Query 032848
Match_columns 132
No_of_seqs 156 out of 647
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 06:40:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032848.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032848hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00018 histone H3; Provision 100.0 5.4E-55 1.2E-59 322.3 12.2 131 1-131 1-135 (136)
2 PLN00161 histone H3; Provision 100.0 6.4E-55 1.4E-59 320.9 12.2 128 1-131 1-129 (135)
3 PLN00121 histone H3; Provision 100.0 6.8E-55 1.5E-59 321.8 12.2 132 1-132 1-136 (136)
4 KOG1745 Histones H3 and H4 [Ch 100.0 8E-51 1.7E-55 299.4 8.7 132 1-132 1-137 (137)
5 smart00428 H3 Histone H3. 100.0 5.7E-47 1.2E-51 269.4 10.3 101 31-131 2-104 (105)
6 PLN00160 histone H3; Provision 100.0 1.7E-46 3.7E-51 263.4 9.0 94 38-131 1-95 (97)
7 COG2036 HHT1 Histones H3 and H 99.9 3.4E-27 7.5E-32 164.1 8.0 87 40-131 1-87 (91)
8 PF00125 Histone: Core histone 99.8 3E-21 6.4E-26 127.9 7.4 75 54-128 1-75 (75)
9 cd07981 TAF12 TATA Binding Pro 99.4 5.2E-13 1.1E-17 88.9 7.9 58 69-126 8-65 (72)
10 cd00076 H4 Histone H4, one of 99.3 6.2E-12 1.3E-16 86.6 7.5 71 55-130 10-80 (85)
11 PLN00035 histone H4; Provision 99.3 1E-11 2.3E-16 88.2 7.5 67 59-130 30-96 (103)
12 PTZ00015 histone H4; Provision 99.3 1.6E-11 3.5E-16 87.2 7.4 69 57-130 29-97 (102)
13 smart00803 TAF TATA box bindin 99.2 3.8E-11 8.3E-16 78.8 6.1 64 58-126 2-65 (65)
14 smart00417 H4 Histone H4. 99.1 7.5E-11 1.6E-15 79.4 5.3 65 54-123 9-73 (74)
15 PTZ00463 histone H2B; Provisio 99.1 1.6E-10 3.4E-15 83.6 7.2 65 60-128 26-94 (117)
16 PLN00158 histone H2B; Provisio 99.1 2E-10 4.3E-15 83.0 7.3 65 60-128 25-93 (116)
17 smart00427 H2B Histone H2B. 99.1 2.4E-10 5.2E-15 79.3 7.4 62 63-128 2-67 (89)
18 cd07979 TAF9 TATA Binding Prot 98.8 2.2E-08 4.7E-13 72.5 8.1 66 64-130 3-68 (117)
19 KOG1744 Histone H2B [Chromatin 98.8 9.7E-09 2.1E-13 75.3 5.5 66 59-128 34-103 (127)
20 PF00808 CBFD_NFYB_HMF: Histon 98.8 2.9E-08 6.2E-13 64.2 6.8 63 59-125 3-65 (65)
21 cd00074 H2A Histone 2A; H2A is 98.4 6.2E-07 1.3E-11 64.9 5.4 67 56-126 18-84 (115)
22 smart00576 BTP Bromodomain tra 98.4 2.3E-06 5E-11 57.3 7.2 54 77-130 20-73 (77)
23 PF03847 TFIID_20kDa: Transcri 98.3 3.2E-06 7E-11 55.9 6.9 59 68-126 5-63 (68)
24 PF15630 CENP-S: Kinetochore c 98.3 2.3E-06 5E-11 57.8 6.0 65 62-126 5-71 (76)
25 KOG0870 DNA polymerase epsilon 98.3 2.7E-06 5.9E-11 65.0 6.6 70 56-127 8-77 (172)
26 cd08050 TAF6 TATA Binding Prot 98.1 1.4E-05 2.9E-10 67.0 7.8 62 68-130 5-66 (343)
27 PF02969 TAF: TATA box binding 98.1 2.1E-05 4.6E-10 51.8 7.0 58 68-126 9-66 (66)
28 PF02291 TFIID-31kDa: Transcri 98.0 4.3E-05 9.3E-10 56.4 7.4 65 65-130 15-79 (129)
29 PF15511 CENP-T: Centromere ki 97.8 3.9E-05 8.5E-10 65.8 5.9 62 59-120 352-414 (414)
30 KOG1142 Transcription initiati 97.8 3E-05 6.5E-10 62.9 4.4 73 50-126 146-218 (258)
31 KOG0869 CCAAT-binding factor, 97.5 0.00031 6.7E-09 53.5 6.5 71 56-129 30-100 (168)
32 KOG3334 Transcription initiati 97.0 0.0044 9.6E-08 46.6 7.7 64 66-130 17-80 (148)
33 KOG3467 Histone H4 [Chromatin 96.9 0.004 8.7E-08 43.4 6.2 66 60-130 31-96 (103)
34 PF07524 Bromo_TP: Bromodomain 96.7 0.0078 1.7E-07 39.8 6.4 52 79-130 22-73 (77)
35 KOG0871 Class 2 transcription 96.5 0.012 2.6E-07 44.5 6.8 72 55-129 9-80 (156)
36 smart00414 H2A Histone 2A. 95.9 0.015 3.3E-07 41.5 4.4 67 56-126 7-73 (106)
37 PLN00154 histone H2A; Provisio 95.8 0.024 5.2E-07 42.3 5.3 68 56-126 36-103 (136)
38 PTZ00017 histone H2A; Provisio 95.7 0.016 3.6E-07 43.1 4.0 67 56-126 25-91 (134)
39 COG5262 HTA1 Histone H2A [Chro 94.9 0.05 1.1E-06 39.8 4.5 58 69-126 33-90 (132)
40 PLN00157 histone H2A; Provisio 94.7 0.039 8.5E-07 41.0 3.5 67 56-126 24-90 (132)
41 PLN00156 histone H2AX; Provisi 94.7 0.051 1.1E-06 40.7 4.0 67 56-126 27-93 (139)
42 KOG2549 Transcription initiati 94.4 0.14 3.1E-06 45.9 6.9 53 77-129 25-77 (576)
43 PF02269 TFIID-18kDa: Transcri 94.4 0.033 7.1E-07 38.7 2.3 58 69-126 8-65 (93)
44 PLN00153 histone H2A; Provisio 94.3 0.062 1.4E-06 39.7 3.8 67 56-126 22-88 (129)
45 COG5094 TAF9 Transcription ini 93.8 0.26 5.6E-06 36.6 6.1 61 66-127 18-81 (145)
46 PTZ00252 histone H2A; Provisio 93.7 0.12 2.7E-06 38.4 4.4 67 56-126 23-91 (134)
47 COG5150 Class 2 transcription 93.5 0.32 7E-06 36.1 6.2 71 54-127 7-77 (148)
48 cd08045 TAF4 TATA Binding Prot 91.9 0.59 1.3E-05 36.6 6.2 56 56-112 42-97 (212)
49 KOG1756 Histone 2A [Chromatin 91.8 0.31 6.6E-06 36.1 4.2 67 56-126 25-91 (131)
50 COG5208 HAP5 CCAAT-binding fac 91.0 0.67 1.4E-05 37.5 5.7 85 41-126 80-173 (286)
51 PF05236 TAF4: Transcription i 90.7 0.29 6.3E-06 39.5 3.5 58 56-114 41-98 (264)
52 cd07978 TAF13 The TATA Binding 90.5 2.6 5.7E-05 29.2 7.7 58 68-126 8-65 (92)
53 KOG4336 TBP-associated transcr 90.0 1.3 2.8E-05 37.2 6.7 51 80-130 22-72 (323)
54 KOG1657 CCAAT-binding factor, 88.7 0.82 1.8E-05 36.9 4.6 72 53-125 66-137 (236)
55 PF09415 CENP-X: CENP-S associ 85.4 1.5 3.2E-05 29.2 3.7 57 67-123 4-63 (72)
56 PF09123 DUF1931: Domain of un 82.4 2.8 6E-05 31.4 4.4 59 64-127 1-59 (138)
57 COG5248 TAF19 Transcription in 82.3 10 0.00022 27.6 7.1 61 64-126 11-71 (126)
58 KOG2389 Predicted bromodomain 80.5 6.2 0.00013 33.7 6.4 53 78-130 44-96 (353)
59 KOG3901 Transcription initiati 79.8 15 0.00032 26.5 7.2 62 62-126 9-70 (109)
60 COG5095 TAF6 Transcription ini 78.8 4.6 0.0001 34.6 5.1 53 77-129 19-71 (450)
61 cd08048 TAF11 TATA Binding Pro 70.0 32 0.00069 23.4 7.9 65 59-128 17-84 (85)
62 COG1224 TIP49 DNA helicase TIP 69.8 11 0.00024 32.9 5.3 72 57-128 354-432 (450)
63 PF13654 AAA_32: AAA domain; P 66.5 37 0.0008 30.2 8.1 66 63-129 431-507 (509)
64 KOG1757 Histone 2A [Chromatin 64.1 11 0.00024 27.5 3.6 66 63-130 32-97 (131)
65 TIGR00764 lon_rel lon-related 63.3 44 0.00095 30.3 8.1 64 65-128 315-391 (608)
66 KOG1658 DNA polymerase epsilon 62.3 5.9 0.00013 30.3 2.0 64 60-125 58-122 (162)
67 TIGR02902 spore_lonB ATP-depen 59.6 40 0.00088 29.9 7.1 50 77-126 279-330 (531)
68 TIGR03015 pepcterm_ATPase puta 56.8 52 0.0011 25.4 6.6 61 66-126 199-264 (269)
69 PF07278 DUF1441: Protein of u 55.5 63 0.0014 24.5 6.5 65 44-108 75-150 (152)
70 COG5624 TAF61 Transcription in 55.1 3.4 7.4E-05 36.3 -0.4 58 68-125 389-447 (505)
71 KOG2680 DNA helicase TIP49, TB 52.8 54 0.0012 28.4 6.4 72 57-128 351-429 (454)
72 PRK07452 DNA polymerase III su 52.2 52 0.0011 26.5 6.1 61 64-126 135-197 (326)
73 PF04719 TAFII28: hTAFII28-lik 50.6 81 0.0018 21.8 6.9 64 59-126 24-88 (90)
74 PF08369 PCP_red: Proto-chloro 49.4 27 0.0006 20.9 3.1 43 81-124 1-44 (45)
75 TIGR02030 BchI-ChlI magnesium 48.1 67 0.0015 27.0 6.3 51 77-127 251-308 (337)
76 PRK08487 DNA polymerase III su 43.1 98 0.0021 25.3 6.5 56 66-125 142-197 (328)
77 TIGR01128 holA DNA polymerase 42.8 1.5E+02 0.0033 23.2 7.3 62 64-127 116-177 (302)
78 PF10911 DUF2717: Protein of u 41.9 51 0.0011 22.3 3.8 60 45-107 2-64 (77)
79 PRK05907 hypothetical protein; 39.6 90 0.002 25.8 5.7 67 59-125 131-200 (311)
80 KOG1659 Class 2 transcription 39.5 99 0.0021 24.9 5.6 65 59-125 11-76 (224)
81 PF08157 NUC129: NUC129 domain 35.7 67 0.0015 20.9 3.4 43 83-125 9-59 (63)
82 PRK06585 holA DNA polymerase I 35.1 1.3E+02 0.0028 24.5 5.9 50 77-126 158-208 (343)
83 TIGR01924 rsbW_low_gc serine-p 34.4 83 0.0018 23.1 4.3 45 61-105 15-59 (159)
84 TIGR02442 Cob-chelat-sub cobal 32.4 1.3E+02 0.0029 27.3 6.0 52 77-128 246-304 (633)
85 COG1466 HolA DNA polymerase II 31.8 1.7E+02 0.0037 24.0 6.2 49 77-125 156-204 (334)
86 PRK13531 regulatory ATPase Rav 31.4 2.2E+02 0.0049 25.5 7.1 75 43-128 207-284 (498)
87 KOG1942 DNA helicase, TBP-inte 31.4 1.4E+02 0.0031 25.8 5.7 71 57-127 360-437 (456)
88 PF13581 HATPase_c_2: Histidin 31.3 1.1E+02 0.0024 20.7 4.3 43 65-107 8-50 (125)
89 PRK05574 holA DNA polymerase I 30.7 2.8E+02 0.006 22.1 7.2 60 65-127 152-212 (340)
90 CHL00081 chlI Mg-protoporyphyr 30.6 1.9E+02 0.0041 24.6 6.3 51 77-127 264-321 (350)
91 PRK10840 transcriptional regul 29.9 63 0.0014 24.0 3.1 28 93-120 182-214 (216)
92 PF13060 DUF3921: Protein of u 28.9 1.2E+02 0.0027 19.0 3.7 28 76-103 21-48 (58)
93 PRK00411 cdc6 cell division co 28.6 3.3E+02 0.0072 22.3 8.0 47 80-126 228-280 (394)
94 PRK05629 hypothetical protein; 27.6 2.2E+02 0.0048 23.0 6.1 48 77-125 142-189 (318)
95 PRK13407 bchI magnesium chelat 27.2 1.9E+02 0.0042 24.2 5.8 51 77-127 248-305 (334)
96 PF07962 Swi3: Replication For 26.4 1E+02 0.0022 20.7 3.3 29 43-71 34-62 (83)
97 PRK04069 serine-protein kinase 25.4 1.4E+02 0.003 21.8 4.2 45 61-105 15-59 (161)
98 PF10788 DUF2603: Protein of u 25.1 67 0.0014 24.0 2.4 32 42-74 97-128 (137)
99 TIGR02031 BchD-ChlD magnesium 25.0 1.9E+02 0.0042 26.0 5.7 52 77-128 200-258 (589)
100 PF12767 SAGA-Tad1: Transcript 24.7 1.2E+02 0.0027 24.0 4.0 31 77-107 219-250 (252)
101 PF15510 CENP-W: Centromere ki 24.2 1.9E+02 0.0041 20.4 4.3 34 94-127 62-95 (102)
102 smart00350 MCM minichromosome 24.0 3.2E+02 0.0069 24.0 6.8 28 102-129 478-505 (509)
103 KOG3219 Transcription initiati 23.4 79 0.0017 25.0 2.6 78 47-129 101-179 (195)
104 cd00913 PCD_DCoH_subfamily_a P 23.2 52 0.0011 21.4 1.4 13 115-127 61-73 (76)
105 PF08681 DUF1778: Protein of u 21.5 1.7E+02 0.0037 19.2 3.6 51 78-128 3-61 (80)
106 cd00488 PCD_DCoH PCD_DCoH: The 21.5 60 0.0013 21.0 1.4 13 116-128 61-73 (75)
107 PF04604 L_biotic_typeA: Type- 21.5 83 0.0018 19.7 1.9 20 84-103 7-26 (51)
108 PRK07914 hypothetical protein; 21.4 2.8E+02 0.0061 22.5 5.6 60 65-125 131-191 (320)
109 COG3682 Predicted transcriptio 21.2 1.8E+02 0.0038 21.3 3.9 66 64-129 45-117 (123)
110 COG1598 Predicted nuclease of 21.2 1.3E+02 0.0029 19.3 3.0 24 83-106 34-57 (73)
111 COG5304 Uncharacterized protei 21.1 69 0.0015 22.4 1.6 16 60-75 73-88 (92)
112 PRK09335 30S ribosomal protein 20.4 26 0.00057 24.6 -0.6 18 103-120 69-86 (95)
113 KOG1969 DNA replication checkp 20.1 2.8E+02 0.0061 26.7 5.8 71 41-113 449-520 (877)
No 1
>PTZ00018 histone H3; Provisional
Probab=100.00 E-value=5.4e-55 Score=322.32 Aligned_cols=131 Identities=96% Similarity=1.346 Sum_probs=123.4
Q ss_pred CCCccccccccCCCCCCCcccccC----CCCCCCCCCCCcccCCCchhhHHHHhhhhhhhhhcccchhHHHHHHHHHhcc
Q 032848 1 MARTKQTARKSTGGKAPRKQLATK----SAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 76 (132)
Q Consensus 1 MARtk~~a~ks~g~kaprk~~~~k----~~~~~~~~k~~~r~~~g~~~l~eIr~~q~st~llipk~pF~rlvreI~~~~~ 76 (132)
|||||+++++++|+++|+++.+++ +.+..++.++++||+||+++|+|||+||+||+|||||+||+||||||++++.
T Consensus 1 MaRtk~~~~k~~~~~~prk~~~~~~~~~~~~~~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~ 80 (136)
T PTZ00018 1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
T ss_pred CCCCCcCccCCCCCCCCcccccccccccCCCCCCCCCCCcccCCchhHHHHHHHHcccchhccccccHHHHHHHHHHHcC
Confidence 999999999999999999988763 3334566788999999999999999999999999999999999999999999
Q ss_pred cCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhccc
Q 032848 77 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 131 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~~ 131 (132)
.++||+++||++||||+|+|||+||||+|+||+||||||||++||+|+.+|||++
T Consensus 81 ~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~~ 135 (136)
T PTZ00018 81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
T ss_pred CcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHhcccC
Confidence 9999999999999999999999999999999999999999999999999999986
No 2
>PLN00161 histone H3; Provisional
Probab=100.00 E-value=6.4e-55 Score=320.88 Aligned_cols=128 Identities=66% Similarity=0.963 Sum_probs=120.3
Q ss_pred CCCccccccccCCCCCCCcccccCCCCCCCCCCCCcccCCCchhhHHHHhhhhhhhhhcccchhHHHHHHHHHhcc-cCc
Q 032848 1 MARTKQTARKSTGGKAPRKQLATKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK-TDL 79 (132)
Q Consensus 1 MARtk~~a~ks~g~kaprk~~~~k~~~~~~~~k~~~r~~~g~~~l~eIr~~q~st~llipk~pF~rlvreI~~~~~-~~~ 79 (132)
||||||+ +++++|+.|++++..+ ...+++++++||+||+++|+|||+||+||++|||++||+||||||++++. .++
T Consensus 1 mar~k~~-~~~~~~~~~~~~~~~~--~~~~~~kk~~r~rpGtvaLrEIR~yQkst~lLIpklPF~RLVREI~~~~~~~~~ 77 (135)
T PLN00161 1 MARRLQG-KRFRKGKKPQKEASGV--TRQELDKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLREPF 77 (135)
T ss_pred CCccccc-ccccCCCCCcccCCCC--CCCCCCCCCccCCCcchHHHHHHHHccccccccccccHHHHHHHHHHhcCCCCc
Confidence 9999999 7788999999998776 23566789999999999999999999999999999999999999999996 579
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhccc
Q 032848 80 RFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 131 (132)
Q Consensus 80 r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~~ 131 (132)
||+++||++||||+|+|||++|||+|+||+||||||||++||+||.+|||+.
T Consensus 78 Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rirg~~ 129 (135)
T PLN00161 78 RWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRGPI 129 (135)
T ss_pred EeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhcccc
Confidence 9999999999999999999999999999999999999999999999999974
No 3
>PLN00121 histone H3; Provisional
Probab=100.00 E-value=6.8e-55 Score=321.80 Aligned_cols=132 Identities=98% Similarity=1.348 Sum_probs=124.2
Q ss_pred CCCccccccccCCCCCCCcccccC----CCCCCCCCCCCcccCCCchhhHHHHhhhhhhhhhcccchhHHHHHHHHHhcc
Q 032848 1 MARTKQTARKSTGGKAPRKQLATK----SAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 76 (132)
Q Consensus 1 MARtk~~a~ks~g~kaprk~~~~k----~~~~~~~~k~~~r~~~g~~~l~eIr~~q~st~llipk~pF~rlvreI~~~~~ 76 (132)
|||||+++++++|+++|+++.+++ +.+..++.+++++|+||+++|+|||+||+||+|||||+||+||||||++++.
T Consensus 1 MaRtk~~~~k~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~ 80 (136)
T PLN00121 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
T ss_pred CCCCCcCccCCCCCCCCcccccccccccCCCCCCCCCCCcccCchhHHHHHHHHhccccccccccccHHHHHHHHHHHhC
Confidence 999999999999999999998763 3334566789999999999999999999999999999999999999999999
Q ss_pred cCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcccC
Q 032848 77 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 132 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~~~ 132 (132)
+++||+++||++||||+|+|||+||||+|+||+|+||||||++||+|+.+|||+++
T Consensus 81 ~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~~~ 136 (136)
T PLN00121 81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136 (136)
T ss_pred ccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHhccccC
Confidence 99999999999999999999999999999999999999999999999999999864
No 4
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=100.00 E-value=8e-51 Score=299.38 Aligned_cols=132 Identities=93% Similarity=1.278 Sum_probs=124.5
Q ss_pred CCCccccccccCCCCCCCcccccCCCCC-----CCCCCCCcccCCCchhhHHHHhhhhhhhhhcccchhHHHHHHHHHhc
Q 032848 1 MARTKQTARKSTGGKAPRKQLATKSAPT-----TGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDF 75 (132)
Q Consensus 1 MARtk~~a~ks~g~kaprk~~~~k~~~~-----~~~~k~~~r~~~g~~~l~eIr~~q~st~llipk~pF~rlvreI~~~~ 75 (132)
|+|++++++++.++++|++..+.++... .+...++++|+||+++++|||+||+||+|||+|+||+|||+||.+++
T Consensus 1 m~r~~~t~~k~~~~~~~r~~~a~~~~~~~~~~~~~~~~k~~r~rpg~~al~eirkyQkstdLlI~K~PFqRlvrei~q~f 80 (137)
T KOG1745|consen 1 MARTKQTARKSTGGKAPRKQLAGKAARKSAAPRTGRVKKPHRYRPGTVALREIRKYQKSTDLLIRKLPFQRLVREIAQDF 80 (137)
T ss_pred CCCCCcccccccCCCCCccccccccccccccccccccCccccccCchHHHHHHHHHHhhhHHHhhcCcHHHHhHHHHhcc
Confidence 8999999999999999999998855443 34567889999999999999999999999999999999999999999
Q ss_pred ccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcccC
Q 032848 76 KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 132 (132)
Q Consensus 76 ~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~~~ 132 (132)
..|+|||+.|+.+||||+|+|||+||||+|+||+||||||||++|||||++|+|+++
T Consensus 81 ~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg~~~ 137 (137)
T KOG1745|consen 81 KTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 137 (137)
T ss_pred cccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhcccCCC
Confidence 999999999999999999999999999999999999999999999999999999874
No 5
>smart00428 H3 Histone H3.
Probab=100.00 E-value=5.7e-47 Score=269.43 Aligned_cols=101 Identities=87% Similarity=1.223 Sum_probs=97.9
Q ss_pred CCCCCcccCCCchhhHHHHhhhhhhhhhcccchhHHHHHHHHHhccc--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032848 31 GVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSHAVLALQEAAEAYLVGLFEDTNLCA 108 (132)
Q Consensus 31 ~~k~~~r~~~g~~~l~eIr~~q~st~llipk~pF~rlvreI~~~~~~--~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a 108 (132)
++++++||+||+++|+|||+||+||++||||+||+||||||++++.+ ++|||++|+++|||++|+||+++||||++||
T Consensus 2 ~~~~~~r~rpg~~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a 81 (105)
T smart00428 2 GKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLA 81 (105)
T ss_pred CCCCCcCCCCcchHHHHHHHHccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999999999999999999999999999999987 9999999999999999999999999999999
Q ss_pred hhcCccccChhhHHHHHHHhccc
Q 032848 109 IHAKRVTIMPKDIQLARRIRGER 131 (132)
Q Consensus 109 ~HakRvTi~~~Diqla~ri~~~~ 131 (132)
+||||||||++||+||.+|||++
T Consensus 82 ~HAkRvTl~~kDi~La~rir~~~ 104 (105)
T smart00428 82 IHAKRVTIMPKDIQLARRIRGER 104 (105)
T ss_pred HHhCCccCcHhhHHHHHHHhccC
Confidence 99999999999999999999985
No 6
>PLN00160 histone H3; Provisional
Probab=100.00 E-value=1.7e-46 Score=263.40 Aligned_cols=94 Identities=71% Similarity=1.082 Sum_probs=91.0
Q ss_pred cCCCchhhHHHHhhhhhhhhhcccchhHHHHHHHHHhcc-cCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCcccc
Q 032848 38 YRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK-TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTI 116 (132)
Q Consensus 38 ~~~g~~~l~eIr~~q~st~llipk~pF~rlvreI~~~~~-~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi 116 (132)
++||+++|+|||+||+||++||||+||+||||||++++. .++||+++|+++||||+|+|||++|||+|+||+|||||||
T Consensus 1 ~rpGt~aLrEIR~yQkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl 80 (97)
T PLN00160 1 MRPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTI 80 (97)
T ss_pred CCCccHHHHHHHHHccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhccccc
Confidence 589999999999999999999999999999999999986 5699999999999999999999999999999999999999
Q ss_pred ChhhHHHHHHHhccc
Q 032848 117 MPKDIQLARRIRGER 131 (132)
Q Consensus 117 ~~~Diqla~ri~~~~ 131 (132)
|++|||||.+|||+.
T Consensus 81 ~~kD~~L~~rirg~~ 95 (97)
T PLN00160 81 MPKDMQLARRIRGQT 95 (97)
T ss_pred chhhHHHHHHhhccc
Confidence 999999999999974
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.94 E-value=3.4e-27 Score=164.12 Aligned_cols=87 Identities=47% Similarity=0.671 Sum_probs=83.0
Q ss_pred CCchhhHHHHhhhhhhhhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChh
Q 032848 40 PGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPK 119 (132)
Q Consensus 40 ~g~~~l~eIr~~q~st~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~ 119 (132)
||+..++|||+||++++++||++||.|++|+... .|||.+|.++||+++|.|+.+++|+|+.||.|+||+||+++
T Consensus 1 ~~~~~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~-----~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~ 75 (91)
T COG2036 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGA-----ERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAE 75 (91)
T ss_pred CCcchHHHHHhhhhhhhhhcCchHHHHHHHHHhH-----HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHH
Confidence 6889999999999999999999999999999954 49999999999999999999999999999999999999999
Q ss_pred hHHHHHHHhccc
Q 032848 120 DIQLARRIRGER 131 (132)
Q Consensus 120 Diqla~ri~~~~ 131 (132)
||+|+.+.+|..
T Consensus 76 DI~la~~~~~~~ 87 (91)
T COG2036 76 DIKLALKRLGRR 87 (91)
T ss_pred HHHHHHHHhccc
Confidence 999999999863
No 8
>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=99.85 E-value=3e-21 Score=127.90 Aligned_cols=75 Identities=48% Similarity=0.665 Sum_probs=71.5
Q ss_pred hhhhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032848 54 STELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 54 st~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~ 128 (132)
++..+||+.||.|++++|..++...++|+.+|+.+||.++|.|++++||+|+.||.|+||+||+++||++|.+++
T Consensus 1 ~~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~ 75 (75)
T PF00125_consen 1 RTRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID 75 (75)
T ss_dssp HHSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred CcccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence 467899999999999999998877799999999999999999999999999999999999999999999999985
No 9
>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=99.44 E-value=5.2e-13 Score=88.94 Aligned_cols=58 Identities=24% Similarity=0.292 Sum_probs=52.5
Q ss_pred HHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 69 REIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 69 reI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
.+.+.++.+..+++++|.++||+.+|+|+.+++++|+.+|.|++|.||.++||+|+..
T Consensus 8 ~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~ 65 (72)
T cd07981 8 QELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLE 65 (72)
T ss_pred HHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 3444555677999999999999999999999999999999999999999999999965
No 10
>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=6.2e-12 Score=86.64 Aligned_cols=71 Identities=24% Similarity=0.253 Sum_probs=66.5
Q ss_pred hhhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032848 55 TELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 55 t~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 130 (132)
+-.-||+.|..||++.- +..|+|.++.+++.++.|.|+.++..||..++.|++|.||+..||.+|.+-.|.
T Consensus 10 ~~~gi~k~~I~RLarr~-----GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~ 80 (85)
T cd00076 10 NIKGITKPAIRRLARRG-----GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 80 (85)
T ss_pred hhccCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCC
Confidence 33449999999999988 889999999999999999999999999999999999999999999999998885
No 11
>PLN00035 histone H4; Provisional
Probab=99.30 E-value=1e-11 Score=88.20 Aligned_cols=67 Identities=22% Similarity=0.263 Sum_probs=64.8
Q ss_pred cccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032848 59 IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 59 ipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 130 (132)
||+.|..||++.- +..|+|.+|.++|.++.|.|+.++..||..+|.||+|+||+.+||.+|.+..|.
T Consensus 30 ipk~~IrRLARr~-----GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~ 96 (103)
T PLN00035 30 ITKPAIRRLARRG-----GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred CCHHHHHHHHHHc-----CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCC
Confidence 9999999999988 899999999999999999999999999999999999999999999999998875
No 12
>PTZ00015 histone H4; Provisional
Probab=99.27 E-value=1.6e-11 Score=87.16 Aligned_cols=69 Identities=22% Similarity=0.229 Sum_probs=65.6
Q ss_pred hhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032848 57 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 57 llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 130 (132)
.-||+.|..||++.- +..|+|.++.+.+.++.|.|+.++..||..+|.||+|.||+.+||.+|.+..|.
T Consensus 29 ~gI~k~~IrRLarr~-----GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~ 97 (102)
T PTZ00015 29 RGITKGAIRRLARRG-----GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR 97 (102)
T ss_pred cCCCHHHHHHHHHHc-----CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC
Confidence 459999999999988 899999999999999999999999999999999999999999999999988875
No 13
>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=99.21 E-value=3.8e-11 Score=78.76 Aligned_cols=64 Identities=20% Similarity=0.214 Sum_probs=60.3
Q ss_pred hcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 58 LIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 58 lipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
.+|+.|..|+.+.+ |-.+++.++..+|.+..|.++.++.++|..++.|++|.||+..||.+|.+
T Consensus 2 ~~p~~~i~ria~~~-----Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESL-----GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHC-----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 57999999999888 88899999999999999999999999999999999999999999999863
No 14
>smart00417 H4 Histone H4.
Probab=99.14 E-value=7.5e-11 Score=79.37 Aligned_cols=65 Identities=20% Similarity=0.193 Sum_probs=60.0
Q ss_pred hhhhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHH
Q 032848 54 STELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL 123 (132)
Q Consensus 54 st~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diql 123 (132)
.+-.-||+.|..||++.- +..|+|.++.+.|.++.|.|+.++..+|..++.|++|+||+..||..
T Consensus 9 d~i~gI~k~~IrRLaRr~-----GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 9 DNIQGITKPAIRRLARRG-----GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred hhhcCCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 333459999999999987 89999999999999999999999999999999999999999999864
No 15
>PTZ00463 histone H2B; Provisional
Probab=99.14 E-value=1.6e-10 Score=83.56 Aligned_cols=65 Identities=18% Similarity=0.293 Sum_probs=60.8
Q ss_pred ccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHH----HHHHHhhcCccccChhhHHHHHHHh
Q 032848 60 RKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFED----TNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 60 pk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~----a~~~a~HakRvTi~~~Diqla~ri~ 128 (132)
++.+|..||+.++.+++++..|+..||..| ++|++|+||. |..++.+.+|.||+++|||.|++|.
T Consensus 26 r~esy~~YI~KVLKqVhPd~gIS~kaM~Im----nSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 26 RYDSYGLYIFKVLKQVHPDTGISRKSMNIM----NSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred ccchHHHHHHHHHHhhCCCCCccHHHHHHH----HHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 356699999999999999999999999999 8999999998 8999999999999999999999985
No 16
>PLN00158 histone H2B; Provisional
Probab=99.13 E-value=2e-10 Score=83.04 Aligned_cols=65 Identities=18% Similarity=0.333 Sum_probs=61.3
Q ss_pred ccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHH----HHHHHhhcCccccChhhHHHHHHHh
Q 032848 60 RKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFED----TNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 60 pk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~----a~~~a~HakRvTi~~~Diqla~ri~ 128 (132)
++..|..||+.++.+++++..|+..||..| ++|++|+||. |..++.+.+|.||+++|||.|++|.
T Consensus 25 r~esy~~YI~kVLKQVhPd~gIS~kaM~Im----nSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 25 KTETYKIYIYKVLKQVHPDTGISSKAMSIM----NSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred ccccHHHHHHHHHHHhCCCCCccHHHHHHH----HHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 467899999999999999999999999999 8999999998 8999999999999999999999985
No 17
>smart00427 H2B Histone H2B.
Probab=99.13 E-value=2.4e-10 Score=79.32 Aligned_cols=62 Identities=19% Similarity=0.331 Sum_probs=58.9
Q ss_pred hhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHH----HHHHHhhcCccccChhhHHHHHHHh
Q 032848 63 PFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFED----TNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 63 pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~----a~~~a~HakRvTi~~~Diqla~ri~ 128 (132)
+|..||++++.++++|..++..||..| ++|++|+||. |..++.+.+|.||+++|||.|+++.
T Consensus 2 sy~~Yi~kvLKqVhpd~giS~kam~im----nSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 2 TYAIYIYKVLKQVHPDTGISSKAMSIM----NSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred cHHHHHHHHHHHhCCCccccHHHHHHH----HHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 689999999999999999999999999 8999999988 8999999999999999999999985
No 18
>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=98.83 E-value=2.2e-08 Score=72.50 Aligned_cols=66 Identities=21% Similarity=0.324 Sum_probs=60.1
Q ss_pred hHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032848 64 FQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 64 F~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 130 (132)
..++|..|+.+. +..++++++...|-|.++.|..+++.||..+|.||+|.||+.+||+||...++.
T Consensus 3 d~~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 3 DARVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 357788887765 567999999999999999999999999999999999999999999999998875
No 19
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=98.80 E-value=9.7e-09 Score=75.32 Aligned_cols=66 Identities=27% Similarity=0.379 Sum_probs=62.0
Q ss_pred cccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHH----HHHHHhhcCccccChhhHHHHHHHh
Q 032848 59 IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFED----TNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 59 ipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~----a~~~a~HakRvTi~~~Diqla~ri~ 128 (132)
..+..|..+|+.++.++++++.+++.|+.+| ++|++++||+ |+.+|.+.+|-||..++||+|.+|.
T Consensus 34 ~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vm----nsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 34 RRKESYSEYVYKVLKQVHPDLGISSKAMGVM----NSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred cccCceeeehhhhhhcccCCCCcCHHHHHHH----HHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 4677899999999999999999999999999 9999999998 9999999999999999999999985
No 20
>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=98.78 E-value=2.9e-08 Score=64.20 Aligned_cols=63 Identities=27% Similarity=0.294 Sum_probs=51.1
Q ss_pred cccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032848 59 IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 59 ipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 125 (132)
+|.....++++.. .+..+++.+|..+|+.++|.|+..|...|+..|.+.+|.||+.+||..|+
T Consensus 3 lP~a~vkri~k~~----~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 3 LPLARVKRIMKSD----PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp S-HHHHHHHHHHT----STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CChHHHHHHhccC----CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 4555555555443 45678999999999999999999999999999999999999999998764
No 21
>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=98.39 E-value=6.2e-07 Score=64.94 Aligned_cols=67 Identities=22% Similarity=0.206 Sum_probs=61.5
Q ss_pred hhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
.|.+|..++.|++++- ....|++.+|...|....|.+..+++|.|...|.|.++.+|+++||++|.+
T Consensus 18 gL~fPV~ri~R~Lk~~----~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~ 84 (115)
T cd00074 18 GLQFPVGRIHRYLKKG----RYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR 84 (115)
T ss_pred CccCcHHHHHHHHHcC----ccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh
Confidence 5889999999999762 145899999999999999999999999999999999999999999999975
No 22
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.36 E-value=2.3e-06 Score=57.30 Aligned_cols=54 Identities=24% Similarity=0.134 Sum_probs=50.7
Q ss_pred cCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032848 77 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 130 (132)
+-.+++++|++.|.+..|.|+..|-+.+..+|.|++|.++.+.||.+|..-.|.
T Consensus 20 Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi 73 (77)
T smart00576 20 GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGI 73 (77)
T ss_pred CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Confidence 567999999999999999999999999999999999999999999999877664
No 23
>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=98.31 E-value=3.2e-06 Score=55.93 Aligned_cols=59 Identities=20% Similarity=0.253 Sum_probs=47.1
Q ss_pred HHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 68 VREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 68 vreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
+.+++.++.+...+.+++.+.|.+.++.|+.++.+.|..+|.|.+--||..+||++...
T Consensus 5 l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le 63 (68)
T PF03847_consen 5 LQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE 63 (68)
T ss_dssp HHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence 34555666889999999999999999999999999999999999999999999999864
No 24
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.30 E-value=2.3e-06 Score=57.83 Aligned_cols=65 Identities=26% Similarity=0.260 Sum_probs=53.7
Q ss_pred chhHHHHHHHHHhc--ccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 62 LPFQRLVREIAQDF--KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 62 ~pF~rlvreI~~~~--~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
+.+..-|-+|.++. ..+..++++.+.+|-|.+=.++..+-+|--..|.||||.||+++|+.|..|
T Consensus 5 aal~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 5 AALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 34555666777766 367899999999999999999999999999999999999999999999764
No 25
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=98.27 E-value=2.7e-06 Score=65.00 Aligned_cols=70 Identities=27% Similarity=0.301 Sum_probs=65.2
Q ss_pred hhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032848 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 127 (132)
Q Consensus 56 ~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri 127 (132)
++.+|++-..|||++++.+. +..++.+|..+|+.+|--|+..|.-.|+..|.-.+|.||++.|+--+..-
T Consensus 8 dl~lP~AiI~rlvke~l~E~--~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~E 77 (172)
T KOG0870|consen 8 DLNLPNAIITRLVKEVLPES--NVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDE 77 (172)
T ss_pred HhhccHHHHHHHHHHhCccc--cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHH
Confidence 68899999999999998876 78999999999999999999999999999999999999999999776643
No 26
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=98.09 E-value=1.4e-05 Score=66.99 Aligned_cols=62 Identities=21% Similarity=0.262 Sum_probs=55.1
Q ss_pred HHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032848 68 VREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 68 vreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 130 (132)
|+.|++.. +..+++.+|..+|.+-+|.++..+.++|..+|.|+||.||+.+||++|.+.++.
T Consensus 5 i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~ 66 (343)
T cd08050 5 IKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNV 66 (343)
T ss_pred HHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCC
Confidence 45555433 456999999999999999999999999999999999999999999999999865
No 27
>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=98.08 E-value=2.1e-05 Score=51.82 Aligned_cols=58 Identities=28% Similarity=0.326 Sum_probs=45.3
Q ss_pred HHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 68 VREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 68 vreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
|+-|++.++ -..++.++...|.+-+|.-|-.+.++|..++.|++|.+|+..||..|.|
T Consensus 9 vk~iAes~G-i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 9 VKDIAESLG-ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp HHHHHHHTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred HHHHHHHcC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 445555443 2368999999999999999999999999999999999999999999875
No 28
>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=97.95 E-value=4.3e-05 Score=56.37 Aligned_cols=65 Identities=29% Similarity=0.359 Sum_probs=52.9
Q ss_pred HHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032848 65 QRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 65 ~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 130 (132)
.++|..|+.+.+ -..+++..+.-|-|.+=.|..++++||...|-||+|.+|...|++||...|..
T Consensus 15 a~~i~~iL~~~G-v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~ 79 (129)
T PF02291_consen 15 ARVIHLILKSMG-VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLD 79 (129)
T ss_dssp HHHHHHHHHHTT----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT--
T ss_pred HHHHHHHHHHcC-CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHh
Confidence 578888888774 34579999999999999999999999999999999999999999999987743
No 29
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.81 E-value=3.9e-05 Score=65.85 Aligned_cols=62 Identities=24% Similarity=0.293 Sum_probs=43.9
Q ss_pred cccchhHHHHHHHHHh-cccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhh
Q 032848 59 IRKLPFQRLVREIAQD-FKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKD 120 (132)
Q Consensus 59 ipk~pF~rlvreI~~~-~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~D 120 (132)
+|..+..+|+.-.++. +....+|+.+||.+|..++|-|..+|-+|--..|.||||+||...|
T Consensus 352 lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 352 LPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4555555555555442 3367899999999999999999999999999999999999999887
No 30
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.78 E-value=3e-05 Score=62.94 Aligned_cols=73 Identities=21% Similarity=0.272 Sum_probs=65.0
Q ss_pred hhhhhhhhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 50 KYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 50 ~~q~st~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
.++-+++.++-|--...||++| .++.-+..++-+.|.|.|++|+.++-..|+.+|.|.|--||-++||+|+..
T Consensus 146 ~~~~~~~~il~k~kl~dLvqqI----d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLE 218 (258)
T KOG1142|consen 146 QDEPGNNPILSKRKLDDLVQQI----DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLE 218 (258)
T ss_pred cccCCCCccccccchhHHHHhh----cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeee
Confidence 5667778888887777777777 678899999999999999999999999999999999999999999999863
No 31
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=97.53 E-value=0.00031 Score=53.50 Aligned_cols=71 Identities=15% Similarity=0.197 Sum_probs=64.6
Q ss_pred hhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032848 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 129 (132)
Q Consensus 56 ~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~ 129 (132)
+.++|.+...|+.+.++ ..+-.|+.+|.+.+||.+-.|+--+--.|+.-+.--+|+||+.+||-.|+--.|
T Consensus 30 Dr~LPIANV~RIMK~~l---P~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 30 DRFLPIANVSRIMKKAL---PANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred hhhccHHHHHHHHHhcC---CcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 45689999999999984 478899999999999999999999999999999999999999999999987665
No 32
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.02 E-value=0.0044 Score=46.60 Aligned_cols=64 Identities=25% Similarity=0.417 Sum_probs=54.3
Q ss_pred HHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032848 66 RLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 66 rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 130 (132)
++|..|+.+++ -.-+....+.-|-|.+=.|.+++++||...+.||++-||..+|++||...++.
T Consensus 17 ~~i~~iL~s~G-I~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~ 80 (148)
T KOG3334|consen 17 RVIASILKSLG-IQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVD 80 (148)
T ss_pred HHHHHHHHHcC-ccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhc
Confidence 56666666554 33566778888889999999999999999999999999999999999988875
No 33
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=96.91 E-value=0.004 Score=43.41 Aligned_cols=66 Identities=23% Similarity=0.254 Sum_probs=56.0
Q ss_pred ccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032848 60 RKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 60 pk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 130 (132)
-|-...||.|.- +--|+..-..+....++..||.+..-+|+..+-||||+||+.-|+--+.+-.|.
T Consensus 31 tKpaIRRlARr~-----GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~ 96 (103)
T KOG3467|consen 31 TKPAIRRLARRG-----GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred chHHHHHHHHhc-----CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCc
Confidence 355666777655 667888888899999999999999999999999999999999999888776554
No 34
>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=96.73 E-value=0.0078 Score=39.83 Aligned_cols=52 Identities=23% Similarity=0.142 Sum_probs=48.6
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032848 79 LRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 79 ~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 130 (132)
..+++.|++.|-+.+..||..|...+...|-|++|-...+.|+.++..-.|.
T Consensus 22 ~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi 73 (77)
T PF07524_consen 22 DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGI 73 (77)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence 4789999999999999999999999999999999999999999999876664
No 35
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=96.52 E-value=0.012 Score=44.53 Aligned_cols=72 Identities=18% Similarity=0.255 Sum_probs=66.2
Q ss_pred hhhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032848 55 TELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 129 (132)
Q Consensus 55 t~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~ 129 (132)
-++-+||+....+|+|++ ..+.||..+|-+.+++..=.|+.-|--.||.++---.+.||.++-+.-|..-.|
T Consensus 9 de~sLPkAtv~KmIke~l---P~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~Lg 80 (156)
T KOG0871|consen 9 DELSLPKATVNKMIKEML---PKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLG 80 (156)
T ss_pred ccccCcHHHHHHHHHHhC---CcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcc
Confidence 467799999999999994 479999999999999999999999999999999999999999999998887665
No 36
>smart00414 H2A Histone 2A.
Probab=95.89 E-value=0.015 Score=41.48 Aligned_cols=67 Identities=25% Similarity=0.223 Sum_probs=57.5
Q ss_pred hhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
+|.+|-.-|.|++++- ....|++..|..-|--..|.+..+++|.|...+...++..|+++|+++|.+
T Consensus 7 gL~fPVgRi~r~Lk~~----~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 7 GLQFPVGRIHRLLRKG----TYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred CccCchHHHHHHHHcC----ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 5677777777887654 235699999999999999999999999999999999999999999999864
No 37
>PLN00154 histone H2A; Provisional
Probab=95.82 E-value=0.024 Score=42.26 Aligned_cols=68 Identities=19% Similarity=0.154 Sum_probs=59.8
Q ss_pred hhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
.|.+|-.-+.|+.++-.. ...|++..|..-|--+.|....+++|-|...|...++..|++++|+||.+
T Consensus 36 gL~FPVgRi~r~Lk~g~~---~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVS---AHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred CccCchHHHHHHHHhhhh---hccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 577888888888887621 35799999999999999999999999999999999999999999999974
No 38
>PTZ00017 histone H2A; Provisional
Probab=95.67 E-value=0.016 Score=43.05 Aligned_cols=67 Identities=24% Similarity=0.210 Sum_probs=58.9
Q ss_pred hhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
.|.+|-.-+.|+.++- ....|++..|..-|--..|.+..+++|.|...+...++.-|++++|+||.+
T Consensus 25 gL~FPVgRi~R~Lk~g----~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKG----RYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CcccchHHHHHHHhcc----chhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 5778888888888664 234699999999999999999999999999999999999999999999975
No 39
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=94.94 E-value=0.05 Score=39.84 Aligned_cols=58 Identities=22% Similarity=0.278 Sum_probs=50.0
Q ss_pred HHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 69 REIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 69 reI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
+.++..-....|++++|...|-...|.....++|-|...|.-.+-..|+|+-+|||.+
T Consensus 33 kr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 33 KRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred HHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 3344433467899999999999999999999999999999999999999999999853
No 40
>PLN00157 histone H2A; Provisional
Probab=94.71 E-value=0.039 Score=40.95 Aligned_cols=67 Identities=25% Similarity=0.224 Sum_probs=57.8
Q ss_pred hhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
.|.+|-.-+.|++++- ....|++..|..-|--..|....+++|.|...+...++.-|++++|+||.+
T Consensus 24 gL~FPVgRi~R~Lk~g----~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 24 GLQFPVGRIARYLKAG----KYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred CcccchHHHHHHHhcC----chhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 4678888888887663 235799999999998889999999999999999999999999999999874
No 41
>PLN00156 histone H2AX; Provisional
Probab=94.68 E-value=0.051 Score=40.68 Aligned_cols=67 Identities=25% Similarity=0.222 Sum_probs=57.4
Q ss_pred hhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
.|.+|-.-+.|++++- ....|++..|..-|--..|....+++|.|...+...++.-|+|+.|+||.+
T Consensus 27 gL~FPVgRi~R~Lk~g----~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 27 GLQFPVGRIARFLKAG----KYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred CcccchHHHHHHHhcC----ChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 4667777777877653 234699999999998889999999999999999999999999999999974
No 42
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=94.42 E-value=0.14 Score=45.88 Aligned_cols=53 Identities=23% Similarity=0.286 Sum_probs=49.6
Q ss_pred cCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032848 77 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 129 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~ 129 (132)
+-..++.+|..+|-+-.|.-+-++.++|..++.|+||-+++..||.-|.+.+.
T Consensus 25 Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 25 GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 56679999999999999999999999999999999999999999999998764
No 43
>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=94.40 E-value=0.033 Score=38.67 Aligned_cols=58 Identities=16% Similarity=0.187 Sum_probs=29.0
Q ss_pred HHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 69 REIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 69 reI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
+.++--++..-.-..+....|.+..-.|++++...|..+|...++.+|..+|+-.+.|
T Consensus 8 ~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR 65 (93)
T PF02269_consen 8 RQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLR 65 (93)
T ss_dssp HHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred HHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHh
Confidence 4444445555678899999999999999999999999999999999999999988765
No 44
>PLN00153 histone H2A; Provisional
Probab=94.34 E-value=0.062 Score=39.74 Aligned_cols=67 Identities=25% Similarity=0.218 Sum_probs=57.7
Q ss_pred hhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
.|.+|-.-+.|++++= ....|++..|..-|--..|....+++|.|...+...+..-|+|+.|+||.+
T Consensus 22 gL~FpVgRi~R~Lr~g----~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 22 GLQFPVGRIARYLKKG----KYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred CcccchHHHHHHHhcC----chhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 4678887788887653 235699999999999999999999999999999999999999999999974
No 45
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=93.81 E-value=0.26 Score=36.56 Aligned_cols=61 Identities=28% Similarity=0.355 Sum_probs=43.0
Q ss_pred HHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccCh---hhHHHHHHH
Q 032848 66 RLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMP---KDIQLARRI 127 (132)
Q Consensus 66 rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~---~Diqla~ri 127 (132)
||+.=|+...+ -.........-|-+-|-.|-.+++|||...|.|++|-.+.. +|+.||.--
T Consensus 18 rlihliL~Slg-i~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at 81 (145)
T COG5094 18 RLIHLILRSLG-IEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALAT 81 (145)
T ss_pred hHHHHHHHhcC-chhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHH
Confidence 44444444332 12334445555668889999999999999999999875555 999999754
No 46
>PTZ00252 histone H2A; Provisional
Probab=93.71 E-value=0.12 Score=38.42 Aligned_cols=67 Identities=19% Similarity=0.196 Sum_probs=55.6
Q ss_pred hhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh--cCccccChhhHHHHHH
Q 032848 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~H--akRvTi~~~Diqla~r 126 (132)
.|.+|-.-+.|++++- ....|+++.|..-|--..|....+++|.|...|.. .++.-|++++|+||.+
T Consensus 23 GL~FPVgRi~R~Lr~g----~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRG----QYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred CccCchHHHHHHHHcC----CcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 4668888888887654 23569999999999888899999999999998864 6778999999999975
No 47
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=93.47 E-value=0.32 Score=36.14 Aligned_cols=71 Identities=21% Similarity=0.180 Sum_probs=63.0
Q ss_pred hhhhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032848 54 STELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 127 (132)
Q Consensus 54 st~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri 127 (132)
+.++-+||+-.+..|-+|+. .++-|+.+|-+.++++.=.|+.-|--.||.++-.-..+||.++-+--|..-
T Consensus 7 dDe~sLPKATVqKMvS~iLp---~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALen 77 (148)
T COG5150 7 DDENSLPKATVQKMVSSILP---KDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALEN 77 (148)
T ss_pred cccccCcHHHHHHHHHHhcc---ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHh
Confidence 34677999999999999954 899999999999999999999999999999999999999999887666543
No 48
>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=91.87 E-value=0.59 Score=36.56 Aligned_cols=56 Identities=18% Similarity=0.209 Sum_probs=50.4
Q ss_pred hhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 032848 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAK 112 (132)
Q Consensus 56 ~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~Hak 112 (132)
..++..-|+...+..|+.+.+.. .++.+.+..|..|+|.+|.+|.+....++.|-.
T Consensus 42 ~~fl~~~~l~~~~~~i~~~~g~~-~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~ 97 (212)
T cd08045 42 PSFLNPSPLAKKIRKIAKKHGLK-EVDEDVLDLISLALEERLRNLLEKLIEVSEHRV 97 (212)
T ss_pred hhccCHHHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 46788899999999998876654 899999999999999999999999999999973
No 49
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=91.82 E-value=0.31 Score=36.09 Aligned_cols=67 Identities=25% Similarity=0.249 Sum_probs=55.4
Q ss_pred hhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
.+.+|---..|++|+ -....|++.+|...|--..|.....++|.|-..|.-.++.-|+|+-++||.+
T Consensus 25 gl~fPvgri~r~Lr~----~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 25 GLQFPVGRIHRLLRK----GRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred ccccCHHHHHHHHHc----cchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 355666656666655 2367899999999998888888899999999999999999999999999975
No 50
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=91.05 E-value=0.67 Score=37.50 Aligned_cols=85 Identities=20% Similarity=0.246 Sum_probs=64.2
Q ss_pred CchhhHHHHhhhhhhhh---------hcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 032848 41 GTVALREIRKYQKSTEL---------LIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHA 111 (132)
Q Consensus 41 g~~~l~eIr~~q~st~l---------lipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~Ha 111 (132)
|...-+-+|.||+..+- -...+||.|+ +++++.-.+--=|+++|=...-.++|-|+..|-=.|-+.|...
T Consensus 80 g~~~e~i~ryWq~ti~~~e~~~q~~~k~h~LPlARI-kkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~N 158 (286)
T COG5208 80 GLLDERISRYWQQTIKAAEEERQILLKDHNLPLARI-KKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEEN 158 (286)
T ss_pred hhHHHHHHHHHHHHHHHHHHhHHHHHHhccCcHHHH-HHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHh
Confidence 44455567888875322 2334799886 5565432223357888888888999999999999999999999
Q ss_pred CccccChhhHHHHHH
Q 032848 112 KRVTIMPKDIQLARR 126 (132)
Q Consensus 112 kRvTi~~~Diqla~r 126 (132)
+|-||...||--|+.
T Consensus 159 kRRtLQksDia~Av~ 173 (286)
T COG5208 159 KRRTLQKSDIAAAVK 173 (286)
T ss_pred hhhHHHHHHHHHHHH
Confidence 999999999988765
No 51
>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=90.69 E-value=0.29 Score=39.45 Aligned_cols=58 Identities=21% Similarity=0.255 Sum_probs=38.7
Q ss_pred hhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCcc
Q 032848 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRV 114 (132)
Q Consensus 56 ~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRv 114 (132)
.+++...|+...+.+|..... ...+.++.+..|-.|+|.+|-+|+|++..++.|....
T Consensus 41 ~~fL~~~~L~~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~ 98 (264)
T PF05236_consen 41 EPFLNPSPLQKRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDS 98 (264)
T ss_dssp ---S-HHHHHHHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred ccccCHHHHHHHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 467888899999999986554 6689999999999999999999999999999996544
No 52
>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=90.48 E-value=2.6 Score=29.16 Aligned_cols=58 Identities=17% Similarity=0.232 Sum_probs=45.3
Q ss_pred HHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 68 VREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 68 vreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
++.++--++..-.-..+.+..|.+..=.|+.+|.-.|..+|. .++--+.++|+..+.|
T Consensus 8 i~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR 65 (92)
T cd07978 8 IRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR 65 (92)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence 344444444455677899999999999999999999999998 5666669999998764
No 53
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=89.95 E-value=1.3 Score=37.25 Aligned_cols=51 Identities=16% Similarity=0.081 Sum_probs=47.7
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032848 80 RFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 80 r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 130 (132)
.++.-|++.|-+..-.|+-.+|+.+-..+.|++|.-.+..|+.|.....|.
T Consensus 22 ~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI 72 (323)
T KOG4336|consen 22 SISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNI 72 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCC
Confidence 478889999999999999999999999999999999999999999988775
No 54
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=88.72 E-value=0.82 Score=36.89 Aligned_cols=72 Identities=19% Similarity=0.223 Sum_probs=61.3
Q ss_pred hhhhhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032848 53 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 53 ~st~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 125 (132)
...++.+..+|..|+ |.|.+.-..---|+.+|...+-.|+|.|+..|-..+..-+--++|.|+.-.|+.-++
T Consensus 66 ~~~d~~~~~lPlaRi-KkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av 137 (236)
T KOG1657|consen 66 GQLDFKNHILPLARI-KKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAV 137 (236)
T ss_pred cccchhhccCcHhhc-cccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHh
Confidence 456788999999986 567554333348999999999999999999999999999999999999999998765
No 55
>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=85.41 E-value=1.5 Score=29.19 Aligned_cols=57 Identities=7% Similarity=0.061 Sum_probs=43.3
Q ss_pred HHHHHHHhc--ccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccc-cChhhHHH
Q 032848 67 LVREIAQDF--KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVT-IMPKDIQL 123 (132)
Q Consensus 67 lvreI~~~~--~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvT-i~~~Diql 123 (132)
+|.+|++.. +..++|+.+|+..+.+..+-|+..-...|+..+.--+-.+ |.++|++=
T Consensus 4 li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEk 63 (72)
T PF09415_consen 4 LIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEK 63 (72)
T ss_dssp HHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHH
T ss_pred HHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence 455555543 3679999999999999999999999999999888777777 99999874
No 56
>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=82.44 E-value=2.8 Score=31.41 Aligned_cols=59 Identities=22% Similarity=0.316 Sum_probs=43.9
Q ss_pred hHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032848 64 FQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 127 (132)
Q Consensus 64 F~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri 127 (132)
|.++.|+. .++-+..+-+.-+-+..|.-+-+||+-|..-|...+|-.|.+.|+-+...+
T Consensus 1 fe~lFR~a-----a~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPITkGl 59 (138)
T PF09123_consen 1 FERLFRKA-----AGLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPITKGL 59 (138)
T ss_dssp HHHHHHHH-----HS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HHH
T ss_pred ChHHHHHH-----hccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCccHHH
Confidence 56777777 456777888888999999999999999999999999999999999877655
No 57
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=82.34 E-value=10 Score=27.62 Aligned_cols=61 Identities=18% Similarity=0.200 Sum_probs=48.1
Q ss_pred hHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 64 FQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 64 F~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
|..=|+..+--++....--.+.+++|.|..-.|++.+.-.|-.+|- .|-.+..+|++.|.+
T Consensus 11 F~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr 71 (126)
T COG5248 11 FMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALR 71 (126)
T ss_pred HHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHh
Confidence 4444555555556666677889999999999999999998888887 777888999999875
No 58
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=80.53 E-value=6.2 Score=33.71 Aligned_cols=53 Identities=21% Similarity=0.090 Sum_probs=47.6
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032848 78 DLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 78 ~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 130 (132)
--.++..|++.|+..+-.|+-+|-+.|-..+-|++|+-....||-+|..-.|.
T Consensus 44 ~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~ 96 (353)
T KOG2389|consen 44 YSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSA 96 (353)
T ss_pred CcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhh
Confidence 34677789999999999999999999999999999999999999999876553
No 59
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=79.79 E-value=15 Score=26.45 Aligned_cols=62 Identities=19% Similarity=0.235 Sum_probs=47.2
Q ss_pred chhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 62 LPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 62 ~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
--|+.=++-.+--|+.+.---.+.+++|.+..=.|++++.+.|..+. +|-.+..+|+..+.|
T Consensus 9 ~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 9 HLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred HHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 34666666666666666666788899998889999999966666555 888899999998765
No 60
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=78.77 E-value=4.6 Score=34.60 Aligned_cols=53 Identities=21% Similarity=0.206 Sum_probs=47.7
Q ss_pred cCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032848 77 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 129 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~ 129 (132)
+---+..+++.+|..-.|.-+-++-+.|...+.|.||--++..||.-|.+-+.
T Consensus 19 Gi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lN 71 (450)
T COG5095 19 GISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLN 71 (450)
T ss_pred CCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcC
Confidence 33467889999999999999999999999999999999999999999988764
No 61
>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=69.99 E-value=32 Score=23.43 Aligned_cols=65 Identities=17% Similarity=0.258 Sum_probs=53.8
Q ss_pred cccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCc---cccChhhHHHHHHHh
Q 032848 59 IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKR---VTIMPKDIQLARRIR 128 (132)
Q Consensus 59 ipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR---vTi~~~Diqla~ri~ 128 (132)
+++....+++..+ .+..++.+.+.+|.-.+..|+..|-|.|..+...-+. --|.|+.|.-|.+..
T Consensus 17 f~k~~iKr~~~~~-----~~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 17 FPKAAIKRLIQSV-----TGQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred ccHHHHHHHHHHH-----cCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 6777767776655 4478899999999999999999999999999887665 788999998887753
No 62
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=69.81 E-value=11 Score=32.93 Aligned_cols=72 Identities=24% Similarity=0.374 Sum_probs=59.6
Q ss_pred hhcccchhHH-HHHHHHHhc--ccCcccCHHHHHHHHHHHH----HHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032848 57 LLIRKLPFQR-LVREIAQDF--KTDLRFQSHAVLALQEAAE----AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 57 llipk~pF~r-lvreI~~~~--~~~~r~~~~Al~aLqea~E----~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~ 128 (132)
++|+-.||.+ =+++|+.-- ..+.-++++|++-|-...+ -|.++|++-|+..|.-.+..+|..+|+.-|..+-
T Consensus 354 lII~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~lF 432 (450)
T COG1224 354 LIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKELF 432 (450)
T ss_pred eEEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHHH
Confidence 6788888876 467775532 3678899999999976655 6999999999999999999999999999887763
No 63
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=66.51 E-value=37 Score=30.23 Aligned_cols=66 Identities=23% Similarity=0.278 Sum_probs=48.6
Q ss_pred hhHHHHHHHHHhcccCcccCHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032848 63 PFQRLVREIAQDFKTDLRFQSHAVLALQEAAE-----------AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 129 (132)
Q Consensus 63 pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E-----------~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~ 129 (132)
.|.++|..++++. +-..|+.+|+..|=+.+- ..|.+|+..|+.+|.-.+...|...||+-|..-|-
T Consensus 431 ~~~~~i~~~~~~~-~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r~ 507 (509)
T PF13654_consen 431 QYARFIASICQKE-GLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEERR 507 (509)
T ss_dssp HHHHHHHHHHHHH-SS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH--
T ss_pred HHHHHHHHHHHhC-CCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHccc
Confidence 5777777776644 345789999988766543 57899999999999999999999999999987553
No 64
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=64.10 E-value=11 Score=27.47 Aligned_cols=66 Identities=24% Similarity=0.305 Sum_probs=49.8
Q ss_pred hhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032848 63 PFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 63 pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 130 (132)
|..|+=+-+-......-|+...|..-+-...|..-..++|-|...+.--|=+.|+|+-+||| |||+
T Consensus 32 pVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLA--iRGD 97 (131)
T KOG1757|consen 32 PVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLA--IRGD 97 (131)
T ss_pred chHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheee--ecCc
Confidence 45555544444455677888888777766678888889999998888888888999999998 4554
No 65
>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=63.29 E-value=44 Score=30.30 Aligned_cols=64 Identities=16% Similarity=0.136 Sum_probs=45.7
Q ss_pred HHHHHHHHHhcccCcccCHHHHHHHHHH-H------------HHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032848 65 QRLVREIAQDFKTDLRFQSHAVLALQEA-A------------EAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 65 ~rlvreI~~~~~~~~r~~~~Al~aLqea-~------------E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~ 128 (132)
.+++.........-..|+.+|+..|-+. + ..-|.+++..|+..|...+..+|+.+|++-|...+
T Consensus 315 ~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 315 VQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred HHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 3444444333323348999999998642 2 36788888889888888899999999999775543
No 66
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=62.34 E-value=5.9 Score=30.34 Aligned_cols=64 Identities=25% Similarity=0.350 Sum_probs=49.4
Q ss_pred ccchhHHHHHHHHHhcccCcccCHH-HHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032848 60 RKLPFQRLVREIAQDFKTDLRFQSH-AVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 60 pk~pF~rlvreI~~~~~~~~r~~~~-Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 125 (132)
-++|.+|+ ++|.. ..+++++..+ |+.++-.++|-|+-.|-..++.|+.-.+|+|+.-+|+..+.
T Consensus 58 ~rLpL~ri-k~vvk-l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai 122 (162)
T KOG1658|consen 58 SRLPLARI-KQVVK-LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAI 122 (162)
T ss_pred hhccHHHH-Hhhcc-CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccc
Confidence 34455443 34422 3578888765 56678899999999999999999999999999999987654
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=59.62 E-value=40 Score=29.89 Aligned_cols=50 Identities=18% Similarity=0.226 Sum_probs=39.9
Q ss_pred cCcccCHHHHHHHHHHHH--HHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 77 TDLRFQSHAVLALQEAAE--AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E--~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
.++.++.+|++.|...+. ..+..+++.|...|...+|.+|+.+|+.-+..
T Consensus 279 ~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~ 330 (531)
T TIGR02902 279 IGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAE 330 (531)
T ss_pred cCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhC
Confidence 347889999988755443 45778888888888888999999999998764
No 68
>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=56.81 E-value=52 Score=25.38 Aligned_cols=61 Identities=11% Similarity=0.066 Sum_probs=46.2
Q ss_pred HHHHHHHHhcc--cCcccCHHHHHHHHHHHHH---HHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 66 RLVREIAQDFK--TDLRFQSHAVLALQEAAEA---YLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 66 rlvreI~~~~~--~~~r~~~~Al~aLqea~E~---~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
.|+...+.... .+..|++++++.|.+.+.- +++.+...+...|.-.+-.+|+.+||..+..
T Consensus 199 ~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~ 264 (269)
T TIGR03015 199 EYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIA 264 (269)
T ss_pred HHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 34444444332 2456999999999999986 7888888888888777888999999988764
No 69
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=55.46 E-value=63 Score=24.51 Aligned_cols=65 Identities=18% Similarity=0.191 Sum_probs=49.3
Q ss_pred hhHHHHhhhhhhhhhcccchh----HHHHHHHHHhc-------ccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032848 44 ALREIRKYQKSTELLIRKLPF----QRLVREIAQDF-------KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCA 108 (132)
Q Consensus 44 ~l~eIr~~q~st~llipk~pF----~rlvreI~~~~-------~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a 108 (132)
+-.|--+|++.+.-|||-.-+ +.+++-|.+.+ .-+..++++++..+|.+......+|.+..+.++
T Consensus 75 sE~eRlk~e~e~g~Lipa~eV~~~~s~~~Kav~q~LetlPD~LERd~gL~p~~v~~vQ~~iD~lR~~l~~~i~~~~ 150 (152)
T PF07278_consen 75 SENERLKFEKETGQLIPAEEVRREMSEMAKAVVQVLETLPDILERDAGLPPEQVARVQSVIDDLRDQLAERIQEAC 150 (152)
T ss_pred HHHHHHHHHHHHcccCcHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445666789999999998754 44555554433 257899999999999999999999988765543
No 70
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=55.06 E-value=3.4 Score=36.27 Aligned_cols=58 Identities=19% Similarity=0.147 Sum_probs=47.9
Q ss_pred HHHHHHhc-ccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032848 68 VREIAQDF-KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 68 vreI~~~~-~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 125 (132)
++|..+.+ .+...|..+.-+.|-+.|..|....-+-++.+|.|.|-.||-++|+||-.
T Consensus 389 L~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhl 447 (505)
T COG5624 389 LEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHL 447 (505)
T ss_pred HHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeee
Confidence 33443333 57788888888888899999999998889999999999999999999854
No 71
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=52.83 E-value=54 Score=28.42 Aligned_cols=72 Identities=21% Similarity=0.352 Sum_probs=58.6
Q ss_pred hhcccchhHH-HHHHHHHh-c-ccCcccCHHHHHHHHHHHH----HHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032848 57 LLIRKLPFQR-LVREIAQD-F-KTDLRFQSHAVLALQEAAE----AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 57 llipk~pF~r-lvreI~~~-~-~~~~r~~~~Al~aLqea~E----~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~ 128 (132)
++|.-.||.. =+++|+.- + ..+.-++++|++.|-...| .|-..|...|++.+...|-.++..+||+-|.+|-
T Consensus 351 lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~LF 429 (454)
T KOG2680|consen 351 LIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYRLF 429 (454)
T ss_pred heeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHHHH
Confidence 6777778754 46666553 2 3678899999999876665 5889999999999999999999999999998874
No 72
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=52.16 E-value=52 Score=26.54 Aligned_cols=61 Identities=18% Similarity=0.233 Sum_probs=46.0
Q ss_pred hHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh--cCccccChhhHHHHHH
Q 032848 64 FQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLARR 126 (132)
Q Consensus 64 F~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~H--akRvTi~~~Diqla~r 126 (132)
...+|++.++. .+..++.+|+..|.+.++.=+..+-..-..++.+ .+..+|+.+||+.++.
T Consensus 135 l~~~i~~~~~~--~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~ 197 (326)
T PRK07452 135 LKQLVERTAQE--LGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVS 197 (326)
T ss_pred HHHHHHHHHHH--cCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhc
Confidence 34455554432 4678999999999888887777777777788888 5688899999997653
No 73
>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=50.65 E-value=81 Score=21.76 Aligned_cols=64 Identities=14% Similarity=0.270 Sum_probs=40.9
Q ss_pred cccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCcc-ccChhhHHHHHH
Q 032848 59 IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRV-TIMPKDIQLARR 126 (132)
Q Consensus 59 ipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRv-Ti~~~Diqla~r 126 (132)
++|....+|+..+ .++..++.....++.-.+-.|+-+|-|.|..+..--+-. .|.|..+.-|.+
T Consensus 24 ~~k~~ikkli~~~----~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~r 88 (90)
T PF04719_consen 24 FNKAAIKKLINQV----LGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYR 88 (90)
T ss_dssp --HHHHHHHHHHH----HS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHH
T ss_pred CCHHHHHHHHHHH----cCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHH
Confidence 6666666665554 455789999999999999999999999998877643322 677777666544
No 74
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=49.36 E-value=27 Score=20.89 Aligned_cols=43 Identities=14% Similarity=0.092 Sum_probs=23.6
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHH-HHHHHhhcCccccChhhHHHH
Q 032848 81 FQSHAVLALQEAAEAYLVGLFED-TNLCAIHAKRVTIMPKDIQLA 124 (132)
Q Consensus 81 ~~~~Al~aLqea~E~~lv~lfe~-a~~~a~HakRvTi~~~Diqla 124 (132)
|+++|...|..+ =.|+-....+ +-.+|...+...|+.++|.-|
T Consensus 1 W~~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 1 WTDEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp E-HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred CCHHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 455555555443 2344444444 556678888888888887755
No 75
>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=48.12 E-value=67 Score=26.98 Aligned_cols=51 Identities=14% Similarity=0.155 Sum_probs=40.8
Q ss_pred cCcccCHHHHHHHHHHHHHHHHH-------HHHHHHHHHhhcCccccChhhHHHHHHH
Q 032848 77 TDLRFQSHAVLALQEAAEAYLVG-------LFEDTNLCAIHAKRVTIMPKDIQLARRI 127 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E~~lv~-------lfe~a~~~a~HakRvTi~~~Diqla~ri 127 (132)
.+..++.+.++.+.+.+.+.-++ ++..|..+|.-.+|-.|+++|++.+..+
T Consensus 251 ~~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~~ 308 (337)
T TIGR02030 251 PQVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAVL 308 (337)
T ss_pred ccCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 56778888888777777665542 6677999999999999999999987765
No 76
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=43.05 E-value=98 Score=25.31 Aligned_cols=56 Identities=25% Similarity=0.166 Sum_probs=42.3
Q ss_pred HHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032848 66 RLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 66 rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 125 (132)
++|++.+++ .+..++.+|++.|-+.++.=+..+-..--.++.+++ +|+.+||+.++
T Consensus 142 ~~i~~~~~~--~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v 197 (328)
T PRK08487 142 ELLQERAKE--LGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELV 197 (328)
T ss_pred HHHHHHHHH--hCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHh
Confidence 344444332 567899999999988888777777777777888876 79999998765
No 77
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=42.82 E-value=1.5e+02 Score=23.18 Aligned_cols=62 Identities=23% Similarity=0.243 Sum_probs=40.7
Q ss_pred hHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032848 64 FQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 127 (132)
Q Consensus 64 F~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri 127 (132)
+..+|++.+.+ .+..++.+|+..|-+.++.=+-.+-.....++.+++-.+|+.+||+-....
T Consensus 116 ~~~~i~~~~~~--~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~ 177 (302)
T TIGR01128 116 LPRWIQARLKK--LGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSD 177 (302)
T ss_pred HHHHHHHHHHH--cCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhh
Confidence 34455555443 467899999999977776544444445555556654447999999866543
No 78
>PF10911 DUF2717: Protein of unknown function (DUF2717); InterPro: IPR020121 The proteins in this entry are uncharacterised.
Probab=41.93 E-value=51 Score=22.33 Aligned_cols=60 Identities=23% Similarity=0.401 Sum_probs=44.1
Q ss_pred hHHHHhhhhhhhhhcccchhHHHHHHHHHh-cccCcccCHHHHHHHHH--HHHHHHHHHHHHHHHH
Q 032848 45 LREIRKYQKSTELLIRKLPFQRLVREIAQD-FKTDLRFQSHAVLALQE--AAEAYLVGLFEDTNLC 107 (132)
Q Consensus 45 l~eIr~~q~st~llipk~pF~rlvreI~~~-~~~~~r~~~~Al~aLqe--a~E~~lv~lfe~a~~~ 107 (132)
|++|.+|+...+ =||-.| |.+.|-++. |+.++-+.+..+..|+. -+|+||-++++-.+.+
T Consensus 2 L~~I~h~l~np~-DiP~ip--ra~aeyLqvrfN~~yl~~sG~i~~lr~~G~SE~~I~Gfl~Gl~~A 64 (77)
T PF10911_consen 2 LKPIQHLLDNPD-DIPDIP--RAAAEYLQVRFNAAYLMASGIISALRKQGWSESYILGFLAGLQYA 64 (77)
T ss_pred cchHHHHhcCCc-ccCCcc--HHHHHHHHHHhcHHHHHHhhhHHHHHHccccHHHHHHHHHHHHHH
Confidence 678888887753 356554 666676653 56777778888888875 4899999999987776
No 79
>PRK05907 hypothetical protein; Provisional
Probab=39.59 E-value=90 Score=25.83 Aligned_cols=67 Identities=12% Similarity=0.025 Sum_probs=49.2
Q ss_pred cccchhHHHHHHHHHhcc-cCcccCHHHHHHHHHHH-HHHHHHHHHHHHHHHhh-cCccccChhhHHHHH
Q 032848 59 IRKLPFQRLVREIAQDFK-TDLRFQSHAVLALQEAA-EAYLVGLFEDTNLCAIH-AKRVTIMPKDIQLAR 125 (132)
Q Consensus 59 ipk~pF~rlvreI~~~~~-~~~r~~~~Al~aLqea~-E~~lv~lfe~a~~~a~H-akRvTi~~~Diqla~ 125 (132)
.+...-..|.+-|.+.+. .+..++.+|++.|-+.+ +.=|..+...-..++.+ +.+.+|+.+||+..+
T Consensus 131 ~~~l~e~~L~~Wi~~~~~~~g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv 200 (311)
T PRK05907 131 WFADRDKRIAQLLIQRAKELGISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFV 200 (311)
T ss_pred cCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHh
Confidence 344444666666666664 67899999999997777 55666666667777778 669999999998764
No 80
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=39.51 E-value=99 Score=24.92 Aligned_cols=65 Identities=18% Similarity=0.253 Sum_probs=44.2
Q ss_pred cccchhHHHHHHHHHhcccCc-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032848 59 IRKLPFQRLVREIAQDFKTDL-RFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 59 ipk~pF~rlvreI~~~~~~~~-r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 125 (132)
+-+.|-.| |++|++.- .|+ ++....=..+-.|.|-||..|...++..+.-.+-+||++.-|+-++
T Consensus 11 ~trfp~aR-iKKIMQ~d-EdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v 76 (224)
T KOG1659|consen 11 KTRFPPAR-IKKIMQSD-EDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAV 76 (224)
T ss_pred hccCCHHH-HHHHHhhh-hhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHH
Confidence 34455555 47787621 222 2222223345667799999999999999999999999988776554
No 81
>PF08157 NUC129: NUC129 domain; InterPro: IPR012579 This C-terminal domain is found in a novel family of hypothetical nucleolar proteins [].; GO: 0005634 nucleus
Probab=35.75 E-value=67 Score=20.91 Aligned_cols=43 Identities=14% Similarity=0.230 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHH--------HHHHHhhcCccccChhhHHHHH
Q 032848 83 SHAVLALQEAAEAYLVGLFED--------TNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 83 ~~Al~aLqea~E~~lv~lfe~--------a~~~a~HakRvTi~~~Diqla~ 125 (132)
.+..+..|+++++||..-+=- --.+.++.||.-++.--+|++-
T Consensus 9 ~~l~~~~QqaAk~Fi~~~LYGpgsnRTT~N~flSL~NKr~~vKkAAvQFv~ 59 (63)
T PF08157_consen 9 QSLRDSQQQAAKDFIQSRLYGPGSNRTTVNEFLSLANKRLPVKKAAVQFVN 59 (63)
T ss_pred chhhhHHHHHHHHHHHHhccCCCCCcccHHHHhhhhhcccccHHHHHHHHh
Confidence 456678899999999876532 3456777777777766666653
No 82
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=35.09 E-value=1.3e+02 Score=24.50 Aligned_cols=50 Identities=16% Similarity=0.092 Sum_probs=39.0
Q ss_pred cCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC-ccccChhhHHHHHH
Q 032848 77 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAK-RVTIMPKDIQLARR 126 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~Hak-RvTi~~~Diqla~r 126 (132)
.+..++.+|++.|-+.++.=+..+-..-..++.+++ ..+|+.+||+-+..
T Consensus 158 ~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 158 AGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred CCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 568899999999988888766677777777777754 46799999976643
No 83
>TIGR01924 rsbW_low_gc serine-protein kinase RsbW. This model describes the anti-sigma B factor also known as serine-protein kinase RsbW. Sigma B controls the general stress regulon in B subtilis and is activated by cell stresses such as stationary phase and heat shock. RsbW binds to sigma B and prevents formation of the transcription complex at the promoter. RsbV (anti-anti-sigma factor) binds to RsbW to inhibit association with sigma B, however RsbW can phosphorylate RsbV, causing disassociation of the RsbV/RsbW complex. Low ATP level or environmental stress causes the dephosphorylation of RsbV.
Probab=34.41 E-value=83 Score=23.08 Aligned_cols=45 Identities=11% Similarity=0.115 Sum_probs=36.0
Q ss_pred cchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHH
Q 032848 61 KLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTN 105 (132)
Q Consensus 61 k~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~ 105 (132)
..-+-+.|+..+..+-....++.+.+..++-+++..+++.++.++
T Consensus 15 ~~~~~~~vr~~~~~~a~~~g~~~~~~~~l~lav~Ea~~Nai~ha~ 59 (159)
T TIGR01924 15 KPEYVGLIRLTLSGIASRAGYTYDDIEDLKIAVSEACTNAVKHAY 59 (159)
T ss_pred cHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhcc
Confidence 445667788888777777889999999998888888888888765
No 84
>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=32.37 E-value=1.3e+02 Score=27.26 Aligned_cols=52 Identities=13% Similarity=0.150 Sum_probs=42.5
Q ss_pred cCcccCHHHHHHHHHHHHHHHH-------HHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032848 77 TDLRFQSHAVLALQEAAEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E~~lv-------~lfe~a~~~a~HakRvTi~~~Diqla~ri~ 128 (132)
....++.++++.|.+.+..+-+ .+..-|--+|.-.+|-+|..+|++.|..+-
T Consensus 246 ~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~lv 304 (633)
T TIGR02442 246 PSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAELV 304 (633)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHH
Confidence 5678899999999888877654 345668888899999999999999988763
No 85
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=31.75 E-value=1.7e+02 Score=24.03 Aligned_cols=49 Identities=20% Similarity=0.229 Sum_probs=35.6
Q ss_pred cCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032848 77 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 125 (132)
...+++.+|++.|-+..|.=+-.+...-+.++..+.=.+|+.+||+.++
T Consensus 156 ~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v 204 (334)
T COG1466 156 LGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVV 204 (334)
T ss_pred cCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHH
Confidence 5789999999999887775555555554555555444499999999875
No 86
>PRK13531 regulatory ATPase RavA; Provisional
Probab=31.40 E-value=2.2e+02 Score=25.53 Aligned_cols=75 Identities=15% Similarity=0.123 Sum_probs=47.9
Q ss_pred hhhHHHHhhhhhhhhhcccchhHHHHHHHHHhcc---cCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChh
Q 032848 43 VALREIRKYQKSTELLIRKLPFQRLVREIAQDFK---TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPK 119 (132)
Q Consensus 43 ~~l~eIr~~q~st~llipk~pF~rlvreI~~~~~---~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~ 119 (132)
....|+..+|+....+---.+...|+.+|..... .+..+|+.+...| ...+..+|.-.+|-.|.+.
T Consensus 207 is~eel~~lq~~v~~V~v~d~v~eyI~~L~~~lr~~r~~~~~SpR~~~~l-----------~~~akA~A~l~GR~~V~p~ 275 (498)
T PRK13531 207 ITDEEYQQWQKEIGKITLPDHVFELIFQLRQQLDALPNAPYVSDRRWKKA-----------IRLLQASAFFSGRDAIAPI 275 (498)
T ss_pred CCHHHHHHHHHHhcceeCCHHHHHHHHHHHHHHhcCCCCCCcCcHHHHHH-----------HHHHHHHHHHCCCCCCCHH
Confidence 4556777777665444333455566666655321 1234666665555 4456778899999999999
Q ss_pred hHHHHHHHh
Q 032848 120 DIQLARRIR 128 (132)
Q Consensus 120 Diqla~ri~ 128 (132)
|++++.-..
T Consensus 276 Dv~ll~~vL 284 (498)
T PRK13531 276 DLILLKDCL 284 (498)
T ss_pred HHHHhHHHh
Confidence 999776543
No 87
>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]
Probab=31.37 E-value=1.4e+02 Score=25.82 Aligned_cols=71 Identities=25% Similarity=0.373 Sum_probs=52.8
Q ss_pred hhcccchhHH-HHHHHHHhc--ccCcccCHHHHHHHHH----HHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032848 57 LLIRKLPFQR-LVREIAQDF--KTDLRFQSHAVLALQE----AAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 127 (132)
Q Consensus 57 llipk~pF~r-lvreI~~~~--~~~~r~~~~Al~aLqe----a~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri 127 (132)
++|+-.|+.- -+++|..-- ..++.+..+|++-|-+ .+=.|.++|+--|+.||.-.+|.-|..+|+.-+..|
T Consensus 360 ~Iirt~~y~~~e~r~Ii~~Ra~~E~l~~~e~a~~~l~~~gt~tsLRy~vqLl~p~~~~ak~~g~~~i~v~dvee~~~L 437 (456)
T KOG1942|consen 360 LIIRTLPYDEEEIRQIIKIRAQVEGLQVEEEALDLLAEIGTSTSLRYAVQLLTPASILAKTNGRKEISVEDVEEVTEL 437 (456)
T ss_pred eEEeeccCCHHHHHHHHHHHHhhhcceecHHHHHHHHhhccchhHHHHHHhcCHHHHHHHHcCCceeecccHHHHHHH
Confidence 4455555432 234443321 2578899999999866 455899999999999999999999999999877665
No 88
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=31.30 E-value=1.1e+02 Score=20.67 Aligned_cols=43 Identities=19% Similarity=0.126 Sum_probs=32.6
Q ss_pred HHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032848 65 QRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLC 107 (132)
Q Consensus 65 ~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~ 107 (132)
-..++..+..+-....|+.+.+..+.-+++..+++.++.++..
T Consensus 8 i~~~r~~~~~~~~~~~~~~~~~~~~~lav~E~~~Nav~H~~~~ 50 (125)
T PF13581_consen 8 IREARAFLREFLERLGLPEEDRDDLELAVSEALTNAVEHGYPG 50 (125)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 3445555555555688999999999889999998888887653
No 89
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=30.66 E-value=2.8e+02 Score=22.13 Aligned_cols=60 Identities=18% Similarity=0.205 Sum_probs=39.8
Q ss_pred HHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhc-CccccChhhHHHHHHH
Q 032848 65 QRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHA-KRVTIMPKDIQLARRI 127 (132)
Q Consensus 65 ~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~Ha-kRvTi~~~Diqla~ri 127 (132)
..+|++.+.+ ....++.+|++.|-+.++.=+..+-.....++..+ +.. |+.+||+-....
T Consensus 152 ~~~i~~~~~~--~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~ 212 (340)
T PRK05574 152 PQWIQQRLKQ--QGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPD 212 (340)
T ss_pred HHHHHHHHHH--cCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhh
Confidence 3444444332 45689999999998887765555555566666665 333 999999866543
No 90
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=30.58 E-value=1.9e+02 Score=24.56 Aligned_cols=51 Identities=14% Similarity=0.127 Sum_probs=37.4
Q ss_pred cCcccCHHHHHHHHHHHHHHHH-------HHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032848 77 TDLRFQSHAVLALQEAAEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRI 127 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E~~lv-------~lfe~a~~~a~HakRvTi~~~Diqla~ri 127 (132)
....++.+.++.+.+.+.+.-+ .+...|..+|.-.+|-.|.++||+.+..+
T Consensus 264 ~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~~ 321 (350)
T CHL00081 264 PKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVITL 321 (350)
T ss_pred CCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 4556666666666666665443 34556888999999999999999988765
No 91
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=29.92 E-value=63 Score=24.00 Aligned_cols=28 Identities=14% Similarity=0.008 Sum_probs=22.6
Q ss_pred HHHHHHHHHHH-----HHHHHhhcCccccChhh
Q 032848 93 AEAYLVGLFED-----TNLCAIHAKRVTIMPKD 120 (132)
Q Consensus 93 ~E~~lv~lfe~-----a~~~a~HakRvTi~~~D 120 (132)
.+.|+..+|.. -..+...+.|||+.+-|
T Consensus 182 V~~h~~~i~~Kl~v~~~~~l~~~~~~~~~~~~~ 214 (216)
T PRK10840 182 ISSQKKSAMMKLGVENDIALLNYLSSVTLSPAD 214 (216)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhcCCccc
Confidence 48899999988 44566789999999877
No 92
>PF13060 DUF3921: Protein of unknown function (DUF3921)
Probab=28.88 E-value=1.2e+02 Score=18.95 Aligned_cols=28 Identities=25% Similarity=0.367 Sum_probs=22.3
Q ss_pred ccCcccCHHHHHHHHHHHHHHHHHHHHH
Q 032848 76 KTDLRFQSHAVLALQEAAEAYLVGLFED 103 (132)
Q Consensus 76 ~~~~r~~~~Al~aLqea~E~~lv~lfe~ 103 (132)
..++-.+.-+.+.+|.|-|.||..|--.
T Consensus 21 gkei~~~g~~~d~i~kaqeeylsals~e 48 (58)
T PF13060_consen 21 GKEIDLQGVIADEIQKAQEEYLSALSHE 48 (58)
T ss_pred hHHhhhcchHHHHHHHHHHHHHHHhhHH
Confidence 4456677888999999999999887544
No 93
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=28.58 E-value=3.3e+02 Score=22.30 Aligned_cols=47 Identities=11% Similarity=0.145 Sum_probs=36.8
Q ss_pred ccCHHHHHHHHHHHHH------HHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032848 80 RFQSHAVLALQEAAEA------YLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 80 r~~~~Al~aLqea~E~------~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 126 (132)
-|+.++++.+.+.+.. ++.+++..|...|...+..+|+.+|+.-|..
T Consensus 228 ~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~ 280 (394)
T PRK00411 228 VVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYE 280 (394)
T ss_pred CCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHH
Confidence 5889999888777744 4456677777788888889999999987764
No 94
>PRK05629 hypothetical protein; Validated
Probab=27.57 E-value=2.2e+02 Score=23.04 Aligned_cols=48 Identities=15% Similarity=0.074 Sum_probs=34.0
Q ss_pred cCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032848 77 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 125 (132)
....++.+|++.|-+.++.=+..+-..--.++.+.+ -+|+.+||+-+.
T Consensus 142 ~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v 189 (318)
T PRK05629 142 HGVRPTPDVVHALLEGVGSDLRELASAISQLVEDTQ-GNVTVEKVRAYY 189 (318)
T ss_pred cCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcCC-CCcCHHHHHHHh
Confidence 568899999999977776555545444445556654 369999998653
No 95
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=27.19 E-value=1.9e+02 Score=24.24 Aligned_cols=51 Identities=8% Similarity=0.018 Sum_probs=37.4
Q ss_pred cCcccCHHHHHHHHHHHHHHHH-------HHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032848 77 TDLRFQSHAVLALQEAAEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRI 127 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E~~lv-------~lfe~a~~~a~HakRvTi~~~Diqla~ri 127 (132)
....++.+.+..+.+.+.+.-+ .|...|..+|+..+|-.|+++||+-+..+
T Consensus 248 ~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~~~ 305 (334)
T PRK13407 248 PQLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVATM 305 (334)
T ss_pred CCcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHHHH
Confidence 4556667666666666655432 16677999999999999999999876654
No 96
>PF07962 Swi3: Replication Fork Protection Component Swi3; InterPro: IPR012923 Replication fork pausing is required to initiate recombination events. More specifically, Swi1 is required for recombination near the mat1 locus. Swi3 has been found to co-purify with Swi1. Together they define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilises stalled replication forks []. This complex is required for accurate replication, fork protection and replication checkpoint signalling [, ].; GO: 0006974 response to DNA damage stimulus, 0007049 cell cycle, 0048478 replication fork protection, 0005634 nucleus
Probab=26.35 E-value=1e+02 Score=20.66 Aligned_cols=29 Identities=21% Similarity=0.282 Sum_probs=24.5
Q ss_pred hhhHHHHhhhhhhhhhcccchhHHHHHHH
Q 032848 43 VALREIRKYQKSTELLIRKLPFQRLVREI 71 (132)
Q Consensus 43 ~~l~eIr~~q~st~llipk~pF~rlvreI 71 (132)
..-+=+..||.=...|.|+++|...|..|
T Consensus 34 dL~~ll~~Yq~W~h~LfPk~~F~d~i~~v 62 (83)
T PF07962_consen 34 DLRRLLQFYQLWAHRLFPKASFEDFIERV 62 (83)
T ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence 34455788998889999999999999888
No 97
>PRK04069 serine-protein kinase RsbW; Provisional
Probab=25.40 E-value=1.4e+02 Score=21.79 Aligned_cols=45 Identities=9% Similarity=0.146 Sum_probs=33.7
Q ss_pred cchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHH
Q 032848 61 KLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTN 105 (132)
Q Consensus 61 k~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~ 105 (132)
..-+.++|+..+..+.....|+.+.++.|+-+++..+.+..+.++
T Consensus 15 ~~~~~~~vr~~v~~~~~~~g~~~~~~~~l~lav~Ea~~Nai~Hg~ 59 (161)
T PRK04069 15 KAEYVSIIRLTLSGVANRMGFSYDDIEDMKIAVSEACTNAVQHAY 59 (161)
T ss_pred cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 445677888888888788899999998887777766666665543
No 98
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=25.06 E-value=67 Score=24.01 Aligned_cols=32 Identities=28% Similarity=0.541 Sum_probs=25.8
Q ss_pred chhhHHHHhhhhhhhhhcccchhHHHHHHHHHh
Q 032848 42 TVALREIRKYQKSTELLIRKLPFQRLVREIAQD 74 (132)
Q Consensus 42 ~~~l~eIr~~q~st~llipk~pF~rlvreI~~~ 74 (132)
.+|+.||+++..+...+ |...+.+||++|=.+
T Consensus 97 ~VAm~ei~~~~~~~~~~-~~id~~~lvk~IKk~ 128 (137)
T PF10788_consen 97 AVAMDEIKKMRQKDGNL-PNIDLDKLVKNIKKE 128 (137)
T ss_pred HHHHHHHHHHHhcCCCc-CCCCHHHHHHHHHHh
Confidence 47899999997665444 999999999999543
No 99
>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=24.97 E-value=1.9e+02 Score=26.05 Aligned_cols=52 Identities=15% Similarity=0.178 Sum_probs=39.3
Q ss_pred cCcccCHHHHHHHHHHHHHHHHH-------HHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032848 77 TDLRFQSHAVLALQEAAEAYLVG-------LFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 77 ~~~r~~~~Al~aLqea~E~~lv~-------lfe~a~~~a~HakRvTi~~~Diqla~ri~ 128 (132)
....++.+.++.|-+.+-.+-+. +...|..+|.-.+|-+|.++|++.|..+-
T Consensus 200 ~~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~lv 258 (589)
T TIGR02031 200 PQVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVELV 258 (589)
T ss_pred CCccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Confidence 56778888887766655444432 44558888999999999999999998763
No 100
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=24.68 E-value=1.2e+02 Score=24.04 Aligned_cols=31 Identities=19% Similarity=0.060 Sum_probs=27.2
Q ss_pred cCc-ccCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032848 77 TDL-RFQSHAVLALQEAAEAYLVGLFEDTNLC 107 (132)
Q Consensus 77 ~~~-r~~~~Al~aLqea~E~~lv~lfe~a~~~ 107 (132)
.++ .++.+|.+.|.-|.|.||-+|++.+...
T Consensus 219 ~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~ 250 (252)
T PF12767_consen 219 HGLGGVSDDCANLLNLALEVHLKNLIKSCLDL 250 (252)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 455 8999999999999999999999987654
No 101
>PF15510 CENP-W: Centromere kinetochore component W
Probab=24.21 E-value=1.9e+02 Score=20.43 Aligned_cols=34 Identities=21% Similarity=0.186 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032848 94 EAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 127 (132)
Q Consensus 94 E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri 127 (132)
=-|+..|.|+|..-|.-.|.-||..+-+.-|.+.
T Consensus 62 LLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaKv 95 (102)
T PF15510_consen 62 LLFVHRLAEEARTNACENKCGTIKKEHVLAAAKV 95 (102)
T ss_pred HHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHH
Confidence 3688899999999999999999999999887653
No 102
>smart00350 MCM minichromosome maintenance proteins.
Probab=23.98 E-value=3.2e+02 Score=24.02 Aligned_cols=28 Identities=14% Similarity=0.011 Sum_probs=21.9
Q ss_pred HHHHHHHhhcCccccChhhHHHHHHHhc
Q 032848 102 EDTNLCAIHAKRVTIMPKDIQLARRIRG 129 (132)
Q Consensus 102 e~a~~~a~HakRvTi~~~Diqla~ri~~ 129 (132)
.-|...|.=..|-+|+++|++.|.+|-.
T Consensus 478 Rla~A~A~l~~r~~V~~~Dv~~ai~l~~ 505 (509)
T smart00350 478 RLSEAHAKMRLSDVVEEADVEEAIRLLR 505 (509)
T ss_pred HHHHHHHHHcCCCccCHHHHHHHHHHHH
Confidence 3344556777899999999999998853
No 103
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=23.45 E-value=79 Score=25.00 Aligned_cols=78 Identities=15% Similarity=0.213 Sum_probs=56.3
Q ss_pred HHHhhhhhhhhhcccchhHHHHHHHHHhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHh-hcCccccChhhHHHHH
Q 032848 47 EIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAI-HAKRVTIMPKDIQLAR 125 (132)
Q Consensus 47 eIr~~q~st~llipk~pF~rlvreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~-HakRvTi~~~Diqla~ 125 (132)
.+.+|-.-....+||+-..+|+.+|+. -.++..+..+++-.+..|+-.+-|.|..+.- -..-=-|.|..|.-|.
T Consensus 101 Ql~RYEvfRrs~f~Ka~iKkL~~~itg-----~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~ 175 (195)
T KOG3219|consen 101 QLSRYEVFRRSAFPKAQIKKLMSSITG-----QSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAY 175 (195)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHhC-----CccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHH
Confidence 345555444556888888889888844 2377777778888899999999999876543 3444568888888777
Q ss_pred HHhc
Q 032848 126 RIRG 129 (132)
Q Consensus 126 ri~~ 129 (132)
+..+
T Consensus 176 rrL~ 179 (195)
T KOG3219|consen 176 RRLK 179 (195)
T ss_pred HHHH
Confidence 6654
No 104
>cd00913 PCD_DCoH_subfamily_a PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein).
Probab=23.23 E-value=52 Score=21.39 Aligned_cols=13 Identities=23% Similarity=0.404 Sum_probs=11.1
Q ss_pred ccChhhHHHHHHH
Q 032848 115 TIMPKDIQLARRI 127 (132)
Q Consensus 115 Ti~~~Diqla~ri 127 (132)
.|+.+|+.||.+|
T Consensus 61 glT~~D~~lA~~i 73 (76)
T cd00913 61 GLSENDFIMAAKI 73 (76)
T ss_pred CCCHHHHHHHHHH
Confidence 3778999999987
No 105
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=21.55 E-value=1.7e+02 Score=19.21 Aligned_cols=51 Identities=14% Similarity=0.137 Sum_probs=30.0
Q ss_pred CcccCHHHHHHHHHHHHHHHH--------HHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032848 78 DLRFQSHAVLALQEAAEAYLV--------GLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 78 ~~r~~~~Al~aLqea~E~~lv--------~lfe~a~~~a~HakRvTi~~~Diqla~ri~ 128 (132)
++|++++..+.|+.|++...+ ..++.|-..-.-...+++..+|.+......
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~aL 61 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMAAL 61 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHHHH
Confidence 467888888888888874332 334444444344456677777777665543
No 106
>cd00488 PCD_DCoH PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon cancer carc
Probab=21.52 E-value=60 Score=20.97 Aligned_cols=13 Identities=31% Similarity=0.475 Sum_probs=11.2
Q ss_pred cChhhHHHHHHHh
Q 032848 116 IMPKDIQLARRIR 128 (132)
Q Consensus 116 i~~~Diqla~ri~ 128 (132)
|+.+|+.||.+|=
T Consensus 61 lt~~D~~lA~~id 73 (75)
T cd00488 61 LTENDFILAAKID 73 (75)
T ss_pred CCHHHHHHHHHHh
Confidence 7889999999873
No 107
>PF04604 L_biotic_typeA: Type-A lantibiotic; InterPro: IPR007682 Lantibiotics are antibiotic peptides distinguished by the presence of the rare thioether amino acids lanthionine and/or methyllanthionine. They are produced by Gram-positive bacteria as gene-encoded precursor peptides and undergo post-translational modification to generate the mature peptide. Based on their structural and functional features lantibiotics are currently divided into two major groups: the flexible amphiphilic type-A and the rather rigid and globular type-B. Type-A lantibiotics act primarily by pore formation in the bacterial membrane by a mechanism involving the interaction with specific docking molecules such as the membrane precursor lipid II [].; GO: 0019748 secondary metabolic process, 0005576 extracellular region
Probab=21.48 E-value=83 Score=19.70 Aligned_cols=20 Identities=25% Similarity=0.308 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 032848 84 HAVLALQEAAEAYLVGLFED 103 (132)
Q Consensus 84 ~Al~aLqea~E~~lv~lfe~ 103 (132)
+|+.+|||.+++-|..+.--
T Consensus 7 ea~~~lqevs~eELd~ilGg 26 (51)
T PF04604_consen 7 EALNSLQEVSDEELDQILGG 26 (51)
T ss_pred HHHHHHHhcCHHHHHHHhCC
Confidence 89999999999999888754
No 108
>PRK07914 hypothetical protein; Reviewed
Probab=21.37 E-value=2.8e+02 Score=22.49 Aligned_cols=60 Identities=12% Similarity=0.112 Sum_probs=39.1
Q ss_pred HHHHHHHHHhc-ccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032848 65 QRLVREIAQDF-KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 65 ~rlvreI~~~~-~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 125 (132)
..+.+=|.+.. ..+..++.+|+..|.+.++.=+..+-..-..++.+.+ .+|+.+||+-++
T Consensus 131 ~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v 191 (320)
T PRK07914 131 AERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYH 191 (320)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHc
Confidence 34444444434 3567899999999988887555555444445555554 468899988654
No 109
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=21.22 E-value=1.8e+02 Score=21.35 Aligned_cols=66 Identities=17% Similarity=0.239 Sum_probs=43.3
Q ss_pred hHHHHHHHHHhcc---cCcccCH--HHHHHHHHHHHHHHHHHHHH--HHHHHhhcCccccChhhHHHHHHHhc
Q 032848 64 FQRLVREIAQDFK---TDLRFQS--HAVLALQEAAEAYLVGLFED--TNLCAIHAKRVTIMPKDIQLARRIRG 129 (132)
Q Consensus 64 F~rlvreI~~~~~---~~~r~~~--~Al~aLqea~E~~lv~lfe~--a~~~a~HakRvTi~~~Diqla~ri~~ 129 (132)
..||+++=+.... ..++|++ +-=+..+..+..+|..+|.- +++++..+.+.+++..|+.....|..
T Consensus 45 l~RL~KKg~l~~~kdgr~~~y~pL~~~~~~~~~~~~~~l~k~~d~~~~~lv~~F~~~~~l~~~eie~L~~il~ 117 (123)
T COG3682 45 LNRLVKKGLLTRKKDGRAFRYSPLLTRDQYVAGESQDLLDKICDGGLASLVAHFAEKEKLTADEIEALKAILD 117 (123)
T ss_pred HHHHHhccchhhhhcCCeeeeecccCHHHHHHHHHHHHHHHHHcccchHHHHHHHHhccCCHHHHHHHHHHHH
Confidence 4577766544332 2333332 11223445567778887776 67889999999999999998887754
No 110
>COG1598 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]
Probab=21.16 E-value=1.3e+02 Score=19.35 Aligned_cols=24 Identities=29% Similarity=0.293 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 032848 83 SHAVLALQEAAEAYLVGLFEDTNL 106 (132)
Q Consensus 83 ~~Al~aLqea~E~~lv~lfe~a~~ 106 (132)
.+|+.-++||.|-|+..+.++...
T Consensus 34 eea~~n~~eai~l~~e~~~~~~~~ 57 (73)
T COG1598 34 EEALQNAKEAIELHLEALLEEGEP 57 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCc
Confidence 578889999999999998887543
No 111
>COG5304 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.13 E-value=69 Score=22.38 Aligned_cols=16 Identities=38% Similarity=0.823 Sum_probs=13.3
Q ss_pred ccchhHHHHHHHHHhc
Q 032848 60 RKLPFQRLVREIAQDF 75 (132)
Q Consensus 60 pk~pF~rlvreI~~~~ 75 (132)
.-+||++|+++|+...
T Consensus 73 ~GlpYQtyIreiLh~~ 88 (92)
T COG5304 73 EGLPYQTYIREILHKY 88 (92)
T ss_pred cCCcHHHHHHHHHHhh
Confidence 5579999999998754
No 112
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=20.36 E-value=26 Score=24.65 Aligned_cols=18 Identities=28% Similarity=0.497 Sum_probs=15.1
Q ss_pred HHHHHHhhcCccccChhh
Q 032848 103 DTNLCAIHAKRVTIMPKD 120 (132)
Q Consensus 103 ~a~~~a~HakRvTi~~~D 120 (132)
.+..||+|.+=|-+-+++
T Consensus 69 YCvSCAiH~~IVrvRs~e 86 (95)
T PRK09335 69 YCVNCAVHLGIIKIRPEE 86 (95)
T ss_pred EechhhhhccccccCChH
Confidence 489999999988887765
No 113
>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=20.09 E-value=2.8e+02 Score=26.66 Aligned_cols=71 Identities=21% Similarity=0.255 Sum_probs=46.3
Q ss_pred CchhhHHHHhhhhhhhhhcccchhHHHHHHHHHhc-ccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCc
Q 032848 41 GTVALREIRKYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKR 113 (132)
Q Consensus 41 g~~~l~eIr~~q~st~llipk~pF~rlvreI~~~~-~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR 113 (132)
.+.+|+..|.|-.= ..++..+-.+||...-.-| ..+++....||.+|-|.++.=+-.-..--..++.-++|
T Consensus 449 YaPaLR~Lr~~A~i--i~f~~p~~s~Lv~RL~~IC~rE~mr~d~~aL~~L~el~~~DIRsCINtLQfLa~~~~r 520 (877)
T KOG1969|consen 449 YAPALRPLRPFAEI--IAFVPPSQSRLVERLNEICHRENMRADSKALNALCELTQNDIRSCINTLQFLASNVDR 520 (877)
T ss_pred cchhhhhcccceEE--EEecCCChhHHHHHHHHHHhhhcCCCCHHHHHHHHHHhcchHHHHHHHHHHHHHhccc
Confidence 67789999887432 4456666778884443333 37899999999999776665444444434455555555
Done!