Query 044287
Match_columns 188
No_of_seqs 150 out of 629
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 13:10:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044287.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044287hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0869 CCAAT-binding factor, 100.0 1.8E-34 3.9E-39 234.9 10.1 105 25-129 21-125 (168)
2 KOG0871 Class 2 transcription 100.0 9E-33 2E-37 223.0 8.9 121 33-153 9-133 (156)
3 COG5150 Class 2 transcription 100.0 1.1E-28 2.3E-33 195.8 6.9 123 32-154 7-133 (148)
4 KOG0870 DNA polymerase epsilon 99.9 2.6E-24 5.6E-29 176.6 9.2 100 30-129 4-104 (172)
5 PF00808 CBFD_NFYB_HMF: Histon 99.7 1E-17 2.2E-22 116.9 6.7 64 36-100 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.7 3.3E-17 7.3E-22 123.5 5.7 82 26-109 9-90 (91)
7 cd00076 H4 Histone H4, one of 99.3 4.8E-12 1E-16 94.4 7.5 72 35-108 12-83 (85)
8 PLN00035 histone H4; Provision 99.3 7E-12 1.5E-16 96.6 6.5 80 25-106 18-97 (103)
9 PTZ00015 histone H4; Provision 99.2 1.8E-11 3.9E-16 94.2 7.1 81 26-108 20-100 (102)
10 smart00417 H4 Histone H4. 99.1 1.3E-10 2.9E-15 84.7 4.9 64 34-99 11-74 (74)
11 smart00803 TAF TATA box bindin 99.1 4.7E-10 1E-14 79.5 6.7 64 36-101 2-65 (65)
12 smart00428 H3 Histone H3. 98.9 4.8E-09 1E-13 81.1 6.3 73 31-103 24-101 (105)
13 PF00125 Histone: Core histone 98.8 8.2E-09 1.8E-13 73.0 5.5 68 34-101 3-73 (75)
14 cd07981 TAF12 TATA Binding Pro 98.8 2E-08 4.3E-13 72.1 7.4 65 37-102 2-66 (72)
15 PLN00160 histone H3; Provision 98.5 3.4E-07 7.3E-12 70.0 6.3 71 31-101 16-90 (97)
16 PLN00121 histone H3; Provision 98.5 2.5E-07 5.3E-12 74.6 5.7 71 31-101 57-130 (136)
17 PLN00161 histone H3; Provision 98.5 5E-07 1.1E-11 72.7 7.3 71 31-101 50-124 (135)
18 KOG3467 Histone H4 [Chromatin 98.4 2E-07 4.4E-12 70.6 4.1 80 25-106 18-97 (103)
19 PTZ00018 histone H3; Provision 98.4 3.6E-07 7.7E-12 73.7 5.8 71 31-101 57-130 (136)
20 smart00576 BTP Bromodomain tra 98.4 1.3E-06 2.7E-11 63.2 7.3 68 37-106 7-74 (77)
21 COG5208 HAP5 CCAAT-binding fac 98.4 2E-07 4.4E-12 80.8 3.3 81 31-112 104-184 (286)
22 cd00074 H2A Histone 2A; H2A is 98.2 2.5E-06 5.4E-11 66.9 6.0 68 34-102 18-85 (115)
23 cd07979 TAF9 TATA Binding Prot 98.1 9.9E-06 2.1E-10 63.4 7.4 77 41-119 6-83 (117)
24 KOG1657 CCAAT-binding factor, 98.1 3.1E-06 6.7E-11 73.6 4.6 89 30-119 68-159 (236)
25 cd08050 TAF6 TATA Binding Prot 97.9 3.8E-05 8.3E-10 69.3 7.3 67 38-106 1-67 (343)
26 cd08048 TAF11 TATA Binding Pro 97.8 0.00012 2.6E-09 54.6 7.2 66 36-103 16-84 (85)
27 PF15511 CENP-T: Centromere ki 97.7 4.2E-05 9E-10 70.9 5.3 63 33-95 348-414 (414)
28 PF07524 Bromo_TP: Bromodomain 97.7 0.00021 4.6E-09 51.2 7.4 66 39-106 9-74 (77)
29 KOG1745 Histones H3 and H4 [Ch 97.7 3E-05 6.6E-10 62.7 3.2 74 31-104 58-134 (137)
30 PF15630 CENP-S: Kinetochore c 97.6 0.0002 4.4E-09 52.4 6.2 62 41-102 10-72 (76)
31 smart00427 H2B Histone H2B. 97.6 0.00025 5.3E-09 53.7 6.5 62 41-103 6-67 (89)
32 PF03847 TFIID_20kDa: Transcri 97.5 0.00033 7.2E-09 50.2 6.3 63 39-102 2-64 (68)
33 PF09415 CENP-X: CENP-S associ 97.4 0.00021 4.6E-09 51.8 3.9 65 38-102 1-67 (72)
34 PLN00158 histone H2B; Provisio 97.3 0.00072 1.6E-08 53.4 6.6 67 36-103 27-93 (116)
35 PF02969 TAF: TATA box binding 97.3 0.0011 2.4E-08 47.5 6.6 64 36-101 3-66 (66)
36 PTZ00463 histone H2B; Provisio 97.3 0.00089 1.9E-08 52.9 6.6 64 40-104 32-95 (117)
37 PF04719 TAFII28: hTAFII28-lik 97.3 0.0008 1.7E-08 50.8 6.0 67 36-103 23-90 (90)
38 KOG1659 Class 2 transcription 97.2 0.00096 2.1E-08 57.6 6.1 86 36-122 13-98 (224)
39 COG5262 HTA1 Histone H2A [Chro 96.9 0.0024 5.2E-08 50.9 5.9 69 33-102 23-91 (132)
40 smart00414 H2A Histone 2A. 96.8 0.0038 8.3E-08 48.4 5.9 68 34-102 7-74 (106)
41 PLN00154 histone H2A; Provisio 96.6 0.012 2.7E-07 47.6 7.7 70 33-102 35-104 (136)
42 COG5247 BUR6 Class 2 transcrip 96.5 0.0047 1E-07 48.2 4.7 78 35-113 22-99 (113)
43 PLN00157 histone H2A; Provisio 96.3 0.015 3.3E-07 46.8 6.9 69 33-102 23-91 (132)
44 PLN00153 histone H2A; Provisio 96.3 0.015 3.2E-07 46.8 6.6 69 33-102 21-89 (129)
45 KOG1142 Transcription initiati 96.3 0.013 2.9E-07 51.8 6.8 69 33-102 151-219 (258)
46 PTZ00017 histone H2A; Provisio 96.2 0.0087 1.9E-07 48.4 5.1 69 33-102 24-92 (134)
47 KOG1744 Histone H2B [Chromatin 96.1 0.017 3.6E-07 46.4 6.1 62 41-103 42-103 (127)
48 KOG1756 Histone 2A [Chromatin 96.1 0.012 2.7E-07 47.3 5.3 68 33-101 24-91 (131)
49 KOG3219 Transcription initiati 96.1 0.0055 1.2E-07 52.3 3.4 69 36-106 112-181 (195)
50 PF15510 CENP-W: Centromere ki 96.1 0.0081 1.7E-07 46.1 3.9 67 35-102 15-95 (102)
51 PF02269 TFIID-18kDa: Transcri 95.9 0.011 2.4E-07 44.4 3.8 60 42-102 7-66 (93)
52 PF02291 TFIID-31kDa: Transcri 95.8 0.033 7.2E-07 44.6 6.4 85 33-119 7-94 (129)
53 PLN00156 histone H2AX; Provisi 95.7 0.022 4.7E-07 46.4 5.3 69 33-102 26-94 (139)
54 KOG1658 DNA polymerase epsilon 95.4 0.013 2.8E-07 48.6 2.7 66 35-102 58-124 (162)
55 PTZ00252 histone H2A; Provisio 93.8 0.16 3.5E-06 41.2 5.5 69 33-102 22-92 (134)
56 cd07978 TAF13 The TATA Binding 93.3 0.41 8.9E-06 36.1 6.7 61 40-102 6-66 (92)
57 KOG3423 Transcription initiati 93.0 0.41 8.9E-06 40.3 6.9 69 36-106 86-168 (176)
58 KOG4336 TBP-associated transcr 92.6 0.53 1.2E-05 42.9 7.6 77 41-121 10-86 (323)
59 KOG2549 Transcription initiati 90.6 0.83 1.8E-05 44.6 6.9 65 38-104 13-77 (576)
60 TIGR03015 pepcterm_ATPase puta 88.8 1.1 2.4E-05 37.4 5.7 69 37-105 192-268 (269)
61 KOG3334 Transcription initiati 85.5 3.7 8.1E-05 33.8 6.8 79 37-117 12-93 (148)
62 KOG2389 Predicted bromodomain 85.5 1.6 3.4E-05 40.5 5.1 69 36-106 29-97 (353)
63 PRK00411 cdc6 cell division co 83.9 3.7 8E-05 36.5 6.7 70 39-108 209-287 (394)
64 TIGR02928 orc1/cdc6 family rep 78.6 5.6 0.00012 34.9 5.8 74 39-112 201-283 (365)
65 PF13654 AAA_32: AAA domain; P 76.7 8 0.00017 37.2 6.7 49 55-103 447-506 (509)
66 COG1067 LonB Predicted ATP-dep 75.9 2.1 4.6E-05 42.4 2.7 33 69-102 366-398 (647)
67 TIGR02902 spore_lonB ATP-depen 73.6 8 0.00017 37.0 5.9 67 39-105 265-334 (531)
68 TIGR00764 lon_rel lon-related 70.2 12 0.00027 36.5 6.4 49 55-103 330-391 (608)
69 COG5162 Transcription initiati 68.8 26 0.00057 29.8 7.2 68 37-106 89-189 (197)
70 cd08045 TAF4 TATA Binding Prot 68.6 21 0.00046 30.1 6.8 72 35-106 43-122 (212)
71 COG5095 TAF6 Transcription ini 68.2 17 0.00037 34.0 6.5 66 39-106 8-73 (450)
72 PF03540 TFIID_30kDa: Transcri 67.5 33 0.00072 23.5 6.3 47 36-85 2-49 (51)
73 PF08369 PCP_red: Proto-chloro 65.8 5.6 0.00012 26.2 2.1 42 57-99 2-44 (45)
74 KOG2680 DNA helicase TIP49, TB 64.9 31 0.00067 32.5 7.5 50 52-101 374-427 (454)
75 PF13335 Mg_chelatase_2: Magne 64.8 18 0.00039 27.0 5.1 48 54-101 41-94 (96)
76 PRK00080 ruvB Holliday junctio 54.5 41 0.00089 29.6 6.3 71 37-107 180-254 (328)
77 TIGR00635 ruvB Holliday juncti 52.5 61 0.0013 27.7 6.9 70 37-106 159-232 (305)
78 KOG3901 Transcription initiati 52.4 29 0.00063 27.3 4.4 49 51-102 23-71 (109)
79 KOG1757 Histone 2A [Chromatin 51.5 23 0.0005 28.3 3.8 64 34-101 28-95 (131)
80 PF02861 Clp_N: Clp amino term 49.3 9.9 0.00021 24.1 1.2 26 79-104 1-26 (53)
81 PRK09862 putative ATP-dependen 46.7 52 0.0011 31.8 6.1 57 54-110 437-499 (506)
82 PF09114 MotA_activ: Transcrip 44.7 39 0.00085 26.0 4.0 34 40-73 51-88 (96)
83 TIGR02442 Cob-chelat-sub cobal 43.5 63 0.0014 31.7 6.2 49 53-101 247-302 (633)
84 TIGR02030 BchI-ChlI magnesium 41.8 81 0.0018 28.7 6.3 54 47-101 247-307 (337)
85 TIGR01128 holA DNA polymerase 41.5 1.2E+02 0.0025 25.7 6.9 66 37-102 111-177 (302)
86 PRK13765 ATP-dependent proteas 41.0 36 0.00079 33.8 4.2 47 55-101 339-398 (637)
87 PRK13406 bchD magnesium chelat 39.9 50 0.0011 32.4 4.9 52 49-101 190-248 (584)
88 PF00531 Death: Death domain; 39.3 35 0.00076 23.4 2.8 30 87-116 54-83 (83)
89 PRK12402 replication factor C 38.9 61 0.0013 27.8 4.8 72 37-110 184-256 (337)
90 PF05236 TAF4: Transcription i 38.4 43 0.00092 29.1 3.8 75 32-106 39-121 (264)
91 COG1474 CDC6 Cdc6-related prot 37.7 88 0.0019 28.8 5.9 73 40-112 193-274 (366)
92 COG1224 TIP49 DNA helicase TIP 37.6 63 0.0014 30.9 4.9 50 52-101 377-430 (450)
93 PF00356 LacI: Bacterial regul 37.6 78 0.0017 20.7 4.1 32 35-70 9-40 (46)
94 TIGR00368 Mg chelatase-related 37.5 62 0.0013 31.1 5.0 47 55-101 445-497 (499)
95 COG5251 TAF40 Transcription in 36.7 24 0.00052 30.2 1.9 61 36-100 115-178 (199)
96 PRK07452 DNA polymerase III su 35.1 92 0.002 27.1 5.4 65 42-106 135-202 (326)
97 COG5248 TAF19 Transcription in 35.0 1.1E+02 0.0024 24.5 5.2 49 52-102 24-72 (126)
98 cd04752 Commd4 COMM_Domain con 34.9 2.5E+02 0.0055 22.9 8.6 52 68-126 44-96 (174)
99 CHL00081 chlI Mg-protoporyphyr 34.1 83 0.0018 29.0 5.1 54 47-101 260-320 (350)
100 PF07647 SAM_2: SAM domain (St 32.1 30 0.00065 23.0 1.5 24 91-114 4-27 (66)
101 PRK13407 bchI magnesium chelat 31.2 1.1E+02 0.0025 27.8 5.5 53 47-100 244-303 (334)
102 PTZ00361 26 proteosome regulat 29.6 49 0.0011 31.3 2.9 31 72-102 393-423 (438)
103 TIGR02031 BchD-ChlD magnesium 29.5 1.3E+02 0.0029 29.3 5.9 54 47-101 196-256 (589)
104 smart00350 MCM minichromosome 29.1 1.7E+02 0.0037 27.8 6.5 69 35-103 416-504 (509)
105 cd00166 SAM Sterile alpha moti 28.5 27 0.00059 22.4 0.8 24 92-115 3-26 (63)
106 PF08823 PG_binding_2: Putativ 28.5 63 0.0014 23.3 2.7 32 94-125 19-56 (74)
107 PF12010 DUF3502: Domain of un 28.3 37 0.00081 26.6 1.6 63 57-123 71-133 (134)
108 PRK05574 holA DNA polymerase I 28.2 1.4E+02 0.0031 25.7 5.4 66 37-102 146-212 (340)
109 PF00536 SAM_1: SAM domain (St 28.0 36 0.00079 22.5 1.3 23 92-114 4-26 (64)
110 TIGR01242 26Sp45 26S proteasom 27.9 56 0.0012 29.2 2.9 32 71-102 331-362 (364)
111 TIGR01052 top6b DNA topoisomer 27.8 67 0.0014 31.1 3.5 59 47-119 426-484 (488)
112 PRK03992 proteasome-activating 27.6 57 0.0012 29.8 2.9 35 70-104 339-373 (389)
113 COG5094 TAF9 Transcription ini 26.5 2.4E+02 0.0053 23.0 6.0 66 55-120 31-100 (145)
114 PF13405 EF-hand_6: EF-hand do 25.2 43 0.00093 19.3 1.1 27 78-104 4-31 (31)
115 PF09123 DUF1931: Domain of un 25.0 62 0.0014 26.5 2.4 54 42-97 1-54 (138)
116 PF02361 CbiQ: Cobalt transpor 24.9 74 0.0016 25.6 2.8 67 55-127 95-173 (224)
117 smart00454 SAM Sterile alpha m 24.1 30 0.00065 22.4 0.3 25 91-115 4-28 (68)
118 PTZ00454 26S protease regulato 23.5 70 0.0015 29.7 2.8 31 72-102 355-385 (398)
119 TIGR02454 CbiQ_TIGR cobalt ABC 23.1 95 0.0021 24.9 3.1 38 89-126 112-160 (198)
120 PF07499 RuvA_C: RuvA, C-termi 23.0 37 0.0008 22.1 0.6 13 94-106 4-16 (47)
121 COG1724 Predicted RNA binding 22.8 37 0.0008 24.5 0.6 17 90-106 6-22 (66)
122 cd08779 Death_PIDD Death Domai 20.8 1.4E+02 0.003 21.7 3.4 34 82-115 52-85 (86)
123 PRK07914 hypothetical protein; 20.2 1.8E+02 0.0039 25.5 4.6 63 38-101 129-192 (320)
124 PF10728 DUF2520: Domain of un 20.0 2.7E+02 0.0059 21.8 5.1 71 40-121 14-87 (132)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=1.8e-34 Score=234.90 Aligned_cols=105 Identities=68% Similarity=1.126 Sum_probs=99.6
Q ss_pred CCCCCCccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcC
Q 044287 25 SDDGGIKEQERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLG 104 (188)
Q Consensus 25 ~~~~~~~~~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LG 104 (188)
+....++++|..||+|+|.||||.+||++.+|||||++.||+|++|||+|||++|+++|..++|||||+|||+|||..||
T Consensus 21 ~~~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 21 QSSLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred ccccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 34457899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcchHHHHHHHHHHHHHHHhhhhh
Q 044287 105 FDDYAGPIRRYLHKYRELEGERANQ 129 (188)
Q Consensus 105 F~dyi~~lk~~L~~~re~~~~K~~~ 129 (188)
|++|+++|+.||..||+++..|...
T Consensus 101 Fe~Y~eplkiyL~kYRe~e~e~~~~ 125 (168)
T KOG0869|consen 101 FENYAEPLKIYLQKYRELEGERGRS 125 (168)
T ss_pred cHhHHHHHHHHHHHHHHHhhhcccc
Confidence 9999999999999999998877543
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.98 E-value=9e-33 Score=222.98 Aligned_cols=121 Identities=32% Similarity=0.513 Sum_probs=116.6
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchHHH
Q 044287 33 QERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAGPI 112 (188)
Q Consensus 33 ~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~~l 112 (188)
+++.||+|+|.+|||+.||.+++|.+||+++|.+||.+||++|+++||++|.++.||||.+|||++||+.|||.+|++.+
T Consensus 9 de~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYiee~ 88 (156)
T KOG0871|consen 9 DELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIEEA 88 (156)
T ss_pred ccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhhhhhccccCCcch----hhhhhhcCCCCCC
Q 044287 113 RRYLHKYRELEGERANQQDKASNSNSNI----NINEEREEPAGSS 153 (188)
Q Consensus 113 k~~L~~~re~~~~K~~~~~K~~~sg~~~----~~~~~~~~~~~~~ 153 (188)
...|++|+...+.|+++++|++++|+++ ++|++.|..+|..
T Consensus 89 ~~vl~~~K~~~~~~~~kssk~e~~Gi~eEEL~~qQqeLf~~ARar 133 (156)
T KOG0871|consen 89 EEVLENCKEEAKKRRRKSSKFEKSGIPEEELLRQQQELFAKARAR 133 (156)
T ss_pred HHHHHHHHHHHHHhhhhhhhHHhcCCCHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999997 5688999988854
No 3
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.95 E-value=1.1e-28 Score=195.83 Aligned_cols=123 Identities=28% Similarity=0.458 Sum_probs=117.9
Q ss_pred cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchHH
Q 044287 32 EQERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAGP 111 (188)
Q Consensus 32 ~~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~~ 111 (188)
.+++.||+|+|.+++.+.||.+..+.+||++.+++||.+||+.|+++||++|.++.+|||.++||++||+.|||.+|++.
T Consensus 7 dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~~ 86 (148)
T COG5150 7 DDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIES 86 (148)
T ss_pred cccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHHH
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhhhhhccccCCcch----hhhhhhcCCCCCCC
Q 044287 112 IRRYLHKYRELEGERANQQDKASNSNSNI----NINEEREEPAGSSY 154 (188)
Q Consensus 112 lk~~L~~~re~~~~K~~~~~K~~~sg~~~----~~~~~~~~~~~~~~ 154 (188)
+.+.+.+|+..++.|.++.+||+++|+++ ++|+++|..++..+
T Consensus 87 ~~e~~~n~k~~qK~ke~k~sKFk~SGls~eELlrQQeeLf~~ar~rf 133 (148)
T COG5150 87 CMEEHENYKSYQKQKESKISKFKDSGLSMEELLRQQEELFQNARLRF 133 (148)
T ss_pred HHHHHHHHHHHHhhchhhhhHHHhcCCCHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999996 66889998888766
No 4
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.91 E-value=2.6e-24 Score=176.61 Aligned_cols=100 Identities=28% Similarity=0.519 Sum_probs=95.5
Q ss_pred CccccccCchhHHHHHHhhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcc
Q 044287 30 IKEQERLLPIANVGRIMKQILPAN-AKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDY 108 (188)
Q Consensus 30 ~~~~d~~LPkA~I~RImK~~LP~~-~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dy 108 (188)
.+.+++.||+|+|.||+|+.||.. +.|||||+.+|+++|++||+||++.|+++|..++||||+++||+.||.+|+|..|
T Consensus 4 eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f 83 (172)
T KOG0870|consen 4 ERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSF 83 (172)
T ss_pred hhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHH
Confidence 467899999999999999999977 9999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHhhhhh
Q 044287 109 AGPIRRYLHKYRELEGERANQ 129 (188)
Q Consensus 109 i~~lk~~L~~~re~~~~K~~~ 129 (188)
..+|+..|+.|+...+.|+..
T Consensus 84 ~~plk~~Le~yk~~~k~Kk~~ 104 (172)
T KOG0870|consen 84 VNPLKSALEAYKKAVKQKKLA 104 (172)
T ss_pred hhHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999887653
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=99.72 E-value=1e-17 Score=116.87 Aligned_cols=64 Identities=39% Similarity=0.635 Sum_probs=59.3
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHh
Q 044287 36 LLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWAL 100 (188)
Q Consensus 36 ~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL 100 (188)
.||.+.|.||||.. |+..+||+||..+|++|+++||.||+.+|++.|..++||||+++||..||
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 88899999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.69 E-value=3.3e-17 Score=123.47 Aligned_cols=82 Identities=33% Similarity=0.434 Sum_probs=76.2
Q ss_pred CCCCCccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCC
Q 044287 26 DDGGIKEQERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGF 105 (188)
Q Consensus 26 ~~~~~~~~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF 105 (188)
..+..+..+..||+++|.||||++++. |||.+|+++|++|+++|+..|+..|+++|.|+|||||+++||..|++.+||
T Consensus 9 ~r~~~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~ 86 (91)
T COG2036 9 IRRYQRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGR 86 (91)
T ss_pred HHhhhhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcc
Confidence 445567788999999999999999964 999999999999999999999999999999999999999999999999999
Q ss_pred Ccch
Q 044287 106 DDYA 109 (188)
Q Consensus 106 ~dyi 109 (188)
..|.
T Consensus 87 ~~~~ 90 (91)
T COG2036 87 RIYG 90 (91)
T ss_pred cccc
Confidence 8764
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=99.33 E-value=4.8e-12 Score=94.40 Aligned_cols=72 Identities=18% Similarity=0.278 Sum_probs=67.7
Q ss_pred ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcc
Q 044287 35 RLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDY 108 (188)
Q Consensus 35 ~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dy 108 (188)
..||+++|.||++... ..+||.|+.+.+.++..+|+..|...|..+|++++||||+++||..||+..|-.-|
T Consensus 12 ~gi~k~~I~RLarr~G--vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 12 KGITKPAIRRLARRGG--VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred ccCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 3599999999999997 78999999999999999999999999999999999999999999999999986544
No 8
>PLN00035 histone H4; Provisional
Probab=99.28 E-value=7e-12 Score=96.56 Aligned_cols=80 Identities=19% Similarity=0.223 Sum_probs=72.2
Q ss_pred CCCCCCccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcC
Q 044287 25 SDDGGIKEQERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLG 104 (188)
Q Consensus 25 ~~~~~~~~~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LG 104 (188)
.+...+......||+++|.||++... ..|||.++.++|.+..++|+..|+..|..+|++++||||+++||..||+.+|
T Consensus 18 r~~k~~~d~i~~ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g 95 (103)
T PLN00035 18 RHRKVLRDNIQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
T ss_pred HHHHHHHhhhccCCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcC
Confidence 45555555666799999999999997 7899999999999999999999999999999999999999999999999876
Q ss_pred CC
Q 044287 105 FD 106 (188)
Q Consensus 105 F~ 106 (188)
=.
T Consensus 96 ~~ 97 (103)
T PLN00035 96 RT 97 (103)
T ss_pred Cc
Confidence 54
No 9
>PTZ00015 histone H4; Provisional
Probab=99.25 E-value=1.8e-11 Score=94.16 Aligned_cols=81 Identities=20% Similarity=0.295 Sum_probs=72.4
Q ss_pred CCCCCccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCC
Q 044287 26 DDGGIKEQERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGF 105 (188)
Q Consensus 26 ~~~~~~~~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF 105 (188)
+.+.++.....||+++|.||++... ..|||.|+.+.+.++.++|+..|...|..+|++++||||+++||..||+..|-
T Consensus 20 ~rk~~r~~i~gI~k~~IrRLarr~G--vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~ 97 (102)
T PTZ00015 20 QKKVLRDNIRGITKGAIRRLARRGG--VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR 97 (102)
T ss_pred HHHHHhhcccCCCHHHHHHHHHHcC--CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC
Confidence 3444555566899999999999997 78999999999999999999999999999999999999999999999999886
Q ss_pred Ccc
Q 044287 106 DDY 108 (188)
Q Consensus 106 ~dy 108 (188)
.-|
T Consensus 98 ~~y 100 (102)
T PTZ00015 98 TLY 100 (102)
T ss_pred CCC
Confidence 543
No 10
>smart00417 H4 Histone H4.
Probab=99.09 E-value=1.3e-10 Score=84.72 Aligned_cols=64 Identities=19% Similarity=0.254 Sum_probs=60.0
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHH
Q 044287 34 ERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWA 99 (188)
Q Consensus 34 d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~A 99 (188)
-..||+++|.||++..+ ..+||.++.+.+.+..++|+..|...|..+|++++||||+++||..|
T Consensus 11 i~gI~k~~IrRLaRr~G--vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 11 IQGITKPAIRRLARRGG--VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred hcCCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 34699999999999997 68999999999999999999999999999999999999999999754
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=99.06 E-value=4.7e-10 Score=79.54 Aligned_cols=64 Identities=28% Similarity=0.280 Sum_probs=61.0
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 36 LLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 36 ~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
.||+++|.||++..+ ..+||.|+..+|.+-++.|+.-|..+|..++++.+||||+++||-.||+
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 589999999999987 5689999999999999999999999999999999999999999999985
No 12
>smart00428 H3 Histone H3.
Probab=98.87 E-value=4.8e-09 Score=81.11 Aligned_cols=73 Identities=18% Similarity=0.223 Sum_probs=66.4
Q ss_pred ccccccCchhHHHHHHhhhCCC-----CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhc
Q 044287 31 KEQERLLPIANVGRIMKQILPA-----NAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTL 103 (188)
Q Consensus 31 ~~~d~~LPkA~I~RImK~~LP~-----~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~L 103 (188)
+..++.+|+.+..|+++++... +.+++.+|..+||++++.|+.-+...|+..|.+.+|+||+++|+.-|..--
T Consensus 24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir 101 (105)
T smart00428 24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIR 101 (105)
T ss_pred cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHh
Confidence 4477899999999999998863 789999999999999999999999999999999999999999998776533
No 13
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=98.81 E-value=8.2e-09 Score=72.96 Aligned_cols=68 Identities=29% Similarity=0.399 Sum_probs=62.9
Q ss_pred cccCchhHHHHHHhhhCCC---CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 34 ERLLPIANVGRIMKQILPA---NAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 34 d~~LPkA~I~RImK~~LP~---~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
...+|+..|.|+.|+..++ ..+||.+|...|+..++.|+.-|...|..+|.+.+|+||++.||..|++
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 4578999999999998863 2699999999999999999999999999999999999999999999985
No 14
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=98.81 E-value=2e-08 Score=72.11 Aligned_cols=65 Identities=17% Similarity=0.354 Sum_probs=61.7
Q ss_pred CchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 37 LPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 37 LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
|++..+..++++.-| ..+++.||.++|++.+..|+.-|+..|..+|.+.||+||.++||.-+|+.
T Consensus 2 ~~k~~l~~lv~~id~-~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 2 LTKRKLQELLKEIDP-REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred CcHHHHHHHHHhhCC-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 678899999999976 69999999999999999999999999999999999999999999999975
No 15
>PLN00160 histone H3; Provisional
Probab=98.49 E-value=3.4e-07 Score=70.04 Aligned_cols=71 Identities=15% Similarity=0.146 Sum_probs=64.9
Q ss_pred ccccccCchhHHHHHHhhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 31 KEQERLLPIANVGRIMKQILP----ANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 31 ~~~d~~LPkA~I~RImK~~LP----~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
+..++.+|+++..|+++++.. .+.++..+|..+||++++.|+.-+...|+-.|.+.+|.||.+.|+.-|..
T Consensus 16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 346789999999999999874 35899999999999999999999999999999999999999999987764
No 16
>PLN00121 histone H3; Provisional
Probab=98.48 E-value=2.5e-07 Score=74.60 Aligned_cols=71 Identities=18% Similarity=0.225 Sum_probs=65.3
Q ss_pred ccccccCchhHHHHHHhhhCCC---CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 31 KEQERLLPIANVGRIMKQILPA---NAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 31 ~~~d~~LPkA~I~RImK~~LP~---~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
+..++.||+....|+++++... ++++..+|..+||++++.|+.-|...++-.|.+.+|.||.+.|+.-|+.
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 4468899999999999998863 7899999999999999999999999999999999999999999987764
No 17
>PLN00161 histone H3; Provisional
Probab=98.47 E-value=5e-07 Score=72.74 Aligned_cols=71 Identities=20% Similarity=0.249 Sum_probs=65.2
Q ss_pred ccccccCchhHHHHHHhhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 31 KEQERLLPIANVGRIMKQILP----ANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 31 ~~~d~~LPkA~I~RImK~~LP----~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
+..++.||+....|+++++.. .++++..+|..+||++++.|+.-|...|+-.|.+.+|.||.+.|+.-|..
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 557889999999999999863 46899999999999999999999999999999999999999999987764
No 18
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=98.45 E-value=2e-07 Score=70.57 Aligned_cols=80 Identities=18% Similarity=0.218 Sum_probs=71.1
Q ss_pred CCCCCCccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcC
Q 044287 25 SDDGGIKEQERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLG 104 (188)
Q Consensus 25 ~~~~~~~~~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LG 104 (188)
.+.++++..-..+.+.+|+||.+... .-+|+.-..+.+...+.+|+..+.+.|..++++++||||++.||+.+|+.+|
T Consensus 18 rHRK~LsDnIqgitKpaIRRlARr~G--VkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G 95 (103)
T KOG3467|consen 18 RHRKVLRDNIQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG 95 (103)
T ss_pred HHHHHHHhhccccchHHHHHHHHhcC--cchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcC
Confidence 45555555555688999999999987 6789999999999999999999999999999999999999999999999987
Q ss_pred CC
Q 044287 105 FD 106 (188)
Q Consensus 105 F~ 106 (188)
--
T Consensus 96 ~~ 97 (103)
T KOG3467|consen 96 RT 97 (103)
T ss_pred ce
Confidence 54
No 19
>PTZ00018 histone H3; Provisional
Probab=98.45 E-value=3.6e-07 Score=73.68 Aligned_cols=71 Identities=18% Similarity=0.230 Sum_probs=65.1
Q ss_pred ccccccCchhHHHHHHhhhCC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 31 KEQERLLPIANVGRIMKQILP---ANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 31 ~~~d~~LPkA~I~RImK~~LP---~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
+..++.||+....|+++++.. .++++..+|.++||++++.|+..|...++-.|.|.+|.||.+.|+.-|..
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence 345889999999999999874 47899999999999999999999999999999999999999999987764
No 20
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.41 E-value=1.3e-06 Score=63.19 Aligned_cols=68 Identities=22% Similarity=0.254 Sum_probs=61.4
Q ss_pred CchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCC
Q 044287 37 LPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFD 106 (188)
Q Consensus 37 LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~ 106 (188)
|=+-.|.+|++.++ --+++..|.+.|.+....|+..|+..+..+|++.||+++++.||..||+.+|+.
T Consensus 7 ll~~~Vaqil~~~G--f~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 7 LLRIAVAQILESAG--FDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 33556788888875 458999999999999999999999999999999999999999999999999974
No 21
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.39 E-value=2e-07 Score=80.76 Aligned_cols=81 Identities=25% Similarity=0.256 Sum_probs=71.1
Q ss_pred ccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchH
Q 044287 31 KEQERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAG 110 (188)
Q Consensus 31 ~~~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~ 110 (188)
...+..||.|.|.|+||---. .-.||.||-.++.+.|+.||..||..|+-.|++++|+|+.-.||..|+++-++-||+-
T Consensus 104 ~~k~h~LPlARIkkvMKtded-VkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLi 182 (286)
T COG5208 104 LLKDHNLPLARIKKVMKTDED-VKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLI 182 (286)
T ss_pred HHHhccCcHHHHHHHHhcccc-hhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHh
Confidence 345678999999999997642 3369999999999999999999999999999999999999999999999988777764
Q ss_pred HH
Q 044287 111 PI 112 (188)
Q Consensus 111 ~l 112 (188)
.+
T Consensus 183 di 184 (286)
T COG5208 183 DI 184 (286)
T ss_pred hh
Confidence 33
No 22
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=98.24 E-value=2.5e-06 Score=66.93 Aligned_cols=68 Identities=12% Similarity=0.191 Sum_probs=62.7
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 34 ERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 34 d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
.+.||.+.|.|+||+... ..|||.+|...|..+.+-+...|...|...|.+.+|++|+++||..|+..
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 489999999999998432 58999999999999999999999999999999999999999999999974
No 23
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=98.13 E-value=9.9e-06 Score=63.35 Aligned_cols=77 Identities=13% Similarity=0.213 Sum_probs=65.2
Q ss_pred HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchHH-HHHHHHHH
Q 044287 41 NVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAGP-IRRYLHKY 119 (188)
Q Consensus 41 ~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~~-lk~~L~~~ 119 (188)
.|.+|+|+.. ..+++.++...|.+.+..++.-|..+|..+|.++||+||+++||.-|++..+-..|..+ -++.|-+.
T Consensus 6 ~v~~iLk~~G--v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~~ 83 (117)
T cd07979 6 VIAAILKSMG--ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLEL 83 (117)
T ss_pred HHHHHHHHCC--CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHHH
Confidence 5888888875 56899999999999999999999999999999999999999999999997665555443 55554433
No 24
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.11 E-value=3.1e-06 Score=73.55 Aligned_cols=89 Identities=24% Similarity=0.318 Sum_probs=74.6
Q ss_pred CccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh---cCCC
Q 044287 30 IKEQERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT---LGFD 106 (188)
Q Consensus 30 ~~~~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~---LGF~ 106 (188)
.+.-...||++.|.+|||..- +.-.|+.||..++.+||+.||..|+..|+..+...+|+|+...|+..|+.. ++|.
T Consensus 68 ~d~~~~~lPlaRiKkimK~de-dv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL 146 (236)
T KOG1657|consen 68 LDFKNHILPLARIKKIMKSDE-DVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFL 146 (236)
T ss_pred cchhhccCcHhhccccccccc-cccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccce
Confidence 334456799999999999875 233799999999999999999999999999999999999999999999986 5555
Q ss_pred cchHHHHHHHHHH
Q 044287 107 DYAGPIRRYLHKY 119 (188)
Q Consensus 107 dyi~~lk~~L~~~ 119 (188)
-.+-+.+..++.|
T Consensus 147 ~DivP~~~~~~~~ 159 (236)
T KOG1657|consen 147 RDIVPRKILAEKY 159 (236)
T ss_pred eccccchhccccc
Confidence 5555666666666
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=97.88 E-value=3.8e-05 Score=69.28 Aligned_cols=67 Identities=21% Similarity=0.253 Sum_probs=59.8
Q ss_pred chhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCC
Q 044287 38 PIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFD 106 (188)
Q Consensus 38 PkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~ 106 (188)
|..+|.-|++..+ ..++++||..+|.+.++.++..|+.+|...+++.+||||+++||-.||+.++.+
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 4567777888775 459999999999999999999999999999999999999999999999975544
No 26
>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=97.76 E-value=0.00012 Score=54.56 Aligned_cols=66 Identities=15% Similarity=0.196 Sum_probs=61.7
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CccCccCHHHHhhhc
Q 044287 36 LLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERR---KTVNGDDICWALGTL 103 (188)
Q Consensus 36 ~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kR---KTIt~eDVl~AL~~L 103 (188)
.||++.|.|||...+ +..++.+...+|.-.+.+||..|..+|.++..+.+. ..|.|+||-.|.+.|
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 599999999999999 489999999999999999999999999999998776 789999999999876
No 27
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.73 E-value=4.2e-05 Score=70.88 Aligned_cols=63 Identities=22% Similarity=0.338 Sum_probs=47.5
Q ss_pred ccccCchhHHHHHHhhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccC
Q 044287 33 QERLLPIANVGRIMKQILP----ANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDD 95 (188)
Q Consensus 33 ~d~~LPkA~I~RImK~~LP----~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eD 95 (188)
.--.||.+.|+|++..... ..++|++||..+|.+|...|-..|+..--.+|.|+|||||..+|
T Consensus 348 ~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 348 PYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ----S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3446999999998877643 57899999999999999999999999999999999999998765
No 28
>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=97.70 E-value=0.00021 Score=51.16 Aligned_cols=66 Identities=20% Similarity=0.244 Sum_probs=57.7
Q ss_pred hhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCC
Q 044287 39 IANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFD 106 (188)
Q Consensus 39 kA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~ 106 (188)
+-.|..|++.++ =-.++..|.+.|...+..||..|+..+..+|++.+|...+..||..||.++|+.
T Consensus 9 ~~~va~il~~~G--F~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 9 RRSVAQILKHAG--FDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 345566666653 237999999999999999999999999999999999999999999999999984
No 29
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=97.69 E-value=3e-05 Score=62.65 Aligned_cols=74 Identities=18% Similarity=0.244 Sum_probs=66.3
Q ss_pred ccccccCchhHHHHHHhhhCC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcC
Q 044287 31 KEQERLLPIANVGRIMKQILP---ANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLG 104 (188)
Q Consensus 31 ~~~d~~LPkA~I~RImK~~LP---~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LG 104 (188)
+..|+.+++....|++++..+ .+.++...|..+||++++.|+.-|...+|-+|.+.+|.||.+.||--|..--|
T Consensus 58 kstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg 134 (137)
T KOG1745|consen 58 KSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 134 (137)
T ss_pred hhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence 467889999999999995554 58899999999999999999999999999999999999999999998876544
No 30
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.60 E-value=0.0002 Score=52.42 Aligned_cols=62 Identities=18% Similarity=0.254 Sum_probs=52.4
Q ss_pred HHHHHHhhhC-CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 41 NVGRIMKQIL-PANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 41 ~I~RImK~~L-P~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
+|.+|+.+.. +.++.+|+.+..+|.+.+-.++..++..--..|+|+||+||+.+||+-..++
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr 72 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 5788888875 5678999999999999999999999999999999999999999999976653
No 31
>smart00427 H2B Histone H2B.
Probab=97.58 E-value=0.00025 Score=53.67 Aligned_cols=62 Identities=26% Similarity=0.402 Sum_probs=58.0
Q ss_pred HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhc
Q 044287 41 NVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTL 103 (188)
Q Consensus 41 ~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~L 103 (188)
-|.|++|++-| +..||..|...|.-.+..+..-|+.+|...|...+|+||++.+|..|.+-+
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 58999999998 689999999999999999999999999999999999999999999998754
No 32
>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=97.52 E-value=0.00033 Score=50.24 Aligned_cols=63 Identities=22% Similarity=0.341 Sum_probs=51.5
Q ss_pred hhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 39 IANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 39 kA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
+..+..+|+++-| +..+..++.++|.+.|.+||.-++..|...|++-+-.||...||.-.|++
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 89999999999999999999999999999999999999999999988874
No 33
>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=97.38 E-value=0.00021 Score=51.81 Aligned_cols=65 Identities=20% Similarity=0.273 Sum_probs=54.7
Q ss_pred chhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-cCccCHHHHhhh
Q 044287 38 PIANVGRIMKQILP-ANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKT-VNGDDICWALGT 102 (188)
Q Consensus 38 PkA~I~RImK~~LP-~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKT-It~eDVl~AL~~ 102 (188)
|+.+|.||++.... +..+|++||..++.+....||..-..-|...+..++..+ |..+|+-+.+-.
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 88999999998774 578999999999999999999999999999999999999 999999887654
No 34
>PLN00158 histone H2B; Provisional
Probab=97.33 E-value=0.00072 Score=53.40 Aligned_cols=67 Identities=22% Similarity=0.315 Sum_probs=60.7
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhc
Q 044287 36 LLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTL 103 (188)
Q Consensus 36 ~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~L 103 (188)
.--..-|.|++|++-| +..||..|...|.-....+..-|+.+|...|...+|.||++.+|..|.+-+
T Consensus 27 esy~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 27 ETYKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred ccHHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 3445679999999998 689999999999999999999999999999999999999999999998754
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=97.30 E-value=0.0011 Score=47.46 Aligned_cols=64 Identities=27% Similarity=0.273 Sum_probs=50.1
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 36 LLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 36 ~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
.+|..+|.-+....+ -..++.|+...|.+-++--|..|..+|...+.+.+|++++++||-.||+
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 467788877776654 3489999999999999999999999999999999999999999999985
No 36
>PTZ00463 histone H2B; Provisional
Probab=97.29 E-value=0.00089 Score=52.94 Aligned_cols=64 Identities=25% Similarity=0.391 Sum_probs=58.6
Q ss_pred hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcC
Q 044287 40 ANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLG 104 (188)
Q Consensus 40 A~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LG 104 (188)
.-|.|++|++-| +..||..|...|.-.......-|+.+|...|...+|.||++.+|..|++-+=
T Consensus 32 ~YI~KVLKqVhP-d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLlL 95 (117)
T PTZ00463 32 LYIFKVLKQVHP-DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVL 95 (117)
T ss_pred HHHHHHHHhhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhcc
Confidence 359999999998 6899999999999999999999999999999999999999999999987543
No 37
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=97.27 E-value=0.0008 Score=50.85 Aligned_cols=67 Identities=18% Similarity=0.216 Sum_probs=51.6
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-ccCccCHHHHhhhc
Q 044287 36 LLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRK-TVNGDDICWALGTL 103 (188)
Q Consensus 36 ~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRK-TIt~eDVl~AL~~L 103 (188)
.||++.|.|||...+. +..|+.....+|.-.+..||-.|-.+|.+++.+.+.. .|.+.|+-.|.++|
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 5999999999999994 4899999999999999999999999999999865544 79999999998765
No 38
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.16 E-value=0.00096 Score=57.64 Aligned_cols=86 Identities=15% Similarity=0.168 Sum_probs=74.0
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchHHHHHH
Q 044287 36 LLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAGPIRRY 115 (188)
Q Consensus 36 ~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~~lk~~ 115 (188)
-||.+.|.|||...- +--+|..-+-..+.++.+.|+.-|...+.++++..+-|||+++|+..|+..-.-.||+..+...
T Consensus 13 rfp~aRiKKIMQ~dE-dIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~v~~ 91 (224)
T KOG1659|consen 13 RFPPARIKKIMQSDE-DIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEVVEK 91 (224)
T ss_pred cCCHHHHHHHHhhhh-hhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHHHHh
Confidence 599999999998754 2348999999999999999999999999999999999999999999999988888888776665
Q ss_pred HHHHHHH
Q 044287 116 LHKYREL 122 (188)
Q Consensus 116 L~~~re~ 122 (188)
+..+...
T Consensus 92 vpd~~~~ 98 (224)
T KOG1659|consen 92 VPDRQQA 98 (224)
T ss_pred cCCCccc
Confidence 5554443
No 39
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=96.93 E-value=0.0024 Score=50.89 Aligned_cols=69 Identities=16% Similarity=0.235 Sum_probs=60.4
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 33 QERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 33 ~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
..+.+|...|.||||.. .-.+||+++|...+.-|.+=.+..|+.-|-..|...++|.|+|.|+-.|+..
T Consensus 23 agl~fpvgrvkr~lk~~-~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrn 91 (132)
T COG5262 23 AGLIFPVGRVKRLLKKG-NYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRN 91 (132)
T ss_pred cCccccHHHHHHHHHcC-ccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcC
Confidence 45789999999999933 3478999999999999998888888888888899999999999999999873
No 40
>smart00414 H2A Histone 2A.
Probab=96.77 E-value=0.0038 Score=48.35 Aligned_cols=68 Identities=9% Similarity=0.210 Sum_probs=59.9
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 34 ERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 34 d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
.+.||-+.|.|+||+.-- ..||+..|...|..+.+-+...|..-|...|...+++.|+++||..|+..
T Consensus 7 gL~fPVgRi~r~Lk~~~~-~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 7 GLQFPVGRIHRLLRKGTY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred CccCchHHHHHHHHcCcc-ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 478999999999998743 46999999999999888888888888888899999999999999999974
No 41
>PLN00154 histone H2A; Provisional
Probab=96.57 E-value=0.012 Score=47.64 Aligned_cols=70 Identities=13% Similarity=0.180 Sum_probs=59.0
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 33 QERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 33 ~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
..+.||-+.|.|++|+...-..||+..|...|.-+.+=+...|..-|-..|...+++-|++.||..|+..
T Consensus 35 AgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 35 AGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred cCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 4678999999999999764357999999999988877666666667777889999999999999999863
No 42
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=96.51 E-value=0.0047 Score=48.16 Aligned_cols=78 Identities=17% Similarity=0.189 Sum_probs=66.3
Q ss_pred ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchHHHH
Q 044287 35 RLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAGPIR 113 (188)
Q Consensus 35 ~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~~lk 113 (188)
..+|.|.|.|||.-.- +--+|+.-.-..+.++.+.|+..|-......|+..+-|-|+++++..|...-+=.||+..+.
T Consensus 22 trFP~ar~KkIMQ~de-DiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~ 99 (113)
T COG5247 22 TRFPIARLKKIMQLDE-DIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNME 99 (113)
T ss_pred hcCCHHHHHHHHHhhh-hhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHH
Confidence 3599999999998654 23489999999999999999999999999999999999999999999998765555554443
No 43
>PLN00157 histone H2A; Provisional
Probab=96.33 E-value=0.015 Score=46.84 Aligned_cols=69 Identities=12% Similarity=0.168 Sum_probs=59.5
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 33 QERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 33 ~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
..+.||...|.|++|+.-- ..||+..|...|.-+.+-.+..|..-|...|...+++-|+++||..|+..
T Consensus 23 agL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 91 (132)
T PLN00157 23 AGLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN 91 (132)
T ss_pred cCcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence 4589999999999999643 46999999999998888777777777888899999999999999999963
No 44
>PLN00153 histone H2A; Provisional
Probab=96.29 E-value=0.015 Score=46.75 Aligned_cols=69 Identities=13% Similarity=0.187 Sum_probs=59.8
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 33 QERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 33 ~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
..+.||...|.|++|+.-. ..||+..|...|.-+.+-.+..|..-|-..|...+++-|+++||..|+..
T Consensus 21 agL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 89 (129)
T PLN00153 21 AGLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN 89 (129)
T ss_pred cCcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence 4589999999999998654 46999999999998888777777777888889999999999999999963
No 45
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.27 E-value=0.013 Score=51.81 Aligned_cols=69 Identities=19% Similarity=0.334 Sum_probs=63.6
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 33 QERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 33 ~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
....|-+-.|.-+++.+- .+..|-.|+.++|.+.|..||..|+..|...|++.+..||-+.||.-.|++
T Consensus 151 ~~~il~k~kl~dLvqqId-~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr 219 (258)
T KOG1142|consen 151 NNPILSKRKLDDLVQQID-GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLER 219 (258)
T ss_pred CCccccccchhHHHHhhc-CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeec
Confidence 445688889999999985 478999999999999999999999999999999999999999999999995
No 46
>PTZ00017 histone H2A; Provisional
Probab=96.25 E-value=0.0087 Score=48.36 Aligned_cols=69 Identities=13% Similarity=0.187 Sum_probs=60.7
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 33 QERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 33 ~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
..+.||-+.|.|+|++.-- ..||+..|...|.-+.+-+...|..-|...|...+++-|+++||..|+..
T Consensus 24 agL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 24 AGLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN 92 (134)
T ss_pred CCcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence 4588999999999998642 46999999999999988888888888888999999999999999999963
No 47
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.14 E-value=0.017 Score=46.41 Aligned_cols=62 Identities=29% Similarity=0.372 Sum_probs=57.0
Q ss_pred HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhc
Q 044287 41 NVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTL 103 (188)
Q Consensus 41 ~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~L 103 (188)
.|.|++|++-|+ ..|+.++...|.-..-.++..|+.+|+..+...+|.||+..+|..|.+-|
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 477899999985 88999999999999999999999999999999999999999999987643
No 48
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.11 E-value=0.012 Score=47.27 Aligned_cols=68 Identities=10% Similarity=0.206 Sum_probs=55.3
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 33 QERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 33 ~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
..+.+|...|.|++|+ ..-..+|+.+|...|.-|.+=.+..|+..|-..+..+++.-|++.||..|+.
T Consensus 24 agl~fPvgri~r~Lr~-~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 24 AGLQFPVGRIHRLLRK-GRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred cccccCHHHHHHHHHc-cchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 4578999999999999 3336799999999999776655555555666677788888999999999996
No 49
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=96.09 E-value=0.0055 Score=52.26 Aligned_cols=69 Identities=17% Similarity=0.214 Sum_probs=61.3
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-ccCccCHHHHhhhcCCC
Q 044287 36 LLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRK-TVNGDDICWALGTLGFD 106 (188)
Q Consensus 36 ~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRK-TIt~eDVl~AL~~LGF~ 106 (188)
.||+++|.|||..+.. -.|+.-+..+|.-.+.+||-.|--+|.++|..-+.. .|.+.||-.|...|+..
T Consensus 112 ~f~Ka~iKkL~~~itg--~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~q 181 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITG--QSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQ 181 (195)
T ss_pred cCCHHHHHHHHHHHhC--CccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhc
Confidence 5999999999999995 339999999999999999999999999999977663 49999999998887654
No 50
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.07 E-value=0.0081 Score=46.06 Aligned_cols=67 Identities=15% Similarity=0.209 Sum_probs=55.1
Q ss_pred ccCchhHHHHHHhhhCCCCccccHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHh
Q 044287 35 RLLPIANVGRIMKQILPANAKISKEAKET--------------MQECVSEFISFITSEASEKCRKERRKTVNGDDICWAL 100 (188)
Q Consensus 35 ~~LPkA~I~RImK~~LP~~~rISkDA~~a--------------l~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL 100 (188)
..-|++.+.|++|..-| ..++...+-.+ +.-.|-.|++-|+.+|...|=+++=.||..+||+.|-
T Consensus 15 rkaPrgfLkrv~Kr~Kp-hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~Aaa 93 (102)
T PF15510_consen 15 RKAPRGFLKRVFKRQKP-HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAA 93 (102)
T ss_pred HhCchHHHHHHHHhcCC-ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHH
Confidence 35799999999998887 56665544444 5566889999999999999999999999999999887
Q ss_pred hh
Q 044287 101 GT 102 (188)
Q Consensus 101 ~~ 102 (188)
+.
T Consensus 94 Kv 95 (102)
T PF15510_consen 94 KV 95 (102)
T ss_pred HH
Confidence 53
No 51
>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=95.86 E-value=0.011 Score=44.40 Aligned_cols=60 Identities=18% Similarity=0.264 Sum_probs=30.0
Q ss_pred HHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 42 VGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 42 I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
|..+|-.-+ +...-..|...+|-+.+.+||..|...|..+|...|+++|+.+|++-+|+.
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 445555544 456788999999999999999999999999999999999999999999985
No 52
>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=95.78 E-value=0.033 Score=44.55 Aligned_cols=85 Identities=20% Similarity=0.259 Sum_probs=49.7
Q ss_pred ccccCchh--HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhh-hcCCCcch
Q 044287 33 QERLLPIA--NVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALG-TLGFDDYA 109 (188)
Q Consensus 33 ~d~~LPkA--~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~-~LGF~dyi 109 (188)
..-.+|+. .|.-|+|+.+ .......+...|.+.+-.|+.-|...|..++.+.+|++|+.+||.-|++ .+++.-..
T Consensus 7 ~~~~~PrDa~~i~~iL~~~G--v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~ 84 (129)
T PF02291_consen 7 QSKSLPRDARVIHLILKSMG--VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQ 84 (129)
T ss_dssp ------HHHHHHHHHHHHTT-----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-------
T ss_pred CCccCChHHHHHHHHHHHcC--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccC
Confidence 33467774 5666667664 3457888999999999999999999999999999999999999999999 57777666
Q ss_pred HHHHHHHHHH
Q 044287 110 GPIRRYLHKY 119 (188)
Q Consensus 110 ~~lk~~L~~~ 119 (188)
++-+++|-+.
T Consensus 85 pppre~llel 94 (129)
T PF02291_consen 85 PPPREFLLEL 94 (129)
T ss_dssp ----------
T ss_pred CCChHHHHHH
Confidence 6666655443
No 53
>PLN00156 histone H2AX; Provisional
Probab=95.74 E-value=0.022 Score=46.39 Aligned_cols=69 Identities=12% Similarity=0.179 Sum_probs=58.2
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 33 QERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 33 ~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
..+.||...|.|++++.-- ..||+..|...|.-+.+=.+..|..-|-..|...+++-|+++||..|+..
T Consensus 26 AgL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrn 94 (139)
T PLN00156 26 AGLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN 94 (139)
T ss_pred cCcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccC
Confidence 3578999999999999643 46999999999998877666667777777888899999999999999963
No 54
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=95.37 E-value=0.013 Score=48.62 Aligned_cols=66 Identities=21% Similarity=0.306 Sum_probs=58.1
Q ss_pred ccCchhHHHHHHhhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 35 RLLPIANVGRIMKQILPANAK-ISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 35 ~~LPkA~I~RImK~~LP~~~r-ISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
..||.+.|..+||. +++.+ ...+++.+|.+++..||..|+..|+..+...+|||+.-.|+-.|++.
T Consensus 58 ~rLpL~rik~vvkl--~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~ 124 (162)
T KOG1658|consen 58 SRLPLARIKQVVKL--DPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEA 124 (162)
T ss_pred hhccHHHHHhhccC--CcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccc
Confidence 57999999999985 45665 56778899999999999999999999999999999999988887765
No 55
>PTZ00252 histone H2A; Provisional
Probab=93.79 E-value=0.16 Score=41.15 Aligned_cols=69 Identities=10% Similarity=0.196 Sum_probs=50.2
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCccCHHHHhhh
Q 044287 33 QERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRK--ERRKTVNGDDICWALGT 102 (188)
Q Consensus 33 ~d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~--~kRKTIt~eDVl~AL~~ 102 (188)
..+.||-+.|.|++++.-- ..||+.-|...|.-+.+=....|..-|...|.. .+++-|+++||..|+..
T Consensus 22 AGL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN 92 (134)
T PTZ00252 22 AGLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH 92 (134)
T ss_pred cCccCchHHHHHHHHcCCc-ccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence 3489999999999998764 469999999888876553333333334444432 46678999999999863
No 56
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=93.29 E-value=0.41 Score=36.10 Aligned_cols=61 Identities=20% Similarity=0.284 Sum_probs=50.1
Q ss_pred hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 40 ANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 40 A~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
.-|..+|-..+ +...-..|...+|-+...+||..|+..|..+|. .++.-|+.||++-+|+.
T Consensus 6 ~ei~~mmy~~G-D~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~ 66 (92)
T cd07978 6 KEIRQMMYGFG-DVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK 66 (92)
T ss_pred HHHHHHHHHcC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence 34667777665 345678899999999999999999999999999 44445699999999974
No 57
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=92.99 E-value=0.41 Score=40.30 Aligned_cols=69 Identities=19% Similarity=0.242 Sum_probs=56.7
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--------------CCccCccCHHHHhh
Q 044287 36 LLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKER--------------RKTVNGDDICWALG 101 (188)
Q Consensus 36 ~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~k--------------RKTIt~eDVl~AL~ 101 (188)
.||-+.+.-.++.++ -.....-.+-+|.=++-.||.-|+..|.++|+-.. |-|++-+|+..||+
T Consensus 86 ~IPDavt~~yL~~aG--f~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~ 163 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKAG--FQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALA 163 (176)
T ss_pred CCcHHHHHHHHHhcC--CCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHH
Confidence 688888888888876 22344556788899999999999999999998443 55899999999999
Q ss_pred hcCCC
Q 044287 102 TLGFD 106 (188)
Q Consensus 102 ~LGF~ 106 (188)
+.|..
T Consensus 164 EyGin 168 (176)
T KOG3423|consen 164 EYGIN 168 (176)
T ss_pred HhCcc
Confidence 98874
No 58
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=92.64 E-value=0.53 Score=42.93 Aligned_cols=77 Identities=21% Similarity=0.248 Sum_probs=64.3
Q ss_pred HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchHHHHHHHHHHH
Q 044287 41 NVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAGPIRRYLHKYR 120 (188)
Q Consensus 41 ~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~~lk~~L~~~r 120 (188)
.|.-|.+..+ =-.|++-|++.|.+....+|.-+...+.-+|+.+||-..+.-||.-+|-.+|+. +..|..+++.+.
T Consensus 10 VV~~Ll~~~g--fd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~ 85 (323)
T KOG4336|consen 10 VVSNLLKTKG--FDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQE 85 (323)
T ss_pred HHHHHHHHhC--chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhcc
Confidence 4444555544 224999999999999999999999999999999999999999999999999998 677777765554
Q ss_pred H
Q 044287 121 E 121 (188)
Q Consensus 121 e 121 (188)
.
T Consensus 86 ~ 86 (323)
T KOG4336|consen 86 F 86 (323)
T ss_pred c
Confidence 4
No 59
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=90.56 E-value=0.83 Score=44.62 Aligned_cols=65 Identities=23% Similarity=0.266 Sum_probs=55.3
Q ss_pred chhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcC
Q 044287 38 PIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLG 104 (188)
Q Consensus 38 PkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LG 104 (188)
|+-.+.-+++..+ -..|+.||..+|.+-.+.=|..|+.+|.+.-.+.+|.+++.+||..||+.+.
T Consensus 13 ~~Es~k~vAEslG--i~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 13 PKESVKVVAESLG--ITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred cHHHHHHHHHHhC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 3555555555543 4569999999999999999999999999999999999999999999999643
No 60
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=88.77 E-value=1.1 Score=37.40 Aligned_cols=69 Identities=12% Similarity=0.227 Sum_probs=54.4
Q ss_pred CchhHHHHHHhhhCC-----CCccccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCC
Q 044287 37 LPIANVGRIMKQILP-----ANAKISKEAKETMQECVSE---FISFITSEASEKCRKERRKTVNGDDICWALGTLGF 105 (188)
Q Consensus 37 LPkA~I~RImK~~LP-----~~~rISkDA~~al~eca~e---FI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF 105 (188)
|...-+..++...+. ....++.++.+.|.+.+.= .|+.++..|...+-..+.++|+.++|..++..+.|
T Consensus 192 l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~ 268 (269)
T TIGR03015 192 LDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF 268 (269)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence 444555555544331 2346999999999998864 79999999999988899999999999999998865
No 61
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=85.53 E-value=3.7 Score=33.83 Aligned_cols=79 Identities=14% Similarity=0.256 Sum_probs=58.7
Q ss_pred Cchh--HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchH-HHH
Q 044287 37 LPIA--NVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAG-PIR 113 (188)
Q Consensus 37 LPkA--~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~-~lk 113 (188)
-|+. .|.-|+|+.. ---...-....|.+.+=.++.-|...|.-++.++++.||.++||..|+.-.+=-+|.+ +=+
T Consensus 12 ~pkDa~~i~~iL~s~G--I~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpR 89 (148)
T KOG3334|consen 12 VPKDARVIASILKSLG--IQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPR 89 (148)
T ss_pred CcHHHHHHHHHHHHcC--ccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCch
Confidence 4554 2444445443 2235666777888899999999999999999999999999999999999777666666 444
Q ss_pred HHHH
Q 044287 114 RYLH 117 (188)
Q Consensus 114 ~~L~ 117 (188)
++|-
T Consensus 90 e~lL 93 (148)
T KOG3334|consen 90 EFLL 93 (148)
T ss_pred HHHH
Confidence 4443
No 62
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=85.45 E-value=1.6 Score=40.45 Aligned_cols=69 Identities=20% Similarity=0.207 Sum_probs=58.3
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCC
Q 044287 36 LLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFD 106 (188)
Q Consensus 36 ~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~ 106 (188)
.|-+..|..|.....-. ....-|.+.|+..+..||+-|+..|..++...||--.+.-||+.||+.|+..
T Consensus 29 sla~~avaQIcqslg~~--~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 29 SLARVAVAQICQSLGYS--STQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHhcCCc--ccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 46667888888776532 3334499999999999999999999999999999999999999999987654
No 63
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=83.91 E-value=3.7 Score=36.49 Aligned_cols=70 Identities=11% Similarity=0.116 Sum_probs=51.7
Q ss_pred hhHHHHHHhhhCCC---CccccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcc
Q 044287 39 IANVGRIMKQILPA---NAKISKEAKETMQECV------SEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDY 108 (188)
Q Consensus 39 kA~I~RImK~~LP~---~~rISkDA~~al~eca------~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dy 108 (188)
...+..|++..+.. ...++.++.+.+.+.+ ...+..+...|...|...++.+|+.+||..|+..+....+
T Consensus 209 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~ 287 (394)
T PRK00411 209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHL 287 (394)
T ss_pred HHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHH
Confidence 45566666655421 2358999999988877 3455566788888999999999999999999998844333
No 64
>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=78.57 E-value=5.6 Score=34.88 Aligned_cols=74 Identities=12% Similarity=0.047 Sum_probs=50.9
Q ss_pred hhHHHHHHhhhCC---CCccccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcch
Q 044287 39 IANVGRIMKQILP---ANAKISKEAKETMQECVS------EFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYA 109 (188)
Q Consensus 39 kA~I~RImK~~LP---~~~rISkDA~~al~eca~------eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi 109 (188)
..-+..|++..+. ....++.++...+.+.+. ..+..+...|...|...++.+|+.+||..|+..+....+.
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 3446677765542 123588888887766442 3445566678888989999999999999999988544444
Q ss_pred HHH
Q 044287 110 GPI 112 (188)
Q Consensus 110 ~~l 112 (188)
..+
T Consensus 281 ~~i 283 (365)
T TIGR02928 281 ELI 283 (365)
T ss_pred HHH
Confidence 333
No 65
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=76.70 E-value=8 Score=37.22 Aligned_cols=49 Identities=18% Similarity=0.232 Sum_probs=38.3
Q ss_pred cccHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhc
Q 044287 55 KISKEAKETMQECVS-----------EFISFITSEASEKCRKERRKTVNGDDICWALGTL 103 (188)
Q Consensus 55 rISkDA~~al~eca~-----------eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~L 103 (188)
-++.+|...|.+.+. .-|.-|..+|+.+|..+++++|+++||..|++.-
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 578888887777664 3567788999999999999999999999999753
No 66
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=75.86 E-value=2.1 Score=42.43 Aligned_cols=33 Identities=24% Similarity=0.339 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 69 SEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 69 ~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
..-...|. +|+.+|..++++-|+++||.+|++.
T Consensus 366 rdl~~lv~-~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 366 RDLGNLVR-EAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred HHHHHHHH-HhhHHHhcCCcccCcHHHHHHHHHh
Confidence 44444444 8999999999999999999999986
No 67
>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=73.64 E-value=8 Score=37.04 Aligned_cols=67 Identities=21% Similarity=0.208 Sum_probs=46.2
Q ss_pred hhHHHHHHhhhCC-CCccccHHHHHHHHHHHHH--HHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCC
Q 044287 39 IANVGRIMKQILP-ANAKISKEAKETMQECVSE--FISFITSEASEKCRKERRKTVNGDDICWALGTLGF 105 (188)
Q Consensus 39 kA~I~RImK~~LP-~~~rISkDA~~al~eca~e--FI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF 105 (188)
..-+..|++..+. -++.++.++.+.|...+.. .+..+...|..+|..++|++|+.+||.|++..-.|
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 3446666666553 2467999999988777652 22233345666888889999999999999764433
No 68
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=70.22 E-value=12 Score=36.55 Aligned_cols=49 Identities=10% Similarity=0.110 Sum_probs=40.5
Q ss_pred cccHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhc
Q 044287 55 KISKEAKETMQECVS-------------EFISFITSEASEKCRKERRKTVNGDDICWALGTL 103 (188)
Q Consensus 55 rISkDA~~al~eca~-------------eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~L 103 (188)
.++.+|...|.+.++ .=+.-|..+|..+|..++..+|+.+||..|++.-
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 689999999886554 3456677788899999999999999999999754
No 69
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=68.78 E-value=26 Score=29.76 Aligned_cols=68 Identities=16% Similarity=0.238 Sum_probs=47.4
Q ss_pred CchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHH-hc-----------------------------
Q 044287 37 LPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCR-KE----------------------------- 86 (188)
Q Consensus 37 LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~-~~----------------------------- 86 (188)
||-+.+.=.|-.+. -.....-.+.+|.-.+..||.-|+-.|.++.+ +.
T Consensus 89 iPd~v~DYyl~k~G--f~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~ 166 (197)
T COG5162 89 IPDSVTDYYLEKAG--FVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRR 166 (197)
T ss_pred ccHHHHHHHHHhcC--ceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccc
Confidence 44444444444432 12344556788888999999999999888654 11
Q ss_pred ---CCCccCccCHHHHhhhcCCC
Q 044287 87 ---RRKTVNGDDICWALGTLGFD 106 (188)
Q Consensus 87 ---kRKTIt~eDVl~AL~~LGF~ 106 (188)
++-+++..|+..||++.|..
T Consensus 167 ~dr~K~vltv~DLs~Al~EyGin 189 (197)
T COG5162 167 GDRKKPVLTVVDLSKALEEYGIN 189 (197)
T ss_pred cccCCceeeehHHHHHHHHhccc
Confidence 55678999999999998864
No 70
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=68.63 E-value=21 Score=30.06 Aligned_cols=72 Identities=10% Similarity=0.103 Sum_probs=53.4
Q ss_pred ccCchhHHHHHHhhhCCC-Cc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCccCccCHHHHhhhcCCC
Q 044287 35 RLLPIANVGRIMKQILPA-NA-KISKEAKETMQECVSEFISFITSEASEKCRKE------RRKTVNGDDICWALGTLGFD 106 (188)
Q Consensus 35 ~~LPkA~I~RImK~~LP~-~~-rISkDA~~al~eca~eFI~~LtseAne~a~~~------kRKTIt~eDVl~AL~~LGF~ 106 (188)
..|....|.+.|...+.. +. .|+.|+..+|.-||..++..|.......|.+- ...++--.||-.-|..|.--
T Consensus 43 ~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~~~ 122 (212)
T cd08045 43 SFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLEQL 122 (212)
T ss_pred hccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHHHH
Confidence 456666666666555532 12 79999999999999999999999999999864 34566677887777655543
No 71
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=68.18 E-value=17 Score=34.00 Aligned_cols=66 Identities=21% Similarity=0.257 Sum_probs=54.2
Q ss_pred hhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCC
Q 044287 39 IANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFD 106 (188)
Q Consensus 39 kA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~ 106 (188)
+.+|.-+... ++ -..|..|+..+|..-.+==|+.+..+|...-.+.+|..++-+||-.||+.|..+
T Consensus 8 ~et~KdvAes-lG-i~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 8 KETLKDVAES-LG-ISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred HHHHHHHHHH-cC-CcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 3444444433 31 357999999999999999999999999999999999999999999999987654
No 72
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=67.48 E-value=33 Score=23.47 Aligned_cols=47 Identities=17% Similarity=0.219 Sum_probs=36.7
Q ss_pred cCchhHHHHHHhhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 044287 36 LLPIANVGRIMKQILPANAK-ISKEAKETMQECVSEFISFITSEASEKCRK 85 (188)
Q Consensus 36 ~LPkA~I~RImK~~LP~~~r-ISkDA~~al~eca~eFI~~LtseAne~a~~ 85 (188)
.+|-+.+.-+++.++ +. -..-.+-+|.=++..||..|+..|.++|+-
T Consensus 2 ~IPD~v~~~yL~~~G---~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSG---FQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCC---CCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 478888888998886 32 233445678888899999999999999873
No 73
>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=65.80 E-value=5.6 Score=26.21 Aligned_cols=42 Identities=17% Similarity=0.180 Sum_probs=29.1
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcCCCccCccCHHHH
Q 044287 57 SKEAKETMQECVSEFISFITSEASE-KCRKERRKTVNGDDICWA 99 (188)
Q Consensus 57 SkDA~~al~eca~eFI~~LtseAne-~a~~~kRKTIt~eDVl~A 99 (188)
+.||...|.+. --|+.--...+.+ +|.+.|...||.++|..|
T Consensus 2 ~~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 2 TDEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp -HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred CHHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 56777777775 6677765555554 899999999999998765
No 74
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=64.94 E-value=31 Score=32.51 Aligned_cols=50 Identities=20% Similarity=0.294 Sum_probs=42.7
Q ss_pred CCccccHHHHHHHHHHHH----HHHHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 52 ANAKISKEAKETMQECVS----EFISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 52 ~~~rISkDA~~al~eca~----eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
.++.++.||++.|..... .|..+|.+.|+.+|.+.+-+++..+||-.+.+
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 467899999999987654 46777888899999999999999999998864
No 75
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=64.79 E-value=18 Score=27.04 Aligned_cols=48 Identities=21% Similarity=0.245 Sum_probs=39.2
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 54 AKISKEAKETMQECVSEF------ISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 54 ~rISkDA~~al~eca~eF------I~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
..++.++..+|..++..| ++-|..-|..+|.=++...|..+||..||.
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 357788888888777655 455667799999999999999999999984
No 76
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=54.46 E-value=41 Score=29.59 Aligned_cols=71 Identities=13% Similarity=0.175 Sum_probs=50.9
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCc
Q 044287 37 LPIANVGRIMKQILP-ANAKISKEAKETMQECVS---EFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDD 107 (188)
Q Consensus 37 LPkA~I~RImK~~LP-~~~rISkDA~~al~eca~---eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~d 107 (188)
++...+..|++.... .++.++.++...|.+.|. -.+..+...+.++|...+...|+.++|..++..++...
T Consensus 180 ~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~ 254 (328)
T PRK00080 180 YTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDE 254 (328)
T ss_pred CCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCc
Confidence 455566666665542 357899999988887773 33555555666777766677899999999999877664
No 77
>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=52.55 E-value=61 Score=27.71 Aligned_cols=70 Identities=17% Similarity=0.165 Sum_probs=48.5
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCC
Q 044287 37 LPIANVGRIMKQILP-ANAKISKEAKETMQECVS---EFISFITSEASEKCRKERRKTVNGDDICWALGTLGFD 106 (188)
Q Consensus 37 LPkA~I~RImK~~LP-~~~rISkDA~~al~eca~---eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~ 106 (188)
++...+..|++.... ....++.++...|.+.+. -++..+...+...+...+...|+.++|..++..++++
T Consensus 159 l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~ 232 (305)
T TIGR00635 159 YTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMID 232 (305)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCC
Confidence 444556666665442 256799999988887653 2344555566677766666779999999999987655
No 78
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=52.37 E-value=29 Score=27.31 Aligned_cols=49 Identities=22% Similarity=0.285 Sum_probs=39.5
Q ss_pred CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 51 PANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 51 P~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
+++..=-.+.+++|-..+.+||..++..|..+. +|--+..||++.+|++
T Consensus 23 GDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRk 71 (109)
T KOG3901|consen 23 GDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRK 71 (109)
T ss_pred CCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHh
Confidence 345556678899999999999999988887777 4555788999999974
No 79
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=51.55 E-value=23 Score=28.34 Aligned_cols=64 Identities=14% Similarity=0.250 Sum_probs=49.3
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC----CCccCccCHHHHhh
Q 044287 34 ERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKER----RKTVNGDDICWALG 101 (188)
Q Consensus 34 d~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~k----RKTIt~eDVl~AL~ 101 (188)
.+.||...|.|.+|.......+|..-+..-+ ...+.||+.+-.+.|.+.. -|-|++.|+--|++
T Consensus 28 GlqFpVgRihr~LK~r~t~h~rVGataavy~----aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 28 GLQFPVGRIHRHLKTRTTSHGRVGATAAVYS----AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred ccccchHHHHHHHHHhcccccccchHHHHHH----HHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 4689999999999999877777765554433 2356799999888887654 36799999988776
No 80
>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=49.30 E-value=9.9 Score=24.10 Aligned_cols=26 Identities=19% Similarity=0.162 Sum_probs=20.8
Q ss_pred HHHHHHhcCCCccCccCHHHHhhhcC
Q 044287 79 ASEKCRKERRKTVNGDDICWALGTLG 104 (188)
Q Consensus 79 Ane~a~~~kRKTIt~eDVl~AL~~LG 104 (188)
|.+.|...+...|+++|++.||=..+
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 56789999999999999999975443
No 81
>PRK09862 putative ATP-dependent protease; Provisional
Probab=46.70 E-value=52 Score=31.81 Aligned_cols=57 Identities=11% Similarity=0.085 Sum_probs=44.4
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchH
Q 044287 54 AKISKEAKETMQECVSEF------ISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAG 110 (188)
Q Consensus 54 ~rISkDA~~al~eca~eF------I~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~ 110 (188)
..++.++...+...+..+ .+.|..-|..+|.=+++..|+.+||..||.--+++...-
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 357888888777765444 567778899999999999999999999998665554433
No 82
>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=44.73 E-value=39 Score=26.01 Aligned_cols=34 Identities=18% Similarity=0.320 Sum_probs=27.6
Q ss_pred hHHHHHHhhhC----CCCccccHHHHHHHHHHHHHHHH
Q 044287 40 ANVGRIMKQIL----PANAKISKEAKETMQECVSEFIS 73 (188)
Q Consensus 40 A~I~RImK~~L----P~~~rISkDA~~al~eca~eFI~ 73 (188)
++|.++||..| +++..++.++.+.|++++..|-.
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 46788999887 45688999999999999998854
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=43.53 E-value=63 Score=31.70 Aligned_cols=49 Identities=20% Similarity=0.215 Sum_probs=42.1
Q ss_pred CccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 53 NAKISKEAKETMQECVSEFI-------SFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 53 ~~rISkDA~~al~eca~eFI-------~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
.+.|+.++...|...+..+- .++...|..+|.=++|.+|+.+||..|+.
T Consensus 247 ~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~ 302 (633)
T TIGR02442 247 SVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAE 302 (633)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence 68899999999999887762 45667788899999999999999999885
No 84
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=41.78 E-value=81 Score=28.70 Aligned_cols=54 Identities=22% Similarity=0.212 Sum_probs=42.2
Q ss_pred hhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 47 KQILPANAKISKEAKETMQECVSEFI-------SFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 47 K~~LP~~~rISkDA~~al~eca~eFI-------~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
++.++ .+.|+.+....+...+..+= .++...|...|--+||..|+++||..+..
T Consensus 247 ~~~~~-~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 247 QNLLP-QVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred HHHhc-cCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 34454 68899999998888776653 34667788899999999999999997763
No 85
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=41.48 E-value=1.2e+02 Score=25.72 Aligned_cols=66 Identities=15% Similarity=0.112 Sum_probs=46.7
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 37 LPIANVGRIMKQILP-ANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 37 LPkA~I~RImK~~LP-~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
+....+.+++++.+. .+..|+.+|...|...+..=+..+..+-...|.-.+.++|+.+||...+..
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 455566666666553 357899999999988887656666666666666544457999999877653
No 86
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=41.00 E-value=36 Score=33.77 Aligned_cols=47 Identities=13% Similarity=0.123 Sum_probs=39.0
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 55 KISKEAKETMQECVSEF-------------ISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 55 rISkDA~~al~eca~eF-------------I~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
.++.+|...|.+.++.- +.-|..+|..+|+.++++.|+++||..|+.
T Consensus 339 ~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~ 398 (637)
T PRK13765 339 HFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKK 398 (637)
T ss_pred CCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHH
Confidence 68999998888766633 333778899999999999999999999984
No 87
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=39.90 E-value=50 Score=32.43 Aligned_cols=52 Identities=17% Similarity=0.159 Sum_probs=45.1
Q ss_pred hCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 49 ILPANAKISKEAKETMQECVSEFI-------SFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 49 ~LP~~~rISkDA~~al~eca~eFI-------~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
.++ ++.|+.+....+.++|..|- .++...|..+|.=++|.+|+.+||..|+.
T Consensus 190 rl~-~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 190 RLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 444 78999999999888888774 47888899999999999999999999985
No 88
>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=39.33 E-value=35 Score=23.38 Aligned_cols=30 Identities=27% Similarity=0.339 Sum_probs=23.9
Q ss_pred CCCccCccCHHHHhhhcCCCcchHHHHHHH
Q 044287 87 RRKTVNGDDICWALGTLGFDDYAGPIRRYL 116 (188)
Q Consensus 87 kRKTIt~eDVl~AL~~LGF~dyi~~lk~~L 116 (188)
....-+..+++.||+.+|..+-+..+..+|
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 345567889999999999999888887654
No 89
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=38.94 E-value=61 Score=27.82 Aligned_cols=72 Identities=10% Similarity=0.059 Sum_probs=44.6
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchH
Q 044287 37 LPIANVGRIMKQILP-ANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAG 110 (188)
Q Consensus 37 LPkA~I~RImK~~LP-~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~ 110 (188)
++...+..+++..+. .+..++.++.+.|.+.+.-=+..+.......|. +..+|+.+||..++.....++.+-
T Consensus 184 ~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~~~i~ 256 (337)
T PRK12402 184 PTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTDEVIE 256 (337)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCHHHHH
Confidence 445566666666543 256799999999988873333333333333442 233799999999888655444333
No 90
>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=38.39 E-value=43 Score=29.10 Aligned_cols=75 Identities=15% Similarity=0.127 Sum_probs=34.2
Q ss_pred cccccCchhHHHHHHhhhCC--CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CccCccCHHHHhhhc
Q 044287 32 EQERLLPIANVGRIMKQILP--ANAKISKEAKETMQECVSEFISFITSEASEKCRKERR------KTVNGDDICWALGTL 103 (188)
Q Consensus 32 ~~d~~LPkA~I~RImK~~LP--~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kR------KTIt~eDVl~AL~~L 103 (188)
.++..|....+.+-|..+.. +...|..|...+|.-||.+++..|...+..+|.+-.. .+....||-..|..|
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 34567887777777766653 1457999999999999999999999999998885322 123466776666655
Q ss_pred CCC
Q 044287 104 GFD 106 (188)
Q Consensus 104 GF~ 106 (188)
.--
T Consensus 119 ~~~ 121 (264)
T PF05236_consen 119 EQL 121 (264)
T ss_dssp ---
T ss_pred HHH
Confidence 543
No 91
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=37.71 E-value=88 Score=28.77 Aligned_cols=73 Identities=15% Similarity=0.143 Sum_probs=50.3
Q ss_pred hHHHHHHhhhCC---CCccccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchH
Q 044287 40 ANVGRIMKQILP---ANAKISKEAKETMQECV------SEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAG 110 (188)
Q Consensus 40 A~I~RImK~~LP---~~~rISkDA~~al~eca------~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~ 110 (188)
.-|.-|+++-.. ....++.++.+++...+ ..+...|...|.++|+.+++.+|+.+||..|-+..+..-+..
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 355666655542 13457777776666433 235566777899999999999999999999977766654444
Q ss_pred HH
Q 044287 111 PI 112 (188)
Q Consensus 111 ~l 112 (188)
.+
T Consensus 273 ~~ 274 (366)
T COG1474 273 VL 274 (366)
T ss_pred HH
Confidence 43
No 92
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=37.64 E-value=63 Score=30.94 Aligned_cols=50 Identities=20% Similarity=0.237 Sum_probs=41.8
Q ss_pred CCccccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 52 ANAKISKEAKETMQECVSE----FISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 52 ~~~rISkDA~~al~eca~e----FI~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
.++.++.||.+.|....++ |..-|..-|+.+|...|+++|..+||..|-+
T Consensus 377 e~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~ 430 (450)
T COG1224 377 EDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKE 430 (450)
T ss_pred hccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHH
Confidence 3678999999999876654 5566667799999999999999999998864
No 93
>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=37.63 E-value=78 Score=20.73 Aligned_cols=32 Identities=22% Similarity=0.387 Sum_probs=27.0
Q ss_pred ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHH
Q 044287 35 RLLPIANVGRIMKQILPANAKISKEAKETMQECVSE 70 (188)
Q Consensus 35 ~~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~e 70 (188)
..+..++|.|++... -+||.+.++-|.+++.+
T Consensus 9 agvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 9 AGVSKSTVSRVLNGP----PRVSEETRERILEAAEE 40 (46)
T ss_dssp HTSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHH
T ss_pred HCcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHH
Confidence 357889999999875 58999999999988775
No 94
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=37.55 E-value=62 Score=31.10 Aligned_cols=47 Identities=13% Similarity=0.184 Sum_probs=41.0
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 55 KISKEAKETMQECVSEF------ISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 55 rISkDA~~al~eca~eF------I~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
.+++++..+|.+++..| .+-|..-|..+|.=++...|..+||..||.
T Consensus 445 ~l~~~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 445 KLSAIDANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred CCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 46889999999888776 566778899999999999999999999984
No 95
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=36.71 E-value=24 Score=30.17 Aligned_cols=61 Identities=16% Similarity=0.034 Sum_probs=46.8
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc---cCccCHHHHh
Q 044287 36 LLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKT---VNGDDICWAL 100 (188)
Q Consensus 36 ~LPkA~I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKT---It~eDVl~AL 100 (188)
.||++.|.+++..++ +-.|+...+.+|+-.+.+|+-.|..-|..+-. ++.| +.+.|+-.|.
T Consensus 115 ~lnKt~VKKlastV~--nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq~--~w~~sgpl~p~h~reay 178 (199)
T COG5251 115 SLNKTQVKKLASTVA--NQTVSPNIRIFLQGVGKVFVGEIIELAMIVQN--KWLTSGPLIPFHKREAY 178 (199)
T ss_pred CCCHHHHHHHHHHHh--ccccCCCeeeeeechhHHHHHHHHHHHHHHHH--HhcccCCCChHHHHHHH
Confidence 699999999999998 56788888888999999999888777655433 2332 6677766554
No 96
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=35.08 E-value=92 Score=27.08 Aligned_cols=65 Identities=12% Similarity=0.166 Sum_probs=46.7
Q ss_pred HHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCccCHHHHhhhcCCC
Q 044287 42 VGRIMKQILP-ANAKISKEAKETMQECVSEFISFITSEASEKCRK--ERRKTVNGDDICWALGTLGFD 106 (188)
Q Consensus 42 I~RImK~~LP-~~~rISkDA~~al~eca~eFI~~LtseAne~a~~--~kRKTIt~eDVl~AL~~LGF~ 106 (188)
+.++|++.+- .+..|+.+|...|..++..=...+..+-...|.- .++.+|+.+||...+....+.
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 3678999999999999886566666666666665 457789999999988766654
No 97
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=34.96 E-value=1.1e+02 Score=24.49 Aligned_cols=49 Identities=18% Similarity=0.326 Sum_probs=41.5
Q ss_pred CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 52 ANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 52 ~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
+.+.=..|..++|.+.+..|++.+...|..+|.. |-.+..||+.-||++
T Consensus 24 Dvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~--rnK~k~eDfkfaLr~ 72 (126)
T COG5248 24 DVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQV--RNKTKTEDFKFALRR 72 (126)
T ss_pred CCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHh--cccchHHHHHHHHhh
Confidence 4566678899999999999999999999999983 444678999999984
No 98
>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=34.94 E-value=2.5e+02 Score=22.93 Aligned_cols=52 Identities=25% Similarity=0.342 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCC-cchHHHHHHHHHHHHHHHhh
Q 044287 68 VSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFD-DYAGPIRRYLHKYRELEGER 126 (188)
Q Consensus 68 a~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~-dyi~~lk~~L~~~re~~~~K 126 (188)
+...+.||-..|. |.-++++++..-|..|||+ +.++.+......+++.....
T Consensus 44 ~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l~~~ 96 (174)
T cd04752 44 SIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKLQES 96 (174)
T ss_pred HHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555443 4559999999999999998 66666666666666544433
No 99
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=34.06 E-value=83 Score=28.96 Aligned_cols=54 Identities=20% Similarity=0.262 Sum_probs=44.2
Q ss_pred hhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 47 KQILPANAKISKEAKETMQECVSEFI-------SFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 47 K~~LP~~~rISkDA~~al~eca~eFI-------~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
++.++ .+.|+.+....|.+.|..+= .++...|...|-=+||..|+++||..+..
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 44454 68899999999999887764 36777888899999999999999998764
No 100
>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=32.13 E-value=30 Score=23.02 Aligned_cols=24 Identities=29% Similarity=0.500 Sum_probs=20.3
Q ss_pred cCccCHHHHhhhcCCCcchHHHHH
Q 044287 91 VNGDDICWALGTLGFDDYAGPIRR 114 (188)
Q Consensus 91 It~eDVl~AL~~LGF~dyi~~lk~ 114 (188)
=++++|..-|..+||.+|.+....
T Consensus 4 w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 4 WSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp HCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCHHHHHHHHHHCCcHHHHHHHHH
Confidence 467889999999999999987764
No 101
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=31.17 E-value=1.1e+02 Score=27.77 Aligned_cols=53 Identities=11% Similarity=0.026 Sum_probs=42.0
Q ss_pred hhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCccCHHHHh
Q 044287 47 KQILPANAKISKEAKETMQECVSEFI-------SFITSEASEKCRKERRKTVNGDDICWAL 100 (188)
Q Consensus 47 K~~LP~~~rISkDA~~al~eca~eFI-------~~LtseAne~a~~~kRKTIt~eDVl~AL 100 (188)
++.++ .+.|+.+....+.+.|..+= .+|...|...|--+||..|+++||..+.
T Consensus 244 ~~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 244 RARLP-QLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred HHhcC-CcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 34443 68899999999998887654 2377788889999999999999996554
No 102
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=29.58 E-value=49 Score=31.33 Aligned_cols=31 Identities=32% Similarity=0.251 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 72 ISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 72 I~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
|..|..+|...|..++|..|+.+||..|++.
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~ 423 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEK 423 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHH
Confidence 5677888999999999999999999999875
No 103
>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=29.48 E-value=1.3e+02 Score=29.30 Aligned_cols=54 Identities=20% Similarity=0.298 Sum_probs=40.9
Q ss_pred hhhCCCCccccHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 47 KQILPANAKISKEAKETMQECVSEF-------ISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 47 K~~LP~~~rISkDA~~al~eca~eF-------I~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
++.++ .+.|+.+....|.+.|..+ -.++...|...|.=++|.+|+.+||..|+.
T Consensus 196 r~~~~-~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 196 RELLP-QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred HHhcC-CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 34444 5789999998887776543 224556777788899999999999999885
No 104
>smart00350 MCM minichromosome maintenance proteins.
Probab=29.11 E-value=1.7e+02 Score=27.84 Aligned_cols=69 Identities=14% Similarity=0.155 Sum_probs=48.7
Q ss_pred ccCchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhcCCCccCcc
Q 044287 35 RLLPIANVGRIMKQILP-ANAKISKEAKETMQECVSEF-------------------ISFITSEASEKCRKERRKTVNGD 94 (188)
Q Consensus 35 ~~LPkA~I~RImK~~LP-~~~rISkDA~~al~eca~eF-------------------I~~LtseAne~a~~~kRKTIt~e 94 (188)
..++...+.+.+.-+=. -...||+++.+.|.+..... +..|...|-..|.-..|.+|+.+
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 35777888877744321 01258999999887655432 24566677778999999999999
Q ss_pred CHHHHhhhc
Q 044287 95 DICWALGTL 103 (188)
Q Consensus 95 DVl~AL~~L 103 (188)
||..|++-+
T Consensus 496 Dv~~ai~l~ 504 (509)
T smart00350 496 DVEEAIRLL 504 (509)
T ss_pred HHHHHHHHH
Confidence 999998643
No 105
>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=28.53 E-value=27 Score=22.39 Aligned_cols=24 Identities=29% Similarity=0.484 Sum_probs=19.7
Q ss_pred CccCHHHHhhhcCCCcchHHHHHH
Q 044287 92 NGDDICWALGTLGFDDYAGPIRRY 115 (188)
Q Consensus 92 t~eDVl~AL~~LGF~dyi~~lk~~ 115 (188)
++++|..-|+.+|+++|++.+...
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 567899999999998888877653
No 106
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=28.50 E-value=63 Score=23.33 Aligned_cols=32 Identities=19% Similarity=0.242 Sum_probs=26.4
Q ss_pred cCHHHHhhhcCC------CcchHHHHHHHHHHHHHHHh
Q 044287 94 DDICWALGTLGF------DDYAGPIRRYLHKYRELEGE 125 (188)
Q Consensus 94 eDVl~AL~~LGF------~dyi~~lk~~L~~~re~~~~ 125 (188)
..|..+|..||| +.+-+.+.++|..|...+.-
T Consensus 19 ~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~ENf 56 (74)
T PF08823_consen 19 REVQEALKRLGYYKGEADGVWDEATEDALRAWAGTENF 56 (74)
T ss_pred HHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhhH
Confidence 356779999999 78889999999999876654
No 107
>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=28.28 E-value=37 Score=26.61 Aligned_cols=63 Identities=10% Similarity=0.175 Sum_probs=42.1
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchHHHHHHHHHHHHHH
Q 044287 57 SKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAGPIRRYLHKYRELE 123 (188)
Q Consensus 57 SkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~~lk~~L~~~re~~ 123 (188)
+...+..|..|..+.-.|...-..-... ---.-..+...|+..|++..+.++...+++|++.+
T Consensus 71 ~s~Vk~Eiaa~~~v~~~Y~~~L~~G~vd----~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~~ 133 (134)
T PF12010_consen 71 PSPVKNEIAACSNVWSEYYPPLETGLVD----PEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAAN 133 (134)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHccCCC----HHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhc
Confidence 3456677777777766665543222111 00123467778899999999999999999998743
No 108
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=28.22 E-value=1.4e+02 Score=25.68 Aligned_cols=66 Identities=15% Similarity=0.075 Sum_probs=46.0
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 37 LPIANVGRIMKQILP-ANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 37 LPkA~I~RImK~~LP-~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
++...+.+.|+..+- .+..|+.+|.+.|.+.+..=+..+..+....|.-.+-+.|+.+||...+..
T Consensus 146 ~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~ 212 (340)
T PRK05574 146 PKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPD 212 (340)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhh
Confidence 455555665555543 357899999999999887666777777777766442223999998876654
No 109
>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=28.04 E-value=36 Score=22.53 Aligned_cols=23 Identities=26% Similarity=0.487 Sum_probs=19.5
Q ss_pred CccCHHHHhhhcCCCcchHHHHH
Q 044287 92 NGDDICWALGTLGFDDYAGPIRR 114 (188)
Q Consensus 92 t~eDVl~AL~~LGF~dyi~~lk~ 114 (188)
++++|..-|+.+|++.|++....
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F~~ 26 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENFEK 26 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHHc
Confidence 57889999999999999987743
No 110
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=27.88 E-value=56 Score=29.24 Aligned_cols=32 Identities=28% Similarity=0.210 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 71 FISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 71 FI~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
-|..|..+|...|...++..|+.+|+..|++.
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 35577778888999999999999999999975
No 111
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=27.78 E-value=67 Score=31.09 Aligned_cols=59 Identities=24% Similarity=0.325 Sum_probs=41.0
Q ss_pred hhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchHHHHHHHHHH
Q 044287 47 KQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAGPIRRYLHKY 119 (188)
Q Consensus 47 K~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~~lk~~L~~~ 119 (188)
|+++.+.--|-+|.+.+|++||...=.||...-...-..+++++ |..|++.+...|...
T Consensus 426 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~~ 484 (488)
T TIGR01052 426 KQSVADIPEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAYI 484 (488)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHH
Confidence 33333334588899999999999999999987666666555554 445666666655543
No 112
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=27.65 E-value=57 Score=29.84 Aligned_cols=35 Identities=20% Similarity=0.161 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcC
Q 044287 70 EFISFITSEASEKCRKERRKTVNGDDICWALGTLG 104 (188)
Q Consensus 70 eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LG 104 (188)
-=|..|..+|...|..+++..|+.+|+..|++..-
T Consensus 339 adl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~ 373 (389)
T PRK03992 339 ADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVM 373 (389)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence 34566777888888899999999999999997653
No 113
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=26.54 E-value=2.4e+02 Score=23.01 Aligned_cols=66 Identities=17% Similarity=0.232 Sum_probs=50.8
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCc---cCHHHHhhh-cCCCcchHHHHHHHHHHH
Q 044287 55 KISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNG---DDICWALGT-LGFDDYAGPIRRYLHKYR 120 (188)
Q Consensus 55 rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~---eDVl~AL~~-LGF~dyi~~lk~~L~~~r 120 (188)
..+.-+...|.+.|-.|..-|...|.-++++.||--+++ +||--|+.. .|..---++-+++|-+.-
T Consensus 31 ~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F~pppPke~llela 100 (145)
T COG5094 31 EYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHFVPPPPKEYLLELA 100 (145)
T ss_pred hhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCcCCCChHHHHHHHH
Confidence 466667778888999999999999999999999987766 999999985 555433445666655443
No 114
>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=25.17 E-value=43 Score=19.32 Aligned_cols=27 Identities=22% Similarity=0.249 Sum_probs=20.8
Q ss_pred HHHHHHHhcCCCccCccCHHHHhh-hcC
Q 044287 78 EASEKCRKERRKTVNGDDICWALG-TLG 104 (188)
Q Consensus 78 eAne~a~~~kRKTIt~eDVl~AL~-~LG 104 (188)
.+......++--+|+.+++..+|+ .||
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 355666778888999999999998 576
No 115
>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=25.00 E-value=62 Score=26.46 Aligned_cols=54 Identities=13% Similarity=0.230 Sum_probs=41.1
Q ss_pred HHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHH
Q 044287 42 VGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDIC 97 (188)
Q Consensus 42 I~RImK~~LP~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl 97 (188)
+.|+++.+. +.-|.|+-..-+...+..=+.-|.-.|...|..++|-+|...|+=
T Consensus 1 fe~lFR~aa--~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLP 54 (138)
T PF09123_consen 1 FERLFRKAA--GLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLP 54 (138)
T ss_dssp HHHHHHHHH--S----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-
T ss_pred ChHHHHHHh--ccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCC
Confidence 357888887 577888888899999998888888899999999999999999863
No 116
>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=24.85 E-value=74 Score=25.55 Aligned_cols=67 Identities=15% Similarity=0.101 Sum_probs=43.4
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCc------------chHHHHHHHHHHHHH
Q 044287 55 KISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDD------------YAGPIRRYLHKYREL 122 (188)
Q Consensus 55 rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~d------------yi~~lk~~L~~~re~ 122 (188)
.+..+. +..++..++..++.-..-..- =.|.+++|++.+|+.+++.. |++.+.+.+..-++.
T Consensus 95 ~i~~~g---~~~~~~~~lr~~~~~~~~~~~---~~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A 168 (224)
T PF02361_consen 95 SITQEG---LIYAALLALRILAILLASLLF---ILTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREA 168 (224)
T ss_pred hhhHHH---HHHHHHHHHHHHHHHHHHHHH---HHHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444 344444444444433333222 24789999999999999988 788888877777777
Q ss_pred HHhhh
Q 044287 123 EGERA 127 (188)
Q Consensus 123 ~~~K~ 127 (188)
++.|-
T Consensus 169 ~~~Rg 173 (224)
T PF02361_consen 169 QRLRG 173 (224)
T ss_pred HHHcC
Confidence 77663
No 117
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=24.13 E-value=30 Score=22.36 Aligned_cols=25 Identities=20% Similarity=0.412 Sum_probs=20.1
Q ss_pred cCccCHHHHhhhcCCCcchHHHHHH
Q 044287 91 VNGDDICWALGTLGFDDYAGPIRRY 115 (188)
Q Consensus 91 It~eDVl~AL~~LGF~dyi~~lk~~ 115 (188)
-+.++|..-|..+||++|++.+...
T Consensus 4 w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 4 WSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCHHHHHHHHHHCChHHHHHHHHHC
Confidence 4567889999999999888877654
No 118
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=23.51 E-value=70 Score=29.70 Aligned_cols=31 Identities=23% Similarity=0.193 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHhcCCCccCccCHHHHhhh
Q 044287 72 ISFITSEASEKCRKERRKTVNGDDICWALGT 102 (188)
Q Consensus 72 I~~LtseAne~a~~~kRKTIt~eDVl~AL~~ 102 (188)
|..|..+|...|...+|..|+.+|+..|++.
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~ 385 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKT 385 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHH
Confidence 6678888999999999999999999999875
No 119
>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=23.06 E-value=95 Score=24.92 Aligned_cols=38 Identities=21% Similarity=0.121 Sum_probs=29.9
Q ss_pred CccCccCHHHHhhhcCCC-----------cchHHHHHHHHHHHHHHHhh
Q 044287 89 KTVNGDDICWALGTLGFD-----------DYAGPIRRYLHKYRELEGER 126 (188)
Q Consensus 89 KTIt~eDVl~AL~~LGF~-----------dyi~~lk~~L~~~re~~~~K 126 (188)
-|....|+..+|+.+|++ .|++.+.+..+.-++.++.|
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 367889999999999986 46777777777777777766
No 120
>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=23.03 E-value=37 Score=22.05 Aligned_cols=13 Identities=38% Similarity=0.524 Sum_probs=11.1
Q ss_pred cCHHHHhhhcCCC
Q 044287 94 DDICWALGTLGFD 106 (188)
Q Consensus 94 eDVl~AL~~LGF~ 106 (188)
+|++.||..|||.
T Consensus 4 ~d~~~AL~~LGy~ 16 (47)
T PF07499_consen 4 EDALEALISLGYS 16 (47)
T ss_dssp HHHHHHHHHTTS-
T ss_pred HHHHHHHHHcCCC
Confidence 5899999999998
No 121
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=22.81 E-value=37 Score=24.55 Aligned_cols=17 Identities=24% Similarity=0.405 Sum_probs=15.1
Q ss_pred ccCccCHHHHhhhcCCC
Q 044287 90 TVNGDDICWALGTLGFD 106 (188)
Q Consensus 90 TIt~eDVl~AL~~LGF~ 106 (188)
.+++.+|+++|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 47889999999999996
No 122
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=20.84 E-value=1.4e+02 Score=21.75 Aligned_cols=34 Identities=18% Similarity=0.157 Sum_probs=24.9
Q ss_pred HHHhcCCCccCccCHHHHhhhcCCCcchHHHHHH
Q 044287 82 KCRKERRKTVNGDDICWALGTLGFDDYAGPIRRY 115 (188)
Q Consensus 82 ~a~~~kRKTIt~eDVl~AL~~LGF~dyi~~lk~~ 115 (188)
.....+...-+.+.++.||...|..+.++.+++.
T Consensus 52 W~~~~~~~~atv~~L~~AL~~~gr~dlae~l~~~ 85 (86)
T cd08779 52 WAQRQAGDPDAVGKLVTALEESGRQDLADEVRAV 85 (86)
T ss_pred HHHhcCCCchHHHHHHHHHHHcCHHHHHHHHHhh
Confidence 3444444444567899999999999998888764
No 123
>PRK07914 hypothetical protein; Reviewed
Probab=20.23 E-value=1.8e+02 Score=25.53 Aligned_cols=63 Identities=10% Similarity=0.128 Sum_probs=41.9
Q ss_pred chhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccCHHHHhh
Q 044287 38 PIANVGRIMKQILP-ANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDICWALG 101 (188)
Q Consensus 38 PkA~I~RImK~~LP-~~~rISkDA~~al~eca~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~ 101 (188)
+...+.+.|++.+- .+..|+.+|...|.+++..=+..+..+--..+...+ .+|+.+||...+.
T Consensus 129 ~~~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 192 (320)
T PRK07914 129 KAAERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHS 192 (320)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcC
Confidence 34444444444432 257899999999999986655666665555554334 5699999988765
No 124
>PF10728 DUF2520: Domain of unknown function (DUF2520); InterPro: IPR018931 This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases. ; PDB: 3D1L_A 2I76_A 3DFU_A.
Probab=20.01 E-value=2.7e+02 Score=21.84 Aligned_cols=71 Identities=17% Similarity=0.170 Sum_probs=47.4
Q ss_pred hHHHHHHhhhCCCCccccHHHHHHHHHHH---HHHHHHHHHHHHHHHHhcCCCccCccCHHHHhhhcCCCcchHHHHHHH
Q 044287 40 ANVGRIMKQILPANAKISKEAKETMQECV---SEFISFITSEASEKCRKERRKTVNGDDICWALGTLGFDDYAGPIRRYL 116 (188)
Q Consensus 40 A~I~RImK~~LP~~~rISkDA~~al~eca---~eFI~~LtseAne~a~~~kRKTIt~eDVl~AL~~LGF~dyi~~lk~~L 116 (188)
..+..|++........|..+-+....-+| ..|+..|...|.+++...| |..++.+.+| .+-+...+
T Consensus 14 ~~l~~l~~~lg~~~~~i~~~~r~~yHaAav~asNf~~~L~~~a~~ll~~~g---i~~~~a~~~L--------~PLi~~t~ 82 (132)
T PF10728_consen 14 EVLQELAKELGGRPFEIDSEQRALYHAAAVFASNFLVALYALAAELLEQAG---IDFEEALEAL--------LPLIRETL 82 (132)
T ss_dssp HHHHHHHHHTTSEEEE--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SHHH--HHH--------HHHHHHHH
T ss_pred HHHHHHHHHhCCceEEeCHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHcC---CCchhHHHHH--------HHHHHHHH
Confidence 46778888877767789999988887765 5889999999999888663 4444433333 45566666
Q ss_pred HHHHH
Q 044287 117 HKYRE 121 (188)
Q Consensus 117 ~~~re 121 (188)
++..+
T Consensus 83 ~n~~~ 87 (132)
T PF10728_consen 83 ENILQ 87 (132)
T ss_dssp HHHHH
T ss_pred HHHHh
Confidence 66654
Done!