Query 038325
Match_columns 231
No_of_seqs 155 out of 629
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 09:51:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038325.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038325hhsearch_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 6E-38 1.3E-42 264.1 13.1 103 51-153 23-125 (168)
2 KOG0871 Class 2 transcription 99.9 2E-25 4.4E-30 186.8 10.2 98 54-151 6-103 (156)
3 KOG0870 DNA polymerase epsilon 99.9 1.7E-24 3.6E-29 183.9 9.7 101 53-153 3-104 (172)
4 COG5150 Class 2 transcription 99.8 2.3E-20 5.1E-25 153.8 8.9 98 55-152 6-103 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.7 1E-17 2.2E-22 120.2 7.8 64 60-124 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.7 7.6E-18 1.6E-22 131.3 5.2 83 49-133 8-90 (91)
7 cd00076 H4 Histone H4, one of 99.4 1.6E-12 3.4E-17 100.3 7.1 80 51-132 4-83 (85)
8 PLN00035 histone H4; Provision 99.3 3.4E-12 7.4E-17 101.7 6.1 83 48-132 17-99 (103)
9 PTZ00015 histone H4; Provision 99.3 7.4E-12 1.6E-16 99.6 7.0 85 46-132 16-100 (102)
10 smart00417 H4 Histone H4. 99.1 7E-11 1.5E-15 89.2 5.2 71 51-123 4-74 (74)
11 smart00803 TAF TATA box bindin 99.0 7.8E-10 1.7E-14 81.1 7.5 64 60-125 2-65 (65)
12 smart00428 H3 Histone H3. 99.0 1.7E-09 3.6E-14 86.6 6.7 76 51-126 20-100 (105)
13 cd07981 TAF12 TATA Binding Pro 98.8 1.9E-08 4.2E-13 74.6 8.0 66 61-127 2-67 (72)
14 PF00125 Histone: Core histone 98.8 1.2E-08 2.6E-13 74.2 6.5 68 58-125 3-73 (75)
15 COG5208 HAP5 CCAAT-binding fac 98.6 2.4E-08 5.1E-13 89.6 3.9 78 56-135 105-183 (286)
16 PLN00121 histone H3; Provision 98.6 6.2E-08 1.4E-12 80.8 5.8 75 51-125 53-130 (136)
17 PLN00160 histone H3; Provision 98.6 1E-07 2.2E-12 75.5 6.5 75 51-125 12-90 (97)
18 PLN00161 histone H3; Provision 98.6 1.5E-07 3.2E-12 78.4 7.6 75 51-125 46-124 (135)
19 PTZ00018 histone H3; Provision 98.6 1.2E-07 2.5E-12 79.1 6.0 75 51-125 53-130 (136)
20 KOG1657 CCAAT-binding factor, 98.5 1.1E-07 2.3E-12 85.3 4.5 105 38-143 50-159 (236)
21 KOG3467 Histone H4 [Chromatin 98.5 1.6E-07 3.4E-12 74.0 4.6 81 48-130 17-97 (103)
22 smart00576 BTP Bromodomain tra 98.4 1.8E-06 4E-11 64.4 7.8 66 63-130 9-74 (77)
23 cd00074 H2A Histone 2A; H2A is 98.2 3.1E-06 6.7E-11 68.7 6.9 68 58-126 18-85 (115)
24 cd07979 TAF9 TATA Binding Prot 98.1 1.7E-05 3.7E-10 64.1 8.1 75 65-141 6-81 (117)
25 cd08050 TAF6 TATA Binding Prot 97.9 4.6E-05 1E-09 70.9 8.0 67 62-130 1-67 (343)
26 KOG1745 Histones H3 and H4 [Ch 97.8 1.1E-05 2.4E-10 67.5 2.7 80 48-127 51-133 (137)
27 PF15511 CENP-T: Centromere ki 97.8 3.8E-05 8.3E-10 73.3 6.1 65 55-119 346-414 (414)
28 PF03847 TFIID_20kDa: Transcri 97.6 0.00028 6.1E-09 52.4 7.1 63 63-126 2-64 (68)
29 PF15630 CENP-S: Kinetochore c 97.6 0.00028 6E-09 53.6 7.2 62 65-126 10-72 (76)
30 PF07524 Bromo_TP: Bromodomain 97.6 0.00041 8.8E-09 51.3 8.0 65 64-130 10-74 (77)
31 smart00427 H2B Histone H2B. 97.5 0.00048 1E-08 54.1 7.1 62 65-127 6-67 (89)
32 cd08048 TAF11 TATA Binding Pro 97.5 0.00063 1.4E-08 52.6 7.6 66 60-127 16-84 (85)
33 KOG1659 Class 2 transcription 97.3 0.00042 9.2E-09 62.0 5.2 87 59-146 12-98 (224)
34 PF09415 CENP-X: CENP-S associ 97.3 0.00048 1E-08 51.8 4.6 65 62-126 1-67 (72)
35 PF02969 TAF: TATA box binding 97.2 0.0023 4.9E-08 47.6 7.5 64 60-125 3-66 (66)
36 PLN00158 histone H2B; Provisio 97.2 0.0016 3.5E-08 53.4 7.1 66 61-127 28-93 (116)
37 PTZ00463 histone H2B; Provisio 97.1 0.0021 4.5E-08 52.8 7.2 62 65-127 33-94 (117)
38 COG5247 BUR6 Class 2 transcrip 97.0 0.0021 4.5E-08 52.1 6.2 77 60-137 23-99 (113)
39 PF04719 TAFII28: hTAFII28-lik 97.0 0.003 6.4E-08 49.5 6.7 67 60-127 23-90 (90)
40 COG5262 HTA1 Histone H2A [Chro 96.8 0.0025 5.5E-08 52.8 5.7 68 57-125 23-90 (132)
41 smart00414 H2A Histone 2A. 96.7 0.0048 1E-07 49.5 6.3 68 58-126 7-74 (106)
42 KOG1142 Transcription initiati 96.6 0.0035 7.7E-08 57.4 5.7 70 56-126 150-219 (258)
43 PLN00154 histone H2A; Provisio 96.4 0.0098 2.1E-07 50.0 6.3 68 58-125 36-103 (136)
44 PTZ00017 histone H2A; Provisio 96.1 0.013 2.9E-07 49.1 5.6 67 58-125 25-91 (134)
45 KOG1658 DNA polymerase epsilon 96.1 0.0045 9.8E-08 53.2 2.8 69 56-126 55-124 (162)
46 PF02269 TFIID-18kDa: Transcri 96.0 0.009 1.9E-07 46.5 3.9 60 66-126 7-66 (93)
47 KOG1744 Histone H2B [Chromatin 95.9 0.027 5.8E-07 46.9 6.5 62 65-127 42-103 (127)
48 KOG1756 Histone 2A [Chromatin 95.6 0.034 7.3E-07 46.5 5.8 68 57-125 24-91 (131)
49 PLN00157 histone H2A; Provisio 95.6 0.027 5.8E-07 47.2 5.3 67 58-125 24-90 (132)
50 PF15510 CENP-W: Centromere ki 95.5 0.023 5E-07 45.4 4.6 66 60-126 16-95 (102)
51 PLN00153 histone H2A; Provisio 95.5 0.032 6.9E-07 46.6 5.4 67 58-125 22-88 (129)
52 PLN00156 histone H2AX; Provisi 95.5 0.037 8E-07 46.7 5.8 67 58-125 27-93 (139)
53 KOG3219 Transcription initiati 94.9 0.029 6.2E-07 49.7 3.8 70 59-130 111-181 (195)
54 cd07978 TAF13 The TATA Binding 94.9 0.37 8E-06 37.7 9.6 60 65-126 7-66 (92)
55 PF02291 TFIID-31kDa: Transcri 94.7 0.15 3.2E-06 42.4 7.1 82 58-141 8-92 (129)
56 PTZ00252 histone H2A; Provisio 93.1 0.28 6.1E-06 41.3 6.1 67 58-125 23-91 (134)
57 KOG4336 TBP-associated transcr 93.1 0.45 9.7E-06 45.0 8.1 77 65-145 10-86 (323)
58 KOG3423 Transcription initiati 91.7 0.85 1.8E-05 39.9 7.4 70 59-130 85-168 (176)
59 TIGR03015 pepcterm_ATPase puta 89.7 1 2.3E-05 38.7 6.3 70 61-130 192-269 (269)
60 KOG2549 Transcription initiati 89.5 1.3 2.8E-05 44.9 7.5 65 63-129 14-78 (576)
61 KOG3334 Transcription initiati 86.0 6.5 0.00014 33.8 8.6 62 80-141 31-93 (148)
62 PRK00411 cdc6 cell division co 85.4 3.4 7.4E-05 37.8 7.3 69 63-131 209-286 (394)
63 TIGR02928 orc1/cdc6 family rep 82.8 4.7 0.0001 36.4 7.0 74 63-136 201-283 (365)
64 KOG2389 Predicted bromodomain 77.0 5.7 0.00012 38.3 5.7 72 57-130 26-97 (353)
65 TIGR02902 spore_lonB ATP-depen 76.6 6.7 0.00014 38.8 6.3 67 63-129 265-334 (531)
66 PF13654 AAA_32: AAA domain; P 72.3 14 0.0003 36.8 7.4 49 79-127 447-506 (509)
67 TIGR00764 lon_rel lon-related 70.5 15 0.00032 37.2 7.2 50 79-128 330-392 (608)
68 COG5095 TAF6 Transcription ini 69.5 9.6 0.00021 37.0 5.3 54 77-130 20-73 (450)
69 cd08045 TAF4 TATA Binding Prot 69.3 24 0.00051 30.8 7.4 78 56-133 40-125 (212)
70 COG1067 LonB Predicted ATP-dep 67.1 4.7 0.0001 41.4 2.9 48 79-126 338-398 (647)
71 KOG2680 DNA helicase TIP49, TB 62.8 29 0.00063 33.9 7.1 50 76-125 374-427 (454)
72 COG5162 Transcription initiati 55.7 67 0.0014 28.5 7.6 69 60-130 88-189 (197)
73 PF13335 Mg_chelatase_2: Magne 55.6 37 0.00081 26.3 5.5 48 78-125 41-94 (96)
74 COG1224 TIP49 DNA helicase TIP 54.7 31 0.00068 34.2 5.9 81 62-145 362-447 (450)
75 PF08369 PCP_red: Proto-chloro 54.6 17 0.00037 24.9 3.1 42 81-123 2-44 (45)
76 PF03540 TFIID_30kDa: Transcri 54.0 79 0.0017 22.6 6.4 48 60-109 2-49 (51)
77 PRK00080 ruvB Holliday junctio 49.5 66 0.0014 29.2 7.0 73 60-132 179-255 (328)
78 TIGR00635 ruvB Holliday juncti 47.9 88 0.0019 27.6 7.3 71 61-131 159-233 (305)
79 KOG3901 Transcription initiati 47.7 80 0.0017 26.0 6.3 50 74-126 22-71 (109)
80 KOG1757 Histone 2A [Chromatin 47.5 30 0.00064 28.9 3.9 65 57-125 27-95 (131)
81 COG5248 TAF19 Transcription in 47.3 91 0.002 26.0 6.7 49 76-126 24-72 (126)
82 PF02861 Clp_N: Clp amino term 46.3 17 0.00036 23.8 2.0 26 103-128 1-26 (53)
83 TIGR02442 Cob-chelat-sub cobal 45.5 64 0.0014 32.7 6.8 50 76-125 246-302 (633)
84 PRK09862 putative ATP-dependen 45.2 62 0.0014 32.4 6.5 57 78-134 437-499 (506)
85 TIGR02030 BchI-ChlI magnesium 44.1 82 0.0018 29.7 6.9 54 71-125 247-307 (337)
86 PF00531 Death: Death domain; 42.3 28 0.0006 24.7 2.8 30 111-140 54-83 (83)
87 PRK12402 replication factor C 41.9 55 0.0012 29.0 5.1 71 61-133 184-255 (337)
88 PF09114 MotA_activ: Transcrip 41.8 41 0.00089 27.0 3.8 34 64-97 51-88 (96)
89 PRK13406 bchD magnesium chelat 41.6 52 0.0011 33.5 5.4 59 65-125 183-248 (584)
90 PF08823 PG_binding_2: Putativ 41.5 37 0.0008 25.5 3.4 34 117-150 18-57 (74)
91 TIGR01128 holA DNA polymerase 41.4 1.2E+02 0.0026 26.5 7.1 66 61-126 111-177 (302)
92 smart00350 MCM minichromosome 37.7 1.3E+02 0.0028 29.6 7.4 69 59-127 416-504 (509)
93 KOG0921 Dosage compensation co 37.4 64 0.0014 35.5 5.4 36 172-207 1207-1249(1282)
94 PRK13765 ATP-dependent proteas 36.2 55 0.0012 33.7 4.7 48 79-126 339-399 (637)
95 COG1331 Highly conserved prote 35.9 45 0.00098 34.8 4.0 16 189-204 243-258 (667)
96 PRK13407 bchI magnesium chelat 35.4 1.1E+02 0.0023 29.0 6.1 53 71-124 244-303 (334)
97 PRK07452 DNA polymerase III su 35.3 84 0.0018 28.2 5.3 65 66-130 135-202 (326)
98 TIGR02454 CbiQ_TIGR cobalt ABC 34.8 54 0.0012 27.2 3.7 38 113-150 112-160 (198)
99 PF08681 DUF1778: Protein of u 34.7 31 0.00067 25.8 2.1 49 77-125 3-59 (80)
100 PF05236 TAF4: Transcription i 34.7 55 0.0012 29.4 4.0 76 56-131 39-122 (264)
101 PTZ00009 heat shock 70 kDa pro 34.6 3.8E+02 0.0081 27.3 10.3 13 61-73 512-524 (653)
102 CHL00081 chlI Mg-protoporyphyr 34.4 1.2E+02 0.0025 29.1 6.3 54 71-125 260-320 (350)
103 TIGR00368 Mg chelatase-related 33.9 84 0.0018 31.3 5.5 48 78-125 444-497 (499)
104 PF00356 LacI: Bacterial regul 33.5 85 0.0019 21.4 3.9 31 60-94 10-40 (46)
105 COG1474 CDC6 Cdc6-related prot 32.1 1.3E+02 0.0028 28.7 6.2 72 64-135 193-273 (366)
106 TIGR02031 BchD-ChlD magnesium 31.8 1.3E+02 0.0029 30.4 6.5 55 70-125 195-256 (589)
107 cd04752 Commd4 COMM_Domain con 31.4 3.3E+02 0.0071 23.1 9.2 53 91-150 43-96 (174)
108 TIGR01052 top6b DNA topoisomer 31.2 52 0.0011 33.0 3.5 44 71-114 426-469 (488)
109 PTZ00361 26 proteosome regulat 30.4 54 0.0012 32.1 3.5 32 96-127 393-424 (438)
110 PRK10423 transcriptional repre 30.4 37 0.0008 29.5 2.1 37 60-101 9-45 (327)
111 PF02361 CbiQ: Cobalt transpor 29.5 66 0.0014 26.7 3.4 40 113-152 123-174 (224)
112 TIGR01242 26Sp45 26S proteasom 28.0 67 0.0015 29.7 3.5 33 95-127 331-363 (364)
113 PRK03992 proteasome-activating 27.9 66 0.0014 30.4 3.5 34 95-128 340-373 (389)
114 PF07647 SAM_2: SAM domain (St 27.7 52 0.0011 22.6 2.1 25 114-138 3-27 (66)
115 PTZ00183 centrin; Provisional 27.4 1.8E+02 0.004 22.4 5.4 19 111-129 30-48 (158)
116 PRK14975 bifunctional 3'-5' ex 26.9 3.8E+02 0.0083 26.8 8.7 93 57-152 160-272 (553)
117 PF12010 DUF3502: Domain of un 26.8 38 0.00083 27.5 1.5 62 81-146 71-132 (134)
118 PRK09526 lacI lac repressor; R 26.7 40 0.00086 29.6 1.7 37 60-101 16-52 (342)
119 COG5251 TAF40 Transcription in 26.6 78 0.0017 28.2 3.4 61 59-123 114-177 (199)
120 PF09123 DUF1931: Domain of un 26.3 64 0.0014 27.5 2.8 69 66-146 1-69 (138)
121 PRK05574 holA DNA polymerase I 26.0 2.8E+02 0.0062 24.6 7.0 65 61-126 146-212 (340)
122 KOG1528 Salt-sensitive 3'-phos 25.8 1.6E+02 0.0034 28.6 5.5 79 51-130 41-126 (351)
123 PTZ00454 26S protease regulato 25.2 75 0.0016 30.6 3.4 32 96-127 355-386 (398)
124 PF13405 EF-hand_6: EF-hand do 24.9 70 0.0015 19.2 2.1 27 102-128 4-31 (31)
125 cd00166 SAM Sterile alpha moti 24.9 42 0.00092 22.3 1.2 24 116-139 3-26 (63)
126 PF00536 SAM_1: SAM domain (St 23.5 65 0.0014 22.1 2.0 22 116-137 4-25 (64)
127 COG1389 DNA topoisomerase VI, 23.3 65 0.0014 32.7 2.6 46 71-116 434-479 (538)
128 PRK14971 DNA polymerase III su 23.1 1.4E+02 0.0031 30.4 5.0 64 61-125 180-244 (614)
129 PRK00440 rfc replication facto 22.0 1.7E+02 0.0036 25.7 4.7 65 61-127 161-226 (319)
130 TIGR01278 DPOR_BchB light-inde 21.7 1.5E+02 0.0033 29.2 4.8 51 77-128 460-511 (511)
131 PF11753 DUF3310: Protein of u 21.1 2E+02 0.0044 20.5 4.2 42 83-126 14-57 (60)
132 COG1724 Predicted RNA binding 21.1 52 0.0011 24.9 1.1 18 114-131 6-23 (66)
133 PRK02910 light-independent pro 20.9 1.6E+02 0.0035 29.2 4.8 52 76-128 466-518 (519)
134 smart00027 EH Eps15 homology d 20.8 1.5E+02 0.0033 22.0 3.7 29 102-130 14-42 (96)
135 PF07499 RuvA_C: RuvA, C-termi 20.8 55 0.0012 22.1 1.1 14 118-131 4-17 (47)
136 PRK06585 holA DNA polymerase I 20.3 2E+02 0.0044 26.0 5.0 50 77-126 159-209 (343)
137 TIGR02903 spore_lon_C ATP-depe 20.0 2E+02 0.0043 29.3 5.3 73 61-134 353-437 (615)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=6e-38 Score=264.08 Aligned_cols=103 Identities=61% Similarity=1.074 Sum_probs=100.0
Q ss_pred CCCCCccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 038325 51 PCVVREQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFD 130 (231)
Q Consensus 51 ~~~v~e~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~ 130 (231)
.+.++++|++||+|||.||||+.||.++|||||||+.||+|++|||+|||++|+++|++++|||||+|||||||..|||+
T Consensus 23 ~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe 102 (168)
T KOG0869|consen 23 SLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFE 102 (168)
T ss_pred ccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcH
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchHHHHHHHHHHHHHHHHHhhh
Q 038325 131 NYVEPLSIFLNRFRDSEHERTAA 153 (231)
Q Consensus 131 dYv~~Lk~~L~~yRe~~~~rk~~ 153 (231)
+|+++|+.||.+|||++++|...
T Consensus 103 ~Y~eplkiyL~kYRe~e~e~~~~ 125 (168)
T KOG0869|consen 103 NYAEPLKIYLQKYRELEGERGRS 125 (168)
T ss_pred hHHHHHHHHHHHHHHHhhhcccc
Confidence 99999999999999999988764
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.92 E-value=2e-25 Score=186.75 Aligned_cols=98 Identities=31% Similarity=0.648 Sum_probs=93.4
Q ss_pred CCccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcch
Q 038325 54 VREQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYV 133 (231)
Q Consensus 54 v~e~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv 133 (231)
-..+++.||+|+|.+|||+.||.+++|.+||+++|.+||.+||+.|+++||++|.++.||||.+|||++||+.|||.+|+
T Consensus 6 ~~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYi 85 (156)
T KOG0871|consen 6 KEDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYI 85 (156)
T ss_pred cccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHH
Confidence 34678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 038325 134 EPLSIFLNRFRDSEHERT 151 (231)
Q Consensus 134 ~~Lk~~L~~yRe~~~~rk 151 (231)
+.+...|+.|+.....|.
T Consensus 86 ee~~~vl~~~K~~~~~~~ 103 (156)
T KOG0871|consen 86 EEAEEVLENCKEEAKKRR 103 (156)
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 999999999999877543
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.91 E-value=1.7e-24 Score=183.91 Aligned_cols=101 Identities=28% Similarity=0.526 Sum_probs=97.7
Q ss_pred CCCccccCCchhHHHHHHHhhCCCC-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCc
Q 038325 53 VVREQDQYMPIANVIRIMRRILPPH-AKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDN 131 (231)
Q Consensus 53 ~v~e~d~~LPkA~I~RImK~aLP~~-~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~d 131 (231)
..+++++.||+|+|.||+|++||+. +.|||||+.+|+++|++||+||++.|+++|+.++||||+++|||.||++|+|..
T Consensus 3 ~eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~ 82 (172)
T KOG0870|consen 3 DERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSS 82 (172)
T ss_pred chhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHH
Confidence 4568899999999999999999987 999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHHHHhhh
Q 038325 132 YVEPLSIFLNRFRDSEHERTAA 153 (231)
Q Consensus 132 Yv~~Lk~~L~~yRe~~~~rk~~ 153 (231)
|+.+|+..|+.||...++||..
T Consensus 83 f~~plk~~Le~yk~~~k~Kk~~ 104 (172)
T KOG0870|consen 83 FVNPLKSALEAYKKAVKQKKLA 104 (172)
T ss_pred HhhHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999985
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.82 E-value=2.3e-20 Score=153.76 Aligned_cols=98 Identities=27% Similarity=0.520 Sum_probs=94.2
Q ss_pred CccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchH
Q 038325 55 REQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYVE 134 (231)
Q Consensus 55 ~e~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv~ 134 (231)
..++..||+|+|.++|-+.||.+..+.|||++.+++||-+||+.|+++|++.|..+.+|||.+|||++||+.|+|.+|++
T Consensus 6 ~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~ 85 (148)
T COG5150 6 NDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIE 85 (148)
T ss_pred ccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHH
Confidence 46788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhh
Q 038325 135 PLSIFLNRFRDSEHERTA 152 (231)
Q Consensus 135 ~Lk~~L~~yRe~~~~rk~ 152 (231)
.+.+.+..|+..++.|.+
T Consensus 86 ~~~e~~~n~k~~qK~ke~ 103 (148)
T COG5150 86 SCMEEHENYKSYQKQKES 103 (148)
T ss_pred HHHHHHHHHHHHHhhchh
Confidence 999999999999887665
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=1e-17 Score=120.23 Aligned_cols=64 Identities=41% Similarity=0.631 Sum_probs=59.4
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHH
Q 038325 60 YMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124 (231)
Q Consensus 60 ~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~AL 124 (231)
.||++.|.||||.. |+..+||+||.++|++|+++||.+|+.+|++.|.+++||||+++||..||
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 59999999999999 88999999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.71 E-value=7.6e-18 Score=131.29 Aligned_cols=83 Identities=34% Similarity=0.445 Sum_probs=77.9
Q ss_pred CCCCCCCccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcC
Q 038325 49 GAPCVVREQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLG 128 (231)
Q Consensus 49 ~~~~~v~e~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LG 128 (231)
+....++..+..||+++|.||||++.++ |||.+|+++|++|+++|+..|+..|+++|.++|||||+++||..||+.+|
T Consensus 8 ~~r~~~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~ 85 (91)
T COG2036 8 EIRRYQRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLG 85 (91)
T ss_pred HHHhhhhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhc
Confidence 3456788999999999999999999975 99999999999999999999999999999999999999999999999999
Q ss_pred CCcch
Q 038325 129 FDNYV 133 (231)
Q Consensus 129 F~dYv 133 (231)
|..|.
T Consensus 86 ~~~~~ 90 (91)
T COG2036 86 RRIYG 90 (91)
T ss_pred ccccc
Confidence 98663
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=1.6e-12 Score=100.31 Aligned_cols=80 Identities=26% Similarity=0.348 Sum_probs=71.5
Q ss_pred CCCCCccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 038325 51 PCVVREQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFD 130 (231)
Q Consensus 51 ~~~v~e~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~ 130 (231)
....+.....||++.|.||+|... ..+||+|+.+++.++.++|+..|..+|..+|++++||||+++||..||++.|-.
T Consensus 4 r~~~~~~~~gi~k~~I~RLarr~G--vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~ 81 (85)
T cd00076 4 RKVLRDNIKGITKPAIRRLARRGG--VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 81 (85)
T ss_pred hHHHHHhhccCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCC
Confidence 334444455699999999999997 679999999999999999999999999999999999999999999999999865
Q ss_pred cc
Q 038325 131 NY 132 (231)
Q Consensus 131 dY 132 (231)
-|
T Consensus 82 ~y 83 (85)
T cd00076 82 LY 83 (85)
T ss_pred cc
Confidence 44
No 8
>PLN00035 histone H4; Provisional
Probab=99.31 E-value=3.4e-12 Score=101.73 Aligned_cols=83 Identities=25% Similarity=0.278 Sum_probs=74.6
Q ss_pred CCCCCCCCccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 038325 48 AGAPCVVREQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKL 127 (231)
Q Consensus 48 ~~~~~~v~e~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~L 127 (231)
.+|....+.....||++.|.||+|+.. ..|||.|+.++|.+..++|+..|..+|..+|++.+||||+++||..||+++
T Consensus 17 kr~~k~~~d~i~~ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~ 94 (103)
T PLN00035 17 KRHRKVLRDNIQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
T ss_pred hHHHHHHHhhhccCCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHc
Confidence 455666666677799999999999997 679999999999999999999999999999999999999999999999988
Q ss_pred CCCcc
Q 038325 128 GFDNY 132 (231)
Q Consensus 128 GF~dY 132 (231)
|=.-|
T Consensus 95 g~~ly 99 (103)
T PLN00035 95 GRTLY 99 (103)
T ss_pred CCcCC
Confidence 76543
No 9
>PTZ00015 histone H4; Provisional
Probab=99.29 E-value=7.4e-12 Score=99.60 Aligned_cols=85 Identities=25% Similarity=0.321 Sum_probs=76.3
Q ss_pred CCCCCCCCCCccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 46 PPAGAPCVVREQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 46 ~~~~~~~~v~e~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
....+....+.....||++.|.||+|... ..|||.|+.+.+.++.++|+..|..+|..+|++.+||||+++||..||+
T Consensus 16 ~~kr~rk~~r~~i~gI~k~~IrRLarr~G--vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlK 93 (102)
T PTZ00015 16 GQKRQKKVLRDNIRGITKGAIRRLARRGG--VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALK 93 (102)
T ss_pred chhhHHHHHhhcccCCCHHHHHHHHHHcC--CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHH
Confidence 33455666777778899999999999997 6799999999999999999999999999999999999999999999999
Q ss_pred hcCCCcc
Q 038325 126 KLGFDNY 132 (231)
Q Consensus 126 ~LGF~dY 132 (231)
++|-.-|
T Consensus 94 r~g~~~y 100 (102)
T PTZ00015 94 RQGRTLY 100 (102)
T ss_pred hcCCCCC
Confidence 9886544
No 10
>smart00417 H4 Histone H4.
Probab=99.13 E-value=7e-11 Score=89.19 Aligned_cols=71 Identities=25% Similarity=0.305 Sum_probs=64.0
Q ss_pred CCCCCccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHH
Q 038325 51 PCVVREQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWA 123 (231)
Q Consensus 51 ~~~v~e~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~A 123 (231)
...++.....||++.|.||+|... ..+||.|+.+.+.+..++|+..|..+|..+|++.+||||+++||..|
T Consensus 4 ~~~~~d~i~gI~k~~IrRLaRr~G--vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 4 KKVLRDNIQGITKPAIRRLARRGG--VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred hHHHHhhhcCCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 344555566799999999999997 67899999999999999999999999999999999999999999754
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=99.05 E-value=7.8e-10 Score=81.09 Aligned_cols=64 Identities=23% Similarity=0.285 Sum_probs=60.9
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 60 YMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 60 ~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
.||++.|.||++... -.+||+|+..+|.+-++.|+.-|..+|...+++.+||||+++||-.||+
T Consensus 2 ~~p~~~i~ria~~~G--i~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLG--IGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCC--CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 589999999999996 5589999999999999999999999999999999999999999999985
No 12
>smart00428 H3 Histone H3.
Probab=98.96 E-value=1.7e-09 Score=86.56 Aligned_cols=76 Identities=20% Similarity=0.209 Sum_probs=69.8
Q ss_pred CCCCCccccCCchhHHHHHHHhhCCC-----CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 51 PCVVREQDQYMPIANVIRIMRRILPP-----HAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 51 ~~~v~e~d~~LPkA~I~RImK~aLP~-----~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
...++..++.+|+..+.|++++...+ +.+|+.+|.++||++++.|+.-+...|+..+.+.||+||.++||.-|..
T Consensus 20 r~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r 99 (105)
T smart00428 20 RKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR 99 (105)
T ss_pred HHHccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence 45678999999999999999998764 6899999999999999999999999999999999999999999988864
Q ss_pred h
Q 038325 126 K 126 (231)
Q Consensus 126 ~ 126 (231)
-
T Consensus 100 i 100 (105)
T smart00428 100 I 100 (105)
T ss_pred H
Confidence 3
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=98.83 E-value=1.9e-08 Score=74.57 Aligned_cols=66 Identities=14% Similarity=0.314 Sum_probs=62.2
Q ss_pred CchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 038325 61 MPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKL 127 (231)
Q Consensus 61 LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~L 127 (231)
|++..+..+||+.-| ..+|+.||.++|++.+++|+.-|+..|...|++.||+||.++||..+|++.
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 678889999999986 689999999999999999999999999999999999999999999999864
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=98.81 E-value=1.2e-08 Score=74.23 Aligned_cols=68 Identities=26% Similarity=0.325 Sum_probs=62.7
Q ss_pred ccCCchhHHHHHHHhhCCC---CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 58 DQYMPIANVIRIMRRILPP---HAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 58 d~~LPkA~I~RImK~aLP~---~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
...+|+..|.|++|+..++ ..+||++|...|+.+++.|+.-|..+|...|.+.||+||+++||..|++
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 4578999999999999864 2699999999999999999999999999999999999999999999986
No 15
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.63 E-value=2.4e-08 Score=89.64 Aligned_cols=78 Identities=21% Similarity=0.279 Sum_probs=71.2
Q ss_pred ccccCCchhHHHHHHHhhCCCCcc-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchH
Q 038325 56 EQDQYMPIANVIRIMRRILPPHAK-ISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYVE 134 (231)
Q Consensus 56 e~d~~LPkA~I~RImK~aLP~~~r-ISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv~ 134 (231)
..++.||.|.|+|+||-.- ++| ||.||..++.++++.||..||..|+-.+++++|+|+...||-.|+++-++-||+-
T Consensus 105 ~k~h~LPlARIkkvMKtde--dVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLi 182 (286)
T COG5208 105 LKDHNLPLARIKKVMKTDE--DVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLI 182 (286)
T ss_pred HHhccCcHHHHHHHHhccc--chhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHh
Confidence 3467899999999999874 665 9999999999999999999999999999999999999999999999998888764
Q ss_pred H
Q 038325 135 P 135 (231)
Q Consensus 135 ~ 135 (231)
.
T Consensus 183 d 183 (286)
T COG5208 183 D 183 (286)
T ss_pred h
Confidence 3
No 16
>PLN00121 histone H3; Provisional
Probab=98.62 E-value=6.2e-08 Score=80.76 Aligned_cols=75 Identities=17% Similarity=0.194 Sum_probs=69.0
Q ss_pred CCCCCccccCCchhHHHHHHHhhCCC---CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 51 PCVVREQDQYMPIANVIRIMRRILPP---HAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 51 ~~~v~e~d~~LPkA~I~RImK~aLP~---~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
...++..+++||+..+.||+++...+ +.++..+|.++||++++.|+.-|...++..|.+.+|.||...||.-++.
T Consensus 53 r~yQkst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 53 RKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred HHhccccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 44567889999999999999999764 7899999999999999999999999999999999999999999987764
No 17
>PLN00160 histone H3; Provisional
Probab=98.61 E-value=1e-07 Score=75.49 Aligned_cols=75 Identities=17% Similarity=0.128 Sum_probs=68.6
Q ss_pred CCCCCccccCCchhHHHHHHHhhCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 51 PCVVREQDQYMPIANVIRIMRRILP----PHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 51 ~~~v~e~d~~LPkA~I~RImK~aLP----~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
...++..++.+|+....|++++... ++.++..+|.++||++++.|+.-+...++..|.+.||.||.+.|+.-|..
T Consensus 12 R~yQkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 12 KMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred HHHccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 3467889999999999999999864 35899999999999999999999999999999999999999999987764
No 18
>PLN00161 histone H3; Provisional
Probab=98.60 E-value=1.5e-07 Score=78.45 Aligned_cols=75 Identities=16% Similarity=0.194 Sum_probs=68.6
Q ss_pred CCCCCccccCCchhHHHHHHHhhCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 51 PCVVREQDQYMPIANVIRIMRRILP----PHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 51 ~~~v~e~d~~LPkA~I~RImK~aLP----~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
...++..+++||+..+.||+++... .++++..+|.++||++++.|+.-|...|+..|.+.+|.||.+.||.-|..
T Consensus 46 R~yQkst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 46 RKYQKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred HHHccccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 4566789999999999999999863 46899999999999999999999999999999999999999999988764
No 19
>PTZ00018 histone H3; Provisional
Probab=98.56 E-value=1.2e-07 Score=79.14 Aligned_cols=75 Identities=17% Similarity=0.201 Sum_probs=68.7
Q ss_pred CCCCCccccCCchhHHHHHHHhhCC---CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 51 PCVVREQDQYMPIANVIRIMRRILP---PHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 51 ~~~v~e~d~~LPkA~I~RImK~aLP---~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
...++..+++||+..+.||+++... .++++..+|.++||++++.|+.-|...++..|.+.+|.||...|+.-+..
T Consensus 53 r~yQkst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PTZ00018 53 RRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred HHHcccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence 4456788999999999999999964 46899999999999999999999999999999999999999999988764
No 20
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.50 E-value=1.1e-07 Score=85.32 Aligned_cols=105 Identities=17% Similarity=0.257 Sum_probs=85.7
Q ss_pred cccccccCCCCC--CCCCCCccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc
Q 038325 38 QLPLQSLLPPAG--APCVVREQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTI 115 (231)
Q Consensus 38 ~~~~q~~~~~~~--~~~~v~e~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTI 115 (231)
.+.++++|.... -+.........||++.|++|||..= +.-+|+.||...+.+||+.||..|+..|+..++..+|+|+
T Consensus 50 ~~~l~~fw~~~~~e~e~~~d~~~~~lPlaRiKkimK~de-dv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl 128 (236)
T KOG1657|consen 50 RQQLQSFWSKQAIEKEGQLDFKNHILPLARIKKIMKSDE-DVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTL 128 (236)
T ss_pred hHHHHhhhhccccccccccchhhccCcHhhccccccccc-cccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccc
Confidence 557888998775 1233335567799999999999884 2236999999999999999999999999999999999999
Q ss_pred CcccHHHHHhhc---CCCcchHHHHHHHHHH
Q 038325 116 TAEDVVWAMGKL---GFDNYVEPLSIFLNRF 143 (231)
Q Consensus 116 taeDVL~ALe~L---GF~dYv~~Lk~~L~~y 143 (231)
...||-.|+..- +|.-.+.+.+..+++|
T Consensus 129 ~~sdia~av~~s~~fdFL~DivP~~~~~~~~ 159 (236)
T KOG1657|consen 129 QKSDIAAAVTQSETFDFLRDIVPRKILAEKY 159 (236)
T ss_pred hHHHHHHHhccCCCccceeccccchhccccc
Confidence 999999999964 4444455777777766
No 21
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=98.49 E-value=1.6e-07 Score=73.97 Aligned_cols=81 Identities=25% Similarity=0.268 Sum_probs=72.6
Q ss_pred CCCCCCCCccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 038325 48 AGAPCVVREQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKL 127 (231)
Q Consensus 48 ~~~~~~v~e~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~L 127 (231)
..|+..++....-+.+..|+||.+... .-+|+--.-+.+..++.+||.-+.+.|..++++.+||||++.||+.+|+++
T Consensus 17 KrHRK~LsDnIqgitKpaIRRlARr~G--VkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~ 94 (103)
T KOG3467|consen 17 KRHRKVLRDNIQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ 94 (103)
T ss_pred HHHHHHHHhhccccchHHHHHHHHhcC--cchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHc
Confidence 455666666666788999999999996 567999999999999999999999999999999999999999999999998
Q ss_pred CCC
Q 038325 128 GFD 130 (231)
Q Consensus 128 GF~ 130 (231)
|.-
T Consensus 95 G~~ 97 (103)
T KOG3467|consen 95 GRT 97 (103)
T ss_pred Cce
Confidence 864
No 22
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.38 E-value=1.8e-06 Score=64.37 Aligned_cols=66 Identities=23% Similarity=0.282 Sum_probs=60.2
Q ss_pred hhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 038325 63 IANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFD 130 (231)
Q Consensus 63 kA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~ 130 (231)
+-.|.+|+|... --+++.+|+++|.+.+..|+..|+..+..+|++.+|++++..||..||+++|+.
T Consensus 9 ~~~Vaqil~~~G--f~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESAG--FDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 446778888875 458999999999999999999999999999999999999999999999999974
No 23
>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=98.24 E-value=3.1e-06 Score=68.66 Aligned_cols=68 Identities=12% Similarity=0.174 Sum_probs=62.2
Q ss_pred ccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 58 DQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 58 d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
.+.||.+.|.|+||+.-- ..||+.+|...|..+.+.+...|...|...|+..+|++|+++||..|+..
T Consensus 18 gL~fPV~ri~R~Lk~~~~-a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 18 GLQFPVGRIHRYLKKGRY-AERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred CccCcHHHHHHHHHcCcc-ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 678999999999998431 57999999999999999999999999999999999999999999999863
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=98.09 E-value=1.7e-05 Score=64.11 Aligned_cols=75 Identities=16% Similarity=0.172 Sum_probs=64.7
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHH-HHHHHH
Q 038325 65 NVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYVEP-LSIFLN 141 (231)
Q Consensus 65 ~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv~~-Lk~~L~ 141 (231)
.|.+|+|+.. ..+++.++...|.+.+..++.-|..+|...+++.+|+||+++||.-|++...-..|..+ -+++|-
T Consensus 6 ~v~~iLk~~G--v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~ 81 (117)
T cd07979 6 VIAAILKSMG--ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLL 81 (117)
T ss_pred HHHHHHHHCC--CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHH
Confidence 5788888874 56899999999999999999999999999999999999999999999997766556554 555554
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=97.87 E-value=4.6e-05 Score=70.88 Aligned_cols=67 Identities=21% Similarity=0.236 Sum_probs=59.2
Q ss_pred chhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 038325 62 PIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFD 130 (231)
Q Consensus 62 PkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~ 130 (231)
|..+|.-|++... -.++++||..+|.+.++.++.-|..+|...+++.|||||+++||-.||+.++.+
T Consensus 1 ~~~~i~~ia~~~G--i~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 1 PQESIKLIAESLG--IDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred ChhHHHHHHHHcC--CCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 4556777777764 449999999999999999999999999999999999999999999999976655
No 26
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=97.83 E-value=1.1e-05 Score=67.53 Aligned_cols=80 Identities=18% Similarity=0.177 Sum_probs=70.4
Q ss_pred CCCCCCCCccccCCchhHHHHHHHhhCC---CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHH
Q 038325 48 AGAPCVVREQDQYMPIANVIRIMRRILP---PHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124 (231)
Q Consensus 48 ~~~~~~v~e~d~~LPkA~I~RImK~aLP---~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~AL 124 (231)
.+-...++..|++|++....|++|+..+ .++++..+|..+||++++.|+.-|.-.+|-.+.+.||.||.+.||--|.
T Consensus 51 ~eirkyQkstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlAr 130 (137)
T KOG1745|consen 51 REIRKYQKSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 130 (137)
T ss_pred HHHHHHHhhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhh
Confidence 3334557799999999999999995544 5889999999999999999999999999999999999999999998887
Q ss_pred hhc
Q 038325 125 GKL 127 (231)
Q Consensus 125 e~L 127 (231)
.--
T Consensus 131 rir 133 (137)
T KOG1745|consen 131 RIR 133 (137)
T ss_pred hcc
Confidence 643
No 27
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.79 E-value=3.8e-05 Score=73.34 Aligned_cols=65 Identities=20% Similarity=0.264 Sum_probs=47.9
Q ss_pred CccccCCchhHHHHHHHhhCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccc
Q 038325 55 REQDQYMPIANVIRIMRRILP----PHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAED 119 (231)
Q Consensus 55 ~e~d~~LPkA~I~RImK~aLP----~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeD 119 (231)
++.--.||.+.|+||+..... .+++|+|||+.+|.+|...|..-|...--.+|+|+|||||..+|
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 355566999999998887753 46899999999999999999999999999999999999999876
No 28
>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=97.61 E-value=0.00028 Score=52.43 Aligned_cols=63 Identities=16% Similarity=0.308 Sum_probs=51.8
Q ss_pred hhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 63 IANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 63 kA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
+..+..+|++.-| +.++.+|+.++|.+.|.+||.-++..|...|++.+-.||...||...|++
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 4567889999865 89999999999999999999999999999999999999999999999885
No 29
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.61 E-value=0.00028 Score=53.61 Aligned_cols=62 Identities=16% Similarity=0.171 Sum_probs=52.4
Q ss_pred HHHHHHHhhC-CCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 65 NVIRIMRRIL-PPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 65 ~I~RImK~aL-P~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
.|.||+.+.. +.++.+|+++..+|.+.+-.++..++..----|+++||+||+.+||+-...+
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 5778898885 5578999999999999999999999998888999999999999999987654
No 30
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=97.61 E-value=0.00041 Score=51.31 Aligned_cols=65 Identities=18% Similarity=0.281 Sum_probs=57.0
Q ss_pred hHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 038325 64 ANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFD 130 (231)
Q Consensus 64 A~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~ 130 (231)
-.|.+|++.+. =-.++..|.+.|...+..||..|+..+...|++.+|...+..||..||+++|+.
T Consensus 10 ~~va~il~~~G--F~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 10 RSVAQILKHAG--FDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 34556666553 236999999999999999999999999999999999999999999999999984
No 31
>smart00427 H2B Histone H2B.
Probab=97.48 E-value=0.00048 Score=54.06 Aligned_cols=62 Identities=16% Similarity=0.349 Sum_probs=57.5
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 038325 65 NVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKL 127 (231)
Q Consensus 65 ~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~L 127 (231)
-|.|+.|++-| +..||..|...|.--+..+..-|+.||...|...+|+||+..+|..|++-+
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 568999999999999999999999999999999999999999999998754
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=97.46 E-value=0.00063 Score=52.56 Aligned_cols=66 Identities=15% Similarity=0.198 Sum_probs=61.3
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CccCcccHHHHHhhc
Q 038325 60 YMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQR---KTITAEDVVWAMGKL 127 (231)
Q Consensus 60 ~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kR---KTItaeDVL~ALe~L 127 (231)
.||++.|.|||...+ +.+++.+...+|.-.+.+||--|..+|.++..+.+. .-|.++||-.|..+|
T Consensus 16 ~f~k~~iKr~~~~~~--~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 16 SFPKAAIKRLIQSVT--GQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hccHHHHHHHHHHHc--CCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 399999999999999 489999999999999999999999999999888766 789999999999876
No 33
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.27 E-value=0.00042 Score=61.98 Aligned_cols=87 Identities=10% Similarity=0.115 Sum_probs=73.1
Q ss_pred cCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHHHHH
Q 038325 59 QYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYVEPLSI 138 (231)
Q Consensus 59 ~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv~~Lk~ 138 (231)
..+|.+.|.|||...= +-.||..-.-..|.++.+.|+.-|...+.++++..+-|||+++|+..|+..-.--+|+..+-.
T Consensus 12 trfp~aRiKKIMQ~dE-dIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~v~ 90 (224)
T KOG1659|consen 12 TRFPPARIKKIMQSDE-DIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEVVE 90 (224)
T ss_pred ccCCHHHHHHHHhhhh-hhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHHHH
Confidence 3599999999999774 345899999999999999999999999999999999999999999999997776677766554
Q ss_pred HHHHHHHH
Q 038325 139 FLNRFRDS 146 (231)
Q Consensus 139 ~L~~yRe~ 146 (231)
.+..+...
T Consensus 91 ~vpd~~~~ 98 (224)
T KOG1659|consen 91 KVPDRQQA 98 (224)
T ss_pred hcCCCccc
Confidence 44444333
No 34
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=97.25 E-value=0.00048 Score=51.79 Aligned_cols=65 Identities=18% Similarity=0.259 Sum_probs=54.0
Q ss_pred chhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-cCcccHHHHHhh
Q 038325 62 PIANVIRIMRRILP-PHAKISDDAKETVQECVSEYISFITGEANERCHREQRKT-ITAEDVVWAMGK 126 (231)
Q Consensus 62 PkA~I~RImK~aLP-~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKT-ItaeDVL~ALe~ 126 (231)
|...|.||++.... +..||++||..++.+....||..-..-|.+.++.++... |..+|+-+.+-.
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 78899999997774 578999999999999999999999999999999999988 999999886643
No 35
>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=97.18 E-value=0.0023 Score=47.56 Aligned_cols=64 Identities=22% Similarity=0.230 Sum_probs=49.2
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 60 YMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 60 ~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
.+|..+|.-+..... -..+++|+...|.+-++--|..|..+|...+++.+|++++.+||-.||+
T Consensus 3 ~~~~esvk~iAes~G--i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESLG--ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHTT-----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHcC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 367777766665554 3479999999999999999999999999999999999999999999985
No 36
>PLN00158 histone H2B; Provisional
Probab=97.17 E-value=0.0016 Score=53.38 Aligned_cols=66 Identities=15% Similarity=0.285 Sum_probs=59.7
Q ss_pred CchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 038325 61 MPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKL 127 (231)
Q Consensus 61 LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~L 127 (231)
--..-|.|++|++-| +..||..+...|.-.+..+..-|+.||...|.-.+|+||+..+|..|++-+
T Consensus 28 sy~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 28 TYKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred cHHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 345569999999997 678999999999999999999999999999999999999999999998754
No 37
>PTZ00463 histone H2B; Provisional
Probab=97.10 E-value=0.0021 Score=52.80 Aligned_cols=62 Identities=16% Similarity=0.378 Sum_probs=57.2
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 038325 65 NVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKL 127 (231)
Q Consensus 65 ~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~L 127 (231)
-|.|++|++-| +.-||..|...|.-.+.....-|+.||...|.-.+|+||+..+|..|++-+
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 48999999997 678999999999999999999999999999999999999999999998754
No 38
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=97.00 E-value=0.0021 Score=52.10 Aligned_cols=77 Identities=16% Similarity=0.211 Sum_probs=65.8
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHHHH
Q 038325 60 YMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYVEPLS 137 (231)
Q Consensus 60 ~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv~~Lk 137 (231)
.+|+|.|.|||...- |-.+|+.-.-....++.+.||..|-.+..+.++..+-|-|+.+.+..|.+.-+=-+|...+.
T Consensus 23 rFP~ar~KkIMQ~de-DiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~ 99 (113)
T COG5247 23 RFPIARLKKIMQLDE-DIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNME 99 (113)
T ss_pred cCCHHHHHHHHHhhh-hhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHH
Confidence 499999999998764 34589999999999999999999999999999999999999999999988655445554433
No 39
>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=96.97 E-value=0.003 Score=49.53 Aligned_cols=67 Identities=13% Similarity=0.195 Sum_probs=51.7
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-ccCcccHHHHHhhc
Q 038325 60 YMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRK-TITAEDVVWAMGKL 127 (231)
Q Consensus 60 ~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRK-TItaeDVL~ALe~L 127 (231)
.||++.|+|||...+. +..|+.....+|.-.+..||-.|-.+|.+++.+.+.. -|.+.|+-.|..+|
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 4999999999999993 4899999999999999999999999999998866543 79999999998775
No 40
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=96.85 E-value=0.0025 Score=52.76 Aligned_cols=68 Identities=15% Similarity=0.190 Sum_probs=60.1
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 57 QDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 57 ~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
..+.+|...|.||||..- -.+||+++|...+..|.+=.+..|+..|-..|+..++|-|.+.|+-.|+.
T Consensus 23 agl~fpvgrvkr~lk~~~-~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 23 AGLIFPVGRVKRLLKKGN-YRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred cCccccHHHHHHHHHcCc-cceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 456799999999999443 47899999999999999888888888888889999999999999999986
No 41
>smart00414 H2A Histone 2A.
Probab=96.72 E-value=0.0048 Score=49.49 Aligned_cols=68 Identities=12% Similarity=0.205 Sum_probs=59.6
Q ss_pred ccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 58 DQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 58 d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
.+.||.+.|.|+||+.-- ..||+..|..-|..|.+-+...|...|...|+..+++.|+++||..|+..
T Consensus 7 gL~fPVgRi~r~Lk~~~~-~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 7 GLQFPVGRIHRLLRKGTY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred CccCchHHHHHHHHcCcc-ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 567999999999999742 46999999999999888888888888888899999999999999999875
No 42
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.65 E-value=0.0035 Score=57.38 Aligned_cols=70 Identities=13% Similarity=0.281 Sum_probs=64.6
Q ss_pred ccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 56 EQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 56 e~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
..+..|-+-.|.-+|+.+- .+.+|-+|+.+.|.+.|..||..|+..|...|++.|..||-+.||...||+
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 4566788889999999995 478999999999999999999999999999999999999999999999995
No 43
>PLN00154 histone H2A; Provisional
Probab=96.40 E-value=0.0098 Score=50.00 Aligned_cols=68 Identities=13% Similarity=0.190 Sum_probs=57.4
Q ss_pred ccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 58 DQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 58 d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
.+.||.+.|.|++|+...-..||+..|..-|..+.+=+...|...|-..|...+++-|++.||..|+.
T Consensus 36 gL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred CccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 67899999999999986445799999999988877666666666677788899999999999999985
No 44
>PTZ00017 histone H2A; Provisional
Probab=96.09 E-value=0.013 Score=49.05 Aligned_cols=67 Identities=13% Similarity=0.183 Sum_probs=59.6
Q ss_pred ccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 58 DQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 58 d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
.+.||...|.|+||+.-- ..||+..|..-|..+.+-+...|...|-..|...+++-|+++||..|+.
T Consensus 25 gL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 678999999999998742 4699999999999998888888888888899999999999999999985
No 45
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=96.08 E-value=0.0045 Score=53.18 Aligned_cols=69 Identities=17% Similarity=0.266 Sum_probs=59.0
Q ss_pred ccccCCchhHHHHHHHhhCCCCcc-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 56 EQDQYMPIANVIRIMRRILPPHAK-ISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 56 e~d~~LPkA~I~RImK~aLP~~~r-ISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
..-..||.+.|..+||.. ++++ ..+|++.+|.+++..||.+|...++..+...+|||+.-.|+=.|++.
T Consensus 55 a~l~rLpL~rik~vvkl~--pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~ 124 (162)
T KOG1658|consen 55 ASLSRLPLARIKQVVKLD--PDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEA 124 (162)
T ss_pred hhhhhccHHHHHhhccCC--cchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccc
Confidence 344579999999999865 5776 66788999999999999999999999999999999998887766654
No 46
>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=95.99 E-value=0.009 Score=46.50 Aligned_cols=60 Identities=25% Similarity=0.321 Sum_probs=29.9
Q ss_pred HHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 66 I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
|..+|-.-. +...-..|...+|-+.+.+||..|+.+|.+.|...+++.|+.||++.+|+.
T Consensus 7 I~~mMy~fG-D~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 7 IRQMMYGFG-DVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp CHHHHHCTT-S-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHHcC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 344555444 456789999999999999999999999999999999999999999999985
No 47
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=95.88 E-value=0.027 Score=46.94 Aligned_cols=62 Identities=24% Similarity=0.378 Sum_probs=56.6
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 038325 65 NVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKL 127 (231)
Q Consensus 65 ~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~L 127 (231)
-|.|++|++-|+ .-|+.++...|.--+-.++.-|+.+|...+.-.+|.||+..+|..|+.-|
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 77999999999999999999999999999999999999999999987644
No 48
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=95.56 E-value=0.034 Score=46.54 Aligned_cols=68 Identities=13% Similarity=0.195 Sum_probs=53.9
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 57 QDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 57 ~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
..+.+|...|.|++|+. .-..+|+.+|...|.-|.+-.+..|+..|-..+..+++.-|+++||..|+.
T Consensus 24 agl~fPvgri~r~Lr~~-~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 24 AGLQFPVGRIHRLLRKG-RYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred cccccCHHHHHHHHHcc-chhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 46789999999999993 235689999999998766554555555555567778899999999999986
No 49
>PLN00157 histone H2A; Provisional
Probab=95.55 E-value=0.027 Score=47.18 Aligned_cols=67 Identities=9% Similarity=0.144 Sum_probs=58.3
Q ss_pred ccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 58 DQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 58 d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
.+.||...|.|++|+.-- ..||+..|..-|..+.+-.+..|...|-..|...+++-|+++||..|+.
T Consensus 24 gL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred CcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 678999999999999642 4699999999998888777777777788889999999999999999985
No 50
>PF15510 CENP-W: Centromere kinetochore component W
Probab=95.54 E-value=0.023 Score=45.38 Aligned_cols=66 Identities=20% Similarity=0.235 Sum_probs=54.8
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 60 YMPIANVIRIMRRILPPHAKISDDAKET--------------VQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 60 ~LPkA~I~RImK~aLP~~~rISkDAkea--------------IqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
.-|++.+.|++|+.-| ..++....-.+ +.--|-.||+-|+.||...+=+++-.||+.+||+.|-+
T Consensus 16 kaPrgfLkrv~Kr~Kp-hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaK 94 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKP-HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAAK 94 (102)
T ss_pred hCchHHHHHHHHhcCC-ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHH
Confidence 4799999999998876 66665544444 55567899999999999999999999999999999876
Q ss_pred h
Q 038325 126 K 126 (231)
Q Consensus 126 ~ 126 (231)
.
T Consensus 95 v 95 (102)
T PF15510_consen 95 V 95 (102)
T ss_pred H
Confidence 4
No 51
>PLN00153 histone H2A; Provisional
Probab=95.47 E-value=0.032 Score=46.56 Aligned_cols=67 Identities=10% Similarity=0.171 Sum_probs=58.5
Q ss_pred ccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 58 DQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 58 d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
.+.||...|.|++|+.-- ..||+..|..-|.-+.+-.+..|...|-..|...+++-|+++||..|+.
T Consensus 22 gL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred CcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 678999999999998653 4699999999998888877777777788889999999999999999985
No 52
>PLN00156 histone H2AX; Provisional
Probab=95.46 E-value=0.037 Score=46.74 Aligned_cols=67 Identities=9% Similarity=0.155 Sum_probs=56.9
Q ss_pred ccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 58 DQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 58 d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
.+.||...|.|+||+.-- ..||+..|...|.-|.+=....|...|-..|...+++-|+++||..|+.
T Consensus 27 gL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred CcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 678999999999999742 4699999999998887766666666777788899999999999999985
No 53
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=94.93 E-value=0.029 Score=49.72 Aligned_cols=70 Identities=13% Similarity=0.197 Sum_probs=60.4
Q ss_pred cCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-ccCcccHHHHHhhcCCC
Q 038325 59 QYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRK-TITAEDVVWAMGKLGFD 130 (231)
Q Consensus 59 ~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRK-TItaeDVL~ALe~LGF~ 130 (231)
..||++.|.|||..... -.|+.-+..+|+-.+.+||-.|--+|.++|..-+.. -|.+.||-.|..+|...
T Consensus 111 s~f~Ka~iKkL~~~itg--~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~q 181 (195)
T KOG3219|consen 111 SAFPKAQIKKLMSSITG--QSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQ 181 (195)
T ss_pred hcCCHHHHHHHHHHHhC--CccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhc
Confidence 45999999999999984 339999999999999999999999999999877653 58888988888777654
No 54
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=94.91 E-value=0.37 Score=37.69 Aligned_cols=60 Identities=18% Similarity=0.298 Sum_probs=49.2
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 65 NVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 65 ~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
-|..+|-.-. +...-..|...+|-+.+.+||.-|+.+|.+.+. .+|.-|+.||++.+|..
T Consensus 7 ei~~mmy~~G-D~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~ 66 (92)
T cd07978 7 EIRQMMYGFG-DVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK 66 (92)
T ss_pred HHHHHHHHcC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence 4566666665 455688999999999999999999999999998 44444599999999964
No 55
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=94.66 E-value=0.15 Score=42.36 Aligned_cols=82 Identities=21% Similarity=0.228 Sum_probs=47.2
Q ss_pred ccCCchh--HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh-hcCCCcchH
Q 038325 58 DQYMPIA--NVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG-KLGFDNYVE 134 (231)
Q Consensus 58 d~~LPkA--~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe-~LGF~dYv~ 134 (231)
.-.+|+. .|.-|+|+.. -......+...|.+.+-.|+.-|...|..++.+.+|++|+.+||.-|++ ++++.-...
T Consensus 8 ~~~~PrDa~~i~~iL~~~G--v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~p 85 (129)
T PF02291_consen 8 SKSLPRDARVIHLILKSMG--VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQP 85 (129)
T ss_dssp -----HHHHHHHHHHHHTT-----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT--------
T ss_pred CccCChHHHHHHHHHHHcC--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccCC
Confidence 3456663 3444455443 2357778889999999999999999999999999999999999999999 667765555
Q ss_pred HHHHHHH
Q 038325 135 PLSIFLN 141 (231)
Q Consensus 135 ~Lk~~L~ 141 (231)
+-+++|-
T Consensus 86 ppre~ll 92 (129)
T PF02291_consen 86 PPREFLL 92 (129)
T ss_dssp -------
T ss_pred CChHHHH
Confidence 5556554
No 56
>PTZ00252 histone H2A; Provisional
Probab=93.13 E-value=0.28 Score=41.28 Aligned_cols=67 Identities=13% Similarity=0.151 Sum_probs=49.0
Q ss_pred ccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCcccHHHHHh
Q 038325 58 DQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHR--EQRKTITAEDVVWAMG 125 (231)
Q Consensus 58 d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~--~kRKTItaeDVL~ALe 125 (231)
.+.||...|.|++|+.-- ..||+.-|..-|..+.+=....|...|...|.. .+++-|+++||..|+.
T Consensus 23 GL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred CccCchHHHHHHHHcCCc-ccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 678999999999998864 468999998888766543333333334444433 5778899999999975
No 57
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=93.11 E-value=0.45 Score=45.00 Aligned_cols=77 Identities=22% Similarity=0.254 Sum_probs=66.0
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHHHHHHHHHHH
Q 038325 65 NVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYVEPLSIFLNRFR 144 (231)
Q Consensus 65 ~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv~~Lk~~L~~yR 144 (231)
.|..|.+..+= -.|++-|++.|.+.+..+|.-|...+...|+..||-..|.-||...|-+||+. +..|..+++++.
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 44555555542 24999999999999999999999999999999999999999999999999997 678888887665
Q ss_pred H
Q 038325 145 D 145 (231)
Q Consensus 145 e 145 (231)
.
T Consensus 86 ~ 86 (323)
T KOG4336|consen 86 F 86 (323)
T ss_pred c
Confidence 5
No 58
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=91.69 E-value=0.85 Score=39.94 Aligned_cols=70 Identities=19% Similarity=0.234 Sum_probs=56.9
Q ss_pred cCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--------------CCccCcccHHHHH
Q 038325 59 QYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQ--------------RKTITAEDVVWAM 124 (231)
Q Consensus 59 ~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~k--------------RKTItaeDVL~AL 124 (231)
-.||-+.+.-.++.+. -...-.-.+-+|.-++-.||+-|+..|.+.|+-.. |-|++-||+..||
T Consensus 85 P~IPDavt~~yL~~aG--f~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL 162 (176)
T KOG3423|consen 85 PTIPDAVTDHYLKKAG--FQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPAL 162 (176)
T ss_pred CCCcHHHHHHHHHhcC--CCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHH
Confidence 3589999999999885 22344556778889999999999999999997443 4489999999999
Q ss_pred hhcCCC
Q 038325 125 GKLGFD 130 (231)
Q Consensus 125 e~LGF~ 130 (231)
++-|..
T Consensus 163 ~EyGin 168 (176)
T KOG3423|consen 163 AEYGIN 168 (176)
T ss_pred HHhCcc
Confidence 998874
No 59
>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=89.67 E-value=1 Score=38.69 Aligned_cols=70 Identities=13% Similarity=0.209 Sum_probs=55.3
Q ss_pred CchhHHHHHHHhhC-----CCCcccCHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 038325 61 MPIANVIRIMRRIL-----PPHAKISDDAKETVQECVSE---YISFITGEANERCHREQRKTITAEDVVWAMGKLGFD 130 (231)
Q Consensus 61 LPkA~I~RImK~aL-----P~~~rISkDAkeaIqecase---FI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~ 130 (231)
|....+..++...+ .....+++++.+.|.+.+.- .|+.+...|...+-..+.++|+.++|..++.++.|+
T Consensus 192 l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~~ 269 (269)
T TIGR03015 192 LDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDFE 269 (269)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhcC
Confidence 44455656555443 12356999999999998875 799999999999888899999999999999998753
No 60
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=89.49 E-value=1.3 Score=44.91 Aligned_cols=65 Identities=23% Similarity=0.288 Sum_probs=54.4
Q ss_pred hhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCC
Q 038325 63 IANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGF 129 (231)
Q Consensus 63 kA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF 129 (231)
+-.+ +.|-+.+ .-..|++|+..+|.+-++.=|..|..+|.+.-.+.||.+++.+||-.||+.+.-
T Consensus 14 ~Es~-k~vAEsl-Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nV 78 (576)
T KOG2549|consen 14 KESV-KVVAESL-GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNV 78 (576)
T ss_pred HHHH-HHHHHHh-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhccc
Confidence 4444 4555555 134599999999999999999999999999999999999999999999996543
No 61
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=85.97 E-value=6.5 Score=33.76 Aligned_cols=62 Identities=21% Similarity=0.220 Sum_probs=50.3
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchH-HHHHHHH
Q 038325 80 ISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYVE-PLSIFLN 141 (231)
Q Consensus 80 ISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv~-~Lk~~L~ 141 (231)
...-....|-+.+=.|+.-|...|.-++.+.++.||.+|||..|+....=-.|.. +=+++|-
T Consensus 31 yEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL 93 (148)
T KOG3334|consen 31 YEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLL 93 (148)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHH
Confidence 4555666777888888888999999999999999999999999999877777776 4444443
No 62
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=85.43 E-value=3.4 Score=37.80 Aligned_cols=69 Identities=16% Similarity=0.189 Sum_probs=50.4
Q ss_pred hhHHHHHHHhhCCC---CcccCHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCc
Q 038325 63 IANVIRIMRRILPP---HAKISDDAKETVQECV------SEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDN 131 (231)
Q Consensus 63 kA~I~RImK~aLP~---~~rISkDAkeaIqeca------seFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~d 131 (231)
...+..|++..+-. ...++.++.+.+.+.+ -..+..+...|.+.|...++.+|+.+||..|++++....
T Consensus 209 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~ 286 (394)
T PRK00411 209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVH 286 (394)
T ss_pred HHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHH
Confidence 45566666654421 2358999998888777 334556667888889999999999999999999884433
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=82.82 E-value=4.7 Score=36.45 Aligned_cols=74 Identities=16% Similarity=0.115 Sum_probs=50.6
Q ss_pred hhHHHHHHHhhCC---CCcccCHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcch
Q 038325 63 IANVIRIMRRILP---PHAKISDDAKETVQECVS------EYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYV 133 (231)
Q Consensus 63 kA~I~RImK~aLP---~~~rISkDAkeaIqecas------eFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv 133 (231)
...+..|++..+. ....+++|+.+.+.+.+. ..+..+...|.+.|..+++.+|+.+||..|++.+....+.
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 4446666665542 123488888877766443 3444566678888988999999999999999988544444
Q ss_pred HHH
Q 038325 134 EPL 136 (231)
Q Consensus 134 ~~L 136 (231)
..+
T Consensus 281 ~~i 283 (365)
T TIGR02928 281 ELI 283 (365)
T ss_pred HHH
Confidence 333
No 64
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=76.96 E-value=5.7 Score=38.26 Aligned_cols=72 Identities=17% Similarity=0.192 Sum_probs=60.3
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 038325 57 QDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFD 130 (231)
Q Consensus 57 ~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~ 130 (231)
-.+.|-+..|..|+....=. ....-|.+.|+-.+..||+-|+..|..+....+|--.+..||+.||++|+..
T Consensus 26 ya~sla~~avaQIcqslg~~--~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 26 YAFSLARVAVAQICQSLGYS--STQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHHHHhcCCc--ccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 34457778888888777533 3444499999999999999999999999999999999999999999987654
No 65
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=76.63 E-value=6.7 Score=38.84 Aligned_cols=67 Identities=21% Similarity=0.196 Sum_probs=46.0
Q ss_pred hhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHH--HHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCC
Q 038325 63 IANVIRIMRRILP-PHAKISDDAKETVQECVSE--YISFITGEANERCHREQRKTITAEDVVWAMGKLGF 129 (231)
Q Consensus 63 kA~I~RImK~aLP-~~~rISkDAkeaIqecase--FI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF 129 (231)
...+.+|++..+. .++.|++++.+.|.+.+.. .+..+...|...|..++|++|+.+||.|++..-.|
T Consensus 265 ~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~~~~ 334 (531)
T TIGR02902 265 DEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAENGNY 334 (531)
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCCccc
Confidence 4456666666653 2467999999988776652 12233345566788889999999999999765433
No 66
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=72.34 E-value=14 Score=36.85 Aligned_cols=49 Identities=27% Similarity=0.263 Sum_probs=38.0
Q ss_pred ccCHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 038325 79 KISDDAKETVQECVSE-----------YISFITGEANERCHREQRKTITAEDVVWAMGKL 127 (231)
Q Consensus 79 rISkDAkeaIqecase-----------FI~~LTseAne~c~~~kRKTItaeDVL~ALe~L 127 (231)
-++.+|...|-+.+.. -|.-|..+|+..|+.+++++|+++||..|++.-
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 4788888777776543 567777999999999999999999999999864
No 67
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=70.46 E-value=15 Score=37.23 Aligned_cols=50 Identities=18% Similarity=0.136 Sum_probs=40.3
Q ss_pred ccCHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcC
Q 038325 79 KISDDAKETVQECVS-------------EYISFITGEANERCHREQRKTITAEDVVWAMGKLG 128 (231)
Q Consensus 79 rISkDAkeaIqecas-------------eFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LG 128 (231)
.++++|.+.|.+-++ .=|.-|..+|..+|..+++.+|+.+||..|++.-.
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 699999998876544 34556677888899999999999999999988543
No 68
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=69.49 E-value=9.6 Score=37.00 Aligned_cols=54 Identities=22% Similarity=0.306 Sum_probs=49.5
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 038325 77 HAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFD 130 (231)
Q Consensus 77 ~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~ 130 (231)
-..|.+|+..+|..-.+-=|..+..+|...-.+.||..++-+||-.||..|..+
T Consensus 20 i~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 20 ISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred CcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 346999999999999999999999999999999999999999999999987654
No 69
>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=69.29 E-value=24 Score=30.85 Aligned_cols=78 Identities=12% Similarity=0.153 Sum_probs=57.3
Q ss_pred ccccCCchhHHHHHHHhhCCCC-c-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCccCcccHHHHHhhc
Q 038325 56 EQDQYMPIANVIRIMRRILPPH-A-KISDDAKETVQECVSEYISFITGEANERCHRE------QRKTITAEDVVWAMGKL 127 (231)
Q Consensus 56 e~d~~LPkA~I~RImK~aLP~~-~-rISkDAkeaIqecaseFI~~LTseAne~c~~~------kRKTItaeDVL~ALe~L 127 (231)
.+..+|....|.+.|...+... . .|+.|+...|.-||.+++..|.......|++- ...++--.||-.-|..|
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 3445677777777666665432 2 79999999999999999999999999988764 33566677887777665
Q ss_pred CCCcch
Q 038325 128 GFDNYV 133 (231)
Q Consensus 128 GF~dYv 133 (231)
.--+-.
T Consensus 120 ~~~ek~ 125 (212)
T cd08045 120 EQLERE 125 (212)
T ss_pred HHHHHH
Confidence 544333
No 70
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=67.06 E-value=4.7 Score=41.42 Aligned_cols=48 Identities=33% Similarity=0.337 Sum_probs=36.2
Q ss_pred ccCHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 79 KISDDAKETVQECVSEY-------------ISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 79 rISkDAkeaIqecaseF-------------I~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
-++++|...|.+-+..- |--|-.+|.++|..++++-|+++||.+|++.
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHh
Confidence 47777776665544432 3334459999999999999999999999987
No 71
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=62.77 E-value=29 Score=33.94 Aligned_cols=50 Identities=14% Similarity=0.266 Sum_probs=42.5
Q ss_pred CCcccCHHHHHHHHHHHH----HHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 76 PHAKISDDAKETVQECVS----EYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 76 ~~~rISkDAkeaIqecas----eFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
+++.++.||++.|.+... .|-..|.+.|+..|.+.|-+++..+||-.+.+
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 578999999999887654 36667777899999999999999999999865
No 72
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=55.65 E-value=67 Score=28.53 Aligned_cols=69 Identities=13% Similarity=0.167 Sum_probs=47.0
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------------------c----------
Q 038325 60 YMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHR-------------------E---------- 110 (231)
Q Consensus 60 ~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~-------------------~---------- 110 (231)
.||-+.+.=.|.++. -.....-.+.+|.-.+..||+-|+-.|.++.+= .
T Consensus 88 liPd~v~DYyl~k~G--f~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~ 165 (197)
T COG5162 88 LIPDSVTDYYLEKAG--FVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGR 165 (197)
T ss_pred CccHHHHHHHHHhcC--ceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhccccccccccc
Confidence 355555554444443 123445567888889999999999888775321 0
Q ss_pred ----CCCccCcccHHHHHhhcCCC
Q 038325 111 ----QRKTITAEDVVWAMGKLGFD 130 (231)
Q Consensus 111 ----kRKTItaeDVL~ALe~LGF~ 130 (231)
++-+++..|+-.||++.|+.
T Consensus 166 ~~dr~K~vltv~DLs~Al~EyGin 189 (197)
T COG5162 166 RGDRKKPVLTVVDLSKALEEYGIN 189 (197)
T ss_pred ccccCCceeeehHHHHHHHHhccc
Confidence 45578999999999988864
No 73
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=55.63 E-value=37 Score=26.30 Aligned_cols=48 Identities=21% Similarity=0.232 Sum_probs=39.5
Q ss_pred cccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 78 AKISDDAKETVQECVSEY------ISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 78 ~rISkDAkeaIqecaseF------I~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
..+++++...|..++..| +.-|..-|..+|--++...|+.+||..||.
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 445667789999999999999999999985
No 74
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=54.72 E-value=31 Score=34.16 Aligned_cols=81 Identities=21% Similarity=0.232 Sum_probs=54.4
Q ss_pred chhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHHH
Q 038325 62 PIANVIRIMRRILP-PHAKISDDAKETVQECVSE----YISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYVEPL 136 (231)
Q Consensus 62 PkA~I~RImK~aLP-~~~rISkDAkeaIqecase----FI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv~~L 136 (231)
++.-|+-|++--.. +++.+++||.+.|....++ |..-|..-|..+|++.++++|..+||-.|-+- |.|-. .-
T Consensus 362 ~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~l--F~D~k-rS 438 (450)
T COG1224 362 SREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKEL--FLDVK-RS 438 (450)
T ss_pred CHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHH--HhhHH-HH
Confidence 44445555554332 4788999999999876554 45556667899999999999999999998442 22222 22
Q ss_pred HHHHHHHHH
Q 038325 137 SIFLNRFRD 145 (231)
Q Consensus 137 k~~L~~yRe 145 (231)
-+|++.|++
T Consensus 439 v~~v~~~~~ 447 (450)
T COG1224 439 VEYVEKYEG 447 (450)
T ss_pred HHHHHHHHh
Confidence 255666554
No 75
>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=54.61 E-value=17 Score=24.87 Aligned_cols=42 Identities=19% Similarity=0.172 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHH-HHHHhcCCCccCcccHHHH
Q 038325 81 SDDAKETVQECVSEYISFITGEAN-ERCHREQRKTITAEDVVWA 123 (231)
Q Consensus 81 SkDAkeaIqecaseFI~~LTseAn-e~c~~~kRKTItaeDVL~A 123 (231)
+.||...|.+. -.|+.--...+. ..|...|...||.++|..|
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 56777777774 567765444444 4888999999999998765
No 76
>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=54.00 E-value=79 Score=22.61 Aligned_cols=48 Identities=19% Similarity=0.147 Sum_probs=35.9
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038325 60 YMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHR 109 (231)
Q Consensus 60 ~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~ 109 (231)
.+|-+.+.-+++++.=+ .-..-.+-+|.=++..||+-|+..|.+.|+-
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 47888888888888621 1223345677888899999999999999863
No 77
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=49.46 E-value=66 Score=29.24 Aligned_cols=73 Identities=14% Similarity=0.180 Sum_probs=51.3
Q ss_pred CCchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcc
Q 038325 60 YMPIANVIRIMRRILP-PHAKISDDAKETVQECVSE---YISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNY 132 (231)
Q Consensus 60 ~LPkA~I~RImK~aLP-~~~rISkDAkeaIqecase---FI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dY 132 (231)
.++...+..|++...- .++.++.|+...|.+.+.- .+..+...+.+.+...+.+.|+.++|..+++.++.+..
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 3556666667765542 3578999999888876633 34445555666666666678999999999999877643
No 78
>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=47.89 E-value=88 Score=27.63 Aligned_cols=71 Identities=13% Similarity=0.128 Sum_probs=48.6
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCc
Q 038325 61 MPIANVIRIMRRILP-PHAKISDDAKETVQECVSE---YISFITGEANERCHREQRKTITAEDVVWAMGKLGFDN 131 (231)
Q Consensus 61 LPkA~I~RImK~aLP-~~~rISkDAkeaIqecase---FI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~d 131 (231)
++...+..|+++... ..+.++.|+.+.|.+.+.- ++.-+...+.+.+...+...|+.++|..++..++++.
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 455566666665542 2567999999888776532 3344455566666666667799999999999876653
No 79
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=47.68 E-value=80 Score=25.97 Aligned_cols=50 Identities=22% Similarity=0.296 Sum_probs=40.6
Q ss_pred CCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 74 LPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 74 LP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
..++..=-.|..++|-..+.+||..++..|.++. +|--+..||++.+|++
T Consensus 22 fGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRk 71 (109)
T KOG3901|consen 22 FGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRK 71 (109)
T ss_pred cCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHh
Confidence 3456666788999999999999999988777766 5556788999999984
No 80
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=47.50 E-value=30 Score=28.94 Aligned_cols=65 Identities=17% Similarity=0.273 Sum_probs=49.8
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC----CCccCcccHHHHHh
Q 038325 57 QDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQ----RKTITAEDVVWAMG 125 (231)
Q Consensus 57 ~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~k----RKTItaeDVL~ALe 125 (231)
..+.+|...|.|.+|.-...+.+|..-+..-. ...+.|||.|-.+.+.... -|-|++.|+..|+.
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 35679999999999999988888875554432 3346799999988877654 47899999887765
No 81
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=47.27 E-value=91 Score=26.02 Aligned_cols=49 Identities=22% Similarity=0.356 Sum_probs=42.3
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 76 PHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 76 ~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
+.+.=..|..++|.+.+..|++.+...|...|+ .|-.+..||...||++
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 566778899999999999999999999999988 4555688999999984
No 82
>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=46.28 E-value=17 Score=23.84 Aligned_cols=26 Identities=19% Similarity=0.190 Sum_probs=21.1
Q ss_pred HHHHHHhcCCCccCcccHHHHHhhcC
Q 038325 103 ANERCHREQRKTITAEDVVWAMGKLG 128 (231)
Q Consensus 103 Ane~c~~~kRKTItaeDVL~ALe~LG 128 (231)
|.+.|+..+...|+.+||+.||=+.+
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 83
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=45.49 E-value=64 Score=32.71 Aligned_cols=50 Identities=28% Similarity=0.308 Sum_probs=42.0
Q ss_pred CCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 76 PHAKISDDAKETVQECVSEYI-------SFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 76 ~~~rISkDAkeaIqecaseFI-------~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
+.+.|+.++++.|.+.+..+- .++...|...|.-++|.+|+.+||..|++
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 468899999999988887762 45667788889999999999999999876
No 84
>PRK09862 putative ATP-dependent protease; Provisional
Probab=45.25 E-value=62 Score=32.41 Aligned_cols=57 Identities=14% Similarity=0.121 Sum_probs=44.5
Q ss_pred cccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchH
Q 038325 78 AKISDDAKETVQECVSEY------ISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYVE 134 (231)
Q Consensus 78 ~rISkDAkeaIqecaseF------I~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv~ 134 (231)
+.+++++...+.+++..+ ...|..-|..+|--++|..|+.+||..||.--+++...-
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 467888888877765544 566778889999999999999999999998666554433
No 85
>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=44.12 E-value=82 Score=29.71 Aligned_cols=54 Identities=22% Similarity=0.235 Sum_probs=40.4
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 71 RRILPPHAKISDDAKETVQECVSEYI-------SFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 71 K~aLP~~~rISkDAkeaIqecaseFI-------~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
++.+ +.+.|+++.++.|.+.+..+= .++...|...|--++|..|+.+||..+..
T Consensus 247 ~~~~-~~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 247 QNLL-PQVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred HHHh-ccCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 4445 378899999888888766542 34556777788888999999999987754
No 86
>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=42.33 E-value=28 Score=24.73 Aligned_cols=30 Identities=17% Similarity=0.371 Sum_probs=24.3
Q ss_pred CCCccCcccHHHHHhhcCCCcchHHHHHHH
Q 038325 111 QRKTITAEDVVWAMGKLGFDNYVEPLSIFL 140 (231)
Q Consensus 111 kRKTItaeDVL~ALe~LGF~dYv~~Lk~~L 140 (231)
....-+..+++.||+++|..+-++.|+.+|
T Consensus 54 ~~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 54 EGPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp HGSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred cCCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 344557889999999999999998888765
No 87
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=41.95 E-value=55 Score=28.98 Aligned_cols=71 Identities=15% Similarity=0.150 Sum_probs=43.7
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcch
Q 038325 61 MPIANVIRIMRRILP-PHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYV 133 (231)
Q Consensus 61 LPkA~I~RImK~aLP-~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv 133 (231)
++...+..++++.+. .++.++.++.+.|.+.+.-=+..+.......|. +.++|+.+||..++.....++-+
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 444566666666543 356799999999888774333333333333342 23479999999988865544433
No 88
>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=41.76 E-value=41 Score=27.02 Aligned_cols=34 Identities=9% Similarity=0.204 Sum_probs=27.5
Q ss_pred hHHHHHHHhhCC----CCcccCHHHHHHHHHHHHHHHH
Q 038325 64 ANVIRIMRRILP----PHAKISDDAKETVQECVSEYIS 97 (231)
Q Consensus 64 A~I~RImK~aLP----~~~rISkDAkeaIqecaseFI~ 97 (231)
++|.+|+|+.|= |+..++.++.+.|+++++.|-.
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 567789999883 5678999999999999998753
No 89
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=41.56 E-value=52 Score=33.45 Aligned_cols=59 Identities=14% Similarity=0.112 Sum_probs=47.8
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 65 NVIRIMRRILPPHAKISDDAKETVQECVSEYI-------SFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 65 ~I~RImK~aLP~~~rISkDAkeaIqecaseFI-------~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
.|.+.- +.++ ++.|+.+....+.++|..|- .+|...|..+|-=++|..|+.+||..|+.
T Consensus 183 ~I~~AR-~rl~-~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 183 DIAAAR-ARLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHHHHH-HHHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 444433 3454 89999999999888888774 47778899999999999999999999987
No 90
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=41.53 E-value=37 Score=25.53 Aligned_cols=34 Identities=24% Similarity=0.306 Sum_probs=29.0
Q ss_pred cccHHHHHhhcCC------CcchHHHHHHHHHHHHHHHHH
Q 038325 117 AEDVVWAMGKLGF------DNYVEPLSIFLNRFRDSEHER 150 (231)
Q Consensus 117 aeDVL~ALe~LGF------~dYv~~Lk~~L~~yRe~~~~r 150 (231)
++.|..+|.+||| ..+-+.++..|..|..+++--
T Consensus 18 ~~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~ENfE 57 (74)
T PF08823_consen 18 AREVQEALKRLGYYKGEADGVWDEATEDALRAWAGTENFE 57 (74)
T ss_pred HHHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhhHH
Confidence 3567889999999 678899999999999988753
No 91
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=41.36 E-value=1.2e+02 Score=26.49 Aligned_cols=66 Identities=23% Similarity=0.150 Sum_probs=46.1
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 61 MPIANVIRIMRRILP-PHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 61 LPkA~I~RImK~aLP-~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
+....+.+++++.+. .+.+|+.++...|.+.+..=+..+..+-...|.-.+.++|+.+||...+..
T Consensus 111 ~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~ 177 (302)
T TIGR01128 111 PKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSD 177 (302)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhh
Confidence 556666666666553 357899999999988877555566666666555444457999999877663
No 92
>smart00350 MCM minichromosome maintenance proteins.
Probab=37.69 E-value=1.3e+02 Score=29.60 Aligned_cols=69 Identities=13% Similarity=0.106 Sum_probs=47.7
Q ss_pred cCCchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHHhcCCCccCcc
Q 038325 59 QYMPIANVIRIMRRILP-PHAKISDDAKETVQECVSE-------------------YISFITGEANERCHREQRKTITAE 118 (231)
Q Consensus 59 ~~LPkA~I~RImK~aLP-~~~rISkDAkeaIqecase-------------------FI~~LTseAne~c~~~kRKTItae 118 (231)
..++...+.+.+.-+=- -..+|++++.+.|.+...+ .+..|...|-..|+-..|.+|+.+
T Consensus 416 ~~~~~~~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~ 495 (509)
T smart00350 416 VPISQEFLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEA 495 (509)
T ss_pred ccCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHH
Confidence 35777777776644421 0125899999888664433 235566677778888999999999
Q ss_pred cHHHHHhhc
Q 038325 119 DVVWAMGKL 127 (231)
Q Consensus 119 DVL~ALe~L 127 (231)
||..|++-+
T Consensus 496 Dv~~ai~l~ 504 (509)
T smart00350 496 DVEEAIRLL 504 (509)
T ss_pred HHHHHHHHH
Confidence 999997643
No 93
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=37.39 E-value=64 Score=35.55 Aligned_cols=36 Identities=22% Similarity=0.232 Sum_probs=22.9
Q ss_pred CCCCCCCCCCCCcccCCCCCCCCCc-------ccccccCCCCC
Q 038325 172 LFGLPPGPFGPVFNMGPQQGVFDPS-------IGGFLREGSGS 207 (231)
Q Consensus 172 ~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~ 207 (231)
++|...+.|.+.+-+|-++|.++.. -||||+.++++
T Consensus 1207 GYGgsa~~~~~~~Gagvg~GyrGvsrgGfrnnggGdyrnpggg 1249 (1282)
T KOG0921|consen 1207 GYGGSAPSARANYGAGVGNGYRGVSRGGFRNNGGGDYRNPGGG 1249 (1282)
T ss_pred CCCCCCCCCCCCccccccCCCccccCCccccCCCCCCCCCCCC
Confidence 3444455666788888888887753 35566666443
No 94
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=36.18 E-value=55 Score=33.69 Aligned_cols=48 Identities=21% Similarity=0.133 Sum_probs=38.8
Q ss_pred ccCHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 79 KISDDAKETVQECVSEY-------------ISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 79 rISkDAkeaIqecaseF-------------I~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
.|+++|...|-+-++.- |.-|..+|..+|+.++++.|+++||..|+..
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 69999998887765522 3337788999999999999999999999843
No 95
>COG1331 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]
Probab=35.85 E-value=45 Score=34.80 Aligned_cols=16 Identities=38% Similarity=0.769 Sum_probs=13.4
Q ss_pred CCCCCCCcccccccCC
Q 038325 189 QQGVFDPSIGGFLREG 204 (231)
Q Consensus 189 ~~~~~~~~~~~~~~~~ 204 (231)
.+|+||..-|||||=.
T Consensus 243 ~GGIyDhlgGGF~RYS 258 (667)
T COG1331 243 RGGIYDHLGGGFFRYS 258 (667)
T ss_pred ccCCccccCCceeeee
Confidence 4699999999999864
No 96
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=35.37 E-value=1.1e+02 Score=28.99 Aligned_cols=53 Identities=11% Similarity=0.026 Sum_probs=41.9
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcccHHHHH
Q 038325 71 RRILPPHAKISDDAKETVQECVSEYI-------SFITGEANERCHREQRKTITAEDVVWAM 124 (231)
Q Consensus 71 K~aLP~~~rISkDAkeaIqecaseFI-------~~LTseAne~c~~~kRKTItaeDVL~AL 124 (231)
++.+ +.+.|+++.+..|.+.+..+= .+|...|...|--++|..|+.+||..+.
T Consensus 244 ~~~~-~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 244 RARL-PQLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred HHhc-CCcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 3444 378899999999988887764 2467778888999999999999996554
No 97
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=35.27 E-value=84 Score=28.22 Aligned_cols=65 Identities=18% Similarity=0.192 Sum_probs=46.8
Q ss_pred HHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCcccHHHHHhhcCCC
Q 038325 66 VIRIMRRILP-PHAKISDDAKETVQECVSEYISFITGEANERCHR--EQRKTITAEDVVWAMGKLGFD 130 (231)
Q Consensus 66 I~RImK~aLP-~~~rISkDAkeaIqecaseFI~~LTseAne~c~~--~kRKTItaeDVL~ALe~LGF~ 130 (231)
+.++|++.+- .+.+|+.+|...|.+++..=+..+..|-...|.- .++++|+.+||...+....+.
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 3678999999999999887566666666666665 457889999999988776644
No 98
>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=34.76 E-value=54 Score=27.23 Aligned_cols=38 Identities=24% Similarity=0.247 Sum_probs=29.4
Q ss_pred CccCcccHHHHHhhcCCCc-----------chHHHHHHHHHHHHHHHHH
Q 038325 113 KTITAEDVVWAMGKLGFDN-----------YVEPLSIFLNRFRDSEHER 150 (231)
Q Consensus 113 KTItaeDVL~ALe~LGF~d-----------Yv~~Lk~~L~~yRe~~~~r 150 (231)
.|...+|++.+|+++|++. |++.+.+..++-++.++.|
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 3668899999999999974 6666777777767766666
No 99
>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=34.72 E-value=31 Score=25.85 Aligned_cols=49 Identities=22% Similarity=0.291 Sum_probs=25.9
Q ss_pred CcccCHHHHHHHHHHHHH-------HHHHHHHHHHHHHH-hcCCCccCcccHHHHHh
Q 038325 77 HAKISDDAKETVQECVSE-------YISFITGEANERCH-REQRKTITAEDVVWAMG 125 (231)
Q Consensus 77 ~~rISkDAkeaIqecase-------FI~~LTseAne~c~-~~kRKTItaeDVL~ALe 125 (231)
++||+.+.++.|.+++.. ||.-.+.++.+... ....-+++.+|.-.-++
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~ 59 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMA 59 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHH
Confidence 478999999999999754 44444433333222 22334555555443333
No 100
>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=34.71 E-value=55 Score=29.42 Aligned_cols=76 Identities=11% Similarity=0.113 Sum_probs=34.9
Q ss_pred ccccCCchhHHHHHHHhhCCC--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CccCcccHHHHHhhc
Q 038325 56 EQDQYMPIANVIRIMRRILPP--HAKISDDAKETVQECVSEYISFITGEANERCHREQR------KTITAEDVVWAMGKL 127 (231)
Q Consensus 56 e~d~~LPkA~I~RImK~aLP~--~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kR------KTItaeDVL~ALe~L 127 (231)
.++.+|-...+.+-|.+.... ...|..|...+|.-||++.|..|...+..+|++-.. .+....||-..|..|
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 556678888888777776633 357999999999999999999999999998875422 133466776666655
Q ss_pred CCCc
Q 038325 128 GFDN 131 (231)
Q Consensus 128 GF~d 131 (231)
.-.+
T Consensus 119 ~~~e 122 (264)
T PF05236_consen 119 EQLE 122 (264)
T ss_dssp ----
T ss_pred HHHH
Confidence 4433
No 101
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=34.63 E-value=3.8e+02 Score=27.34 Aligned_cols=13 Identities=15% Similarity=0.353 Sum_probs=5.7
Q ss_pred CchhHHHHHHHhh
Q 038325 61 MPIANVIRIMRRI 73 (231)
Q Consensus 61 LPkA~I~RImK~a 73 (231)
|....|.++.+..
T Consensus 512 ls~~~i~~~~~~~ 524 (653)
T PTZ00009 512 LSKADIDRMVNEA 524 (653)
T ss_pred ccHHHHHHHHHHH
Confidence 4444444444443
No 102
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=34.39 E-value=1.2e+02 Score=29.06 Aligned_cols=54 Identities=20% Similarity=0.280 Sum_probs=43.4
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 71 RRILPPHAKISDDAKETVQECVSEYI-------SFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 71 K~aLP~~~rISkDAkeaIqecaseFI-------~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
++.++ .+.|+++.+..|.+.|..+= .++...|...|--++|..|+++||..+..
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 44453 68899999999888887763 35667778888899999999999998865
No 103
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=33.95 E-value=84 Score=31.27 Aligned_cols=48 Identities=17% Similarity=0.169 Sum_probs=41.1
Q ss_pred cccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 78 AKISDDAKETVQECVSEY------ISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 78 ~rISkDAkeaIqecaseF------I~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
..++++++..|.+++..| .+-|..-|..+|.=+++..|+.+||..||.
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 357889999999888876 556777899999999999999999999985
No 104
>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=33.53 E-value=85 Score=21.43 Aligned_cols=31 Identities=19% Similarity=0.392 Sum_probs=25.9
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHH
Q 038325 60 YMPIANVIRIMRRILPPHAKISDDAKETVQECVSE 94 (231)
Q Consensus 60 ~LPkA~I~RImK~aLP~~~rISkDAkeaIqecase 94 (231)
.+-+++|.|++... -+||.+.++.|.+++.+
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 46778898888776 48999999999998876
No 105
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=32.05 E-value=1.3e+02 Score=28.69 Aligned_cols=72 Identities=21% Similarity=0.208 Sum_probs=48.7
Q ss_pred hHHHHHHHhhCC---CCcccCHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchH
Q 038325 64 ANVIRIMRRILP---PHAKISDDAKETVQECV------SEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYVE 134 (231)
Q Consensus 64 A~I~RImK~aLP---~~~rISkDAkeaIqeca------seFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv~ 134 (231)
.-|.-|+++-.- ....++.++.+.+..-+ ..+..-|...|.++|+++++.+|+.+||..|-++.+..-+.+
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 345556555442 13457777766665322 234456777899999999999999999999977776664444
Q ss_pred H
Q 038325 135 P 135 (231)
Q Consensus 135 ~ 135 (231)
.
T Consensus 273 ~ 273 (366)
T COG1474 273 V 273 (366)
T ss_pred H
Confidence 4
No 106
>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=31.79 E-value=1.3e+02 Score=30.35 Aligned_cols=55 Identities=22% Similarity=0.290 Sum_probs=39.7
Q ss_pred HHhhCCCCcccCHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 70 MRRILPPHAKISDDAKETVQECVSEY-------ISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 70 mK~aLP~~~rISkDAkeaIqecaseF-------I~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
+++.++ .+.|+++..+.|.+.+..+ -.++...|...|.-++|.+|+.+||..|+.
T Consensus 195 ar~~~~-~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 195 ARELLP-QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred HHHhcC-CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 344443 6889999987777666443 124456667778888999999999999876
No 107
>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=31.35 E-value=3.3e+02 Score=23.13 Aligned_cols=53 Identities=17% Similarity=0.215 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCC-cchHHHHHHHHHHHHHHHHH
Q 038325 91 CVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFD-NYVEPLSIFLNRFRDSEHER 150 (231)
Q Consensus 91 caseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~-dYv~~Lk~~L~~yRe~~~~r 150 (231)
.+-+.+.||..+|.. .-++.+++..-|+.|||+ +.++.+...+..+|+.....
T Consensus 43 ~~va~l~fiL~~A~k-------~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l~~~ 96 (174)
T cd04752 43 ASIAVLSFILSSAAK-------YNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKLQES 96 (174)
T ss_pred HHHHHHHHHHHHHHH-------cCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 345556666666543 348999999999999998 56666666666666655543
No 108
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=31.20 E-value=52 Score=32.99 Aligned_cols=44 Identities=16% Similarity=0.262 Sum_probs=33.9
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc
Q 038325 71 RRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKT 114 (231)
Q Consensus 71 K~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKT 114 (231)
|+++-+.--|-+|.+.||++||...=.||...-...-+++++++
T Consensus 426 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~ 469 (488)
T TIGR01052 426 KQSVADIPEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT 469 (488)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444445689999999999999999999987666666666555
No 109
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=30.39 E-value=54 Score=32.13 Aligned_cols=32 Identities=34% Similarity=0.286 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 038325 96 ISFITGEANERCHREQRKTITAEDVVWAMGKL 127 (231)
Q Consensus 96 I~~LTseAne~c~~~kRKTItaeDVL~ALe~L 127 (231)
|..|..+|...|.+++|..|+.+||..|+++.
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v 424 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEKV 424 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence 55677889999999999999999999998863
No 110
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=30.39 E-value=37 Score=29.55 Aligned_cols=37 Identities=11% Similarity=0.248 Sum_probs=28.5
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHH
Q 038325 60 YMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITG 101 (231)
Q Consensus 60 ~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTs 101 (231)
.+-+++|.|.+... -+||++.++.|.+++++. .|.-.
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 35678999998653 479999999999999874 45443
No 111
>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=29.53 E-value=66 Score=26.69 Aligned_cols=40 Identities=23% Similarity=0.329 Sum_probs=31.4
Q ss_pred CccCcccHHHHHhhcCCCc------------chHHHHHHHHHHHHHHHHHhh
Q 038325 113 KTITAEDVVWAMGKLGFDN------------YVEPLSIFLNRFRDSEHERTA 152 (231)
Q Consensus 113 KTItaeDVL~ALe~LGF~d------------Yv~~Lk~~L~~yRe~~~~rk~ 152 (231)
.|.+.+|++.+|+.++++. |++.+.+.+++-++.++.|..
T Consensus 123 ~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A~~~Rg~ 174 (224)
T PF02361_consen 123 LTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREAQRLRGV 174 (224)
T ss_pred HHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 4779999999999999987 677777777777776666654
No 112
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=27.96 E-value=67 Score=29.71 Aligned_cols=33 Identities=30% Similarity=0.337 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 038325 95 YISFITGEANERCHREQRKTITAEDVVWAMGKL 127 (231)
Q Consensus 95 FI~~LTseAne~c~~~kRKTItaeDVL~ALe~L 127 (231)
-|..|..+|...|.+.+|..|+.+|+..|+++.
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~~ 363 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEKV 363 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHh
Confidence 355677788888999999999999999999863
No 113
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=27.90 E-value=66 Score=30.45 Aligned_cols=34 Identities=29% Similarity=0.295 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcC
Q 038325 95 YISFITGEANERCHREQRKTITAEDVVWAMGKLG 128 (231)
Q Consensus 95 FI~~LTseAne~c~~~kRKTItaeDVL~ALe~LG 128 (231)
=|..|..+|...|.+++++.|+.+|+..|+++.-
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~ 373 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVM 373 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence 3556777888888899999999999999988653
No 114
>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=27.71 E-value=52 Score=22.64 Aligned_cols=25 Identities=28% Similarity=0.441 Sum_probs=20.5
Q ss_pred ccCcccHHHHHhhcCCCcchHHHHH
Q 038325 114 TITAEDVVWAMGKLGFDNYVEPLSI 138 (231)
Q Consensus 114 TItaeDVL~ALe~LGF~dYv~~Lk~ 138 (231)
+=+.+||..-|+.+||++|.+.++.
T Consensus 3 ~w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 3 TWSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp GHCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCCHHHHHHHHHHCCcHHHHHHHHH
Confidence 3467899999999999999887664
No 115
>PTZ00183 centrin; Provisional
Probab=27.41 E-value=1.8e+02 Score=22.37 Aligned_cols=19 Identities=37% Similarity=0.515 Sum_probs=9.3
Q ss_pred CCCccCcccHHHHHhhcCC
Q 038325 111 QRKTITAEDVVWAMGKLGF 129 (231)
Q Consensus 111 kRKTItaeDVL~ALe~LGF 129 (231)
+.-+|+.+++..+|+.+|+
T Consensus 30 ~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 30 GSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred CCCcccHHHHHHHHHHhCC
Confidence 3444555555555554443
No 116
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=26.85 E-value=3.8e+02 Score=26.79 Aligned_cols=93 Identities=15% Similarity=0.095 Sum_probs=62.2
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHH----------HHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 57 QDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVS----------EYISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 57 ~d~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecas----------eFI~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
.++++|.+.|---|... ++.|..+....+..-.. .-+.-|..+..+......=.-=++.+|..+|++
T Consensus 160 ~~~E~~~~~~l~~me~~---Gi~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~g~~~~n~~S~~ql~~~L~~ 236 (553)
T PRK14975 160 AAAESAGALAAAEMELA---GLPWDTDVHEALLAELLGPRPAAGGRPARLAELAAEIREALGRPRLNPDSPQQVLRALRR 236 (553)
T ss_pred HHHHhhHHHHHHHHHHh---CeEeCHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHH
Confidence 45678888888888877 48899998877766555 556666666666552211123467889999999
Q ss_pred cCCC----------cchHHHHHHHHHHHHHHHHHhh
Q 038325 127 LGFD----------NYVEPLSIFLNRFRDSEHERTA 152 (231)
Q Consensus 127 LGF~----------dYv~~Lk~~L~~yRe~~~~rk~ 152 (231)
+|+. .-..|+-..|-+||+..+....
T Consensus 237 ~g~~~~~t~~~~L~~~~hp~~~~ile~r~~~kl~st 272 (553)
T PRK14975 237 AGIELPSTRKWELREIDHPAVEPLLEYRKLSKLLSA 272 (553)
T ss_pred CCCCCCCCcHHHhccCCCchHHHHHHHHHHHHHHHH
Confidence 8885 1112445567788888777554
No 117
>PF12010 DUF3502: Domain of unknown function (DUF3502); InterPro: IPR022627 This domain is about 140 amino acids in length and is functionally uncharacterised. It is found in bacteria C-terminal to PF01547 from PFAM.
Probab=26.80 E-value=38 Score=27.55 Aligned_cols=62 Identities=11% Similarity=0.185 Sum_probs=43.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHHHHHHHHHHHHH
Q 038325 81 SDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYVEPLSIFLNRFRDS 146 (231)
Q Consensus 81 SkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv~~Lk~~L~~yRe~ 146 (231)
+...+..|..|..+.-.|......=... ---.-.+++..|+..|++..+.+++..|++|++.
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 4566777888877776665543322111 1123567788899999999999999999999874
No 118
>PRK09526 lacI lac repressor; Reviewed
Probab=26.69 E-value=40 Score=29.64 Aligned_cols=37 Identities=16% Similarity=0.445 Sum_probs=29.4
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHH
Q 038325 60 YMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITG 101 (231)
Q Consensus 60 ~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTs 101 (231)
..-+++|.|++... .+||++.++.|.+++++ +.|.-.
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 46678898888653 47999999999999999 566543
No 119
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=26.55 E-value=78 Score=28.24 Aligned_cols=61 Identities=11% Similarity=0.037 Sum_probs=44.7
Q ss_pred cCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc---cCcccHHHH
Q 038325 59 QYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKT---ITAEDVVWA 123 (231)
Q Consensus 59 ~~LPkA~I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKT---ItaeDVL~A 123 (231)
..||+++|.+++..++ +-.|+...+..|+-.+.+|+-.|.-.|..+ .+++.| +.+.|+-.|
T Consensus 114 t~lnKt~VKKlastV~--nQtVspNi~I~l~g~~KVfvGEiIElA~~V--q~~w~~sgpl~p~h~rea 177 (199)
T COG5251 114 TSLNKTQVKKLASTVA--NQTVSPNIRIFLQGVGKVFVGEIIELAMIV--QNKWLTSGPLIPFHKREA 177 (199)
T ss_pred cCCCHHHHHHHHHHHh--ccccCCCeeeeeechhHHHHHHHHHHHHHH--HHHhcccCCCChHHHHHH
Confidence 4699999999999998 567788888889999999998887766543 233332 455555544
No 120
>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=26.30 E-value=64 Score=27.47 Aligned_cols=69 Identities=16% Similarity=0.213 Sum_probs=47.8
Q ss_pred HHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhcCCCcchHHHHHHHHHHHH
Q 038325 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNYVEPLSIFLNRFRD 145 (231)
Q Consensus 66 I~RImK~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~LGF~dYv~~Lk~~L~~yRe 145 (231)
+.||++.+. +.-|-|+-..-+...++.=+.-|.--|.+.|+.++|.+|...|+=- -.-+++.++.||+
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 FERLFRKAA--GLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPI----------TKGLQESIREFRK 68 (138)
T ss_dssp HHHHHHHHH--S----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-------------HHHHHHHHHHHT
T ss_pred ChHHHHHHh--ccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCc----------cHHHHHHHHHHHH
Confidence 357888887 6777888888888888888888888899999999999999988632 2345566666666
Q ss_pred H
Q 038325 146 S 146 (231)
Q Consensus 146 ~ 146 (231)
.
T Consensus 69 l 69 (138)
T PF09123_consen 69 L 69 (138)
T ss_dssp T
T ss_pred c
Confidence 5
No 121
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=26.03 E-value=2.8e+02 Score=24.63 Aligned_cols=65 Identities=22% Similarity=0.127 Sum_probs=46.4
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCccCcccHHHHHhh
Q 038325 61 MPIANVIRIMRRILP-PHAKISDDAKETVQECVSEYISFITGEANERCHRE-QRKTITAEDVVWAMGK 126 (231)
Q Consensus 61 LPkA~I~RImK~aLP-~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~-kRKTItaeDVL~ALe~ 126 (231)
+....+.+.|+..+- .++.|+.+|.+.|.+.+..=+..+..|-...|.-. +++ |+.+||-..+..
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 556666666666553 35789999999999988876677777777766543 233 999998877654
No 122
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=25.75 E-value=1.6e+02 Score=28.58 Aligned_cols=79 Identities=19% Similarity=0.208 Sum_probs=52.3
Q ss_pred CCCCCccccCCchhHHHHHHHhhCCCCc--ccCHHHHHHHHHH-HHHHHHHHHHHHHH-HHHhc--CC-CccCcccHHHH
Q 038325 51 PCVVREQDQYMPIANVIRIMRRILPPHA--KISDDAKETVQEC-VSEYISFITGEANE-RCHRE--QR-KTITAEDVVWA 123 (231)
Q Consensus 51 ~~~v~e~d~~LPkA~I~RImK~aLP~~~--rISkDAkeaIqec-aseFI~~LTseAne-~c~~~--kR-KTItaeDVL~A 123 (231)
..++..-|+- --|.|.-.+++.+|++- .|..|--..|.+. ++.|+.-|+..-++ ++..+ +- ..++.+||++|
T Consensus 41 ~SPVTvaDyG-~QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~a 119 (351)
T KOG1528|consen 41 KSPVTVADYG-SQAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLKA 119 (351)
T ss_pred CCCcchhhhh-HHHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHHH
Confidence 3444444432 35788899999999765 6777776666665 56677777774444 22222 22 78999999999
Q ss_pred HhhcCCC
Q 038325 124 MGKLGFD 130 (231)
Q Consensus 124 Le~LGF~ 130 (231)
++.-+.+
T Consensus 120 ID~G~s~ 126 (351)
T KOG1528|consen 120 IDRGNSE 126 (351)
T ss_pred Hhccccc
Confidence 9865544
No 123
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=25.17 E-value=75 Score=30.56 Aligned_cols=32 Identities=25% Similarity=0.248 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 038325 96 ISFITGEANERCHREQRKTITAEDVVWAMGKL 127 (231)
Q Consensus 96 I~~LTseAne~c~~~kRKTItaeDVL~ALe~L 127 (231)
|..|..+|...|.+++|+.|+.+|+..|+++.
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 66778889999999999999999999998763
No 124
>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=24.92 E-value=70 Score=19.17 Aligned_cols=27 Identities=22% Similarity=0.233 Sum_probs=20.7
Q ss_pred HHHHHHHhcCCCccCcccHHHHHh-hcC
Q 038325 102 EANERCHREQRKTITAEDVVWAMG-KLG 128 (231)
Q Consensus 102 eAne~c~~~kRKTItaeDVL~ALe-~LG 128 (231)
.+....-.++.-+|+.+++..+|+ .||
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 345566677888999999999999 576
No 125
>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=24.92 E-value=42 Score=22.25 Aligned_cols=24 Identities=25% Similarity=0.375 Sum_probs=19.7
Q ss_pred CcccHHHHHhhcCCCcchHHHHHH
Q 038325 116 TAEDVVWAMGKLGFDNYVEPLSIF 139 (231)
Q Consensus 116 taeDVL~ALe~LGF~dYv~~Lk~~ 139 (231)
+.++|..-|+.+|+++|++.++..
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 578899999999998888877653
No 126
>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=23.50 E-value=65 Score=22.08 Aligned_cols=22 Identities=32% Similarity=0.531 Sum_probs=19.1
Q ss_pred CcccHHHHHhhcCCCcchHHHH
Q 038325 116 TAEDVVWAMGKLGFDNYVEPLS 137 (231)
Q Consensus 116 taeDVL~ALe~LGF~dYv~~Lk 137 (231)
+.++|..-|+.+|++.|++..+
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 127
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=23.33 E-value=65 Score=32.74 Aligned_cols=46 Identities=17% Similarity=0.325 Sum_probs=36.7
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC
Q 038325 71 RRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTIT 116 (231)
Q Consensus 71 K~aLP~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTIt 116 (231)
|+++.+.--|-+|.+.|+++||.+.=.||.....+.-+.+++++|.
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 3344334468899999999999999999999998887777777753
No 128
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=23.08 E-value=1.4e+02 Score=30.44 Aligned_cols=64 Identities=8% Similarity=0.086 Sum_probs=33.2
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHh
Q 038325 61 MPIANVIRIMRRILP-PHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMG 125 (231)
Q Consensus 61 LPkA~I~RImK~aLP-~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe 125 (231)
|+...|.+.+++.+- .++.|+.++...|.+.+.-=+..+-.+....+.-.+++ |+.++|...+.
T Consensus 180 ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~ 244 (614)
T PRK14971 180 IQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLN 244 (614)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhC
Confidence 444445544544332 25778888888877665443333333333333333333 66666655544
No 129
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=21.97 E-value=1.7e+02 Score=25.66 Aligned_cols=65 Identities=20% Similarity=0.160 Sum_probs=39.7
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhhc
Q 038325 61 MPIANVIRIMRRILP-PHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKL 127 (231)
Q Consensus 61 LPkA~I~RImK~aLP-~~~rISkDAkeaIqecaseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~L 127 (231)
++...+.++++..+. .++.|+.++.+.|.+.+.--+..+-.+-...+.. .++|+.+||..++...
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 445555555555442 3567999999998887654333333333223332 4689999998887654
No 130
>TIGR01278 DPOR_BchB light-independent protochlorophyllide reductase, B subunit. This enzyme describes the B subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme. This subunit shows homology to the nitrogenase molybdenum-iron protein. It catalyzes a step in bacteriochlorophyll biosynthesis.
Probab=21.71 E-value=1.5e+02 Score=29.16 Aligned_cols=51 Identities=14% Similarity=0.139 Sum_probs=38.8
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHH-HHHHHHHHhcCCCccCcccHHHHHhhcC
Q 038325 77 HAKISDDAKETVQECVSEYISFIT-GEANERCHREQRKTITAEDVVWAMGKLG 128 (231)
Q Consensus 77 ~~rISkDAkeaIqecaseFI~~LT-seAne~c~~~kRKTItaeDVL~ALe~LG 128 (231)
.+.++.||...|.+ +--|+.-=. ..+-+.|++.+...||.+.|..|=..+|
T Consensus 460 ~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 511 (511)
T TIGR01278 460 ELGWTAEAEAELKK-VPFFVRGKVRRNTENFARERGYSVITLEVIYAAKEHFG 511 (511)
T ss_pred CCCcCHHHHHHHhh-CChhhhHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhcC
Confidence 46899999999965 566665333 3444588999999999999999876654
No 131
>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=21.11 E-value=2e+02 Score=20.54 Aligned_cols=42 Identities=21% Similarity=0.248 Sum_probs=32.2
Q ss_pred HHHHHHHHH--HHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHhh
Q 038325 83 DAKETVQEC--VSEYISFITGEANERCHREQRKTITAEDVVWAMGK 126 (231)
Q Consensus 83 DAkeaIqec--aseFI~~LTseAne~c~~~kRKTItaeDVL~ALe~ 126 (231)
|+.+.| +. ...|+.|...-|..++-+.++|. .-+|+.+|..=
T Consensus 14 e~id~~-~~~~~~~~~~f~~gnaiKY~~R~~~K~-~~eDl~KA~~Y 57 (60)
T PF11753_consen 14 ECIDFI-EQFTEEQFLGFCLGNAIKYLWRAGKKN-GIEDLKKAKWY 57 (60)
T ss_pred cHHHHH-HHhcchhhhhHHHHHHHHHHHHHcccC-cHHHHHHHHHH
Confidence 445555 33 44899999999999999999994 48888888653
No 132
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=21.09 E-value=52 Score=24.86 Aligned_cols=18 Identities=33% Similarity=0.497 Sum_probs=15.7
Q ss_pred ccCcccHHHHHhhcCCCc
Q 038325 114 TITAEDVVWAMGKLGFDN 131 (231)
Q Consensus 114 TItaeDVL~ALe~LGF~d 131 (231)
.+++.||+++|+.+||..
T Consensus 6 ~~~~ke~ik~Le~~Gf~~ 23 (66)
T COG1724 6 RMKAKEVIKALEKDGFQL 23 (66)
T ss_pred cCCHHHHHHHHHhCCcEE
Confidence 478899999999999963
No 133
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=20.89 E-value=1.6e+02 Score=29.15 Aligned_cols=52 Identities=12% Similarity=0.114 Sum_probs=40.1
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHH-HHHHHHHhcCCCccCcccHHHHHhhcC
Q 038325 76 PHAKISDDAKETVQECVSEYISFITG-EANERCHREQRKTITAEDVVWAMGKLG 128 (231)
Q Consensus 76 ~~~rISkDAkeaIqecaseFI~~LTs-eAne~c~~~kRKTItaeDVL~ALe~LG 128 (231)
+.+.++.||...|.+ +--|+.-=.. .+-+.|+..+...||.|.|..|-..+|
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 467899999999965 6667664443 444478999999999999999977654
No 134
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=20.81 E-value=1.5e+02 Score=22.04 Aligned_cols=29 Identities=17% Similarity=0.132 Sum_probs=22.6
Q ss_pred HHHHHHHhcCCCccCcccHHHHHhhcCCC
Q 038325 102 EANERCHREQRKTITAEDVVWAMGKLGFD 130 (231)
Q Consensus 102 eAne~c~~~kRKTItaeDVL~ALe~LGF~ 130 (231)
++...+-.++.-.|+.++|..+|..+|+.
T Consensus 14 ~~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 14 QIFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 35556667777889999999999888875
No 135
>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=20.81 E-value=55 Score=22.09 Aligned_cols=14 Identities=36% Similarity=0.565 Sum_probs=11.8
Q ss_pred ccHHHHHhhcCCCc
Q 038325 118 EDVVWAMGKLGFDN 131 (231)
Q Consensus 118 eDVL~ALe~LGF~d 131 (231)
+|++.||..|||..
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 68999999999984
No 136
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=20.29 E-value=2e+02 Score=26.02 Aligned_cols=50 Identities=18% Similarity=0.149 Sum_probs=36.5
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCccCcccHHHHHhh
Q 038325 77 HAKISDDAKETVQECVSEYISFITGEANERCHR-EQRKTITAEDVVWAMGK 126 (231)
Q Consensus 77 ~~rISkDAkeaIqecaseFI~~LTseAne~c~~-~kRKTItaeDVL~ALe~ 126 (231)
+.+|+.||...|.+++..=+..+..+-...+.- ...++|+.+||...+..
T Consensus 159 g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~ 209 (343)
T PRK06585 159 GLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGD 209 (343)
T ss_pred CCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC
Confidence 678999999999998876555555555555554 34568999999877653
No 137
>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=20.04 E-value=2e+02 Score=29.28 Aligned_cols=73 Identities=11% Similarity=0.174 Sum_probs=46.0
Q ss_pred CchhHHHHHHHhhCCC-CcccCHHHHHHHHHHH---HHHHHHHHHHHHHH--------HHhcCCCccCcccHHHHHhhcC
Q 038325 61 MPIANVIRIMRRILPP-HAKISDDAKETVQECV---SEYISFITGEANER--------CHREQRKTITAEDVVWAMGKLG 128 (231)
Q Consensus 61 LPkA~I~RImK~aLP~-~~rISkDAkeaIqeca---seFI~~LTseAne~--------c~~~kRKTItaeDVL~ALe~LG 128 (231)
|....+..|++..+.. .+.++.++.++|.+++ ...+..|... ... +...++.+|+.+||..++..--
T Consensus 353 ls~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~~gRraln~L~~~-~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r 431 (615)
T TIGR02903 353 LTPEDIALIVLNAAEKINVHLAAGVEELIARYTIEGRKAVNILADV-YGYALYRAAEAGKENDKVTITQDDVYEVIQISR 431 (615)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCcHHHHHHHHHHH-HHHHHHHHHHhccCCCCeeECHHHHHHHhCCCc
Confidence 3345577777776542 3568999999988765 3334433221 111 2233456899999999998877
Q ss_pred CCcchH
Q 038325 129 FDNYVE 134 (231)
Q Consensus 129 F~dYv~ 134 (231)
|..|..
T Consensus 432 ~~~~~~ 437 (615)
T TIGR02903 432 LSPYEK 437 (615)
T ss_pred Cccchh
Confidence 776653
Done!