Query 031980
Match_columns 149
No_of_seqs 158 out of 587
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 07:59:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031980.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031980hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00161 histone H3; Provision 100.0 1.7E-58 3.6E-63 353.6 12.2 130 1-147 1-130 (135)
2 PTZ00018 histone H3; Provision 100.0 3E-58 6.4E-63 353.1 11.6 135 1-146 1-135 (136)
3 PLN00121 histone H3; Provision 100.0 5.8E-58 1.3E-62 351.4 11.5 135 1-146 1-135 (136)
4 KOG1745 Histones H3 and H4 [Ch 100.0 1.6E-55 3.4E-60 337.6 7.8 135 1-146 1-136 (137)
5 smart00428 H3 Histone H3. 100.0 9.6E-51 2.1E-55 300.0 10.5 103 44-146 2-104 (105)
6 PLN00160 histone H3; Provision 100.0 1.3E-50 2.8E-55 295.7 9.1 95 51-146 1-95 (97)
7 COG2036 HHT1 Histones H3 and H 99.9 1.3E-27 2.8E-32 172.9 8.1 87 53-146 1-87 (91)
8 PF00125 Histone: Core histone 99.8 1.2E-20 2.6E-25 128.8 7.5 75 67-143 1-75 (75)
9 cd07981 TAF12 TATA Binding Pro 99.4 2.2E-12 4.8E-17 89.0 6.7 64 72-141 2-65 (72)
10 cd00076 H4 Histone H4, one of 99.1 1.9E-10 4E-15 82.5 6.8 68 71-145 13-80 (85)
11 PLN00035 histone H4; Provision 99.1 4.6E-10 9.9E-15 83.1 6.9 67 72-145 30-96 (103)
12 PTZ00015 histone H4; Provision 99.1 5.3E-10 1.2E-14 82.6 7.0 69 70-145 29-97 (102)
13 smart00803 TAF TATA box bindin 99.0 1.2E-09 2.5E-14 74.5 5.7 64 71-141 2-65 (65)
14 smart00417 H4 Histone H4. 98.9 2.2E-09 4.8E-14 75.2 4.7 62 70-138 12-73 (74)
15 PF00808 CBFD_NFYB_HMF: Histon 98.6 1.4E-07 3.1E-12 63.0 6.0 62 72-139 3-64 (65)
16 cd07979 TAF9 TATA Binding Prot 98.6 2.9E-07 6.3E-12 69.1 7.3 65 78-145 4-68 (117)
17 PF15630 CENP-S: Kinetochore c 98.3 3.6E-06 7.7E-11 59.2 6.5 67 75-141 5-71 (76)
18 smart00576 BTP Bromodomain tra 98.2 5.9E-06 1.3E-10 57.3 6.3 52 94-145 22-73 (77)
19 cd00074 H2A Histone 2A; H2A is 97.9 2.1E-05 4.5E-10 59.3 5.2 67 69-141 18-84 (115)
20 cd08050 TAF6 TATA Binding Prot 97.9 4.2E-05 9.1E-10 66.2 7.5 65 79-146 3-67 (343)
21 KOG0870 DNA polymerase epsilon 97.7 6.9E-05 1.5E-09 59.8 5.4 69 69-141 8-76 (172)
22 PF02969 TAF: TATA box binding 97.6 0.00018 3.9E-09 49.4 6.0 59 80-141 8-66 (66)
23 PF03847 TFIID_20kDa: Transcri 97.6 0.00015 3.4E-09 49.8 5.5 60 76-141 4-63 (68)
24 PF15511 CENP-T: Centromere ki 97.6 0.00012 2.5E-09 65.2 5.8 63 72-135 352-414 (414)
25 PF02291 TFIID-31kDa: Transcri 97.4 0.00056 1.2E-08 52.5 6.9 65 78-145 15-79 (129)
26 KOG1142 Transcription initiati 97.1 0.00082 1.8E-08 56.9 4.8 73 63-141 146-218 (258)
27 PF07524 Bromo_TP: Bromodomain 96.3 0.028 6E-07 38.5 7.2 51 94-144 22-72 (77)
28 KOG3334 Transcription initiati 95.4 0.043 9.3E-07 43.2 5.5 65 79-146 17-81 (148)
29 KOG3467 Histone H4 [Chromatin 94.9 0.097 2.1E-06 38.3 5.9 67 72-145 30-96 (103)
30 smart00414 H2A Histone 2A. 94.6 0.037 8E-07 41.1 3.2 67 69-141 7-73 (106)
31 KOG0869 CCAAT-binding factor, 94.0 0.14 3E-06 41.0 5.5 74 56-141 24-97 (168)
32 PTZ00017 histone H2A; Provisio 92.6 0.19 4.1E-06 39.0 4.1 67 69-141 25-91 (134)
33 PLN00158 histone H2B; Provisio 92.4 0.88 1.9E-05 34.6 7.4 51 93-143 43-93 (116)
34 smart00427 H2B Histone H2B. 92.3 0.99 2.2E-05 32.8 7.3 51 93-143 17-67 (89)
35 PTZ00463 histone H2B; Provisio 91.8 1.1 2.5E-05 34.0 7.3 51 93-143 44-94 (117)
36 PLN00154 histone H2A; Provisio 91.4 0.52 1.1E-05 36.7 5.4 68 69-141 36-103 (136)
37 PF02269 TFIID-18kDa: Transcri 90.8 0.38 8.3E-06 34.6 3.8 52 90-141 14-65 (93)
38 KOG0871 Class 2 transcription 90.2 1.2 2.6E-05 35.3 6.4 69 68-141 9-77 (156)
39 PLN00156 histone H2AX; Provisi 90.2 0.49 1.1E-05 37.0 4.2 67 69-141 27-93 (139)
40 PLN00157 histone H2A; Provisio 89.8 0.46 1E-05 36.8 3.7 67 69-141 24-90 (132)
41 COG5262 HTA1 Histone H2A [Chro 89.6 0.64 1.4E-05 35.7 4.3 51 91-141 40-90 (132)
42 PLN00153 histone H2A; Provisio 89.1 0.61 1.3E-05 36.0 3.9 67 69-141 22-88 (129)
43 COG5094 TAF9 Transcription ini 87.3 1.8 3.9E-05 33.7 5.4 47 96-142 32-81 (145)
44 cd08045 TAF4 TATA Binding Prot 87.1 2.4 5.2E-05 34.3 6.5 57 69-128 42-98 (212)
45 PTZ00252 histone H2A; Provisio 86.7 1.2 2.5E-05 34.7 4.2 67 69-141 23-91 (134)
46 KOG2549 Transcription initiati 86.5 1.9 4.2E-05 40.4 6.2 51 94-144 27-77 (576)
47 PF05236 TAF4: Transcription i 86.0 1.1 2.4E-05 37.4 4.1 58 69-129 41-98 (264)
48 KOG1744 Histone H2B [Chromatin 83.7 3.7 8.1E-05 31.7 5.7 62 76-143 42-103 (127)
49 KOG2389 Predicted bromodomain 83.6 2.8 6.1E-05 37.2 5.6 49 94-142 45-93 (353)
50 COG5150 Class 2 transcription 82.6 5.1 0.00011 31.3 6.1 68 67-139 7-74 (148)
51 KOG1756 Histone 2A [Chromatin 79.9 3.7 7.9E-05 31.8 4.4 67 69-141 25-91 (131)
52 cd07978 TAF13 The TATA Binding 79.4 14 0.0003 26.6 7.1 51 90-141 15-65 (92)
53 PF09415 CENP-X: CENP-S associ 74.2 5.8 0.00012 27.5 3.8 58 80-137 4-62 (72)
54 KOG4336 TBP-associated transcr 74.0 7.8 0.00017 34.1 5.3 50 96-145 23-72 (323)
55 KOG3901 Transcription initiati 70.0 30 0.00064 26.1 6.9 64 73-141 7-70 (109)
56 COG1224 TIP49 DNA helicase TIP 65.7 11 0.00024 34.3 4.7 73 70-142 354-431 (450)
57 KOG1757 Histone 2A [Chromatin 63.7 14 0.0003 28.3 4.2 68 75-146 31-98 (131)
58 COG5248 TAF19 Transcription in 63.2 43 0.00092 25.6 6.7 61 77-141 11-71 (126)
59 COG5095 TAF6 Transcription ini 60.0 33 0.00072 30.9 6.5 63 79-144 9-71 (450)
60 PF10911 DUF2717: Protein of u 57.2 30 0.00064 24.6 4.7 61 58-122 2-64 (77)
61 KOG1657 CCAAT-binding factor, 53.6 23 0.0005 29.8 4.3 72 66-140 66-137 (236)
62 TIGR02902 spore_lonB ATP-depen 52.1 28 0.0006 32.0 4.9 60 82-141 269-330 (531)
63 KOG2680 DNA helicase TIP49, TB 51.2 47 0.001 30.0 6.0 73 70-142 351-428 (454)
64 KOG1658 DNA polymerase epsilon 49.6 14 0.0003 29.6 2.2 65 72-140 57-122 (162)
65 PRK07452 DNA polymerase III su 48.2 53 0.0011 27.4 5.7 60 77-140 135-196 (326)
66 PF09123 DUF1931: Domain of un 45.2 39 0.00084 26.5 4.1 59 77-142 1-59 (138)
67 COG5208 HAP5 CCAAT-binding fac 44.5 53 0.0011 28.0 5.0 85 54-141 80-173 (286)
68 KOG1942 DNA helicase, TBP-inte 41.3 65 0.0014 29.1 5.3 73 70-142 360-437 (456)
69 PF13654 AAA_32: AAA domain; P 35.1 1.5E+02 0.0033 27.4 7.0 66 75-143 430-506 (509)
70 TIGR00764 lon_rel lon-related 34.0 1.9E+02 0.0041 27.2 7.5 48 94-141 329-389 (608)
71 PF10788 DUF2603: Protein of u 33.7 41 0.00088 26.3 2.6 32 55-87 97-128 (137)
72 TIGR01128 holA DNA polymerase 33.0 1.6E+02 0.0035 23.7 6.2 62 77-142 116-177 (302)
73 PRK05574 holA DNA polymerase I 31.7 1.7E+02 0.0037 24.1 6.2 61 78-143 152-213 (340)
74 TIGR03015 pepcterm_ATPase puta 31.5 1.9E+02 0.0041 22.9 6.3 49 93-141 213-264 (269)
75 PRK08487 DNA polymerase III su 29.9 1.6E+02 0.0034 24.9 5.8 57 78-140 141-197 (328)
76 PF13060 DUF3921: Protein of u 28.2 1.3E+02 0.0029 19.9 3.9 26 94-119 24-49 (58)
77 PRK14562 haloacid dehalogenase 28.0 84 0.0018 25.5 3.7 26 91-116 70-95 (204)
78 PF08369 PCP_red: Proto-chloro 25.9 1E+02 0.0022 19.2 3.0 19 121-139 26-44 (45)
79 PRK06585 holA DNA polymerase I 24.6 1.4E+02 0.003 25.1 4.6 59 78-140 148-207 (343)
80 PF00540 Gag_p17: gag gene pro 23.8 3.3E+02 0.0071 21.3 6.1 76 46-141 25-101 (140)
81 PRK05629 hypothetical protein; 23.6 2.3E+02 0.005 23.7 5.7 57 78-139 132-188 (318)
82 COG2118 DNA-binding protein [G 23.3 1.2E+02 0.0027 23.1 3.5 32 103-142 67-98 (116)
83 COG1466 HolA DNA polymerase II 22.0 2.3E+02 0.0051 24.0 5.5 59 77-140 145-204 (334)
84 COG1598 Predicted nuclease of 21.2 1.4E+02 0.0029 20.2 3.2 25 98-122 34-58 (73)
85 PF04604 L_biotic_typeA: Type- 20.9 88 0.0019 20.6 2.0 20 99-118 7-26 (51)
No 1
>PLN00161 histone H3; Provisional
Probab=100.00 E-value=1.7e-58 Score=353.62 Aligned_cols=130 Identities=50% Similarity=0.721 Sum_probs=117.9
Q ss_pred CCCcccccccccCcccccccCCCCCCCCcchhhhhhcCCCCCCccCCcccCCCCchhhHHHHhhhhcccccCCcchHHHH
Q 031980 1 MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEAGEGTPTAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIRE 80 (149)
Q Consensus 1 MartK~~a~k~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~kk~~r~rpgt~alrEIr~yQkst~lLIpk~PF~RL 80 (149)
||||||+ +|+++|+.|.+++.. +..+++++++||||||||||+|||+||+||+|||||+||+||
T Consensus 1 mar~k~~-~~~~~~~~~~~~~~~---------------~~~~~~~kk~~r~rpGtvaLrEIR~yQkst~lLIpklPF~RL 64 (135)
T PLN00161 1 MARRLQG-KRFRKGKKPQKEASG---------------VTRQELDKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARL 64 (135)
T ss_pred CCccccc-ccccCCCCCcccCCC---------------CCCCCCCCCCccCCCcchHHHHHHHHccccccccccccHHHH
Confidence 9999999 777888888776641 012267899999999999999999999999999999999999
Q ss_pred HHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccCCC
Q 031980 81 VRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKGQ 147 (149)
Q Consensus 81 VrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~~~ 147 (149)
||||++++ ..+++|||++||+|||||+|+|||+||||+|+||+||||||||++||+||++|||++.
T Consensus 65 VREI~~~~-~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rirg~~~ 130 (135)
T PLN00161 65 VREISNEM-LREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRGPIY 130 (135)
T ss_pred HHHHHHhc-CCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhccccc
Confidence 99999994 3468999999999999999999999999999999999999999999999999999854
No 2
>PTZ00018 histone H3; Provisional
Probab=100.00 E-value=3e-58 Score=353.06 Aligned_cols=135 Identities=49% Similarity=0.678 Sum_probs=120.9
Q ss_pred CCCcccccccccCcccccccCCCCCCCCcchhhhhhcCCCCCCccCCcccCCCCchhhHHHHhhhhcccccCCcchHHHH
Q 031980 1 MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEAGEGTPTAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIRE 80 (149)
Q Consensus 1 MartK~~a~k~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~kk~~r~rpgt~alrEIr~yQkst~lLIpk~PF~RL 80 (149)
||||||+++|++++++|+++.+. +...+..+. .++.++++||+||+|||+|||+||+||+|||||+||+||
T Consensus 1 MaRtk~~~~k~~~~~~prk~~~~--------~~~~~~~~~-~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RL 71 (136)
T PTZ00018 1 MARTKQTARKSTGGKAPRKQLAS--------KAARKSAPV-TGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRL 71 (136)
T ss_pred CCCCCcCccCCCCCCCCcccccc--------cccccCCCC-CCCCCCCcccCCchhHHHHHHHHcccchhccccccHHHH
Confidence 99999999999999998887752 111112222 267899999999999999999999999999999999999
Q ss_pred HHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccCC
Q 031980 81 VRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKG 146 (149)
Q Consensus 81 VrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~~ 146 (149)
||||+++ +.+++|||++||+|||||+|+|||+||||+|+||+||||||||++||+|+++|||+.
T Consensus 72 VREI~~~--~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~~ 135 (136)
T PTZ00018 72 VREIAQD--FKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
T ss_pred HHHHHHH--cCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHhcccC
Confidence 9999999 467899999999999999999999999999999999999999999999999999984
No 3
>PLN00121 histone H3; Provisional
Probab=100.00 E-value=5.8e-58 Score=351.44 Aligned_cols=135 Identities=48% Similarity=0.683 Sum_probs=121.1
Q ss_pred CCCcccccccccCcccccccCCCCCCCCcchhhhhhcCCCCCCccCCcccCCCCchhhHHHHhhhhcccccCCcchHHHH
Q 031980 1 MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEAGEGTPTAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIRE 80 (149)
Q Consensus 1 MartK~~a~k~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~kk~~r~rpgt~alrEIr~yQkst~lLIpk~PF~RL 80 (149)
||||||++++++++++|+++.+. +...+..+. .++.++++||+||++||+|||+||+||+|||||+||+||
T Consensus 1 MaRtk~~~~k~~~~~~p~~~~~~--------~~~~~~~~~-~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RL 71 (136)
T PLN00121 1 MARTKQTARKSTGGKAPRKQLAT--------KAARKSAPA-TGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRL 71 (136)
T ss_pred CCCCCcCccCCCCCCCCcccccc--------cccccCCCC-CCCCCCCcccCchhHHHHHHHHhccccccccccccHHHH
Confidence 99999999999999999887752 111112222 267899999999999999999999999999999999999
Q ss_pred HHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccCC
Q 031980 81 VRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKG 146 (149)
Q Consensus 81 VrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~~ 146 (149)
||||+++ +.+++|||++||+|||||+|+|||+||||+|+||+||||||||++||+|+++|||+.
T Consensus 72 VREI~~~--~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~~ 135 (136)
T PLN00121 72 VREIAQD--FKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
T ss_pred HHHHHHH--hCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHhcccc
Confidence 9999999 467899999999999999999999999999999999999999999999999999984
No 4
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=100.00 E-value=1.6e-55 Score=337.59 Aligned_cols=135 Identities=49% Similarity=0.667 Sum_probs=121.9
Q ss_pred CCCcccccccccCcccccccCCCCCCCCcchhhhhhc-CCCCCCccCCcccCCCCchhhHHHHhhhhcccccCCcchHHH
Q 031980 1 MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEA-GEGTPTAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIR 79 (149)
Q Consensus 1 MartK~~a~k~~~~~~~~~~~~~~~~~~~~~k~~~~~-~~~~~~~~kk~~r~rpgt~alrEIr~yQkst~lLIpk~PF~R 79 (149)
|+|++++++|++++++++++.+.. ..++. .+. .+.++|++||+||+|+|+|||+||+||||||+|+||+|
T Consensus 1 m~r~~~t~~k~~~~~~~r~~~a~~--------~~~~~~~~~-~~~~~k~~r~rpg~~al~eirkyQkstdLlI~K~PFqR 71 (137)
T KOG1745|consen 1 MARTKQTARKSTGGKAPRKQLAGK--------AARKSAAPR-TGRVKKPHRYRPGTVALREIRKYQKSTDLLIRKLPFQR 71 (137)
T ss_pred CCCCCcccccccCCCCCccccccc--------ccccccccc-ccccCccccccCchHHHHHHHHHHhhhHHHhhcCcHHH
Confidence 899999999999999999987632 11111 111 15688999999999999999999999999999999999
Q ss_pred HHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccCC
Q 031980 80 EVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKG 146 (149)
Q Consensus 80 LVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~~ 146 (149)
|||||+++ |..|+|||++|+.|||||+|+|||+||||+|+||+|||||||||+|||||++|+|++
T Consensus 72 lvrei~q~--f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg~~ 136 (137)
T KOG1745|consen 72 LVREIAQD--FKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 136 (137)
T ss_pred HhHHHHhc--ccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhcccCC
Confidence 99999998 778999999999999999999999999999999999999999999999999999985
No 5
>smart00428 H3 Histone H3.
Probab=100.00 E-value=9.6e-51 Score=300.01 Aligned_cols=103 Identities=52% Similarity=0.756 Sum_probs=98.0
Q ss_pred ccCCcccCCCCchhhHHHHhhhhcccccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 031980 44 AQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCA 123 (149)
Q Consensus 44 ~~kk~~r~rpgt~alrEIr~yQkst~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA 123 (149)
+++++||||||++||+|||+||+||+|||||+||+||||||++++....++|||++|++|||||+|+|||++|||+|+||
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 57889999999999999999999999999999999999999999543348999999999999999999999999999999
Q ss_pred hhcCccccccccHHHHHHHccCC
Q 031980 124 IHAKRVTLMKKDFELARRLGGKG 146 (149)
Q Consensus 124 ~HAkRvTi~~kDiqLa~rirg~~ 146 (149)
+||||||||++||+||.+|||+.
T Consensus 82 ~HAkRvTl~~kDi~La~rir~~~ 104 (105)
T smart00428 82 IHAKRVTIMPKDIQLARRIRGER 104 (105)
T ss_pred HHhCCccCcHhhHHHHHHHhccC
Confidence 99999999999999999999974
No 6
>PLN00160 histone H3; Provisional
Probab=100.00 E-value=1.3e-50 Score=295.66 Aligned_cols=95 Identities=56% Similarity=0.893 Sum_probs=91.3
Q ss_pred CCCCchhhHHHHhhhhcccccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccc
Q 031980 51 LRPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVT 130 (149)
Q Consensus 51 ~rpgt~alrEIr~yQkst~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvT 130 (149)
|||||+||+|||+||+||+|||||+||+||||||++++ ..+++|||++||+|||||+|+|||+||||+|+||+||||||
T Consensus 1 ~rpGt~aLrEIR~yQkst~lLI~k~pF~RLVREI~~~~-~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVT 79 (97)
T PLN00160 1 MRPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEM-SREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVT 79 (97)
T ss_pred CCCccHHHHHHHHHccchhhhhccccHHHHHHHHHHHc-CCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccc
Confidence 79999999999999999999999999999999999984 35679999999999999999999999999999999999999
Q ss_pred cccccHHHHHHHccCC
Q 031980 131 LMKKDFELARRLGGKG 146 (149)
Q Consensus 131 i~~kDiqLa~rirg~~ 146 (149)
||++||+|+++|||+.
T Consensus 80 l~~kD~~L~~rirg~~ 95 (97)
T PLN00160 80 IMPKDMQLARRIRGQT 95 (97)
T ss_pred cchhhHHHHHHhhccc
Confidence 9999999999999985
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.95 E-value=1.3e-27 Score=172.91 Aligned_cols=87 Identities=40% Similarity=0.569 Sum_probs=84.0
Q ss_pred CCchhhHHHHhhhhcccccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccc
Q 031980 53 PGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLM 132 (149)
Q Consensus 53 pgt~alrEIr~yQkst~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~ 132 (149)
||.++++|||+||++++++||++||+||+|+.+.+ ||+.+|+++||+++|.|+++++|+|++||.|+||+||+
T Consensus 1 ~~~~~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~~-------Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~ 73 (91)
T COG2036 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAE-------RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVK 73 (91)
T ss_pred CCcchHHHHHhhhhhhhhhcCchHHHHHHHHHhHH-------HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeec
Confidence 68999999999999999999999999999999985 99999999999999999999999999999999999999
Q ss_pred cccHHHHHHHccCC
Q 031980 133 KKDFELARRLGGKG 146 (149)
Q Consensus 133 ~kDiqLa~rirg~~ 146 (149)
++||+|+.+..|..
T Consensus 74 ~~DI~la~~~~~~~ 87 (91)
T COG2036 74 AEDIKLALKRLGRR 87 (91)
T ss_pred HHHHHHHHHHhccc
Confidence 99999999998763
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=99.83 E-value=1.2e-20 Score=128.79 Aligned_cols=75 Identities=37% Similarity=0.485 Sum_probs=69.7
Q ss_pred cccccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHc
Q 031980 67 SVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLG 143 (149)
Q Consensus 67 st~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rir 143 (149)
+|.++|+++||.|++++|..++ ...+||+++|+..||+++|+|++++||+|+.||.|+||+||+++||++|.+++
T Consensus 1 ~~~~~~~~~~~~r~~r~i~~~~--~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~ 75 (75)
T PF00125_consen 1 RTRRLIPKFPFSRLLREIGEEI--LSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID 75 (75)
T ss_dssp HHSHSSSHHHHHHHHHHHHHTT--SSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred CcccccCceEEeeeeehhhccc--ccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence 4678999999999999999983 33489999999999999999999999999999999999999999999999875
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=99.36 E-value=2.2e-12 Score=89.04 Aligned_cols=64 Identities=27% Similarity=0.297 Sum_probs=56.3
Q ss_pred CCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 72 IPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 72 Ipk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
+++--.+.||++|.. ..|++++|.++||+.+|+|+.++++++..||.|++|.||+++||+|+..
T Consensus 2 ~~k~~l~~lv~~id~------~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~ 65 (72)
T cd07981 2 LTKRKLQELLKEIDP------REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLE 65 (72)
T ss_pred CcHHHHHHHHHhhCC------CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 344555677777754 3899999999999999999999999999999999999999999999964
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=99.12 E-value=1.9e-10 Score=82.49 Aligned_cols=68 Identities=22% Similarity=0.236 Sum_probs=64.1
Q ss_pred cCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccC
Q 031980 71 LIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGK 145 (149)
Q Consensus 71 LIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~ 145 (149)
-|++.|..||+|.-+. .|++.++.+++.++.|.||.++..|+..++.||+|.||+..||.+|.+-.|.
T Consensus 13 gi~k~~I~RLarr~Gv-------kRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~ 80 (85)
T cd00076 13 GITKPAIRRLARRGGV-------KRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 80 (85)
T ss_pred cCCHHHHHHHHHHcCc-------chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCC
Confidence 4999999999998776 5999999999999999999999999999999999999999999999988774
No 11
>PLN00035 histone H4; Provisional
Probab=99.06 E-value=4.6e-10 Score=83.11 Aligned_cols=67 Identities=24% Similarity=0.222 Sum_probs=63.7
Q ss_pred CCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccC
Q 031980 72 IPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGK 145 (149)
Q Consensus 72 Ipk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~ 145 (149)
||+.|..||.|..+. .|++.+|.++|.++.|.||..+..|+...+.||+|.||+.+||.+|.+-.|.
T Consensus 30 ipk~~IrRLARr~Gv-------kRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~ 96 (103)
T PLN00035 30 ITKPAIRRLARRGGV-------KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred CCHHHHHHHHHHcCc-------ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCC
Confidence 999999999998876 5999999999999999999999999999999999999999999999887765
No 12
>PTZ00015 histone H4; Provisional
Probab=99.06 E-value=5.3e-10 Score=82.62 Aligned_cols=69 Identities=20% Similarity=0.177 Sum_probs=64.4
Q ss_pred ccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccC
Q 031980 70 LLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGK 145 (149)
Q Consensus 70 lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~ 145 (149)
--|++.|..||.|..+. .|++.++.+.|.++.|.||.++..|+..+|-||+|.||+..||.+|.+-.|.
T Consensus 29 ~gI~k~~IrRLarr~Gv-------kRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~ 97 (102)
T PTZ00015 29 RGITKGAIRRLARRGGV-------KRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR 97 (102)
T ss_pred cCCCHHHHHHHHHHcCC-------ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC
Confidence 34999999999998877 4999999999999999999999999999999999999999999999887765
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=98.98 E-value=1.2e-09 Score=74.51 Aligned_cols=64 Identities=23% Similarity=0.297 Sum_probs=59.3
Q ss_pred cCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 71 LIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 71 LIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
.+|+.|..|+.+.++. .|++.+|..+|.+..|.++-++.++|..++.|++|.||+..||.+|.+
T Consensus 2 ~~p~~~i~ria~~~Gi-------~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLGI-------GNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCCC-------ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 5789999999988776 489999999999999999999999999999999999999999999863
No 14
>smart00417 H4 Histone H4.
Probab=98.89 E-value=2.2e-09 Score=75.19 Aligned_cols=62 Identities=23% Similarity=0.181 Sum_probs=57.8
Q ss_pred ccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHH
Q 031980 70 LLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFEL 138 (149)
Q Consensus 70 lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqL 138 (149)
--||+.|..||.|.-+. .|++.++.+.|.++.|.||..+..|+..++.||+|.||+..|+..
T Consensus 12 ~gI~k~~IrRLaRr~Gv-------kRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 12 QGITKPAIRRLARRGGV-------KRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred cCCCHHHHHHHHHHcCc-------chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 34999999999998776 499999999999999999999999999999999999999999864
No 15
>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=98.59 E-value=1.4e-07 Score=63.02 Aligned_cols=62 Identities=34% Similarity=0.381 Sum_probs=52.0
Q ss_pred CCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHH
Q 031980 72 IPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELA 139 (149)
Q Consensus 72 Ipk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa 139 (149)
+|.....|++|+. +++.+++.+|+.+|+.++|.|+..|-..++.+|.+.+|.||+++||.-|
T Consensus 3 lP~a~vkri~k~~------~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~A 64 (65)
T PF00808_consen 3 LPLARVKRIMKSD------PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKA 64 (65)
T ss_dssp S-HHHHHHHHHHT------STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHH
T ss_pred CChHHHHHHhccC------CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHH
Confidence 5666777777765 2357899999999999999999999999999999999999999999876
No 16
>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=98.55 E-value=2.9e-07 Score=69.09 Aligned_cols=65 Identities=20% Similarity=0.276 Sum_probs=58.9
Q ss_pred HHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccC
Q 031980 78 IREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGK 145 (149)
Q Consensus 78 ~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~ 145 (149)
.++|..|..+ -...+|+.+++..|-|.+|.|..++..||...|.||+|.||..+||+||...++.
T Consensus 4 ~~~v~~iLk~---~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 4 ARVIAAILKS---MGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHH---CCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 5677778775 2346999999999999999999999999999999999999999999999998876
No 17
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.26 E-value=3.6e-06 Score=59.20 Aligned_cols=67 Identities=28% Similarity=0.211 Sum_probs=54.0
Q ss_pred chHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 75 MSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 75 ~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
+-+.--|-+|+++.....+..|+.+.+.+|-|.+=.++..+-+|--..|.||||.||.++|+.|..|
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 3344556666666444567899999999999999999999999999999999999999999999754
No 18
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.18 E-value=5.9e-06 Score=57.34 Aligned_cols=52 Identities=23% Similarity=0.135 Sum_probs=48.4
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccC
Q 031980 94 NRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGK 145 (149)
Q Consensus 94 ~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~ 145 (149)
.+++.+|++.|.+..|.|+..|-+.+...+.|++|.++.+.||.+|..--|.
T Consensus 22 ~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi 73 (77)
T smart00576 22 DSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGI 73 (77)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Confidence 5999999999999999999999999999999999999999999999765443
No 19
>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=97.91 E-value=2.1e-05 Score=59.26 Aligned_cols=67 Identities=21% Similarity=0.194 Sum_probs=60.9
Q ss_pred cccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 69 DLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 69 ~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
.|.+|-.++.|+.++-.. ..|+.++|...|..+.|.+..+++|-+...|.|.++.+|+|+||+||.+
T Consensus 18 gL~fPV~ri~R~Lk~~~~------a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~ 84 (115)
T cd00074 18 GLQFPVGRIHRYLKKGRY------AERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR 84 (115)
T ss_pred CccCcHHHHHHHHHcCcc------ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh
Confidence 688999999999986322 2699999999999999999999999999999999999999999999964
No 20
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=97.89 E-value=4.2e-05 Score=66.24 Aligned_cols=65 Identities=23% Similarity=0.230 Sum_probs=57.3
Q ss_pred HHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccCC
Q 031980 79 REVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKG 146 (149)
Q Consensus 79 RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~~ 146 (149)
..|+.|+.. . ...|.+.+|..+|.+-+|.++-++.++|..++.|+||.||+.+||++|.+.++..
T Consensus 3 ~~i~~ia~~--~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 3 ESIKLIAES--L-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred hHHHHHHHH--c-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 356777775 1 2359999999999999999999999999999999999999999999999988763
No 21
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=97.70 E-value=6.9e-05 Score=59.85 Aligned_cols=69 Identities=26% Similarity=0.206 Sum_probs=63.1
Q ss_pred cccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 69 DLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 69 ~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
+|.+|++-..|||++...+. +.-++.+|+.|++++|--|+.-|.--++..|.-.+|.||+++|+-=+..
T Consensus 8 dl~lP~AiI~rlvke~l~E~----~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~ 76 (172)
T KOG0870|consen 8 DLNLPNAIITRLVKEVLPES----NVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALD 76 (172)
T ss_pred HhhccHHHHHHHHHHhCccc----cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHH
Confidence 57899999999999999872 5789999999999999999999999999999999999999999865543
No 22
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=97.64 E-value=0.00018 Score=49.38 Aligned_cols=59 Identities=29% Similarity=0.332 Sum_probs=46.5
Q ss_pred HHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 80 EVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 80 LVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
-|+.|+..+ + ..-.+.++...|.+-+|.-|-++.++|..++.|+||.+++..||..|.|
T Consensus 8 svk~iAes~--G-i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 8 SVKDIAESL--G-ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp HHHHHHHHT--T----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred HHHHHHHHc--C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 466677652 1 2357899999999999999999999999999999999999999999864
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=97.62 E-value=0.00015 Score=49.83 Aligned_cols=60 Identities=28% Similarity=0.274 Sum_probs=48.1
Q ss_pred hHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 76 SFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 76 PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
-++.||++|.. ...+.+++-+.|.+.+++|+.+..+.+-.+|.|-+--||.++||+|...
T Consensus 4 ~l~~Lv~~iDp------~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le 63 (68)
T PF03847_consen 4 KLQELVKQIDP------NEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE 63 (68)
T ss_dssp HHHHHHHCC-S------S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred HHHHHHHHcCC------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence 45778888854 3789999999999999999999999999999999999999999999864
No 24
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.59 E-value=0.00012 Score=65.16 Aligned_cols=63 Identities=24% Similarity=0.226 Sum_probs=43.7
Q ss_pred CCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccccccc
Q 031980 72 IPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKD 135 (149)
Q Consensus 72 Ipk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kD 135 (149)
+|..+..+|+.-.++- .+....++..+||.+|..|+|-|.-+|-+|---.|.||+|+||...|
T Consensus 352 lP~~~vK~la~~~ak~-s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 352 LPPGVVKKLAQHFAKS-SGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp S-HHHHHHHHHHHH--------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCccHHHHHHHHHHHh-hcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4444555555555442 24456899999999999999999999999999999999999999877
No 25
>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=97.44 E-value=0.00056 Score=52.47 Aligned_cols=65 Identities=26% Similarity=0.268 Sum_probs=51.8
Q ss_pred HHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccC
Q 031980 78 IREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGK 145 (149)
Q Consensus 78 ~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~ 145 (149)
.++|..|..+ . ...-|+...+.-|-|-+=.|..++++||...|-||+|.+|...|++||...+..
T Consensus 15 a~~i~~iL~~--~-Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~ 79 (129)
T PF02291_consen 15 ARVIHLILKS--M-GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLD 79 (129)
T ss_dssp HHHHHHHHHH--T-T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT--
T ss_pred HHHHHHHHHH--c-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHh
Confidence 5778888876 2 234589999999999999999999999999999999999999999999987654
No 26
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.08 E-value=0.00082 Score=56.93 Aligned_cols=73 Identities=18% Similarity=0.185 Sum_probs=66.5
Q ss_pred hhhhcccccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 63 RFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 63 ~yQkst~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
.++-+++.++-|--...||++|..+ .-...++-+.|.|.|++|+-.+---+-.+|.|.|--||.++||+|..+
T Consensus 146 ~~~~~~~~il~k~kl~dLvqqId~~------~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLE 218 (258)
T KOG1142|consen 146 QDEPGNNPILSKRKLDDLVQQIDGT------TKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLE 218 (258)
T ss_pred cccCCCCccccccchhHHHHhhcCc------ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeee
Confidence 7788889999999999999999553 567789999999999999999999999999999999999999999863
No 27
>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=96.31 E-value=0.028 Score=38.50 Aligned_cols=51 Identities=29% Similarity=0.236 Sum_probs=47.2
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHcc
Q 031980 94 NRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGG 144 (149)
Q Consensus 94 ~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg 144 (149)
..++.+||+.|-+.++.||..|...+...|-|++|-...+.|+.++..--|
T Consensus 22 ~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~g 72 (77)
T PF07524_consen 22 DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMG 72 (77)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhC
Confidence 378999999999999999999999999999999999999999999876544
No 28
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.36 E-value=0.043 Score=43.16 Aligned_cols=65 Identities=23% Similarity=0.353 Sum_probs=52.8
Q ss_pred HHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccCC
Q 031980 79 REVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKG 146 (149)
Q Consensus 79 RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~~ 146 (149)
++|..|..++ ...-|....+.-|=|-+=.|...+++||...+-||++-||..+|++||...++..
T Consensus 17 ~~i~~iL~s~---GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~ 81 (148)
T KOG3334|consen 17 RVIASILKSL---GIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDH 81 (148)
T ss_pred HHHHHHHHHc---CccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhcc
Confidence 4455555441 1234667788889999999999999999999999999999999999999887654
No 29
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=94.92 E-value=0.097 Score=38.34 Aligned_cols=67 Identities=25% Similarity=0.229 Sum_probs=53.8
Q ss_pred CCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccC
Q 031980 72 IPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGK 145 (149)
Q Consensus 72 Ipk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~ 145 (149)
|-|-...||.|.-+- -|+..-..+....++..||.+...+|...+-||||.||..-|+--+.+-.|.
T Consensus 30 itKpaIRRlARr~GV-------kRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~ 96 (103)
T KOG3467|consen 30 ITKPAIRRLARRGGV-------KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred cchHHHHHHHHhcCc-------chhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCc
Confidence 345566666664443 4777888888999999999999999999999999999999999777665443
No 30
>smart00414 H2A Histone 2A.
Probab=94.61 E-value=0.037 Score=41.13 Aligned_cols=67 Identities=24% Similarity=0.213 Sum_probs=56.8
Q ss_pred cccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 69 DLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 69 ~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
+|.+|---|.|+.++-.. ..|+.++|..-|--+.|....+++|-+...+...++..|+|+||++|.+
T Consensus 7 gL~fPVgRi~r~Lk~~~~------~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 7 GLQFPVGRIHRLLRKGTY------AKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred CccCchHHHHHHHHcCcc------ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 566777777777765432 2599999999999999999999999999999999999999999999963
No 31
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=94.03 E-value=0.14 Score=40.96 Aligned_cols=74 Identities=24% Similarity=0.279 Sum_probs=60.8
Q ss_pred hhhHHHHhhhhcccccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccccccc
Q 031980 56 KALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKD 135 (149)
Q Consensus 56 ~alrEIr~yQkst~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kD 135 (149)
..+||=-+| +|-+-..|+.|.+.- .+-.+..+|-+.+||.+-.|+-=+--.|..-+---||+||..+|
T Consensus 24 ~~~reqDr~-------LPIANV~RIMK~~lP-----~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdD 91 (168)
T KOG0869|consen 24 LSLREQDRF-------LPIANVSRIMKKALP-----ANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDD 91 (168)
T ss_pred cccchhhhh-------ccHHHHHHHHHhcCC-----cccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHH
Confidence 445554444 889999999988754 35789999999999999998888887888877888999999999
Q ss_pred HHHHHH
Q 031980 136 FELARR 141 (149)
Q Consensus 136 iqLa~r 141 (149)
|-.|+-
T Consensus 92 llwAm~ 97 (168)
T KOG0869|consen 92 LLWAMS 97 (168)
T ss_pred HHHHHH
Confidence 988764
No 32
>PTZ00017 histone H2A; Provisional
Probab=92.64 E-value=0.19 Score=38.99 Aligned_cols=67 Identities=21% Similarity=0.183 Sum_probs=58.2
Q ss_pred cccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 69 DLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 69 ~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
.|.+|---+.|+.++-.. ..|+.+.|..-|--+.|....+++|-+-..+...++..|+|++|+||.+
T Consensus 25 gL~FPVgRi~R~Lk~g~~------a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGRY------AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CcccchHHHHHHHhccch------hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 567788888888776432 2599999999999999999999999999999999999999999999964
No 33
>PLN00158 histone H2B; Provisional
Probab=92.41 E-value=0.88 Score=34.59 Aligned_cols=51 Identities=18% Similarity=0.151 Sum_probs=44.9
Q ss_pred ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHc
Q 031980 93 VNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLG 143 (149)
Q Consensus 93 ~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rir 143 (149)
|.-+++.|+..+---..+.+..+...|..++...+|.||..+|||-|.++-
T Consensus 43 d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 43 DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 467899999998888888888888888889999999999999999998863
No 34
>smart00427 H2B Histone H2B.
Probab=92.34 E-value=0.99 Score=32.78 Aligned_cols=51 Identities=20% Similarity=0.192 Sum_probs=44.4
Q ss_pred ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHc
Q 031980 93 VNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLG 143 (149)
Q Consensus 93 ~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rir 143 (149)
|.-+++.|+.-+---.-+....+...|..++...+|.||..+|||-|.++-
T Consensus 17 d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 17 DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 468999999988877778777888888888889999999999999998863
No 35
>PTZ00463 histone H2B; Provisional
Probab=91.78 E-value=1.1 Score=34.04 Aligned_cols=51 Identities=16% Similarity=0.111 Sum_probs=44.9
Q ss_pred ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHc
Q 031980 93 VNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLG 143 (149)
Q Consensus 93 ~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rir 143 (149)
|.-+++.|+.-+---..+.+..+...|..++...+|-||..+|||-|.+|-
T Consensus 44 d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 44 DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 467899999998888888888888888888999999999999999998874
No 36
>PLN00154 histone H2A; Provisional
Probab=91.45 E-value=0.52 Score=36.69 Aligned_cols=68 Identities=16% Similarity=0.105 Sum_probs=59.1
Q ss_pred cccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 69 DLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 69 ~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
.|.+|---..|+.|+-... ..|+.+.|..-|--+.|....+++|-+-..|...++..|+|++|+||.+
T Consensus 36 gL~FPVgRi~r~Lk~g~~~-----~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSA-----HGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred CccCchHHHHHHHHhhhhh-----ccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 5677877888888876421 2699999999999999999999999999999999999999999999964
No 37
>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=90.77 E-value=0.38 Score=34.60 Aligned_cols=52 Identities=19% Similarity=0.266 Sum_probs=26.4
Q ss_pred CCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 90 PPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 90 ~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
+++...=..+.+..+.+..=.|++.+...|..+|...++..|..+|+-.+.|
T Consensus 14 fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR 65 (93)
T PF02269_consen 14 FGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLR 65 (93)
T ss_dssp TTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred cCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHh
Confidence 5666667789999999999999999999999999999999999999988764
No 38
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=90.21 E-value=1.2 Score=35.35 Aligned_cols=69 Identities=13% Similarity=0.112 Sum_probs=62.0
Q ss_pred ccccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 68 VDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 68 t~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
-++-+||+-.+.+|+|+.- .+.||..+|-+.|+++.=.|+--+-..||..+---.+.||-++-+.=|..
T Consensus 9 de~sLPkAtv~KmIke~lP-----~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe 77 (156)
T KOG0871|consen 9 DELSLPKATVNKMIKEMLP-----KDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALE 77 (156)
T ss_pred ccccCcHHHHHHHHHHhCC-----cccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHH
Confidence 4677999999999999975 36899999999999999999999999999999999999999998866654
No 39
>PLN00156 histone H2AX; Provisional
Probab=90.20 E-value=0.49 Score=36.97 Aligned_cols=67 Identities=21% Similarity=0.205 Sum_probs=56.9
Q ss_pred cccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 69 DLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 69 ~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
.|.+|---+.|+.++-.. ..|+.+.|..-|--..|....+++|-+-..+...++..|+|++|+||.+
T Consensus 27 gL~FPVgRi~R~Lk~g~y------a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKY------AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred CcccchHHHHHHHhcCCh------hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 466777777777766422 3699999999999999999999999999999999999999999999964
No 40
>PLN00157 histone H2A; Provisional
Probab=89.76 E-value=0.46 Score=36.79 Aligned_cols=67 Identities=21% Similarity=0.213 Sum_probs=56.9
Q ss_pred cccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 69 DLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 69 ~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
.|.+|---+.|+.++-.. ..|+.+.|..-|--..|....+++|-+...+...++.-|+|++|+||.+
T Consensus 24 gL~FPVgRi~R~Lk~g~~------a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKY------ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred CcccchHHHHHHHhcCch------hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 566777777777766322 3699999999999999999999999999999999999999999999964
No 41
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=89.63 E-value=0.64 Score=35.71 Aligned_cols=51 Identities=20% Similarity=0.135 Sum_probs=47.2
Q ss_pred CCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 91 PDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 91 ~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
....|+.+.|...|-...|....+++|-|-..|.--|-..|||+-+|||.+
T Consensus 40 ~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 40 NYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred ccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 346899999999999999999999999999999999999999999999953
No 42
>PLN00153 histone H2A; Provisional
Probab=89.12 E-value=0.61 Score=35.99 Aligned_cols=67 Identities=21% Similarity=0.208 Sum_probs=56.8
Q ss_pred cccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 69 DLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 69 ~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
.|.+|---+.|+.++-.. ..|+.+.|..-|--..|....+++|-+...|...+..-|+|+.|+||.+
T Consensus 22 gL~FpVgRi~R~Lr~g~~------a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKY------AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred CcccchHHHHHHHhcCch------hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 466777777777765322 3699999999999999999999999999999999999999999999964
No 43
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=87.26 E-value=1.8 Score=33.66 Aligned_cols=47 Identities=26% Similarity=0.398 Sum_probs=38.1
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccccc---ccHHHHHHH
Q 031980 96 WTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMK---KDFELARRL 142 (149)
Q Consensus 96 fq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~---kDiqLa~ri 142 (149)
+......-|-+-|--|-.+++|||...|-|++|-.+.+ +|+.||.--
T Consensus 32 ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at 81 (145)
T COG5094 32 YEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALAT 81 (145)
T ss_pred hCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHH
Confidence 44455566778889999999999999999999876655 999998643
No 44
>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=87.06 E-value=2.4 Score=34.30 Aligned_cols=57 Identities=16% Similarity=0.168 Sum_probs=49.4
Q ss_pred cccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCc
Q 031980 69 DLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKR 128 (149)
Q Consensus 69 ~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkR 128 (149)
..++..-|+...+..|+.....+ -+..+.+..|-.|+|.||-+|.++...++.|-..
T Consensus 42 ~~fl~~~~l~~~~~~i~~~~g~~---~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~ 98 (212)
T cd08045 42 PSFLNPSPLAKKIRKIAKKHGLK---EVDEDVLDLISLALEERLRNLLEKLIEVSEHRVD 98 (212)
T ss_pred hhccCHHHHHHHHHHHHHHcCCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 45789999999999999972211 7899999999999999999999999999999743
No 45
>PTZ00252 histone H2A; Provisional
Probab=86.70 E-value=1.2 Score=34.68 Aligned_cols=67 Identities=19% Similarity=0.194 Sum_probs=54.4
Q ss_pred cccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCccccccccHHHHHH
Q 031980 69 DLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIH--AKRVTLMKKDFELARR 141 (149)
Q Consensus 69 ~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~H--AkRvTi~~kDiqLa~r 141 (149)
.|.+|---+.|+.++-.. ..|+.+.|..-|--..|....+++|-+...|.. -++..|.|++|+||.+
T Consensus 23 GL~FPVgRi~R~Lr~g~y------a~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRGQY------ARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred CccCchHHHHHHHHcCCc------ccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 466777777777765432 369999999999999999999999999988864 5778899999999964
No 46
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=86.51 E-value=1.9 Score=40.41 Aligned_cols=51 Identities=27% Similarity=0.292 Sum_probs=47.2
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHcc
Q 031980 94 NRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGG 144 (149)
Q Consensus 94 ~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg 144 (149)
.....+|..+|-+=.|.-+-++.+|+..+..|+||-++...||.-|.+.+.
T Consensus 27 ~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 27 TNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 467899999999999999999999999999999999999999999987653
No 47
>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=86.01 E-value=1.1 Score=37.35 Aligned_cols=58 Identities=17% Similarity=0.253 Sum_probs=38.8
Q ss_pred cccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCcc
Q 031980 69 DLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRV 129 (149)
Q Consensus 69 ~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRv 129 (149)
++++...|++.-|.+|+.. .+ ..-+..+.+..|--|+|.+|-+|+|++..++.|-...
T Consensus 41 ~~fL~~~~L~~~i~~i~~~--~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~ 98 (264)
T PF05236_consen 41 EPFLNPSPLQKRIQKIAKK--HG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDS 98 (264)
T ss_dssp ---S-HHHHHHHHHHHHHC--TT---EE-TCHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred ccccCHHHHHHHHHHHHHH--cC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 4578889999999999985 22 4678999999999999999999999999999996554
No 48
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=83.66 E-value=3.7 Score=31.66 Aligned_cols=62 Identities=16% Similarity=0.151 Sum_probs=49.4
Q ss_pred hHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHc
Q 031980 76 SFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLG 143 (149)
Q Consensus 76 PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rir 143 (149)
+|.|..+++-.+ .-+.+.|+..+---.-+++-.+...++.+|..-+|-||..++||.+.+|-
T Consensus 42 yv~kvlk~Vhpd------~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 42 YVYKVLKQVHPD------LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred ehhhhhhcccCC------CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 344455554443 55889999988877777777888889999999999999999999999874
No 49
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=83.58 E-value=2.8 Score=37.23 Aligned_cols=49 Identities=22% Similarity=0.098 Sum_probs=45.5
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHH
Q 031980 94 NRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRL 142 (149)
Q Consensus 94 ~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~ri 142 (149)
.-++.+|++.|+..+-.|+-+|-++|-..+-|++|+-....||-+|..-
T Consensus 45 ~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~d 93 (353)
T KOG2389|consen 45 SSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQD 93 (353)
T ss_pred cccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHH
Confidence 3678889999999999999999999999999999999999999988754
No 50
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=82.64 E-value=5.1 Score=31.27 Aligned_cols=68 Identities=18% Similarity=0.125 Sum_probs=59.4
Q ss_pred cccccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHH
Q 031980 67 SVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELA 139 (149)
Q Consensus 67 st~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa 139 (149)
+-++-+||+-.|..|.+|... |+=|+.+|-+-++++.=.|+--|--.||.++-.-...||-++-+--|
T Consensus 7 dDe~sLPKATVqKMvS~iLp~-----dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKA 74 (148)
T COG5150 7 DDENSLPKATVQKMVSSILPK-----DLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKA 74 (148)
T ss_pred cccccCcHHHHHHHHHHhccc-----cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHH
Confidence 346678999999999999753 78999999999999999999999999999999999999998876444
No 51
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=79.94 E-value=3.7 Score=31.84 Aligned_cols=67 Identities=21% Similarity=0.170 Sum_probs=54.3
Q ss_pred cccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 69 DLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 69 ~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
++..|---..|+.|+ ++ .-.|+..+|...|--..|....+++|.+-..|.-.++..|+|+-++||.+
T Consensus 25 gl~fPvgri~r~Lr~-~~-----~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 25 GLQFPVGRIHRLLRK-GR-----YAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred ccccCHHHHHHHHHc-cc-----hhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 344555555566665 22 24799999999999888888899999999999999999999999999964
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=79.44 E-value=14 Score=26.64 Aligned_cols=51 Identities=22% Similarity=0.256 Sum_probs=42.3
Q ss_pred CCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 90 PPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 90 ~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
++++-.=..+.+..|.+..=.|++++.-.|..+|. .++--+.++|+..+.|
T Consensus 15 ~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR 65 (92)
T cd07978 15 FGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR 65 (92)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence 45555556788999999999999999999999998 6666669999988764
No 53
>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=74.20 E-value=5.8 Score=27.46 Aligned_cols=58 Identities=16% Similarity=0.028 Sum_probs=42.2
Q ss_pred HHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccc-cccccHH
Q 031980 80 EVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVT-LMKKDFE 137 (149)
Q Consensus 80 LVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvT-i~~kDiq 137 (149)
+|..|.+..+.....|++.+|+..+.+..+-|..+-+--|+.-+.--+--. |.++|++
T Consensus 4 li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LE 62 (72)
T PF09415_consen 4 LIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLE 62 (72)
T ss_dssp HHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHH
T ss_pred HHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence 556666654445778999999999999999999988888877666666666 8888875
No 54
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=74.00 E-value=7.8 Score=34.07 Aligned_cols=50 Identities=16% Similarity=0.030 Sum_probs=46.0
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccC
Q 031980 96 WTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGK 145 (149)
Q Consensus 96 fq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~ 145 (149)
+...|++.|-|..-.|+-++|+.+-..+-|++|--....|+.|....-|.
T Consensus 23 is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI 72 (323)
T KOG4336|consen 23 ISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNI 72 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCC
Confidence 67889999999999999999999999999999999999999999876654
No 55
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=70.04 E-value=30 Score=26.09 Aligned_cols=64 Identities=23% Similarity=0.327 Sum_probs=48.0
Q ss_pred CcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 73 PRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 73 pk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
++--|++=++...-. ++++--=-.+.+++|.+..=.|++.+...+..+. +|=.+.++||..+.|
T Consensus 7 rk~lF~Kdl~~mmYg--fGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 7 RKHLFSKDLRSMMYG--FGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred HHHHHHHHHHHHHHh--cCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 344577777776664 5555444577899999999999999977666665 888899999988754
No 56
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=65.75 E-value=11 Score=34.32 Aligned_cols=73 Identities=26% Similarity=0.316 Sum_probs=59.2
Q ss_pred ccCCcchHHH-HHHHHhhhcCCCCccccCHHHHHHHHHHHHH----HHHHHHHHHHHHhhhcCccccccccHHHHHHH
Q 031980 70 LLIPRMSFIR-EVRTITYRVAPPDVNRWTPEALIALQEAAED----FLVNLFGDAMLCAIHAKRVTLMKKDFELARRL 142 (149)
Q Consensus 70 lLIpk~PF~R-LVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~----yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~ri 142 (149)
|+|.-.||.+ =+|||..--....+.-.+++|++-|-...|. |.++|++-++..|.-.+..+|..+|++-|..+
T Consensus 354 lII~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~l 431 (450)
T COG1224 354 LIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKEL 431 (450)
T ss_pred eEEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHH
Confidence 6778888874 5777765322345678899999999776665 99999999999999999999999999887654
No 57
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=63.69 E-value=14 Score=28.32 Aligned_cols=68 Identities=16% Similarity=0.120 Sum_probs=52.8
Q ss_pred chHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccCC
Q 031980 75 MSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKG 146 (149)
Q Consensus 75 ~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~~ 146 (149)
.|..|+-|.+-+. ...+.|+...|..-.-...|..-.+.+|-+-..+.--|-..|.|+-+||| |||+.
T Consensus 31 FpVgRihr~LK~r--~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLA--iRGDe 98 (131)
T KOG1757|consen 31 FPVGRIHRHLKTR--TTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLA--IRGDE 98 (131)
T ss_pred cchHHHHHHHHHh--cccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheee--ecCcH
Confidence 4666766666554 34467898888887777788888888998888888888888999999999 57764
No 58
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=63.18 E-value=43 Score=25.60 Aligned_cols=61 Identities=26% Similarity=0.328 Sum_probs=46.1
Q ss_pred HHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 77 FIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 77 F~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
|..=|+....- ++++--=..+.+++|.|..-+|++.+.-++--.|- .|-.+..+|++.+.|
T Consensus 11 F~KDikslmYa--yGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr 71 (126)
T COG5248 11 FMKDIKSLMYA--YGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALR 71 (126)
T ss_pred HHHHHHHHHHH--hCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHh
Confidence 44445555543 45555555788999999999999999888777776 677888999999875
No 59
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=60.01 E-value=33 Score=30.85 Aligned_cols=63 Identities=21% Similarity=0.208 Sum_probs=53.4
Q ss_pred HHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHcc
Q 031980 79 REVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGG 144 (149)
Q Consensus 79 RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg 144 (149)
.-++.+++. ..-.-+..+++.||.--.|.-+-++-+.+.....|.||--+...||.-|.|-..
T Consensus 9 et~KdvAes---lGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lN 71 (450)
T COG5095 9 ETLKDVAES---LGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLN 71 (450)
T ss_pred HHHHHHHHH---cCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcC
Confidence 346677764 223467899999999999999999999999999999999999999999988654
No 60
>PF10911 DUF2717: Protein of unknown function (DUF2717); InterPro: IPR020121 The proteins in this entry are uncharacterised.
Probab=57.24 E-value=30 Score=24.61 Aligned_cols=61 Identities=15% Similarity=0.218 Sum_probs=41.0
Q ss_pred hHHHHhhhhcccccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHH--HHHHHHHHHHHHHHHH
Q 031980 58 LREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQE--AAEDFLVNLFGDAMLC 122 (149)
Q Consensus 58 lrEIr~yQkst~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQe--AaE~yLv~Lfeda~lc 122 (149)
|.+|.+|+...+= ||-.| |.+.|-.+- -+..++=.++..+..|+. -+|+|+.++++..+.|
T Consensus 2 L~~I~h~l~np~D-iP~ip--ra~aeyLqv-rfN~~yl~~sG~i~~lr~~G~SE~~I~Gfl~Gl~~A 64 (77)
T PF10911_consen 2 LKPIQHLLDNPDD-IPDIP--RAAAEYLQV-RFNAAYLMASGIISALRKQGWSESYILGFLAGLQYA 64 (77)
T ss_pred cchHHHHhcCCcc-cCCcc--HHHHHHHHH-HhcHHHHHHhhhHHHHHHccccHHHHHHHHHHHHHH
Confidence 6899999998753 45554 555555553 122233344556666764 5899999999999888
No 61
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=53.63 E-value=23 Score=29.75 Aligned_cols=72 Identities=26% Similarity=0.242 Sum_probs=60.0
Q ss_pred hcccccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHH
Q 031980 66 KSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELAR 140 (149)
Q Consensus 66 kst~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~ 140 (149)
...++.+..+|..|+.+ |... ..+.--+..+|..-.-.|+|.|+..|-.-+..-+--.+|.|+.-.||.-+.
T Consensus 66 ~~~d~~~~~lPlaRiKk-imK~--dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av 137 (236)
T KOG1657|consen 66 GQLDFKNHILPLARIKK-IMKS--DEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAV 137 (236)
T ss_pred cccchhhccCcHhhccc-cccc--cccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHh
Confidence 45688999999999864 4331 233347999999999999999999999999999999999999999987664
No 62
>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=52.08 E-value=28 Score=32.00 Aligned_cols=60 Identities=20% Similarity=0.102 Sum_probs=44.8
Q ss_pred HHHhhhcCCCCccccCHHHHHHHHHHHH--HHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 82 RTITYRVAPPDVNRWTPEALIALQEAAE--DFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 82 rEI~~~~~~~~~~Rfq~~Al~aLQeAaE--~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
.+|+.....+.+..+..+|++.|...+. ..++.+++.+...|..-+|.+|..+|++-+..
T Consensus 269 ~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~ 330 (531)
T TIGR02902 269 KEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAE 330 (531)
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhC
Confidence 3444433333457889999998766555 37888999988888888999999999988864
No 63
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=51.18 E-value=47 Score=30.05 Aligned_cols=73 Identities=22% Similarity=0.325 Sum_probs=58.3
Q ss_pred ccCCcchHH-HHHHHHhhhcCCCCccccCHHHHHHHHHHHHH----HHHHHHHHHHHHhhhcCccccccccHHHHHHH
Q 031980 70 LLIPRMSFI-REVRTITYRVAPPDVNRWTPEALIALQEAAED----FLVNLFGDAMLCAIHAKRVTLMKKDFELARRL 142 (149)
Q Consensus 70 lLIpk~PF~-RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~----yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~ri 142 (149)
|+|.-.|+. +=+++|..--....|.-.+++|++-|-...|+ |...|...+++.+...|-.++..+||+-|.++
T Consensus 351 lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~L 428 (454)
T KOG2680|consen 351 LIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYRL 428 (454)
T ss_pred heeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHHH
Confidence 567777775 34666654322456778899999998777776 99999999999999999999999999988776
No 64
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=49.62 E-value=14 Score=29.63 Aligned_cols=65 Identities=23% Similarity=0.210 Sum_probs=51.0
Q ss_pred CCcchHHHHHHHHhhhcCCCCccccCHH-HHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHH
Q 031980 72 IPRMSFIREVRTITYRVAPPDVNRWTPE-ALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELAR 140 (149)
Q Consensus 72 Ipk~PF~RLVrEI~~~~~~~~~~Rfq~~-Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~ 140 (149)
+.++|.+|+ +++.. ...+++|-.+ |+..+-.|+|.|+-.|-.+++-|+--.+|+|+..+|+..+.
T Consensus 57 l~rLpL~ri-k~vvk---l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai 122 (162)
T KOG1658|consen 57 LSRLPLARI-KQVVK---LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAI 122 (162)
T ss_pred hhhccHHHH-Hhhcc---CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccc
Confidence 356666664 45554 3457787654 56678899999999999999999999999999999987653
No 65
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=48.24 E-value=53 Score=27.36 Aligned_cols=60 Identities=17% Similarity=0.089 Sum_probs=48.5
Q ss_pred HHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCccccccccHHHHH
Q 031980 77 FIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIH--AKRVTLMKKDFELAR 140 (149)
Q Consensus 77 F~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~H--AkRvTi~~kDiqLa~ 140 (149)
..+.|++.++. .+..+..+|+..|.+.++.-+..+-.....++.. .+..+|..+||+.+.
T Consensus 135 l~~~i~~~~~~----~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v 196 (326)
T PRK07452 135 LKQLVERTAQE----LGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALV 196 (326)
T ss_pred HHHHHHHHHHH----cCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHh
Confidence 45666666664 4578999999999999999888888888888888 567889999998654
No 66
>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=45.16 E-value=39 Score=26.46 Aligned_cols=59 Identities=19% Similarity=0.100 Sum_probs=43.2
Q ss_pred HHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHH
Q 031980 77 FIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRL 142 (149)
Q Consensus 77 F~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~ri 142 (149)
|++|.|+.+. +=+..+=+.-+-+..|.-+..||+-+..-|.--+|-.|.+.|+.+...+
T Consensus 1 fe~lFR~aa~-------LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPITkGl 59 (138)
T PF09123_consen 1 FERLFRKAAG-------LDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPITKGL 59 (138)
T ss_dssp HHHHHHHHHS-----------HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HHH
T ss_pred ChHHHHHHhc-------cCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCccHHH
Confidence 6777777765 3344666778889999999999999999999999999999999876554
No 67
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=44.48 E-value=53 Score=28.00 Aligned_cols=85 Identities=25% Similarity=0.246 Sum_probs=61.9
Q ss_pred CchhhHHHHhhhhcccc---------cCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 031980 54 GTKALREIRRFQKSVDL---------LIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAI 124 (149)
Q Consensus 54 gt~alrEIr~yQkst~l---------LIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~ 124 (149)
|...-+-+|.||+..+- -...+||.|+-|=.--| .+.-=+.++|=...-.++|-|+.+|-=-|-+.|-
T Consensus 80 g~~~e~i~ryWq~ti~~~e~~~q~~~k~h~LPlARIkkvMKtd---edVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae 156 (286)
T COG5208 80 GLLDERISRYWQQTIKAAEEERQILLKDHNLPLARIKKVMKTD---EDVKMISAEAPVLFAKITEIFIEELTMRAWINAE 156 (286)
T ss_pred hhHHHHHHHHHHHHHHHHHHhHHHHHHhccCcHHHHHHHHhcc---cchhheecccchHHHHHHHHHHHHHHHHHHHHHh
Confidence 44556678888875322 12348999975533221 1222466777777889999999999999999999
Q ss_pred hcCccccccccHHHHHH
Q 031980 125 HAKRVTLMKKDFELARR 141 (149)
Q Consensus 125 HAkRvTi~~kDiqLa~r 141 (149)
..||-||...||--|..
T Consensus 157 ~NkRRtLQksDia~Av~ 173 (286)
T COG5208 157 ENKRRTLQKSDIAAAVK 173 (286)
T ss_pred HhhhhHHHHHHHHHHHH
Confidence 99999999999977654
No 68
>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]
Probab=41.31 E-value=65 Score=29.10 Aligned_cols=73 Identities=26% Similarity=0.257 Sum_probs=53.3
Q ss_pred ccCCcchHH-HHHHHHhhhcCCCCccccCHHHHHHHHH----HHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHH
Q 031980 70 LLIPRMSFI-REVRTITYRVAPPDVNRWTPEALIALQE----AAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRL 142 (149)
Q Consensus 70 lLIpk~PF~-RLVrEI~~~~~~~~~~Rfq~~Al~aLQe----AaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~ri 142 (149)
++|+-+|+. .-+|+|..--....++-+.++|+.-|-+ .+=-|.++|+.-+++||.-.+|..|..+|++-+..+
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 345555553 2344444322234567889999998876 455699999999999999999999999999876554
No 69
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=35.06 E-value=1.5e+02 Score=27.38 Aligned_cols=66 Identities=17% Similarity=0.190 Sum_probs=50.3
Q ss_pred chHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHH-----------HHHHHHHHHHHHHhhhcCccccccccHHHHHHHc
Q 031980 75 MSFIREVRTITYRVAPPDVNRWTPEALIALQEAAE-----------DFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLG 143 (149)
Q Consensus 75 ~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE-----------~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rir 143 (149)
..|.++|..++++. .-.-|+.+|+..|=+.+= ..|..|+..|+..|--.+...|...||+-|..-|
T Consensus 430 ~~~~~~i~~~~~~~---~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 430 RQYARFIASICQKE---GLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHHHHHHH---SS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHHHHHHHhC---CCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 45788999988872 234799999999766553 4789999999999999999999999999987654
No 70
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=34.04 E-value=1.9e+02 Score=27.22 Aligned_cols=48 Identities=19% Similarity=0.095 Sum_probs=39.2
Q ss_pred cccCHHHHHHHHH-HH------------HHHHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 94 NRWTPEALIALQE-AA------------EDFLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 94 ~Rfq~~Al~aLQe-Aa------------E~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
..|+.+|+..|-+ ++ +..|.++...|+..|...+..+|..+|++-|..
T Consensus 329 ~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~ 389 (608)
T TIGR00764 329 PHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKK 389 (608)
T ss_pred CcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHH
Confidence 4899999999864 23 467888999998888888899999999987644
No 71
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=33.67 E-value=41 Score=26.27 Aligned_cols=32 Identities=22% Similarity=0.394 Sum_probs=27.2
Q ss_pred chhhHHHHhhhhcccccCCcchHHHHHHHHhhh
Q 031980 55 TKALREIRRFQKSVDLLIPRMSFIREVRTITYR 87 (149)
Q Consensus 55 t~alrEIr~yQkst~lLIpk~PF~RLVrEI~~~ 87 (149)
.||+.||+++-.+..-+ +..-+-+||++|=.+
T Consensus 97 ~VAm~ei~~~~~~~~~~-~~id~~~lvk~IKk~ 128 (137)
T PF10788_consen 97 AVAMDEIKKMRQKDGNL-PNIDLDKLVKNIKKE 128 (137)
T ss_pred HHHHHHHHHHHhcCCCc-CCCCHHHHHHHHHHh
Confidence 68999999997666555 999999999999775
No 72
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=32.96 E-value=1.6e+02 Score=23.72 Aligned_cols=62 Identities=21% Similarity=0.100 Sum_probs=39.8
Q ss_pred HHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHH
Q 031980 77 FIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRL 142 (149)
Q Consensus 77 F~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~ri 142 (149)
+...|++.+.+ .+..+..+|+..|-+.++.=+-.+-.....++.-++-.+|..+||+-....
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 34456666554 457899999999988887644444444444444443336889999765543
No 73
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=31.73 E-value=1.7e+02 Score=24.11 Aligned_cols=61 Identities=18% Similarity=0.025 Sum_probs=40.3
Q ss_pred HHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhc-CccccccccHHHHHHHc
Q 031980 78 IREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHA-KRVTLMKKDFELARRLG 143 (149)
Q Consensus 78 ~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HA-kRvTi~~kDiqLa~rir 143 (149)
...|++++.+ .+..++.+|+..|-+.++.-+-.+-.....++.-+ ... |..+||+-.....
T Consensus 152 ~~~i~~~~~~----~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~~ 213 (340)
T PRK05574 152 PQWIQQRLKQ----QGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPDS 213 (340)
T ss_pred HHHHHHHHHH----cCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhhh
Confidence 3444444443 35689999999999998876666665556666554 333 8889987654433
No 74
>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=31.54 E-value=1.9e+02 Score=22.89 Aligned_cols=49 Identities=10% Similarity=0.114 Sum_probs=38.5
Q ss_pred ccccCHHHHHHHHHHHHH---HHHHHHHHHHHHhhhcCccccccccHHHHHH
Q 031980 93 VNRWTPEALIALQEAAED---FLVNLFGDAMLCAIHAKRVTLMKKDFELARR 141 (149)
Q Consensus 93 ~~Rfq~~Al~aLQeAaE~---yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~r 141 (149)
+..|+.+++..|.+.+.- ++..+...+.+.|.-.+--+|..+||+-+..
T Consensus 213 ~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~ 264 (269)
T TIGR03015 213 APVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIA 264 (269)
T ss_pred CCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 346999999999999987 6777777777777666777899999976643
No 75
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=29.91 E-value=1.6e+02 Score=24.95 Aligned_cols=57 Identities=14% Similarity=-0.049 Sum_probs=45.3
Q ss_pred HHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHH
Q 031980 78 IREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELAR 140 (149)
Q Consensus 78 ~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~ 140 (149)
.+.|++.+++ .+..++.+|+..|-+..+.-+..+-..-..++...+ +|..+||+.+.
T Consensus 141 ~~~i~~~~~~----~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v 197 (328)
T PRK08487 141 LELLQERAKE----LGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELV 197 (328)
T ss_pred HHHHHHHHHH----hCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHh
Confidence 4555666554 457899999999999999988888888888888876 68999997654
No 76
>PF13060 DUF3921: Protein of unknown function (DUF3921)
Probab=28.23 E-value=1.3e+02 Score=19.87 Aligned_cols=26 Identities=19% Similarity=0.169 Sum_probs=20.8
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHH
Q 031980 94 NRWTPEALIALQEAAEDFLVNLFGDA 119 (149)
Q Consensus 94 ~Rfq~~Al~aLQeAaE~yLv~Lfeda 119 (149)
.-.|.-+.+.+|.|-|.||-.|--.+
T Consensus 24 i~~~g~~~d~i~kaqeeylsals~et 49 (58)
T PF13060_consen 24 IDLQGVIADEIQKAQEEYLSALSHET 49 (58)
T ss_pred hhhcchHHHHHHHHHHHHHHHhhHHH
Confidence 44567888999999999998886443
No 77
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=28.04 E-value=84 Score=25.46 Aligned_cols=26 Identities=27% Similarity=0.115 Sum_probs=19.7
Q ss_pred CCccccCHHHHHHHHHHHHHHHHHHH
Q 031980 91 PDVNRWTPEALIALQEAAEDFLVNLF 116 (149)
Q Consensus 91 ~~~~Rfq~~Al~aLQeAaE~yLv~Lf 116 (149)
..+++|+...-.++||.+|++....|
T Consensus 70 ~~~~~y~~~~~~~lQEyvEA~~f~~~ 95 (204)
T PRK14562 70 HPELYYAGYVGTALQEYVEALLVYSL 95 (204)
T ss_pred CchhhhhhhcchHHHHHHHHHHHHHH
Confidence 34678888888899999988665544
No 78
>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=25.90 E-value=1e+02 Score=19.22 Aligned_cols=19 Identities=11% Similarity=-0.101 Sum_probs=11.0
Q ss_pred HHhhhcCccccccccHHHH
Q 031980 121 LCAIHAKRVTLMKKDFELA 139 (149)
Q Consensus 121 lcA~HAkRvTi~~kDiqLa 139 (149)
.+|...+...|++++|.-|
T Consensus 26 ~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 26 KYARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHHCT-SEE-HHHHHHH
T ss_pred HHHHHcCCCeECHHHHHhh
Confidence 3467777777777766544
No 79
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=24.61 E-value=1.4e+02 Score=25.08 Aligned_cols=59 Identities=15% Similarity=-0.003 Sum_probs=43.9
Q ss_pred HHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC-ccccccccHHHHH
Q 031980 78 IREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAK-RVTLMKKDFELAR 140 (149)
Q Consensus 78 ~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAk-RvTi~~kDiqLa~ 140 (149)
.+.|++.+++ .+..+..+|+..|-+.++.-+..+-..-..++..++ .-+|..+||+-+.
T Consensus 148 ~~~i~~~~~~----~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv 207 (343)
T PRK06585 148 ARLIDDELAE----AGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVV 207 (343)
T ss_pred HHHHHHHHHH----CCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHh
Confidence 4456666654 468999999999999999977777777777777643 4578899996553
No 80
>PF00540 Gag_p17: gag gene protein p17 (matrix protein); InterPro: IPR000071 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from immunodeficiency lentiviruses, such as Human immunodeficiency virus (HIV) and Simian immunodeficiency virus (SIV-cpz) []. The structure of the HIV protein consists of 5 alpha helices, a short 3.10 helix and a 3-stranded mixed beta-sheet [].; GO: 0005198 structural molecule activity; PDB: 2JMG_A 1L6N_A 2NV3_A 1ED1_A 1ECW_A 2C7U_C 2H3F_A 1HIW_S 2H3V_A 2H3I_A ....
Probab=23.78 E-value=3.3e+02 Score=21.34 Aligned_cols=76 Identities=28% Similarity=0.329 Sum_probs=46.6
Q ss_pred CCcccCCCCchhhHHHHhhhhcccccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHH-HHHHHhh
Q 031980 46 RKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFG-DAMLCAI 124 (149)
Q Consensus 46 kk~~r~rpgt~alrEIr~yQkst~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfe-da~lcA~ 124 (149)
||+.+.+-=-.|.+|.-+|-=+..||=-.---+.|+..+..- |+.-+|. |-+||. -+.+.++
T Consensus 25 KKkY~lKHlVWasrELeRFalnp~LLeT~EGC~qIl~qL~P~----------------l~TGSee-LkSL~NtvavLyCV 87 (140)
T PF00540_consen 25 KKKYRLKHLVWASRELERFALNPGLLETAEGCQQILEQLQPL----------------LPTGSEE-LKSLFNTVAVLYCV 87 (140)
T ss_dssp SCBE-HHHHHHHHHHHHHTTSSGGGGCSHHHHHHHHHHHGGG----------------CTTSHHH-HHHHHHHHHHHHHH
T ss_pred CcceecceeeccccccccccccccccchhhhhhcceeccCCC----------------CcCCccc-cchhhhccceeEEE
Confidence 343444444568899999988877665555555555544332 2233555 778887 6788888
Q ss_pred hcCccccccccHHHHHH
Q 031980 125 HAKRVTLMKKDFELARR 141 (149)
Q Consensus 125 HAkRvTi~~kDiqLa~r 141 (149)
|++ |.++|-+=|..
T Consensus 88 H~~---i~VkDTkEAl~ 101 (140)
T PF00540_consen 88 HQR---IEVKDTKEALD 101 (140)
T ss_dssp HTT------SBHHHHHH
T ss_pred ecC---cccccHHHHHH
Confidence 875 88889877653
No 81
>PRK05629 hypothetical protein; Validated
Probab=23.62 E-value=2.3e+02 Score=23.71 Aligned_cols=57 Identities=16% Similarity=-0.028 Sum_probs=40.0
Q ss_pred HHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHH
Q 031980 78 IREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELA 139 (149)
Q Consensus 78 ~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa 139 (149)
.+.|++.++. .+..+..+|++.|-+.++.=+..+-.....++.+.+ -+|..+||+-+
T Consensus 132 ~~wi~~~~~~----~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~ 188 (318)
T PRK05629 132 PGWVTQEFKN----HGVRPTPDVVHALLEGVGSDLRELASAISQLVEDTQ-GNVTVEKVRAY 188 (318)
T ss_pred HHHHHHHHHH----cCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcCC-CCcCHHHHHHH
Confidence 3445555543 567899999999999998866666665555556654 36889998765
No 82
>COG2118 DNA-binding protein [General function prediction only]
Probab=23.29 E-value=1.2e+02 Score=23.06 Aligned_cols=32 Identities=34% Similarity=0.384 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHH
Q 031980 103 ALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRL 142 (149)
Q Consensus 103 aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~ri 142 (149)
.|-|++|.||+.|. -.+||+.+..|=+|..-+
T Consensus 67 e~AeavE~qLi~La--------qtGri~~~I~e~~lk~IL 98 (116)
T COG2118 67 ELAEAVENQLIQLA--------QTGRITHKIDEEELKEIL 98 (116)
T ss_pred HHHHHHHHHHHHHH--------HcCCCCCCCCHHHHHHHH
Confidence 37899999999996 589999999998887644
No 83
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=22.03 E-value=2.3e+02 Score=24.05 Aligned_cols=59 Identities=15% Similarity=0.088 Sum_probs=41.8
Q ss_pred HHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHH-HHHHhhhcCccccccccHHHHH
Q 031980 77 FIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGD-AMLCAIHAKRVTLMKKDFELAR 140 (149)
Q Consensus 77 F~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfed-a~lcA~HAkRvTi~~kDiqLa~ 140 (149)
+.++|...+.+ ...++..+|++.|-+..|.=+-.+... --++.+..+. +|..+||+.+.
T Consensus 145 l~~~i~~~~~~----~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~-~I~~~~V~~~v 204 (334)
T COG1466 145 LPQWIKKRAKE----LGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDK-EITLEDVEEVV 204 (334)
T ss_pred HHHHHHHHHHH----cCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCC-cCCHHHHHHHH
Confidence 44455555543 568999999999999999755555444 4455555566 99999998764
No 84
>COG1598 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]
Probab=21.21 E-value=1.4e+02 Score=20.16 Aligned_cols=25 Identities=32% Similarity=0.230 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 031980 98 PEALIALQEAAEDFLVNLFGDAMLC 122 (149)
Q Consensus 98 ~~Al~aLQeAaE~yLv~Lfeda~lc 122 (149)
.+|+.-++||.|-|+..+.++.+..
T Consensus 34 eea~~n~~eai~l~~e~~~~~~~~i 58 (73)
T COG1598 34 EEALQNAKEAIELHLEALLEEGEPI 58 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCcC
Confidence 6899999999999999999887665
No 85
>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=20.93 E-value=88 Score=20.57 Aligned_cols=20 Identities=40% Similarity=0.577 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 031980 99 EALIALQEAAEDFLVNLFGD 118 (149)
Q Consensus 99 ~Al~aLQeAaE~yLv~Lfed 118 (149)
+|+.+|||.++.-|-++.-.
T Consensus 7 ea~~~lqevs~eELd~ilGg 26 (51)
T PF04604_consen 7 EALNSLQEVSDEELDQILGG 26 (51)
T ss_pred HHHHHHHhcCHHHHHHHhCC
Confidence 89999999999999888754
Done!