262 Sum_probs=66.4
Q ss_pred cccccCCchhHHHHHHHhhCCC---CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 57 REQDRFMPIANVIRIMRKILPQ---HAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 57 ~e~D~~LPkA~I~RImKeaLp~---~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
+.+|+.||+....||+++...+ +.++..+|.++||++++.|+.-|..+++..|.+.||.||.+.||..+..
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 6689999999999999998764 6899999999999999999999999999999999999999999988763
No 18
>PLN00160 histone H3; Provisional
Probab=98.58 E-value=1.3e-07 Score=75.26 Aligned_cols=71 Identities=18% Similarity=0.184 Sum_probs=65.6
Q ss_pred cccccCCchhHHHHHHHhhCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 57 REQDRFMPIANVIRIMRKILP----QHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 57 ~e~D~~LPkA~I~RImKeaLp----~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
+.+++.+|++...|++++... ++.|+..+|..+||++++.|+.-+...++..|.++||.||.+.|+..|..
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 568899999999999999864 35899999999999999999999999999999999999999999988764
No 19
>PTZ00018 histone H3; Provisional
Probab=98.53 E-value=1.4e-07 Score=79.10 Aligned_cols=71 Identities=18% Similarity=0.258 Sum_probs=66.0
Q ss_pred cccccCCchhHHHHHHHhhCC---CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 57 REQDRFMPIANVIRIMRKILP---QHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 57 ~e~D~~LPkA~I~RImKeaLp---~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
+.+|+.||+....||+++... .+.++..+|.++||++++.|+.-|..+++..|.+.||.||.+.|+..|..
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 678999999999999999864 36899999999999999999999999999999999999999999988764
No 20
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.47 E-value=8.6e-07 Score=66.41 Aligned_cols=66 Identities=21% Similarity=0.274 Sum_probs=60.5
Q ss_pred hhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 026469 65 IANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFD 132 (238)
Q Consensus 65 kA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~ 132 (238)
+-.|.+|+|...= -+++.+|.+.|.+....|+..|+..+..+|++.+|++++.+||..||+++|+.
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 4467888888764 68999999999999999999999999999999999999999999999999974
No 21
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=98.37 E-value=1.1e-06 Score=69.55 Aligned_cols=69 Identities=22% Similarity=0.271 Sum_probs=64.4
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFD 132 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~ 132 (238)
.+.+-+|.||.+.... -||+.-..+.+..++.+||.-+.+.|..+++++|||||++.||+.+|+++|--
T Consensus 29 gitKpaIRRlARr~GV--kRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 29 GITKPAIRRLARRGGV--KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred ccchHHHHHHHHhcCc--chhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 4678899999999875 78999999999999999999999999999999999999999999999998864
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=98.37 E-value=1e-06 Score=71.77 Aligned_cols=69 Identities=13% Similarity=0.178 Sum_probs=62.8
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 59 QDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 59 ~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
..+.||.+.|.|+||+.-- ..||+.+|...|..+.+.+...|...|...|++.+||+|+++||..|+..
T Consensus 17 agL~fPV~ri~R~Lk~~~~-a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 17 AGLQFPVGRIHRYLKKGRY-AERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred cCccCcHHHHHHHHHcCcc-ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 4678999999999998422 38999999999999999999999999999999999999999999999863
No 23
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.33 E-value=5.5e-07 Score=81.11 Aligned_cols=91 Identities=18% Similarity=0.293 Sum_probs=74.8
Q ss_pred ccccccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCc
Q 026469 54 CTVREQDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDD 133 (238)
Q Consensus 54 ~~v~e~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~d 133 (238)
.....-...||++.|++|||..-. .-.|+.||..++.+||+.||..|+..|+..++..+|+|+...||..|+..-.-.|
T Consensus 66 ~~~d~~~~~lPlaRiKkimK~ded-v~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fd 144 (236)
T KOG1657|consen 66 GQLDFKNHILPLARIKKIMKSDED-VSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFD 144 (236)
T ss_pred cccchhhccCcHhhcccccccccc-ccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCcc
Confidence 334445567999999999998643 3379999999999999999999999999999999999999999999999766555
Q ss_pred c---hHHHHHHHHHH
Q 026469 134 Y---IEPLTVYLHRY 145 (238)
Q Consensus 134 y---ve~Lk~~L~~y 145 (238)
| +-+.+..+++|
T Consensus 145 FL~DivP~~~~~~~~ 159 (236)
T KOG1657|consen 145 FLRDIVPRKILAEKY 159 (236)
T ss_pred ceeccccchhccccc
Confidence 5 33445555555
No 24
>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=98.28 E-value=3.3e-06 Score=68.50 Aligned_cols=77 Identities=14% Similarity=0.175 Sum_probs=65.5
Q ss_pred hHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHH-HHHHHHH
Q 026469 66 ANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIEP-LTVYLHR 144 (238)
Q Consensus 66 A~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve~-Lk~~L~~ 144 (238)
..|.+|+|+... .+++.+++..|.+.+..++.-|..+|..+|++++|+||+++||..|++...-..|..+ -++.|-.
T Consensus 5 ~~v~~iLk~~Gv--~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~ 82 (117)
T cd07979 5 RVIAAILKSMGI--TEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLE 82 (117)
T ss_pred HHHHHHHHHCCC--CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHH
Confidence 357889998754 6999999999999999999999999999999999999999999999997766566544 4555433
No 25
>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=98.08 E-value=1.1e-05 Score=75.21 Aligned_cols=67 Identities=21% Similarity=0.245 Sum_probs=60.0
Q ss_pred chhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 026469 64 PIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFD 132 (238)
Q Consensus 64 PkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~ 132 (238)
|..+|+-|++...- .++++||..+|.+.++.++..|+.+|.+.+++.|||||+++||-.||+.++.+
T Consensus 1 ~~~~i~~ia~~~Gi--~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 1 PQESIKLIAESLGI--DSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred ChhHHHHHHHHcCC--CcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 45677777777654 59999999999999999999999999999999999999999999999977665
No 26
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=97.91 E-value=6.5e-06 Score=69.22 Aligned_cols=73 Identities=19% Similarity=0.264 Sum_probs=65.9
Q ss_pred cccccCCchhHHHHHHHhh---CCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 026469 57 REQDRFMPIANVIRIMRKI---LPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKL 129 (238)
Q Consensus 57 ~e~D~~LPkA~I~RImKea---Lp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~L 129 (238)
+.+|+.|++....||+|+. .-.+.++..+|..+||++++.|+.-|...+|-.|.++||.||.+.||-.|..--
T Consensus 58 kstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrir 133 (137)
T KOG1745|consen 58 KSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 133 (137)
T ss_pred hhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhcc
Confidence 5789999999999999944 445789999999999999999999999999999999999999999999887643
No 27
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.88 E-value=2.2e-05 Score=75.27 Aligned_cols=65 Identities=20% Similarity=0.264 Sum_probs=48.0
Q ss_pred cccccCCchhHHHHHHHhhCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccc
Q 026469 57 REQDRFMPIANVIRIMRKILP----QHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAED 121 (238)
Q Consensus 57 ~e~D~~LPkA~I~RImKeaLp----~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaED 121 (238)
.+.--.||.+.|+||+..... .+++|++||.++|.+|...|-.-|+..--.||+|+|||||..+|
T Consensus 346 gi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 346 GIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 444556999999999877744 57899999999999999999999999999999999999999876
No 28
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.83 E-value=7e-05 Score=57.11 Aligned_cols=62 Identities=16% Similarity=0.199 Sum_probs=52.8
Q ss_pred HHHHHHHhhC-CCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 67 NVIRIMRKIL-PQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 67 ~I~RImKeaL-p~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
.|.||+.+.. ..++.+|+++..+|.+.+-.++..++.+--..|+++||+||+.|||+....+
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr 72 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 5788888875 4578999999999999999999999999999999999999999999987654
No 29
>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=97.71 E-value=0.00024 Score=52.71 Aligned_cols=64 Identities=19% Similarity=0.281 Sum_probs=56.6
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 026469 67 NVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFD 132 (238)
Q Consensus 67 ~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~ 132 (238)
.|.+|++.+.= -.++..|.+.|.+.+..||..|++.+..+|++.+|...+..||..||+++|+.
T Consensus 11 ~va~il~~~GF--~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 11 SVAQILKHAGF--DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHcCc--cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 45566655432 47999999999999999999999999999999999999999999999999984
No 30
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=97.66 E-value=0.0002 Score=53.47 Aligned_cols=63 Identities=16% Similarity=0.323 Sum_probs=51.6
Q ss_pred hhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 65 IANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 65 kA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
|..+..||++.-| +.++.+|+.++|.+.+.+||.-+...|...|++-+-.||...||...|++
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 4567888988754 89999999999999999999999999999999999999999999999875
No 31
>smart00427 H2B Histone H2B.
Probab=97.56 E-value=0.00031 Score=55.37 Aligned_cols=62 Identities=16% Similarity=0.362 Sum_probs=57.3
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 026469 67 NVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKL 129 (238)
Q Consensus 67 ~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~L 129 (238)
-|.|++|++-| +..||..|...+.--+..+..-|+.||...|...+|+||+.++|..|++-+
T Consensus 6 Yi~kvLKqVhp-d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 6 YIYKVLKQVHP-DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHHhCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 48999999998 668999999999999999999999999999999999999999999998644
No 32
>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=97.54 E-value=0.00047 Score=53.48 Aligned_cols=66 Identities=14% Similarity=0.202 Sum_probs=61.6
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CccCcccHHHHHhhc
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQR---KTITAEDVLWAMSKL 129 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kR---KTItaEDVL~ALe~L 129 (238)
.||++.|+|||...++ ..++++...+|.-.+.+||-.|..+|.++..+.+. .-|.++||-.|..+|
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 4999999999999997 89999999999999999999999999999988766 789999999999876
No 33
>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=97.49 E-value=0.00058 Score=50.94 Aligned_cols=64 Identities=22% Similarity=0.246 Sum_probs=49.5
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
.+|..+|+-+.....- ..+++|+...|.+-++--|..|..+|.....+.+|++++.+||-.||+
T Consensus 3 ~~~~esvk~iAes~Gi--~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESLGI--SNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHTT-----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHcCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 4677777776655543 479999999999999999999999999999999999999999999985
No 34
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.42 E-value=0.00025 Score=63.73 Aligned_cols=79 Identities=14% Similarity=0.164 Sum_probs=69.6
Q ss_pred cCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHHHHH
Q 026469 61 RFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIEPLTV 140 (238)
Q Consensus 61 ~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve~Lk~ 140 (238)
..+|.+.|.|||...-. --||+.-+...+.++.+.|+.-|...+.+++...+-|||+++|+..|+..-.-.||+..+-.
T Consensus 12 trfp~aRiKKIMQ~dEd-IGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~v~ 90 (224)
T KOG1659|consen 12 TRFPPARIKKIMQSDED-IGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEVVE 90 (224)
T ss_pred ccCCHHHHHHHHhhhhh-hhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHHHH
Confidence 36899999999986532 45899999999999999999999999999999999999999999999998777788776433
No 35
>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=97.36 E-value=0.00028 Score=53.31 Aligned_cols=65 Identities=18% Similarity=0.279 Sum_probs=54.0
Q ss_pred chhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-cCcccHHHHHhh
Q 026469 64 PIANVIRIMRKILP-QHAKISDDAKETIQECVSEYISFITGEANERCQREQRKT-ITAEDVLWAMSK 128 (238)
Q Consensus 64 PkA~I~RImKeaLp-~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKT-ItaEDVL~ALe~ 128 (238)
|+..|.||++.... +..||++||..++++....||..-..-|.+.++.++..+ |..+|+-+.+-.
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq 67 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ 67 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 78999999997764 578999999999999999999999999999999999988 999999876643
No 36
>PLN00158 histone H2B; Provisional
Probab=97.28 E-value=0.001 Score=54.79 Aligned_cols=65 Identities=15% Similarity=0.305 Sum_probs=59.0
Q ss_pred chhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 026469 64 PIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKL 129 (238)
Q Consensus 64 PkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~L 129 (238)
-..-|+|++|++-| +..||..+...|.--+..+..-|+.||...|...+|+||++.+|..|++-+
T Consensus 29 y~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 29 YKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred HHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 34569999999988 678999999999999999999999999999999999999999999998644
No 37
>PTZ00463 histone H2B; Provisional
Probab=97.24 E-value=0.0012 Score=54.43 Aligned_cols=62 Identities=16% Similarity=0.391 Sum_probs=57.1
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 026469 67 NVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKL 129 (238)
Q Consensus 67 ~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~L 129 (238)
-|+|++|++-| +.-||..|...|.--+.....-|+.||...|...+|+||++.||..|++-+
T Consensus 33 YI~KVLKqVhP-d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 33 YIFKVLKQVHP-DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred HHHHHHHhhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 48999999988 678999999999999999999999999999999999999999999998644
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=97.04 E-value=0.0025 Score=50.20 Aligned_cols=67 Identities=12% Similarity=0.198 Sum_probs=51.6
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-ccCcccHHHHHhhc
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRK-TITAEDVLWAMSKL 129 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRK-TItaEDVL~ALe~L 129 (238)
.||++.|+|||...+. +..|+.....+|.-.+..||-.|-.+|.+++.+.+.. -|.+.|+-.|..+|
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 4999999999999985 6899999999999999999999999999999865544 79999999998765
No 39
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.00 E-value=0.0014 Score=54.51 Aligned_cols=68 Identities=16% Similarity=0.227 Sum_probs=59.8
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 59 QDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 59 ~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
+-+.+|...|.||||+. .-.+||+++|...+..|.+=.+..|+.-|-..|...++|-|.+.|+-.|+.
T Consensus 23 agl~fpvgrvkr~lk~~-~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 23 AGLIFPVGRVKRLLKKG-NYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred cCccccHHHHHHHHHcC-ccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 45679999999999943 336999999999999999888888888888889999999999999999986
No 40
>smart00414 H2A Histone 2A.
Probab=96.97 E-value=0.0023 Score=51.57 Aligned_cols=69 Identities=13% Similarity=0.209 Sum_probs=60.0
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 59 QDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 59 ~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
-.+.||.+.|.|+||+.-- ..||+..|...|.-|.+-+...|..-|...|...+++.|+++||..|+..
T Consensus 6 agL~fPVgRi~r~Lk~~~~-~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 6 AGLQFPVGRIHRLLRKGTY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred CCccCchHHHHHHHHcCcc-ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 3578999999999998643 36999999999999988888888888888899999999999999999864
No 41
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=96.87 E-value=0.0022 Score=52.23 Aligned_cols=77 Identities=17% Similarity=0.221 Sum_probs=66.0
Q ss_pred cCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHHH
Q 026469 61 RFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIEPL 138 (238)
Q Consensus 61 ~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve~L 138 (238)
..+|.|.|.|||.-.-+ --+|+.-......++.+.|+..|-.++.+.|...+-|-|+.+++..|.+.-+=.||+..+
T Consensus 22 trFP~ar~KkIMQ~deD-iGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~ 98 (113)
T COG5247 22 TRFPIARLKKIMQLDED-IGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNM 98 (113)
T ss_pred hcCCHHHHHHHHHhhhh-hhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHH
Confidence 46999999999976532 458999999999999999999999999999999999999999999998866555555443
No 42
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.75 E-value=0.0027 Score=58.39 Aligned_cols=70 Identities=13% Similarity=0.302 Sum_probs=62.8
Q ss_pred ccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 58 EQDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 58 e~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
..+..|-+-.|.-+++++- .+.+|-+|+.++|.+.|..||..|+.-|...|++-|..||-+.||...||+
T Consensus 150 ~~~~il~k~kl~dLvqqId-~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr 219 (258)
T KOG1142|consen 150 GNNPILSKRKLDDLVQQID-GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLER 219 (258)
T ss_pred CCCccccccchhHHHHhhc-CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeec
Confidence 3455677778888899884 488999999999999999999999999999999999999999999999983
No 43
>PLN00154 histone H2A; Provisional
Probab=96.66 E-value=0.0051 Score=51.94 Aligned_cols=69 Identities=13% Similarity=0.182 Sum_probs=58.3
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 59 QDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 59 ~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
..+.||.+.|.|++|+..--..||+..|...|.-+.+=+...|..-|-..|...+++-|++.||..|+.
T Consensus 35 AgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 35 AGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred cCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 467899999999999976445799999999998877666666666677788899999999999999985
No 44
>PTZ00017 histone H2A; Provisional
Probab=96.49 E-value=0.0058 Score=51.44 Aligned_cols=68 Identities=15% Similarity=0.187 Sum_probs=60.0
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 59 QDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 59 ~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
..+.||.+.|.|+||+.-- ..||+..|...|.-+.+-+...|..-|...|...+++-|+++||..|+.
T Consensus 24 agL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 24 AGLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CCcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 4678999999999998633 3699999999999998888888888888899999999999999999985
No 45
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.25 E-value=0.014 Score=48.85 Aligned_cols=62 Identities=23% Similarity=0.369 Sum_probs=56.2
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 026469 67 NVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKL 129 (238)
Q Consensus 67 ~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~L 129 (238)
-|+|++|++-|+ .-|+.++...+.--+-++..-|+++|...+...+|.||+..+|..|+.-|
T Consensus 42 yv~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 42 YVYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred ehhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 467799999986 77999999999999999999999999999999999999999999987543
No 46
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.19 E-value=0.0084 Score=48.09 Aligned_cols=67 Identities=19% Similarity=0.249 Sum_probs=56.3
Q ss_pred cCCchhHHHHHHHhhCCCCcccCHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHH
Q 026469 61 RFMPIANVIRIMRKILPQHAKISDDAKET--------------IQECVSEYISFITGEANERCQREQRKTITAEDVLWAM 126 (238)
Q Consensus 61 ~~LPkA~I~RImKeaLp~~~rISkDAkea--------------LqecaseFI~~LaseAne~A~~~kRKTItaEDVL~AL 126 (238)
..-|++.+.|++|+.-| +.|+....-.+ +.--|-.||+-|+.||...|=++|-.||..|||+.|-
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 35699999999998877 67766555444 5666889999999999999999999999999999987
Q ss_pred hh
Q 026469 127 SK 128 (238)
Q Consensus 127 e~ 128 (238)
+.
T Consensus 94 Kv 95 (102)
T PF15510_consen 94 KV 95 (102)
T ss_pred HH
Confidence 64
No 47
>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=96.17 E-value=0.022 Score=47.41 Aligned_cols=85 Identities=20% Similarity=0.236 Sum_probs=48.2
Q ss_pred cccccCCchh--HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh-hcCCCc
Q 026469 57 REQDRFMPIA--NVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS-KLGFDD 133 (238)
Q Consensus 57 ~e~D~~LPkA--~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe-~LGF~d 133 (238)
..+.-.+|+. .|.-|+|+..- ......+...|.+.+-.|+.-|..+|..++.+++|++|+.+||..|++ ++++.-
T Consensus 5 ~~~~~~~PrDa~~i~~iL~~~Gv--~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f 82 (129)
T PF02291_consen 5 DSQSKSLPRDARVIHLILKSMGV--TEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSF 82 (129)
T ss_dssp --------HHHHHHHHHHHHTT-----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-----
T ss_pred CCCCccCChHHHHHHHHHHHcCC--cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhc
Confidence 3445567763 34455555543 357888899999999999999999999999999999999999999999 666655
Q ss_pred chHHHHHHHH
Q 026469 134 YIEPLTVYLH 143 (238)
Q Consensus 134 yve~Lk~~L~ 143 (238)
..++-+++|-
T Consensus 83 ~~pppre~ll 92 (129)
T PF02291_consen 83 TQPPPREFLL 92 (129)
T ss_dssp ----------
T ss_pred cCCCChHHHH
Confidence 5555555543
No 48
>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=96.12 E-value=0.0071 Score=47.27 Aligned_cols=59 Identities=27% Similarity=0.357 Sum_probs=29.0
Q ss_pred HHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 69 IRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 69 ~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
..+|-.- .+...-..|+..+|-+.+.+||..|..+|.++|...++++|+.||++.+|..
T Consensus 8 ~~mMy~f-GD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 8 RQMMYGF-GDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp HHHHHCT-TS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHc-CCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 4445433 3456788999999999999999999999999999999999999999999984
No 49
>PLN00157 histone H2A; Provisional
Probab=96.11 E-value=0.012 Score=49.56 Aligned_cols=68 Identities=9% Similarity=0.148 Sum_probs=59.0
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 59 QDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 59 ~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
..+.||...|.|++|+.-- ..||+..|...|.-+.+-.+..|..-|...|...+++-|+++||..|+.
T Consensus 23 agL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 23 AGLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred cCcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 4678999999999998533 4799999999999888777777777788888999999999999999985
No 50
>PLN00153 histone H2A; Provisional
Probab=96.05 E-value=0.014 Score=48.92 Aligned_cols=68 Identities=12% Similarity=0.175 Sum_probs=59.3
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 59 QDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 59 ~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
..+.||...|.|++|+.-- ..||+..|...|.-|.+-.+..|..-|...|...+++-|+++||..|+.
T Consensus 21 agL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 21 AGLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred cCcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 4678999999999998644 4699999999999988877777777788888999999999999999985
No 51
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.04 E-value=0.016 Score=48.66 Aligned_cols=68 Identities=15% Similarity=0.210 Sum_probs=53.7
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 59 QDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 59 ~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
..+.+|...|.|++|+ .---.||+.+|...+.-|.+-.+..|+.-|-..+..+++.-|+++||..|+.
T Consensus 24 agl~fPvgri~r~Lr~-~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 24 AGLQFPVGRIHRLLRK-GRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred cccccCHHHHHHHHHc-cchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 5678999999999999 3335799999999998766544445555555566777889999999999986
No 52
>PLN00156 histone H2AX; Provisional
Probab=96.02 E-value=0.016 Score=49.14 Aligned_cols=68 Identities=9% Similarity=0.158 Sum_probs=57.6
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 59 QDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 59 ~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
..+.||...|.|++|+.-- ..||+..|...|.-|.+=.+..|..-|-..|...+++-|+++||..|+.
T Consensus 26 AgL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 26 AGLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred cCcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 4678999999999998643 4699999999998887766667777777788899999999999999985
No 53
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=95.84 E-value=0.005 Score=53.19 Aligned_cols=70 Identities=19% Similarity=0.252 Sum_probs=59.5
Q ss_pred ccccCCchhHHHHHHHhhCCCCcc-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 026469 58 EQDRFMPIANVIRIMRKILPQHAK-ISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKL 129 (238)
Q Consensus 58 e~D~~LPkA~I~RImKeaLp~~~r-ISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~L 129 (238)
..-..||.+.|..+||. +++.+ ..+|++.+|.+++..||.+|...+...+...+|||+.-.|+-.|++.-
T Consensus 55 a~l~rLpL~rik~vvkl--~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~ 125 (162)
T KOG1658|consen 55 ASLSRLPLARIKQVVKL--DPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAV 125 (162)
T ss_pred hhhhhccHHHHHhhccC--CcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccch
Confidence 34467999999999985 45665 567889999999999999999999999999999999998887776643
No 54
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=95.62 E-value=0.15 Score=40.10 Aligned_cols=60 Identities=20% Similarity=0.314 Sum_probs=49.5
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 67 NVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 67 ~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
-|..+|--... ...-..|...+|-+.+.+||..|+.+|.+.|. .+|.-|+.||++-+|..
T Consensus 7 ei~~mmy~~GD-~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~ 66 (92)
T cd07978 7 EIRQMMYGFGD-VQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK 66 (92)
T ss_pred HHHHHHHHcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence 46667765544 55678999999999999999999999999999 45555699999999964
No 55
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=95.29 E-value=0.021 Score=50.79 Aligned_cols=69 Identities=14% Similarity=0.227 Sum_probs=59.5
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-ccCcccHHHHHhhcCCC
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRK-TITAEDVLWAMSKLGFD 132 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRK-TItaEDVL~ALe~LGF~ 132 (238)
.||++.|.|||...... .|+.-+..+++-.+.+||-.|--+|.++|..-+.. -|.+.||-.|..+|...
T Consensus 112 ~f~Ka~iKkL~~~itg~--~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~q 181 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITGQ--SVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQ 181 (195)
T ss_pred cCCHHHHHHHHHHHhCC--ccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhc
Confidence 49999999999999873 39999999999999999999999999999877654 58888888887776554
No 56
>PTZ00252 histone H2A; Provisional
Probab=94.40 E-value=0.11 Score=43.82 Aligned_cols=68 Identities=12% Similarity=0.149 Sum_probs=49.7
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCcccHHHHHh
Q 026469 59 QDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQR--EQRKTITAEDVLWAMS 127 (238)
Q Consensus 59 ~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~--~kRKTItaEDVL~ALe 127 (238)
..+.||.+.|.|++|+.-- ..||+..|...|.-+.+=....|..-|...|.. .+++-|+++||..|+.
T Consensus 22 AGL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 22 AGLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred cCccCchHHHHHHHHcCCc-ccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 4678999999999998754 469999999988776543333333333334433 4778999999999985
No 57
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=93.52 E-value=0.82 Score=43.51 Aligned_cols=77 Identities=22% Similarity=0.298 Sum_probs=63.8
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHHHHHHHHHHH
Q 026469 67 NVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIEPLTVYLHRYR 146 (238)
Q Consensus 67 ~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve~Lk~~L~~yR 146 (238)
.|.-|.++.+= -.|++-|++.|.+.+..+|..|..++.-+|+.++|-..+.-||...|-++|+. +..|..+++++.
T Consensus 10 VV~~Ll~~~gf--d~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~ 85 (323)
T KOG4336|consen 10 VVSNLLKTKGF--DSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQE 85 (323)
T ss_pred HHHHHHHHhCc--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhcc
Confidence 34444555443 34999999999999999999999999999999999999999999999999997 566666666554
Q ss_pred H
Q 026469 147 E 147 (238)
Q Consensus 147 E 147 (238)
.
T Consensus 86 ~ 86 (323)
T KOG4336|consen 86 F 86 (323)
T ss_pred c
Confidence 4
No 58
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=92.92 E-value=0.35 Score=49.01 Aligned_cols=66 Identities=24% Similarity=0.289 Sum_probs=55.2
Q ss_pred chhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCC
Q 026469 64 PIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGF 131 (238)
Q Consensus 64 PkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF 131 (238)
|+-.+.-++ +.+. -..|++|+..+|.+-++.=|..|+.+|.+.-.+.||.+++.+||..||+.+..
T Consensus 13 ~~Es~k~vA-EslG-i~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nV 78 (576)
T KOG2549|consen 13 PKESVKVVA-ESLG-ITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNV 78 (576)
T ss_pred cHHHHHHHH-HHhC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhccc
Confidence 355554444 4443 25699999999999999999999999999999999999999999999996654
No 59
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=92.67 E-value=0.53 Score=41.38 Aligned_cols=69 Identities=19% Similarity=0.229 Sum_probs=57.0
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--------------CCCccCcccHHHHHh
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQRE--------------QRKTITAEDVLWAMS 127 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~--------------kRKTItaEDVL~ALe 127 (238)
.||-+.+.-.++.+.- .-...-.+.+|.=++..||+-|+..|.++|+-. +|-|++-||+..||+
T Consensus 86 ~IPDavt~~yL~~aGf--~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~ 163 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKAGF--QTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALA 163 (176)
T ss_pred CCcHHHHHHHHHhcCC--CcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHH
Confidence 5899999999998864 334455678899999999999999999999733 344899999999999
Q ss_pred hcCCC
Q 026469 128 KLGFD 132 (238)
Q Consensus 128 ~LGF~ 132 (238)
+.|..
T Consensus 164 EyGin 168 (176)
T KOG3423|consen 164 EYGIN 168 (176)
T ss_pred HhCcc
Confidence 98874
No 60
>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=91.31 E-value=0.64 Score=40.12 Aligned_cols=70 Identities=14% Similarity=0.182 Sum_probs=55.9
Q ss_pred CCchhHHHHHHHhhCC-----CCcccCHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCC
Q 026469 62 FMPIANVIRIMRKILP-----QHAKISDDAKETIQECVSE---YISFITGEANERCQREQRKTITAEDVLWAMSKLGF 131 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp-----~~~rISkDAkeaLqecase---FI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF 131 (238)
.|....+..++...+. ....+++++.+.|.+.+.= .|+.++..|...+-..+.++|+.++|..++.++.|
T Consensus 191 ~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~ 268 (269)
T TIGR03015 191 PLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF 268 (269)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence 3455566666554432 2356999999999998875 79999999999998899999999999999999875
No 61
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=86.63 E-value=2.8 Score=38.53 Aligned_cols=71 Identities=17% Similarity=0.209 Sum_probs=52.3
Q ss_pred chhHHHHHHHhhCCC---CcccCHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcc
Q 026469 64 PIANVIRIMRKILPQ---HAKISDDAKETIQECV------SEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDY 134 (238)
Q Consensus 64 PkA~I~RImKeaLp~---~~rISkDAkeaLqeca------seFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dy 134 (238)
....+..|++..+.. ...+++++.+.+.+.+ -..+..+...|.+.|...++.+|+.+||..|++++....+
T Consensus 208 ~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~ 287 (394)
T PRK00411 208 TADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHL 287 (394)
T ss_pred CHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHH
Confidence 345566666655422 2358999999888877 3345566788889999999999999999999998854433
No 62
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=86.21 E-value=4.3 Score=34.97 Aligned_cols=64 Identities=19% Similarity=0.229 Sum_probs=51.8
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchH-HHHHHHHH
Q 026469 81 KISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIE-PLTVYLHR 144 (238)
Q Consensus 81 rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve-~Lk~~L~~ 144 (238)
-...-+.-.|-+.+=.++.-|...|.-++.++++.||.+|||..|+....=..|.. +=+++|-+
T Consensus 30 eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~ 94 (148)
T KOG3334|consen 30 EYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLE 94 (148)
T ss_pred ccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHH
Confidence 35556667777888888999999999999999999999999999999877777776 44444433
No 63
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=83.39 E-value=3.7 Score=37.22 Aligned_cols=75 Identities=16% Similarity=0.124 Sum_probs=52.2
Q ss_pred hhHHHHHHHhhCC---CCcccCHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcch
Q 026469 65 IANVIRIMRKILP---QHAKISDDAKETIQECVS------EYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYI 135 (238)
Q Consensus 65 kA~I~RImKeaLp---~~~rISkDAkeaLqecas------eFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyv 135 (238)
..-+..|++..+. ....+++|+.+.+.+.+. ..+..+...|.+.|..+++.+|+.+||..|++.+....++
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 4456666665543 123588888887766543 3445566788888999999999999999999988655554
Q ss_pred HHHH
Q 026469 136 EPLT 139 (238)
Q Consensus 136 e~Lk 139 (238)
..++
T Consensus 281 ~~i~ 284 (365)
T TIGR02928 281 ELIR 284 (365)
T ss_pred HHHH
Confidence 4443
No 64
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=82.76 E-value=3.5 Score=39.87 Aligned_cols=69 Identities=16% Similarity=0.223 Sum_probs=57.8
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFD 132 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~ 132 (238)
.|-+..|..|.....-... ..-|.+.|+..+..||+-|+..|..++...+|--.+..||+.||+.|+..
T Consensus 29 sla~~avaQIcqslg~~~~--~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 29 SLARVAVAQICQSLGYSST--QNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHhcCCccc--ccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 4667777888766554333 33499999999999999999999999999999999999999999988764
No 65
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=78.85 E-value=6.9 Score=38.16 Aligned_cols=53 Identities=23% Similarity=0.333 Sum_probs=49.4
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 026469 80 AKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFD 132 (238)
Q Consensus 80 ~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~ 132 (238)
..|.+|+..+|..-.+-=|..+..+|...-.+.||..++-+||-.||..|..+
T Consensus 21 ~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 21 SNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred cccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 57999999999999999999999999999999999999999999999988654
No 66
>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=77.94 E-value=5.6 Score=39.49 Aligned_cols=68 Identities=22% Similarity=0.211 Sum_probs=47.0
Q ss_pred chhHHHHHHHhhCCC-CcccCHHHHHHHHHHHHH--HHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCC
Q 026469 64 PIANVIRIMRKILPQ-HAKISDDAKETIQECVSE--YISFITGEANERCQREQRKTITAEDVLWAMSKLGF 131 (238)
Q Consensus 64 PkA~I~RImKeaLp~-~~rISkDAkeaLqecase--FI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF 131 (238)
...-+.+|++..+.. +..|++++.+.|.+.+.. .+.-+...|..+|..++|++|+.+||.+++..-.|
T Consensus 264 ~~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~~~~ 334 (531)
T TIGR02902 264 LDEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAENGNY 334 (531)
T ss_pred CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCCccc
Confidence 345566667666542 467999999988776652 22233445666788889999999999999765433
No 67
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=76.88 E-value=8.8 Score=38.38 Aligned_cols=49 Identities=27% Similarity=0.276 Sum_probs=38.4
Q ss_pred ccCHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 026469 81 KISDDAKETIQECVSE-----------YISFITGEANERCQREQRKTITAEDVLWAMSKL 129 (238)
Q Consensus 81 rISkDAkeaLqecase-----------FI~~LaseAne~A~~~kRKTItaEDVL~ALe~L 129 (238)
-++.+|+..|-+.+.. -|.-|..+|+.+|..+++++|+++||..|++.-
T Consensus 447 ~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 447 PFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp -BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred CCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 5788888877776653 567788999999999999999999999999864
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=73.67 E-value=17 Score=31.90 Aligned_cols=80 Identities=16% Similarity=0.202 Sum_probs=59.9
Q ss_pred ccccCCchhHHHHHHHhhCCCCc--ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCccCcccHHHHHhhc
Q 026469 58 EQDRFMPIANVIRIMRKILPQHA--KISDDAKETIQECVSEYISFITGEANERCQRE------QRKTITAEDVLWAMSKL 129 (238)
Q Consensus 58 e~D~~LPkA~I~RImKeaLp~~~--rISkDAkeaLqecaseFI~~LaseAne~A~~~------kRKTItaEDVL~ALe~L 129 (238)
....+|....|.+.|.+.+...- .|+.|+..+|.-||++++..|.......|++- .-.++--.||-.-|..|
T Consensus 40 ~~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l 119 (212)
T cd08045 40 KDPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFL 119 (212)
T ss_pred chhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHH
Confidence 34557777777777766665432 79999999999999999999999999998764 34566778888877666
Q ss_pred CCCcchHH
Q 026469 130 GFDDYIEP 137 (238)
Q Consensus 130 GF~dyve~ 137 (238)
+--+-.+.
T Consensus 120 ~~~ek~e~ 127 (212)
T cd08045 120 EQLEREEE 127 (212)
T ss_pred HHHHHHHH
Confidence 55444443
No 69
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=72.92 E-value=3 Score=43.05 Aligned_cols=47 Identities=34% Similarity=0.376 Sum_probs=35.2
Q ss_pred ccCHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 81 KISDDAKETIQECVS--------------EYISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 81 rISkDAkeaLqecas--------------eFI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
-++++|...|.+-+. .-...| .+|.++|..++++-|+++||.+|++.
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv-~~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLV-REAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHH-HHhhHHHhcCCcccCcHHHHHHHHHh
Confidence 466666655554443 333334 49999999999999999999999987
No 70
>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=71.78 E-value=13 Score=37.86 Aligned_cols=50 Identities=22% Similarity=0.170 Sum_probs=40.3
Q ss_pred ccCHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcC
Q 026469 81 KISDDAKETIQECVS-------------EYISFITGEANERCQREQRKTITAEDVLWAMSKLG 130 (238)
Q Consensus 81 rISkDAkeaLqecas-------------eFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LG 130 (238)
.++++|.+.|.+-++ .=|.-|..+|..+|..+++++|+.+||.+|++.-.
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~ 392 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAK 392 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence 799999988876444 34556677888899999999999999999987543
No 71
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=69.54 E-value=26 Score=31.20 Aligned_cols=69 Identities=14% Similarity=0.170 Sum_probs=50.0
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------------------c----------
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQR-------------------E---------- 112 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~-------------------~---------- 112 (238)
.||-+.+.=.|-++.- .....-.|.+|.-.+..||+-|+..|.++.+= .
T Consensus 88 liPd~v~DYyl~k~Gf--~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~ 165 (197)
T COG5162 88 LIPDSVTDYYLEKAGF--VTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGR 165 (197)
T ss_pred CccHHHHHHHHHhcCc--eeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhccccccccccc
Confidence 4666666666655532 33445677888999999999999999886531 1
Q ss_pred ----CCCccCcccHHHHHhhcCCC
Q 026469 113 ----QRKTITAEDVLWAMSKLGFD 132 (238)
Q Consensus 113 ----kRKTItaEDVL~ALe~LGF~ 132 (238)
++-+++..|+-.||++.|..
T Consensus 166 ~~dr~K~vltv~DLs~Al~EyGin 189 (197)
T COG5162 166 RGDRKKPVLTVVDLSKALEEYGIN 189 (197)
T ss_pred ccccCCceeeehHHHHHHHHhccc
Confidence 45578999999999988863
No 72
>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=69.41 E-value=27 Score=25.08 Aligned_cols=48 Identities=17% Similarity=0.155 Sum_probs=37.0
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQR 111 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~ 111 (238)
.+|-+.+.-++++++-+ --..-.+-+|.=++..||..|+..|.++|+-
T Consensus 2 ~IPD~v~~~yL~~~G~~--~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSGFQ--TSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCCCC--CCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 47888888888887642 1233456788889999999999999999864
No 73
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=68.51 E-value=9.9 Score=27.20 Aligned_cols=61 Identities=21% Similarity=0.297 Sum_probs=39.7
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHHHHHHH
Q 026469 81 KISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIEPLTVYL 142 (238)
Q Consensus 81 rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve~Lk~~L 142 (238)
-++.+-.+.|..+... ...-+.+............-+.++++.||+++|..+-++.|+.+|
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 4666666666665432 333333444445554556678889999999999999998887764
No 74
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=66.35 E-value=13 Score=30.61 Aligned_cols=48 Identities=23% Similarity=0.326 Sum_probs=39.6
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 78 QHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 78 ~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
++..=-.|.+++|.+.+.+||..++..|.++. +|--+..||++.+|++
T Consensus 24 Dd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRk 71 (109)
T KOG3901|consen 24 DDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRK 71 (109)
T ss_pred CCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHh
Confidence 45556678999999999999999988777777 5666788999999974
No 75
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=65.70 E-value=9.7 Score=31.92 Aligned_cols=65 Identities=17% Similarity=0.274 Sum_probs=51.6
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc----CCCccCcccHHHHHh
Q 026469 59 QDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQRE----QRKTITAEDVLWAMS 127 (238)
Q Consensus 59 ~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~----kRKTItaEDVL~ALe 127 (238)
.-+.+|...|.|.+|.....+.||..-+..-. ...+.||+.|-.+.|... |-|-|++.|+..|+.
T Consensus 27 aGlqFpVgRihr~LK~r~t~h~rVGataavy~----aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 27 AGLQFPVGRIHRHLKTRTTSHGRVGATAAVYS----AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred cccccchHHHHHHHHHhcccccccchHHHHHH----HHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 45689999999999999988888877665543 335689999998887655 457899999988875
No 76
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=65.38 E-value=20 Score=27.99 Aligned_cols=48 Identities=23% Similarity=0.246 Sum_probs=39.7
Q ss_pred cccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 80 AKISDDAKETIQECVSEY------ISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 80 ~rISkDAkeaLqecaseF------I~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
..+++++..+|.+++..+ ++-|..-|..+|.-++...|..+||..||.
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 467888888888877765 455667889999999999999999999984
No 77
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=59.23 E-value=22 Score=29.77 Aligned_cols=49 Identities=24% Similarity=0.386 Sum_probs=42.4
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 78 QHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 78 ~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
+.+.=..|..++|.+.+..+++.+..+|...|+ .|-.+..||...||++
T Consensus 24 Dvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~ 72 (126)
T COG5248 24 DVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRR 72 (126)
T ss_pred CCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhh
Confidence 456677899999999999999999999999998 5666788999999973
No 78
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=55.72 E-value=45 Score=30.44 Aligned_cols=73 Identities=16% Similarity=0.199 Sum_probs=52.0
Q ss_pred CCchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcc
Q 026469 62 FMPIANVIRIMRKILP-QHAKISDDAKETIQECVSE---YISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDY 134 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp-~~~rISkDAkeaLqecase---FI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dy 134 (238)
.++...+..|++.... .++.++.|+...|.+.|.- .+..+...+.+++...+.+.|+.++|..+++.++.+..
T Consensus 179 ~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~~ 255 (328)
T PRK00080 179 FYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDEL 255 (328)
T ss_pred CCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCcC
Confidence 4556667777765533 3578999999888877632 34455556666776666779999999999998877643
No 79
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=54.65 E-value=54 Score=29.06 Aligned_cols=71 Identities=15% Similarity=0.163 Sum_probs=49.5
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCc
Q 026469 63 MPIANVIRIMRKILP-QHAKISDDAKETIQECVS---EYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDD 133 (238)
Q Consensus 63 LPkA~I~RImKeaLp-~~~rISkDAkeaLqecas---eFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~d 133 (238)
++...+..|+++... ....++.|+.+.|.+.+. -++.-+...+.+.+...+...|+.++|..++..++++.
T Consensus 159 l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~~ 233 (305)
T TIGR00635 159 YTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMIDE 233 (305)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCCC
Confidence 455566666665543 246799999988877653 23445555666777666667899999999999976653
No 80
>PRK09862 putative ATP-dependent protease; Provisional
Probab=53.67 E-value=38 Score=34.03 Aligned_cols=57 Identities=16% Similarity=0.142 Sum_probs=45.1
Q ss_pred cccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchH
Q 026469 80 AKISDDAKETIQECVSEY------ISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIE 136 (238)
Q Consensus 80 ~rISkDAkeaLqecaseF------I~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve 136 (238)
..+++++...+.++...+ ...|..-|..+|.-++|..|+.+||..|+.--+++..+-
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~~~~ 499 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDRLLI 499 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccHHHH
Confidence 468888888887766544 566778889999999999999999999998666554433
No 81
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=52.91 E-value=50 Score=28.91 Aligned_cols=65 Identities=25% Similarity=0.181 Sum_probs=48.0
Q ss_pred CchhHHHHHHHhhCCC-CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 63 MPIANVIRIMRKILPQ-HAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 63 LPkA~I~RImKeaLp~-~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
+....+.+++++.+.. +..|+.++...|.+.+.-=+..+-.+-...|.-.+.++|+.+||...+.
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 5566666666665443 5789999999998888766667777777766655555899999988776
No 82
>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=51.33 E-value=18 Score=24.90 Aligned_cols=42 Identities=21% Similarity=0.197 Sum_probs=27.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcCCCccCcccHHHH
Q 026469 83 SDDAKETIQECVSEYISFITGEANE-RCQREQRKTITAEDVLWA 125 (238)
Q Consensus 83 SkDAkeaLqecaseFI~~LaseAne-~A~~~kRKTItaEDVL~A 125 (238)
+.||...|.+. =-|+.--...+.+ +|...|...||.++|..|
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 56777777775 4466655554444 889999999999998776
No 83
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=50.10 E-value=45 Score=32.83 Aligned_cols=50 Identities=14% Similarity=0.288 Sum_probs=42.2
Q ss_pred CCcccCHHHHHHHHHHHH----HHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 78 QHAKISDDAKETIQECVS----EYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 78 ~~~rISkDAkeaLqecas----eFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
+++.++.||++.|.+..+ .|...|-+.|+.+|.+.|-+++..+||-.+.+
T Consensus 374 Edv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 374 EDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred hccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 467899999999877554 46677888899999999999999999999864
No 84
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=49.71 E-value=59 Score=30.78 Aligned_cols=54 Identities=20% Similarity=0.253 Sum_probs=41.2
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 73 RKILPQHAKISDDAKETIQECVSEYI-------SFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 73 KeaLp~~~rISkDAkeaLqecaseFI-------~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
++.++ .+.|+++.++.+.+.|..+= .++...|...|--++|..|+++||..+..
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 33343 68899999998888776653 24566777788889999999999998763
No 85
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=48.48 E-value=40 Score=30.43 Aligned_cols=65 Identities=18% Similarity=0.199 Sum_probs=49.0
Q ss_pred HHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCcccHHHHHhhcCCC
Q 026469 68 VIRIMRKILP-QHAKISDDAKETIQECVSEYISFITGEANERCQR--EQRKTITAEDVLWAMSKLGFD 132 (238)
Q Consensus 68 I~RImKeaLp-~~~rISkDAkeaLqecaseFI~~LaseAne~A~~--~kRKTItaEDVL~ALe~LGF~ 132 (238)
+.+.|++.+. .+..|+.+|.+.|.+++..=...+..|-...|.- .++++|+.+||...+....+.
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 4444444332 3578999999999999887677777777777766 568899999999998876654
No 86
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=48.43 E-value=63 Score=32.27 Aligned_cols=62 Identities=26% Similarity=0.267 Sum_probs=46.0
Q ss_pred hhHHHHHHHhh-CCCCcccCHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccCcccHHHHH
Q 026469 65 IANVIRIMRKI-LPQHAKISDDAKETIQECVSE----YISFITGEANERCQREQRKTITAEDVLWAM 126 (238)
Q Consensus 65 kA~I~RImKea-Lp~~~rISkDAkeaLqecase----FI~~LaseAne~A~~~kRKTItaEDVL~AL 126 (238)
+.-|+-|++-- .-+++.+++||.+.|....++ |..-|..-|..+|+..++++|..+||-.|-
T Consensus 363 ~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~ 429 (450)
T COG1224 363 REEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAK 429 (450)
T ss_pred HHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHH
Confidence 33344444322 224678999999999876554 555667789999999999999999999985
No 87
>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=48.30 E-value=46 Score=33.89 Aligned_cols=50 Identities=28% Similarity=0.271 Sum_probs=42.1
Q ss_pred CCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 78 QHAKISDDAKETIQECVSEYI-------SFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 78 ~~~rISkDAkeaLqecaseFI-------~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
+.+.|++++++.|.+.+..+- .++...|...|--++|.+|+.+||..|++
T Consensus 246 ~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~ 302 (633)
T TIGR02442 246 PSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAE 302 (633)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence 368899999999999887763 45667788889999999999999999875
No 88
>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=47.66 E-value=14 Score=24.31 Aligned_cols=26 Identities=23% Similarity=0.259 Sum_probs=21.2
Q ss_pred HHHHHHhcCCCccCcccHHHHHhhcC
Q 026469 105 ANERCQREQRKTITAEDVLWAMSKLG 130 (238)
Q Consensus 105 Ane~A~~~kRKTItaEDVL~ALe~LG 130 (238)
|.+.|...+...|+.+|++.||=+.+
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 56789999999999999999976544
No 89
>COG4187 RocB Arginine degradation protein (predicted deacylase) [Amino acid transport and metabolism]
Probab=47.31 E-value=17 Score=36.89 Aligned_cols=102 Identities=19% Similarity=0.100 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---------ccCcccHHHHHhhcC-CCcchHHHHHHHHHHHHHHh-hhcC
Q 026469 86 AKETIQECVSEYISFITGEANERCQREQRK---------TITAEDVLWAMSKLG-FDDYIEPLTVYLHRYREMEG-ERGS 154 (238)
Q Consensus 86 AkeaLqecaseFI~~LaseAne~A~~~kRK---------TItaEDVL~ALe~LG-F~dyve~Lk~~L~~yRE~~~-~rks 154 (238)
.++...++|++-|.-+...+-++|+..+|+ .++.++++...+..| ++.....++..+..=-+..- .+.-
T Consensus 318 l~~~a~~A~~e~i~~~~~~~~~y~k~~n~~~~~l~~~~~Vlt~~ell~raR~~g~~d~~~~~~e~~f~~~~~ld~r~~s~ 397 (553)
T COG4187 318 LKEEAETAAEEAIETLRDRYEEYGKLVNRPAGPLPAKPRVLTFQELLERARVRGHIDAEYAEKEYEFAQNGELDLRLRST 397 (553)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCceEEEHHHHHHHHHhcCCCCHHHHHHHHHhhhCcccCchHHHH
Confidence 345556788999999999999999988654 588889888888777 76554433322211000000 0000
Q ss_pred CCCCCCCCCCCCCcccCCccccccCCccccccCCC
Q 026469 155 IRGEPPLVKRPPVEFRTLGVAAFAAPAAAFHHMGL 189 (238)
Q Consensus 155 ~k~~~p~~k~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 (238)
+-.+- +.+= ..+.|+.-+-+|+||++|..|+..
T Consensus 398 ~~~~~-L~~l-~~~~gp~iVlffapp~yP~n~L~~ 430 (553)
T COG4187 398 QLTEW-LVGL-AGLSGPAIVLFFAPPHYPHNTLRV 430 (553)
T ss_pred HHHHH-HHhh-ccccCCeEEEEecCCCCCcchhcc
Confidence 00000 1111 234455545579999888665543
No 90
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=45.94 E-value=41 Score=34.35 Aligned_cols=52 Identities=15% Similarity=0.129 Sum_probs=44.9
Q ss_pred hCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 75 ILPQHAKISDDAKETIQECVSEYI-------SFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 75 aLp~~~rISkDAkeaLqecaseFI-------~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
.++ ++.|+++..+.+.++|..|- ..|...|..+|-=++|..|+.+||..|+.
T Consensus 190 rl~-~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 190 RLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 444 78999999999988888874 47788899999999999999999999985
No 91
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=45.39 E-value=44 Score=29.72 Aligned_cols=71 Identities=17% Similarity=0.156 Sum_probs=44.5
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcch
Q 026469 63 MPIANVIRIMRKILP-QHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYI 135 (238)
Q Consensus 63 LPkA~I~RImKeaLp-~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyv 135 (238)
++...+.+++++.+. .+..++.++.+.|.+.+.-=+..+.......|. +.++|+.+||..++.....++-+
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 444566666665443 246799999999988774334444333334442 33479999999988865544333
No 92
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=44.34 E-value=48 Score=34.27 Aligned_cols=48 Identities=25% Similarity=0.169 Sum_probs=38.8
Q ss_pred ccCHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 81 KISDDAKETIQECVSEY-------------ISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 81 rISkDAkeaLqecaseF-------------I~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
.++++|...|.+-.+.- |.-|..+|..+|..++++.|+.+||..|+..
T Consensus 339 ~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~ 399 (637)
T PRK13765 339 HFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKKI 399 (637)
T ss_pred CCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence 68999998887755532 3337788999999999999999999999843
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=44.22 E-value=35 Score=30.82 Aligned_cols=76 Identities=13% Similarity=0.149 Sum_probs=35.1
Q ss_pred ccccCCchhHHHHHHHhhCCC--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CccCcccHHHHHhhc
Q 026469 58 EQDRFMPIANVIRIMRKILPQ--HAKISDDAKETIQECVSEYISFITGEANERCQREQR------KTITAEDVLWAMSKL 129 (238)
Q Consensus 58 e~D~~LPkA~I~RImKeaLp~--~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kR------KTItaEDVL~ALe~L 129 (238)
.++.+|-...+.+-|.+.... ...|..|...+|.-||++.|..|...+..+|++-.. .+....||-..|..|
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 456688888888777776643 357999999999999999999999999998875321 233466777766655
Q ss_pred CCCc
Q 026469 130 GFDD 133 (238)
Q Consensus 130 GF~d 133 (238)
.-.+
T Consensus 119 ~~~e 122 (264)
T PF05236_consen 119 EQLE 122 (264)
T ss_dssp ----
T ss_pred HHHH
Confidence 5433
No 94
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=41.58 E-value=76 Score=30.43 Aligned_cols=54 Identities=22% Similarity=0.320 Sum_probs=43.2
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 73 RKILPQHAKISDDAKETIQECVSEYI-------SFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 73 KeaLp~~~rISkDAkeaLqecaseFI-------~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
++.++ .+.|+++.++.|.+.|..+= .++...|...|--++|..|+++||..+..
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 33443 68899999999988888764 35667777888899999999999998864
No 95
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=41.28 E-value=57 Score=22.45 Aligned_cols=31 Identities=23% Similarity=0.387 Sum_probs=26.2
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHH
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSE 96 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecase 96 (238)
.+.+++|.|++... -+||.+.++.|.+++++
T Consensus 10 gvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 10 GVSKSTVSRVLNGP----PRVSEETRERILEAAEE 40 (46)
T ss_dssp TSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHH
Confidence 46788999988765 58999999999998876
No 96
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=41.09 E-value=55 Score=32.67 Aligned_cols=48 Identities=17% Similarity=0.178 Sum_probs=41.7
Q ss_pred cccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 80 AKISDDAKETIQECVSEY------ISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 80 ~rISkDAkeaLqecaseF------I~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
..+++++++.|.+++..+ .+-|..-|..+|.=+++..|..+||..|+.
T Consensus 444 ~~l~~~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 444 CKLSAIDANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred cCCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 356899999999988876 566778899999999999999999999984
No 97
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=40.54 E-value=75 Score=30.10 Aligned_cols=48 Identities=6% Similarity=-0.068 Sum_probs=39.9
Q ss_pred CcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcccHHHHH
Q 026469 79 HAKISDDAKETIQECVSEYI-------SFITGEANERCQREQRKTITAEDVLWAM 126 (238)
Q Consensus 79 ~~rISkDAkeaLqecaseFI-------~~LaseAne~A~~~kRKTItaEDVL~AL 126 (238)
.+.|+++..+.|.+.|..+= .+|...|...|--++|..|+++||..+.
T Consensus 249 ~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 249 QLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred CcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 68899999999988887764 2477788889999999999999996654
No 98
>smart00350 MCM minichromosome maintenance proteins.
Probab=39.48 E-value=1.2e+02 Score=29.93 Aligned_cols=65 Identities=14% Similarity=0.152 Sum_probs=46.9
Q ss_pred cCCchhHHHHHHHhh----CCCCcccCHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhcCCCcc
Q 026469 61 RFMPIANVIRIMRKI----LPQHAKISDDAKETIQECVSEY-------------------ISFITGEANERCQREQRKTI 117 (238)
Q Consensus 61 ~~LPkA~I~RImKea----Lp~~~rISkDAkeaLqecaseF-------------------I~~LaseAne~A~~~kRKTI 117 (238)
..++...+.+.+.-+ .| +|++++.+.|.+...+. +..|..-|-..|.-..|.+|
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 357777777766333 34 68999999887654442 24555667778888899999
Q ss_pred CcccHHHHHhh
Q 026469 118 TAEDVLWAMSK 128 (238)
Q Consensus 118 taEDVL~ALe~ 128 (238)
+.+||..|++-
T Consensus 493 ~~~Dv~~ai~l 503 (509)
T smart00350 493 EEADVEEAIRL 503 (509)
T ss_pred CHHHHHHHHHH
Confidence 99999999764
No 99
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=38.24 E-value=1.1e+02 Score=27.32 Aligned_cols=65 Identities=23% Similarity=0.154 Sum_probs=47.7
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCccCcccHHHHHhh
Q 026469 63 MPIANVIRIMRKILP-QHAKISDDAKETIQECVSEYISFITGEANERCQRE-QRKTITAEDVLWAMSK 128 (238)
Q Consensus 63 LPkA~I~RImKeaLp-~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~-kRKTItaEDVL~ALe~ 128 (238)
+....+.+.|++.+. .+..|+.+|.+.|.+.+..=+..+..|-...|.-. +++ |+.+||-..+..
T Consensus 146 ~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~ 212 (340)
T PRK05574 146 PKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPD 212 (340)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhh
Confidence 556666666655554 35789999999999998877777777777776644 334 999999877654
No 100
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=37.37 E-value=35 Score=34.26 Aligned_cols=59 Identities=15% Similarity=0.304 Sum_probs=42.9
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHHHHHHHHHH
Q 026469 73 RKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIEPLTVYLHRY 145 (238)
Q Consensus 73 KeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve~Lk~~L~~y 145 (238)
|+++.+.--|-+|.+.+|++||.+.=.||...-...-.++++++ |..|++.+-..|...
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 45555455788999999999999999999987666666666555 346677666655543
No 101
>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=36.81 E-value=26 Score=26.36 Aligned_cols=47 Identities=23% Similarity=0.336 Sum_probs=26.1
Q ss_pred CcccCHHHHHHHHHHHH-------HHHHHHHHHHHHHH-HhcCCCccCcccHHHH
Q 026469 79 HAKISDDAKETIQECVS-------EYISFITGEANERC-QREQRKTITAEDVLWA 125 (238)
Q Consensus 79 ~~rISkDAkeaLqecas-------eFI~~LaseAne~A-~~~kRKTItaEDVL~A 125 (238)
++||+.+.++.|.+++. .||.-.+.++.+.. ..+.+-+++.+|.-.-
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f 57 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAF 57 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHH
Confidence 37899999999999975 45555444443322 2333345555554333
No 102
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=35.29 E-value=51 Score=26.66 Aligned_cols=34 Identities=15% Similarity=0.233 Sum_probs=27.3
Q ss_pred hHHHHHHHhhCC----CCcccCHHHHHHHHHHHHHHHH
Q 026469 66 ANVIRIMRKILP----QHAKISDDAKETIQECVSEYIS 99 (238)
Q Consensus 66 A~I~RImKeaLp----~~~rISkDAkeaLqecaseFI~ 99 (238)
++|.+|+|+.+- |+..++.++.+.|+++++.|-.
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~a~ 88 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELWAQ 88 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHHHh
Confidence 567789998876 3578999999999999998754
No 103
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=35.15 E-value=1.1e+02 Score=29.31 Aligned_cols=74 Identities=23% Similarity=0.237 Sum_probs=50.5
Q ss_pred hHHHHHHHhhCCC---CcccCHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchH
Q 026469 66 ANVIRIMRKILPQ---HAKISDDAKETIQECV------SEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIE 136 (238)
Q Consensus 66 A~I~RImKeaLp~---~~rISkDAkeaLqeca------seFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve 136 (238)
.-|.-|+++-... ...+++++.+++..-+ ..+..-|...|.++|+.+++.+|+.+||..|-++.+..-+.+
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 4455666554432 3457777776665332 234566778899999999999999999999977777655544
Q ss_pred HHH
Q 026469 137 PLT 139 (238)
Q Consensus 137 ~Lk 139 (238)
.++
T Consensus 273 ~~~ 275 (366)
T COG1474 273 VLK 275 (366)
T ss_pred HHH
Confidence 443
No 104
>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=34.39 E-value=1.1e+02 Score=30.97 Aligned_cols=49 Identities=18% Similarity=0.208 Sum_probs=37.4
Q ss_pred CcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 79 HAKISDDAKETIQECVSEYI-------SFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 79 ~~rISkDAkeaLqecaseFI-------~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
.+.|+++..+.|.+.+..+- .++...|...|.-++|.+|+.+||..|+.
T Consensus 201 ~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 201 QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 57899999887777665432 24456666778888999999999999974
No 105
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=33.56 E-value=44 Score=32.87 Aligned_cols=31 Identities=35% Similarity=0.288 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 98 ISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 98 I~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
|..|..+|...|.+++|..|+.+||..|+++
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~ 423 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEK 423 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHH
Confidence 6677888999999999999999999999875
No 106
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=32.46 E-value=1.1e+02 Score=27.81 Aligned_cols=50 Identities=16% Similarity=0.111 Sum_probs=38.6
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCccCcccHHHHHh
Q 026469 78 QHAKISDDAKETIQECVSEYISFITGEANERCQR-EQRKTITAEDVLWAMS 127 (238)
Q Consensus 78 ~~~rISkDAkeaLqecaseFI~~LaseAne~A~~-~kRKTItaEDVL~ALe 127 (238)
.+.+|+.||.+.|.+++.-=...+..|-...+.- ...++|+.+||...+.
T Consensus 158 ~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 158 AGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred CCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 3579999999999999887666666666666664 3457899999988765
No 107
>PF09123 DUF1931: Domain of unknown function (DUF1931); InterPro: IPR015207 This entry represents a set of hypothetical bacterial proteins containing a core of six alpha-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined []. ; PDB: 1WWS_A 1WWI_A 1R4V_A.
Probab=31.83 E-value=45 Score=28.57 Aligned_cols=69 Identities=16% Similarity=0.242 Sum_probs=48.6
Q ss_pred HHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHHHHHHHHHHHH
Q 026469 68 VIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIEPLTVYLHRYRE 147 (238)
Q Consensus 68 I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve~Lk~~L~~yRE 147 (238)
+.||++.+.. .-|.|+-.+-+.+.++.=+.-|.--|.+.|+.++|.+|...|+=- -..+++.++.||+
T Consensus 1 fe~lFR~aa~--LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPI----------TkGlqesi~~Fr~ 68 (138)
T PF09123_consen 1 FERLFRKAAG--LDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPI----------TKGLQESIREFRK 68 (138)
T ss_dssp HHHHHHHHHS------HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-------------HHHHHHHHHHHT
T ss_pred ChHHHHHHhc--cCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCc----------cHHHHHHHHHHHH
Confidence 3578888876 667788888888888888888888899999999999999988632 2445566677776
Q ss_pred H
Q 026469 148 M 148 (238)
Q Consensus 148 ~ 148 (238)
+
T Consensus 69 l 69 (138)
T PF09123_consen 69 L 69 (138)
T ss_dssp T
T ss_pred c
Confidence 5
No 108
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=30.44 E-value=56 Score=31.05 Aligned_cols=34 Identities=32% Similarity=0.363 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 026469 96 EYISFITGEANERCQREQRKTITAEDVLWAMSKL 129 (238)
Q Consensus 96 eFI~~LaseAne~A~~~kRKTItaEDVL~ALe~L 129 (238)
.-|..|..+|...|.+++++.|+.+|+..|+++.
T Consensus 339 adl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~ 372 (389)
T PRK03992 339 ADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKV 372 (389)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 3456677888889999999999999999998754
No 109
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=30.29 E-value=64 Score=28.92 Aligned_cols=60 Identities=12% Similarity=0.028 Sum_probs=42.6
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc---cCcccHHHH
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKT---ITAEDVLWA 125 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKT---ItaEDVL~A 125 (238)
.||++.|.+++..++. --|+...+.+|+-.+.+|+-.|-.-|..+ .+++.| +.+.|+-.|
T Consensus 115 ~lnKt~VKKlastV~n--QtVspNi~I~l~g~~KVfvGEiIElA~~V--q~~w~~sgpl~p~h~rea 177 (199)
T COG5251 115 SLNKTQVKKLASTVAN--QTVSPNIRIFLQGVGKVFVGEIIELAMIV--QNKWLTSGPLIPFHKREA 177 (199)
T ss_pred CCCHHHHHHHHHHHhc--cccCCCeeeeeechhHHHHHHHHHHHHHH--HHHhcccCCCChHHHHHH
Confidence 5999999999999886 66777777888888889988777655443 233333 445555444
No 110
>PF02361 CbiQ: Cobalt transport protein; InterPro: IPR003339 Cobalt transport proteins are most often found in cobalamin (vitamin B12) biosynthesis operons. Salmonella typhimurium synthesizes cobalamin (vitamin B12) de novo under anaerobic conditions. Not all Salmonella and Pseudomonas cobalamin synthetic genes have apparent homologs in the other species suggesting that the cobalamin biosynthetic pathways differ between the two organisms [].; GO: 0015087 cobalt ion transmembrane transporter activity, 0006824 cobalt ion transport, 0009236 cobalamin biosynthetic process
Probab=29.82 E-value=63 Score=26.89 Aligned_cols=63 Identities=19% Similarity=0.114 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCc------------chHHHHHHHHHHHHHHhhhcCC
Q 026469 90 IQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDD------------YIEPLTVYLHRYREMEGERGSI 155 (238)
Q Consensus 90 LqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~d------------yve~Lk~~L~~yRE~~~~rks~ 155 (238)
+..++..++..+..-..-.. =-.|.+.+|++.+++.+.+.. |++.+.+.+++-++.++.|...
T Consensus 101 ~~~~~~~~lr~~~~~~~~~~---~~~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A~~~Rg~~ 175 (224)
T PF02361_consen 101 LIYAALLALRILAILLASLL---FILTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREAQRLRGVG 175 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHH---HHHHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 44444444444443333322 134778999999999999987 7777777777777776666543
No 111
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=29.50 E-value=61 Score=30.12 Aligned_cols=32 Identities=31% Similarity=0.339 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 97 YISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 97 FI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
-|..|..+|...|...+|..|+.+|+..|+++
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 45577788889999999999999999999976
No 112
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=29.24 E-value=43 Score=29.21 Aligned_cols=37 Identities=11% Similarity=0.239 Sum_probs=28.7
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHH
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITG 103 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~Las 103 (238)
..-+++|.|.+... -+||++.++.|.+++++. .|.-.
T Consensus 9 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l-gY~pn 45 (327)
T PRK10423 9 GVSTSTVSHVINKD----RFVSEAITAKVEAAIKEL-NYAPS 45 (327)
T ss_pred CCcHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCcc
Confidence 45688999998643 479999999999999874 45443
No 113
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=29.24 E-value=1.1e+02 Score=28.38 Aligned_cols=64 Identities=22% Similarity=0.171 Sum_probs=47.2
Q ss_pred HHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCC
Q 026469 68 VIRIMRKILP-QHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGF 131 (238)
Q Consensus 68 I~RImKeaLp-~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF 131 (238)
+.+.+++.+- .+++|++||.+.|.++..-=+..|.+|-...+--..-++|+.+||..++.+-.-
T Consensus 145 l~~~i~~~~~~~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~~~~ 209 (334)
T COG1466 145 LPQWIKKRAKELGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSDVAE 209 (334)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhcccc
Confidence 4444444332 257999999999999998777777777777666555559999999999875443
No 114
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=29.18 E-value=2.6e+02 Score=22.13 Aligned_cols=73 Identities=12% Similarity=0.167 Sum_probs=42.4
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHH-----HHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchH
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQE-----CVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIE 136 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqe-----caseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve 136 (238)
.+|...+.+++++- .+|.-..+.|.. +.+.-+.. .........++=+.++++.||..+++..-.+
T Consensus 17 ~~~~~~wK~faR~l-----glse~~Id~I~~~~~~d~~Eq~~qm-----L~~W~~~~G~~a~~~~Li~aLr~~~l~~~Ad 86 (97)
T cd08316 17 VMTLKDVKKFVRKS-----GLSEPKIDEIKLDNPQDTAEQKVQL-----LRAWYQSHGKTGAYRTLIKTLRKAKLCTKAD 86 (97)
T ss_pred HcCHHHHHHHHHHc-----CCCHHHHHHHHHcCCCChHHHHHHH-----HHHHHHHhCCCchHHHHHHHHHHccchhHHH
Confidence 36667777777764 344444444331 11111111 2333333334446799999999999998888
Q ss_pred HHHHHHHH
Q 026469 137 PLTVYLHR 144 (238)
Q Consensus 137 ~Lk~~L~~ 144 (238)
.++..|.+
T Consensus 87 ~I~~~l~~ 94 (97)
T cd08316 87 KIQDIIEA 94 (97)
T ss_pred HHHHHHHh
Confidence 88776543
No 115
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=28.46 E-value=57 Score=33.20 Aligned_cols=56 Identities=11% Similarity=0.301 Sum_probs=40.9
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC--cccHHHHHhh
Q 026469 73 RKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTIT--AEDVLWAMSK 128 (238)
Q Consensus 73 KeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTIt--aEDVL~ALe~ 128 (238)
|+++.+.--|-+|.+.+|++||...=.||...-...-..++++++. -.+|..+|.+
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 4555555578899999999999999999999777766666666654 2345555543
No 116
>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=27.61 E-value=45 Score=27.26 Aligned_cols=62 Identities=13% Similarity=0.176 Sum_probs=39.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHHHHHHHHHHHHH
Q 026469 83 SDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFDDYIEPLTVYLHRYREM 148 (238)
Q Consensus 83 SkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~dyve~Lk~~L~~yRE~ 148 (238)
+..++..|..|..+.-.|...-..=... ---.-.++...|+..|++..+.+++..|++|++.
T Consensus 71 ~s~Vk~Eiaa~~~v~~~Y~~~L~~G~vd----~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~ 132 (134)
T PF12010_consen 71 PSPVKNEIAACSNVWSEYYPPLETGLVD----PEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAA 132 (134)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHccCCC----HHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHh
Confidence 3455666666666655554431111110 0113456788899999999999999999999864
No 117
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=26.96 E-value=1.5e+02 Score=28.85 Aligned_cols=81 Identities=19% Similarity=0.233 Sum_probs=54.7
Q ss_pred CCCcccccccccCCchhHHHHHHHhhCCCCc--ccCHHHHHHHHHH-HHHHHHHHHHHHHH-HHHhc--CC-CccCcccH
Q 026469 50 EDNECTVREQDRFMPIANVIRIMRKILPQHA--KISDDAKETIQEC-VSEYISFITGEANE-RCQRE--QR-KTITAEDV 122 (238)
Q Consensus 50 ~~~e~~v~e~D~~LPkA~I~RImKeaLp~~~--rISkDAkeaLqec-aseFI~~LaseAne-~A~~~--kR-KTItaEDV 122 (238)
-++..+|...|+. -.|.|.-.+++.+|+.- .|..|--.-|.+. ++.|+.-|+.--++ ++..+ +- +.++.+||
T Consensus 38 K~D~SPVTvaDyG-~QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dv 116 (351)
T KOG1528|consen 38 KSDKSPVTVADYG-SQAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDV 116 (351)
T ss_pred cCCCCCcchhhhh-HHHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHH
Confidence 3446677777754 47889999999999765 5666666666655 55667777764444 33222 22 78999999
Q ss_pred HHHHhhcCC
Q 026469 123 LWAMSKLGF 131 (238)
Q Consensus 123 L~ALe~LGF 131 (238)
++|+..-+.
T Consensus 117 l~aID~G~s 125 (351)
T KOG1528|consen 117 LKAIDRGNS 125 (351)
T ss_pred HHHHhcccc
Confidence 999975444
No 118
>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=26.90 E-value=1.4e+02 Score=21.60 Aligned_cols=41 Identities=24% Similarity=0.265 Sum_probs=32.0
Q ss_pred HHHHHHHHH--HHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 85 DAKETIQEC--VSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 85 DAkeaLqec--aseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
|+.+.| +. ...|+.|....|..++-+.++|. .-+|+.+|..
T Consensus 14 e~id~~-~~~~~~~~~~f~~gnaiKY~~R~~~K~-~~eDl~KA~~ 56 (60)
T PF11753_consen 14 ECIDFI-EQFTEEQFLGFCLGNAIKYLWRAGKKN-GIEDLKKAKW 56 (60)
T ss_pred cHHHHH-HHhcchhhhhHHHHHHHHHHHHHcccC-cHHHHHHHHH
Confidence 445555 33 44899999999999999999994 4888888864
No 119
>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=26.60 E-value=56 Score=22.58 Aligned_cols=24 Identities=25% Similarity=0.425 Sum_probs=20.3
Q ss_pred cCcccHHHHHhhcCCCcchHHHHH
Q 026469 117 ITAEDVLWAMSKLGFDDYIEPLTV 140 (238)
Q Consensus 117 ItaEDVL~ALe~LGF~dyve~Lk~ 140 (238)
=+.+||..-|+.+||++|++..+.
T Consensus 4 w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 4 WSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp HCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCHHHHHHHHHHCCcHHHHHHHHH
Confidence 367899999999999999887664
No 120
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=26.54 E-value=71 Score=30.84 Aligned_cols=33 Identities=24% Similarity=0.202 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 96 EYISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 96 eFI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
.=|..|..+|...|.+++|+.|+.+|+..|+++
T Consensus 353 aDI~~l~~eA~~~A~r~~~~~i~~~df~~A~~~ 385 (398)
T PTZ00454 353 ADIAAICQEAGMQAVRKNRYVILPKDFEKGYKT 385 (398)
T ss_pred HHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHH
Confidence 336778889999999999999999999999875
No 121
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=26.51 E-value=1.1e+02 Score=31.44 Aligned_cols=65 Identities=9% Similarity=0.092 Sum_probs=35.9
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 026469 63 MPIANVIRIMRKILP-QHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSK 128 (238)
Q Consensus 63 LPkA~I~RImKeaLp-~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~ 128 (238)
|+...|.+.+++.+. .++.++.++...|.+.+.-=+..+-.+....+.-.+++ |+.++|...+..
T Consensus 180 ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~~ 245 (614)
T PRK14971 180 IQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLNI 245 (614)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhCC
Confidence 444555555544332 25788999888887765443444444433333333433 777777665543
No 122
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=26.51 E-value=1.2e+02 Score=26.67 Aligned_cols=65 Identities=20% Similarity=0.152 Sum_probs=40.4
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 026469 63 MPIANVIRIMRKILP-QHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSKL 129 (238)
Q Consensus 63 LPkA~I~RImKeaLp-~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~L 129 (238)
++...+.++++..+. .+..|+.++.+.|.+.+.--+..+-.+-...+.. .++|+.+||..++...
T Consensus 161 l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~--~~~it~~~v~~~~~~~ 226 (319)
T PRK00440 161 LKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAAT--GKEVTEEAVYKITGTA 226 (319)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc--CCCCCHHHHHHHhCCC
Confidence 445555555655443 2567999999999887654333333333233332 4789999999887654
No 123
>PRK09526 lacI lac repressor; Reviewed
Probab=26.13 E-value=45 Score=29.41 Aligned_cols=37 Identities=14% Similarity=0.432 Sum_probs=29.7
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHH
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITG 103 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~Las 103 (238)
..-+++|.|++... .+||++.++.|.+++++ +.|.-.
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 56788999988643 47999999999999999 556543
No 124
>PRK07914 hypothetical protein; Reviewed
Probab=25.85 E-value=1.2e+02 Score=27.62 Aligned_cols=62 Identities=16% Similarity=0.182 Sum_probs=43.5
Q ss_pred hhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 026469 65 IANVIRIMRKILP-QHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS 127 (238)
Q Consensus 65 kA~I~RImKeaLp-~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe 127 (238)
...+.+.|++.+. .+.+|+.||.+.|.+++..=+..|..|--..+...+ .+|+.+||...+.
T Consensus 130 ~~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 192 (320)
T PRK07914 130 AAERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHS 192 (320)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcC
Confidence 4444444444433 246899999999999997767777777666554333 5799999998876
No 125
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=25.58 E-value=52 Score=33.55 Aligned_cols=46 Identities=17% Similarity=0.354 Sum_probs=37.7
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC
Q 026469 73 RKILPQHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTIT 118 (238)
Q Consensus 73 KeaLp~~~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTIt 118 (238)
|+++.+.--|-+|.+.++++||.+.=.||.....+.-+.+++++|.
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 3444444567899999999999999999999999888888888764
No 126
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=25.28 E-value=4.4e+02 Score=22.65 Aligned_cols=65 Identities=18% Similarity=0.207 Sum_probs=48.6
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCc---ccHHHHHhhcCCCcchHH-HHHHHHHH
Q 026469 81 KISDDAKETIQECVSEYISFITGEANERCQREQRKTITA---EDVLWAMSKLGFDDYIEP-LTVYLHRY 145 (238)
Q Consensus 81 rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTIta---EDVL~ALe~LGF~dyve~-Lk~~L~~y 145 (238)
..+..+...|.+.+-.+-.-+..+|.-++++.+|--++. |||-.|+..-==-.|+++ -+++|-+.
T Consensus 31 ~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F~pppPke~llel 99 (145)
T COG5094 31 EYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHFVPPPPKEYLLEL 99 (145)
T ss_pred hhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCcCCCChHHHHHHH
Confidence 456666677778888888999999999999999986666 999999984433456544 56665443
No 127
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=25.11 E-value=1.1e+02 Score=30.35 Aligned_cols=52 Identities=12% Similarity=0.133 Sum_probs=39.7
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHHH-HHHHHHhcCCCccCcccHHHHHhhcC
Q 026469 78 QHAKISDDAKETIQECVSEYISFITGE-ANERCQREQRKTITAEDVLWAMSKLG 130 (238)
Q Consensus 78 ~~~rISkDAkeaLqecaseFI~~Lase-Ane~A~~~kRKTItaEDVL~ALe~LG 130 (238)
+.+.++.||...|.+ +=-|+.-=... +-++|++.+...|+.|.|..|-..+|
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 45566544444 44488999999999999999976654
No 128
>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=24.26 E-value=1.2e+02 Score=30.12 Aligned_cols=52 Identities=13% Similarity=0.155 Sum_probs=38.9
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHH-HHHHHHHhcCCCccCcccHHHHHhhcC
Q 026469 78 QHAKISDDAKETIQECVSEYISFITG-EANERCQREQRKTITAEDVLWAMSKLG 130 (238)
Q Consensus 78 ~~~rISkDAkeaLqecaseFI~~Las-eAne~A~~~kRKTItaEDVL~ALe~LG 130 (238)
+.+.++.||...|.+ +=-|+.-=.. .+-++|.+.+...|+.|.|..|=+.+|
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 347899999999965 4455553333 444588999999999999999876654
No 129
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=23.61 E-value=1.1e+02 Score=23.17 Aligned_cols=33 Identities=24% Similarity=0.283 Sum_probs=26.8
Q ss_pred cccHHHHHhhcCC------CcchHHHHHHHHHHHHHHhh
Q 026469 119 AEDVLWAMSKLGF------DDYIEPLTVYLHRYREMEGE 151 (238)
Q Consensus 119 aEDVL~ALe~LGF------~dyve~Lk~~L~~yRE~~~~ 151 (238)
++.|..+|++||| ..+-+.++..|..|..+++-
T Consensus 18 ~~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~ENf 56 (74)
T PF08823_consen 18 AREVQEALKRLGYYKGEADGVWDEATEDALRAWAGTENF 56 (74)
T ss_pred HHHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhhH
Confidence 3467889999999 67888888999988887763
No 130
>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=23.41 E-value=48 Score=22.09 Aligned_cols=23 Identities=26% Similarity=0.433 Sum_probs=19.4
Q ss_pred CcccHHHHHhhcCCCcchHHHHH
Q 026469 118 TAEDVLWAMSKLGFDDYIEPLTV 140 (238)
Q Consensus 118 taEDVL~ALe~LGF~dyve~Lk~ 140 (238)
+.++|..-|+.+|+++|++.++.
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~ 25 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFRE 25 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHH
Confidence 57899999999999888887765
No 131
>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=23.27 E-value=1.5e+02 Score=30.29 Aligned_cols=71 Identities=13% Similarity=0.189 Sum_probs=45.1
Q ss_pred chhHHHHHHHhhCCC-CcccCHHHHHHHHHHH---HHHHHHHHHHHHHH--------HHhcCCCccCcccHHHHHhhcCC
Q 026469 64 PIANVIRIMRKILPQ-HAKISDDAKETIQECV---SEYISFITGEANER--------CQREQRKTITAEDVLWAMSKLGF 131 (238)
Q Consensus 64 PkA~I~RImKeaLp~-~~rISkDAkeaLqeca---seFI~~LaseAne~--------A~~~kRKTItaEDVL~ALe~LGF 131 (238)
...-+..|++..+.. ...+++++.++|.+++ ...+..|... ... ++..++.+|+.+||.++++.--|
T Consensus 354 s~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~~gRraln~L~~~-~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r~ 432 (615)
T TIGR02903 354 TPEDIALIVLNAAEKINVHLAAGVEELIARYTIEGRKAVNILADV-YGYALYRAAEAGKENDKVTITQDDVYEVIQISRL 432 (615)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCcHHHHHHHHHHH-HHHHHHHHHHhccCCCCeeECHHHHHHHhCCCcC
Confidence 345566677766543 3568999999998765 3334433222 111 22334568999999999988777
Q ss_pred Ccch
Q 026469 132 DDYI 135 (238)
Q Consensus 132 ~dyv 135 (238)
..|.
T Consensus 433 ~~~~ 436 (615)
T TIGR02903 433 SPYE 436 (615)
T ss_pred ccch
Confidence 6665
No 132
>PRK06130 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=22.92 E-value=1.2e+02 Score=27.32 Aligned_cols=60 Identities=18% Similarity=0.188 Sum_probs=33.7
Q ss_pred hHHHHHHHhhCCCCcccCHHHH-HHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh-hcCCC
Q 026469 66 ANVIRIMRKILPQHAKISDDAK-ETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMS-KLGFD 132 (238)
Q Consensus 66 A~I~RImKeaLp~~~rISkDAk-eaLqecaseFI~~LaseAne~A~~~kRKTItaEDVL~ALe-~LGF~ 132 (238)
..|..+++...-.-+.+.+|.. .++.+. +.-+..||...+++.+ ++++||..+|. .+||.
T Consensus 162 ~~v~~l~~~~G~~~v~~~~d~~G~i~nr~----~~~~~~Ea~~l~~~g~---~~~~~id~~~~~~~g~~ 223 (311)
T PRK06130 162 ATTMALLRSIGKRPVLVKKDIPGFIANRI----QHALAREAISLLEKGV---ASAEDIDEVVKWSLGIR 223 (311)
T ss_pred HHHHHHHHHcCCEEEEEcCCCCCcHHHHH----HHHHHHHHHHHHHcCC---CCHHHHHHHHHhcCCCC
Confidence 3455566554432344554532 233332 2344566766665443 79999999996 66664
No 133
>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=22.70 E-value=1.4e+02 Score=25.94 Aligned_cols=45 Identities=11% Similarity=0.248 Sum_probs=32.5
Q ss_pred ccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHH
Q 026469 58 EQDRFMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITGEA 105 (238)
Q Consensus 58 e~D~~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~LaseA 105 (238)
.-...+|-.... |+++.+.--|-+|.+.+|++||...=.||...-
T Consensus 99 i~St~VPfts~~---KeaIadvpEI~~EIrlAl~~~~R~L~~~l~kk~ 143 (151)
T cd00823 99 VASTKVPFTSEG---KEAIADIPEIEEEIKLALQEVARKLKRYLSKKR 143 (151)
T ss_pred EeecCCCcCCcc---hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455554443 455655557899999999999999999998743
No 134
>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=22.61 E-value=16 Score=25.42 Aligned_cols=57 Identities=28% Similarity=0.442 Sum_probs=31.1
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC---cccHHHHHhhcCCCcch-HHHHH
Q 026469 80 AKISDDAKETIQECVSEYISFITGEANERCQREQRKTIT---AEDVLWAMSKLGFDDYI-EPLTV 140 (238)
Q Consensus 80 ~rISkDAkeaLqecaseFI~~LaseAne~A~~~kRKTIt---aEDVL~ALe~LGF~dyv-e~Lk~ 140 (238)
.+|.++...+|.+++. .+..|+ .++-..+=.|.+. +...+..|.++|+-+++ +.++.
T Consensus 2 F~ie~~t~~ai~~~~~-~L~~is---~ERi~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~ 62 (64)
T PF12627_consen 2 FKIEPETEEAIKENAE-LLSKIS---KERIREELEKILSSPNPSRAFKLLDELGLLEYIFPELDA 62 (64)
T ss_dssp -EE-HHHHHHHHHHGG-GGGGS----HHHHHHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT
T ss_pred CccCHHHHHHHHHHHH-HHhcCC---HHHHHHHHHHHHcCCCHHHHHHHHHHcCCHHHHCccccc
Confidence 5678888888888766 333433 3444444344444 34455666677876653 54443
No 135
>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=22.15 E-value=72 Score=21.96 Aligned_cols=22 Identities=32% Similarity=0.518 Sum_probs=19.2
Q ss_pred CcccHHHHHhhcCCCcchHHHH
Q 026469 118 TAEDVLWAMSKLGFDDYIEPLT 139 (238)
Q Consensus 118 taEDVL~ALe~LGF~dyve~Lk 139 (238)
+++||..-|+.+|+++|++..+
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 5789999999999999998763
No 136
>KOG0093 consensus GTPase Rab3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.66 E-value=78 Score=28.18 Aligned_cols=53 Identities=13% Similarity=0.370 Sum_probs=35.2
Q ss_pred CHHHHHHHHHHHHHHHHHHHHH-----HHHHHHhcCCCccCcccHHHHHhhcCCCcch
Q 026469 83 SDDAKETIQECVSEYISFITGE-----ANERCQREQRKTITAEDVLWAMSKLGFDDYI 135 (238)
Q Consensus 83 SkDAkeaLqecaseFI~~Lase-----Ane~A~~~kRKTItaEDVL~ALe~LGF~dyv 135 (238)
.++...++|.-++..-.|--.. +-..|.-+..++|+.|.++.-.++|||+-|-
T Consensus 105 NeeSf~svqdw~tqIktysw~naqvilvgnKCDmd~eRvis~e~g~~l~~~LGfefFE 162 (193)
T KOG0093|consen 105 NEESFNSVQDWITQIKTYSWDNAQVILVGNKCDMDSERVISHERGRQLADQLGFEFFE 162 (193)
T ss_pred CHHHHHHHHHHHHHheeeeccCceEEEEecccCCccceeeeHHHHHHHHHHhChHHhh
Confidence 4555666666655543331111 1235777889999999999999999995443
No 137
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=21.54 E-value=58 Score=28.69 Aligned_cols=37 Identities=19% Similarity=0.313 Sum_probs=28.5
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHH
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFITG 103 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~Las 103 (238)
..-+++|.|++... .+||.+.++.+.+++++ +.|.-.
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 46678888888543 47999999999999988 456543
No 138
>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=21.08 E-value=53 Score=22.29 Aligned_cols=14 Identities=43% Similarity=0.674 Sum_probs=11.8
Q ss_pred ccHHHHHhhcCCCc
Q 026469 120 EDVLWAMSKLGFDD 133 (238)
Q Consensus 120 EDVL~ALe~LGF~d 133 (238)
+|++.||..|||..
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 139
>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=21.00 E-value=5.3e+02 Score=21.98 Aligned_cols=50 Identities=16% Similarity=0.201 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC-cchHHHHHHHHHHHHHHh
Q 026469 94 VSEYISFITGEANERCQREQRKTITAEDVLWAMSKLGFD-DYIEPLTVYLHRYREMEG 150 (238)
Q Consensus 94 aseFI~~LaseAne~A~~~kRKTItaEDVL~ALe~LGF~-dyve~Lk~~L~~yRE~~~ 150 (238)
+.+.+.||..+|. |.-++.+++..-|+.|||+ +.++.+......+|+...
T Consensus 44 ~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l~ 94 (174)
T cd04752 44 SIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKLQ 94 (174)
T ss_pred HHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH
Confidence 4455666666554 3448999999999999998 556666666666665544
No 140
>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=20.72 E-value=82 Score=18.99 Aligned_cols=27 Identities=22% Similarity=0.246 Sum_probs=20.4
Q ss_pred HHHHHHHhcCCCccCcccHHHHHh-hcC
Q 026469 104 EANERCQREQRKTITAEDVLWAMS-KLG 130 (238)
Q Consensus 104 eAne~A~~~kRKTItaEDVL~ALe-~LG 130 (238)
++....-.++.-+|+.+|+..+|+ .||
T Consensus 4 ~~F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 4 EAFKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 344566677888999999999998 576
No 141
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=20.68 E-value=1.6e+02 Score=29.29 Aligned_cols=52 Identities=12% Similarity=0.093 Sum_probs=40.1
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHH-HHHHHHHhcCCCccCcccHHHHHhhcC
Q 026469 78 QHAKISDDAKETIQECVSEYISFITG-EANERCQREQRKTITAEDVLWAMSKLG 130 (238)
Q Consensus 78 ~~~rISkDAkeaLqecaseFI~~Las-eAne~A~~~kRKTItaEDVL~ALe~LG 130 (238)
+.+.++.||.+.|.+. =-|+.-=.. .+-++|++.+...||.|.|..|=.++|
T Consensus 460 ~~~~w~~ea~~~l~~i-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 512 (513)
T CHL00076 460 SDLIWSPESQLELSKI-PGFVRGKVKRNTEKFARQNGITNITVEVMYAAKEALS 512 (513)
T ss_pred CCCCCCHHHHHHHHhC-CHHhHHHHHHHHHHHHHHcCCCeEcHHHHHHHHHhhC
Confidence 3468999999999987 455553333 444588999999999999999977665
No 142
>TIGR02454 CbiQ_TIGR cobalt ABC transporter, permease protein CbiQ. This model represents the permease component of the cobalt-specific ABC transporter. This model finds permeases which are generally next to the other subunits of the complex (CbiN and CbiO) or the cobalamin biosynthesis protein CbiM which is a transmembrane protein which likely interacts with the complex in some manner. In genomes which possess all of these subunits the ATPase is most likely running in the direction of import (for the biosynthesis of coenzyme B12). In other genomes, this subunit may be involved in the export of cobalt and/or other closely related heavy metals.
Probab=20.36 E-value=1.3e+02 Score=25.13 Aligned_cols=38 Identities=26% Similarity=0.280 Sum_probs=26.3
Q ss_pred CccCcccHHHHHhhcCCC-----------cchHHHHHHHHHHHHHHhhh
Q 026469 115 KTITAEDVLWAMSKLGFD-----------DYIEPLTVYLHRYREMEGER 152 (238)
Q Consensus 115 KTItaEDVL~ALe~LGF~-----------dyve~Lk~~L~~yRE~~~~r 152 (238)
-|...+|+..+|+++++. .|++.+.+..++-++.++.|
T Consensus 112 ~TT~~~~l~~~l~~l~~P~~~~~~~~l~~Rfip~l~~e~~~i~~Aq~aR 160 (198)
T TIGR02454 112 LTTPFPELLSALRRLGVPPLLVEILLLTYRYLFVLLEELRRMLLAQRSR 160 (198)
T ss_pred HcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 467889999999999986 35555555555555555544
No 143
>PRK09492 treR trehalose repressor; Provisional
Probab=20.23 E-value=82 Score=27.41 Aligned_cols=36 Identities=14% Similarity=0.337 Sum_probs=28.2
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHH
Q 026469 62 FMPIANVIRIMRKILPQHAKISDDAKETIQECVSEYISFIT 102 (238)
Q Consensus 62 ~LPkA~I~RImKeaLp~~~rISkDAkeaLqecaseFI~~La 102 (238)
.+-+++|.|++... .+||.+.++.|.+++++. .|.-
T Consensus 15 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~el-gY~p 50 (315)
T PRK09492 15 GVGKSTVSRVLNNE----SGVSEETRERVEAVINQH-GFSP 50 (315)
T ss_pred CCCHHHHhHHhCCC----CCCCHHHHHHHHHHHHHH-CCCc
Confidence 46788999988752 489999999999999884 3543
Done!